Archaea & Eubacteria: 09/2007

Bioenergetics

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Bioenergetics of the Archaea. [Microbiol Mol Biol Rev. 1999]
In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a separate domain, Archaea display an enormous diversity of lifestyles and metabolic capabilities. Many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic pH. This has posed the challenge of studying the molecular and mechanistic bases on which these organisms can cope with such adverse conditions. This review considers our cumulative knowledge on archaeal mechanisms of primary energy conservation, in relationship to those of bacteria and eucarya. Although the universal principle of chemiosmotic energy conservation also holds for Archaea, distinct features have been discovered with respect to novel ion-transducing, membrane-residing protein complexes and the use of novel cofactors in bioenergetics of methanogenesis. From aerobically respiring Archaea, unusual electron-transporting supercomplexes could be isolated and functionally resolved, and a proposal on the organization of archaeal electron transport chains has been presented. The unique functions of archaeal rhodopsins as sensory systems and as proton or chloride pumps have been elucidated on the basis of recent structural information on the atomic scale. Whereas components of methanogenesis and of phototrophic energy transduction in halobacteria appear to be unique to Archaea, respiratory complexes and the ATP synthase exhibit some chimeric features with respect to their evolutionary origin. Nevertheless, archaeal ATP synthases are to be considered distinct members of this family of secondary energy transducers. A major challenge to future investigations is the development of archaeal genetic transformation systems, in order to gain access to the regulation of bioenergetic systems and to overproducers of archaeal membrane proteins as a prerequisite for their crystallization.
Schafer G, Engelhard M, Muller V. Bioenergetics of the Archaea. (Free Full Text Article) Microbiol Mol Biol Rev. 1999 Sep;63(3):570-620.

Related Links
On the origin of respiration: electron transport proteins from archaea to man. [FEMS Microbiol Rev. 1996] PMID: 8639327
Stress genes and proteins in the archaea. [Microbiol Mol Biol Rev. 1999] PMID: 10585970
Bioenergetics of the archaebacterium Sulfolobus. [Biochim Biophys Acta. 1996] PMID: 8982385
Bioenergetics of archaea: ATP synthesis under harsh environmental conditions. [J Mol Microbiol Biotechnol. 2005] PMID: 16645313
Respiratory chains of archaea and extremophiles. [Biochim Biophys Acta. 1996] PMID: 8688447

Gene cluster of Rhodothermus marinus high-potential iron-sulfur Protein: oxygen
A novel scenario for the evolution of haem-copper oxygen reductases. [Biochim Biophys Acta. 2001] PMID: 11334784
New genes encoding subunits of a cytochrome bc1-analogous complex in the respiratory chain of the hyperthermoacidophilic crenarchaeon Sulfolobus acidocaldarius. [J Bioenerg Biomembr. 2003] PMID: 12887010
Evolution of the cytochrome c oxidase proton pump. [J Mol Evol. 1998] PMID: 9545462

Control of gene expression

Bacteria have operons, which are protein-encoding gene clusters. Prokaryotic genes lack introns. RNA transcribed from prokaryotic operons is polycistronic – multiple proteins are encoded in a single transcript.

In prokaryotes, operons are defined as groups of genes transcribed under the control of a single operator gene. The operon comprises a functionally integrated genetic unit for the control of gene expression, and comprises one or more genes together with an adjacent promoter (activator or repressor) and an operator that controls expression through interaction with a regulator protein.

Control of prokaryotic gene expression is brought about by control of the rate of transcriptional initiation by two DNA promoter sequence elements. In prokaryotic cells, all RNA classes are synthesized by a single polymerase. Regulatory accessory proteins alter the activity of RNA polymerase at a given promoter by affecting the ability of RNA polymerase to recognize start-sites. These regulatory proteins can act both positively (activators) and negatively (repressors).

In bacteria, regulons comprise several operons, and are global regulatory systems that participate in pleiotropic regulatory domains.

Table gene regulation in E.coli :

More detail:

Control of prokaryotic gene expression is brought about by control of the rate of transcriptional initiation by two DNA promoter sequence elements – the -35 and -10 positions. These elements are approximately 35 bases and 10 bases upstream of the site of transcriptional initiation. These promoter sequences promote recognition of transcriptional start sites by RNA polymerase. The consensus sequence for the -35 position is TTGACA, and for the -10 position, TATAAT. (The -10 position is also known as the Pribnow-box.) These promoter sequences are recognized and contacted by RNA polymerase.

Regulatory accessory proteins alter the activity of RNA polymerase at a given promoter by affecting the ability of RNA polymerase to recognize start-sites. These regulatory proteins can act both positively (activators) and negatively (repressors). Proteins with sequences termed operators regulate the accessibility of promoter regions to prokaryotic DNA. The operator region is adjacent to the promoter elements in most operons, and in most cases the sequences of the operator bind a repressor protein. However, E. coli possesses several operons that contain overlapping sequence elements, one that binds a repressor and one that binds an activator.

Two major modes of transcriptional regulation in bacteria (E. coli) utilize repressor proteins to control the expression of operons.
1. Catabolite-regulated operons employ repressor proteins to down-regulate operons that produce gene products necessary for the utilization of energy. A classic example of a catabolite-regulated operon is the lac operon, responsible for obtaining energy from b-galactosides such as lactose.
2. Attenuated operons regulate operons that produce gene products necessary for the synthesis of small biomolecules such as amino acids. Expression of the an attenuated operon class of operons is repressed by sequences within the transcribed RNA. A classic example of an attenuated operon is the trp operon, responsible for the biosynthesis of tryptophan.

Table gene regulation in E.coli :

E. Coli Research Identifies Two New Keys To Regulation Of Bacterial Gene Expression :
Gourse investigated the interaction between RNA polymerase and promoters from the E. coli chromosome. RNA polymerase reads the information in DNA and transcribes it into chains of RNA, which are later translated into proteins. Promoter regions are specific sequences within the DNA chain that tell RNA polymerase when and where to begin transcription, and how much product to make from specific genes.

Gourse's group found that there is a specific region within DNA promoters that makes contact with a highly conserved but previously underappreciated segment of the sigma subunit of RNA polymerase. While the contact with sigma is very strong at promoters for most genes, it is particularly weak at promoters that make ribosomal RNA, which means that other factors like nutritional and environmental signals ultimately regulate the expression of those genes.

"In this case, regulation is achieved not because the promoter makes a special contact, but because it can't establish contact at all," says Gourse. "This is an example of how sometimes less is more, and a probably very ancient example of one of the methods that arose through evolution to regulate gene expression."

Ribosomal RNA makes up the bulk of ribosomes, the molecular machines that make proteins and are present in huge numbers in all cells. Since so much of the cell's energy is used to make ribosomes, control of ribosomal RNA transcription is particularly crucial to a cell's well-being.

Translation in prokaryotes

Bacteria utilize N-formylmethionine (f-Met) rather than methionine (Met) at the N-terminal of the translated polypeptide.

N-Formylmethionine (fMet) is an amino acid that is found in all living cells. It is a derivative of the amino acid methionine, in which a formyl group has been added to methionine's amino group (catalyzed by the enzyme transformylase when Met is attached to tRNA.fMet, but not to tRNA.Met).

N-Formylmethionine is delivered to the 30S ribosome-mRNA complex by the specialized tRNA (tRNA.fMet), which possesses a 5'-CAU-3' anticodon that is capable of binding with the mRNA’s AUG start codon. N-Formylmethionine is coded for by AUG, which is the Met codon. However, AUG is also the translation initiation codon. When the AUG codon is employed for initiation, prokaryotes and plastids insert N-formylmethionine instead of methionine at the N-terminal of the nascent peptide chain. When the AUG codon appears farther along the mRNA, unmodified Met is inserted. Many organisms employ varations of this basic mechanism.

Thus, N-Formylmethionine plays a crucial role in the protein biosynthesis of bacteria, archaea, mitochondria and chloroplasts. However, f-Met is not employed in eukaryotic translation within the cytoplasm, where eukaryotic nuclear genes are translated into proteins.

Physical and Functional Interaction between the Eukaryotic Orthologs of Prokaryotic Translation Initiation Factors IF1 and IF2.
The fundamental process of translation initiation has been conserved between prokaryotes and eukaryotes. The initiator Met-tRNA is bound to the small ribosomal subunit, and this complex is localized to the AUG start codon of an mRNA. Three translation initiation factors (IFs) have been identified in prokaryotes (reviewed in references 7 and 18). Factor IF2 is responsible for binding fMet-tRNAiMet to the 30S ribosomal subunit. Factor IF1 binds to the 30S subunit and protects the same region of the ribosome (A site) as the elongation factor EF-Tu–GTP–aminoacyl-tRNA complex (28). Although a unique function has not been attributed to IF1, it does promote IF2 activities (reviewed in references 7, 18, 22, and 31. Factor IF3 dissociates ribosomal complexes, presumably to generate a pool of small ribosomal subunits for translation initiation. In addition, IF3 has recently been implicated in the process of ribosome recycling following termination of translation (21).

Sang Ki Choi, DeAnne S. Olsen, Antonina Roll-Mecak, Agnes Martung, Keith L. Remo, Stephen K. Burley, Alan G. Hinnebusch, and Thomas E. Dever Physical and Functional Interaction between the Eukaryotic Orthologs of Prokaryotic Translation Initiation Factors IF1 and IF2 Mol Cell Biol. 2000 October; 20(19): 7183–7191.

Restriction Enzymes

Bacterial restriction enzymes cut the sugar-phosphate backbone of the DNA molecule at specific recognition sequences, so these DNA-cutting enzymes are often called restriction endonucleases. Restriction enzymes hydrolyze the backbone of DNA between deoxyribose and phosphate groups, leaving a phosphate group at the 5' ends and a hydroxyl at the 3' ends of both strands. A few restriction enzymes inefficiently cleave single stranded DNA.

A consensus sequence may be a short sequence of nucleotides that is found several times in the genome and is thought to play the same role in its different locations. Restriction enzymes usually have palindromic consensus recognition sequences, which correspond to the site where they cut the DNA. For example, the bacterium Hemophilus aegypticus produces a restriction endonucleases termed HaeIII that cuts DNA between the adjacent G and C wherever it encounters the sequence:

5'GGCC3'
3'CCGG5'

Some features of recognition sequences:
1. Variable length (4-8 bp). Length of the recognition sequence dictates how frequently the enzyme will cut a random sequence of DNA – on average, every 256 bp for a 4 bp recognition site, every 4096 bp for a 6 bp recognition sequence, and every 4⁸ bp for an 8 bp recognition site.
2. Most sequences are palindromic – displaying the same sequence in both direction
3. Isoschizomers – where different restriction enzymes cut the DNA backbone at different recognition sequences.
4. Ambiguous or unambiguous – ambiguous restriction enzymes cut the DNA at recognition sites that begin and end with specific nucleotid sequences, but which can have variable nucleotides (n, pu, py) inserted between the specific 5' and 3' ends, unambiguous recognition sites have invariable sequences.
5. The recognition site for one restriction endonuclease may include the restriction site for another

Compare:
BamHI GGATCC & CCTAGG
NotI GCGGCCGC & CGCCGGCG
Sau3AI GATC & CTAG
SacI GAGCTC & CTCGAG
SstI GAGCTC & CTCGAG
HinfI GAnTC & CtnAG
XhoII puGATCpy & pyCTAGpu

HaeIII and AluI cut straight across the double helix producing "blunt" ends. However, many restriction enzymes cut in an offset fashion, generating an overlapping segment of single-stranded DNA. Such extensions are called "sticky ends" because they are able to form base pairs with any DNA molecule that contains the complementary sticky end. Such a union can be made permanent by another enzyme, DNA ligase, which forms covalent bonds along the backbone of each strand, producing a molecule of recombinant DNA (rDNA).

AluI and HaeIII produce blunt ends, while BamHI, HindIII, and EcoRI produce offset, “sticky” ends. Restriction enzyme, recognition sequences, bacterial genus and species:

AluI....................................... 5’ … AGcutCT … 3’
Arthrobacter luteus............................. 3’ … TCcutGA … 5’

HaeIII..................................... 5’ … GGcutCC … 3’
Haemophilus influenzae.......................... 3’ … CCcutGG … 5’

BamHI.................................... 5’ … GcutGATCC … 3’
Bacillus amyloliquefaciens................. 3’ … CCTAGcutG … 5’

HindIII.................................... 5’ … AcutAGCTT … 3’
Haemophilus influenzae ....................3’ …TTCGAcutA … 5’

EcoRI..................................... 5’ … GcutAATTC … 3’
Escherichia coli................................... 3’ … CTTAAcutG … 5’

Most restriction enzymes occur in bacteria, where they play a role in defense by chopping up - restricting - the genomes of bacteriophages. In almost all cases, a bacterium that produces a particular restriction endonuclease also synthesizes a companion DNA methyltransferase, which methylates the DNA target sequence for that restriction enzyme, thereby protecting the bacterial genome from cleavage. This combination of restriction endonuclease with methylase is referred to as a restriction-modification system.

The ability to produce recombinant DNA molecules revolutionized the study of genetics, and has proved important to biotechnology. Recombinant DNA technology has been utilized to produce human insulin (for diabetics), human factor VIII (for hemophilia A), and other useful proteins.

Stress genes, proteins, molecular chaperones

Activation of stress genes is an important component of the stress response (90, 120, 205, 208, 219, 253, 254, 279)[s]. Stress (physical or chemical) also inactivates or down-regulates many genes, including many housekeeping genes.

Stress proteins, which are encoded by stress genes, play critical roles in physiological protein biogenesis. These proteins assist in the folding, translocation, and assembly of other proteins (191, 214, 235, 236, 247), so many stress proteins are also called molecular chaperones (72). Not all stress proteins are chaperones and, conversely, not every molecular chaperone is a stress protein. : image 24 unit Archaebacterial heat shock protein :

Molecular chaperones interact with unfolded or partially folded protein subunits, such as nascent chains emerging from the ribosome or extended chains undergoing translocation across subcellular membranes. The chief function of chaperones is to prevent inappropriate association or aggregation of exposed hydrophobic surfaces by directing their substrates into productive folding, transport or degradation pathways. Chaperones stabilize non-native conformation and facilitate correct folding of protein subunits, often coupling ATP binding/hydrolysis to the folding process. They do not interact with native proteins, nor do they form part of the final folded structures. Some chaperones are non-specific in that they interact with a wide variety of polypeptide chains, while other chaperoness are restricted to specific targets. Chaperones are essential for viability, so their expression is often increased by cellular stress. : image substrate binding by chaperones : image Hsp60 chaperonin GroEL : image Hsp70 : more :

Stress proteins help other cellular proteins to (i) fold correctly during and after translation; (ii) migrate to the cell's locale, where they will reside and function; and (iii) assemble into the quaternary structure that will make them useful to the cell when the proteins function as polymers. Further, some stress proteins participate in the degradation of other polypeptides such as those that are denatured beyond recovery and could pose a serious threat to the cell if they were to aggregate (39, 92, 97, 98, 122, 123, 133).

Thermophilic cell lines adapted for survival at high temperatures constitutively synthesize the stress protein hsp70 at high levels, whereas temperature-sensitive cell-lines do not. Several stress protein families, including hsp90, hsp70, chaperonin60, hsp40, the low molecular weight stress proteins, and ubiquitin, are expressed in diverse phyla. Studies comparing the stress protein repetoir of closely related species inhabiting different environments have demonstrated that differences in the heat-stress response are correlated with thermal resistance, suggesting that stress proteins help organisms adapt to harsh or unpredictable environments.

. cellular stress response .

Stress genes and proteins in the archaea.
The field covered in this review is new; the first sequence of a gene encoding the molecular chaperone Hsp70 and the first description of a chaperonin in the archaea were reported in 1991. These findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular biology and biochemistry of life in extreme environments, and stress tolerance at the cellular and molecular levels. In the last 8 years, archaeal stress genes and proteins belonging to the families Hsp70, Hsp60 (chaperonins), Hsp40(DnaJ), and small heat-shock proteins (sHsp) have been studied. The hsp70(dnaK), hsp40(dnaJ), and grpE genes (the chaperone machine) have been sequenced in seven, four, and two species, respectively, but their expression has been examined in detail only in the mesophilic methanogen Methanosarcina mazei S-6. The proteins possess markers typical of bacterial homologs but none of the signatures distinctive of eukaryotes. In contrast, gene expression and transcription initiation signals and factors are of the eucaryal type, which suggests a hybrid archaeal-bacterial complexion for the Hsp70 system. Another remarkable feature is that several archaeal species in different phylogenetic branches do not have the gene hsp70(dnaK), an evolutionary puzzle that raises the important question of what replaces the product of this gene, Hsp70(DnaK), in protein biogenesis and refolding and for stress resistance. Although archaea are prokaryotes like bacteria, their Hsp60 (chaperonin) family is of type (group) II, similar to that of the eukaryotic cytosol; however, unlike the latter, which has several different members, the archaeal chaperonin system usually includes only two (in some species one and in others possibly three) related subunits of approximately 60 kDa. These form, in various combinations depending on the species, a large structure or chaperonin complex sometimes called the thermosome. This multimolecular assembly is similar to the bacterial chaperonin complex GroEL/S, but it is made of only the large, double-ring oligomers each with eight (or nine) subunits instead of seven as in the bacterial complex. Like Hsp70(DnaK), the archaeal chaperonin subunits are remarkable for their evolution, but for a different reason. Ubiquitous among archaea, the chaperonins show a pattern of recurrent gene duplication-hetero-oligomeric chaperonin complexes appear to have evolved several times independently. The stress response and stress tolerance in the archaea involve chaperones, chaperonins, other heat shock (stress) proteins including sHsp, thermoprotectants, the proteasome, as yet incompletely understood thermoresistant features of many molecules, and formation of multicellular structures. The latter structures include single- and mixed-species (bacterial-archaeal) types. Many questions remain unanswered, and the field offers extraordinary opportunities owing to the diversity, genetic makeup, and phylogenetic position of archaea and the variety of ecosystems they inhabit. Specific aspects that deserve investigation are elucidation of the mechanism of action of the chaperonin complex at different temperatures, identification of the partners and substitutes for the Hsp70 chaperone machine, analysis of protein folding and refolding in hyperthermophiles, and determination of the molecular mechanisms involved in stress gene regulation in archaeal species that thrive under widely different conditions (temperature, pH, osmolarity, and barometric pressure). These studies are now possible with uni- and multicellular archaeal models and are relevant to various areas of basic and applied research, including exploration and conquest of ecosystems inhospitable to humans and many mammals and plants.
Macario AJ, Lange M, Ahring BK, De Macario EC. Stress genes and proteins in the archaea. (Free Full Text Article) Microbiol Mol Biol Rev. 1999 Dec;63(4):923-67, table of contents.

The archaeal molecular chaperone machine: peculiarities and paradoxes. [Genetics. 1999] PMID: 10430558
Molecular biology of stress genes in methanogens: potential for bioreactor technology. [Adv Biochem Eng Biotechnol. 2003] PMID: 12747562
The molecular chaperone system and other anti-stress mechanisms in archaea. [Front Biosci. 2001] PMID: 11171552
Evolution of assisted protein folding: the distribution of the main chaperoning systems within the phylogenetic domain archaea. [Front Biosci. 2004] PMID: 14977547
The basal transcription factors TBP and TFB from the mesophilic archaeon Methanosarcina mazeii: structure and conformational changes upon interaction with stress-gene promoters. [J Mol Biol. 2001] PMID: 11397082

Horizontal Gene Transfer

Horizontal gene transfer - gene swapping - has blurred the evolutionary relationships (phylogeny) of prokaryotes (left, adapted - click to enlarge), and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria. (see The net of life: Reconstructing the microbial phylogenetic networkV. Kunin, L. Goldovsky, N. Darzentas, and C. A. OuzounisGenome Res. 1 July 2005. pdf)

Three mechanisms of horizontal (lateral) gene transfer are recognized: direct bacterial conjugation, bacteriophage mediated transduction between bacteria, and bacterial transformation by uptake of DNA fragments.

A major form of vertical gene transfer followed serial endosymbiotic events, in which ingested purple bacteria and Cyanobacteria became eukaryotic mitochondria and chloroplasts respectively. The ingested prokaryotes are believed to have relinquished certain genes to the nuclei of their host cells, a process known as endosymbiotic gene transfer.

Horizontal Genomics: Mobile genetic elements: the agents of open source evolution.
Mobile genetic elements: the agents of open source evolution.: "Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage - and avoid the dangers - of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics."

Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005 Sep;3(9):722-32.Nat Rev Microbiol. 2005 Sep;3(9):722-32.

The Balance of Driving Forces During Genome Evolution in Prokaryotes.

Genomes are shaped by evolutionary processes such as gene genesis, horizontal gene transfer (HGT), and gene loss. To quantify the relative contributions of these processes, we analyze the distribution of 12,762 protein families on a phylogenetic tree, derived from entire genomes of 41 Bacteria and 10 Archaea. We show that gene loss is the most important factor in shaping genome content, being up to three times more frequent than HGT, followed by gene genesis, which may contribute up to twice as many genes as HGT. We suggest that gene gain and gene loss in prokaryotes are balanced; thus, on average, prokaryotic genome size is kept constant. Despite the importance of HGT, our results indicate that the majority of protein families have only been transmitted by vertical inheritance. To test our method, we present a study of strain-specific genes of Helicobacter pylori, and demonstrate correct predictions of gene loss and HGT for at least 81% of validated cases. This approach indicates that it is possible to trace genome content history and quantify the factors that shape contemporary prokaryotic genomes.

Victor Kunin and Christos A. Ouzounis The Balance of Driving Forces During Genome Evolution in Prokaryotes Genome Research 13:1589-1594, 2003 Full Text Full Text (PDF)

Examining bacterial species under the specter of gene transfer and exchange.
Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene transfer (LGT) among lineages at virtually all phylogenetic levels. In most bacterial genomes, large proportions of genes are introduced by LGT, as indicated by their compositional features and/or phylogenetic distributions, and there is also clear evidence of LGT between very distantly related organisms. By adopting a whole-genome approach, which examined the history of every gene in numerous bacterial genomes, we show that LGT does not hamper phylogenetic reconstruction at many of the shallower taxonomic levels. Despite the high levels of gene acquisition, the only taxonomic group for which appreciable amounts of homologous recombination were detected was within bacterial species. Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species.

Howard Ochman, Emmanuelle Lerat, and Vincent Daubin Examining bacterial species under the specter of gene transfer and exchange PNAS May 3, 2005 vol. 102 Suppl. 1 6595-6599 Full Text Full Text (PDF)

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.: "Numerous studies have considered the emergence of metabolic pathways, but the modes of recent evolution of metabolic networks are poorly understood. Here, we integrate comparative genomics with flux balance analysis to examine (i) the contribution of different genetic mechanisms to network growth in bacteria, (ii) the selective forces driving network evolution and (iii) the integration of new nodes into the network. Most changes to the metabolic network of Escherichia coli in the past 100 million years are due to horizontal gene transfer, with little contribution from gene duplicates. Networks grow by acquiring genes involved in the transport and catalysis of external nutrients, driven by adaptations to changing environments. Accordingly, horizontally transferred genes are integrated at the periphery of the network, whereas central parts remain evolutionarily stable. Genes encoding physiologically coupled reactions are often transferred together, frequently in operons. Thus, bacterial metabolic networks evolve by direct uptake of peripheral reactions in response to changed environments."
Pal C, Papp B, Lercher MJ. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet. 2005 Dec;37(12):1372-5. Epub 2005 Nov 20.

Horizontal gene transfer in bacterial and archaeal complete genomes.
There is growing evidence that horizontal gene transfer is a potent evolutionary force in prokaryotes, although exactly how potent is not known. We have developed a statistical procedure for predicting whether genes of a complete genome have been acquired by horizontal gene transfer. It is based on the analysis of G+C contents, codon usage, amino acid usage, and gene position. When we applied this procedure to 17 bacterial complete genomes and seven archaeal ones, we found that the percentage of horizontally transferred genes varied from 1.5% to 14.5%. Archaea and nonpathogenic bacteria had the highest percentages and pathogenic bacteria, except for Mycoplasma genitalium, had the lowest. As reported in the literature, we found that informational genes were less likely to be transferred than operational genes. Most of the horizontally transferred genes were only present in one or two lineages. Some of these transferred genes include genes that form part of prophages, pathogenecity islands, transposases, integrases, recombinases, genes present only in one of the two Helicobacter pylori strains, and regions of genes functionally related. All of these findings support the important role of horizontal gene transfer in the molecular evolution of microorganisms and speciation.

Garcia-Vallve S, Romeu A, Palau J. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 2000 Nov;10(11):1719-25. Free Full Text Article.

Stochastic Models for Horizontal Gene Transfer : Taking a Random Walk Through Tree Space.
Horizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in "tree space" that allows for the development of a joint probabilistic distribution over multiple gene trees and an unknown, but estimable species tree. I consider two general forms of random walks. The first form is derived from the subtree prune and regraft (SPR) operator that mirrors the observed effects that HGT has on inferred trees. The second form is based on walks over complete graphs and offers numerically tractable solutions for an increasing number of taxa. The bottom level of the hierarchy utilizes standard phylogenetic models to reconstruct gene trees given multiple gene alignments conditional on the random walk process. I develop a well-mixing Markov chain Monte Carlo algorithm to fit the models in a Bayesian framework. I demonstrate the flexibility of these stochastic models to test competing ideas about HGT by examining the complexity hypothesis. Using 144 orthologous gene alignments from six prokaryotes previously collected and analyzed, Bayesian model selection finds support for (1) the SPR model over the alternative form, (2) the 16S rRNA reconstruction as the most likely species tree, and (3) increased HGT of operational genes compared to informational genes.

Marc A. Suchard Stochastic Models for Horizontal Gene Transfer Taking a Random Walk Through Tree Space Genetics, Vol. 170, 419-431, May 2005 Full Text Full Text (PDF)

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.
In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the -, ß- and -herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.

Aristotelis Tsirigos and Isidore Rigoutsos, A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Research 2005 33(12):3699-3707; doi:10.1093/nar/gki660 Full Text Free

The fate of laterally transferred genes: Life in the fast lane to adaptation or death.

Large-scale genome arrangement plays an important role in bacterial genome evolution. A substantial number of genes can be inserted into, deleted from, or rearranged within genomes during evolution. Detecting or inferring gene insertions/deletions is of interest because such information provides insights into bacterial genome evolution and speciation. However, efficient inference of genome events is difficult because genome comparisons alone do not generally supply enough information to distinguish insertions, deletions, and other rearrangements. In this study, homologous genes from the complete genomes of 13 closely related bacteria were examined. The presence or absence of genes from each genome was cataloged, and a maximum likelihood method was used to infer insertion/deletion rates according to the phylogenetic history of the taxa. It was found that whole gene insertions/deletions in genomes occur at rates comparable to or greater than the rate of nucleotide substitution and that higher insertion/deletion rates are often inferred to be present at the tips of the phylogeny with lower rates on more ancient interior branches. Recently transferred genes are under faster and relaxed evolution compared with more ancient genes. Together, this implies that many of the lineage-specific insertions are lost quickly during evolution and that perhaps a few of the genes inserted by lateral transfer are niche specific.

Weilong Hao and G. Brian Golding The fate of laterally transferred genes: Life in the fast lane to adaptation or death Genome Research 16:636-643, 2006

GENSTYLE: exploration and analysis of DNA sequences with genomic signature Full Text free

Conjugation

Conjugation enables bacteria to exchange genetic material because of tube-like connections called pili.

Conjugation is often likened to a form of sexual reproduction or mating, though it is merely a process by which donor bacteria deliver genetic material to recipient bacteria, utilizing tube-like connections called pili.

Bacteria often contain small circular, double-stranded DNA molecules that are termed plasmids. Bacterial plasmids are not connected to the main bacterial chromosomes and replicate independently. The donor bacterium contains conjugative or mobilizable genetic elements, usually a conjugative plasmid or episome plasmid that can integrate itself into the bacterial chromosome by genetic recombination. One such conjugative plasmid is called the F-plasmid. This is an episome about 100 thousand base-pairs in length, which carries its own origin of replication, called oriV. Most conjugative plasmids have systems ensuring that the recipient cell does not already contain a similar element, ensuring that there is only one copy of the F-plasmid in the F-positive bacterium. diagram of conjugation events diagram of molecular events

One cell contains an F-plasmid (pink), distinct from the prokaryotic genome (blue). The cell with an F-plasmid also possesses pili, which make contact with the F-negative cell, which does not have pili (top right diagram).

The middle diagram (right) indicates passage of genetic material through a pilum from the F+ bacterium to a F- bacterium. This mechanism is under debate. (Compare with a 27,000 x magnification tem image tem conjugation E. coli)

Transfer through the pili (middle, right) may not be a strictly accurate depiction of the actual transfer mechanism. The mechanism utilizes proteins coded by the tra or trb loci, and these may open a channel between the bacteria (bottom diagram). In this case, the pili are probably utilized to anchor and draw together the donor and recipient bacteria (top diagram). (Compare with conjugation in alga Conjugation of Spirogyra and a protist Conjugation of Paramecium.)

Once conjugation has been initiated by a mating signal, a complex of proteins called the relaxosome opens up one plasmid DNA strand at the origin of transfer, or oriT. The relaxosome system of the F-plasmid system comprises proteins TraI, TraY, TraM, and a protein that functions as the integrated host factor, IHF. The transferred strand – the T-strand – is unwound from the duplex before transfer into the recipient bacterium in a 5'-terminus to 3'-terminus direction. The remaining strand is replicated. Replication in concert with conjugation is termed conjugative replication, and is similar to the rolling circle replication of lambda phage. Replication may also occur independent of conjugative action – this is vegetative replication, and begins at the oriV.

Transduction

In transduction, a bacteriophage that has packaged a head-full of donor DNA then injects that DNA into the recipient.

Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts.
The movement of genes between organisms is an important mechanism in evolution. As agents of gene transfer, phages play a role in host evolution by supplying the host with new genetic material [11–15] and by displacing “host” genes with viral-encoded homologues [16–18]. Phage evolution is in turn influenced by the acquisition of DNA from their hosts [13,19–22] and by the swapping of genes within the phage gene pool [23,24]. Recent evidence suggests that gene flow within the global phage gene pool extends across ecosystems [25–27].
Cyanophage genomes bearing key photosynthesis genes psbA and psbD provide a notable example of the co-option of “host” genes for phage purposes [13,22,28–30]. The psbA and psbD genes encode the two photosystem II core reaction center proteins, D1 and D2 (denoted here as PsbA and PsbD, respectively), found in all oxygenic photosynthetic organisms. It has recently been shown that the phage-encoded psbA gene is expressed during infection [31,32]. Because maximal cyanophage production is dependent on photosynthesis [31,33], and the host PsbA protein turns over rapidly [34] and declines during infection [31], expression of these phage-encoded genes likely enhances photosynthesis during infection, thus increasing cyanophage fitness.
Matthew B. Sullivan, Debbie Lindell, Jessica A. Lee, Luke R. Thompson, Joseph P. Bielawski, Sallie W. Chisholm Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts. PLoS Biology Volume 4 Issue 8 AUGUST 2006
Volume 4 Issue 8 AUGUST 2006

Transformation

In transformation, naked DNA from the donor is taken up by the recipient.

The ability to adsorb, fragment, up-take, and recombine foreign DNA (as ssDNA) is termed competence. Natural competence involves a genetically programmed physiological state achieved by some strains of gram-negative (H. influenzae, N. gonorrhoeae) and gram-positive (S. pneumoniae, B. subtilis) bacteria. Artificial competence may be induced in some strains of bacteria (E. coli) through techniques utilizing CaCl2 and temperature manipulation.

More detail: Bacterial Transformation

Symbiosis

Biologist Lynn Margulis proposed that eukaryotic organisms acquired mitochondria and chloroplasts by symbiosis of prokaryotic organisms. Below is a proposed scheme for these transfers within the origins of the Kingdoms of Life.