PLPA 608 lecture 1

Bacterium-Host Genomics: BIOMI/PLPA 608
Lecture 10/25/04
Microbial genomics: How, what, why, where, and when

When - some genomics landmarks
1995 Haemophilus influenzae - first bacterium (Fleischmann et al. 1995)
1996 Saccharomyces cerevisiae - first eucaryote (Goffeau et al. 1996)
2000 Arabidopsis - first plant (Initiative 2000)
2000 Xylella fastidiosa - first plant pathogen (excluding viruses) (Simpson et al. 2000)

How
· The shotgun sequencing, assembly, editing, and annotation process pioneered by TIGR and now being applied to Pseudomonas syringae pv. tomato DC3000 (Fleischmann et al. 1995; Fraser et al. 2000; Fouts et al. 2002; Pennisi 2002)
· The debate over the value of complete vs. draft sequences

Why
· Explore pathogenesis in the context of the whole organism
   o nutrition (Schaad et al. 2001)
   o virulence factor redundancy(Parkhill 2002)
   o virulence regulons (Fouts et al. 2002)
   o systems biology (Oltvai and Barabasi 2002)
· Blueprint for high throughput hypothesis testing
· Explore virulence mechanisms in the context of a web of information on model organisms and proteins (Greenbaum et al. 2001)
· Explore pathogenesis in the context of new paradigms in microbiology:
   o More accurate phylogeny (Preston et al. 1998; Brown et al. 2001)
   o Minimal genome concept (Hutchison et al. 1999; Koonin 2003)
   o Core genome concept (Boucher et al. 2001)
   o Surprising plasticity among closely related bacteria (Dobrindt and Hacker 2001)
   o Importance of horizontal gene transfer and pathogenicity islands (Hacker and Kaper 2000; Kim and Alfano 2002)
   o Redefining concepts of virulence in the genomics era (Wassenaar and Gaastra 2001)
· Challenges we continue to face, e.g., citrus canker (Schubert et al. 2001; Graham et al. 2004)

Where
· TIGR (Comprehensive Microbial Resource)(Peterson et al. 2001)
· Sanger Centre (England)
· Joint Genome Institute (JGI) of DOE
· NCBI (GenBank, Entrez, PubMed, and many other resources)
· Updated list of all databases (Galperin 2004)

What
The list of completed, draft, and pending bacterial genome projects is growing exponentially. For an updated list of plant pathogen projects, see Puhler et al. (Puhler et al. 2004) or http://www.tigr.org/~vinita/PPwebpage.html.

Assignments:
· Read:
   o Fraser, C. M., Eisen, J. A., and Salzberg, S. L. 2000. Microbial genome sequencing. Nature 406:799-803.
   o Parkhill, J. 2002. The importance of complete genome sequences. Trends Microbiol 10:219-20 and the associate response letter.
   o Wassenaar, T. M., and Gaastra, W. 2001. Bacterial virulence: can we draw the line? FEMS Microbiol. Lett. 201:1-7.
· Explore the tools in the TIGR CMR, using the Pseudomonas syringae pv. tomato DC3000 genome as an example.

Bacterium-Host Genomics: BIOMI/PLPA 608
Lecture 10/25/04

References:

Boucher, Y., Nesbo, C. L., and Doolittle, W. F. 2001. Microbial genomes: dealing with diversity. Curr. Opin. Microbiol. 4:285-289.

Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E., and Stanhope, M. J. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:281-5.

Dobrindt, U., and Hacker, J. 2001. Whole genome plasticity in pathogenic bacteria. Curr. Opin. Microbiol. 4:550-557.

Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M., and et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.

Fouts, D. E., Abramovitch, R. B., Alfano, J. R., Baldo, A. M., Buell, C. R., Cartinhour, S., Chatterjee, A. K., D'Ascenzo, M., Gwinn, M. L., Lazarowitz, S. G., Lin, N.-C., Martin, G. B., Rehm, A. H., Schneider, D. J., van Dijk, K., Tang, X., and Collmer, A. 2002. Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl. Acad. Sci. USA 99:2275-2280.

Fraser, C. M., Eisen, J. A., and Salzberg, S. L. 2000. Microbial genome sequencing. Nature 406:799-803.

Galperin, M. Y. 2004. The Molecular Biology Database Collection: 2004 update. Nucleic Acids Res 32 Database issue:D3-22.

Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P., Tettelin, H., and Oliver, S. G. 1996. Life with 6000 genes. Science 274:546, 563-7.

Graham, J. H., Gottwald, T. R., Cubero, J., and Achor, D. S. 2004. Xanthomonas axonopodis pv. citri: factors affecting successful eradication of citrus canker. Mol. Plant Pathol. 5:1-15.

Greenbaum, D., Luscombe, N. M., Jansen, R., Qian, J., and Gerstein, M. 2001. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res 11:1463-8.

Hacker, J., and Kaper, J. B. 2000. Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641-679.

Hutchison, C. A., Peterson, S. N., Gill, S. R., Cline, R. T., White, O., Fraser, C. M., Smith, H. O., and Venter, J. C. 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165-9.

Initiative, T. A. G. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. The Arabidopsis Genome Initiative. Nature 408:796-815.

Kim, J. F., and Alfano, J. R. 2002. Pathogenicity islands and virulence plasmids of bacterial plant pathogens. Curr. Topic Microbiol. Immunol. 264/2:127-147.

Koonin, E. V. 2003. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1:127-36.

Oltvai, Z. N., and Barabasi, A. L. 2002. Systems biology. Life's complexity pyramid. Science 298:763-4.

Parkhill, J. 2002. The importance of complete genome sequences. Trends Microbiol 10:219-20.

Pennisi, E. 2002. Claire Fraser profile. TIGR's chief: results without the roar. Science 296:1957-8.

Peterson, J. D., Umayam, L. A., Dickinson, T., Hickey, E. K., and White, O. 2001. The Comprehensive Microbial Resource. Nucleic Acids Res 29:123-5.

Preston, G. M., Haubold, B., and Rainey, P. B. 1998. Bacterial genomics and adaptation to life on plants: implications for the evolution of pathogenicity and symbiosis. Curr. Opin. Microbiol. 1:589-597.

Puhler, A., Arlat, M., Becker, A., Gottfert, M., Morrissey, J. P., and O'Gara, F. 2004. What can bacterial genome research teach us about bacteria-plant interactions? Curr Opin Plant Biol 7:137-47.

Schaad, N. W., Jones, J. B., and Chun, W. 2001. Laboratory Guide for the Identification of Plant Pathogenic Bacteria, Third Edition. APS Press, St. Paul.

Schubert, T. S., Rizvi, S. A., Sun, X., Gottwald, T. R., Graham, J. H., and Dixon, W. N. 2001. Meeting the challenge of eradicating citrus canker in Florida--again. Plant Disease 85:340-356.

Simpson, A. J. G., Reinach, F. C., Arruda, P., Abreu, F. A., Acencio, M., Avarenga, R., Alves, L. M., Araya, J. E., Baia, G. S., and Baptista, C. S., et al. 2000. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406:151-157.

Wassenaar, T. M., and Gaastra, W. 2001. Bacterial virulence: can we draw the line? FEMS Microbiol. Lett. 201:1-7.

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