Chapter 12 : Genome Architecture and Evolution of Bacterial Pathogens

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

Genome Architecture and Evolution of Bacterial Pathogens, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815639/9781555814144_Chap12-1.gif /docserver/preview/fulltext/10.1128/9781555815639/9781555814144_Chap12-2.gif


Bacterial genomes are usually packed with genes occupying around 90% of their DNA, and no structures resembling isochores or telomeres have been identified. A second source of heterogeneity could come from structural domains in the genome, which would make some areas of the chromosome more accessible than others to foreign DNA sequences and influence intrachromosomal recombination. With the advent of genomic data and the improvement of methods for replication origin and terminus detection, it is now possible to review the genome balance hypothesis. The mutation probability has been proposed to vary within a bacterial chromosome for genes located at different positions relative to the replication origin. Electron micrographs of the Escherichia coli chromosome displayed a rossette-like organization with loops of supercoiled DNA distributed around a central node. Species such as Staphylococcus aureus and E. coli display an increase in horizontally acquired genes closer to the terminus, whereas transposable elements seem unaffected. Sequence repeats, in all their variants, are one of the main evolutionary tools to generate variability, this being structural (rearrangements) or functional (generation of new genes). The plethora of genomic data has unexpectedly suggested that the traditional view of IS Elements (ISs) as detrimental selfish elements is probably an oversimplification. In relation to bacterial pathogens, the data suggest that their genomes are more flexible than related nonpathogenic species, as if their need for fast adaptation and plasticity had relaxed organizational constraints.

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1.
Figure 1.

Expression and location. Putative expression level, measured as the Codon Adaptation Index (Sharp and Li, 1987) and chromosomal location of E. coli O157 genes. Many genes of predicted high and low expression levels appear clustered in some areas or domains.

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

Location of paralogous sequences. (a) Distance between paralogous genes in Clostridium acetubutylicum. Gene pairs with high sequence similarity are closely located. (b) Genomic distance of paralogous genes in Mycoplasma gallisepticum. Vertical patterns appear, showing gradients of sequence similarity among clustered genes.

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Alokam, S.,, S. L. Liu,, K. Said, and, K. E. Sanderson. 2002. Inversions over the terminus region in Salmonella and Escherichia coli: IS200s as the sites of homologous recombination inverting the chromosome of Salmonella enterica serovar Typhi. J. Bacteriol. 184:61906197.
2. Aras, R. A.,, J. Kang,, A. I. Tschumi,, Y. Harasaki, and, M. J. Blazer. 2003. Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc. Natl. Acad. Sci. USA 100:1357913584.
3. Bailly-Bechet, M.,, A. Danchin,, M. Iqbal,, M. Marsili, and, M. Vergassola. 2006. Codon usage domains over bacterial chromosomes. PLoS Comput. Biol. 2:e37.
4. Bi, X., and, L. F. Liu. 1994. RecA-independent and recA-dependent intramolecular plasmid recombination. Differential homology requirement and distance effect. J. Mol. Biol. 234:414423.
5. Birky, C. W., Jr., and, J. B. Walsh. 1992. Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes. Genetics 130:677683.
6. Bremer, H., and, P. P. Dennis. 1996. Modulation of chemical composition and other parameters of the cell by growth rate, p. 15531569. In F. Neidhardt et al. (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC.
7. Brewer, B. J. 1988. When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53:679686.
8. Campo, N.,, M. J. Dias,, M. L. Daveran-Mingot,, P. Ritzenthaler, and, P. Le Bourgeois. 2004. Chromosomal constraints in gram-positive bacteria revealed by artificial inversions. Mol. Microbiol. 51:511522.
9. Carlson, C. R.,, A. B. Kolsto. 1994. A small (2.4 Mb) Bacillus cereus chromosome corresponds to a conserved region of a larger (5.3 Mb) Bacillus cereus chromosome. Mol. Microbiol. 13:161169.
10. Casjens, S. 1998. The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32:339377.
11. Cerdeno-Tarraga, A. M.,, S. Patrick,, L. C. Crossman,, G. Blakely,, V. Abratt,, N. Lennard,, I. Poxton,, B. Duerden,, B. Harris,, M. A. Quail, et al. 2005. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science. 307:14631465.
12. Cole, S. T.,, K. Eiglmeier,, J. Parkhill,, K. D. James,, N. R. Thomson, et al. 2001. Massive gene decay in the leprosy bacillus. Nature 409:10071011.
13. Cole, S. T., and, I. Saint-Girons. 1999. Bacterial genomes—all shapes and sizes, p. 3562. In R. L. Charlebois (ed.), Organization of the Prokaryotic Genome. ASM Press, Washington, DC.
14. Couturier, E., and, E. P. Rocha. 2006. Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes. Mol. Microbiol. 59:15061518.
15. Csonka, L. N., and, W. Epstein. 1996. Osmoregulation, p. 12101223. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed, vol. 1. ASM Press, Washington DC.
16. Daubin, V., and, H. Ochman. 2004. Start-up entities in the origin of new genes. Curr. Opin. Genet. Dev. 14:616619.
17. Daubin, V., and, G. Perriere. 2003. G+C3 structuring along the genome: a common feature in prokaryotes. Mol. Biol. Evol. 20:471483.
18. Egan, E. S.,, M. A. Fogel, and, M. K. Waldor. 2005. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56:11291138.
19. 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:research 0011.1–research0011.9.
20. Ellwood, M., and, M. Nomura. 1982. Chromosomal locations of the genes for rRNA in Escherichia coli K-12. J. Bacteriol. 149:458468.
21. Eshed, V.,, A. Gopher,, T. B. Gage, and, I. Hershkovitz. 2004. Has the transition to agriculture reshaped the demographic structure of prehistoric populations? New evidence from the Levant. Am. J. Phys. Anthropol. 124:315329.
22. Fijalkowska, I. J.,, P. Jonczyk,, M. M. Tkaczyk,, M. Bialoskorska, and, R. M. Schaaper. 1998. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. USA 95:1002010025.
23. Forterre, P. 1999. Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol. Microbiol. 33:457465.
24. Foster, J. W., and, M. Moreno. 1999. Inducible acid tolerance mechanisms in enteric bacteria, p. 5569. Bacterial Responses to pH. (Novartis Foundation Symposium 221). Wiley, Chichester, United Kingdom.
25. 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.
26. Frank, A. C.,, H. Amiri, and, S. G. Andersson. 2002. Genome deterioration: loss of repeated sequences and accumulation of junk DNA. Genetica 115:112.
27. Frank, A. C., and, J. R. Lobry. 1999. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238:6577.
28. French, S. 1992. Consequences of replication fork movement through transcription units in vivo. Science 258:13621365.
29. García-Russell, N.,, T. G. Harmon,, T. Q. Le,, N. H. Amaladas,, R. D. Mathewson, and, A. M. Segall. 2004. Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements. Mol. Microbiol. 52:329344.
30. Garcia-Vallve, S.,, E. Guzman,, M. A. Montero, and, A. Romeu. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31:187189.
31. Gil, R.,, F. J. Silva,, J. Pereto, and, A. Moya. 2004. Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68:518537.
32. Hacker, J., and, J. B. Kaper. 2000. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54:641679.
33. Hill, C. W., and, J. A. Gray. 1988. Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics 119:771778.
34. Hill, C. W., and, B. W. Harnish. 1981. Inversions between ribosomal RNA genes of Escherichia coli. Proc. Natl. Acad. Sci. USA 78:70697072.
35. Hudson, R. E.,, U. Bergthorsson,, J. R. Roth, and, H. Ochman. 2002. Effect of chromosome location on bacterial mutation rates. Mol. Biol. Evol. 19:8592.
36. Hughes, D. 2000a. Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol. 1:reviews0006.
37. Hughes, D. 1999. Impact of homologous recombination on genome organization and stability. In R. Charlebois (ed.), Organization of the Prokaryotic Genome. ASM Press, Washington, DC.
38. Hughes, D. 2000b. Co-evolution of the tuf genes links gene conversion with the generation of chromosomal inversions. J. Mol. Biol. 297:355364.
39. Hutchison, C. A.,, S. N. Peterson,, S. R. Gill,, R. T. Cline,, O. White,, C. M. Fraser,, H. O. Smith, and, J. C. Venter. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:21652169.
40. Iyer, L. M.,, E. V. Koonin, and, L. Aravind. 2004. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335:7388.
41. Jacob, F., and, J. Monod. 1962. On the regulation of gene activity. Cold Spring Harbor Symp. Quant. Biol. 26:193211.
42. Jordan, I. K.,, K. S. Makarova,, J. L. Spouge,, Y. I. Wolf, and, E. V. Koonin. 2001. Lineage specific gene expansions in bacterial and archaeal genomes. Genome Res 11:555565.
43. Kaneko, T.,, Y. Nakamura,, S. Sato,, E. Asamizu,, T. Kato,, S. Sasamoto,, A. Watanabe,, K. Idesawa,, A. Ishikawa,, K. Kawashima, et al. 2000. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:331338.
44. Kavenoff, R., and, B. C. Bowen. 1976. Electron microscopy of membrane-free folded chromosomes from Escherichia coli. Chromosoma 59:89101.
45. Krawiec, S., and, M. Riley. 1990. Organization of the bacterial chromosome. Microb. Rev. 54:502539.
46. Kresse, A. U.,, S. D. Dinesh,, K. Larbig, and, U. Romling. 2003. Impact of large chromosomal inversion on the adaptation and evolution of Pseudomonas aeruginosa chronically colonizing cystic fibrosis lungs. Mol. Microbiol. 47:145158.
47. Lawrence, J. G. 2003. Gene organization: selection, selfishness, and serendipity. Annu. Rev. Microbiol. 57:419440.
48. Leach, D. R. F. 1994. Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. BioEssays 16:893900.
49. Legault, B. A.,, A. Lopez-Lopez,, J. C. Alba-Casado,, W. F. Doolittle,, H. Bolhuis,, F. Rodriguez-Valera, and, R. T. Papke RT. 2006. Environmental genomics of “Haloquadratum walsbyi” in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 7:171.
50. Lerat, E.,, V. Daubin,, H. Ochman, and, N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3:e130.
51. Lerat, E., and, H. Ochman. 2004. Psi-Phi: exploring the outer limits of bacterial pseudogenes. Genome Res. 14:22732278.
52. Lindroos, H. L.,, A. Mira,, D. Repsilber,, O. Vinnere,, K. Naslund,, M. Dehio,, C. Dehio, and, S. G. Andersson. 2005. Characterization of the genome composition of Bartonella koehlerae by microarray comparative genomic hybridization profiling. J. Bacteriol. 187:61556165.
53. Liu, G. R.,, W. Q. Liu,, R. N. Johnston,, K. E. Sanderson,, S. X. Li, and, S. L. Liu. 2006. Genome plasticity and oriter rebalancing in Salmonella typhi. Mol. Biol. Evol. 23:365371.
54. Liu, G. R.,, A. Rahn,, W. Q. Liu,, K. E. Sanderson,, R. N. Johnston, and, S. L. Liu. 2002. The evolving genome of Salmonella enterica serovar Pullorum. J. Bacteriol. 184:26262633.
55. Liu, S. L., and, K. E. Sanderson. 1996. Highly plastic chromosomal organization in Salmonella typhi. Proc. Natl. Acad. Sci. USA 93:1030310308.
56. Lovett, S. T. 2004. Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences. Mol. Microb. 52:12431253.
57. Lundgren, M.,, A. Andersson,, L. Chen,, P. Nilsson, and, R. Bernander. 2004. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc. Natl. Acad. Sci. USA 101:70467051.
58. Mackiewicz, P.,, D. Mackiewicz,, M. Kowalczuk, and, S. Cebrat. 2001. Flip-flop around the origin and terminus of replication in prokaryotic genomes. Genome Biol. 2:interactions1004.
59. May, B. J.,, Q. Zhang,, L. L. Li,, M. L. Paustian,, T. S. Whittam, and, V. Kapur. 2001. Complete genomic sequence of Pasteurella multocida, Pm70. Proc. Natl. Acad. Sci. USA 98:34603465.
60. McKeown, T. 1988. The Origins of Human Disease. Blackwell, Oxford, United Kingdom.
61. McLean, M. J.,, K. H. Wolfe, and, K. M. Devine. 1998. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47:691696.
62. Mira, A.,, L. Klasson, and, S. G. E. Andersson. 2002. Microbial genome evolution: sources of variability. Curr. Opin. Microb. 5:506512.
63. Mira, A.,, H. Ochman, and, N. A. Moran. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589596.
64. Mira, A., and, H. Ochman. 2002. Gene location and bacterial sequence divergence. Mol. Biol. Evol. 19:13501358.
65. Mira, A.,, R. Pushker,, B. A. Legault,, D. Moreira, and, F. Rodriguez-Valera. 2004. Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol. Biol. 4:50.
66. Mira, A.,, R. Pushker, and, F. Rodriguez-Valera. 2006. The Neolithic revolution of bacterial genomes. Trends Microbiol. 14:200206.
67. Mira, A., and, R. Pushker. 2005. The silencing of pseudogenes. Mol. Biol. Evol. 22:21352138.
68. Mongodin, E. F.,, K. E. Nelson,, S. Daugherty,, R. T. Deboy,, J. Wister,, H. Khouri,, J. Weidman,, D. A. Walsh,, R. T. Papke,, G. Sanchez Perez,, A. K. Sharma,, C. L. Nesbo,, D. MacLeod,, E. Bapteste,, W. F. Doolittle,, R. L. Charlebois,, B. Legault, and, F. Rodriguez-Valera. 2005. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. USA 102:1814718152.
69. Moran, N. A., and, A. Mira. 2001. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol. 2:research0054.
70. Moran, N. A., and, G. R. Plague. 2004. Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev. 14:627633.
71. Moran, N. A. 2003. Tracing the evolution of gene loss in obligate bacterial symbionts. Curr. Opin. Microbiol. 6:512518.
72. Moreno, E. 1998. Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome? FEMS Microbiol. Rev. 22:255275.
73. Mushegian, A. 1999. The minimal genome concept. Curr. Opin. Genet. Dev. 9:709714.
74. Nomura, M., and, E. A. Morgan. 1977. Genetics of bacterial ribosomes. Annu. Rev. Genet. 11:297347.
75. Ochman, H.,, J. G. Lawrence, and, E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299304.
76. Ochman, H., and, A. C. Wilson. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:7486.
77. Ochman, H. 2002a. Bacterial evolution: chromosome arithmetic and geometry. Curr. Biol. 12:R427R428.
78. Ochman, H. 2002b. Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes. Trends Genet. 18:335337.
79. Ochman, H. 2005. Genomes on the shrink. Proc. Natl. Acad. Sci. USA 102:1195911960.
80. Pal, C.,, B. Papp, and, M. J. Lercher. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37:13721375.
81. Parkhill, J.,, M. Sebaihia,, A. Preston,, L. D. Murphy,, N. Thomson,, D. E. Harris,, M. T. G. Holden,, C. M. Churcher,, S. D. Bentley,, K. L. Mungall, et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Gen. 35:3240.
82. Parkhill, J.,, B. W. Wren,, N. R. Thomson,, R. W. Titball,, M. T. Holden,, M. B. Prentice,, M. Sebaihia,, K. D. James,, C. Churcher,, K. L. Mungall, et al. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523527.
83. Perna, N. T.,, G. Plunkett, III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick, et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529533.
84. Pósfai, G.,, G. Plunkett, III,, T. Feher,, D. Frisch,, G. M. Keil,, K. Umenhoffer,, V. Kolisnychenko,, B. Stahl,, S. S. Sharma,, M. de Arruda,, V. Burland,, S. W. Harcum, and, F. R Blattner. 2006. Emergent properties of reduced-genome Escherichia coli. Science 312:10441046.
85. Pushker, R.,, A. Mira, and, F. Rodriguez-Valera. 2004. Comparative genomics of gene-family size in closely related bacteria. Genome Biol. 5:R27.
86. Reams, A. B., and, E. L. Neidle. 2003. Genome plasticity in Acinetobacter: new degradative capabilities acquired by the spontaneous amplification of large chromosomal segments. Mol.Microb. 47:12911304.
87. Rocha, E. 2002. Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes? Trends Microbiol. 10:393395.
88. Rocha, E. P., and, A. Danchin. 2003. Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31:65706577.
89. Rocha, E. P. C.,, P. Guerdoux-Jamet,, I. Moszer,, A. Viari, and, A. Danchin. 2000. Implication of gene distribution in the bacterial chromosome for the bacterial cell factory. J. Biotechnol. 78:209219.
90. Rocha, E. P. C. 2004a. The replication-related organization of bacterial genomes. Microbiology 150:16091627.
91. Rocha, E. P. C. 2004b. Order and disorder in bacterial genomes. Curr. Opin. Microbiol. 7:519527.
92. Romero, D., and, R. Palacios. 1997. Gene amplification and genomic plasticity in prokaryotes. Annu. Rev. Genet. 31:91111.
93. Rowe-Magnus, D. A.,, A. M. Guerout,, P. Ploncard,, B. Dychinco,, J. Davies, and, D. Mazel. 2001. The evolutionary history of chromosomal super-integrons provides an ancestry for multi-resistant integrons. Proc. Natl. Acad. Sci. USA 98:652657.
94. Salama, N.,, K. Guillemin,, T. K. McDaniel,, G. Sherlock,, L. Tompkins, and, S. Falkow. 2000. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:1466814673.
95. Santamaria, D.,, E. Viguera,, M. L. Martinez-Robles,, O. Hyrien,, P. Hernandez,, D. B. Krimer, and, J. B. Schvartzman. 2000. Bidirectional replication and random termination. Nucleic Acids Res. 28:20992107.
96. Santoyo, G., and, D. Romero. 2005. Gene conversión and concerted evolution in bacterial genomes. FEMS Microbiol. Rev. 29:169183.
97. Schmid, M. B., and, Roth, J. R. 1987. Gene location affects expression level in Salmonella typhimurium. J. Bacteriol. 169:28722875.
98. 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.
99. Sharp, P. M.,, D. C. Shields,, K. H. Wolfe, and, W. H. Li. 1989. Chromosomal location and evolutionary rate variation in enter-obacterial genes. Science 246:808810.
100. 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.
101. Sinden, R. R., and, D. E. Pettijohn. 1981. Chromosomes in living Escherichia coli cells are segregated into domains of super-coiling. Proc. Natl. Acad. Sci. USA 78:224228.
102. Smith, C. L.,, G. Condemine, and, S. Ringquist. 1990. Electro-phoretic analysis of large DNA: application to the structure and dynamics of the Escherichia coli chromosome, p. 205210. In K. Drlica and, M. Roley (eds.), The Bacterial Chromosome. ASM Press, Washington, DC.
103. Snyder, L. A.,, J. K. Davies, and, N. J. Saunders. 2004. Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neis-serial genes associated with minimal mobile elements. BMC Genomics 5:23.
104. Stone, M. D.,, Z. Bryant,, N. J. Crisona,, S. B. Smith,, A. Vologodskii,, C. Bustamante, and, N. R. Cozzarelli. 2003. Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc. Natl. Acad. Sci. USA 100:86548659.
105. Suyama, M., and, P. Bork. 2001. Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet 17:1013.
106. Svetic, R. E.,, C. R. MacCluer,, C. O. Buckley,, K. L. Smythe, and, J. H. Jackson. 2004. A metabolic force for gene clustering. Bull. Math. Biol. 66:559581.
107. Szczepanik, D.,, P. Mackiewicz,, M. Kowalczuk,, A. Gierlik,, A. Nowicka,, M. R. Dudek, and, S. Cebrat. 2001. Evolution rates of genes on leading and lagging DNA strands. J. Mol. Evol. 52:426433.
108. Tamas, I.,, L. Klasson,, B. Canback,, A. K. Naslund,, A. S. Eriksson,, J. J. Wernegreen,, J. P. Sandstrom,, N. A. Moran, and, S. G. Andersson. 2002. 50 million years of genomic stasis in endosym-biotic bacteria. Science 296:23762379.
109. Tettelin, H.,, V. Masignani,, M. J. Cieslewicz,, C. Donati,, D. Medini,, N. L. Ward,, S. V. Angiuoli,, J. Crabtree,, A. L. Jones,, A. S. Durkin, et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.” Proc. Natl. Acad. Sci. USA 102:1395013955.
110. Tillier, E. R., and, R. A. Collins. 2000a. Replication orientation affects the rate and direction of bacterial gene evolution. J. Mol. Evol. 51:459463.
111. Tillier, E. R. M., and, R. A. Collins. 2000b. Genome rearrangement by replication directed translocation. Nat. Genet. 26:184186.
112. Trigueros, S.,, J. Salceda,, I. Bermudez,, X. Fernandez, and, J. J. Roca. 2004. Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. Mol. Biol. 335:723731.
113. Willenbrock, H., and, D. W. Ussery. 2004. Chromatin architecture and gene expression in Escherichia coli. Genome Biol. 5:252.
114. Worning, P.,, L. J. Jensen,, P. F. Hallin,, H. H. Staerfeldt, and, D. W. Ussery. 2006. Origin of replication in circular prokaryotic chromosomes. Environ. Microbiol. 8:353361.
115. Zhou, D.,, Y. Han,, Y. Song,, Z. Tong,, J. Wang,, Z. Guo,, D. Pei,, X. Pang,, J. Zhai,, M. Li, et al. 2004. DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation. J. Bacteriol. 186:51385146.


Generic image for table
Table 1.

Genome balance across bacterial taxa

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
Generic image for table
Table 2.

Density of antibiotic-resistance genes in chromosomes and plasmids c

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12

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