Chapter 2 : The Dynamic Bacterial Genome

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

The Dynamic Bacterial Genome, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap02-1.gif /docserver/preview/fulltext/10.1128/9781555817640/9781555812324_Chap02-2.gif


The model of a static bacterial chromosome arose from early comparisons of the genetic maps of and . Analyses of complete genome sequences by several methods revealed that the differences in gene content were the result of two complementary processes: the gain of new genes by horizontal gene transfer from distantly related organisms, and the loss of ancestral genes from descendent lineages. Directional mutation pressures provide a distinct ‘‘fingerprint’’ to a bacterial genome owing to the differential mutational proclivities of DNA polymerases, the nature and number of mismatch correction systems, the numbers and abundances of tRNA species, and even relative concentrations of precursor nucleotide pools. Thus, genes which appear atypical in their current genomic context may reflect the direction pressures of a donor genome. Aside from changes in gene content, gene order has also been found to be more plastic than once assumed. Mechanisms for DNA rearrangement are well known and have been well measured in the laboratory. Yet despite the opportunities for chromosomal rearrangement, the genetic maps of and seemed to be largely congruent, save the inversion about the terminus of replication. The genome, with all its dynamic parts, steers the organism into the environmental space it is best suited to exploit. Rather than a stale collection of genes having reached optimal performance after billions of years of evolution, one may view a bacterial genome as an ever-changing consortium of genes which cooperate in perpetuating their host organism.

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2

Key Concept Ranking

Mobile Genetic Elements
Multilocus Sequence Typing
Genetic Elements
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1.
Figure 1.

Correspondence between the first genetic maps of ( ), whose loci are denoted on the inside of the circle, and serovar Typhimurium ( ), whose loci are denoted on the outside of the circle. Genes whose positions were less defined are depicted in parentheses; spacing between genes was adjusted to allow for facile alignment of the two maps. The loci shared between the maps show remarkable conservation of order.

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Mechanisms of gene transfer and their effects on inferring phylogeny. Homologous recombination serves to unify strains within bacterial taxa; as a result, phylogenies of different genes within these groups will not be congruent, but phylogenies of the same genes found in different lineages—that is, those which do not exchange genes because of the imposition of mismatch correction systems ( )—will be congruent. This system has been invoked to define bacterial species ( ). Gene exchange across large phylogenetic distances does not disrupt these patterns as long as the donor taxa are not included in the analyses. Limitations of this approach are discussed elsewhere ( ).

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

The distribution of recently acquired DNA, inferred from the numbers of atypical genes, in various bacterial genomes. Gray bars denote amounts of typical protein-coding sequences, while black bars denote atypical protein-coding sequences, identified as having aberrant composition, dinucleotide fingerprints, and patterns of codon usage bias.

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4.
Figure 4.

Disruption of the operon in serogroup A strain Z2491 ( ). Letters indicate genes; non- genes are indicated by the gray boxes. The nucleotide composition plot shows the %G+C for a 200-base window starting at the position indicated.

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5.
Figure 5.

Distribution of oligomers in the genome. Sequence is from Fleischmann et al. ( ); origin and terminus of replication are inferred from strand asymmetry analysis; triangles represent positions as direction of transcription of rRNA operons. The lower panel shows the effects of mutation biases. Strand asymmetry in the genome of is manifested by 14 different octameric oligonucleotides, which are drawn on either the forward or reverse strand. The middle panel shows sequences with both strand asymmetry and a biased distribution with respect to the terminus of replication; the distribution of 23 octamers is shown. The top panel shows a histogram of the distribution of the octamers shown in the middle panel on the leading and lagging strands for 50-kb intervals; intervals were chosen so that the terminus of replication fell between two intervals.

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6.
Figure 6.

Relationship between the amount of recently acquired DNA and information content in bacterial genomes. Genomes used for analysis are shown in Fig. 3 ; information content is measured as corrected, length-normalized average χ of codon usage as described elsewhere ( ).

Citation: Lawrence J. 2005. The Dynamic Bacterial Genome, p 19-37. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch2
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Achtman, M.,, T. Azuma,, D. E. Berg,, Y. Ito,, G. Morelli,, Z. J. Pan,, S. Suerbaum,, S. A. Thompson,, A. van der Ende,, and L. J. van Doorn. 1999. Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol. Microbiol. 32:459470.
2. Achtman, M.,, M. Heuzenroeder,, B. Kusecek,, H. Ochman,, D. Caugant,, R. K. Selander,, V. Vaisanen-Rhen,, T. K. Korhonen,, S. Stuart,, F. Orskov,, and I. Orskov. 1986. Clonal analysis of Escherichia coli O2:K1 isolated from diseased humans and animals. Infect. Immun. 51:268276.
3. Achtman, M.,, A. Mercer,, B. Kusecek,, A. Pohl,, M. Heuzenroeder,, W. Aaronson,, and R. Silver. 1983. Six widespread bacterial clones among E. coli K1 isolates. Infect. Immun. 39:315335.
4. Allison, G. E.,, D. Angeles,, N. Tran-Dinh,, and N. K. Verma. 2002. Complete genomic sequence of SfV, a serotypeconverting temperate bacteriophage of Shigella flexneri. J. Bacteriol. 184:19741987.
5. Andersen, P. A.,, A. A. Griffiths,, I. G. Duggin,, and R. G. Wake. 2000. Functional specificity of the replication forkarrest complexes of Bacillus subtilis and Escherichia coli: significant specificity for Tus-Ter functioning in E. coli. Mol. Microbiol 36:13271335.
6. Andersson, J. O. 2000. Evolutionary genomics: is Buchnera a bacterium or an organelle? Curr. Biol. 10:R866R868.
7. Andersson, J. O.,, and S. G. Andersson. 1999. Genome degradation is an ongoing process in Rickettsia. Mol. Biol. Evol. 16:11781191.
8. Andersson, J. O.,, and S. G. Andersson. 1999. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9:664671.
9. Andersson, S. G.,, A. Zomorodipour,, J. O. Andersson,, T. Sicheritz-Ponten,, U. C. Alsmark,, R. M. Podowski,, A. K. Naslund,, A. S. Eriksson,, H. H. Winkler,, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133140.
10. Bachellier, S.,, J. M. Clement,, M. Hofnung,, and E. Gilson. 1997. Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence. Genetics 145:551562.
11. Bender, R. A., 1996. Variations on a theme by Escherichia, p. 49. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 1. ASM Press, Washington, D.C..
12.. Blattner, F. R.,, G. R. Plunkett,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:14531474.
13. Boucher, Y.,, H. Huber,, S. L’Haridon,, K. O. Stetter,, and W. F. Doolittle. 2001. Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders thermoplasmatales and archaeoglobales. Mol. Biol. Evol. 18:13781388.
14. Boyd, E. F.,, K. Nelson,, F. S. Wang,, T. S. Whittam,, and R. K. Selander. 1994. Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. USA 91:12801284.
15. Brenner, D. J. 1978. Characterization and clinical identification of Enterobacteriaceae by DNA hybridization. Prog. Clin. Pathol. 7:71117.
16. Brenner, D. J.,, and D. B. Cowie. 1968. Thermal stability of Escherichia coli-Salmonella typhimurium deoxyribonucleic acid duplexes. J. Bacteriol. 95:22582262.
17. Brenner, D. J.,, and S. Falkow. 1971. Molecular relationships among members of the Enterobacteriaceae. Adv. Genet. 16:81118.
18. Brenner, D. J.,, G. R. Fanning,, K. E. Johnson,, R. V. Citarella,, and S. Falkow. 1969. Polynucleotide sequence relationships among members of the Enterobacteriaceae. J. Bacteriol. 98:637650.
19. Brenner, D. J.,, G. R. Fanning,, F. J. Skerman,, and S. Falkow. 1972. Polynucleotide sequence divergence among strains of Escherichia coli and closely related organisms. J. Bacteriol. 109:953965.
20. Brenner, D. J.,, M. A. Martin,, and B. H. Hoyer. 1967. Deoxyribonucleic acid homologies among some bacteria. J. Bacteriol. 94:486487.
21. Brochier, C.,, H. Philippe,, and D. Moreira. 2000. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16:529533.
22. Capiaux, H.,, F. Cornet,, J. Corre,, M. Guijo,, K. Perals,, J. E. Rebollo,, and J. Louarn. 2001. Polarization of the Escherichia coli chromosome. A view from the terminus. Biochimie 83:161170.
23.Reference deleted.
24. Caugant, D. A.,, B. R. Levin,, and R. K. Selander. 1984. Distribution of multilocus genotypes of Escherichia coli within and between host families. J. Hyg. Camb. 92:377384.
25. Caugant, D. A.,, B. R. Levin,, and R. K. Selander. 1981. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics 98:467490.
26. Chang, H. W.,, and D. A. Julin. 2001. Structure and function of the Escherichia coli RecE protein, a member of the RecB nuclease domain family. J. Biol. Chem. 276:4600446010.
27. Chistoserdova, L.,, J. A. Vorholt,, R. K. Thauer,, and M. E. Lidstrom. 1998. C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic Archaea. Science 281:99102.
28. Clark, M. A.,, L. Baumann,, M. L. Thao,, N. A. Moran,, and P. Baumann. 2001. Degenerative minimalism in the genome of a psyllid endosymbiont. J. Bacteriol. 183:18531861.
29. Clarke, G. D.,, R. G. Beiko,, M. A. Ragan,, and R. L. Charlebois. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184:20722080.
30. Cohan, F. M. 2001. Bacterial species and speciation. Syst. Biol. 50:513524.
31. Cole, S. T.,, K. Eiglmeier,, J. Parkhill,, K. D. James,, N. R. Thomson,, P. R. Wheeler,, N. Honore,, T. Garnier,, C. Churcher,, D. Harris,, K. Mungall,, D. Basham,, D. Brown,, T. Chillingworth,, R. Connor,, R. M. Davies,, K. Devlin,, S. Duthoy,, T. Feltwell,, A. Fraser,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, C. Lacroix,, J. Maclean,, S. Moule,, L. Murphy,, K. Oliver,, M. A. Quail,, M. A. Rajandream,, K.M. Rutherford,, S. Rutter,, K. Seeger,, S. Simon,, M. Simmonds,, J. Skelton,, R. Squares,, S. Squares,, K. Stevens,, K. Taylor,, S. Whitehead,, J. R. Woodward,, and B. G. Barrell. 2001. Massive gene decay in the leprosy bacillus. Nature 409:10071011.
32. Coskun-Ari, F. F.,, and T. M. Hill. 1997. Sequence-specific interactions in the Tus-Ter complex and the effect of base pair substitutions on arrest of DNA replication in Escherichia coli. J. Biol. Chem. 272:2644826456.
33. Dandekar, T.,, B. Snel,, M. Huynen,, and P. Bork. 1998. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23:324328.
34. Davies, J. 1996. Origins and evolution of antibiotic resistance. Microbiologia 12:916.
35. Dimri, G. P.,, K. E. Rudd,, M. K. Morgan,, H. Bayat,, and G. F. Ames. 1992. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J. Bacteriol. 174:45834593.
36. Doolittle, R. F.,, D. F. Feng,, K. L. Anderson,, and M. R. Alberro. 1990. A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote. J. Mol. Evol. 31:383388.
37. Doolittle, W. F. 1999. Lateral genomics. Trends Cell Biol. 9:M5M8.
38. Doolittle, W. F. 2000. The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10:355358.
39. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:21242129.
40. DuBose, R. F.,, D. E. Dykhuizen,, and D. L. Hartl. 1988. Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 85:70367040.
41. DuBose, R. F.,, and D. L. Hartl. 1990. The molecular evolution of alkaline phosphatase: correlating variation among enteric bacteria to experimental manipulations of the protein. Mol. Biol. Evol. 7:547577.
42. Dykhuizen, D. E.,, and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:72577268.
43. Edwards, R. A.,, G. J. Olsen,, and S. R. Maloy. 2002. Comparative genomics of closely related Salmonellae. Trends Microbiol. 10:9499.
44. Eisen, J. A.,, J. F. Heidelberg,, O. White,, and S. L. Salzberg. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol. 1:111.
45. Falush, D.,, C. Kraft,, N. S. Taylor,, P. Correa,, J. G. Fox,, M. Achtman,, and S. Suerbaum. 2001. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl. Acad. Sci. USA 98:1505615061.
46. Feil, E. J.,, E. C. Holmes,, D. E. Bessen,, M. S. Chan,, N. P. Day,, M. C. Enright,, R. Goldstein,, D. W. Hood,, A. Kalia,, C. E. Moore,, J. Zhou,, and B. G. Spratt. 2001. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. USA 98:182187.
47. Feil, E. J.,, J. M. Smith,, M. C. Enright,, and B. G. Spratt. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:14391450.
48. Felsenstein, J. 1974. The evolutionary advantage of recombination. Genetics 78:737756.
49. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
50. Francino, M. P.,, L. Chao,, M. A. Riley,, and H. Ochman. 1996. Asymmetrics generated by transcription-coupled repair in enterobacterial genes. Science 272:107109.
51. Francino, M. P.,, and H. Ochman. 1999. A comparative genomics approach to DNA asymmetry. Ann. N. Y. Acad. Sci. 870:428431.
52. Francino, M. P.,, and H. Ochman. 2001. Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 18:11471150.
53. Francino, M. P.,, and H. Ochman. 1997. Strand asymmetries in DNA evolution. Trends Genet. 13:240245.
54. Francino, M. P.,, and H. Ochman. 2000. Strand symmetry around the beta-globin origin of replication in primates. Mol. Biol. Evol. 17:416422.
55. Galitski, T.,, and J. R. Roth. 1997. Pathways for homologous recombination between chromosomal direct repeats in Salmonella typhimurium. Genetics 146:751767.
56. Gruss, A.,, V. Moretto,, S. D. Ehrlich,, P. Duwat,, and P. Dabert. 1991. GC-rich DNA sequences block homologous recombination. J. Biol. Chem. 266:66676669.
57. Guttman, D. S.,, and D. E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266:13801383.
58. Guttman, D. S.,, and D. E. Dykhuizen. 1994. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138:9931003.
59. Haack, K. R.,, and J. R. Roth. 1995. Recombination between chromosomal IS200 elements supports frequent duplication formation in Salmonella typhimurium. Genetics 141:12451252.
60. Hall, R. M.,, and C. M. Collis. 1995. Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination. Mol. Microbiol. 15:593600.
61. Hall, R. M.,, C. M. Collis,, M. J. Kim,, S. R. Partridge,, G. D. Recchia,, and H. W. Stokes. 1999. Mobile gene cassettes and integrons in evolution. Ann. N. Y. Acad. Sci. 870:6880.
62. Hartl, D. L.,, and D. E. Dykhuizen. 1984. The population genetics of Escherichia coli. Annu. Rev. Genet. 18:3168.
63. Hayes, W. S.,, and M. Borodovsky. 1998. How to interpret an anonymous bacterial genome: machine learning approach to gene identification. Genome Res. 8:11541171.
64. Himmelreich, R.,, H. Hilbert,, H. Plagens,, E. Pirkl,, B. C. Li,, and R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:44204449.
65. Hiraga, S. 1993. Chromosome partition in Escherichia coli. Curr. Opin. Genet. Dev. 3:789801.
66. Holmes, E. C.,, R. Urwin,, and M. C. J. Maiden. 1999. The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol. Biol. Evol. 16:741749.
67. Hulton, C. S.,, C. F. Higgins,, and P. M. Sharp. 1991. ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol. Microbiol. 5:825834.
68. Ibba, M.,, S. Morgan,, A. W. Curnow,, D. R. Pridmore,, U. C. Vothknecht,, W. Gardner,, W. Lin,, C. R. Woese,, and D. Soll. 1997. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278:11191122.
69. Itoh, T.,, K. Takemoto,, H. Mori,, and T. Gojobori. 1999. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16:332346.
70. Jain, R.,, M. C. Rivera,, and J. A. Lake. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:38013806.
71. Jiang, W.,, W. W. Metcalf,, K. S. Lee,, and B. L. Wanner. 1995. Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2. J. Bacteriol. 177:64116421.
72. Kaneko, T.,, S. Sato,, H. Kotani,, A. Tanaka,, E. Asamizu,, Y. Nakamura,, N. Miyajima,, M. Hirosawa,, M. Sugiura,, S. Sasamoto,, T. Kimura,, T. Hosouchi,, A. Matsuno,, A. Muraki,, N. Nakazaki,, K. Naruo,, S. Okumura,, S. Shimpo,, C. Takeuchi,, T. Wada,, A. Watanabe,, M. Yamada,, M. Yasuda,, and S. Tabata. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:109136.
73. Karlin, S. 1998. Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1:598610.
74. Karlin, S.,, and C. Burge. 1995. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11:283290.
75. Karlin, S.,, A. M. Campbell,, and J. Mrázek. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32:185225.
76. Karlin, S.,, and J. Mrazek. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182:52385250.
77. Karlin, S.,, J. Mrazek,, and A. M. Campbell. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29:13411355.
78. Katz, L. A. 1996. Transkingdom transfer of the phosphoglucose isomerase gene. J. Mol. Evol. 43:453459.
79. Ke, D.,, M. Boissinot,, A. Huletsky,, F. J. Picard,, J. Frenette,, M. Ouellette,, P. H. Roy,, and M. G. Bergeron. 2000. Evidence for horizontal gene transfer in evolution of elongation factor Tu in enterococci. J. Bacteriol. 182:69136920.
80. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, United Kingdom.
81. Koski, L. B.,, R. A. Morton,, and G. B. Golding. 2001. Codon bias and base composition are poor indicators of horizontally transferred genes. Mol. Biol. Evol. 18:404412.
82. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25:156165.
83. Kowalczykowski, S. C.,, D. A. Dixon,, A. K. Eggleston,, S. D. Lauder,, and W. M. Rehrauer. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58:401465.
84. Kranz, R. G.,, and B. S. Goldman. 1998. Evolution and horizontal transfer of an entire biosynthetic pathway for cytochrome c biogenesis: Helicobacter, Deinococcus, Archae and more. Mol. Microbiol. 27:871874.
85. Kroll, J. S.,, K. E. Wilks,, J. L. Farrant,, and P. R. Langford. 1998. Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens. Proc. Natl. Acad. Sci. USA 95:1238112385.
86. Kusano, K.,, N. K. Takahashi,, H. Yoshikura,, and I. Kobayashi. 1994. Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination. Gene 138:1725.
87. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16:373384.
88. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63:751813.
89. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50:479496.
90. Lawrence, J. G. 2002. Gene transfer in bacteria: speciation without species? Theor. Popul. Biol. 61:449460.
91. Lawrence, J. G. 1997. Selfish operons and speciation by gene transfer. Trends Microbiol. 5:355359.
92. Lawrence, J. G. 1999. Selfish operons: the evolutionary impact of gene clustering in the prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9:642648.
93. Lawrence, J. G.,, D. E. Dykhuizen,, R. F. DuBose,, and D. L. Hartl. 1989. Phylogenetic analysis using insertion sequence fingerprinting in Escherichia coli. Mol. Biol. Evol. 6:114.
94. Lawrence, J. G.,, R. W. Hendrix,, and S. Casjens. 2001. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9:535540.
95. Lawrence, J. G.,, and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:383397.
96. Lawrence, J. G.,, and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:94139417.
97. Lawrence, J. G.,, and H. Ochman. 2002. Reconciling the many faces of gene transfer. Trends Microbiol. 10:14.
98. Lawrence, J. G.,, H. Ochman,, and D. L. Hartl. 1992. The evolution of insertion sequences within enteric bacteria. Genetics 131:920.
99. Lawrence, J. G.,, and J. R. Roth. 1995. The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli. J. Bacteriol. 177:63716380.
100. Lawrence, J. G.,, and J. R. Roth. 1996. Evolution of coenzyme B12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142:1124.
101. Lawrence, J. G.,, and J. R. Roth,. 1999. Genomic flux: genome evolution by gene loss and acquisition, p. 263289. In R. L. Charlebois (ed.), Organization of the Prokaryotic Genome. ASM Press, Washington, D.C..
102. Lawrence, J. G.,, and J. R. Roth,. 1998. Roles of horizontal transfer in bacterial evolution, p. 208225. In M. Syvanen, and C. I. Kado (ed.), Horizontal Transfer. Chapman and Hall, London, England.
103. Lawrence, J. G.,, and J. R. Roth. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:18431860.
104. Lederberg, J. 1947. Gene recombination and linked segregations in Escherichia coli. Genetics 32:505525.
105. Lederberg, J.,, and E. L. Tatum. 1946. Gene recombination in Escherichia coli. Nature 158:558.
106. Levin, B. 1981. Periodic selection, infectious gene exchange, and the genetic structure of E. coli populations. Genetics 99:123.
107. Liu, S. L.,, and K. E. Sanderson. 1996. Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93:1030310308.
108. Liu, S. L.,, and K. E. Sanderson. 1995. Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92:10181022.
109. Logsdon, J. M.,, and D. M. Fuguy. 1999. Thermotoga heats up lateral gene transfer. Curr. Biol. 9:R747R751.
110. Losick, R.,, and L. Shapiro. 1999. Changing views on the nature of the bacterial cell: from biochemistry to cytology. J. Bacteriol. 181:41434145.
111. Majewski, J.,, and F. M. Cohan. 1999. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153:15251533.
112. Majewski, J.,, and F. M. Cohan. 1998. The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148:1318.
113. Majewski, J.,, P. Zawadzki,, P. Pickerill,, F. M. Cohan,, and C. G. Dowson. 2000. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182:10161023.
114. Makarova, K. S.,, L. Aravind,, M. Y. Galperin,, N. V. Grishin,, R. L. Tatusov,, Y. I. Wolf,, and E. V. Koonin. 1999. Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9:608628.
115. Martin, W. 1999. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays 21:99104.
116. Maurelli, A. T. 1994. Virulence protein export systems in Salmonella and Shigella: a new family or lost relatives. Trends Cell Biol. 4:240242.
117. Maynard Smith, J.,, N. H. Smith,, M. O’Rourke,, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:43844388.
118. McClelland, M.,, K. E. Sanderson,, J. Spieth,, S. W. Clifton,, P. Latreille,, L. Courtney,, S. Porwollik,, J. Ali,, M. Dante,, F. Du,, S. Hou,, D. Layman,, S. Leonard,, C. Nguyen,, K. Scott,, A. Holmes,, N. Grewal,, E. Mulvaney,, E. Ryan,, H. Sun,, L. Florea,, W. Miller,, T. Stoneking,, M. Nhan,, R. Waterston,, and R. K. Wilson. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852856.
119. McKane, M.,, and R. Milkman. 1995. Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139:3543.
120. Metcalf, W. W.,, and B. L. Wanner. 1993. Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli. Gene 129:2732.
121. Milkman, R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science 182:10241026.
122. Milkman, R.,, and M. M. Bridges. 1990. Molecular evolution of the E. coli chromosome. III. Clonal frames. Genetics 126:505517.
123. Milkman, R.,, and I. P. Crawford. 1983. Clustered third-base substitutions among wild strains of Escherichia coli. Science 221:378379.
124. Milkman, R.,, and A. Stoltzfus. 1988. Molecular evolution of the Escherichia coli chromosome. II. Clonal segments. Genetics 120:359366.
125. Mira, A.,, H. Ochman,, and N. A. Moran. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589596.
126. Moran, N. A. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583586.
127. Moran, N. A.,, and A. Mira. 2001. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2(12):research0054.1research0054.12. [Online.]
128. Moszer, I.,, E. P. Rocha,, and A. Danchin. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2:524528.
129. Müller, H. 1932. Some genetic aspects of sex. Am. Nat. 66:118138.
130. Musser, J. M.,, A. Amin,, and S. Ramaswamy. 2000. Negligible genetic diversity of Mycobacterium tuberculosis host immune system protein targets: evidence of limited selective pressure. Genetics 155:716.
131. Muto, A.,, and S. Osawa. 1987. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84:166169.
132. Mylvaganam, S.,, and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399410.
133. Naas, T.,, M. Blot,, W. M. Fitch,, and W. Arber. 1994. Insertion sequence-related genetic variation in resting Escherichia coli K-12. Genetics 136:721730.
134. Nakata, N.,, T. Tobe,, I. Fukuda,, T. Suzuki,, K. Komatsu,, M. Yoshikawa,, and C. Sasakawa. 1993. The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci. Mol. Microbiol. 9:459468.
135. Nelson, K.,, and R. K. Selander. 1992. Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J. Bacteriol. 174:68866895.
136. Nelson, K. E.,, R. A. Clayton,, S. R. Gill,, M. L. Gwinn,, R. J. Dodson,, D. H. Haft,, E. K. Hickey,, J. D. Peterson,, W. C. Nelson,, K. A. Ketchum,, L. McDonald,, T. R. Utterback,, J. A. Malek,, K. D. Linher,, M. M. Garrett,, A. M. Stewart,, M. D. Cotton,, M. S. Pratt,, C. A. Phillips,, D. Richardson,, J. Heidelberg,, G. G. Sutton,, R. D. Fleischmann,, J. A. Eisen,, and C. M. Fraser. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323329.
137. Nesbo, C. L.,, S. L’Haridon,, K. O. Stetter,, and W. F. Doolittle. 2001. Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria. Mol. Biol. Evol. 18:362375.
138. Neylon, C.,, S. E. Brown,, A. V. Kralicek,, C. S. Miles,, C. A. Love,, and N. E. Dixon. 2000. Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: a model derived from DNA-binding studies of mutant proteins by surface plasmon resonance. Biochemistry 39:1198911999.
139. Ng, I.,, S.-L. Liu,, and K. Sanderson. 1999. Role of genomic rearrangements in producing new ribotypes of Salmonella typhi. J. Bacteriol. 181:35363541.
140. Ochman, H.,, and I. B. Jones. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19: 66376643.
141. Ochman, H.,, and J. G. Lawrence,. 1996. Phylogenetics and the amelioration of bacterial genomes, p. 26272637. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
142. Ochman, H.,, J. G. Lawrence,, and E. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299304.
143. Ochman, H.,, and N. A. Moran. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:10961099.
144. Ochman, H.,, and R. K. Selander. 1984. Evidence for clonal population structure in Escherichia coli. Proc. Natl. Acad. Sci. USA 81:198201.
145. Ochman, H.,, T. S. Whittam,, D. A. Caugant,, and R. K. Selander. 1983. Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. J. Gen. Microbiol. 129:27152726.
146. Ochman, H.,, and A. C. Wilson. 1988. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:7486.
147. Ochman, H.,, and A. C. Wilson,. 1987. Evolutionary history of enteric bacteria, p. 16491654. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.
148. Ohta, T. 1976. Role of very slightly deleterious mutations in molecular evolution and polymorphism. Theor. Popul. Biol. 10:254275.
149. Ohta, T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 264:9698.
150. Olendzenski, L.,, L. Liu,, O. Zhaxybayeva,, R. Murphey,, D. G. Shin,, and J. P. Gogarten. 2000. Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches. J. Mol. Evol. 51:587599.
151. Papadopoulos, D.,, D. Schneider,, J. Meier-Eiss,, W. Arber,, R. E. Lenski,, and M. Blot. 1999. Genomic evolution during a 10,000-generation experiment with bacteria. Proc. Natl. Acad. Sci. USA 96:38073812.
152. Parkhill, J.,, M. Achtman,, K. D. James,, S. D. Bentley,, C. Churcher,, S. R. Klee,, G. Morelli,, D. Basham,, D. Brown,, T. Chillingworth,, R. M. Davies,, P. Davis,, K. Devlin,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, S. Leather,, S. Moule,, K. Mungall,, M. A. Quail,, M. A. Rajandream,, K. M. Rutherford,, M. Simmonds,, J. Skelton,, S. Whitehead,, B. G. Spratt,, and B. G. Barrell. 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404:502506.
153. Parkhill, J.,, G. Dougan,, K. D. James,, N. R. Thomson,, D. Pickard,, J. Wain,, C. Churcher,, K. L. Mungall,, S. D. Bentley,, M. T. Holden,, M. Sebaihia,, S. Baker,, D. Basham,, K. Brooks,, T. Chillingworth,, P. Connerton,, A. Cronin,, P. Davis,, R. M. Davies,, L. Dowd,, N. White,, J. Farrar,, T. Feltwell,, N. Hamlin,, A. Haque,, T. T. Hien,, S. Holroyd,, K. Jagels,, A. Krogh,, T. S. Larsen,, S. Leather,, S. Moule,, P. O’Gaora,, C. Parry,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead,, and B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848852.
154. Perals, K.,, F. Cornet,, Y. Merlet,, I. Delon,, and J. M. Louarn. 2000. Functional polarization of the Escherichia coli chromosome terminus: the dif site acts in chromosome dimer resolution only when located between long stretches of opposite polarity. Mol. Microbiol. 36:3343.
155. Perna, N. T.,, G. Plunkett,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grotbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch,, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529533.
156. Pesole, G.,, C. Gissi,, C. Lanave,, and C. Saccone. 1995. Glutamine synthetase gene evolution in bacteria. Mol. Biol. Evol. 12:189197.
157. Ragan, M. A. 2001. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11:620626.
158. Ragan, M. A. 2001. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:187191.
159. Rainey, P. B.,, and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:6972.
160. Rayssiguier, C.,, D. S. Thaler,, and M. Radman. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396401.
161. Roth, J.,, N. Benson,, T. Galitski,, K. Haack,, J. G. Lawrence,, and L. Miesel,. 1996. Rearrangements of the bacterial chromosome: formation and applications, p. 22562276. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
162. Salyers, A. A.,, N. B. Shoemaker,, A.M. Stevens,, and L. Y. Li. 1995. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59:579590.
163. Salzberg, S. L.,, A. J. Salzberg,, A. R. Kerlavage,, and J. F. Tomb. 1998. Skewed oligomers and origins of replication. Gene 217:5767.
164. Sanderson, K. E. 1970. Current linkage map of Salmonella typhimurium. Bacteriol. Rev. 34:176193.
165. Sanderson, K. E. 1967. Revised linkage map of Salmonella typhimurium. Bacteriol. Rev. 31:354372.
166. Sanderson, K. E.,, and M. Demerec. 1965. The linkage map of Salmonella typhimurium. Genetics 51:897913.
167. Sanderson, K. E.,, and C. A. Hall. 1970. F-prime factors of Salmonella typhimurium and an inversion between S. typhimurium and Escherichia coli. Genetics 64:215228.
168. Saunders, N. J.,, D. W. Hood,, and E. R. Moxon. 1999. Bacterial evolution: bacteria play pass the gene. Curr. Biol. 11:R180R183.
169. Sawyer, S. A.,, D. E. Dykhuizen,, R. F. DuBose,, L. Green,, T. Mutangadura-Mhlanga,, D. F. Wolczyk,, and D. L. Hartl. 1987. Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics 115:5163.
170. Schicklmaier, P.,, E. Moser,, T. Wieland,, W. Rabsch,, and H. Schmieger. 1998. A comparative study on the frequency of prophages among natural isolates of Salmonella and Escherichia coli with emphasis on generalized transducers. Antonie Leeuwenhoek 73:4954.
171. Schmid, M. B.,, and J. R. Roth. 1983. Genetic methods for analysis and manipulation of inversion mutations in bacteria. Genetics 105:517537.
172. Schmid, M. B.,, and J. R. Roth. 1983. Selection and endpoint distribution of bacterial inversion mutations. Genetics 105:539557.
173. Segall, A.,, M. J. Mahan,, and J. R. Roth. 1988. Rearrangement of the bacterial chromosome: forbidden inversions. Science 241:13141318.
174. Segall, A. M.,, and J. R. Roth. 1994. Approaches to halftetrad analysis in bacteria: recombination between repeated, inverse-order chromosomal sequences. Genetics 136:2739.
175. Segall, A. M.,, and J. R. Roth. 1989. Recombination between homologies in direct and inverse orientation in the chromosome of Salmonella: intervals which are nonpermissive for inversion formation. Genetics 122:737747.
176. Shapiro, L.,, and R. Losick. 1997. Protein localization and cell fate in bacteria. Science 276:712718.
177. Sharp, P. M. 1991. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J. Mol. Evol. 33:2333.
178. Sharp, P. M.,, M. Averof,, A. T. Lloyd,, G. Matassi,, and J. F. Peden. 1995. DNA sequence evolution: the sounds of silence. Philos. Trans. R. Soc. Lond. B 349:241247.
179. Sharp, P. M.,, E. Cowe,, D. G. Higgins,, D. C. Shields,, K. H. Wolfe,, and F. Wright. 1988. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16:82078211.
180. Sharp, P. M.,, and W.-H. Li. 1987. The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:12811295.
181. Sharp, P. M.,, and W.-H. Li. 1986. Codon usage in regulatory genes in Escherichia coli does not reflect selection for "rare" codons. Nucleic Acids Res. 14:77377749.
182. Sharp, P. M.,, and W.-H. Li. 1987. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Mol. Biol. Evol. 4:222230.
183. Shimomura, S.,, S. Shigenobu,, M. Morioka,, and H. Ishikawa. 2002. An experimental validation of orphan genes of Buchnera, a symbiont of aphids. Biochem. Biophys. Res. Commun. 292:263267.
184. Smith, G. R. 1994. Hotspots of homologous recombination. Experientia 50:234241.
185. Smith, G. R.,, S. K. Amundsen,, P. Dabert,, and A. F. Taylor. 1995. The initiation and control of homologous recombination in Escherichia coli. Philos. Trans. R. Soc. Lond. B 347:1320.
186. Smith, J. M.,, C. G. Dowson,, and B. G. Spratt. 1991. Localized sex in bacteria. Nature 349:2931.
187. Smith, M. W.,, D.-W. Feng,, and R. F. Doolittle. 1992. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17:489493.
188. Smith, N. H.,, E. C. Holmes,, G. M. Donovan,, G. A. Carpenter,, and B. G. Spratt. 1999. Networks and groups within the genus Neisseria: analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. Mol. Biol. Evol. 16:773783.
189. Sreevatsan, S.,, X. Pan,, K. E. Stockbauer,, N. D. Connell,, B. N. Kreiswirth,, T. S. Whittam,, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94:98699874.
190. Stambuk, S.,, and M. Radman. 1998. Mechanism and control of interspecies recombination in Escherichia coli. I. Mismatch repair, methylation, recombination and replication functions. Genetics 150:553542.
191. Sueoka, N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85:26532657.
192. Sueoka, N. 1993. Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J. Mol. Evol. 37:137153.
193. Sueoka, N. 1992. Directional mutation pressure, selective constraints, and genetic equilibria. J. Mol. Evol. 34:95114.
194. Sueoka, N. 1962. On the genetic basis of variation and heterogeneity in base composition. Proc. Natl. Acad. Sci. USA 48:582592.
195. Suerbaum, S.,, J. M. Smith,, K. Bapumia,, G. Morelli,, N. H. Smith,, E. Kunstmann,, I. Dyrek,, and M. Achtman. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95:1261912624.
196. Tamas, I.,, L. Klasson,, B. Canback,, A. K. Näslund,, A.-S. Eriksson,, J. J. Wernegreen,, J. P. Sandstro¨m,, N. A. Moran,, and S. G. E. Andersson. 2002. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296:23762379.
197. Taylor, A. L.,, and M. S. Thoman. 1964. The genetic map of Escherichia coli K-12. Genetics 50:659677.
198. Taylor, A. L. 1970. Current linkage map of Escherichia coli. Bacteriol. Rev. 34:155175.
199. Taylor, A. L.,, and C. D. Trotter. 1967. Revised linkage map of Escherichia coli. Bacteriol. Rev. 31:332353.
200. Treves, D. S.,, S. Manning,, and J. Adams. 1998. Repeated evolution of an acetate-crossfeeding polymorphism in longterm populations of Escherichia coli. Mol. Biol. Evol. 15: 789797.
201. Vulic, M.,, F. Dionisio,, F. Taddei,, and M. Radman. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in Enterobacteria. Proc. Natl. Acad. Sci. USA 94:97639767.
202. Vulic, M.,, R. E. Lenski,, and M. Radman. 1999. Mutation, recombination, and incipient speciation of bacteria in the laboratory. Proc. Natl. Acad. Sci. USA 96:73487351.
203. Waldor, M. K.,, and J. J. Mekalanos. 1996. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272:19101914.
204. Wang, B. 2001. Limitations of compositional approach to identifying horizontally transferred genes. J. Mol. Evol. 53:244250.
205. Wernegreen, J. J.,, H. Ochman,, I. B. Jones,, and N. A. Moran. 2000. Decoupling of genome size and sequence divergence in a symbiotic bacterium. J. Bacteriol. 182:38673869.
206. Whittam, T. S., 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 27082720. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C..
207. Whittam, T. S.,, and S. Ake,. 1992. Genetic polymorphisms and recombination in natural populations of Escherichia coli, p. 223246. In N. Takahata, and A. G. Clark (ed.), Mechanisms of Molecular Evolution. Japan Scientific Society Press, Tokyo, Japan.
208. Whittam, T. S.,, H. Ochman,, and R. K. Selander. 1984. Geographical components of linkage disequilibrium in natural populations of Escherichia coli. Mol. Biol. Evol. 1:6783.
209. Whittam, T. S.,, H. Ochman,, and R. K. Selander. 1983. Multilocus genetic structure in natural populations of Escherichia coli. Proc. Natl. Acad. Sci. USA 80:17511755.
210. Woese, C. R.,, G. J. Olsen,, M. Ibba,, and D. Soll. 2000. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64:202236.
211. Wolf, Y. I.,, L. Aravind,, N. V. Grishin,, and E. V. Koonin. 1999. Evolution of aminoacyl-tRNA synthetases—analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9:689710.
212. Worning, P.,, L. J. Jensen,, K. E. Nelson,, S. Brunak,, and D. W. Ussery. 2000. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima. Nucleic Acids Res. 28:706709.
213. Xiong, J.,, K. Inoue,, and C. E. Bauer. 1998. Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc. Natl. Acad. Sci. USA 95:1485114856.
214. Yap, W. H.,, Z. Zhang,, and Y. Wang. 1999. Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J. Bacteriol. 181:52015209.
215. Zawadzki, P.,, M. S. Roberts,, and F. M. Cohan. 1995. The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics 140:917932.
216. Zinder, N. D.,, and J. Lederberg. 1952. Genetic exchange in Salmonella. J. Bacteriol. 64:679697.
217. Zuckerkandl, E. 1965. The evolution of hemoglobin. Sci. Am. 212:110118.
218. Zuckerkandl, E.,, and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357366.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error