With more than 200 bacterial and archaeal genomes completely sequenced, and more than 500 genomes at various stages of completion, we begin to appreciate the enormous diversity of prokaryotic genomes in terms of chromosomal structure, gene content and organization, and the abundance and fluidity of accessory and mobile genetic elements. The genome of a bacterial species is composed of conserved core genes and variable accessory genes. Mobile genetic elements, such as plasmids, transposons, insertion sequences, integrons, prophages, genomic islands, and pathogenicity islands, are part of the accessory genes, which can have a significant influence on the phenotype and biology of the organism. These mobile elements facilitate interspecies and intraspecies genetic exchange. They play an important role in the pathogenicity of bacteria, and are a major contributor to species diversity. Further genomic analysis will likely uncover more interesting genetic elements like small (noncoding) RNA genes that can play a significant role in gene regulation.

Key Words

Genome diversity plasmids insertion elements genomic islands prophages small RNA 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Fleischmann, R. D., Adams, M. D., White, O., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512.PubMedCrossRefGoogle Scholar
  2. 2.
    Sakzberg, S. L. and Delcher, A. L. (2004) Tools for gene finding and whole genome composition, in Microbial Genomes (Fraser, C. M., Read, T. D., and Nelson, K. E., eds.). Humana Press, Totowa, NJ, pp. 19–31.Google Scholar
  3. 3.
    Cole, S. T. and Saint Girons, I. (1994) Bacterial genomics. FEMS Microbiol. Rev. 14, 139–160.PubMedCrossRefGoogle Scholar
  4. 4.
    Fonstein, M. and Haselkorn, R. (1995) Physical mapping of bacterial genomes. J. Bacteriol. 177, 3361–3369.PubMedGoogle Scholar
  5. 5.
    Casjens, S. (1998) The diverse and dynamic structure of bacterial genomes. Ann. Rev. Genet. 32, 339–377.PubMedCrossRefGoogle Scholar
  6. 6.
    Danchin, A., Guerdoux-Jamet, P., Moszer, I., and Nitschke, P. (2000) Mapping the bacterial cell architecture into the chromosome. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355, 179–190.PubMedCrossRefGoogle Scholar
  7. 7.
    Fraser, C. M., Gocayne, J. D., White, O., et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397–403.PubMedCrossRefGoogle Scholar
  8. 8.
    Kaneko, T., Nakamura, Y., Sato, S., et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189–197.PubMedCrossRefGoogle Scholar
  9. 9.
    Waters, E., Hohn, M. J., Ahel, I., et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA 100, 12,984–12,988.PubMedCrossRefGoogle Scholar
  10. 10.
    Galagan, J. E., Nusbaum, C., Roy, A., et al. (2002) The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12, 532–542.PubMedCrossRefGoogle Scholar
  11. 11.
    Volff, J.-N. and Altenbuchner, J. (2000) A new begininng with new ends:linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Letts. 186, 143–150.CrossRefGoogle Scholar
  12. 12.
    Ferdows, M. S. and Barbour, A. G. (1989) Megabase-sized linear DNA in the bacterium Borrelia burgdorferi, the lyme disease agent. Proc. Natl. Acad. Sci. USA 86, 5969–5973.PubMedCrossRefGoogle Scholar
  13. 13.
    Lin, Y.-L., Kieser, H. M., Hopwood, D. A., and Chen, C. W. (1993) The chromosomal DNA of Streptomyces lividans 66 is linear. Mol. Microbiol. 10, 923–933.PubMedCrossRefGoogle Scholar
  14. 14.
    Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M., et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147.PubMedCrossRefGoogle Scholar
  15. 15.
    Ikeda, H., Ishikawa, J., Hanamoto, A., et al. (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat. Biotechnol. 21, 526–531.PubMedCrossRefGoogle Scholar
  16. 16.
    Wood, D. W., Setubal, J. C., Kaul, R., et al. (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294, 2317–2323.PubMedCrossRefGoogle Scholar
  17. 17.
    Goodner, B., Hinkle, G., Gattung, S., et al. (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294, 2323–2328.PubMedCrossRefGoogle Scholar
  18. 18.
    Paulsen, I. T., Seshadri, R., Nelson, K. E., et al. (2002) The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. USA 99, 13,148–13,153.PubMedCrossRefGoogle Scholar
  19. 19.
    Jumas-Bailak, E., Michaux-Charachon, S., Bourg, G., O’Callaghan, D., and Ramuz, M. (1998) Differences in chromosome number and genome rearrangements in the genus Brucella. Mol. Microbiol. 27, 99–106.CrossRefGoogle Scholar
  20. 20.
    Ren, S. X., Fu, G., Jiang, X. G., et al. (2003) Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature 422, 888–893.PubMedCrossRefGoogle Scholar
  21. 21.
    Nascimento, A. L., Ko, A. I., Martins, E. A., et al. (2004) Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. J. Bacteriol. 186, 2164–2172.PubMedCrossRefGoogle Scholar
  22. 22.
    Fraser, C. M., Norris, S. J., Weinstock, G. M., et al. (1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281, 375–388.PubMedCrossRefGoogle Scholar
  23. 23.
    Fraser, C. M., Casjens, S., Huang, W. M., et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390, 580–586.PubMedCrossRefGoogle Scholar
  24. 24.
    Heidelberg, J. F., Eisen, J. A., Nelson, W. C., et al. (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483.PubMedCrossRefGoogle Scholar
  25. 25.
    Chen, C. Y., Wu, K. M., Chang, Y. C., et al. (2003) Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res. 13, 2577–2587.PubMedCrossRefGoogle Scholar
  26. 26.
    Makino, K., Oshima, K., Kurokawa, K., et al. (2003) Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae. Lancet 361, 743–749.PubMedCrossRefGoogle Scholar
  27. 27.
    Lessie, T. G., Hendrickson, W., Manning, B. D., and Devereux, R. (1996) Genomic complexity and plasticity of Burkholderia cepacia. FEMS Microbiol. Lett. 144, 117–128.PubMedCrossRefGoogle Scholar
  28. 28.
    Wigley, P. and Burton, N. F. (2000) Multiple chromosomes in Burkholderia cepacia and B. gladioli and their distribution in clinical and environmental strains of B. cepacia. J. Appl. Microbiol. 88, 914–918.PubMedCrossRefGoogle Scholar
  29. 29.
    White, O., Eisen, J. A., Heidelberg, J. F., et al. (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286, 1571–1577.PubMedCrossRefGoogle Scholar
  30. 30.
    Jaffe, J. D., Stange-Thomann, N., Smith, C., et al. (2004) The complete genome and proteome of Mycoplasma mobile. Genome Res. 14, 1447–1461.PubMedCrossRefGoogle Scholar
  31. 31.
    McLeod, M. P., Qin, X., Karpathy, S. E., et al. (2004) Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J. Bacteriol. 18, 5842–5855.CrossRefGoogle Scholar
  32. 32.
    Malek, J. A., Wierzbowski, J. M., Tao, W., et al. (2004) Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica. Nucleic Acids Res. 32, 1059–1064.PubMedCrossRefGoogle Scholar
  33. 33.
    Ogata, H., Audic, S., Renesto-Audiffren, P., et al. (2001) Mechanisms of evolution in Rickettsia conorii and R. prowazekii. Science 293, 2093–2098.PubMedCrossRefGoogle Scholar
  34. 34.
    Andersson, S. G., Zomorodipour, A., Andersson, J. O., et al. (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396, 133–140.PubMedCrossRefGoogle Scholar
  35. 35.
    Minion, F. C., Lefkowitz, E. J., Madsen, M. L., Cleary, B. J., Swartzell, S. M., and Mahairas, G. G. (2004) The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J. Bacteriol. 186, 7123–7133.PubMedCrossRefGoogle Scholar
  36. 36.
    Papazisi, L., Gorton, T. S., Kutish, G., et al. (2003) The complete genome sequence of the avian pathogen Mycoplasma gallisepticum strain R(low). Microbiology 149, 2307–2316.PubMedCrossRefGoogle Scholar
  37. 37.
    Chambaud, I., Heilig, R., Ferris, S., et al. (2001) The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 29, 2145–2153.PubMedCrossRefGoogle Scholar
  38. 38.
    Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B. C., and Herrmann, R. (1996) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24, 4420–4449.PubMedCrossRefGoogle Scholar
  39. 39.
    Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.PubMedCrossRefGoogle Scholar
  40. 40.
    Perna, N. T., Plunkett, G. 3rd, Burland, V., et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533.PubMedCrossRefGoogle Scholar
  41. 41.
    Lindsay, J. A. and Holden, M. T. (2004) Staphylococcus aureus: superbug, super genome? Trends Microbiol. 12, 378–385.PubMedCrossRefGoogle Scholar
  42. 42.
    Lan, R. and Reeves, P. R. (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8, 396–401.PubMedCrossRefGoogle Scholar
  43. 43.
    Cohan, F. M. (2002) What are bacterial species? Annu. Rev. Microbiol. 56, 457–487.PubMedCrossRefGoogle Scholar
  44. 44.
    Anderson, S., Bankier, A. T., Barrell, B. G., et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290, 457–465.PubMedCrossRefGoogle Scholar
  45. 45.
    Osawa, S., Jukes, T. H., Watanabe, K., and Muto, A. (1992) Recent evidence for evolution of the genetic code. Microbiol. Rev. 56, 229–264.PubMedGoogle Scholar
  46. 46.
    Santos, M. A., Ueda, T., Watanabe, K., and Tuite, M. F. (1997) The non-standard genetic code of Candida spp.: an evolving genetic code of a novel mechanism for adaptation? Mol. Microbiol. 26, 423–431.PubMedCrossRefGoogle Scholar
  47. 47.
    Kano, A., Ohama, T., Abe, R., and Osawa, S. (1993) Unassigned or nonsense codons in Micrococcus luteus. J. Mol. Biol. 230, 51–56.PubMedCrossRefGoogle Scholar
  48. 48.
    Grantham, R., Gautier, C., and Gouy, M. (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 8, 1893–1912.PubMedCrossRefGoogle Scholar
  49. 49.
    Ochman, H., Lawrence, J. G., and Grolsman, E. A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304.PubMedCrossRefGoogle Scholar
  50. 50.
    Kanaya, S., Kinouchi, M., Abe, T., et al. (2001) Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 276, 89–99.PubMedCrossRefGoogle Scholar
  51. 51.
    Wang, H. C., Badger, J., Kearney, P., and Li, M. (2001) Analysis of codon usage patterns of bacterial genomes using the self-organizing map. Mol. Biol. Evol. 18, 792–800.PubMedGoogle Scholar
  52. 52.
    Chen, L. L. and Zhang, C. T. (2003) Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. Biochem. Biophys. Res. Commun. 306, 310–317.PubMedCrossRefGoogle Scholar
  53. 53.
    Lynn, D. J., Singer, G. A., and Hickey, D. A. (2002) Synonymous codon usage is subjectto selection in thermophilic bacteria. Nucleic Acids Res. 30, 4272–4277.PubMedCrossRefGoogle Scholar
  54. 54.
    Mackiewicz, P., Zakrzewska-Czerwinska, J., Zawilak, A., Dudek, M. R., and Cebrat, S. (2004) Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res. 32, 3781–3791.PubMedCrossRefGoogle Scholar
  55. 55.
    Lobry, J. R. (1996) Origin of replication of Mycoplasma genitalium. Science 272, 745–746.PubMedCrossRefGoogle Scholar
  56. 56.
    Frank, A. C. and Lobry, J. R. (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16, 560–561.PubMedCrossRefGoogle Scholar
  57. 57.
    Zawilak, A., Cebrat, S., Mackiewicz, P., et al. (2001) Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA. Nucleic Acids Res. 29, 2251–2259.PubMedCrossRefGoogle Scholar
  58. 58.
    Akman, L., Yamashita, A., Watanabe, H., et al.(2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat. Genet. 32, 402–407.PubMedCrossRefGoogle Scholar
  59. 59.
    Gil, R., Silva, F. J., Zientz, E., et al. (2003) The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc. Natl. Acad. Sci. USA 100, 9388–9393.PubMedCrossRefGoogle Scholar
  60. 60.
    Lawrence, J. G. and Roth, J. R. (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843–1860.PubMedGoogle Scholar
  61. 61.
    Watanabe, H., Mori, H., Itoh, T., and Gojobori, T. (1997) Genome plasticity as a paradigm of eubacteria evolution. J. Mol. Evol. 44, S57–S64.PubMedCrossRefGoogle Scholar
  62. 62.
    Siefert, J. L., Martin, K. A., Abdi, F., Widger, W. R., and Fox, G. E. (1997) Conserved gene clusters in bacterial genomes provide further support for the primacy of RNA. J. Mol. Evol. 45, 467–472.PubMedCrossRefGoogle Scholar
  63. 63.
    Wolf, Y. I., Rogozin, I. B., Kondrashov, A. S., and Koonin, E. V. (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11, 356–372.PubMedCrossRefGoogle Scholar
  64. 64.
    Eppinger, M., Baar, C., Raddatz, G., Huson, D. H., and Schuster, S. C. (2004) Comparative analysis of four Campylobacterales. Nat. Rev. Microbiol. 2, 872–885.PubMedCrossRefGoogle Scholar
  65. 65.
    Hinnebusch, J. and Tilly, K. (1993) Linear plasmids and chromosomes in bacteria. Mol. Microbiol. 10, 917–922.PubMedCrossRefGoogle Scholar
  66. 66.
    Crespi, M., Messens, E., Caplan, A. B., van Montagu, M., and Desomer, J. (1992) Fasciation induction by the phytopathogen Rhodococcus fascians depends upon a linear plasmid encoding a cytokinin synthase gene. EMBO J. 11, 795–804.PubMedGoogle Scholar
  67. 67.
    Kalkus, J., Reh, M., and Schlegel, H. G. (1990) Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids. J. Gen. Microbiol. 136, 1145–1151.PubMedGoogle Scholar
  68. 68.
    Brown, S. E., Knudson, D. L., and Ishimaru, C. A. (2002) Linear plasmid in the genome of Clavibacter michiganensissubsp. sepedonicus. J. Bacteriol. 184, 2841–2844.PubMedCrossRefGoogle Scholar
  69. 69.
    Davis, B. M. and Waldor, M. K. (2002) Mobile genetic elements and bacterial pathogenesis, in Mobile DNA II (Craig, N. L., Gellert, M., and Lambowitz, A. M., eds.). ASM Press, Washington, DC, pp. 1040–1059.Google Scholar
  70. 70.
    Thomas, C. M. (2000) Paradigms of plasmid organization. Mol. Microbiol. 37, 485–491.PubMedCrossRefGoogle Scholar
  71. 71.
    Chandler, M. and Mahillon, J. (2002) Insertion sequences revisited, in Mobile DNA II (Craig, N. L., Gellert, M., and Lambowitz, A. M., eds.). ASM Press, Washington, DC, pp. 305–366.Google Scholar
  72. 72.
    Curcio, M. J. and Derbyshire, K. M. (2003) The outs and ins of transposition: from mu to kangaroo. Nat. Rev. Mol. Cell. Biol. 4, 865–877.CrossRefGoogle Scholar
  73. 73.
    Parkhill, J., Sebaihia, M., Preston, A., et al. (2003) Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35, 32–40.PubMedCrossRefGoogle Scholar
  74. 74.
    Preston, A., Parkhill, J., and Maskell, D. J. (2004) The bordetellae: lessons from genomics. Nat. Rev. Microbiol. 2, 379–390.PubMedCrossRefGoogle Scholar
  75. 75.
    Nierman, W. C., DeShazer, D., Kim, H. S., et al. (2004) Structural flexibility in the Burkholderia mallei genome. Proc. Natl. Acad. Sci. USA 101, 14,246–14,251.PubMedCrossRefGoogle Scholar
  76. 76.
    Parkhill, J., Wren, B. W., Thomson, N. R., et al. (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413, 523–527.PubMedCrossRefGoogle Scholar
  77. 77.
    Wei, J., Goldberg, M. B., Burland, V., et al. (2003) Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71, 2775–2786.PubMedCrossRefGoogle Scholar
  78. 78.
    Jin, Q., Yuan, Z., Xu, J., et al. (2002) Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30, 4432–4441.PubMedCrossRefGoogle Scholar
  79. 79.
    Scott, K. P., Melville, C. M., Barbosa, T. M., and Flint, H. J. (2000) Occurrence of the new tetracycline resistance gene tet(W) in bacteria from the human gut. Antimicrob. Agents Chemother. 44, 775–777.PubMedCrossRefGoogle Scholar
  80. 80.
    Scott, K. P. (2002) The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract. Cell. Mol. Life Sci. 59, 2071–2082.PubMedCrossRefGoogle Scholar
  81. 81.
    Burrus, V. and Waldor, M. K. (2004) Shaping bacterial genomes with integrative and conjugative elements. Res. Microbiol. 155, 376–386.PubMedCrossRefGoogle Scholar
  82. 82.
    Nunes-Duby, S. E., Kwon, H. J., Tirumalai, R. S., Ellenberger, T., and Landy, A. (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26, 391–406.PubMedCrossRefGoogle Scholar
  83. 83.
    Hall, R. M., Brookes, D. E., and Stokes, H. W. (1991) Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination crossover point. Mol. Microbiol. 5, 1941–1959.PubMedCrossRefGoogle Scholar
  84. 84.
    Naas, T., Mikami, Y., Imai, T., Poirel, L., and Nordmann, P. (2001) Characterization of In53, a class 1 plasmid-and composite transposon-located integron of Escherichia coli which carries an unusual array of gene cassettes. J. Bacteriol. 183, 235–249.PubMedCrossRefGoogle Scholar
  85. 85.
    Mazel, D., Dychinco, B., Webb, V. A., and Davies, J. (1998) A distinctive class of integron in the Vibrio cholerae genome. Science 280, 605–608.PubMedCrossRefGoogle Scholar
  86. 86.
    Rowe-Magnus, D. A., Guerout, A. M., Ploncard, P., Dychinco, B., Davies, J., and Mazel, D. (2001) The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proc. Natl. Acad. Sci. USA 98, 652–657.PubMedCrossRefGoogle Scholar
  87. 87.
    Vaisvila, R., Morgan, R. D., Posfai, J., and Raleigh, E. A. (2001) Discovery and distribution of super-integrons among pseudomonads. Mol. Microbiol. 42, 587–601.PubMedCrossRefGoogle Scholar
  88. 88.
    Belfort, M., Reaban, M. E., Coetzee, T., and Dalgaard, J. Z. (1995) Prokaryotic introns and inteins: a panoply of form and function. J. Bacteriol. 177, 3897–3903.PubMedGoogle Scholar
  89. 89.
    Chu, F. K., Maley, G. F., Maley, F., and Belfort, M. (1984) Intervening sequence in the thymidylate synthase gene of bacteriophage T4. Proc. Natl. Acad. Sci. USA 81, 3049–3053.PubMedCrossRefGoogle Scholar
  90. 90.
    Edgell, D. R., Belfort, M., and Shub, D. A. (2000) Barriers to intron promiscuity in bacteria. J. Bacteriol. 182, 5281–5289.PubMedCrossRefGoogle Scholar
  91. 91.
    Ko, M., Choi, H., and Park, C. (2002). Group I sel-splicing intron in the recA gene of Bacillus anthracis. J. Bacteriol. 184, 3917–3922.PubMedCrossRefGoogle Scholar
  92. 92.
    Dai, L. and Zimmerly, S. (2002) Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res. 30, 1091–1102.PubMedCrossRefGoogle Scholar
  93. 93.
    Michel, F. and Ferat, J. L. (1995) Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435–461.PubMedCrossRefGoogle Scholar
  94. 94.
    Qin, P. Z. and Pyle, A. M. (1998) The architectural organization and mechanistic function of group II intron structural elements. Curr. Opin. Struct. Biol. 8, 301–308.PubMedCrossRefGoogle Scholar
  95. 95.
    Cousineau, B., Lawrence, S., Smith, D., and Belfort, M. (2000) Retrotransposition of bacterial group II intron. Nature 404, 1018–1021.PubMedCrossRefGoogle Scholar
  96. 96.
    Belhocine, K., Plante, I., and Cousineau, B. (2004) Conjugation mediates transfer of the Ll.LtrB group II intron between different bacterial species. Mol. Microbiol. 51, 1459–1469.PubMedCrossRefGoogle Scholar
  97. 97.
    Casjens, S. (2003) Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49, 277–300.PubMedCrossRefGoogle Scholar
  98. 98.
    Canchaya, C., Fournous, G., and Brussow, H. (2004) The impact of prophages on bacterial chromosomes. Mol. Microbiol. 53, 9–18.PubMedCrossRefGoogle Scholar
  99. 99.
    Freeman, V. J. (1951) Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J. Bacteriol. 61, 675–688.PubMedGoogle Scholar
  100. 100.
    Brussow, H., Canchaya, C., and Hardt, W. D. (2004) Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68, 560–602.PubMedCrossRefGoogle Scholar
  101. 101.
    Hendrix, R. W., Lawrence, J. G., Hatfull, G. F., and Casjens, S. (2000) The origins and ongoing evolution of viruses. Trends Microbiol. 8, 504–508.PubMedCrossRefGoogle Scholar
  102. 102.
    Campbell, A. M. (1992) Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174, 7495–7499.PubMedGoogle Scholar
  103. 103.
    Campbell, A. (2002) Eubacterial genomes, in Mobile DNA II (Craig, N. L., Gellert, M., and Lambowitz, A. M., eds.). ASM Press, Washington, DC, pp. 1024–1039.Google Scholar
  104. 104.
    Blum, G., Ott, M., Lischewski, A., et al. (1994) Excision of large DNA regions termed pathogenicity islands from tRNA-specific loci in the chromosome of an Escherichia coli wild-type pathogen. Infect. Immun. 62, 606–614.PubMedGoogle Scholar
  105. 105.
    Hacker, J. and Carniel, E. (2001) Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2, 376–381.PubMedGoogle Scholar
  106. 106.
    Dobrindt, U., Hochhut, B., Hentschel, U., and Hacker, J. (2004) Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2, 414–424.PubMedCrossRefGoogle Scholar
  107. 107.
    Hershberg, R., Altuvia, S., and Margalit, H. (2003) A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res. 31, 1813–1820.PubMedCrossRefGoogle Scholar
  108. 108.
    Argaman, L., Hershberg, R., Vogel, J., et al. (2001) Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr. Biol. 11, 941–950.PubMedCrossRefGoogle Scholar
  109. 109.
    Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G., and Gottesman, S. (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev. 15, 1637–1651.PubMedCrossRefGoogle Scholar
  110. 110.
    Rivas, E., Klein, R. J., Jones, T. A., and Eddy, S. R. (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr. Biol. 11, 1369–1373.PubMedCrossRefGoogle Scholar
  111. 111.
    Chen, S., Lesnik, E. A., Hall, T. A., et al. (2002) A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems 65, 157–177.PubMedCrossRefGoogle Scholar
  112. 112.
    Tjaden, B., Saxena, R. M., Stolyar, S., Haynor, D. R., Kolker, E., and Rosenow, C. (2002) Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 30, 3732–3738.PubMedCrossRefGoogle Scholar
  113. 113.
    Vogel, J., Bartels, V., Tang, T. H., et al. (2003) RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res. 31, 6435–6443.PubMedCrossRefGoogle Scholar
  114. 114.
    Masse, E., Majdalani, N., and Gottesman, S. (2003) Regulatory roles for small RNAs in bacteria. Curr. Opin. Microbiol. 6, 120–124.PubMedCrossRefGoogle Scholar
  115. 115.
    Storz, G., Opdyke, J. A., and Zhang, A. (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7, 140–144.PubMedCrossRefGoogle Scholar
  116. 116.
    Altuvia, S. (2004) Regulatory small RNAs: the key to coordinating global regulatory circuits. J. Bacteriol. 186, 6679–6680.PubMedCrossRefGoogle Scholar
  117. 117.
    Romeo, T. (1998) Global regulation by the small RNA-binding protein CsrA and the noncoding RNA molecule CsrB. Mol. Microbiol. 29, 1321–1330.PubMedCrossRefGoogle Scholar
  118. 118.
    Zhang, A., Altuvia, S., Tiwari, A., Argaman, L., Hengge-Aronis, R., and Storz, G. (1998) The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) protein. EMBO J. 17, 6061–6068.PubMedCrossRefGoogle Scholar
  119. 119.
    Repoila, F., Majdalani, N., and Gottesman, S. (2003) Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm. Mol. Microbiol. 48, 855–861.PubMedCrossRefGoogle Scholar
  120. 120.
    Opdyke, J. A., Kang, J. G., and Storz, G. (2004) GadY, a small-RNA regulator of acid response genes in Escherichia coli. J. Bacteriol. 186, 6698–6705.PubMedCrossRefGoogle Scholar
  121. 121.
    Chen, S., Zhang, A., Blyn, L. B., and Storz, G. (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J. Bacteriol. 186, 6689–6697.PubMedCrossRefGoogle Scholar
  122. 122.
    Lenz, D. H., Mok, K. C., Lilley, B. N., Kulkarni, R. V., Wingreen, N. S., and Bassler, B. L. (2004) The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell 118, 69–82.PubMedCrossRefGoogle Scholar
  123. 123.
    Henke, J. M. and Bassler, B. L. (2004) Three parallel quorum-sensing systems regulate gene expression in Vibrio harveyi. J. Bacteriol. 186, 6902–6914.PubMedCrossRefGoogle Scholar
  124. 124.
    Masse, E., Escorcia, F. E., and Gottesman, S. (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes and Dev. 17, 2374–2383.PubMedCrossRefGoogle Scholar
  125. 125.
    Wilderman, P. J., Sowa, N. A., FitzGerald, D. J., et al. (2004) Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc. Natl. Acad. Sci. USA 101, 9792–9797.PubMedCrossRefGoogle Scholar
  126. 126.
    McLeod, M. P., Qin, X., Karpathy, S. E., et al. (2004) Complete genome sequence of Rickettsia typhi and comparison with sequences of other rickettsiae. J. Bacteriol. 186, 5842–5855PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2006

Authors and Affiliations

  • Voon Loong Chan
    • 1
  1. 1.Department of Medical Genetics and MicrobiologyUniversity of TorontoTorontoCanada

Personalised recommendations