Bacterial Genetics Genetic information Genetic elements Replication Genetic information transfer Regulation of gene expression Mutation and recombination.

Bacterial Genetics

• Genetic information • Genetic elements • Replication • Genetic information transfer • Regulation of gene expression• Mutation and recombination

Sugar backbone (ribose or deoxiribose) Antiparallel – complementary

(phosphate diester bond)

purine – pyrimidine

A TG C

Deoxi-nucleotide triphosphate units:dATP, dTTP, dGTP, dCTP

The three key processes of macromolecular synthesis are:

• DNA replication;

• transcription (the synthesis of RNA from a DNA template); and

• translation (the synthesis of proteins using messenger RNA as template).

DNA vs. RNA

Deoxyribose

Thymine

T-A G-C

Double stranded

Ribose

Uracil

U-A G-C

Single but

Loop-forming

Types of RNA

mRNA – messengertRNA – transferrRNA – ribosomal--------------------------------------------------Roles: Genetic (informational)

Functional: structure (ribosomes) function (ribozymes)

• Bacteria: promoters are recognized by the sigma subunit of RNA polymerase. These promoters have very similar sequences.

• Eukarya: the major classes of RNA are transcribed by three different RNA polymerases, with RNA polymerase II producing most mRNA.

• Archaea: have a single RNA that resembles in structure and function the RNA polymerase II.

Although the basic processes are the same in

both prokaryotes and eukaryotes, but more

complex in eukaryotes.

1. Eukaryotic genes have both:• Exons (coding regions and • Introns (noncoding regions).

2. Both are transcribed to primary mRNA3. Introns are excised Exons ligated 4. A cap is added at 3’ end 5. A poly-A tail added at 5’ end is clipped

and a6. Mature mRNA leaves the nucleus7. Translation takes place in cytoplasm

Transformation: Free DNA transfer; Requires competence factor

Transduction: Virus mediated transfer Generalized: Accidental DNA fragments packed in the virion (at random; lytic cycle)Specialized: Genes next to prophage are transducted (lysogenic cycle)

Conjugation: Plasmid-stimulated transferF- Recipient w/o plasmidF+ Plasmid only is transferredHfr Plasmid is integrated in the

chromosome both transferredF’ Plasmid w. chromosomal genes

Bacterial Genetics 2

• Mutation • Recombination• In vivo – techniques, transformation

transduction, conjugation • Plasmids, Transposalbe elements• In vitro – techniques• Bacterial genomics• Genetic engineering

Ch. 10, 15, 31

Different types of mutations can occur at different frequencies. For a typical bacterium, mutation rates of 10–7–10–11 per base pair are generally seen. Although RNA and DNA polymerases make errors at about the same rate, RNA genomes typically accumulate mutations at much higher frequencies than DNA genomes.

Genetic Recombination

General: RecASite-specific: Transposase

Eukaryotes: mating + crossing over

Prokaryotes:transformationtransductionconjungation

Transformation: Free DNA transfer; Requires competence factor

Transduction: Virus mediated transfer Generalized: Accidental DNA fragments packed in the virion (at random; lytic cycle)Specialized: Genes next to prophage are transducted (lysogenic cycle)

Conjugation: Plasmid-stimulated transferF- Recipient w/o plasmidF+ Plasmid only is transferredHfr Plasmid is integrated in the

chromosome both transferredF’ Plasmid w. chromosomal genes

Recombination General: homologous: same sequence-different source --- complement partial heteroduplex (prokaryotes). --- crossing-over (eukaryotes) Plasmids: mobilize external receptors & pilus F- no plasmid (competent vs. incompetent) F+ complete transfer regular--- separate circular Hfr complete transfer rare --- integrated F' plasmid + chromosomal genes  Interrupted mating

Site-specific: Transposable elements: transposase, inverted sequences & repeats

ConservativeReplicativeIntegronsInversions

1. Target DNA (organismal)2. Oligonucleotide primers flanking the target sequence,3. DNA polymerase of a hyperthermophile (Taq)4. Heat denaturation of the target dsDNA5. Cooling – annealing of the Primers6. Primer extension by polymerase in both directions7. Repeat of the cycle 8. Accumulated sequence 10-6 – 10-9

(Taq = Thermus aquaticus)

PCR – Polymerase Chain Reaction

Brock Biology of Microorganisms

Microbial Evolution and Systematics

Copyright © 2006 Pearson Prentice Hall, Inc.

EARLY EARTH, THE ORIGIN OF LIFE, AND MICROBIAL DIVERSIFICATION

Origin of Earth, Evidence for Microbial Life on Early Earth, Conditions on Early Earth: Hot and Anoxic.

Origin of Life

Catalysis and the Importance of Montmorillonite

Primitive Life: The RNA World and Molecular Coding

RNA Life

The Modern Cell: DNA —> RNA —> Protein

Cambrian stromatolite, ca. 500 My. Old,South AustraliaScale is in inches, Courtesy of Stanley M. Awramik

Great Slave Lake, CanadaGreat Slave Lake, Canada

Ancient ca. 2 Ancient ca. 2 • 10• 1099 y.y.

RecentRecent

Hamelin Pool,Hamelin Pool,Shark Bay, Shark Bay, W. AustraliaW. Australia

Stromatolitesmatolitesdominated 5/6 of the dominated 5/6 of the etire history of Earthetire history of Earth

CryptozoonKalkowsky, V.H. 1908: Kalkowsky, V.H. 1908: Oolith und Stromatolith im Oolith und Stromatolith im Norddeutschen BuntsandsteinNorddeutschen Buntsandstein

Early Proterozoic stromatoliteca. 3000 My. old,

South AfricaScale bar is 10 cm long

Modern subtidal stromatolitesModern subtidal stromatolitesShark Bay, AustraliaShark Bay, Australia

Modern Modern ConophytonConophyton equivalent equivalent

Old Faithful Geyser

Microbially guidedsilica deposition

Yellowstone National Park

Microbial reefsMicrobial reefswith silica deposition

Yellowstone National Park

Tom Brock in Yellowstone

1975

Modern subtidal stromatolites, Lee Stocking Island, Bahamas

Microbial mat (red) – Stromatolite (yellow)S

edim

ent a

ccum

ulat

ion

Eoentophysalis belcherensis Entophysalis major Hofmann Ercegovic

Fossil 2000 My old stromatolite Modern marine stromatolite Belcher Island Formation, Canada Shark bay, Western Australia

Entophysalis majorBaja California, Mexico

Eoentophysalis belcherensis Mesoproterozoic, ca. 1400 Ma. Gauyuzhuang Formation, China

Planet Earth is approximately 4.6 billion years old. The first evidence for microbial life can be found in rocks about 3.86 billion years old. Early Earth was anoxic and much hotter than the present. The first biochemical compounds were made by abiotic syntheses that set the stage for the origin of life.

Condition on Early Earth: Condition on Early Earth:

Hot and AnoxicHot and AnoxicOrganic synthesis and stabilityOrganic synthesis and stabilityCatalysis on clay and pyrite surfacesCatalysis on clay and pyrite surfacesRNA and molecular codingRNA and molecular coding

The Modern Cell: DNA —> RNA —> Protein

The first life forms may have been self-replicating RNAs. These were both catalytic and informational. Eventually, DNA became the genetic repository of cells and the three part system, DNA, RNA, and protein, became universal among cells.

Primitive Life: Energy and Carbon Metabolism

Molecular Oxygen:Banded Iron Formations

Oxygenation of the Atmosphere: New Metabolisms and the Ozone

Shield

• Primitive metabolism was anaerobic and likely chemolithotrophic, exploiting the abundant sources of FeS and H2S present.• Carbon metabolism may have included autotrophy. • Oxygenic photosynthesis led to development of banded iron formations, an oxic environment, and great bursts of biological evolution.

Phanerozoic 0-0.54

Neoproterozoic 0.54-1.0

Mesoproterozoic 1.0-1.6

Paleoproterozoic 1.6-2.5

Late Archaean 2.5-3.0

Early Archaean 3.0-3.5

Hadean 3.5-4.6

• Origin of the Nucleus• Origin of organelles as organisms • Endosymbiosis • Lateral flow of genetic information• Reduction of redundancies

EvoluntionaryEvoluntionary history of endosymbiosis: history of endosymbiosis:

Mitochondria and ChloroplastsMitochondria and Chloroplasts

EvoluntionaryEvoluntionary history of chloroplast endosymbiosishistory of chloroplast endosymbiosis

2

3

1.1. Cyanobacteria Cyanobacteria 6. Euglenophyta6. Euglenophyta 2.2. GlaucophytaGlaucophyta 7. Chlorachniophyta7. Chlorachniophyta3.3. Cryptomonads Cryptomonads 8. Dinoflagellata (green) . 8. Dinoflagellata (green) . 4.4. RhodophytaRhodophyta 9. Dinoflagellata (brown)9. Dinoflagellata (brown)5.5. Chlorophyta 10. Chrysophyta, Heterocontae, DiatomsChlorophyta 10. Chrysophyta, Heterocontae, Diatoms

EvoluntionaryEvoluntionary history of history of

chloroplast chloroplast endosymbiosis:endosymbiosis:

The HostsThe Hosts

Evidence of EndosymbiosisEvidence of Endosymbiosis

• Size of ribosomes 80S vs. 70SSize of ribosomes 80S vs. 70S• Organellar DNA presentOrganellar DNA present• Organellar DNA is circularOrganellar DNA is circular• Multiple membranesMultiple membranes• Sensitivity to antibiotics Sensitivity to antibiotics

• Models of SymbiosesModels of Symbioses

• The eukaryotic nucleus and mitotic apparatus probably arose as a necessity for ensuring the orderly partitioning of DNA in large-genome organisms. • Mitochondria and chloroplasts, the principal energy-producing organelles of eukaryotes, arose from symbiotic association of prokaryotes of the domain Bacteria within eukaryotic cells, • The process is called endosymbiosis. • Assuming that an RNA world existed, self-replicating entities have populated Earth for over 4 billion years.

Fossil record vs. vs. Molecular view of evolution DNA composition GC to AT ratio DNA-DNA-hybridization: melting – reanealing DNA-sequence similarity and interrelatedness DNA-sequencing: in vivo vs. in vitro Synthetic DNA – PCR – Molecular cloning

Fossil record, and endosymbiotic events Phylogenetic classification Bacterial Classification by phenotypes

Microbial evolution, phylogeny and classification

Criteria for Molecular Chronometers

• Universal distributionUniversal distribution• Functional homologyFunctional homology• Conserved sequences for alignmentConserved sequences for alignment• Slow rates of evolutionary changeSlow rates of evolutionary change• Lack of functional constraintLack of functional constraint

• Ribosomal database Project (RDP)Ribosomal database Project (RDP) >100,000 sequences.>100,000 sequences.

• Ribosomal RNAs as Evolutionary Chronometers • Ribosomal RNA Sequences as a Tool of Molecular Evolution • Sequencing Methodology• Generating Phylogenetic Trees from RNA Sequences

• Comparisons of sequences of ribosomal RNA can be used to determine the evolutionary relationships between organisms. • Phylogenetic trees based on ribosomal RNA have now been prepared for all the major prokaryotic and eukaryotic groups.

• Comparative ribosomal RNA sequencing is now a routine procedure involving:• Amplification of the gene encoding 16S rRNA, • Sequencing it, and • Analyzing the sequence in reference to other sequences. • Two major treeing algorithms are: distance and parsimony.

Signature sequences, short oligonucleotides found within a ribosomal RNA molecule, can be highly diagnostic of a particular organism or group of related organisms. Signature sequences can be used to generate specific phylogenetic probes, useful for FISH or microbial community analyses.

Archaea

4 phyla: CrenarchaeotaEuryarchaeota

KorarchaeotaNanoarchaeota

Life on Earth evolved along three major lines, called domains, all derived from a common ancestor. Each domain contains several phyla. Two of the domains, Bacteria and Archaea, remained prokaryotic, whereas the third line, Eukarya, evolved into the modern eukaryotic cell.

• Although the three domains of living organisms were originally defined by ribosomal RNA sequencing, subsequent studies have shown that they differ in many other ways. • In particular, the Bacteria and Archaea differ extensively in cell wall and lipid chemistry and in features of transcription and protein synthesis.

Conventional bacterial taxonomy places heavy emphasis on analyses of phenotypic properties of the organism. Determining the guanine plus cytosine base ratio of the DNA of the organism can be part of this process.

Chemotaxonomy

DNA-DNA hybridizationRibotyping

MultiLocus Sequence TypingLipid profiling

The species concept applies to prokaryotes as well as eukaryotes, and a similar taxonomic hierarchy exists, with the domain as the highest level taxon. Bacterial speciation may occur from a combination of repeated periodic selection for a favorable trait within an ecotype and lateral gene flow.

Domain Bacteria

Phylum Gamma Proteobacteria

Class Zymobacteria

Order Chromatiales

Family Chromatiaceae

Genus Allochromatium

Species warmingii

Prokaryotes are given descriptive genus names and species epithets. Formal recognition of a new prokaryotic species requires depositing a sample of the organism in a culture collection and official publication of the new species name and description. Bergey’s Manual of Systematic Bacteriology is a major taxonomic compilation of Bacteria and Archaea.

International Journal of Systematic and Evolutionary Microbiology

IJSEM

Methods in Microbial Ecology

The enrichment culture technique is a means of obtaining microorganisms from natural samples. Specific reactions can be investigated by enrichment methods by choosing media and incubation conditions selective for particular organisms.

Once a successful enrichment culture has been established, a pure culture can be obtained by conventional microbiological procedures, including streak plates, agar shakes, and dilution methods. Laser tweezers allow one to “pick” a cell from a microscope field and literally move it away from contaminants.

DAPI is a general stain for identifying microorganisms in natural samples. Some stains can differentiate live versus dead cells, and fluorescent antibodies that are specific for one or a small group of related cells can be prepared. The green fluorescent protein makes cells autofluorescent and is a means for tracking cells introduced into the environment. Unlike pure cultures, in natural samples, morphologically similar cells may actually be quite different genetically.

The polymerase chain reaction (PCR) can be used to amplify specific target genes such as small subunit ribosomal RNA genes or key metabolic genes. Denaturing gradient gel electrophoresis (DGGE) can be used to resolve slightly to greatly different versions of these genes present in the different species inhabiting a natural sample.

The activity of microorganisms in natural samples can be assessed very sensitively using radioisotopes and/or microelectrodes. In most cases, measurements are of the net activity of a microbial community rather than of a population of a single species.

Isotopic fractionation can reveal the biological origin of various substances. Fractionation is a result of the activity of enzymes that discriminate against the heavier form of an element when binding their substrates.

1. Microbial impact on global nutrient cycling Carbon - Nitrogen - Sulfur - Phosphorus – Iron

2. Aquatic environments, nutrients & microbes Benthos – Plankton. Biofilms – DeeP Sea – Hydrotermal vents – Coastal environments – Microbial endoliths – bioerosion – Freshwater eutrophication and pollution – Thermal springs.

3. Aquatic environments Soil microbiology – Rhizobium symbiosis - Mycorhzae

Microbial communities consist of guilds of metabolically related organisms. Microorganisms play major roles in energy transformations and biogeochemical processes that result in the recycling of elements essential to living systems.

Microorganisms are very small and their habitats are likewise small. The microenvironment is the place in which the microorganism actually lives. Microorganisms in nature often live a feast-or-famine existence such that only the best-adapted species thrive in a given niche. Cooperation among microorganisms is also important in many microbial interrelationships.

The soil is a complex habitat with numerous microenvironments and niches. Microorganisms are present in the soil primarily attached to soil particles. The most important factor influencing microbial activity in surface soil is the availability of water, whereas in deep soil (the subsurface environment) nutrient availability plays a major role.

In aquatic ecosystems phototrophic microorganisms are usually the main primary producers. Most of the organic matter produced is consumed by bacteria, which can lead to depletion of oxygen in the environment. BOD is a measure of the oxygen-consuming properties of a water sample.

Marine waters are more nutrient deficient than many freshwaters, yet substantial numbers of microorganisms exist there. Many of these use light to drive ATP synthesis. In terms of prokaryotes, species of the domain Bacteria tend to predominate in oceanic surface waters whereas Archaea are more prevalent in deeper waters.

Donors Acceptors Products

H2 S°, S2O3 H2SH2 CO CH4

H2 O2 , NO3 H2O, NO2

NH4+, NO2 O2 NO2, NO3

HS, S°, S2O3 O2, NO3 S°, SO4

CH4, CO O2 CO2

Fe 2+, Mn 2+ O2 Fe3+, Mn4+

Energetic Base for Chemolithotrophy at the

Deep Ocean Hydrothermal Vents

S - reduciersMethanogensH - oxidizersNitrifyiersS - oxidizersMethylotrophsFe - Mn oxidizers

Iron exists in nature primarily in two oxidation states, ferrous (Fe2+) and ferric (Fe3+), and bacterial and chemical transformation of these metals is of geological and ecological importance. Bacterial ferric iron reduction occurs in anoxic environments and results in the mobilization of iron from swamps, bogs, and other iron-rich aquatic habitats. Bacterial oxidation of ferrous iron occurs on a large scale at low pH and is very common in coal-mining regions, where it results in a type of pollution called acid mine drainage.

• The principal form of nitrogen on Earth is nitrogen gas (N2), which can be used as a nitrogen source only by the nitrogen-fixing bacteria. • Ammonia produced by nitrogen fixation or by ammonification from organic nitrogen compounds can be assimilated into organic matter or • it can be oxidized to nitrate by the nitrifying bacteria. • Losses of nitrogen from the biosphere occur as a result of denitrification, in which nitrate is converted back to N2.

• Bacteria play major roles in both the oxidative and reductive sides of the sulfur cycle. • Sulfur- and sulfide-oxidizing bacteria produce sulfate, while sulfate-reducing bacteria consume sulfate as an electron acceptor in anaerobic respiration, producing hydrogen sulfide. Because sulfide is toxic and also reacts with various metals, sulfate reduction is an important biogeochemical process. • Dimethyl sulfide is the major organic sulfur compound of ecological significance in nature.