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. 2000 Sep-Oct;6(5):496–504. doi: 10.3201/eid0605.000509

Genomics and bacterial pathogenesis.

G M Weinstock 1
PMCID: PMC2627964  PMID: 10998381

Abstract

Whole-genome sequencing is transforming the study of pathogenic bacteria. Searches for single virulence genes can now be performed on a genomewide scale by a variety of computer and genetic techniques. These techniques are discussed to provide a perspective on the developing field of genomics.

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Selected References

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  1. Akerley B. J., Rubin E. J., Camilli A., Lampe D. J., Robertson H. M., Mekalanos J. J. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8927–8932. doi: 10.1073/pnas.95.15.8927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Andersson S. G., Zomorodipour A., Andersson J. O., Sicheritz-Pontén T., Alsmark U. C., Podowski R. M., Näslund A. K., Eriksson A. S., Winkler H. H., Kurland C. G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 1998 Nov 12;396(6707):133–140. doi: 10.1038/24094. [DOI] [PubMed] [Google Scholar]
  5. Barry M. A., Lai W. C., Johnston S. A. Protection against mycoplasma infection using expression-library immunization. Nature. 1995 Oct 19;377(6550):632–635. doi: 10.1038/377632a0. [DOI] [PubMed] [Google Scholar]
  6. Blattner F. R., Plunkett G., 3rd, Bloch C. A., Perna N. T., Burland V., Riley M., Collado-Vides J., Glasner J. D., Rode C. K., Mayhew G. F. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453–1462. doi: 10.1126/science.277.5331.1453. [DOI] [PubMed] [Google Scholar]
  7. Chiang S. L., Mekalanos J. J. Use of signature-tagged transposon mutagenesis to identify Vibrio cholerae genes critical for colonization. Mol Microbiol. 1998 Feb;27(4):797–805. doi: 10.1046/j.1365-2958.1998.00726.x. [DOI] [PubMed] [Google Scholar]
  8. Claros M. G., Brunak S., von Heijne G. Prediction of N-terminal protein sorting signals. Curr Opin Struct Biol. 1997 Jun;7(3):394–398. doi: 10.1016/s0959-440x(97)80057-7. [DOI] [PubMed] [Google Scholar]
  9. Corpet F., Gouzy J., Kahn D. Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res. 1999 Jan 1;27(1):263–267. doi: 10.1093/nar/27.1.263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Darwin A. J., Miller V. L. Identification of Yersinia enterocolitica genes affecting survival in an animal host using signature-tagged transposon mutagenesis. Mol Microbiol. 1999 Apr;32(1):51–62. doi: 10.1046/j.1365-2958.1999.01324.x. [DOI] [PubMed] [Google Scholar]
  11. Edelstein P. H., Edelstein M. A., Higa F., Falkow S. Discovery of virulence genes of Legionella pneumophila by using signature tagged mutagenesis in a guinea pig pneumonia model. Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):8190–8195. doi: 10.1073/pnas.96.14.8190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  13. Fraser C. M., Gocayne J. D., White O., Adams M. D., Clayton R. A., Fleischmann R. D., Bult C. J., Kerlavage A. R., Sutton G., Kelley J. M. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. doi: 10.1126/science.270.5235.397. [DOI] [PubMed] [Google Scholar]
  14. Henikoff J. G., Henikoff S., Pietrokovski S. New features of the Blocks Database servers. Nucleic Acids Res. 1999 Jan 1;27(1):226–228. doi: 10.1093/nar/27.1.226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Henikoff S., Henikoff J. G. Protein family classification based on searching a database of blocks. Genomics. 1994 Jan 1;19(1):97–107. doi: 10.1006/geno.1994.1018. [DOI] [PubMed] [Google Scholar]
  16. Hensel M., Shea J. E., Gleeson C., Jones M. D., Dalton E., Holden D. W. Simultaneous identification of bacterial virulence genes by negative selection. Science. 1995 Jul 21;269(5222):400–403. doi: 10.1126/science.7618105. [DOI] [PubMed] [Google Scholar]
  17. Hensel M. Whole genome scan for habitat-specific genes by signature-tagged mutagenesis. Electrophoresis. 1998 Apr;19(4):608–612. doi: 10.1002/elps.1150190425. [DOI] [PubMed] [Google Scholar]
  18. Herrmann R., Reiner B. Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species. Curr Opin Microbiol. 1998 Oct;1(5):572–579. doi: 10.1016/s1369-5274(98)80091-x. [DOI] [PubMed] [Google Scholar]
  19. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B. C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 1996 Nov 15;24(22):4420–4449. doi: 10.1093/nar/24.22.4420. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Himmelreich R., Plagens H., Hilbert H., Reiner B., Herrmann R. Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res. 1997 Feb 15;25(4):701–712. doi: 10.1093/nar/25.4.701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hood D. W., Deadman M. E., Jennings M. P., Bisercic M., Fleischmann R. D., Venter J. C., Moxon E. R. DNA repeats identify novel virulence genes in Haemophilus influenzae. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):11121–11125. doi: 10.1073/pnas.93.20.11121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Johnston S. A., Barry M. A. Genetic to genomic vaccination. Vaccine. 1997 Jun;15(8):808–809. doi: 10.1016/s0264-410x(96)00276-9. [DOI] [PubMed] [Google Scholar]
  23. Kalman S., Mitchell W., Marathe R., Lammel C., Fan J., Hyman R. W., Olinger L., Grimwood J., Davis R. W., Stephens R. S. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat Genet. 1999 Apr;21(4):385–389. doi: 10.1038/7716. [DOI] [PubMed] [Google Scholar]
  24. Lai W. C., Bennett M., Johnston S. A., Barry M. A., Pakes S. P. Protection against Mycoplasma pulmonis infection by genetic vaccination. DNA Cell Biol. 1995 Jul;14(7):643–651. doi: 10.1089/dna.1995.14.643. [DOI] [PubMed] [Google Scholar]
  25. Lehoux D. E., Sanschagrin F., Levesque R. C. Defined oligonucleotide tag pools and PCR screening in signature-tagged mutagenesis of essential genes from bacteria. Biotechniques. 1999 Mar;26(3):473-8, 480. doi: 10.2144/99263st02. [DOI] [PubMed] [Google Scholar]
  26. Link A. J., Phillips D., Church G. M. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol. 1997 Oct;179(20):6228–6237. doi: 10.1128/jb.179.20.6228-6237.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. McClelland M., Wilson R. K. Comparison of sample sequences of the Salmonella typhi genome to the sequence of the complete Escherichia coli K-12 genome. Infect Immun. 1998 Sep;66(9):4305–4312. doi: 10.1128/iai.66.9.4305-4312.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Mei J. M., Nourbakhsh F., Ford C. W., Holden D. W. Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature-tagged mutagenesis. Mol Microbiol. 1997 Oct;26(2):399–407. doi: 10.1046/j.1365-2958.1997.5911966.x. [DOI] [PubMed] [Google Scholar]
  29. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997 Jan;10(1):1–6. doi: 10.1093/protein/10.1.1. [DOI] [PubMed] [Google Scholar]
  30. Rost B., Fariselli P., Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 1996 Aug;5(8):1704–1718. doi: 10.1002/pro.5560050824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Rost B. PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol. 1996;266:525–539. doi: 10.1016/s0076-6879(96)66033-9. [DOI] [PubMed] [Google Scholar]
  32. Rubin E. J., Akerley B. J., Novik V. N., Lampe D. J., Husson R. N., Mekalanos J. J. In vivo transposition of mariner-based elements in enteric bacteria and mycobacteria. Proc Natl Acad Sci U S A. 1999 Feb 16;96(4):1645–1650. doi: 10.1073/pnas.96.4.1645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Saunders N. J., Peden J. F., Hood D. W., Moxon E. R. Simple sequence repeats in the Helicobacter pylori genome. Mol Microbiol. 1998 Mar;27(6):1091–1098. doi: 10.1046/j.1365-2958.1998.00768.x. [DOI] [PubMed] [Google Scholar]
  34. Smith V., Botstein D., Brown P. O. Genetic footprinting: a genomic strategy for determining a gene's function given its sequence. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6479–6483. doi: 10.1073/pnas.92.14.6479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Smith V., Chou K. N., Lashkari D., Botstein D., Brown P. O. Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science. 1996 Dec 20;274(5295):2069–2074. doi: 10.1126/science.274.5295.2069. [DOI] [PubMed] [Google Scholar]
  36. Stephens R. S., Kalman S., Lammel C., Fan J., Marathe R., Aravind L., Mitchell W., Olinger L., Tatusov R. L., Zhao Q. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science. 1998 Oct 23;282(5389):754–759. doi: 10.1126/science.282.5389.754. [DOI] [PubMed] [Google Scholar]
  37. Taylor R. K., Miller V. L., Furlong D. B., Mekalanos J. J. Use of phoA gene fusions to identify a pilus colonization factor coordinately regulated with cholera toxin. Proc Natl Acad Sci U S A. 1987 May;84(9):2833–2837. doi: 10.1073/pnas.84.9.2833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Weinstock G. M., Hardham J. M., McLeod M. P., Sodergren E. J., Norris S. J. The genome of Treponema pallidum: new light on the agent of syphilis. FEMS Microbiol Rev. 1998 Oct;22(4):323–332. doi: 10.1111/j.1574-6976.1998.tb00373.x. [DOI] [PubMed] [Google Scholar]
  39. Wong R. M., Wong K. K., Benson N. R., McClelland M. Sample sequencing of a Salmonella typhimurium LT2 lambda library: comparison to the Escherichia coli K12 genome. FEMS Microbiol Lett. 1999 Apr 15;173(2):411–423. doi: 10.1111/j.1574-6968.1999.tb13533.x. [DOI] [PubMed] [Google Scholar]

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