Sequencing microbial genomes - What will it do for microbiology?

Journal of Medical Microbiology

Volumn 47, Issue 5, 1998, Pages 375-382

  Jenks, P J ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; BACTERIAL VACCINE;

BACTERIAL INFECTION; BACTERIAL VIRULENCE; BACTERIUM MUTANT; DATA BASE; DNA SEQUENCE; ESCHERICHIA COLI; GENOME; HAEMOPHILUS INFLUENZAE; HELICOBACTER PYLORI; MICROBIOLOGY; MUTAGENESIS; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; RECOMBINANT DNA TECHNOLOGY; REVIEW; SALMONELLA;

HAEMOPHILUS INFLUENZAE;

EID: 0031944844     PISSN: 00222615     EISSN: None     Source Type: Journal    
DOI: 10.1099/00222615-47-5-375     Document Type: Review

References (43)

1. Sanger F, Air GM, Barrell BG et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 1977; 265: 687-695.
2. Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB. Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol 1982; 162: 729-773.
3. Bankier AT, Beck S, Bohni R et al. The DNA sequence of the human cytomegalovirus genome. DNA Seq 1991; 2: 1-12.
4. Goebel SJ, Johnson GP, Perkus ME, Davis SW, Winslow JP, Paoletti E. The complete DNA sequence of vaccinia virus. Virology 1990; 179: 247-266.
5. Massung RF, Esposito JJ, Liu L et al. Potential virulence determinants in terminal regions of variola smallpox virus genome. Nature 1993; 366: 748-751.
6. Adams MD, Kelly JM, Gocayne JD et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991; 252: 1651-1656.
7. Adams MD, Dubnick M, Kervalage AR et al. Sequence identification of 2,375 human brain genes. Nature 1992; 355: 632-634.
8. Fleischmann RD, Adams MD, White O et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995; 269: 496-512.
9. Davies JE. Redundant genome sequencing? Science 1996; 273: 1155.
10. Strauss EJ, Falkow F. Microbial pathogenesis: genomics and beyond. Science 1997; 276: 707-712.
11. Hood DW, Deadman ME, Allen T et al. Use of the complete genome sequence information of Haemophilus influenzae strain Rd to investigate lipopolysaccharide biosynthesis. Mol Microbiol 1996; 22: 951-965.
12. Hood DW, Deadman ME, Jennings MP et al. DNA repeats identify novel virulence genes in Haemophilus influenzae. Proc Natl Acad Sci USA 1996; 93: 11121-11125.
13. Hacker J, Blum-Oehler G, Mühldorfer I, Tschäpe H. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 1997; 23: 1089-1097.
14. Mushegian AR, Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 1996; 93: 10268-10273.
15. Tomb J-F, White O, Kerlavage AR et al. The complete genome sequence of the gastric pathogen Helicobacter priori. Nature 1997; 388: 539-547.
16. Blattner FR, Plunkett G, Block CA et al. The complete genome sequence of Escherichia coli K-12. Science 1997; 277: 1453-1462.
17. Fraser CM, Gocayne JD, White O et al. The minimal gene complement of Mycoplasma genitalium. Science 1995; 270: 397-403.
18. Bull CJ, White O, Olsen GJ et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996; 273: 1058-1073.
19. Hensel M, Shea JE, Gleeson C, Jones MD, Dalton E, Holden DW. Simultaneous identification of bacterial virulence genes by negative selection. Science 1995; 269: 400-403.
20. Shea JE, Hensel M, Gleeson C, Holden DW. Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Proc Natl Acad Sci USA 1996; 93: 2593-2597.
21. Mahan MJ, Slauch JM, Mekalanos JJ. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 1993; 259: 686-688.
22. Wang J, Mushegian A, Lory S, Jin S. Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection. Proc Natl Acad Sci USA 1996; 93: 10434-10439.
23. Wang J, Lory S, Ramphal R, Jin S. Isolation and characterization of Pseudomonas aeruginosa genes inducible by respiratory mucus derived from cystic fibrosis patients. Mol Microbiol 1996; 22: 1005-1012.
24. Valdivia RH, Falkow S. Bacterial genetics by flow cytometry: rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction. Mol Microbiol 1996; 22: 367-378.
25. Buchmeier NA, Heffron F. Induction of Salmonella stress proteins upon infection of macrophages. Science 1990; 248: 730-732.
26. McGowen CC, Necheva AS, Cover TL, Blaser MJ. Acid-induced expression of oxidative stress protein homologs in Helicobacter pylori. In: Abstracts of the 97th General Meeting of the American Society for Microbiology 1997. Washington, DC, American Society for Microbiology. 1997: 38.
27. McGowan CC, Cover TL, Blaser MJ. Helicobacter pylori and gastric acid: biological and therapeutic implications. Gastroenterology 1996; 110: 926-938.
28. Liang P, Pardee AB. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 1992; 257: 967-971.
29. Wong KK, McClelland M. Stress-inducible gene of Salmonella typhimurium identified by arbitrary primer PCR of RNA. Proc Natl Acad Sci USA 1994; 91: 639-643.
30. Lockhart DJ, Dong H, Byrne MC et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotech 1996; 14: 1675-1680.
31. Southern EM. DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale. Trends Genet 1996; 12: 110-115.
32. Fodor SPA, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991; 251: 767-773.
33. Southern EM, Maskos U, Elder JK. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 1992; 13: 1008-1017.
34. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995; 270: 467-470.
35. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SPA. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 1994; 91: 5022-5026.
36. Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat Genet 1996; 14: 450-456.
37. Kozal MJ, Shah N, Shea N et al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Med 1996; 2: 753-759.
38. Cronin MT, Fucini RV, Kim SM, Masino RS, Wespi RM, Miyada CG. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Human Mutat 1996; 7: 244-255.
39. Hacia JG, Brody LC, Chee MS, Fodor SPA, Collins FS. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat Genet 1996; 14: 441-447.
40. Tugendreich S, Bassett DE, McKusick VA, Boguski MS, Hieter P. Genes conserved in yeast and humans. Hum Mol Genet 1994; 3: 1509-1517.
41. Bassett DE, Boguski MS, Hieter P. Yeast genes and human disease. Nature 1996; 379: 589-590.
42. Mushegian AR, Bassett DE, Boguski MS, Bork P, Koonin EV. Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci USA 1997; 94: 5831-5836.
43. Oliver SG. From DNA sequence to biological function. Nature 1996; 379: 597-600.