ISOLATION AND CHARACTERIZATION OF mer GENE FROM MERCURY-RESISTANT BACTERIA ISOLATED FROM POLLUTED SOIL Tan Boon Khai Bachelor of Science with Honours QR 201 (Resource Biotechnology) A6 2009 T161 2009
ISOLATION AND CHARACTERIZATION OF mer GENE FROM MERCURY-RESISTANT BACTERIA ISOLATED FROM
POLLUTED SOIL
Tan Boon Khai
Bachelor of Science with HonoursQR 201 (Resource Biotechnology) A6 2009 T161 2009
Puut IQfdmat Maldut Akademnmiddot UNlVEKSm MALAYSIA SARAWAK
ISOLATION AND CHARACTERIZATION OF mer
GENE FROM MERCURY-RESISTANT BACTERIA
ISOLATED FROM POLLUTED SOIL
TAN BOON KHAI
This report is submitted in partial fulfillment of requirements for the degree
of Bachelor of Science with Honours (Resource Biotechnology)
Faculty of Resource Science and Technology
UNIVERSITI MALAYSIA SARA W AK
2009
ACKNOWLEDGEMENT
Foremost I would like record my utmost sincere gratitude towards my supervisor Dr Awang
Ahmad Sallehin Awang Husaini for providing me the opportunity to carry out this project in
Genetic Molecular Lab (GML) I would like to thank for all his constructive comments
encouragement and understanding which serve him as a good host despite his warm and
humorous personality
Special thanks to Frazer Midot Nur Hafizah George Deng Kolly Lee the postshy
graduates from GML I am indebted to you all for your willingness to share your expertise
experiences and advice all the time You all have been being the ultimate lab-neighbours
providing a great research environment And hereby I wish all the best to you all and I know
a note ofThank you doesnt seem sufficient but it is said with appreciation and truly respect
To all the members in GML thanks again for this too short but really wonderful time spending
together I am glad to bear chance to get to knowing you all
During this project I have collaborated with other lab members for whom I have great
regard and I wish to extend my warmest thanks to all those who have helped given valuable
advice and sacrificed their precious time to guide me through
I would like to gratefully acknowledge the support of this special person Mr Kuah
Meng Kiat who has been actively and always been available to advise me giving me his
untiring help His wide knowledge and logical way of thinking have been of great value for
11
me I believe that his personal guidance for me through this project will leave a remarkable
influence on my future work for the time to come
I have not travelled in a vacuum in this journey There are some people who made this
journey easier with words of encouragement and moral supports thanks for being there for me
and I am truly lucky to have you all Needless to say I would like to dedicate my love and
thanks to my beloved family
III
middot If JChfdmlt Mlkluf 4kd8 UNJVERSrrf MALAYSIA SARAWAK
TABLE OF CONTENTS
Page
ACKNOWLEDGEMENT 11
LIST OF TABLES Vlll
ABSTRACT
A BSTRAK
TABLE OF CONTENTS IV
LIST OF FIGURES IX
LIST OF ABBREVIA nONS XI
10 INTRODUCTION 2
20 LITERATURE REVIEW
21 Mercury 5
22 Toxicity of Mercury 5
23 The mer Operon 7
24 merA 13
25 Application ofmer Operon and Future Prospect 14
I
IV
30 MATERIALS AND METHODS
31 Mercury-resistant Bacteria Strains 17
32 Working Culture
321 LB Agar Plate 17
322 LB Agar Broth 17
33 Preservation of Bacteria Culture 18
34 Isolation of Bacteria Total DNA and Plasmid DNA 18
35 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 19
36 DNA Manipulation 20
361 Cloning of Putative merA Amplicon 20
362 Competent Cell 20
363 Heat Shock Transformation 21
364 BluelWhite Colony Screening 22
365 Colony-PCR 22
37 Sequencing ofDNA 22
38 Development ofMercury-resistant Bacteria Pure Culture 23
39 Preliminary Characterization of Isolated MRB 24
391 Colony Morphology Characterization 24
392 Gram Staining 24
393 Biochemical Test 25
3931 Methyl Red Voges-Proskauer (MRVP) Test 25
253932 Citrate Utilization Test
3933 Motility Test 26
310 16S rDNA Sequencing 26
v
j
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
Puut IQfdmat Maldut Akademnmiddot UNlVEKSm MALAYSIA SARAWAK
ISOLATION AND CHARACTERIZATION OF mer
GENE FROM MERCURY-RESISTANT BACTERIA
ISOLATED FROM POLLUTED SOIL
TAN BOON KHAI
This report is submitted in partial fulfillment of requirements for the degree
of Bachelor of Science with Honours (Resource Biotechnology)
Faculty of Resource Science and Technology
UNIVERSITI MALAYSIA SARA W AK
2009
ACKNOWLEDGEMENT
Foremost I would like record my utmost sincere gratitude towards my supervisor Dr Awang
Ahmad Sallehin Awang Husaini for providing me the opportunity to carry out this project in
Genetic Molecular Lab (GML) I would like to thank for all his constructive comments
encouragement and understanding which serve him as a good host despite his warm and
humorous personality
Special thanks to Frazer Midot Nur Hafizah George Deng Kolly Lee the postshy
graduates from GML I am indebted to you all for your willingness to share your expertise
experiences and advice all the time You all have been being the ultimate lab-neighbours
providing a great research environment And hereby I wish all the best to you all and I know
a note ofThank you doesnt seem sufficient but it is said with appreciation and truly respect
To all the members in GML thanks again for this too short but really wonderful time spending
together I am glad to bear chance to get to knowing you all
During this project I have collaborated with other lab members for whom I have great
regard and I wish to extend my warmest thanks to all those who have helped given valuable
advice and sacrificed their precious time to guide me through
I would like to gratefully acknowledge the support of this special person Mr Kuah
Meng Kiat who has been actively and always been available to advise me giving me his
untiring help His wide knowledge and logical way of thinking have been of great value for
11
me I believe that his personal guidance for me through this project will leave a remarkable
influence on my future work for the time to come
I have not travelled in a vacuum in this journey There are some people who made this
journey easier with words of encouragement and moral supports thanks for being there for me
and I am truly lucky to have you all Needless to say I would like to dedicate my love and
thanks to my beloved family
III
middot If JChfdmlt Mlkluf 4kd8 UNJVERSrrf MALAYSIA SARAWAK
TABLE OF CONTENTS
Page
ACKNOWLEDGEMENT 11
LIST OF TABLES Vlll
ABSTRACT
A BSTRAK
TABLE OF CONTENTS IV
LIST OF FIGURES IX
LIST OF ABBREVIA nONS XI
10 INTRODUCTION 2
20 LITERATURE REVIEW
21 Mercury 5
22 Toxicity of Mercury 5
23 The mer Operon 7
24 merA 13
25 Application ofmer Operon and Future Prospect 14
I
IV
30 MATERIALS AND METHODS
31 Mercury-resistant Bacteria Strains 17
32 Working Culture
321 LB Agar Plate 17
322 LB Agar Broth 17
33 Preservation of Bacteria Culture 18
34 Isolation of Bacteria Total DNA and Plasmid DNA 18
35 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 19
36 DNA Manipulation 20
361 Cloning of Putative merA Amplicon 20
362 Competent Cell 20
363 Heat Shock Transformation 21
364 BluelWhite Colony Screening 22
365 Colony-PCR 22
37 Sequencing ofDNA 22
38 Development ofMercury-resistant Bacteria Pure Culture 23
39 Preliminary Characterization of Isolated MRB 24
391 Colony Morphology Characterization 24
392 Gram Staining 24
393 Biochemical Test 25
3931 Methyl Red Voges-Proskauer (MRVP) Test 25
253932 Citrate Utilization Test
3933 Motility Test 26
310 16S rDNA Sequencing 26
v
j
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
ACKNOWLEDGEMENT
Foremost I would like record my utmost sincere gratitude towards my supervisor Dr Awang
Ahmad Sallehin Awang Husaini for providing me the opportunity to carry out this project in
Genetic Molecular Lab (GML) I would like to thank for all his constructive comments
encouragement and understanding which serve him as a good host despite his warm and
humorous personality
Special thanks to Frazer Midot Nur Hafizah George Deng Kolly Lee the postshy
graduates from GML I am indebted to you all for your willingness to share your expertise
experiences and advice all the time You all have been being the ultimate lab-neighbours
providing a great research environment And hereby I wish all the best to you all and I know
a note ofThank you doesnt seem sufficient but it is said with appreciation and truly respect
To all the members in GML thanks again for this too short but really wonderful time spending
together I am glad to bear chance to get to knowing you all
During this project I have collaborated with other lab members for whom I have great
regard and I wish to extend my warmest thanks to all those who have helped given valuable
advice and sacrificed their precious time to guide me through
I would like to gratefully acknowledge the support of this special person Mr Kuah
Meng Kiat who has been actively and always been available to advise me giving me his
untiring help His wide knowledge and logical way of thinking have been of great value for
11
me I believe that his personal guidance for me through this project will leave a remarkable
influence on my future work for the time to come
I have not travelled in a vacuum in this journey There are some people who made this
journey easier with words of encouragement and moral supports thanks for being there for me
and I am truly lucky to have you all Needless to say I would like to dedicate my love and
thanks to my beloved family
III
middot If JChfdmlt Mlkluf 4kd8 UNJVERSrrf MALAYSIA SARAWAK
TABLE OF CONTENTS
Page
ACKNOWLEDGEMENT 11
LIST OF TABLES Vlll
ABSTRACT
A BSTRAK
TABLE OF CONTENTS IV
LIST OF FIGURES IX
LIST OF ABBREVIA nONS XI
10 INTRODUCTION 2
20 LITERATURE REVIEW
21 Mercury 5
22 Toxicity of Mercury 5
23 The mer Operon 7
24 merA 13
25 Application ofmer Operon and Future Prospect 14
I
IV
30 MATERIALS AND METHODS
31 Mercury-resistant Bacteria Strains 17
32 Working Culture
321 LB Agar Plate 17
322 LB Agar Broth 17
33 Preservation of Bacteria Culture 18
34 Isolation of Bacteria Total DNA and Plasmid DNA 18
35 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 19
36 DNA Manipulation 20
361 Cloning of Putative merA Amplicon 20
362 Competent Cell 20
363 Heat Shock Transformation 21
364 BluelWhite Colony Screening 22
365 Colony-PCR 22
37 Sequencing ofDNA 22
38 Development ofMercury-resistant Bacteria Pure Culture 23
39 Preliminary Characterization of Isolated MRB 24
391 Colony Morphology Characterization 24
392 Gram Staining 24
393 Biochemical Test 25
3931 Methyl Red Voges-Proskauer (MRVP) Test 25
253932 Citrate Utilization Test
3933 Motility Test 26
310 16S rDNA Sequencing 26
v
j
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
me I believe that his personal guidance for me through this project will leave a remarkable
influence on my future work for the time to come
I have not travelled in a vacuum in this journey There are some people who made this
journey easier with words of encouragement and moral supports thanks for being there for me
and I am truly lucky to have you all Needless to say I would like to dedicate my love and
thanks to my beloved family
III
middot If JChfdmlt Mlkluf 4kd8 UNJVERSrrf MALAYSIA SARAWAK
TABLE OF CONTENTS
Page
ACKNOWLEDGEMENT 11
LIST OF TABLES Vlll
ABSTRACT
A BSTRAK
TABLE OF CONTENTS IV
LIST OF FIGURES IX
LIST OF ABBREVIA nONS XI
10 INTRODUCTION 2
20 LITERATURE REVIEW
21 Mercury 5
22 Toxicity of Mercury 5
23 The mer Operon 7
24 merA 13
25 Application ofmer Operon and Future Prospect 14
I
IV
30 MATERIALS AND METHODS
31 Mercury-resistant Bacteria Strains 17
32 Working Culture
321 LB Agar Plate 17
322 LB Agar Broth 17
33 Preservation of Bacteria Culture 18
34 Isolation of Bacteria Total DNA and Plasmid DNA 18
35 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 19
36 DNA Manipulation 20
361 Cloning of Putative merA Amplicon 20
362 Competent Cell 20
363 Heat Shock Transformation 21
364 BluelWhite Colony Screening 22
365 Colony-PCR 22
37 Sequencing ofDNA 22
38 Development ofMercury-resistant Bacteria Pure Culture 23
39 Preliminary Characterization of Isolated MRB 24
391 Colony Morphology Characterization 24
392 Gram Staining 24
393 Biochemical Test 25
3931 Methyl Red Voges-Proskauer (MRVP) Test 25
253932 Citrate Utilization Test
3933 Motility Test 26
310 16S rDNA Sequencing 26
v
j
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
middot If JChfdmlt Mlkluf 4kd8 UNJVERSrrf MALAYSIA SARAWAK
TABLE OF CONTENTS
Page
ACKNOWLEDGEMENT 11
LIST OF TABLES Vlll
ABSTRACT
A BSTRAK
TABLE OF CONTENTS IV
LIST OF FIGURES IX
LIST OF ABBREVIA nONS XI
10 INTRODUCTION 2
20 LITERATURE REVIEW
21 Mercury 5
22 Toxicity of Mercury 5
23 The mer Operon 7
24 merA 13
25 Application ofmer Operon and Future Prospect 14
I
IV
30 MATERIALS AND METHODS
31 Mercury-resistant Bacteria Strains 17
32 Working Culture
321 LB Agar Plate 17
322 LB Agar Broth 17
33 Preservation of Bacteria Culture 18
34 Isolation of Bacteria Total DNA and Plasmid DNA 18
35 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 19
36 DNA Manipulation 20
361 Cloning of Putative merA Amplicon 20
362 Competent Cell 20
363 Heat Shock Transformation 21
364 BluelWhite Colony Screening 22
365 Colony-PCR 22
37 Sequencing ofDNA 22
38 Development ofMercury-resistant Bacteria Pure Culture 23
39 Preliminary Characterization of Isolated MRB 24
391 Colony Morphology Characterization 24
392 Gram Staining 24
393 Biochemical Test 25
3931 Methyl Red Voges-Proskauer (MRVP) Test 25
253932 Citrate Utilization Test
3933 Motility Test 26
310 16S rDNA Sequencing 26
v
j
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
30 MATERIALS AND METHODS
31 Mercury-resistant Bacteria Strains 17
32 Working Culture
321 LB Agar Plate 17
322 LB Agar Broth 17
33 Preservation of Bacteria Culture 18
34 Isolation of Bacteria Total DNA and Plasmid DNA 18
35 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 19
36 DNA Manipulation 20
361 Cloning of Putative merA Amplicon 20
362 Competent Cell 20
363 Heat Shock Transformation 21
364 BluelWhite Colony Screening 22
365 Colony-PCR 22
37 Sequencing ofDNA 22
38 Development ofMercury-resistant Bacteria Pure Culture 23
39 Preliminary Characterization of Isolated MRB 24
391 Colony Morphology Characterization 24
392 Gram Staining 24
393 Biochemical Test 25
3931 Methyl Red Voges-Proskauer (MRVP) Test 25
253932 Citrate Utilization Test
3933 Motility Test 26
310 16S rDNA Sequencing 26
v
j
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
40 RESULTS
41 Mercury-resistant Bacteria Culture 28
42 Polymerase Chain Reaction (PCR) Amplification of Putative merA Gene 29
43 BluelWhite Colony Screening 31
44 Colony-PCR 32
45 Sequencing Result of Putative merA Gene 34
46 Isolation of Mercury-Resistant Bacteria from Polluted Soils Sampled at Miri 37
47 Preliminary Characterization of Isolated MRB 37
471 Colony Morphology Characterization 37
48 Biochemical Test 39
49 16S rDNA Sequencing 39
50 DISCUSSION
51 Mercury-resistant Bacteria Culture 46
52 Genomic and Plasmid DNA Extraction 46
53 Primer Pair ofmerAlImerA5 47
54 Polymerase Chain Reaction (PCR) Amplification ofPutative merA Gene 47
55 Sequencing Result ofPutative merA Gene 49
56 Isolation ofMercury-Resistant Bacteria from Polluted Soils Sampled at Miri 53
57 16S rDNA Sequencing 53
60 CONCLUSION AND RECOMMENDA nON 55
VI
I
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
REFERENCES 57
APPENDICES 66
Vll
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
LIST OF TABLES
Table Descriptions Page
Table 1 Primer description of merAl and merA5 19
Table 2 Primer description ofpA and pH 27
Table 3 Isolates ofmercury-resistant bacteria sampled from polluted soil at Miri with the characteristic of colony morphologies 38
Table 4 Biochemical test result ofIsolate 1 Isolate 3 and Isolate 4 39
TableS Identities of isolates after 16S rONA sequencing 45
viii
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
LIST OF FIGURES
Figure Descriptions Page
Figure 1 Diversity ofmer operons Sequenced mer operons from Gram-positive and Gram-negative bacteria 10
Figure 1 Model of a typical Gram-negative mercury resistance (mer) operon 11
Figure 3 Bacterial colonies ofKlebsiella pnellmoniae formed on LB agar containing 10 ppm HgCh 28
Figure 4 PCR product ofputative positive merA gene from Klebsiella pneumoniae genomic and plasmid DNA 29
Figure 5 Purified PCR product ofputative positive merA gene from Klebsiella pnellmoniae genomic DNA 30
Figure 6 Purified PCR product ofputative positive merA gene from Klebsiella pneumoniae plasmid DNA 31
Figure 7 Bluewhite screening onto the transformed E coli XL I Blu cells with pGEMT -Easy vector with inserts 31
Figure 8 Colony-PCR onto the transformed E coli XLI Blue cells containing pGEMT -Easy vector with inserts 32
Figure 9 Plasmid Mini-preps from the transformed E coli XL I Blue cells containing pGEMT -Easy vector with inserts 33
Figure 10 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pnellmoniae genomic DNA 35
Figure 11 BLASTN nucleotide search result of partially sequenced clone fragment amplified from Klebsiella pneumoniae plasmid DNA 36
Figure 12 LB agar (supplemented 10 ppm HgCh) with dilution factor 10-2 harbouring the MRB isolated from polluted soil sampled at Miri 37
IX
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
I
Figure Descriptions Page
Figure 13 Bacterial colonies formed on LB agar containing 10 ppm HgCh for pure cultures of mercury-resistant bacteria 38
Figure 14 16S rDNA PCR product amplified from Isolate I Isolate 3 and Isolate 4 40
Figure 15 Purified 16S rDNA PCR product from Isolate I Isolate 3 and Isolate 4 41
Figure 16 BLASTN nucleotide search result of partially sequenced 16S rDNA amplified fragment oflsolate 1 42
Figure 17 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 3 43
Figure 18 BLASTN nucleotide search result ofpartially sequenced 16S rDNA amplified fragment oflsolate 4 44
x
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
A
C
C
dNTPs
G
H20
H2S
Hg+
HgO
Hg2+
HgCh
IPTG
L
LB
mg
MgCh
min(s)
mL
MRB
NADH
NADPH
NB
LIST OF ABBREVIATIONS
Adenosine (DNA base)
Carbon
Cytosine (DNA base)
deoxynucleoside-5 -triphosphates
Guanosine (DNA base)
Water
Hydrogen sulfide
Mercurous mercury
Elemental mercury
Mercuricionic mercury
Mercury (II) Chloride
Isopropyl-(3-D-thioglactopyranoside
Liter
Luria Bertani
Milligram
Magnesium (II) Chloride
minute(s)
Milliliter
Mercury-resistant Bacteria
Nicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide phosphate
Nutrient Broth
Xl
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
OC Degree Celcius
PBS Phosphate-buffered Saline
PCR Polymerase Chain Reaction
ppm Parts per Million
RT Room temperature
sec(s) Second(s)
SH Thiol
T Tyrosine (DNA base)
UV Ultra Violet
V Volts
vv Volume over volume
X-gal 5-bromo-4-chloro-3-indoly-(j-D-galactoside
xu
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
Isolation and Characterization of mer Gene from Mercury-Resistant Bacteria Isolated from Polluted Soil
Tan Boon Khai
Resource Biotechnology Programme Faculty of Resource Science and Technology
Universiti Malaysia Sarawak
ABSTRACT The anthropogenic activities have subsequently caused the arisen levels of mercury in the environment Mercury pollution has caused severe problem to human due to its toxicity It was discovered that the prokaryotes have developed the astonishing arrays of resistance system to defend against the polluted environments Mercury resistance operon (mer operon) is one of the best understood biological systems to date for detoxifying organometallic or inorganic compounds where the mercury reductase enzyme that encoded by merA gene mediated the reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile elemental mercury Hgo Through the study of mer operon it can be utilized for bioremediation purpose global recycling of mercury and also allow the study of horizontal gene transfer in the natural population In this study Klebsiella pneumoniae which had been isolated from Sungai Bera Brunei Darussalam was screened for presence of merA gene using Polymerase Chain Reaction (PCR) The putative merA gene was cloned and sequenced -- where the nucleotide sequence was revealed to show 77 similarity to the polysaccharide deacetylase domain protein of Klebsiella pneumoniae Three additional mercury-resistant bacteria were successfully isolated from polluted soil sampled at Miri The three isolates were subjected to 16S rONA sequencing and successfully identified as Bacillus pumilus Bacillus thuringiensis and Bacillus aquimaris respectively
Key words mercury-resistant bacteria Klebsiella pnetmon iae merA gene mercury Bacillus
ABSTRAK Aktiviti-aktiviti antropogenik telah menyebabkan peningkatan paras merkuri dalam alam persekitaran Pencemaran merkuri telah menyebabkan masalah rumit terhadap mantsia akibat ketoksikannya Penemuan lelah dijllmpai bahawa prokariot telah memperkembangkan sistem pertahanan yang menabjukkan terhadap persekitaran tercemar Operon rintang merkuri (mer operon) adalah sistem biologi yang paling difahami sampai kini dalam penyahtoksikan sebatian merkllri di mana enzim merkuri reduktase yang dikodkan oleh gen merA terlibat dalam tindakbalas menllrunkan ion merkllri Hi+ yang amat toksik kepada unsllr merkuri Hl yang kurang toksik dan bersifat mentap Melalui kajian mer operon ia boleh digunakan untuk tujuan bioremediasi kitar semula merkuri dan juga membenarkan kajian pemindahan gen secara mengufuk dalam populasi Dalam kajian ini kehadiran gen merA dalam Klebsiella pneumoniae yand dipencilkan dari sampel tanah Sungai Bera Bnmei Darussalam telah dikaji dengan Tindakbalas Polimerasi Berantai (peR) Gen merA secara putatif lelah diklon dan dijujukkan - di mana jujukan nllkleotida telah menunjllkkan persamaan sebanyak 77 dengan domain protein polisakarida deacetilase dalam Klebsiella pneumoniae Selain illl tiga jenis bakteria tahan merkurijllga telah berjaya dipencilkan dari sampel tanah tercemar di Miri Ketiga-tiga pendlan bakteria tersebut telah tertakluk kepada penjujllkan 16S rDNA dan identitinya telah dikenalpastikan sebagai Bacillus pumilus Bacillus thuringiensis and Bacillus aqllimaris secara
ing-masing
Kat nei bakteria tahan merkuri Klebsiella onellmoniae gen merA merkuri Bacillus
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
CHAPTER 10
INTRODUCTION
enury is present in the environment as a result of natural processes and from anthropogenic
aources (Nascimento and Chartone-Souza 2003) The introduction of metallic mercury into
Ibe environment is one of the major aggressions against man and environment (Nascimento
and Chartone-Souza 2003) due to its toxicity For example Minamata disease which was
discovered in 1956 around Minamata Bay Japan is the first instance on record of severe
methylmercury poisoning having affected thousands of people 887 of whom were killed
(Daher 1999)
It was discovered that the prokaryotes have developed the astonishing arrays of
resistance system to defense against the polluted environments (Huang et at 1999) Mercury
resistance operon (mer operon) is one of the best understood biological systems to date for
detoxifying organometallic or inorganic compounds (Nascimento and Chartone-Souza 2003)
The reduction of highly toxic ionic mercury Hg2+ to relatively less toxic and volatile
elemental mercury HgO is mediated by mercury reductase enzyme which is encoded by merA
gene in the mer operon (Jaysankar 2004 Barkay and Wagner-Dobler 2005 Chadhain et at
2006) Through the study of mer operon it can be utilized for bioremediation purpose global
ncycling of mercury and also allow the study of horizontal gene transfer in the natural
population The use of bacteria in remediating the polluted environment is a promising
2
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
technology (Nascimento and Chartone-Souza 2003) as they are at a lower cost and higher
efficiency and could be promoted to pilot scale operation in future (Barkay et al 2003)
In this study the mercury resistant bacteria (MRB) Klebsiella pneumoniae which had
been successfully isolated from the polluted soil sampled at outflow of Seria crude oil tenninal
plant Sungai Bera Bnmei Darussalam in the previously done work will be screened for the
presence of merA gene using Polymerase Chain Reaction (PCR) amplification using the
sequence specific merAlImerA5 primer pair The putative merA gene amplicons will be
cloned and sequenced The sequence will be used as query to compare to known sequences in
NCBI database (httpwwwncbinlmnihgov) using BLASTN nucleotide search There will
be the attempts onto the isolation of mercury resistant bacteria from the polluted soils sampled
at Miri as well Despite the Gram staining biochemical testing and microscopic examination
the 16S rDNA sequencing method will be conducted to identity the MRB isolates at molecular
level
The Research Rationale
Is the presence ofme rA gene detected in the mercury-resistant bacteria that had been isolated
Hypothesis
Bacteria that able to colonize in polluted soil (such as oil sludge) should have possessed the
mercury resistance ability which is rendered by mercury reductase which is encoded by mer
gene Thus it is possible to isolate and characterize the merA gene from the isolated mercuryshy
tant bacteria
3
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
1_W4~b Objectives
To identify the mercury-resistant bacteria morphologically and molecularly
To isolate and characterize merA gene from the mercury-resistant bacteria
4
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
t mt MJklrma Akaemf~ UNlVERSm MALAYSIA SARAWAK
CHAPTER 20
LITERATURE REVIEW
21Mercury
Mercury its chemical symbol Hg derived from the word Hydragyrum which means liquid
silver or quick silver in Greek (Tekranreg Instrument Corporation 2006) Mercury can exist
as a metallic liquid or vapor (Summers 1986) and exist as liquid at room temperature
(Michael 2005) The Elemental form of mercury Hgo has high vapor pressure (Henrys
constant of 03 very low aqueous solubility (6 fJg per 100 mL of water at 25degC) and it is
volatile at a Iiquidair interface but may coalesce into a liquid in a closed system (Barkay et al
2003) Due to its unique properties mercury use is widespread particularly in the production
of gold vaccines antimicrobials amalgams in dentistry and electronics (Schelert et al 2004)
As a consequent of anthropogenic activities the release of mercury into the air water and on
the land leads to environment pollution and it is an increasing problem both for developing
and developed countries (Nascimento and Chartone-Souza 2003)
11 Toxicity of Mercury
Mercury the 6th most toxic in a universe of 6 million substances exists naturally in small
amounts in the environment being the 16th most rare element on Earth (Nascimento and
Chartone-Souza 2003) Mercury can exist in three oxidation states namely elemental mercury
0 mercurous mercury Hg+ or mercuric mercury Hg2+ The latter two can combine with
5
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
other elements to fonn either organic or inorganic mercury compounds (Hu 1998) Among
those the organic mercury compound in fonn of methylmercury (palmer 2001) is the most
toxic (Goldwater amp Clarkson 1972 Hu 1998)
Mercury has no known biological function (Wagner-Dobler 2003) and it has very high
affinity to thiol (SH) groups in proteins (Glendinning and Brown 2005) Mercury toxicity is
mainly due to the fonnation of covalent bonds of both ionic and organic mercury with sulfur
atoms in cysteine residues of target proteins (Sche1ert et ai 2004) causing disruption of metal
thiolate bonds ofproteins and alters the protein structure the change in redox status of the cell
and the interference with essential metal uptake (Sigaud-Kutner et al 2003)
Organic mercury is able to reach the Central Nervous System (CNS) where it is
oxidized to Hg2+ and leads to neurological damage (Taylor amp Francis 1995) Several years
ago there has been some concern that mercury contained in dental amalgams adversely affects
human health produces illnesses including multiple sclerosis and Alzheimers disease but this
conjecture has not been conclusively proven (Hu 1998 Baldwin amp Marshall 1999) Mercury
bull also genotoxic the inorganic mercury is capable of strong reversible interactions with the
nitrogen in purines and pyrimidines while the organic mercury compounds such as
methylmercury can cause irreversible damage to nucleic acids (Sletten and Nerdal 1997)
ercury poisonings have been reported from ingestion of mercuric chloride (an inorganic
compound which is used as a disinfectant) and also from contaminated illegal drugs such as
amphetamines or from the exposure to fungicides containing organic mercury compounds and
industrial accidents in which mercury vapour was inhaled (Jaysankar 2004)
6
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
Mercury is primarily deposited in the environment as ionic mercury Hg2+ and it may
to the neurotoxic substance methylmercury Following methylmercury
blOlICClllDl~lallon and biomagnifications in food chains it poses a risk to consumers at the
upper trophic levels (Barkay et ai 2003 Barkay and Wagner-Dobler 2005) for having higher
mercury concentrations accumulated within bodies (Nascimento and Chartone-Souza 2003)
Minamata disease was discovered in 1956 around Minamata Bay Japan It is the first instance
on record ofsevere methylmercury poisoning affected thousands ofpeople 887 of whom were
killed (Daher 1999) due the consumption mainly by fishermen and their families of large
amounts of fish and shellfish which had been contaminated with methylmercury and the
methylmercury was resulted resulting from the transformation of the HgCb discharged from a
chemical plant (Nascimento and Chartone-Souza 2003)
23 The mer Operon
Mercury resistance to inorganic and orgamc mercury compounds was first reported in
SlIlphylococcus aureus by Moore (1960) and this mercury resistance mediated by the
microbial mer operon was discovered in the early 1970s (Summers amp Lewis 1973)
Detoxification of mercury by enzymatic reduction was proposed more than three decades ago
(Summers amp Silver 1972) and it has been realized later that the mer operon which confers
both resistance and detoxification capabilities to its possessor is almost universally distributed
in resistant bacteria populations (Okino et al 2002 Barkay et al 2003 Jaysankar 2004) and
the mer operon is fairly highly conselVed (Jaysankar et al 2008) The reported genera to
posses resistance to mercury are Acinetobacter Aeromonas Alcaligenes Azotobacter
Bacteriodes Be ijerinckia Chromobacterium Citrobacter Clostridium
sporium Deinococcus Desulfovibrio Enterobacter Escherichia Erwinia
7
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
Klebsiella Micrococcus Moraxella Morganella Mycobacterium
Planococcus Proteus Rhodococcus Staphylococcus Streptococcus
_iPlOntyceS Xanthomonas Hyphomonas Thiobacillus Vibrio and Yersinia (Robinson and
~lVi1lIflll 1984 Baldi et at 1989 Osborn et al 1997 Nascimento and Chartone-Souza
Bacteria may respond to mercury exposure usmg several strategies however
fllUmllllism involving enzymatic reduction of mercuric ion Hg2+ to elemental mercury HgO
11U1ialYzed by products of the mer operon is the only resistance mechanism that has been
damb4~ (Schelert et ai 2004)
The operons designated mer operons consist of a cluster of linked genes in an operon
most known naturally occurring systems (Silver amp Phung 1996 Barkay et aI 2003) Most
operons contain at least the mercury-resistance genes merR merD merT merP and merA
1oi1lVII amp Phung 1996 Osborn et ai 1997)
The mer resistance components can be sub-grouped into three categories based on the
constituted that encodes for the functional protein ie merR (regulators of operon
_lSicln) merA (ezymatical converters of toxic mercuric compounds Hg2+ into a relatively
IOlll-olOXIC fonn HgO and merT with merP (transporters of Hg2+ into the cells) (Misra 1992
1993 Silver and Phung 1996 Osborn et al 1997 Jaysankar 2004)
In some cases regarded as broad-spectrum resistance by which the bacteria exhibits
to both inorganic and organic mercunc compounds despite of merA gene
8
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
lIkllIticaal merB genes
2003 Felske et al 2003)
~-
are required to degrade organomercurials such as phenylmercuric
I_tate (PMA) by cleaving the C-Hg bond before Hg2+ reduction by mercuric reductase
eacOCScxl by merA (Osborn et al 1997 Huang et al 1999) For the resistance only to
iIDCIlrganlc mercuric compounds is called as narrow spectrum resistance which only involves
that encodes for mercury reductase to reduce the toxic reactive ionic mercury Hg2+
to volatile relatively inert and relatively less toxic elemental form HgO vapor (Barkay et
Mercury-resistance determinants have been found in a wide range of Gram-negative
Gram-positive bacteria isolated from different environments (Nascimento and Chartoneshy
2(03) and it usually located on plasmids (Summers and Silver 1972 Brown et al
86 Griffin et aI 1987 Radstrom et al 1994) and chromosomes (Wang et al 1987 Inoue
al 1991) and are often components of transposons (Misra et al 1984 Kholodii et al
993) and integrons (Liebert et al 1999) Further suggestion is that transposable element may
involved in the horizontal dissemination of mer operons among Gram-positive bacteria
Bacterial mer operons are not all the same it may vary in the number of genes as well
their nature and organization (lohara et al 2001) Interesting findings also pointed out the
IlelatllgClllCIt) of the mer operon that (i) merB is more common in Gram-positive mer operons
~UILl~ to date than in Gram-negative operons (ii) merR in low-GC Gram-positive operons
transcribed in the same direction as the rest of the operons genes but in the high-GC Gramshy
_n Streptomyces operons and all Gram-negative operons merR is transcribed divergently
9
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
------------------------------------------------------------
_~rnkl~
merR mer( merT merP maC merE merA mere maD
tiIllDlmiddotmiddotne2atlve bacteria
the structural genes while the Gram-negative manne bacterium Pseudoalteromonas
is the exception with merR cotranscribed with merTPCAD (Barkay et al 2003)
Bacillus cereus Clostridium r11I1-11I7gtI
Staphylococcus aureus pl258
Streptomyces ividans
Streptomyces pRJ28
I I Exiguobacterium sp
1- Pseudomonas sp ED-23
Pseudomonas stutzeri OX pPB
_ ~ Pseudomonas sp K62 pMR26
Serratia marccens pDU 1358
Pseudomonas aeruginosa Tn50 1
Shigellaflexneri Tn21
Alcaligenes pMER610
-- t-- Pseudomonas sp ADP
Xanthomonas campestris Tn5044~--Imiddot=- Xanthomonas sp Tn5053
Pseudomonas fluorescens
Shewanella plltrejaciens pMERPH
Thiobacillus jerrooxidans
Pseudoalteromonas I Diversity ofmer operons Sequenced mer operons from Gram-positive (above line) and Gram-negative line) bacteria Arrows indicate the direction of translation of each gene product Colorless arrows indicate
with unknown functions Several variations on the structure and organization of known mer operons reflect mosaic nature of the operon (Barkay et al 2003)
Typically mer operons of Gram-negative bacteria are organized in the gene order
merT merP(then sometimes merC) merA and merD as in transposon Tn21 (lohara et
2(01) According to Nascimento and Chartone-Souza (2003) merB seldom occurs in
10
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
11
HgX2 HgO
J Merp
Periplasm
Cytosol
N-termlnus MerD
t---------______~a~c~tI~vation antagonist
~
2 Model of a typical Gram-negative mercury resistance (mer) operon The symbolmiddot indicates a cysteine X refers to a generic solvent nuceophile RSH is the low-molecular-mass cytosolic thiol redox buffer
as glutalhione Parentheses around gene or protein designations indicate proteinsgenes that do not occur in examples of the operon (Barkay et ai 2003)
reference to Figure 2 (Barkay et at 2003 page 7)
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