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ResearchArticleNature Biotechnology 22, 55 - 61 (2004) Published
online: 14 December 2003 | doi:10.1038/nbt923
Complete genome sequence of the metabolically
versatilephotosynthetic bacterium Rhodopseudomonas palustrisFrank W
Larimer1,2, Patrick Chain2,3, Loren Hauser1,2, Jane Lamerdin2,3,7,
StephanieMalfatti2,3, Long Do2,3,7, Miriam L Land1,2, Dale A
Pelletier1,2, J Thomas Beatty4, Andrew SLang4, F Robert Tabita5,
Janet L Gibson5, Thomas E Hanson5,7, Cedric Bobst5, Janelle L
Torresy Torres6, Caroline Peres6,7, Faith H Harrison6, Jane Gibson6
& Caroline S Harwood6
This article is distributed under the terms of the Creative
Commons Attribution-Non-Commercial-Share Alikelicense
(http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits
distribution, andreproduction in any medium, provided the original
author and source are credited. This license does notpermit
commercial exploitation, and derivative works must be licensed
under the same or similar license.
Rhodopseudomonas palustris is among the most metabolically
versatile bacteriaknown. It uses light, inorganic compounds, or
organic compounds, for energy. Itacquires carbon from many types of
green plant–derived compounds or by carbondioxide fixation, and it
fixes nitrogen. Here we describe the genome sequence of
R.palustris, which consists of a 5,459,213-base-pair (bp) circular
chromosome with4,836 predicted genes and a plasmid of 8,427 bp. The
sequence reveals genes thatconfer a remarkably large number of
options within a given type of metabolism,including three
nitrogenases, five benzene ring cleavage pathways and four
lightharvesting 2 systems. R. palustris encodes 63 signal
transduction histidine kinasesand 79 response regulator receiver
domains. Almost 15% of the genome is devotedto transport. This
genome sequence is a starting point to use R. palustris as amodel
to explore how organisms integrate metabolic modules in response
toenvironmental perturbations.
R. palustris is a purple photosynthetic bacterium that belongs
to the alpha proteobacteria and is widely
distributed in nature as indicated by its isolation from sources
as diverse as swine waste lagoons, earthworm
droppings, marine coastal sediments and pond water. It has
extraordinary metabolic versatility and grows by
any one of the four modes of metabolism that support life:
photoautotrophic or photosynthetic (energy from
light and carbon from carbon dioxide), photoheterotrophic
(energy from light and carbon from organic
compounds), chemoheterotrophic (carbon and energy from organic
compounds) and chemoautotrophic
(energy from inorganic compounds and carbon from carbon dioxide)
(Fig. 1). R. palustris enjoys exceptional
flexibility within each of these modes of metabolism. It grows
with or without oxygen and uses many
alternative forms of inorganic electron donors, carbon and
nitrogen. It degrades plant biomass and chlorinated
pollutants and it generates hydrogen as a product of nitrogen
fixation1, 2. Thus R. palustris is a model
organism to probe how the web of metabolic reactions that
operates within the confines of a single cell adjusts
and reweaves itself in response to changes in light, carbon,
nitrogen and electron sources that are easily
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Figure 2: The chromosome of R. palustris strain CGA009.
Major metabolic features and the locations of the genes that
encode them areindicated on the outer circle. Progressing inward,
the second circle depictspredicted coding regions on the plus
strand colored by functional category:white, hypothetical; dark
gray, unknown function; red, replication and repair;green, energy
metabolism; blue, carbon and carbohydrate metabolism; cyan,lipid
metabolism; magenta, transcription; yellow, translation; pale
green,structural RNAs; sky blue, cellular processes; orange, amino
acid metabolism;brown, general function prediction; pink,
metabolism of cofactors and vitamins;light gray, conserved
hypothetical; dark green, transport; lavender, signaltransduction;
light red, purine and pyrimidine metabolism. Third circle,
Figure 1: Overview of the physiology of R. palustris.
Schematic representations of the four types of metabolism that
support itsgrowth are shown. The multicolored circle in each cell
represents the enzymaticreactions of central metabolism.
Full size image (75 KB)
manipulated experimentally. As a critical step in the further
development of this model we have sequenced and
annotated the R. palustris genome. The genome comprises one
circular chromosome that is 5.46 Mb in size.
The sequenced strain also harbors a 8.4-kilobase (kb) circular
plasmid.
Results
Major features of the genome
The R. palustris genome has very few repeat nucleotide
sequences, insertion sequence elements or
transposons. It has just 16 insertion sequence elements
including representatives of the 'phage' integrase
family, four ISR1-like elements and two xerD type elements. No
horizontally transferred islands of DNA are
apparent based on anomalous G + C content. R. palustris has
4,836 predicted protein-encoding genes (Table 1
and http://genome.ornl.gov/microbial/rpal/). These include genes
required for the biosynthesis of all its
cellular components from carbon dioxide in keeping with its
robust growth in media lacking organic carbon
sources. R. palustris has many genes associated with energy
metabolism, reflecting its metabolic versatility
(Fig. 2). The chromosomal positions and numbered designations of
these genes can be found in
Supplementary Table 1 online. There are genes allowing oxidation
of hydrogen, thiosulfate and carbon
monoxide as energy and reductant sources. Two homologous NADH
dehydrogenase complexes that are
encoded in the genome likely broker the catabolism of a wide
variety of organic compounds, including fatty
acids, dicarboxylic acids and lignin monomers. The conditions
under which these two seemingly redundant
enzyme systems are expressed have not been defined. Terminal
oxidase genes should enable R. palustris to use
nitrite, nitric oxide and nitrous oxide as electron acceptors
during anaerobic respiration3. There are four sets of
genes for terminal oxidases that can function with oxygen: a
cytochrome aa3 oxidase, a cytochrome cbb3
oxidase, a cytochrome d quinol oxidase and a quinol bd oxidase.
Photosynthesis genes enable the use of light as
an energy source by cyclic photophosphorylation under anaerobic
conditions.
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Table 1: General features of the R. palustris genome
Full table
predicted coding regions on minus strand (same color scheme as
the secondcircle). Fourth circle, G + C content (deviation from
average); fifth circle, G + Cskew in purple and olive. Scale (in
bp) is indicated along the outside of the circle.
Full size image (88 KB)
Phototrophy
Genes rpa1505–rpa1554 required for the generation of energy by
photophosphorylation reside in a 55-kb
region of the R. palustris chromosome. These include genes for
bacteriochlorophyll and carotenoid
biosynthesis as well as genes encoding the L, M and H
polypeptides that form the membrane-bound reaction
center complex, where light energy is absorbed to initiate
electron transfer reactions. The reaction center genes
rpa1527, rpa1528 and rpa1548 are the most highly conserved
aspect of this region, sharing from 45 to 60%
predicted amino acid identity with the corresponding genes from
Rhodobacter sphaeroides, a model organism
for the study of anoxygenic photosynthesis4. However the R.
palustris reaction center proteins are most
similar (on the order of 75% amino acid identity) to homologs in
the unusual photosynthetic Bradyrhizobium
sp. strain ORS278 (ref. 5). This strain forms nitrogen-fixing
nodules on the stems of the plant Aeschynomene
sensitiva, a tropical legume that grows in water logged soils6.
In addition to a conserved arrangement of
photosynthesis genes, the A. sensitiva symbiont and R. palustris
each contain a bacteriophytochrome
regulatory gene that is absent in other purple phototrophs. The
symbiont's bacteriophytochrome absorbs far-
red light and is required for expression of photosynthesis in
response to illumination at 740 nm7. In our strain
the homologous bacteriophytochrome gene rpa1537 contains a
frameshift mutation and is probably inactive.
Analysis of rRNA sequences indicates that R. palustris is
closely related to the A. sensitiva symbiont as well as
to the soybean symbiont B. japonicum8. However, R. palustris has
never been found in symbiotic association
with plants, and its genome lacks nodulation genes.
R. palustris, like other purple phototrophic bacteria, responds
to lowered light intensity by increasing the
amount of light harvesting (LH) complexes. These consist of α
and ! polypeptides bound to bacteriochlorophylland a carotenoid, to
form a unit that oligomerizes to produce complexes that transfer
light energy to the
reaction center9. The pathway of light energy transfer is LH2
LH1 reaction center. R. palustris differs from
other phototrophs in that it has multiple LH2 complexes that
differ slightly in the wavelengths of light
absorbed. It tunes its complement of LH2 complexes to harvest
light of differing qualities and intensities10.
The genome sequence reveals four complete sets of LH2 genes
(pucBA) and one incomplete set (Fig. 2 and
Supplementary Table 1 online). Two of the four complete sets of
pucBA genes are located near
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bacteriophytochrome genes rpa3015, rpa3016 and rpa1490 that may
function in the regulation of LH2
complex gene expression.
R. palustris has genes (rpa0008 and rpa0009) that are similar to
the circadian clock genes, kaiB and kaiC
previously identified only in oxygenic photosynthetic
bacteria11. R. palustris cells present in anoxic
environments generate ample energy by photophosphorylation
during daylight hours, but may be energy
limited at night. Circadian regulation of energy consuming
reactions such as nitrogen fixation would make
sense, but has yet to be shown in R. palustris.
Carbon dioxide fixation
The R. palustris genome encodes two active forms of
RubisCO, the key enzyme of the Calvin-Benson-Bassham
(CBB) pathway of CO2 fixation12. The form I (cbbLS,
rpa1559 and rpa1560) and form II (cbbM, rpa4641)
RubisCO genes are located on almost opposite sides of the
chromosome. The cbbM gene is linked to other CBB pathway
genes in an arrangement that is similar, but not identical
to
form II cbb operons from other purple phototrophs. The R.
palustris RubisCO form I gene cluster includes an expected
divergently transcribed LysR type regulatory gene cbbR, but
it differs from form I gene clusters in other species in that
it
includes three additional regulatory genes situated between
cbbR and the cbbLS structural genes. These encode two
predicted response regulators (Rpa1556 and Rpa1557) and a
hybrid sensor kinase/response regulator (Rpa1558) that contains
two PAS domains.
Inorganic compounds as a source of reducing power
R. palustris oxidizes inorganic compounds such as thiosulfate
and hydrogen gas as energy sources for
respiratory growth and as sources of reducing power for carbon
dioxide and nitrogen fixation. R. palustris has
a large cluster of genes (rpa0959–rpa0979) for the synthesis and
assembly of a nickel-containing uptake
hydrogenase. Its periplasmic thiosulfate:cytochrome c
oxidoreductase complex is encoded by genes rpa4459–
rpa4467 that are very similar to sox genes that are found in
many other sulfur oxidizing organisms13. Its use of
reduced sulfur compounds as electron donors sets R. palustris
apart from closely related phototrophic
bacteria14. The genome also encodes carbon monoxide
dehydrogenases and a formate dehydrogenase (Fig. 2
and Supplementary Table 1 online). These can potentially
function to supply reductant and substrate for
carbon dioxide fixation during anaerobic phototrophic growth or
to supply reductant for both energy
generation and carbon dioxide fixation under aerobic
chemoautotrophic growth conditions.
RubisCO-like proteins
R. palustris is the only organism known to date that encodes two
RubisCO-like proteins (RLPs)12, 15. RLPs
contain varying numbers of substitutions in conserved active
site residues. The single RLP from the green
sulfur bacterium Chlorobium tepidum contains nine active site
substitutions and cannot function as a
RubisCO15. One of the R. palustris RLPs (RLP2, Rpa0262) is 66%
identical to the C. tepidum RLP protein and
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contains the same pattern of active site substitutions. R.
palustris RLP1 (Rpa2169) has seven active site
substitutions dis-tinct from those in its RLP2. A C. tepidum rlp
mutant is defective in its ability to oxidize
reduced sulfur compounds and from this we infer that the R.
palustris RLPs are probably involved in sulfur
metabolism16.
Biodegradation
Purple photosynthetic bacteria are a major component of
microbial populations found in wastewater treatment
facilities exposed to sunlight17, 18. R. palustris thrives in
such environments because it metabolizes
structurally diverse compounds found as components of degrading
plant and animal wastes. These include
lignin monomers, fatty acids and dicarboxylic acids of the types
derived from green plants, animal fats and
seed oils. R. palustris also degrades nitrogen-containing
compounds including amino acids and heterocyclic
aromatic compounds2, and it dehalogenates and degrades
chlorinated benzoates and chlorinated fatty acids19,
20, compounds that are sometimes found in industrial wastes.
Although R. palustris has been studied for its biodegradation
abilities and is a model for molecular studies of
aromatic ring degradation in the absence of molecular oxygen21,
its genome has revealed a much larger
inventory of degradation genes than expected. It encodes four
distinct oxygenase-dependent ring cleavage
pathways for the aerobic degradation of the aromatic compounds
protocatechuate, homoprotocatechuate,
homogentisate and phenylacetate (Fig. 2 and Supplementary Table
1 online). R. palustris has the potential
to combine oxygen-sensitive and oxygen-requiring enzyme reaction
sequences to accomplish complete
degradation. An example is the anaerobic transformation of
phenol to 4-hydroxyphenylacetate, which is then
degraded aerobically via either the homogentisate or
homoprotocatechuate pathways22. These types of
transformations would be expected to occur in populations
straddling oxic to anoxic transition zones. The
genome contains 19 mono- or dioxygenase and four cytochrome P450
genes. Additional genes that may be
useful in bioremediation or biocatalysis include nitrile
hydratase (rpa2805 and rpa2806) and amidase
(rpa2415) genes, phosphonate utilization genes (rpa0687–rpa0700)
and carboxylesterase genes (rpa1568,
rpa2627, rpa3893 and rpa4646). The R. palustris genome has 16
glutathione S–transferase genes, some of
which may catalyze the cleavage of !-aryl ether bonds23.
R. palustris encodes a complete tricarboxylic acid cycle, an
Embden-Meyerhof pathway and a pentose
phosphate pathway. A predicted glyoxylate shunt permits use of
acetate as a sole carbon source, and the
genome sequence indicates the synthesis of glycogen and poly
!–hydroxyalkanoates as carbon storagepolymers. Other genes encode
enzymes to mobilize and degrade these polymers during times of
carbon
starvation. R. palustris has a limited ability to grow on sugars
and this is reflected by the absence in its genome
sequence of glucose or fructose transporters or a hexokinase
gene. Genes of the Entner-Doudoroff pathway are
absent.
Nitrogen fixation and nitrogen assimilation
We were surprised to find that R. palustris has structural genes
for three different nitrogenases as well as the
related cofactor and assembly genes for these nitrogenases (Fig.
2 and Supplementary Table 1 online).
Previously, only Azotobacter sp., a heterotrophic obligate
aerobe, had been found to encode three nitrogenases.
R. palustris encodes a molybdenum-dependent nitrogenase, found
in all nitrogen-fixing bacteria, and also a
vanadium-dependent and an alternative iron nitrogenase. R.
palustris encodes dinitrogenase reductase ADP-
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Table 2: R. palustris regulatory and signaling proteins
Full table
ribosyltransferase (DraT) (Rpa1431 and Rpa2405) and
dinitrogenase reductase activating glycohydrolase
(DraG) (Rpa2406) enzymes that likely modulate the activity of
dinitrogenase reductase by reversible ADP
ribosylation. Homologs of NifA (Rpa4632), VnfA (Rpa1374) and
AnfA (Rpa1439) regulators are present to
potentially activate their cognate clusters of nitrogenase genes
in conjunction with the single RNA polymerase
sigma factor, RpoN (Rpa0050).
Its genome sequence indicates that R. palustris incorporates
ammonia exclusively through glutamine
synthetase and glutamine:oxoglutarate aminotransferase
reactions. It encodes four glutamine synthetases and
genes for post-translational control of glutamine synthetase
activity by reversible adenylylation are present. R.
palustris has contiguous duplicated, although not identical,
amtB genes rpa0273 and rpa0275 encoding
ammonium transporters. Additional transport and metabolic
capacity exists to use cyanate (rpa2115), urea
(rpa3658–rpa3664) and ethanolamine (rpa3747–rpa3749) as
potential nitrogen sources.
Regulation and signal transduction
Because it is a successful metabolic opportunist, R. palustris
should be able to sense diverse environmental
conditions to appropriately regulate gene expression for
survival and growth. It also needs to integrate its
metabolism and distribute limited pools of ATP and reductant to
competing processes such as nitrogen fixation
and carbon dioxide fixation. R. palustris has 451 potential
regulatory and signaling genes, many of which
encode multiple domain motifs (Table 2; see Supplementary Table
2 online for a complete list)24. It
devotes about the same proportion of its genes (9.3%) to
regulation as do the soil bacteria Pseudomonas
putida, Streptomyces coelicolor and Streptomyces avermitilis
(http://www.tigr.org/). Regulatory genes
comprise 5–6% of the genomes of most free-living bacteria. The
great variety in the domain architecture of R.
palustris' 63 signal transduction histidine kinases points to
their involvement in regulating many different
processes. Half of these genes encode from one to ten predicted
transmembrane regions, 20 have PAS
domains, 9 have GAF domains (which are characteristic of
phytochromes) and 2 have very large, novel
cytoplasmic domains. The genome has genes for 19 different RNA
polymerase sigma factors, 16 of which are
classified as extracytoplasmic function (ECF) sigma factors25.
Two of the ECF sigma factor genes (rpa0639
and rpa1635) are located near flagella biosynthesis genes and
another (rpa0550) is translationally coupled to a
gene resembling the cytochrome c2 anti-sigma factor gene chrR26,
suggesting specific functions.
R. palustris has an acylhomoserine lactone (HSL) synthase gene
(rpa0320) that is adjacent to the HSL-
responsive regulator gene rpa0321. HSLs produced by
gram-negative bacteria serve as intercellular signals
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that allow cells to monitor their population density. Generally,
HSLs activate expression of genes that are
advantageous to a species when cells of that species are at a
population density perceived as a quorum. R.
palustris genes that might be controlled by quorum sensing
include genes rpa1885–rpa1906 for a phage-like
particle called a gene transfer agent27, polyketide synthase
gene rpa3339, and genes rpa3342–rpa3357 for the
production and export of exopolysaccharides28, 29.
R. palustris has genes for three complete chemotaxis signal
transduction complexes and it has 30 chemotaxis
sensory transducer genes. All but five of the transducers are
predicted to be membrane-bound proteins. Four of
the transducer genes (rpa4202, rpa4311, rpa4481 and rpa4483) are
translationally coupled to or located just a
few base pairs away from a sensor gene with a PAS domain. These
gene pairs may have originally existed as
single genes but have been translationally frameshifted. The
existence of the same split genes in
Magnetospirillum magnetotacticum and Rhodospirillum rubrum
suggests that this arrangement may have
been present in an ancestor common to these three organisms.
Transport
The genome of R. palustris encodes about 325 transport systems
comprising at least 700 genes, adding up to
almost 15% of the genome. Transport genes account for 5–6% of
most bacterial genomes30. A complete listing,
classified using the TC Number system31 can be found as
Supplementary Table 3 online. There are 102
primary transport systems, defined as systems powered directly
by ATP hydrolysis. These include 86 ATP-
binding cassette (ABC) systems and 7 P-type ATPases and type II,
III and IV secretion systems. The P-type
ATPases likely confer resistance to heavy metals32. Separate R.
palustris Type II secretion systems are likely
used for the biogenesis of type IV pili and general protein
secretion (the Sec system), with a type III secretion
system for flagella biosynthesis. R. palustris has two sets of
type IV secretion genes (rpa2224–rpa2233 and
rpa4115–rpa4124) similar to the Trb genes from Agrobacterium
tumefaciens for conjugal transfer of DNA33.
R. palustris encodes 137 secondary transport systems including
36 major facilitator superfamily (MFS)
members, 22 resistance-nodulation-cell division (RND) pumps, 15
divalent metal transport (DMT) members
and 8 tripartate ATP-independent periplasmic (TRAP)
tranporters34, 35. All but two of the RND systems are
classified as heavy metal and drug efflux pumps. This is the
largest number of RND pumps observed in any
bacterium to date and may explain the high intrinsic resistance
of R. palustris to antibiotics. R. palustris has
been isolated in high numbers from polluted environments36.
Heavy metal efflux transporters should allow R.
palustris to live in a variety of environments and still acquire
the necessary nutrients while resisting heavy
metal toxicity.
Of the 86 ABC systems, 20 are related to the branched chain
amino acid uptake (ilvFGHKL) system of E. coli.
Isoleucine, leucine and valine are hydrophobic amino acids and
we speculate that other members of this
amplified family are specific for other sorts of hydrophobic
compounds such as lignin monomers, fatty acids
and dicarboxylic acids derived from oils and fats. One system of
this ilv ABC family (Rpa0665–Rpa0668) has
tentatively been identified as a 4-hydroxybenzoate transport
system21. Another (rpa1789 and rpa1791–1793)
lies adjacent to a feruloyl CoA ligase gene implying that it
catalyzes the uptake of the lignin monomer ferulate.
A third example is an ilv family ABC system (rpa3719–3725) that
is next to genes for the degradation of the
dicarboxylic acid pimelate. An analysis of 73 other microbial
genomes shows that 34 of them have no ilv-like
transport systems. Another 25 microbes have between one and five
of these systems and 11 microbes have
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between six and ten ilv family ABC transporters. Only three
other species, Burkholderia fungorum LB400 and
Ralstonia eutropha, both !-proteobacteria, and B. japonicum,
have 19 or more versions of the ilv-like ABCtransport operon.
Iron acquisition appears to be particularly important for R.
palustris. It encodes 24 outer membrane ferric iron
siderophore receptors, and 7 TonB systems for powering these and
other outer membrane receptors
(Supplementary Table 3 online). This implies that R. palustris
uses a large number of different types of
siderophores for iron acquisition. However, genes
rpa2388–rpa2390 to synthesize only one siderophore,
rhizobactin37, were detected suggesting that R. palustris may
transport iron-loaded siderophores produced by
other soil bacteria. As many as seven of the ECF sigma factors
encoded by R. palustris are either translationally
coupled to ferrisiderophore-like receptor genes or are located
very close to genes involved in iron acquisition;
in one case siderophore biosynthesis genes and in another, a
predicted heme uptake system. This suggests a
role for multiple alternative sigma factors in activating gene
expression in response to iron starvation38.
Discussion
R. palustris owes much of its metabolic versatility to known
genes encoding metabolic modules of carbon
dioxide fixation and photophosphorylation that act in concert
with dehydrogenases, oxidoreductases and
carbon degradation pathways to support its four modes of growth
(Fig. 1). The number of options that R.
palustris has within the major metabolic modes to take advantage
of fluctuating supplies of carbon, nitrogen,
light and oxygen is unusually large. The existence of genes for
three nitrogenases, multiple aromatic
degradation pathways and multiple oxidoreductases was not known
before the genome sequence. Its large
inventory of transport and chemotaxis genes implies that R.
palustris is adept at sensing and acquiring diverse
compounds from its environment. The groundwork has now been laid
to explore regulatory strategies used by
R. palustris to appropriately select and integrate its large
number of metabolic choices.
R. palustris is ideally suited for use as a biocatalyst because
it generates ample supplies of ATP from light thus
catalyzing reactions that are thermodynamically unfavorable and
beyond the potential of chemotrophic
organisms. The metabolic group of purple phototrophic bacteria
to which it belongs have been evaluated as
sources of single cell protein, for the synthesis of
polyhydroxyalkanoate 'bioplastics' and for the production of
hydrogen, which they generate as a product of nitrogen
fixation39. Its genome sequence reveals that R.
palustris has additional capabilities, not shared by other
purple bacteria, that enhance its potential for use in
biotechnological applications. These include modulating
photosynthesis according to light quality and
degrading aromatic compounds that are typically found in
agricultural and industrial wastes. That the genome
encodes oxygen-requiring, as well as anaerobic reductive
pathways, for the degrada-tion of aromatic rings,
suggests the possibility of designing hybrid degradation
pathways of broader substrate specificity than those
that occur naturally. R. palustris has physical attributes that
are well suited for process development. It
undergoes asymmetric cell division and produces a cell surface
adhesin at one end of the cell that causes cells
to stick to solid substrates. R. palustris has especially good
potential for use as a biocatalyst for hydrogen
production. It is unique among purple phototrophic bacteria in
encoding a vanadium-containing nitrogenase
that catalyzes the production of approximately three times as
much hydrogen as do molybdenum-containing
nitrogenases40. R. palustris derives reductant for hydrogen
generation from plant biomass, and energy
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captured from sunlight drives the process. Manipulating R.
palustris to produce hydrogen efficiently will
require a detailed knowledge of how each of its three
nitrogenases is regulated. It will also be important to
know in detail how the metabolic modules of
photophosphorylation, biodegradation, carbon dioxide fixation
and hydrogen uptake are regulated and how their activities are
integrated.
Methods
Construction, isolation and sequencing of small-insert and
large-insert libraries.
Genomic DNA, isolated from the R. palustris CGA009, was
sequenced using a conventional whole genome
shotgun strategy41. Briefly, random 2–3 kb-DNA fragments were
isolated after mechanical shearing. These
gel-extracted fragments were concentrated, end-repaired and
cloned into pUC18. Double-ended plasmid
sequencing reactions were carried out using PE BigDye Terminator
chemistry (Perkin Elmer) and sequencing
ladders were resolved on PE 3700 Automated DNA Sequencers. One
round (117,510 reads) of small-insert
library sequencing was done, generating roughly 9.6-fold
redundancy.
A large insert (~30 kb) fosmid library was also constructed by
Sau3AI partial digestion of genomic DNA and
cloning into the pFos1 cloning vector42. End sequencing of ~300
fosmid clones (0.02-fold redundancy)
generated roughly 2-fold genome scaffold coverage. The fosmids
were fingerprinted with EcoRI to aid in
assembly verification and determination of gap sizes and
provided a minimal scaffold used for order and
orientation across assembly gaps. The 8.4-kb plasmid was
assembled from a total of 107 reads.
Sequence assembly and gap closure.
Sequence traces were processed with Phred43, 44 for base calling
and assessment of data quality before
assembly with Phrap (P. Green, University of Washington,
Seattle, Washington, USA) and visualization with
Consed45. Gaps were closed by primer walking on gap-spanning
library clones (identified using linking
information from forward and reverse reads). Alternatively, some
of the larger gaps, including the larger
regions covered only by fosmid clones, were closed by primer
walking on PCR products. Remaining physical
(uncaptured) gaps were closed by combinatorial (multiplex) PCR.
Sequence finishing and polishing added a
total of 300 reads and assessment of final assembly quality was
done as previously described46.
Sequence analysis and annotation.
Gene modeling was done using the Critica47, Glimmer48 and
Generation
(http://compbio.ornl.gov/generation/index.shtml) modeling
packages, the results were combined and
a basic local alignment search tool (BLAST) for proteins (P)
search of the translations versus GenBank's
nonredundant database (NR) was conducted. The alignment of the N
terminus of each gene model versus the
best NR match was used to pick a preferred gene model. If no
BLAST match was returned, the Critica model
was retained. Gene models that overlapped by greater than 10% of
their length were flagged, giving preference
to genes with a BLAST match. The revised gene/protein set was
searched against the KEGG GENES, InterPro
(incorporating Pfam, TIGRFams, SmartHMM, PROSITE, PRINTS and
ProDom) and Clusters of Orthologous
Groups of proteins (COGs) databases, in addition to BLASTP
versus NR. From these results, categorizations
were developed using the KEGG and COGs hierarchies. Initial
criteria for automated functional assignment
required a minimum 50% residue identity over 80% of the length
of the match for BLASTP alignments, plus
concurring evidence from pattern or profile methods. Putative
assignments were made for identities down to
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30%, over 80% of the length. Automated assignments were reviewed
and curated manually using a web-based
editing environment.
Nucleotide sequence accession number.
The sequence of the complete genome of R. palustris CGA009 is
available under GenBank/EMBL/DDBJ
accession numbers BX571963 (chromosome) and BX571964
(plasmid).
Note: Supplementary information is available on the Nature
Biotechnology website.
Acknowledgments
The Biological and Environmental Research program of the US
Department of Energy's Office of Science
funded this research. The Joint Genome Institute managed the
overall sequencing effort. The University of
California, Lawrence Livermore National Laboratory, carried out
genome finishing under the auspices of the
US Department of Energy (DOE). Computational annotation was
carried out at the Oak Ridge National
Laboratory, managed by UT-BATTELLE for the DOE. The DOE provided
additional support to J.T.B., F.R.T.
and C.S.H. The US Army Research Office provided support to
C.S.H.
Competing interests statement
The authors declare no competing financial interests.
Received 24 September 2003; Accepted 3 November 2003; Published
online 14 December 2003.
References
1. Barbosa, M.J., Rocha, J.M., Tramper, J. & Wijffels, R.H.
Acetate as a carbon source for hydrogen
production by photosynthetic bacteria. J. Biotechnol. 85,
25–33
(2001). | Article | PubMed | ISI | ChemPort |
2. Sasikala, C. & Ramana, C.V. Biodegradation and metabolism
of unusual carbon compounds by
anoxygenic phototrophic bacteria. Adv. Microb. Physiol. 39,
339–377
(1998). | PubMed | ISI | ChemPort |
3. Philippot, L. Denitrifying genes in bacterial and archaeal
genomes. Biochim. Biophys. Acta. 1577, 355–
376 (2002). | Article | PubMed | ISI | ChemPort |
4. Hu, X., Ritz, T., Damjanovic, A., Autenrieth, F. &
Schulten, K. Photosynthetic apparatus of purple
bacteria. Q. Rev. Biophys. 35, 1–62 (2002). | Article | PubMed |
ISI | ChemPort |
5. Giraud, E., Hannibal, L., Fardoux, J., Vermeglio, A. &
Dreyfus, B. Effect of Bradyrhizobium
photosynthesis on stem nodulation of Aeschynomene sensitiva.
Proc. Natl. Acad. Sci. USA 97, 14795–
14800 (2000). | Article | PubMed | ChemPort |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=search&term=BX571963http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=search&term=BX571964http://www.nature.com/nbt/journal/v22/n1/suppinfo/nbt923_S1.htmlhttp://dx.doi.org/10.1016/S0168-1656(00)00368-0http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11164959&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000166884300004&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXntl2ntA%3D%3D&pissn=1087-0156&pyear=2003&md5=b8d25e7b8d5aa25f2ab22246870aca55http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9328651&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1998BJ77Y00007&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK2sXnt1ygsbc%3D&pissn=1087-0156&pyear=2003&md5=245361593d5cb42359c63f33035e147bhttp://dx.doi.org/10.1016/S0167-4781(02)00420-7http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12359326&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000178519500001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38XnsVSmt78%3D&pissn=1087-0156&pyear=2003&md5=dad0899fcd185d3a6ad13c222fbd065dhttp://dx.doi.org/10.1017/S0033583501003754http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11997980&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000175365400001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38XktlSjtrc%3D&pissn=1087-0156&pyear=2003&md5=df9bebdfde21e82b1dfec0cfc5e8f25fhttp://dx.doi.org/10.1073/pnas.250484097http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11114184&dopt=Abstracthttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXitVGntQ%3D%3D&pissn=1087-0156&pyear=2003&md5=d103fa34e147af3fbb320d5323efbcf8
-
2015-05-04 15.08Complete genome sequence of the metabolically
versatile photosynt…erium Rhodopseudomonas palustris : Article :
Nature Biotechnology
Sida 11 av
15http://www.nature.com/nbt/journal/v22/n1/full/nbt923.html
6. Boivin, C. et al. Stem nodulation in legumes: diversity,
mechanisms, and unusual characteristics. Crit.
Rev. Plant Sci. 16, 1–30 (1997). | ISI | ChemPort |
7. Giraud, E. et al. Bacteriophytochrome controls photosystem
synthesis in anoxygenic bacteria. Nature
417, 202–205 (2002). | Article | PubMed | ISI | ChemPort |
8. van Berkum, P. et al. Discordant pylogenies within the rrn
loci of Rhizobia. J. Bacteriol. 185, 2988–
2998 (2003). | Article | PubMed | ISI | ChemPort |
9. Cogdell, R.J. et al. How photosynthetic bacteria harvest
solar energy. J. Bacteriol. 181, 3869–3879
(1999). | PubMed | ISI | ChemPort |
10. Gall, A. & Robert, B. Characterization of the different
peripheral light-harvesting complexes from high-
and low-light grown cells from Rhodopseudomonas palustris.
Biochemistry 38, 5185–5190
(1999). | Article | PubMed | ISI | ChemPort |
11. Johnson, C.H. & Golden, S.S. Circadian programs in
cyanobacteria: adaptiveness and mechanism. Annu.
Rev. Microbiol. 53, 389–409 (1999). | Article | PubMed | ISI |
ChemPort |
12. Tabita, F.R. Microbial ribulose–1,5–bisphosphate
carboxylase/oxygenase: a different perspective.
Photosynthesis Res. 60, 1–28 (1999). | Article | ISI | ChemPort
|
13. Friedrich, C.G., Rother, D., Bardischewsky, F., Quentmeier,
A. & Fischer, J. Oxidation of reduced
inorganic sulfur compounds by bacteria: emergence of a common
mechanism? Appl. Environ.
Microbiol. 67, 2873–2882 (2001). | Article | PubMed | ISI |
ChemPort |
14. Rolls, J.P. & Lindstrom, E.S. Effect of thiosulfate on
the photosynthetic growth of Rhodopseudomonas
palustris. J. Bacteriol. 94, 860–869 (1967). | PubMed | ISI |
ChemPort |
15. Hanson, T.E. & Tabita, F.R. A ribulose–1,5–bisphosphate
carboxylase/oxygenase (RubisCO)–like
protein from Chlorobium tepidum that is involved with sulfur
metabolism and the response to oxidative
stress. Proc. Natl. Acad. Sci. USA 98, 4397–4402 (2001). |
Article | PubMed | ChemPort |
16. Hanson, T.E. & Tabita, F.R. Insights into the stress
response and sulfur metabolism revealed by
proteome analysis of a Chlorobium tepidum mutant lacking the
RubisCO-like protein. Photosynthesis
Res. 78, 231–248 (2003). | Article | ISI | ChemPort |
17. Do, Y.S. et al. Role of Rhodobacter sp. strain PS9, a purple
non-sulfur photosynthetic bacterium isolated
from an anaerobic swine waste lagoon, in odor remediation. Appl.
Environ. Microbiol. 69, 1710–1720
(2003). | Article | PubMed | ISI | ChemPort |
18. Kobayashi, M. & Kobayashi, M. in Anoxygenic
Photosynthetic Bacteria (eds. Blankenship, R.E.,
Madigan, M.T. & Bauer, C.E.) 1269–1282 (Kluwer Academic
Publishers, Dordrecht, The Netherlands,
1995).
19. McGrath, J.E. & Harfoot, C.G. Reductive dehalogenation
of halocarboxylic acids by the phototrophic
genera Rhodospirillum and Rhodopseudomonas. Appl. Environ.
Microbiol. 63, 3333–3335
(1997). | PubMed | ISI | ChemPort |
http://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1997WF92500001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK2sXhtlKmtL8%3D&pissn=1087-0156&pyear=2003&md5=e8a589db8dbca94ba207d44bfa0a9248http://www.nature.com/doifinder/10.1038/417202ahttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12000965&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000175460200049&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38Xjs1Sqtr8%3D&pissn=1087-0156&pyear=2003&md5=7d009362d766936a97f457cf9676778bhttp://dx.doi.org/10.1128/JB.185.10.2988-2998.2003http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12730157&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000182686900003&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3sXjs1aqu7g%3D&pissn=1087-0156&pyear=2003&md5=17cdd84b5273d9502d6dde9df34a1320http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=10383951&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000081158300001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1MXktFCisr4%3D&pissn=1087-0156&pyear=2003&md5=6ee1546dbf6f4237e48916767636dfa9http://dx.doi.org/10.1021/bi982486qhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=10213625&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000079924500035&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1MXitVagtbg%3D&pissn=1087-0156&pyear=2003&md5=4859889ecb198e3723ebacef3bd09ca7http://dx.doi.org/10.1146/annurev.micro.53.1.389http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=10547696&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000083208500013&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1MXmvVOnsbw%3D&pissn=1087-0156&pyear=2003&md5=4f0809d977e76a317aa2c9a527169c41http://dx.doi.org/10.1023/A:1006211417981http://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000081922900001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1MXlslSgsbo%3D&pissn=1087-0156&pyear=2003&md5=5de750aedd9643ede4a639ad798fc54fhttp://dx.doi.org/10.1128/AEM.67.7.2873-2882.2001http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11425697&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000169605400001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXkvFSnt7s%3D&pissn=1087-0156&pyear=2003&md5=feb7b4d1c113e598761a679d3e29def2http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=6051358&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1967A098900013&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaF2sXltVKitro%3D&pissn=1087-0156&pyear=2003&md5=88ab5148f93a2f94f7d5df0834daff90http://dx.doi.org/10.1073/pnas.081610398http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11287671&dopt=Abstracthttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXjtVagtr4%3D&pissn=1087-0156&pyear=2003&md5=f2682e5ea82b95eaa31ffee4f1e61348http://dx.doi.org/10.1023/B:PRES.0000006829.41444.3dhttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000186986200005&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3sXpsV2kt7Y%3D&pissn=1087-0156&pyear=2003&md5=8c73a6742f93e5ca2c14641890378fe3http://dx.doi.org/10.1128/AEM.69.3.1710-1720.2003http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12620863&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000181435600050&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3sXitlClsbc%3D&pissn=1087-0156&pyear=2003&md5=38759d3723968ccc90078fca93d56719http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9251226&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1997XP06700063&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK2sXlt1Witr4%3D&pissn=1087-0156&pyear=2003&md5=cb0c6d81c8c0bfd1a66ea6112bbad0a9
-
2015-05-04 15.08Complete genome sequence of the metabolically
versatile photosynt…erium Rhodopseudomonas palustris : Article :
Nature Biotechnology
Sida 12 av
15http://www.nature.com/nbt/journal/v22/n1/full/nbt923.html
20. Egland, P.G., Gibson, J. & Harwood, C.S. Reductive,
coenzyme A–mediated pathway for 3–
chlorobenzoate degradation in the phototrophic bacterium
Rhodopseudomonas palustris. Appl.
Environ. Microbiol. 67, 1396–1399 (2001). | Article | PubMed |
ISI | ChemPort |
21. Egland, P.G., Pelletier, D.A., Dispensa, M., Gibson J. &
Harwood, C.S. A cluster of bacterial genes for
anaerobic benzene ring biodegradation. Proc. Natl. Acad. Sci.
USA 94, 6484–6489
(1997). | Article | PubMed | ChemPort |
22. Noh, U., Heck, S., Giffhorn, F. & Kohring, G.W.
Phototrophic transformation of phenol to 4-
hydroxyphenylacetate by Rhodopseudomonas palustris. Appl.
Microbiol. Biotechnol. 58, 830–835
(2002). | Article | PubMed | ISI | ChemPort |
23. Masai, E. et al. Roles of the enantioselective glutathione
S-transferases in cleavage of beta-aryl ether. J.
Bacteriol. 185, 1768–1775 (2003). | Article | PubMed | ISI |
ChemPort |
24. Galperin, M.Y., Nikolskaya, A.N. & Koonin, E.V. Novel
domains of the prokaryotic two-component signal
transduction systems. FEMS Microbiol. Lett. 203, 11–21
(2001). | Article | PubMed | ISI | ChemPort |
25. Helmann, J.D. The extracytoplasmic function (ECF) sigma
factors. Adv. Microb. Physiol. 46, 47–110
(2002). | PubMed | ISI | ChemPort |
26. Newman, J.D., Anthony, J.R. & Donohue, T.J. The
importance of zinc-binding to the function of
Rhodobacter sphaeroides ChrR as an anti-sigma factor. J. Mol.
Biol. 313, 485–499
(2001). | Article | PubMed | ISI | ChemPort |
27. Lang, A.S. & Beatty, J.T. The gene transfer agent of
Rhodobacter capsulatus and "constitutive
transduction" in prokaryotes. Arch. Microbiol. 175, 241–249
(2001). | Article | PubMed | ISI | ChemPort |
28. Marketon, M.M., Glenn, S.A., Eberhard, A. & Gonzalez,
J.E. Quorum sensing controls exopolysaccharide
production in Sinorhizobium meliloti. J. Bacteriol. 185,
325–331
(2003). | Article | PubMed | ISI | ChemPort |
29. Schaefer, A.L., Taylor, T.A., Beatty, J.T. & Greenberg,
E.P. Long-chain acyl-homoserine lactone quorum-
sensing regulation of Rhodobacter capsulatus gene transfer agent
production. J. Bacteriol. 184, 6515–
6521 (2002). | Article | PubMed | ISI | ChemPort |
30. Paulson, I.T., Nguyen, L., Sliwinski, M.K., Rabus, R. &
Saier, M.H. Jr. Microbial genome analysis:
comparative transport capabilities in eighteen prokaryotes. J.
Mol. Biol. 301, 75–100
(2000). | Article | PubMed | ISI | ChemPort |
31. Saier, M.H. Jr. A functional-phylogenetic classification
system for transmembrane solute transporters.
Microbiol. Mol. Biol. Rev. 64, 354–411 (2000). | Article |
PubMed | ISI | ChemPort |
32. Rosen, B.P. Transport and detoxification systems for
transition metals, heavy metals and metalloids in
eukaryotic and prokaryotic microbes. Comp. Biochem. Physiol. A
Mol. Integr. Physiol. 133, 689–693
(2002). | Article | PubMed | ISI |
http://dx.doi.org/10.1128/AEM.67.3.1396-1399.2001http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11229940&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000167266200054&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXhslSjt7w%3D&pissn=1087-0156&pyear=2003&md5=b0363bcc02060fa47a5c3acf1a9d5288http://dx.doi.org/10.1073/pnas.94.12.6484http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9177244&dopt=Abstracthttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK2sXjvFGgsL0%3D&pissn=1087-0156&pyear=2003&md5=134e69065e379201aeabcbdf69257fc2http://dx.doi.org/10.1007/s00253-002-0954-3http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12021805&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000175863900019&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38XktFCqurY%3D&pissn=1087-0156&pyear=2003&md5=c8309516ad73f7e7508f01bc122806aahttp://dx.doi.org/10.1128/JB.185.6.1768-1775.2003http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12618439&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000181448900002&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3sXitFWktrw%3D&pissn=1087-0156&pyear=2003&md5=ec920822d87335c892ab067a3e3fef3dhttp://dx.doi.org/10.1016/S0378-1097(01)00326-3http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11557134&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000171084400002&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXmsleiur4%3D&pissn=1087-0156&pyear=2003&md5=155688d8f33e09a756b2a8e0f0b71182http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12073657&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000176466600002&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38XlsVKmsro%3D&pissn=1087-0156&pyear=2003&md5=353031075c9f46ef92e6fac1fc940be9http://dx.doi.org/10.1006/jmbi.2001.5069http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11676534&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000171979000005&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXnslCrtr8%3D&pissn=1087-0156&pyear=2003&md5=c5384153d5b8429f5accab0862941244http://dx.doi.org/10.1007/s002030100260http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11382219&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000168520700001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXjvFKjtb4%3D&pissn=1087-0156&pyear=2003&md5=63f3994471c2701553e5096741a17f5fhttp://dx.doi.org/10.1128/JB.185.1.325-331.2003http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12486070&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000180050900037&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3sXht1Gisw%3D%3D&pissn=1087-0156&pyear=2003&md5=883143d9ca829a66f31f7b1ea1e154d0http://dx.doi.org/10.1128/JB.184.23.6515-6521.2002http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12426339&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000179242600016&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38XovFOnsbg%3D&pissn=1087-0156&pyear=2003&md5=c7822f3299dc3fcfd5fe7d4897821deahttp://dx.doi.org/10.1016/S0168-9525(98)01518-2http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=10926494&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000088705300008&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3cXltlCjs74%3D&pissn=1087-0156&pyear=2003&md5=d172c5cffbd0a02d1ffd7604b3e0fd49http://dx.doi.org/10.1128/MMBR.64.2.354-411.2000http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=10839820&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000087486200004&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3cXksVGis7w%3D&pissn=1087-0156&pyear=2003&md5=bf7f165004b395c2ea0ba4a1a3145a33http://dx.doi.org/10.1016/S1095-6433(02)00201-5http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12443926&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000180019200024&DestApp=WOS_CPL
-
2015-05-04 15.08Complete genome sequence of the metabolically
versatile photosynt…erium Rhodopseudomonas palustris : Article :
Nature Biotechnology
Sida 13 av
15http://www.nature.com/nbt/journal/v22/n1/full/nbt923.html
33. Cao, T.B. & Saier, M.H. Jr. Conjugal type IV
macromolecular transfer systems of Gram–negative
bacteria: organismal distribution, structural constraints and
evolutionary conclusions. Microbiology
147, 3201–3214 (2001). | PubMed | ISI | ChemPort |
34. Saier, M.H. Jr. & Paulsen, I.T. Phylogeny of multidrug
transporters. Semin. Cell Dev. Biol. 12, 205–213
(2001). | Article | PubMed | ISI | ChemPort |
35. Kelly, D.J. & Thomas, G.H. The tripartite
ATP-independent periplasmic (TRAP) transporters of bacteria
and archaea. FEMS Microbiol. Rev. 25, 405–424 (2001). | Article
| PubMed | ISI | ChemPort |
36. Oda, Y. et al. Genotypic and phenotypic diversity within
species of purple nonsulfur bacteria isolated
from aquatic sediments. Appl. Environ. Microbiol. 68,
3467–3477
(2002). | Article | PubMed | ISI | ChemPort |
37. Lynch, D. et al. Genetic organization of the region encoding
regulation, biosynthesis, and transport of
rhizobactin 1021, a siderophore produced by Sinorhizobium
meliloti. J. Bacteriol. 183, 2576–2585
(2001). | Article | PubMed | ISI | ChemPort |
38. Visca, P., Leoni, L., Wilson, M.J. & Lamont, I.L. Iron
transport and regulation, cell signalling and
genomics: lessons from Escherichia coli and Pseudomonas. Mol.
Microbiol. 45, 1177–1190
(2002). | Article | PubMed | ISI | ChemPort |
39. Sasikala, C. & Ramana, C.V. Biotechnological potentials
of anoxygenic phototrophic bacteria. II.
Biopolyesters, biopesticide, biofuel, and biofertilizer. Adv.
Appl. Microbiol. 41, 227–278
(1995). | PubMed | ISI | ChemPort |
40. Eady, R.R. Structure–function relationships of alternative
nitrogenases. Chem. Rev. 96, 3013–3030
(1996). | Article | PubMed | ISI | ChemPort |
41. Fleischmann, R.D. et al. Whole genome random sequencing and
assembly of Haemophilus influenzae
Rd. Science 269, 496–512 (1995). | Article | PubMed | ISI |
ChemPort |
42. Kim, U.J., Shizuya, H., deJong, P.J., Birren, B. &
Simon, M.I. Stable propagation of cosmid sized human
DNA inserts in an F factor based vector. Nucleic Acids Res. 20,
1083–1085
(1992). | Article | PubMed | ISI | ChemPort |
43. Ewing, B. & Green, P. Base-calling of automated
sequencer traces using phred. II. Error probabilities.
Genome Res. 8, 186–194 (1998). | PubMed | ISI | ChemPort |
44. Ewing, B., Hillier, L., Wendl, M.C. & Green, P.
Base-calling of automated sequencer traces using phred.
I. Accuracy assessment. Genome Res. 8, 175–185 (1998). | PubMed
| ISI | ChemPort |
45. Gordon, D., Abajian, C. & Green, P. Consed: a graphical
tool for sequence finishing. Genome Res. 8,
195–202 (1998). | PubMed | ISI | ChemPort |
46. Chain, P. et al. Complete genome sequence of the
ammonia-oxidizing bacterium and obligate
chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185,
2759–2773
(2003). | Article | PubMed | ISI | ChemPort |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11739753&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000172735500004&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXptlelu78%3D&pissn=1087-0156&pyear=2003&md5=b99caa4434f6064ab3b70158f8323d18http://dx.doi.org/10.1006/scdb.2000.0246http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11428913&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000169859800002&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXlvVKru7c%3D&pissn=1087-0156&pyear=2003&md5=45f4d6658f040c9d35b0b342a83cb89ahttp://dx.doi.org/10.1016/S0168-6445(01)00061-4http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11524131&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000170864700002&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXmt1Kls7s%3D&pissn=1087-0156&pyear=2003&md5=082b25a4a5dc525bf4fe9e2976df7e0chttp://dx.doi.org/10.1128/AEM.68.7.3467-3477.2002http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12089030&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000176631600038&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38Xlt1SntLc%3D&pissn=1087-0156&pyear=2003&md5=11582e18073aee7e3f6c01732ba98642http://dx.doi.org/10.1128/JB.183.8.2576-2585.2001http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11274118&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000167794600023&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3MXis1art7g%3D&pissn=1087-0156&pyear=2003&md5=55b88850aa528d176e7059913e5161adhttp://dx.doi.org/10.1046/j.1365-2958.2002.03088.xhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12207687&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000177750400001&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD38XntFGktL8%3D&pissn=1087-0156&pyear=2003&md5=ff1bcd40abc51687cba900700ed6eab7http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=7572334&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1995BE46K00006&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK2sXivVOqsg%3D%3D&pissn=1087-0156&pyear=2003&md5=fc6e82b4937f7d903a88e57d3bd68aa6http://dx.doi.org/10.1021/cr950057hhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=11848850&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1996VT05300024&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK28Xmt1Gmsrs%3D&pissn=1087-0156&pyear=2003&md5=ccd23fe00f74517c6432e738ab64bd4bhttp://dx.doi.org/10.1126/science.7542800http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=7542800&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1995RL49500017&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK2MXntF2ksLc%3D&pissn=1087-0156&pyear=2003&md5=e8d8437a4c6560879cdd822c3e67f24chttp://dx.doi.org/10.1093/nar/20.5.1083http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=1549470&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=A1992HK00100017&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK38XitVyrt7g%3D&pissn=1087-0156&pyear=2003&md5=17f0e993f035cdfe2f7d90e0dd04d9f4http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9521922&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000072838200007&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1cXitlWlu7g%3D&pissn=1087-0156&pyear=2003&md5=ac6d2736d12cc38e5b175abd65973473http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9521921&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000072838200006&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1cXitlWlu78%3D&pissn=1087-0156&pyear=2003&md5=d5631f07add910ce63741815f9480229http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=9521923&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000072838200008&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DyaK1cXitlWksr0%3D&pissn=1087-0156&pyear=2003&md5=9e4c84b2666b5976c1886d55ed7bf4aehttp://dx.doi.org/10.1128/JB.185.9.2759-2773.2003http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12700255&dopt=Abstracthttp://links.isiglobalnet2.com/gateway/Gateway.cgi?&GWVersion=2&SrcAuth=Nature&SrcApp=Nature&DestLinkType=FullRecord&KeyUT=000182459500011&DestApp=WOS_CPLhttp://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BD3sXjt1Gmsro%3D&pissn=1087-0156&pyear=2003&md5=b7f30c1aac09783a3aa2d9e57a4fcc10
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2015-05-04 15.08Complete genome sequence of the metabolically
versatile photosynt…erium Rhodopseudomonas palustris : Article :
Nature Biotechnology
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15http://www.nature.com/nbt/journal/v22/n1/full/nbt923.html
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Nature Biotechnology ISSN 1087-0156 EISSN 1546-1696
47. Badger, J.H. & Olsen, G.J. CRITICA: coding region
identification tool invoking comparative analysis.
Mol. Biol. Evol. 16, 512–524 (1999). | PubMed | ISI | ChemPort
|
48. Delcher, A.L., Harmon, D., Kasif, S., White, O. &
Salzberg, S.L. Improved microbial gene identification
with GLIMMER. Nucleic Acids Res. 27, 4636–4641 (1999). | Article
| PubMed | ISI | ChemPort |
1. Genome Analysis and Systems Modeling, Oak Ridge National
Laboratory, One Bethel Valley Rd., OakRidge, Tennessee 37831,
USA.
2. Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek,
California 94598, USA.3. Lawrence Livermore National Laboratory,
7000 East Ave., Livermore, California 94550, USA.4. Department of
Microbiology and Immunology, The University of British Columbia,
6174 University
Blvd., Vancouver, British Columbia, Canada V6T 1Z3.5. Department
of Microbiology, The Ohio State University, 484 West 12th Ave.,
Columbus, Ohio 43210,
USA.6. Department of Microbiology, 3-432 Bowen Science Bldg.,
The University of Iowa, Iowa City, Iowa 52242,
USA.7. Present addresses: Odyssey Thera, 4550 Norris Canyon Rd.,
San Ramon, California 94583, USA (J.L.),
Department of Biology, University of California San Diego, 9500
Gilman Dr., La Jolla, California 92093,USA (L.D.), Delaware
Biotechnology Institute, The University of Delaware, 15 Innovation
Way, Newark,Delaware 19711, USA (T.E.H.), Genencor International,
925 Page Mill Rd., Palo Alto, California 94304,USA (C.P.).
Correspondence to: Caroline S Harwood6 e-mail:
[email protected]
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