1887

Chapter 2 : The Dynamic Bacterial Genome

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

Preview this chapter:
Zoom in
Zoomout

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

Abstract:

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
0.60828227
Multilocus Sequence Typing
0.40966958
Genetic Elements
0.4055215
0.60828227
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

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

References

/content/book/10.1128/9781555817640.chap2
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: 459 470.
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: 268 276.
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: 315 335.
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: 1974 1987.
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: 1327 1335.
6. Andersson, J. O. 2000. Evolutionary genomics: is Buchnera a bacterium or an organelle? Curr. Biol. 10: R866 R868.
7. Andersson, J. O.,, and S. G. Andersson. 1999. Genome degradation is an ongoing process in Rickettsia. Mol. Biol. Evol. 16: 1178 1191.
8. Andersson, J. O.,, and S. G. Andersson. 1999. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9: 664 671.
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: 133 140.
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: 551 562.
11. Bender, R. A., 1996. Variations on a theme by Escherichia, p. 4 9. 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: 1453 1474.
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: 1378 1388.
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: 1280 1284.
15. Brenner, D. J. 1978. Characterization and clinical identification of Enterobacteriaceae by DNA hybridization. Prog. Clin. Pathol. 7: 71 117.
16. Brenner, D. J.,, and D. B. Cowie. 1968. Thermal stability of Escherichia coli-Salmonella typhimurium deoxyribonucleic acid duplexes. J. Bacteriol. 95: 2258 2262.
17. Brenner, D. J.,, and S. Falkow. 1971. Molecular relationships among members of the Enterobacteriaceae. Adv. Genet. 16: 81 118.
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: 637 650.
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: 953 965.
20. Brenner, D. J.,, M. A. Martin,, and B. H. Hoyer. 1967. Deoxyribonucleic acid homologies among some bacteria. J. Bacteriol. 94: 486 487.
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: 529 533.
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: 161 170.
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: 377 384.
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: 467 490.
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: 46004 46010.
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: 99 102.
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: 1853 1861.
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: 2072 2080.
30. Cohan, F. M. 2001. Bacterial species and speciation. Syst. Biol. 50: 513 524.
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: 1007 1011.
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: 26448 26456.
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: 324 328.
34. Davies, J. 1996. Origins and evolution of antibiotic resistance. Microbiologia 12: 9 16.
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: 4583 4593.
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: 383 388.
37. Doolittle, W. F. 1999. Lateral genomics. Trends Cell Biol. 9: M5 M8.
38. Doolittle, W. F. 2000. The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10: 355 358.
39. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124 2129.
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: 7036 7040.
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: 547 577.
42. Dykhuizen, D. E.,, and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173: 7257 7268.
43. Edwards, R. A.,, G. J. Olsen,, and S. R. Maloy. 2002. Comparative genomics of closely related Salmonellae. Trends Microbiol. 10: 94 99.
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: 1 11.
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: 15056 15061.
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: 182 187.
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: 1439 1450.
48. Felsenstein, J. 1974. The evolutionary advantage of recombination. Genetics 78: 737 756.
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: 496 512.
50. Francino, M. P.,, L. Chao,, M. A. Riley,, and H. Ochman. 1996. Asymmetrics generated by transcription-coupled repair in enterobacterial genes. Science 272: 107 109.
51. Francino, M. P.,, and H. Ochman. 1999. A comparative genomics approach to DNA asymmetry. Ann. N. Y. Acad. Sci. 870: 428 431.
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: 1147 1150.
53. Francino, M. P.,, and H. Ochman. 1997. Strand asymmetries in DNA evolution. Trends Genet. 13: 240 245.
54. Francino, M. P.,, and H. Ochman. 2000. Strand symmetry around the beta-globin origin of replication in primates. Mol. Biol. Evol. 17: 416 422.
55. Galitski, T.,, and J. R. Roth. 1997. Pathways for homologous recombination between chromosomal direct repeats in Salmonella typhimurium. Genetics 146: 751 767.
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: 6667 6669.
57. Guttman, D. S.,, and D. E. Dykhuizen. 1994. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266: 1380 1383.
58. Guttman, D. S.,, and D. E. Dykhuizen. 1994. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138: 993 1003.
59. Haack, K. R.,, and J. R. Roth. 1995. Recombination between chromosomal IS200 elements supports frequent duplication formation in Salmonella typhimurium. Genetics 141: 1245 1252.
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: 593 600.
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: 68 80.
62. Hartl, D. L.,, and D. E. Dykhuizen. 1984. The population genetics of Escherichia coli. Annu. Rev. Genet. 18: 31 68.
63. Hayes, W. S.,, and M. Borodovsky. 1998. How to interpret an anonymous bacterial genome: machine learning approach to gene identification. Genome Res. 8: 1154 1171.
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: 4420 4449.
65. Hiraga, S. 1993. Chromosome partition in Escherichia coli. Curr. Opin. Genet. Dev. 3: 789 801.
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: 741 749.
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: 825 834.
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: 1119 1122.
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: 332 346.
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: 3801 3806.
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: 6411 6421.
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: 109 136.
73. Karlin, S. 1998. Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1: 598 610.
74. Karlin, S.,, and C. Burge. 1995. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 11: 283 290.
75. Karlin, S.,, A. M. Campbell,, and J. Mrázek. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32: 185 225.
76. Karlin, S.,, and J. Mrazek. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J. Bacteriol. 182: 5238 5250.
77. Karlin, S.,, J. Mrazek,, and A. M. Campbell. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29: 1341 1355.
78. Katz, L. A. 1996. Transkingdom transfer of the phosphoglucose isomerase gene. J. Mol. Evol. 43: 453 459.
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: 6913 6920.
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: 404 412.
82. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25: 156 165.
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: 401 465.
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: 871 874.
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: 12381 12385.
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: 17 25.
87. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli. Mol. Microbiol. 16: 373 384.
88. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63: 751 813.
89. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50: 479 496.
90. Lawrence, J. G. 2002. Gene transfer in bacteria: speciation without species? Theor. Popul. Biol. 61: 449 460.
91. Lawrence, J. G. 1997. Selfish operons and speciation by gene transfer. Trends Microbiol. 5: 355 359.
92. Lawrence, J. G. 1999. Selfish operons: the evolutionary impact of gene clustering in the prokaryotes and eukaryotes. Curr. Opin. Genet. Dev. 9: 642 648.
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: 1 14.
94. Lawrence, J. G.,, R. W. Hendrix,, and S. Casjens. 2001. Where are the pseudogenes in bacterial genomes? Trends Microbiol. 9: 535 540.
95. Lawrence, J. G.,, and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44: 383 397.
96. Lawrence, J. G.,, and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95: 9413 9417.
97. Lawrence, J. G.,, and H. Ochman. 2002. Reconciling the many faces of gene transfer. Trends Microbiol. 10: 1 4.
98. Lawrence, J. G.,, H. Ochman,, and D. L. Hartl. 1992. The evolution of insertion sequences within enteric bacteria. Genetics 131: 9 20.
99. Lawrence, J. G.,, and J. R. Roth. 1995. The cobalamin (coenzyme B 12) biosynthetic genes of Escherichia coli. J. Bacteriol. 177: 6371 6380.
100. Lawrence, J. G.,, and J. R. Roth. 1996. Evolution of coenzyme B 12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142: 11 24.
101. Lawrence, J. G.,, and J. R. Roth,. 1999. Genomic flux: genome evolution by gene loss and acquisition, p. 263 289. 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. 208 225. 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: 1843 1860.
104. Lederberg, J. 1947. Gene recombination and linked segregations in Escherichia coli. Genetics 32: 505 525.
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: 1 23.
107. Liu, S. L.,, and K. E. Sanderson. 1996. Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93: 10303 10308.
108. Liu, S. L.,, and K. E. Sanderson. 1995. Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92: 1018 1022.
109. Logsdon, J. M.,, and D. M. Fuguy. 1999. Thermotoga heats up lateral gene transfer. Curr. Biol. 9: R747 R751.
110. Losick, R.,, and L. Shapiro. 1999. Changing views on the nature of the bacterial cell: from biochemistry to cytology. J. Bacteriol. 181: 4143 4145.
111. Majewski, J.,, and F. M. Cohan. 1999. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153: 1525 1533.
112. Majewski, J.,, and F. M. Cohan. 1998. The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148: 13 18.
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: 1016 1023.
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: 608 628.
115. Martin, W. 1999. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays 21: 99 104.
116. Maurelli, A. T. 1994. Virulence protein export systems in Salmonella and Shigella: a new family or lost relatives. Trends Cell Biol. 4: 240 242.
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: 4384 4388.
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: 852 856.
119. McKane, M.,, and R. Milkman. 1995. Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139: 35 43.
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: 27 32.
121. Milkman, R. 1973. Electrophoretic variation in Escherichia coli from natural sources. Science 182: 1024 1026.
122. Milkman, R.,, and M. M. Bridges. 1990. Molecular evolution of the E. coli chromosome. III. Clonal frames. Genetics 126: 505 517.
123. Milkman, R.,, and I. P. Crawford. 1983. Clustered third-base substitutions among wild strains of Escherichia coli. Science 221: 378 379.
124. Milkman, R.,, and A. Stoltzfus. 1988. Molecular evolution of the Escherichia coli chromosome. II. Clonal segments. Genetics 120: 359 366.
125. Mira, A.,, H. Ochman,, and N. A. Moran. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17: 589 596.
126. Moran, N. A. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108: 583 586.
127. Moran, N. A.,, and A. Mira. 2001. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2(12): research0054.1 research0054.12. [Online.]
128. Moszer, I.,, E. P. Rocha,, and A. Danchin. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2: 524 528.
129. Müller, H. 1932. Some genetic aspects of sex. Am. Nat. 66: 118 138.
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: 7 16.
131. Muto, A.,, and S. Osawa. 1987. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. USA 84: 166 169.
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: 399 410.
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: 721 730.
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: 459 468.
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: 6886 6895.
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: 323 329.
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: 362 375.
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: 11989 11999.
139. Ng, I.,, S.-L. Liu,, and K. Sanderson. 1999. Role of genomic rearrangements in producing new ribotypes of Salmonella typhi. J. Bacteriol. 181: 3536 3541.
140. Ochman, H.,, and I. B. Jones. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19: 6637 6643.
141. Ochman, H.,, and J. G. Lawrence,. 1996. Phylogenetics and the amelioration of bacterial genomes, p. 2627 2637. 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: 299 304.
143. Ochman, H.,, and N. A. Moran. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292: 1096 1099.
144. Ochman, H.,, and R. K. Selander. 1984. Evidence for clonal population structure in Escherichia coli. Proc. Natl. Acad. Sci. USA 81: 198 201.
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: 2715 2726.
146. Ochman, H.,, and A. C. Wilson. 1988. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26: 74 86.
147. Ochman, H.,, and A. C. Wilson,. 1987. Evolutionary history of enteric bacteria, p. 1649 1654. 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: 254 275.
149. Ohta, T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 264: 96 98.
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: 587 599.
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: 3807 3812.
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: 502 506.
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: 848 852.
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: 33 43.
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: 529 533.
156. Pesole, G.,, C. Gissi,, C. Lanave,, and C. Saccone. 1995. Glutamine synthetase gene evolution in bacteria. Mol. Biol. Evol. 12: 189 197.
157. Ragan, M. A. 2001. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11: 620 626.
158. Ragan, M. A. 2001. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201: 187 191.
159. Rainey, P. B.,, and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394: 69 72.
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: 396 401.
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. 2256 2276. 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: 579 590.
163. Salzberg, S. L.,, A. J. Salzberg,, A. R. Kerlavage,, and J. F. Tomb. 1998. Skewed oligomers and origins of replication. Gene 217: 57 67.
164. Sanderson, K. E. 1970. Current linkage map of Salmonella typhimurium. Bacteriol. Rev. 34: 176 193.
165. Sanderson, K. E. 1967. Revised linkage map of Salmonella typhimurium. Bacteriol. Rev. 31: 354 372.
166. Sanderson, K. E.,, and M. Demerec. 1965. The linkage map of Salmonella typhimurium. Genetics 51: 897 913.
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: 215 228.
168. Saunders, N. J.,, D. W. Hood,, and E. R. Moxon. 1999. Bacterial evolution: bacteria play pass the gene. Curr. Biol. 11: R180 R183.
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: 51 63.
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: 49 54.
171. Schmid, M. B.,, and J. R. Roth. 1983. Genetic methods for analysis and manipulation of inversion mutations in bacteria. Genetics 105: 517 537.
172. Schmid, M. B.,, and J. R. Roth. 1983. Selection and endpoint distribution of bacterial inversion mutations. Genetics 105: 539 557.
173. Segall, A.,, M. J. Mahan,, and J. R. Roth. 1988. Rearrangement of the bacterial chromosome: forbidden inversions. Science 241: 1314 1318.
174. Segall, A. M.,, and J. R. Roth. 1994. Approaches to halftetrad analysis in bacteria: recombination between repeated, inverse-order chromosomal sequences. Genetics 136: 27 39.
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: 737 747.
176. Shapiro, L.,, and R. Losick. 1997. Protein localization and cell fate in bacteria. Science 276: 712 718.
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: 23 33.
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: 241 247.
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: 8207 8211.
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: 1281 1295.
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: 7737 7749.
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: 222 230.
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: 263 267.
184. Smith, G. R. 1994. Hotspots of homologous recombination. Experientia 50: 234 241.
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: 13 20.
186. Smith, J. M.,, C. G. Dowson,, and B. G. Spratt. 1991. Localized sex in bacteria. Nature 349: 29 31.
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: 489 493.
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: 773 783.
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: 9869 9874.
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: 553 542.
191. Sueoka, N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85: 2653 2657.
192. Sueoka, N. 1993. Directional mutation pressure, mutator mutations, and dynamics of molecular evolution. J. Mol. Evol. 37: 137 153.
193. Sueoka, N. 1992. Directional mutation pressure, selective constraints, and genetic equilibria. J. Mol. Evol. 34: 95 114.
194. Sueoka, N. 1962. On the genetic basis of variation and heterogeneity in base composition. Proc. Natl. Acad. Sci. USA 48: 582 592.
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: 12619 12624.
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: 2376 2379.
197. Taylor, A. L.,, and M. S. Thoman. 1964. The genetic map of Escherichia coli K-12. Genetics 50: 659 677.
198. Taylor, A. L. 1970. Current linkage map of Escherichia coli. Bacteriol. Rev. 34: 155 175.
199. Taylor, A. L.,, and C. D. Trotter. 1967. Revised linkage map of Escherichia coli. Bacteriol. Rev. 31: 332 353.
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: 789 797.
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: 9763 9767.
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: 7348 7351.
203. Waldor, M. K.,, and J. J. Mekalanos. 1996. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272: 1910 1914.
204. Wang, B. 2001. Limitations of compositional approach to identifying horizontally transferred genes. J. Mol. Evol. 53: 244 250.
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: 3867 3869.
206. Whittam, T. S., 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708 2720. 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. 223 246. 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: 67 83.
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: 1751 1755.
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: 202 236.
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: 689 710.
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: 706 709.
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: 14851 14856.
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: 5201 5209.
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: 917 932.
216. Zinder, N. D.,, and J. Lederberg. 1952. Genetic exchange in Salmonella. J. Bacteriol. 64: 679 697.
217. Zuckerkandl, E. 1965. The evolution of hemoglobin. Sci. Am. 212: 110 118.
218. Zuckerkandl, E.,, and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357 366.

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