Genomics of Bacterium-Host Interactions: BIOMI/PLPA 6080
Lecture 10/6/10
Genome Structure
1. Genome sequencing has revealed surprising variations in pathogen genome structure (Bentley and
Parkhill 2004).
2. Pathogen genome sizes reflect pathogen lifestyle (e.g., obligate versus facultative association with
host) (Bentley and Parkhill 2004).
3. The percentage of regulatory genes increases with bacterial genome size (Stover et al. 2000).
4. Multiple processes enable the gain and loss of genes in a bacterial genome, and gene loss is also
important in pathogen evolution, as exemplified by Yersinia pestis (Abby and Daubin 2007).
5. Multiple classes of mobile genetic elements carry virulence genes (Pallen and Wren 2007).
6. Genomic islands can be identified in multiple ways (Dobrindt et al. 2004; Langille et al. 2008).
7. Genomic islands have several typical structural features, and the subset of GIs known as
pathogenicity islands may encode functional virulence system modules and possess additional
structural complexities (Alfano et al. 2000; Dobrindt et al. 2004; Gal-Mor and Finlay 2006).
8. Excision of the PPHGI-1 genomic island from Pseudomonas syringae pv. phaseolicola in bean leaves
carrying a resistance (R) gene that detects PPHGI-1-encoded AvrPphB provides an example of rapid
pathogen evolution (Pitman et al. 2005).
9. Identification of genomic islands in a pathogen provides a roadmap to regions likely to harbor
virulence genes (Lindeberg et al. 2008).
10. Simple sequence DNA repeats in contingency loci promote hypermutation through polymerase
slippage and thereby generate high levels of phenotypic variation in pathogen populations in the face
of host defenses (Medini et al. 2008; Moxon et al. 2006).
11. The pan-genome of some bacteria, such as Streptococcus agalactiae, may be extremely large
(Medini et al. 2005).
12. Ecological and genetic diversity (driven largely by horizontal gene transfer) within bacterial species
challenges the concept and convention of species designations, but genomics brings new
perspectives and a new “gold standard” to this issue (Didelot and Maiden 2010; Doolittle and Papke
2006; Konstantinidis et al. 2006; Richter and Rossello-Mora 2009).
References
Abby, S., and Daubin, V. 2007. Comparative genomics and the evolution of prokaryotes. Trends Microbiol
15:135-41.
Alfano, J. R., Charkowski, A. O., Deng, W.-L., Badel, J. L., Petnicki-Ocwieja, T., van Dijk, K., and Collmer,
A. 2000. The Pseudomonas syringae Hrp pathogenicity island has a tripartite mosaic structure
composed of a cluster of type III secretion genes bounded by exchangeable effector and
conserved effector loci that contribute to parasitic fitness and pathogenicity in plants. Proc. Natl.
Acad. Sci. USA 97:4856-4861.
Bentley, S. D., and Parkhill, J. 2004. Comparative genomic structure of prokaryotes. Annu Rev Genet
38:771-92.
Didelot, X., and Maiden, M. C. 2010. Impact of recombination on bacterial evolution. Trends Microbiol
18:315-22.
Dobrindt, U., Hochhut, B., Hentschel, U., and Hacker, J. 2004. Genomic islands in pathogenic and
environmental microorganisms. Nat Rev Microbiol 2:414-424.
Doolittle, W. F., and Papke, R. T. 2006. Genomics and the bacterial species problem. Genome Biol
7:116.
Gal-Mor, O., and Finlay, B. B. 2006. Pathogenicity islands: a molecular toolbox for bacterial virulence.
Cell Microbiol 8:1707-19.
Konstantinidis, K. T., Ramette, A., and Tiedje, J. M. 2006. The bacterial species definition in the genomic
era. Philos Trans R Soc Lond B Biol Sci 361:1929-40.
Langille, M. G., Hsiao, W. W., and Brinkman, F. S. 2008. Evaluation of genomic island predictors using a
comparative genomics approach. BMC Bioinformatics 9:329.
Lindeberg, M., Myers, C. R., Collmer, A., and Schneider, D. J. 2008. Roadmap to new virulence
determinants in Pseudomonas syringae: Insights from comparative genomics and genome
organization. Mol. Plant-Microbe Interact. 21:685-700.
Medini, D., Donati, C., Tettelin, H., Masignani, V., and Rappuoli, R. 2005. The microbial pan-genome.
Curr Opin Genet Dev 15:589-94.
Medini, D., Serruto, D., Parkhill, J., Relman, D. A., Donati, C., Moxon, R., Falkow, S., and Rappuoli, R.
2008. Microbiology in the post-genomic era. Nat Rev Microbiol 6:419-30.
Moxon, R., Bayliss, C., and Hood, D. 2006. Bacterial contingency loci: the role of simple sequence DNA
repeats in bacterial adaptation. Annu Rev Genet 40:307-33.
Pallen, M. J., and Wren, B. W. 2007. Bacterial pathogenomics. Nature 449:835-842.
Pitman, A. R., Jackson, R. W., Mansfield, J. W., Kaitell, V., Thwaites, R., and Arnold, D. L. 2005.
Exposure to host resistance mechanisms drives evolution of bacterial virulence in plants. Curr.
Biol. 15:2230-2235.
Richter, M., and Rossello-Mora, R. 2009. Shifting the genomic gold standard for the prokaryotic species
definition. Proc Natl Acad Sci U S A 106:19126-31.
Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S.,
Hufnagle, W. O., Kowalik, D. J., Lagrou, M., Garber, R. L., Goltry, L., Tolentino, E., WestbrockWadman, S., Yuan, Y., Brody, L. L., Coulter, S. N., Folger, K. R., Kas, A., Larbig, K., Lim, R.,
Smith, K., Spencer, D., Wong, G. K., Wu, Z., and Paulsen, I. T. 2000. Complete genome
sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.