Hendrickson, H., and J.G. Lawrence (2006) Selection for chromosome architecture in bacteria. J. Mol. Evol. 62:615-629
Bacterial chromosomes are immense polymers whose faithful replication and segregation are crucial to cell survival. The ability of proteins such as FtsK to move unidirectionally toward the replication terminus, and direct DNA translocation into the appropriate daughter cell during cell division, requires that bacterial genomes maintain an architecture for the orderly replication and segregation of chromosomes. We suggest that proteins that locate the replication terminus exploit strand-biased sequences that are overrepresented on one DNA strand, and that selection increases with decreased distance to the replication terminus. We report a generalized method for detecting these architecture imparting sequences (AIMS) and have identified AIMS in nearly all bacterial genomes. Their increased abundance on leading strands and decreased abundance on lagging strands toward replication termini are not the result of changes in mutational bias; rather, they reflect a gradient of long-term positive selection for AIMS. The maintenance of the pattern of AIMS across the genomes of related bacteria independent of their positions within individual genes suggests a well-conserved role in genome biology. The stable gradient of AIMS abundance from replication origin to terminus suggests that the replicore acts as a target of selection, where selection for chromosome architecture results in the maintenance of gene order and in the lack of high-frequency DNA inversion within replicores.
Azad, R.K., and J.G. Lawrence (2005) Use of artificial genomes in assessing methods for atypical gene detection. PLoS Comp. Biol. 1:461-473
Parametric methods for identifying laterally transferred genes exploit the directional mutational biases unique to each genome. Yet the development of new, more robust methods - as well as the evaluation and proper implementation of existing methods - relies on an arbitrary assessment of performance using real genomes, where the evolutionary histories of genes are not known. We have used the framework of a generalized hidden Markov model (HMM) to create artificial genomes modeled after genuine genomes. To model a genome, 'core' genes - those displaying patterns of mutational biases shared among large numbers of genes - are identified by a novel gene clustering approach based on the Akaike Information Criterion. Gene models derived from multiple 'core' gene clusters are used to generate an artificial genome which models the properties of a genuine genome. Chimeric artificial genomes - representing those having experienced lateral gene transfer - were created by combining genes from multiple artificial genomes, and the performance of the parametric methods for identifying 'atypical' genes was assessed directly. We found that an HMM that included multiple gene models, each trained on sets of genes representing the range of genotypic variability within a genome, could produce artificial genomes that mimicked the properties of genuine genomes. Moreover, different methods for detecting foreign genes performed differently - that is, they had different sets of strengths and weaknesses - when identifying atypical genes within chimeric artificial genomes.
Lawrence, J.G. (2005) Common themes in the genome strategies of pathogens. Curr. Op. Genet. Dev. 15:584-588
Genomes of pathogenic bacteria evolve by large-scale changes in gene inventory. The continual acquisition of genomic islands, which refines their metabolic arsenal, is offset by gene loss. Far from a passive deletion of genes no longer useful to pathogens, the removal of genes encoding problematic metabolic process and immunogenic surface antigens may be strongly beneficial. Genomes of virulent eukaryotes show the footprint of similar genomic alterations, including acquisition of genes by lateral transfer and genome degradation in obligate pathogens. These common features suggest that unicellular pathogens share common strategies for adaptation.
Gevers, D., F.M. Cohan, J.G. Lawrence, B.G. Spratt, T. Coenye, E.J. Feil, E. Stackebrandt, d.e. .P.e. Van, P. Vandamme, F.L. Thompson, and J. Swings (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733-739
There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.
Lawrence, J.G., and H. Hendrickson (2005) Genome evolution in bacteria: order beneath chaos. Curr. Op. Microbiol. 8:572-578
The historical view of bacterial genomes as collections of genes, with each genome evolving more-or-less independently through the acquisition of mutational changes, has been overturned by the finding that genomes of even closely-related taxa differ widely in gene content. Yet genomes are more than ever-shuffling collections of genes. Some genes are more transient than others, conferring a layer of phenotypic lability over a core of genotypic stability; this core decreases in size with increasing diversity of taxa. In addition, some lineages no longer experience high rates of gene turnover, and gene content changes primarily through slow rates of gene loss. More importantly, the molecular and cell biology of the bacterial cell imposes constraints on chromosome composition, maintaining a stable architecture in the face of gene turnover. As a result, genomes reflect the sum of processes introducing variability arbitrated by processes maintaining stability.
Lawrence, J.G. (2005) Studying evolution using genome sequence data. Pp 000-000 in The Evolution of Microbial Pathogens, Seifert, H., Ed. ASM Press, Washington, D.C.
Lawrence, J.G. (2005) Horizontal and vertical gene transfer: The life history of pathogens. Contrib. Microbiol. 12:255-271
Viewpoints regarding the evolution of pathogenic bacteria have themselves evolved over the past two decades. Although it is perhaps extreme to suggest different teleological camps have been established, it is fair to say that opinions regarding the evolution of pathogens are varied, and the strength of different points of view have waxed and waned. Initially, many view pathogenic bacteria as being specialized, highly-derived bacteria, which evolved complex and intimate associations with their hosts. In this way, special evolutionary mechanism were perhaps responsible for the origin or persistence of pathogens. Gradually, a viewpoint that every micro÷rganism was adapted to a particular niche was widely accepted, and pathogenicity represented just another bacterial lifestyle; therefore, no special evolutionary forces were at play. The evolution of well-studied pathogens could even be used as models for how other bacteria adapted to their environment. Somewhat surprisingly, perhaps, data collected in the "genomic era" has brought opinion back to the view that the evolution of pathogens indeed may encompass evolutionary paths typically not experienced by non-pathogenic bacteria. That is, the association of pathogens with particular hosts results in smaller effective population sizes, low genetic diversity, infrequent recombination and other factors influencing their evolution as dictated by their population genetics. As a result, pathogens would not serve as good models for the evolution of non-pathogenic bacteria that do not share these population genetic constraints. As discussed below, both viewpoints are perhaps true, when applied to the different stages of pathogen evolution. At the heart of the difference between stages of pathogen evolution are the relative roles of gene acquisition via horizontal gene exchange versus gene loss (genome degradation). Rather than representing different paths of pathogen creation or modification, these modes of genomic evolution likely represent a continuum or pathway along which a single lineage may travel.
Lawrence, J.G. (2004) Why genomics is more than genomes. Genome Biol. 5:357
Wildschutte, H., D.M. Wolfe, A. Tamewitz, and J.G. Lawrence (2004) Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella. Proc. Natl. Acad. Sci., USA 101:10644-10649
Extensive population-level genetic variability at the Salmonella rfb locus, which encodes enzymes responsible for synthesis of the O-antigen polysaccharide, is thought to have arisen through frequency-dependent selection (FDS) by means of exposure of this pathogen to host immune systems. The FDS hypothesis works well for pathogens such as Haemophilus influenzae and Neisseria meningitis, which alter the composition of their O-antigens during the course of bloodborne infections. In contrast, Salmonella remains resident in epithelial cells or macrophages during infection and does not have phase variability in its O-antigen. More importantly, Salmonella shows host-serovar specificity, whereby strains bearing certain O-antigens cause disease primarily in specific hosts; this behavior is inconsistent with FDS providing selection for the origin or maintenance of extensive polymorphism at the rfb locus. Alternatively, selective pressure may originate from the host intestinal environment itself, wherein diversifying selection mediated by protozoan predation allows for the continued existence of Salmonella able to avoid consumption by host-specific protozoa. This selective pressure would result in high population-level diversity at the Salmonella rfb locus without phase variation. We show here that intestinal protozoa recognize antigenically diverse Salmonella with different efficiencies and demonstrate that differences solely in the O-antigen are sufficient to allow for prey discrimination. Combined with observations of the differential distributions of both serotypes of bacterial species and their protozoan predators among environments, our data provides a framework for the evolution of high genetic diversity at the rfb locus and host-specific pathogenicity in Salmonella.
Dobbins, A.T., M. George Jr., D.A. Basham, M.E. Ford, J.M. Houtz, M.L. Pedulla, J.G. Lawrence, G.F. Hatfull, and R.W. Hendrix (2004) Complete genomic sequence of the virulent Salmonella bacteriophage SP6. J. Bacteriol. 186:1933-1944
We report the complete genome sequence of Enterobacteriophage SP6, which infects Salmonella enterica serovar Typhimurium. The genome contains 43,769 bp, including a 174 bp direct terminal repeat. The gene content and organization clearly places SP6 in the coliphage T7 group of phages, but it has ~5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes 1.3 through 3 appear to have undergone an unusual reorganization. Sequence analysis identifies 10 putative promoters for the SP6-encoded RNA polymerase and 7 putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provides clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcates exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggests that DNA replication occurs in large part through a bi-directional mechanism, possibly with circular intermediates.
Lawrence, J.G. (2004) Methods for detecting horizontal transfer of genes. Pp 000-000 in Encyclopedia of Genetics and Genomics, Jorde, L.B., P.F.R. Little, M.J. Dunn, and S. Subrmaniam, Ed. J. Wiley and Sons, London
Horizontal gene transfers are events that have no eyewitnesses; therefore, inferences regarding the nature and even existence of transfer events rely solely upon circumstantial evidence. Two general approaches have been taken to identify genes having participated in gene exchange: either examining the evolutionary history of a gene within its phylogenetic context and equating an incongruity with a transfer, or examining the sequence composition of a gene within its genomic context and attributing incongruity with differential history. In both cases, discordance can arise from sources aside from gene transfer, and the degree of the discordance can provide some measure of confidence that a transfer has occurred.
Lawrence, J.G., and H. Hendrickson (2004) Chromosome structure and constraints on lateral gene transfer. Dynamical Genet. 2004:319-336
Lateral gene transfer among bacterial lineages results in organisms whose genomes contain genes with disparate evolutionary histories. Despite mounting evidence for frequent and widespread gene transfer, there are apparently robust taxonomic relationships among more inclusive hierarchical groups of Bacteria and Archaea. The question is raised, then, as to why rampant lateral gene transfer has not obfuscated relationships among higher taxonomic groupings in prokaryotes. Herein we discuss facets of bacterial molecular biology - DNA replication and chromosome segregation - that may rely upon polarized sequences (found primarily on one DNA strand) which are distributed asymmetrically within the genome. These sequences may prevent the accumulation of internal genome rearrangements, but also constrain lateral gene transfer by limiting the suite of potential taxa that may donate genetic material into any one recipient. In this way, even very high rates of lateral gene transfer may not lead to panmixia, that is, the random distribution of genes among genomes regardless of the identities of donor or recipient. This phenomenon may lead to groups of bacterial taxa that reflect high rates of gene exchange within the clade in addition to their descent from a common ancestor.
Lawrence, J.G. (2003) When ELFs are ORFs but don't act like them. Trends Genet. 19:131-132
When they are very small, open reading frames (ORFs) are among the most difficult features of a newly sequenced genome to annotate. Although it has been suggested that degree of conservation of these sequences among closely related genomes might assist this process, there are some classes of ORF that will defy identification because little or none of the protein sequence is under selection.
Lawrence, J.G., and H. Hendrickson (2003) Lateral gene transfer: when will adoloscence end? Mol. Microbiol. 50:739-749
The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification, to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fueled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints likely stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Herein we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.
Lawrence, J.G. (2003) Gene organization: Selection, selfishness and serendipity. Annu. Rev. Microbiol. 57:419-440
The apparati behind the replication, transcription, and translation of prokaryotic and eukaryotic genes are quite different. Yet in both classes of organisms, genes may be organized in their respective chromosomes in similar ways by virtue of similarly acting selective forces. In addition, some gene organizations reflect biology unique to each class of organisms. Levels of organization are more complex than those of the simple operon. Multiple transcription units may be organized into larger units, local control regions may act over large chromosomal regions in eukaryotic chromosomes, and cis-acting genes may control the expression of downstream genes in all classes of organisms. All these mechanisms lead to genomes being far more organized, in both prokaryotes and eukaryotes, than hitherto imagined.
Pedulla, M.L., M.E. Ford, J.M. Houtz, T. Karthikeyan, C. Wadsworth, J.A. Lewis, D. Jacobs-Sera, J. Falbo, J. Gross, N.R. Pannunzio, W. Brucker, V. Kumar, J. Kandasamy, L. Keenan, S. Bardarov, J. Kriakov, J.G. Lawrence, W.R. Jacobs, R.W. Hendrix, and G.F. Hatfull (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113:171-182
Bacteriophages are the most abundant organisms in the biosphere and play major roles in the ecological balance of microbial life. The genomic sequences of ten newly isolated mycobacteriophages suggest that the bacteriophage population as a whole is amazingly diverse and may represent the largest unexplored reservoir of sequence information in the biosphere. Genomic comparison of these mycobacteriophages contributes to our understanding of the mechanisms of viral evolution and provides compelling evidence for the role of illegitimate recombination in horizontal genetic exchange. The promiscuity of these recombination events results in the inclusion of many unexpected genes including those implicated in mycobacterial latency, the cellular and immune responses to mycobacterial infections, and autoimmune diseases such as human lupus. While the role of phages as vehicles of toxin genes is well established, these observations suggest a much broader involvement of phages in bacterial virulence and the host response to bacterial infections.
Lawrence, J.G. (2002) Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 110:407-413
Although genes in prokaryotes and eukaryotes are transcribed and translated by very different mechanisms, they may be organized in their respective chromosomes in surprisingly similar ways. Here I examine common modes of maintaining non-random gene organization in both prokaryotes and eukaryotes, the different ways these organizations have likely arisen, and classes of organization that may be unique to one group or the other.
Gogarten, J.P., W.F. Doolittle, and J.G. Lawrence (2002) Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19:2226-2238
Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss or other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm - some of whose implications we explore here. In particular, we discuss (i) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (ii) the implications of these processes for the reconstruction and meaning of "phylogeny", and (iii) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.
Lawrence, J.G., G.F. Hatfull, and R.W. Hendrix (2002) Imbroglios of viral taxonomy : Genetic exchange and the failings of phenetic approaches. J. Bacteriol. 184:4891-4905
The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linneaus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. While long established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task, and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms obligates a reŰvaluation of the concept of viral species, genera, families and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnean paradigm that necessitate a new view of viral evolution, classification and taxonomy.
Lawrence, J.G. (2002) Gene transfer in bacteria: Speciation without species? Theor. Pop. Biol. 61:449-460
Although Bacteria and Archaea reproduce by binary fission, exchange of genes among lineages has shaped the diversity of their populations and the diversification of their lineages. Gene exchange can occur by two distinct routes, each differentially impacting the recipient genome. First, homologous recombination mediates the exchange of DNA between closely related individuals (those whose sequences are sufficient similarly to allow efficient integration). As a result, homologous recombination mediates the dispersal of advantageous alleles that may rise to high frequency among genetically related individuals via periodic selection events. Second, lateral gene transfer can introduce novel DNA into a genome from completely unrelated lineages via illegitimate recombination. Gene exchange by this route serves to distribute genes throughout distantly-related clades and therefore may confer complex abilities - not otherwise found among closely-related lineages - onto the recipient organisms. These two mechanisms of gene exchange play complementary roles in the diversification of microbial populations into independent, ecologically distinct lineages. Although the delineation of microbial "species" then becomes difficult - if not impossible - to achieve, a cogent process of speciation can be predicted.
Lawrence, J.G. (2002) The dynamics of bacterial genomes. Pp 95-110 in Horizontal Gene Transfer, Syvanen, M., and C.I. Kado, Ed. Academic Press, San Diego, CA
The availability of complete genome sequences for large numbers of micro÷rganisms has catalyzed a paradigm shift on how evolutionary biologists view the bacterial chromosome. No longer a mere collection of genes, each to be studied independently, a bacterial chromosome can be considered a complex document that both establishes its unique set of biological functions and reflects the long series of evolutionary events that shaped its current composition. Examination of genes en masse, and across multiple species, reveal evolutionary processes not evident in studies of individual genes. Two sets of processes affect the character of microbial genomes, mutation and recombination, and their roles in microbial evolution are quite different.
Lawrence, J.G., and H. Ochman (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10:1-4
The various methods for detecting potential lateral gene transfer events typically uncover different sets of genes. Because the procedures used to recognize transferred genes ask different types of questions, the sets of genes identified by each must be interpreted in the appropriate context. The integration of biological information, and long with these analytical procedures, makes it possible to assess the total impact of lateral gene transfer on microbial genomes.
Lawrence, J.G., R.W. Hendrix, and S. Casjens (2001) Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9:535-540
Most bacterial genomes have very few pseudogenes; notable exceptions include the genomes of the intracellular parasites Rickettsia prowezekii and Mycobacterium leprae. We propose that the influx of dangerous genetic elements (transposons and bacteriophages) selects for the maintenance of relatively high deletion rates in most bacteria; the sheltered lifestyle of intracellular parasites removes this threat, leading to reduced deletion rates and larger pseudogene loads.
Lawrence, J.G. (2001) Catalyzing bacterial speciation : Correlating lateral gene transfer and genetic headroom. Syst. Biol. 50:479-496
Unlike crown eukaryotic species, microbial species are created by continual processes of gene loss and acquisition promoted by horizontal genetic transfer. The amounts of foreign DNA in bacterial genomes, and the rate at which its acquired, are consistent with gene transfer as the primary catalyst for microbial differentiation. However, the rate of successful gene transfer varies among bacterial lineages. The heterogeneity in foreign DNA content is directly correlated with amount of genetic headroom intrinsic to a bacterial species. Genetic headroom reflects the amount of potentially dispensable information - reflected in codon usage bias and codon context bias - that can be transiently sacrificed to allow experimentation with functions introduced by gene transfer. In this way, genetic headroom offers potential metric for the propensity of a lineage to speciate.
Kolko, M.M., L.A. Kapetanovich, and J.G. Lawrence (2001) Alternative pathways for siroheme biosynthesis in Klebsiella aerogenes. J. Bacteriol. 183:328-335
Siroheme, the cofactor for sulfite and nitrite reductases, is formed by methylation, oxidation, and iron insertion into the tetrapyrrole uroporphyrinogen III (Uro-III). The CysG protein performs all three steps of siroheme biosynthesis in the enteric bacteria Escherichia coli and Salmonella enterica. In either taxon, cysG mutants cannot reduce sulfite to sulfide and require a source of sulfide or cysteine for growth. In addition, CysG-mediated methylation of Uro-III is required for de novo synthesis of cobalamin (coenzyme B12) in Salmonella enterica. We have determined that cysG mutants of the related enteric bacterium Klebsiella aerogenes have no defect in the reduction of sulfite to sulfide. These data suggest that an alternative enzyme allows for siroheme biosynthesis in CysG-deficient strains of Klebsiella. However, Klebsiella cysG mutants fail to synthesize coenzyme B12, suggesting that the alternative siroheme biosynthetic pathway proceeds by a different route. A gene, cysF, encoding an alternative siroheme synthase homologous to CysG, has been identified by genetic analysis and lies within the cysFDNC operon; the cysF gene is absent from the E. coli and S. enterica genomes. While the cysG is coregulated with the siroheme-dependent nitrite reductase, the cysF gene is regulated by sulfur starvation. Models for alternative regulation of the CysF and CysG siroheme synthases in Klebsiella, and for the loss of the cysF gene from the ancestor of E. coli and S. enterica, are presented.
Seiflein, T.A., and J.G. Lawrence (2001) Methionine to cysteine recycling in Klebsiella aerogenes. J. Bacteriol. 183:336-346
In the enteric bacteria Escherichia coli and Salmonella enterica, sulfate is reduced to sulfide and assimilated into the amino acid cysteine; in turn, cysteine provides the sulfur atom for other sulfur-bearing molecules in the cell, including methionine. These organisms cannot use methionine as a sole source of sulfur. Here we report that this constraint is not shared by many other enteric bacteria, which can use either cysteine or methionine as a sole source of sulfur. The enteric bacterium Klebsiella aerogenes appears to use at least two pathways to allow the reduced sulfur of methionine to be recycled into cysteine. In addition, the ability to recycle methionine appears to be different on solid media - where cys mutants cannot use methionine as a sulfur source - vs. liquid media, where they can. One pathway likely uses a cystathionine intermediate to convert homocysteine to cysteine and is induced under conditions of sulfur starvation, which is likely sensed by low levels of the sulfate-reduction intermediate APS. The CysB regulatory proteins appears to control activation of this pathway. A second pathway may use a methanesulfonate intermediate to convert methionine-derived methanethiol to sulfite. While the transsulfurylation pathway may be directed toward recovery of methionine, the methanethiol pathway likely represents a general salvage mechanism for recovery of alkane-sulfide and alkane-sulfonates. Therefore, the relatively distinct biosyntheses of cysteine and methionine in E. coli and Salmonella appear to be more intertwined in Klebsiella.
Hendrix, R.W., J.G. Lawrence, G.F. Hatfull, and S. Casjens (2000) The origins and ongoing evolution of viruses. Trends Microbiol. 8:504-508
Genome analyses of dsDNA tailed bacteriophages argue that they evolve by recombinational reassortment of genes, and by the acquisition of novel genes as simple genetic elements termed morons. These processes suggest a model for early virus evolution, wherein viruses can be regarded less as having derived from cells and more as being partners in their mutual co-evolution.
Ochman, H.O., J.G. Lawrence, and E.A. Groisman (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304
Unlike eukaryotes, which evolve principally through the modification of existing genetic information, a significant portion of the diversity observed in bacteria has originated through the acquisition of sequences from distantly related organisms. Horizontal genetic processes result in extremely dynamic genomes in which substantial amounts of DNA are introduced into, and deleted from, the chromosome and have effectively changed the ecological and pathogenic character of bacterial species.
Lawrence, J.G. (2000) Beyond the selfish operon : Clustering and hitchhiking among antibiotic resistance genes. ASM News 66:281-286
Lawrence, J.G. (1999) Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Op. Genet. Dev. 9:642-648
The Selfish Operon Model postulates that the organization of bacterial genes into operons is beneficial to the constituent genes in that proximity allows horizontal cotransfer of all genes required for a selectable phenotype; eukaryotic operons formed for very different reasons. Horizontal transfer of selfish operons likely promotes bacterial diversification.
Lawrence, J.G. (1999) Gene transfer, speciation, and the evolution of bacterial genomes. Curr. Op. Microbiol. 2:519-523
Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.
Lawrence, J.G., and J.R. Roth (1999) Genomic flux : Genome evolution by gene loss and acquisition. Pp 263 - 289 in Bacterial Genomics, Charlebois, R., Ed. ASM Press, Washington, D.C.
Genome evolution is the process by which the content and organization of a species' genetic information changes over time. This process involves four sorts of changes: (a) Point mutations and gene conversion events gradually alter internal information; (b) rearrangements (e.g. inversions, translocations, plasmid integration, and transpositions) alter chromosome topology with little change in information content; (c) deletions cause irreversible loss of information; (d) insertions of foreign material can add novel information to a genome. Although the first two processes can create new genes, they act very slowly. Gene loss and acquisition are genomic changes that can radically and rapidly increase fitness or alter some aspect of lifestyle.
Most evolutionary thought on genome evolution has focused on how the slow sequence changes can cause divergence of gene functions. This is understandable, because available data suggests that horizontal genetic transfer has been a minor contributor to the evolution of eukaryotic lineages (with notable exceptions such as the introduction mitochondria and chloroplasts). In bacteria, however, both genetics and genome analysis provide extensive evidence for gene loss and horizontal genetic transfer. Analyses of these data suggest that gene loss and acquisition are likely to be the primary mechanisms by which bacteria adapt genetically to novel environments, and by which bacterial populations diverge and form separate, evolutionarily distinct species. We suggest that bacterial adaptation and speciation is determined predominantly by acquisition of selectively valuable genes (by horizontal transfer) and by loss of weakly contributing genes (by mutation, deletion and drift from the population) during periods of relaxed selection.
We propose that a limitation of genome expansion couples the rates of gene acquisition and loss. Genome size may be limited in part by population-based factors that limit the ability of cells to selectively maintain information; some limitation may also be imposed by physiological considerations. The balance between selective gene acquisition and secondarily-imposed gene loss, implies that addition of a foreign gene increases the probability of loss of some resident function of lower selective value. The interaction of these factors, we suggest, drives divergence of bacterial types.
Lawrence, J.G. (1999) Gene transfer and minimal genome size. Pp 32-38 in Size Limits of Very Small Microorganisms, , Ed. National Research Council, Washington, D.C.
Throughout all domains of life, genetic material is exchanged within and among genomes. Horizontal transfer typically denotes rare transfer of genetic material between diverse lineages. This process does not constrain genome size in significant ways. Intraspecific recombination is more common than horizontal exchange, allows for the removal of deleterious mutations, and helps maintenance of species identity. Recombination enables organisms to maintain maximum genome sizes that are larger than those capable without gene exchange (escape of Muller's ratchet), but does not mediate potential reduction of genome size. In these cases, gene exchange allows transfer of non-essential gene among organisms, or reassortment of essential genes within a taxon. Neither process permits a cell to maintain fewer than the minimal complement of genes required for life. A model is presented whereby the frequency of gene exchange is much greater than the frequency of cell division. In this model, cells may be considered way-stations for gene replication and transfer; such organisms need not maintain a full complement of genes, and genome sizes may decrease. Simulations predict the propagation of organisms where the average cell contains, on average over time, fewer than 1 gene.
Brodsky, J.L., J.G. Lawrence, and A.J. Caplan (1998) Mutations in the cytosolic DnaJ-homologue, YDJ1, delay and compromise the efficient translation of heterologous proteins in yeast. Biochemistry 37:18045-18055
The Saccharomyces cerevisiae YDJ1 gene encodes a yeast homologue of DnaJ, an Escherichia coli molecular chaperone and regulator of Hsp70 function. We examined the function of Ydj1p in vivo by analyzing the activity and production of firefly luciferase (FFLux) and green fluorescent protein (GFP) after inducible expression in yeast strains containing a wild type or a mutant YDJ1 gene. Although FFLux and GFP mRNA levels were similar in the wild type and mutant strains, the FFLux protein was translated about half as efficiently in the ydj1-151 mutant compared to the wild type strain; the lower FFLux level was not the result of increased FFLux turnover in the mutant. In contrast, GFP translation was significantly delayed in the ydj1-151 mutant compared to the wild type strain. Surprisingly, we observed that FFLux and GFP mRNA bound efficiently to polysomes in the ydj1-151 mutant. Analysis of polysome profiles also revealed a modest increase in the amount of 60S ribosomal subunits in the ydj1-151 strain, consistent with a translation defect in the mutant, although the Ydj1 protein was not found to be associated with polysomes. To determine whether the inducible expression of an endogenous yeast protein was also less efficient in the ydj1-151 strain, we examined the inducible synthesis of the yeast TATA-binding protein (TBP) but observed no translation defect. Statistical analysis of the FFLux, GFP, and TBP encoding genes suggests that Ydj1p facilitates the expression of proteins that are poorly translated because both FFLux and GFP contain an abundance of codons that are rarely used in yeast.
Lawrence, J.G., and H. Ochman (1998) Molecular archaeology of bacterial genomes. Proc. Natl. Acad. Sci., USA 95:9413-9417
The availability of the complete sequence of Escherichia coli MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. We found that 755 of 4288 ORFs (547.8 kilobases) have been introduced into the E. coli genome in at least 234 lateral transfer events since this species diverged from the Salmonella lineage 100 million years ago. The average age of introduced genes was 14.4 Myr, yielding a rate of transfer 16 kb per Myr per lineage since divergence. Although most of the acquired genes were subsequently deleted, the sequences that have persisted (~18% of the current chromosome) have conferred properties permitting E. coli to explore otherwise unreachable ecological niches.
Lawrence, J.G., and J.R. Roth (1998) Roles of horizontal transfer in bacterial evolution. Pp 208-225 in Horizontal Gene Transfer, Syvanen, M., and C.I. Kado, Ed. Chapman and Hall, London
Gene loss and reacquisition may be key aspects of bacterial evolution. This was suggested by the history of B12 metabolism in enteric bacteria, which includes loss of multiple functions and reacquisition of genes from a foreign source. Many bacterial genes are located in cotranscribed clusters or operons; together, the genes in an operon generally provide a single function or selectable phenotype. Conditionally dispensable functions are usually encoded by operons; essential genes are less likely to be clustered. Operon formation may be driven by gene loss (by mutation during periods of dispensability) and reacquisition (by horizontal acquisition of small chromosome fragments followed by selection). Clustered genes can be cotransferred horizontally and therefore can spread faster than identical unclustered alleles; thus clustered alleles have higher fitness. Gene clustering may provide no immediate fitness benefit to the host organism and can be considered a selfish property of genes. Recently acquired genes may show atypical patterns of base composition and codon usage bias. With time, such sequences ameliorate toward the patterns of the new host. From the degree of sequence amelioration, one can estimate the time at which a sequence was introduced. We estimate that 31 kb of foreign DNA are introduced and substantially fixed in the E. coli genome every million years; a corresponding amount of DNA is presumably lost. We predict that the genomes of S. enterica and E. coli each include sequences - up to 30% of each genome - that are absent from the other genome. Horizontal transfer may drive bacterial speciation since it allows an organism to suddenly acquire a well-developed capability.
Lawrence, J.G. (1997) Selfish operons and speciation by gene transfer. Trends Microbiol. 5:355-359
Bacterial genes providing for single metabolic functions may be found in operons because this organization allows efficient horizontal transfer among organisms. Transferred genes can confer novel metabolic phenotypes to their new hosts and allow rapid, effective exploitation of new environmental niches. The mobility of selfish operons may facilitate bacterial speciation.
Lawrence, J.G., and H. Ochman (1997) Amelioration of bacterial genes: rates of change and exchange. J. Mol. Evol. 44:383-397
Although bacterial species display wide variation in their overall GC contents, the genes within a particular species' genome are relatively similar in base composition. As a result, sequences that are novel to a bacterial genome - i.e., DNA introduced through recent horizontal transfer - often bear unusual sequence characteristics and can be distinguished from ancestral DNA. At the time of introgression, horizontally-transferred genes reflect the base composition of the donor genome; but, over time, these sequences will ameliorate to reflect the DNA composition of the new genome because the introgressed genes are subject to the same mutational processes affecting all genes in the recipient genome. This process of amelioration is evident in a large group of genes involved in host cell invasion by enteric bacteria and can be modeled to predict the amount of time required after transfer for foreign DNA to resemble native DNA. Furthermore, models of amelioration can be used to estimate the time of introgression of foreign genes in a chromosome. Applying this approach to a 1.43 megabase continuous sequence, we have calculated that the entire Escherichia coli chromosome contains more than 600 kilobases of horizontally-transferred, protein-coding DNA. Estimates of amelioration times indicate that this DNA has accumulated at a rate of 31 kilobases per million years, which is on the order of the amount of variant DNA introduced by point mutations. This rate predicts that the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases of novel DNA since their divergence.
Ochman, H., and J.G. Lawrence (1996) Phylogenetics and the amelioration of bacterial genomes. Pp 2627-2637 in Escherichia coli and Salmonella: Cellular and molecular biology, Second edition, Neidhardt, F.C., R. Curtiss III, J.L Ingraham, E.C.C. Lin, K. Brooks Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter, and H.E. Umbarger, Ed. ASM Press, Washington, D.C.
Roth, J.R., N. Benson, T. Galitski, K. Haack, J.G. Lawrence, and L. Miesel (1996) Rearrangements of the bacterial chromosome -- Formation and applications. Pp 2256-2276 in Escherichia coli and Salmonella: Cellular and molecular biology, Second edition, Neidhardt, F.C, R. Curtiss III, J.L Ingraham, E.C.C. Lin, K. Brooks Low, B. Magasanik, W.S. Reznikoff, M. Riley, M. Schaechter, and H.E. Umbarger, Ed. ASM Press, Washington, D.C.
Roth, J.R., J.G. Lawrence, and T.A. Bobik (1996) Cobalamin (coenzyme B12): synthesis and biological significance. Annu. Rev. Microbiol. 50:137-181
This review examines deoxyadenosylcobalamin (Ado-B12) biosynthesis, transport, use, and uneven distribution among living forms. We describe how genetic analysis of enteric bacteria has contributed to these issues. Two pathways for corrin ring formation have been found-an aerobic pathway (in P. denitrificans) and an anaerobic pathway (in P. shermanii and S. typhimurium)-that differ in the point of cobalt insertion. Analysis of B12 transport in E. coli reveals two systems: one (with two proteins) for the outer membrane, and one (with three proteins) for the inner membrane. To account for the uneven distribution of B12 in living forms, we suggest that the B12 synthetic pathway may have evolved to allow anaerobic fermentation of small molecules in the absence of an external electron acceptor. Later, evolution of the pathway produced siroheme, (allowing use of inorganic electron acceptors), chlorophyll (O2 production), and heme (aerobic respiration). As oxygen became a larger part of the atmosphere, many organisms lost fermentative functions and retained dependence on newer, B12 functions that did not involve fermentation. Paradoxically, Salmonella spp. synthesize B12 only anaerobically but can use B12 (for degradation of ethanolamine and propanediol) only with oxygen. Genetic analysis of the operons for these degradative functions indicate that anaerobic degradation is important. Recent results suggest that B12 can be synthesized and used during anaerobic respiration using tetrathionate (but not nitrate or fumarate) as an electron acceptor. The branch of enteric taxa from which Salmonella spp. and E. coli evolved appears to have lost the ability to synthesize B12 and the ability to use it in propanediol and glycerol degradation. Salmonella spp., but not E. coli, have acquired by horizontal transfer the ability to synthesize B12 and degrade propanediol. The acquired ability to degrade propanediol provides the selective force that maintains B12 synthesis in this group.
Lawrence, J.G., and J.R. Roth (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860
A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa.Bacterial operons are typically comprised of genes whose products contribute to a single function. If this function is subject to weak selection, or to long periods with no selection, the contributing genes may accumulate mutations and be lost by genetic drift. From a cell's perspective, once several genes are lost, the function can be restored only if all missing genes were acquired simultaneously by lateral transfer. The probability of transfer of multiple genes increases when genes are physically proximate. From a gene's perspective, horizontal transfer provides a way to escape evolutionary loss by allowing colonization of organisms lacking the encoded functions. Since organisms bearing clustered genes are more likely to act as successful donors, clustered genes would spread among bacterial genomes. The physical proximity of genes may be considered a selfish property of the operon since it affects the probability of successful horizontal transfer, but may provide no physiological benefit to the host. This process predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.
Lawrence, J.G., and J.R. Roth (1996) Evolution of coenzyme B12synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142:11-24
We have examined the distribution of cobalamin (coenzyme B12) synthetic ability and cobalamin-dependent metabolism among enteric bacteria. Most species of enteric bacteria tested synthesize cobalamin under both aerobic and anaerobic conditions and ferment glycerol in a cobalamin-dependent fashion. The group of species including Escherichia coli and S. typhimurium cannot ferment glycerol. E. coli strains cannot synthesize cobalamin de novo, and Salmonella spp. synthesize cobalamin only under anaerobic conditions. In addition, the cobalamin synthetic genes of Salmonella spp. (cob) show a regulatory pattern different from that of other enteric taxa tested. We propose that the cobalamin synthetic genes, as well as genes providing cobalamin-dependent diol dehydratase, were lost by a common ancestor of E. coli and Salmonella spp. and were both reintroduced as a single fragment into the Salmonella lineage from an exogenous source. Consistent with this hypothesis, the S. typhimurium cob genes do not hybridize with the genomes of other enteric species. The Salmonella cob operon may represent a class of genes characterized by periodic loss and reacquisition by host genomes. This process may be an important aspect of bacterial population genetics and evolution.
Lawrence, J.G., and J.R. Roth (1995) The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli. J. Bacteriol. 177:6371-6380
The enteric bacterium Escherichia coli synthesizes cobalamin (vitamin B12) only when provided with the complex intermediate cobinamide. Three cobalamin biosynthetic genes have been cloned from Escherichia coli K-12 and their nucleotide sequences have been determined. The three genes form an operon (cob) under the control of several promoters and are induced by cobinamide, a precursor of cobalamin. The cob operon of E. coli comprises the cobU gene, encoding the bifunctional cobinamide kinase-guanylyltransferase, the cobS gene, encoding cobalamin synthetase, and the cobT gene, encoding DMB phosphoribosyltransferase. The physiological roles of these sequences were verified by the isolation of Tn10 insertion mutations in the cobS and cobT genes. All genes were named after their Salmonella typhimurium homologues, and are located at the corresponding position on the E. coli genetic map. Although the nucleotide sequences of the Salmonella cob genes and the E. coli cob genes are homologous, they are too divergent to have been derived from an operon present in their most recent common ancestor. Based on comparisons of G+C content, codon usage bias, dinucleotide frequencies, and patterns of synonymous and nonsynonymous substitutions, we conclude that the cob operon was introduced into the Salmonella genome from an exogenous source. The cob operon of E. coli may be related to cobalamin synthetic genes now found among non-Salmonella enteric bacteria.
Lawrence, J.G., D.L. Hartl, and H. Ochman (1993) Sequencing products of the polymerase chain reaction. Meth. Enzymol. 218:26-35
Roth, J.R., J.G. Lawrence, S. Kieffer-Higgins, and G.C. Church (1993) Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175:3303-3316
Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Of the 30 cobalamin synthetic genes, 25 are clustered in one operon, cob, and are arranged in three groups, each group encoding enzymes for a biochemically distinct portion of the biosynthetic pathway. We have determined the DNA sequence for the promoter region and the proximal 17.1 kb of the cob operon. This sequence includes 20 translationally coupled genes that encode the enzymes involved in parts I and III of the cobalamin biosynthetic pathway. A comparison of these genes with the cobalamin synthetic genes from Pseudomonas denitrificans allows assignment of likely functions to 12 of the 20 sequenced Salmonella genes. Three additional Salmonella genes encode proteins likely to be involved in the transport of cobalt, a component of vitamin B12. However, not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species. These differences suggest that the cobalamin biosynthetic pathways differ between the two organisms. The evolution of these genes and their chromosomal positions is discussed.
Hartl, D.L., E.R. Lozovskaya, and J.G. Lawrence (1992) Nonautonomous transposable elements in prokaryotes and eukaryotes. Genetica 86:47-53
Defective (nonautonomous) copies of transposable elements are relatively common in the genomes of eukaryotes but less common in the genomes of prokaryotes. With regard to transposable elements that exist exclusively in the form of DNA (nonretroviral transposable elements), nonautonomous elements may play a role in the regulation of transposition. In prokaryotes, plasmid-mediated horizontal transmission probably imposes a selection against nonautonomous elements, since nonautonomous elements are incapable of mobilizing themselves. The lower relative frequency of nonautonomous elements in prokaryotes may also reflect the coupling of transcription and translation, which may bias toward the cis activation of transposition. The cis bias we suggest need not be absolute in order to militate against the long-term maintenance of prokaryotic elements unable to transpose on their own. Furthermore, any cis bias in transposition would also decrease the opportunity for trans repression of transposition by nonautonomous elements.
Lawrence, J.G., and D.L. Hartl (1992) Inference of horizontal genetic transfer: An approach using the bootstrap. Genetics 131:753-760
Inconsistencies in taxonomic relationships implicit in different sets of nucleic acid sequences potentially result from horizontal transfer of genetic material between genomes. A nonparametric method is proposed to determine whether such inconsistencies are statistically significant. A similarity coefficient is calculated from ranked pairwise identities and evaluated against a distribution of similarity coefficients generated from resampled data. Subsequent analyses of partial data sets, obtained by the elimination of individual taxa, identify particular taxa to which the significance may be attributed, and can sometimes help in distinguishing horizontal genetic transfer from inconsistencies due to convergent evolution or variation in evolutionary rate. The method was successfully applied to data sets that were not found to be significantly different with existing methods that use comparisons of phylogenetic trees. The new statistical framework is also applicable to the inference of horizontal transfer from restriction fragment length polymorphism distributions and protein sequences.
Lawrence, J.G., H. Ochman, and D.L. Hartl (1992) The evolution of insertion sequences in enteric bacteria. Genetics 131:9-20
To identify mechanisms that influence the evolution of bacterial transposons, DNA sequence variation was evaluated among homologs of insertion sequences IS1, IS3 and IS30 from natural strains of Escherichia coli and related enteric bacteria. The nucleotide sequences within each class of IS were highly conserved among E. coli strains, over 99.7% similar to a consensus sequence. When compared to the range of nucleotide divergence among chromosomal genes, these data indicate high turnover and rapid movement of the transposons among clonal lineages of E. coli. In addition, length polymorphism among IS appears to be far less frequent than in eukaryotic transposons, indicating that nonfunctional elements comprise a smaller fraction of bacterial transposon populations than found in eukaryotes. IS present in other species of enteric bacteria are substantially divergent from E. coli elements, indicating that IS are mobilized among bacterial species at a reduced rate. However, homologs of IS1 and IS3 from diverse species provide evidence that recombination events and horizontal transfer of IS among species have both played major roles in the evolution of these elements. IS3 elements from E. coli and Shigella show multiple, nested, intragenic recombinations with a distantly related transposon, and IS1 homologs from diverse taxa reveal a mosaic structure indicative of multiple recombination and horizontal transfer events.
Lawrence, J.G., D.L. Hartl, and H. Ochman (1991) Molecular considerations in the evolution of bacterial genes. J. Mol. Evol. 33:241-250
Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationships, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of the gap and ompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of the ompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzyme in these lineages.
Lawrence, J.G., H. Ochman, and D.L. Hartl (1991) Molecular and evolutionary relationships among enteric bacteria. J. Gen. Microbiol. 137:1911-1921
Classification of bacterial species into genera has traditionally relied upon variation in phenotypic characteristics. However, these phenotypes often have a multifactorial genetic basis, making unambiguous taxonomic placement of new species difficult. By designing evolutionarily conserved oligonucleotide primers, it is possible to amplify homologous regions of genes in diverse taxa using the polymerase chain reaction and determine their nucleotide sequences. We have constructed a phylogeny of some enteric bacteria, including five species classified as members of the genus Escherichia, based on nucleotide sequence variation at the loci encoding glyceraldehyde-3-phosphate dehydrogenase and outer membrane protein 3A, and compared this genealogy with the relationships inferred by biotyping. The DNA sequences of these genes defined congruent and robust phylogenetic trees indicating that they are an accurate reflection of the evolutionary history of the bacterial species. The five species of Escherichia were found to be distantly related and, contrary to their placement in the same genus, do not form a monophyletic group. These data provide a framework which allows the relationships of additional species of enteric bacteria to be inferred. These procedures have general applicability for analysis of the classification, evolution, and epidemiology of bacterial taxa.
Lawrence, J.G., A.C. Colwell, and O.J. Sexton (1991) The ecological impact of allelopathy in Ailanthus altissima. Am. J. Bot. 78:948-958
Lawrence, J.G., and D.L. Hartl (1991) Unusual codon usage bias occurring within insertion sequences in Escherichia coli. Genetica 84:23-29
The large open reading frames of insertion sequences from Escherichia coli were examined for their spatial pattern of codon usage bias and distribution of rarely used codons. There is a bias in codon usage that is generally lower toward the terminal ends of the coding regions, which is reflected in the occurrence of an excess of nonpreferred codons in the 3' portions of the coding regions as compared with the 5' portions. In contrast, typical chromosomal genes have a lower codon usage bias toward the 5' ends of the coding regions. These results imply that the selective forces reflected in codon usage bias may differ according to position within the coding sequence. In addition, these constraints apparently differ in important ways between genes contained in insertion sequences and those in the chromosome.
Lawrence, J.G., D.E. Dykhuizen, R.F. DuBose, and D.L. Hartl (1989) Phylogenetic analysis of Escherichia coli using insertion sequence fingerprinting. Mol. Biol. Evol. 6:1-14
Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these characters yielded a unique phylogenetic tree. This analysis not only distinguished among bacterial strains that were otherwise identical in their biochemical characteristics and enzyme electrophoretic mobilities, but certain aspects of the topology of the tree were consistent across several unrelated insertion elements. The distribution of IS elements was then reexamined in light of the inferred phylogenetic relationships to investigate the biological properties of the elements, such as rates of insertion and deletion, and to discover apparent recombinational events. The analysis shows that the pattern of distribution of insertion elements in the bacterial genome is sufficiently stable for epidemiological studies. Although the rate of recombination by conjugation has been postulated to be low, at least two such events appear to have taken place.
Last Updated 14 August 2006, by JG Lawrence