1887

Chapter 20 : Mechanisms of Variation in Microbial Pathogenesis

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
Zoomout

Mechanisms of Variation in Microbial Pathogenesis, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815639/9781555814144_Chap20-1.gif /docserver/preview/fulltext/10.1128/9781555815639/9781555814144_Chap20-2.gif

Abstract:

Variation that occurs in pathogens is based firmly upon one of three prime mechanisms of genetic variability: point mutations, genetic rearrangements, or lateral gene transfer (LGT). As LGT recently has been the focus of significant new insights into pathogen evolution it will be highlighted in this chapter. The intensive sequencing of microbial genomes and the comparisons made among them expanded our understanding of the scope of LGT in bacterial gene evolution. The main distinction is that the environment and ecology of pathogens is played out within another living organism-the host. The pan-genome represents the most accessible set of building blocks available for use in LGT. In the current environment, however, the widespread selective adaptation has spread because antibiotics are added to everything from cutting boards to cattle feed. The discussion of pathogenic gene content, style, and core distribution is intimately linked to the problem of defining both the species in bacteria and the events most likely to lead to new speciation. Multilocus sequence typing (MLST) involves the sampling of DNA sequences for a subset of housekeeping genes and the assessing of alleles for the purpose of studying the extent of recombination. LGT can cause shifts in the immediate pathogenesis of a clonally evolving group such as the clonal complex. The chapter reviews the way in which LGT has been an architect in the virulence, the genes, the genome, and the pan-genome of pathogens.

Citation: Hollingshead S. 2008. Mechanisms of Variation in Microbial Pathogenesis, p 221-229. 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.ch20
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1.
Figure 1.

The pan-genome. The set of all genes within all members of a species is known as the pan-genome. It contains core genes and noncore genes. The noncore for the species is larger than shown here and bigger than the core. Within the core are sets of genes that are shared with the strain, the species, the genus, and all bacteria (hard core).

Citation: Hollingshead S. 2008. Mechanisms of Variation in Microbial Pathogenesis, p 221-229. 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.ch20
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815639.ch20
1. Aertsen, A., and, C. W. Michiels. 2005. Diversify or die: generation of diversity in response to stress. Crit. Rev. Microbiol. 31:6978.
2. Aras, R. A.,, J. Kang,, A. I. Tschumi,, Y. Harasaki, and, M. J. Blaser. 2003. Extensive repetitive DNA facilitates prokaryotic genome plasticity. Proc. Natl. Acad. Sci. USA 100:1357913584.
3. Arber, W. 2000. Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol. Rev. 24:17.
4. Baquero, F. 2004. From pieces to patterns: evolutionary engineering in bacterial pathogens. Nat. Rev. 2:510518.
5. Bayliss, C. D.,, D. Field, and, E. R. Moxon. 2001. The simple sequence contingency loci of Haemophilus influenzae and Neisseria meningitidis. J. Clin. Invest. 107:657662.
6. Charlebois, R. L., and, W. F. Doolittle. 2004. Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res. 14:24692477.
7. Claverys, J. P.,, M. Prudhomme,, I. Mortier-Barriere, and, B. Martin. 2000. Adaptation to the environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity? Mol. Microbiol. 35:251259.
8. Cohan, F. M. 2006. Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philos. Trans. R. Soc. London 361:19851996.
9. Cohan, F. M. 2002. What are bacterial species? Ann. Rev. Microbiol. 56:457487.
10. Deitsch, K. W.,, E. R. Moxon, and, T. E. Wellems. 1997. Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections. Microbiol. Mol. Biol. Rev. 61:281293.
11. Feil, E. J.,, M. C. Enright, and, B. G. Spratt. 2000a. Estimating the relative contributions of mutation and recombination to clonal diversification: a comparison between Neisseria meningitidis and Streptococcus pneumoniae. Res. Microbiol. 151:465469.
12. Feil, E. J., and, M. C. Enright. 2004. Analyses of clonality and the evolution of bacterial pathogens. Curr. Opin. Microbiol. 7:308313.
13. Feil, E. J.,, M. C. Maiden,, M. Achtman, and, B. G. Spratt. 1999. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol. Biol. Evol. 16:14961502.
14. Feil, E. J.,, J. M. Smith,, M. C. Enright, and, B. G. Spratt. 2000b. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:14391450.
15. Field, D.,, M. O. Magnasco,, E. R. Moxon,, D. Metzgar,, M. M. Tanaka,, C. Wills, et al. 1999. Contingency loci, mutator alleles, and their interactions. Synergistic strategies for microbial evolution and adaptation in pathogenesis. Ann. N. Y. Acad. Sci. 870:378382.
16. Fuda, C. C.,, J. F. Fisher, and, S. Mobashery. 2005. Beta-lactam resistance in Staphylococcus aureus: the adaptive resistance of a plastic genome. Cell. Mol. Life Sci. 62:26172633.
17. Gevers, D.,, F. M. Cohan,, J. G. Lawrence,, B. G. Spratt,, T. Coenye,, E. J. Feil, et al. 2005. Opinion: re-evaluating prokaryotic species. Nat. Rev. 3:733739.
18. Godreuil, S.,, F. Cohan,, H. Shah, and, M. Tibayrenc. 2005. Which species concept for pathogenic bacteria? An E-Debate. Infect. Genet. Evol. 5:375387.
19. Gordon, V. M.,, K. R. Klimpel,, N. Arora,, M. A. Henderson, and, S. H. Leppla. 1995. Proteolytic activation of bacterial toxins by eukaryotic cells is performed by furin and by additional cellular proteases. Infect. Immun. 63:8287.
20. Hacker, J.,, G. Blum-Oehler,, I. Muhldorfer, and, H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:10891097.
21. Hanage, W. P.,, C. Fraser, and, B. G. Spratt. 2006. The impact of homologous recombination on the generation of diversity in bacteria. J. Theor. Biol. 239:210219.
22. Hanage, W. P.,, T. Kaijalainen,, E. Herva,, A. Saukkoriipi,, R. Syrjanen, and, B. G. Spratt. 2005. Using multilocus sequence data to define the pneumococcus. J. Bacteriol. 187:62236230.
23. Hollingshead, S. K. 2001. Mosaic proteins, not reinventing the wheel. In M. Syvannen, and, C. I. Kado (ed.), Horizontal Gene Transfer, 2nd ed. Academic Press, London, United Kingdom.
24. Jain, R.,, M. C. Rivera,, J. E. Moore, and, J. A. Lake. 2002. Horizontal gene transfer in microbial genome evolution. Theor. Popul. Biol. 61:489495.
25. Kang, J., and, M. J. Blaser. 2006. Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori. Nat. Rev. 4:826836.
26. Karlin, S.,, J. Mrazek, and, A. J. Gentles. 2003. Genome comparisons and analysis. Curr. Opin. Struct. Biol. 13:344352.
27. Karlin, S. 1998. Global dinucleotide signatures and analysis of genomic heterogeneity. Curr. Opin. Microbiol. 1:598610.
28. Konstantinidis, K. T.,, A. Ramette, and, J. M. Tiedje. 2006. The bacterial species definition in the genomic era. Philos. Trans. R. Soc. London 361:19291940.
29. Konstantinidis, K. T., and, J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Nat. Acad. Sci. USA 102:25672572.
30. Lawrence, J. G.,, D. L. Hartl, and, H. Ochman. 1991. Molecular considerations in the evolution of bacterial genes. J. Mol. Evol. 33:241250.
31. Lawrence, J. G., and, H. Hendrickson. 2005. Genome evolution in bacteria: order beneath chaos. Curr. Opin. Microbiol. 8:572578.
32. Lawrence, J. G., and, H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:94139417.
33. Lawrence, J. G. 2001. Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Syst. Biol. 50:479496.
34. Lawrence, J. G. 1999. Gene transfer, speciation, and the evolution of bacterial genomes. Curr. Opin. Microbiol. 2:519523.
35. Lawrence, J. G. 2005. Horizontal and vertical gene transfer: the life history of pathogens. Contrib. Microbiol. 12:255271.
36. Maiden, M. C.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Urwin, et al. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:31403145.
37. Majewski, J.,, P. Zawadzki,, P. Pickerill,, F. M. Cohan, and, C. G. Dowson. 2000. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182:10161023.
38. Marraffini, L. A.,, A. C. Dedent, and, O. Schneewind. 2006. Sortases and the art of anchoring proteins to the envelopes of gram-positive bacteria. Microbiol. Mol. Biol. Rev. 70:192221.
39. Medini, D.,, C. Donati,, H. Tettelin,, V. Masignani, and, R. Rappuoli. 2005. The microbial pan-genome. Curr. Opin. Genet. Dev. 15:589594.
40. Merrell, D. S.,, S. M. Butler,, F. Qadri,, N. A. Dolganov,, A. Alam,, M. B. Cohen, et al. 2002. Host-induced epidemic spread of the cholera bacterium. Nature 417:642645.
41. Morschhauser, J.,, G. Kohler,, W. Ziebuhr,, G. Blum-Oehler,, U. Dobrindt, and, J. Hacker. 2000. Evolution of microbial pathogens. Philos. Trans. R. Soc. London 355:695704.
42. Mortier-Barriere, I.,, O. Humbert,, B. Martin,, M. Prudhomme, and, J. P. Claverys. 1997. Control of recombination rate during transformation of Streptococcus pneumoniae: an overview. Microb. Drug Resist. 3:233242.
43. Moszer, I.,, E. P. Rocha, and, A. Danchin. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2:524528.
44. Moxon, E. R.,, P. B. Rainey,, M. A. Nowak, and, R. E. Lenski. 1994. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4:2433.
45. Moxon, R.,, C. Bayliss, and, D. Hood. 2006. Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation. Ann. Rev. Genet. 40:307333.
46. Nakamura, Y.,, T. Itoh,, H. Matsuda, and, T. Gojobori. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36:760766.
47. Ochman, H.,, J. G. Lawrence, and, E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299304.
48. Pascal, G.,, C. Medigue, and, A. Danchin. 2006. Persistent biases in the amino acid composition of prokaryotic proteins. Bioessays 28:726738.
49. Rayssiguier, C.,, D. S. Thaler, and, M. Radman. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396401.
50. Saunders, N. J.,, J. F. Peden,, D. W. Hood, and, E. R. Moxon. 1998. Simple sequence repeats in the Helicobacter pylori genome. Mol. Microbiol. 27:10911098.
51. Silverman, M.,, J. Zieg,, M. Hilmen, and, M. Simon. 1999. Phase variation in Salmonella: genetic analysis of a recombinational switch. Proc. Natl. Acad. Sci. USA 76:391395.
52. Smith, J. M.,, N. H. Smith,, M. O’Rourke, and, B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:43844388.
53. Snel, B.,, P. Bork, and, M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108110.
54. Snel, B.,, P. Bork, and, M. A. Huynen. 2002. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 12:1725.
55. Spratt, B. G.,, W. P. Hanage, and, E. J. Feil. 2001. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr. Opin. Microbiol. 4:602606.
56. Spratt, B. G.,, J. T. Staley, and, M. C. Fisher. 2006. Introduction: species and speciation in microorganisms. Philos. Trans. R. Soc. London 361:18971898.
57. Staley, J. T. 2006. The bacterial species dilemma and the genomicphylogenetic species concept. Philos. Trans. R. Soc. London 361:18991909.
58. Syvanen, M., and, C. I. Kado. 2002. Horizontal Gene Transfer, 2nd ed. Academic Press, San Diego, CA.
59. Tettelin, H.,, V. Masignani,, M. J. Cieslewicz,, C. Donati,, D. Medini,, N. L. Ward, 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.
60. Thomas, G. 2002. Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat. Rev. Mol. Cell. Biol. 3:753766.
61. Vetsigian, K., and, N. Goldenfeld. 2005. Global divergence of microbial genome sequences mediated by propagating fronts. Proc. Natl. Acad. Sci. USA 102:73327337.
62. Vulic, M.,, F. Dionisio,, F. Taddei, and, M. Radman. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Sci. USA 94:97639767.
63. Welch, R. A.,, V. Burland,, G. Plunkett, III,, P. Redford,, P. Roesch,, D. Rasko, et al. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:1702017024.

Tables

Generic image for table
Table 1.

Distribution of genes within the pan-genome

Citation: Hollingshead S. 2008. Mechanisms of Variation in Microbial Pathogenesis, p 221-229. 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.ch20
Generic image for table
Table 2.

Elements of pathogen style relating to the effect of lateral gene transfer

Citation: Hollingshead S. 2008. Mechanisms of Variation in Microbial Pathogenesis, p 221-229. 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.ch20

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