1887

Abstract

Using the complete genome sequence of PAO1, sequenced by the Genome Project (ftp://ftp.pseudomonas.com/data/pacontigs.121599), a genome database (http://pseudomonas.bit.uq.edu.au/) has been developed containing information on more than 95% of all ORFs in . The database is searchable by a variety of means, including gene name, position, keyword, sequence similarity and Pfam domain. Automated and manual annotation, nucleotide and peptide sequences, Pfam and SMART domains (where available), Medline and GenBank links and a scrollable, graphical representation of the surrounding genomic landscape are available for each ORF. Using the database has revealed, among other things, that contains four chemotaxis systems, two novel general secretion pathways, at least three loci encoding F17-like thin fimbriae, six novel filamentous haemagglutinin-like genes, a number of unusual composite genetic loci related to / elements in , a number of -like genes encoding a micro-oxic respiration system, novel biosynthetic pathways and 38 genes containing domains of unknown function (DUF1/DUF2). It is anticipated that this database will be a useful bioinformatic tool for the community that will continue to evolve.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-146-10-2351
2000-10-01
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/146/10/1462351a.html?itemId=/content/journal/micro/10.1099/00221287-146-10-2351&mimeType=html&fmt=ahah

References

  1. Albano, M., Breeitling, R. & Dubnau, D. A. ( 1989; ). Nucleotide sequence and genetic organisation of the Bacillus subtilis comG operon. J Bacteriol 171, 5386-5404.
    [Google Scholar]
  2. Aldridge, P. & Jenal, U. ( 1999; ). Cell cycle-dependent degradation of a flagellar motor component requires a novel-type response regulator. Mol Microbiol 32, 379-391.[CrossRef]
    [Google Scholar]
  3. Alm, R. A. & Mattick, J. S. ( 1996; ). Identification of two genes with prepilin-like leader sequences required for type 4 fimbrial biogenesis in Pseudomonas aeruginosa. J Bacteriol 178, 3809-3817.
    [Google Scholar]
  4. Alm, R. A. & Mattick, J. S. ( 1997; ). Genes involved in the biogenesis and function of type-4 fimbriae in Pseudomonas aeruginosa. Gene 192, 89-98.[CrossRef]
    [Google Scholar]
  5. Alm, R. A., Hallinan, J. P., Watson, A. A. & Mattick, J. S. ( 1996; ). Fimbrial biogenesis genes of Pseudomonas aeruginosa pilW and pilX increase the similarity of type 4 fimbriae to the GSP protein-secretion systems and pilY1 encodes a gonococcal PilC homologue. Mol Microbiol 22, 161-173.[CrossRef]
    [Google Scholar]
  6. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.[CrossRef]
    [Google Scholar]
  7. Aravind, L. & Ponting, C. P. ( 1997; ). The GAF domain: an evolutionary link between diverse phototransducing proteins. Trends Biochem Sci 22, 458-459.[CrossRef]
    [Google Scholar]
  8. Aravind, L. & Ponting, C. P. ( 1999; ). The cytoplasmic helical linker domain of receptor histidine kinase and methyl-accepting proteins is common to many prokaryotic signalling proteins. FEMS Microbiol Lett 176, 111-116.[CrossRef]
    [Google Scholar]
  9. Barenkamp, S. J. & Leininger, E. ( 1992; ). Cloning, expression, and DNA sequence analysis of genes encoding nontypeable Haemophilus influenzae high-molecular-weight surface-exposed proteins related to filamentous hemagglutinin of Bordetella pertussis. Infect Immun 60, 1302-1313.
    [Google Scholar]
  10. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Howe, K. L. & Sonnhammer, E. L. ( 2000; ). The Pfam protein families database. Nucleic Acids Res 28, 263-266.[CrossRef]
    [Google Scholar]
  11. Bleves, S., Voulhoux, R., Michel, G., Lazdunski, A., Tommassen, J. & Filloux, A. ( 1998; ). The secretion apparatus of Pseudomonas aeruginosa: identification of a fifth pseudopilin, XcpX (GspK family). Mol Microbiol 27, 31-40.[CrossRef]
    [Google Scholar]
  12. Buchrieser, C., Prentice, M. & Carniel, E. ( 1998; ). The 102-kilobase unstable region of Yersinia pestis comprises a high-pathogenicity island linked to a pigmentation segment which undergoes internal rearrangement. J Bacteriol 180, 2321-2329.
    [Google Scholar]
  13. Buchrieser, C., Rusniok, C., Frangeul, L., Couve, E., Billault, A., Kunst, F., Carniel, E. & Glaser, P. ( 1999; ). The 102-kilobase pgm locus of Yersinia pestis: sequence analysis and comparison of selected regions among different Yersinia pestis and Yersinia pseudotuberculosis strains. Infect Immun 67, 4851-4861.
    [Google Scholar]
  14. Cope, L. D., Thomas, S. E., Latimer, J. L., Slaughter, C. A., Muller-Eberhard, U. & Hansen, E. J. ( 1994; ). The 100 kDa haem:haemopexin-binding protein of Haemophilus influenzae: structure and localization. Mol Microbiol 13, 863-873.[CrossRef]
    [Google Scholar]
  15. Darzins, A. ( 1993; ). The pilG gene product, required for Pseudomonas aeruginosa pilus production and twitching motility, is homologous to the enteric, single-domain response regulator CheY. J Bacteriol 175, 5934-5944.
    [Google Scholar]
  16. Darzins, A. ( 1994; ). Characterization of a Pseudomonas aeruginosa gene cluster involved in pilus biosynthesis and twitching motility: sequence similarity to the chemotaxis proteins of enterics and the gliding bacterium Myxococcus xanthus. Mol Microbiol 11, 137-153.[CrossRef]
    [Google Scholar]
  17. Darzins, A. ( 1995; ). The Pseudomonas aeruginosa pilK gene encodes a chemotactic methyltransferase (CheR) homologue that is translationally regulated. Mol Microbiol 15, 703-717.
    [Google Scholar]
  18. Domenighini, M., Relman, D., Capiau, C., Falkow, S., Prugnola, A., Scarlato, V. & Rappuoli, R. ( 1990; ). Genetic characterization of Bordetella pertussis filamentous haemagglutinin: a protein processed from an unusually large precursor. Mol Microbiol 4, 787-800.[CrossRef]
    [Google Scholar]
  19. Eisenbach, M. ( 1996; ). Control of bacterial chemotaxis. Mol Microbiol 20, 903-910.[CrossRef]
    [Google Scholar]
  20. Fernandez-Canon, J. & Penalva, M. ( 1995; ). Molecular characterization of a gene encoding a homogentisate dioxygenase from Aspergillus nidulans and identification of its human and plant homologues. J Biol Chem 270, 21199-21205.[CrossRef]
    [Google Scholar]
  21. Fischer, H. M. ( 1994; ). Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 58, 352-386.
    [Google Scholar]
  22. Hecht, G. B. & Newton, A. ( 1995; ). Identification of a novel response regulator required for the swarmer-to-stalked-cell transition in Caulobacter crescentus. J Bacteriol 177, 6223-6229.
    [Google Scholar]
  23. Hill, C. W., Feulner, G., Brody, M. S., Zhao, S., Sadosky, A. B. & Sandt, C. H. ( 1995; ). Correlation of Rhs elements with Escherichia coli population structure. Genetics 141, 15-24.
    [Google Scholar]
  24. Hobbs, M. & Mattick, J. S. ( 1993; ). Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and protein secretion apparatus; a general system for the formation of surface-associated protein complexes. Mol Microbiol 10, 233-243.[CrossRef]
    [Google Scholar]
  25. Holmgren, A., Kuehn, M. J., Branden, C. I. & Hultgren, S. J. ( 1992; ). Conserved immunoglobulin-like features in a family of periplasmic pilus chaperones in bacteria. EMBO J 11, 1617-1622.
    [Google Scholar]
  26. Hultgren, S. J., Abraham, S., Caparon, M., Falk, P., St Geme, J. W. D. & Normark, S. ( 1993; ). Pilus and nonpilus bacterial adhesins: assembly and function in cell recognition. Cell 73, 887-901.[CrossRef]
    [Google Scholar]
  27. Hung, D. L. & Hultgren, S. J. ( 1998; ). Pilus biogenesis via the chaperone/usher pathway: an integration of structure and function. J Struct Biol 124, 201-220.[CrossRef]
    [Google Scholar]
  28. Jones, C. H., Pinkner, J. S., Nicholes, A. V., Slonim, L. N., Abraham, S. N. & Hultgren, S. J. ( 1993; ). FimC is a periplasmic PapD-like chaperone that directs assembly of type 1 pili in bacteria. Proc Natl Acad Sci USA 90, 8397-8401.[CrossRef]
    [Google Scholar]
  29. Kato, J., Nakamura, T., Kuroda, A. & Ohtake, H. ( 1999; ). Cloning and characterization of chemotaxis genes in Pseudomonas aeruginosa. Biosci Biotechnol Biochem 63, 155-161.[CrossRef]
    [Google Scholar]
  30. Klemm, P., Jorgensen, B. J., Kreft, B. & Christiansen, G. ( 1995; ). The export systems of type 1 and F1C fimbriae are interchangeable but work in parental pairs. J Bacteriol 177, 621-627.
    [Google Scholar]
  31. Kuroda, A., Kumano, T., Taguchi, K., Nikata, T., Kato, J. & Ohtake, H. ( 1995; ). Molecular cloning and characterization of a chemotactic transducer gene in Pseudomonas aeruginosa. J Bacteriol 177, 7019-7025.
    [Google Scholar]
  32. Lindberg, F., Tennent, J. M., Hultgren, S. J., Lund, B. & Normark, S. ( 1989; ). PapD, a periplasmic transport protein in P-pilus biogenesis. J Bacteriol 171, 6052-6058.
    [Google Scholar]
  33. Locht, C., Bertin, P., Menozzi, F. D. & Renauld, G. ( 1993; ). The filamentous haemagglutinin, a multifaceted adhesion produced by virulent Bordetella spp. Mol Microbiol 9, 653-660.[CrossRef]
    [Google Scholar]
  34. Martinez, A., Ostrovsky, P. & Nunn, D. ( 1998; ). Identification of an additional member of the secretin superfamily of proteins in Pseudomonas aeruginosa that is able to function in type II protein secretion. Mol Microbiol 28, 1235-1246.[CrossRef]
    [Google Scholar]
  35. Masduki, A., Nakamura, J., Ohga, T., Umezaki, R., Kato, J. & Ohtake, H. ( 1995; ). Isolation and characterization of chemotaxis mutants and genes of Pseudomonas aeruginosa. J Bacteriol 177, 948-952.
    [Google Scholar]
  36. Mattick, J. S. & Alm, R. A. ( 1995; ). Common architecture of type 4 fimbriae and complexes involved in macromolecular traffic. Trends Microbiol 3, 411-413.[CrossRef]
    [Google Scholar]
  37. Motallebi-Veshareh, M., Rouch, D. A. & Thomas, C. M. ( 1990; ). A family of ATPases involved in active partitioning of diverse bacterial plasmids. Mol Microbiol 4, 1455-1463.[CrossRef]
    [Google Scholar]
  38. Parge, H. E., Forest, K. T., Hickey, M. J., Christensen, D. A., Getzoff, E. D. & Tainer, J. A. ( 1995; ). Structure of the fibre-forming protein pilin at 2·6Å resolution. Nature 378, 32-38.[CrossRef]
    [Google Scholar]
  39. Parkinson, J. S. ( 1993; ). Signal transduction schemes of bacteria. Cell 73, 857-871.[CrossRef]
    [Google Scholar]
  40. Pestova, E. V. & Morrison, D. A. ( 1998; ). Isolation and characterization of three Streptococcus pneumoniae transformation-specific loci by use of a lacZ reporter insertion vector. J Bacteriol 180, 2701-2710.
    [Google Scholar]
  41. Ponting, C. P. & Aravind, L. ( 1997; ). PAS: a multifunctional domain family comes to light. Curr Biol 7, R674-R677.[CrossRef]
    [Google Scholar]
  42. Poole, K., Schiebel, E. & Braun, V. ( 1988; ). Molecular characterization of the hemolysin determinant of Serratia marcescens. J Bacteriol 170, 3177-3188.
    [Google Scholar]
  43. Pugsley, A. P. ( 1993; ). The complete general secretory pathway in Gram negative bacteria. Microbiol Rev 57, 50-108.
    [Google Scholar]
  44. Read, T. D., Dowdell, M., Satola, S. W. & Farley, M. M. ( 1996; ). Duplication of pilus gene complexes of Haemophilus influenzae biogroup aegyptius. J Bacteriol 178, 6564-6570.
    [Google Scholar]
  45. Relman, D., Tuomanen, E., Falkow, S., Golenbock, D. T., Saukkonen, K. & Wright, S. D. ( 1990; ). Recognition of a bacterial adhesion by an integrin: macrophage CR3 (alpha M beta 2, CD11b/CD18) binds filamentous hemagglutinin of Bordetella pertussis. Cell 61, 1375-1382.[CrossRef]
    [Google Scholar]
  46. Rosario, M. M. & Ordal, G. W. ( 1996; ). CheC and CheD interact to regulate methylation of Bacillus subtilis methyl-accepting chemotaxis proteins. Mol Microbiol 21, 511-518.[CrossRef]
    [Google Scholar]
  47. Schultz, J., Copley, R. R., Doerks, T., Ponting, C. P. & Bork, P. ( 2000; ). smart: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28, 231-234.[CrossRef]
    [Google Scholar]
  48. Semmler, A. B. T., Whitchurch, C. B. & Mattick, J. S. ( 1999; ). A re-examination of twitching motility in Pseudomonas aeruginosa. Microbiology 145, 2863-2873.
    [Google Scholar]
  49. Semmler, A. B. T., Whitchurch, C. B., Leech, A. J. & Mattick, J. S. ( 2000; ). Identification of a novel gene, fimV, involved in twitching motility in Pseudomonas aeruginosa. Microbiology 146, 1321-1332.
    [Google Scholar]
  50. Soto, G. E. & Hultgren, S. J. ( 1999; ). Bacterial adhesins: common themes and variations in architecture and assembly. J Bacteriol 181, 1059-1071.
    [Google Scholar]
  51. Stibitz, S., Weiss, A. A. & Falkow, S. ( 1988; ). Genetic analysis of a region of the Bordetella pertussis chromosome encoding filamentous hemagglutinin and the pleiotropic regulatory locus vir. J Bacteriol 170, 2904-2913.
    [Google Scholar]
  52. Stover, C. K., Pham, X. Q., Erwin, A. L. & 28 other authors ( 2000; ). Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406, 959–964.[CrossRef]
    [Google Scholar]
  53. Strom, M. S. & Lory, S. ( 1991; ). Amino acid substitutions in pilin of Pseudomonas aeruginosa – effect on leader peptide cleavage, amino-terminal methylation, and pilus assembly. J Biol Chem 266, 1656-1664.
    [Google Scholar]
  54. Taguchi, K., Fukutomi, H., Kuroda, A., Kato, J. & Ohtake, H. ( 1997; ). Genetic identification of chemotactic transducers for amino acids in Pseudomonas aeruginosa. Microbiology 143, 3223-3229.[CrossRef]
    [Google Scholar]
  55. Tal, R., Wong, H. C., Calhoon, R. & 11 other authors ( 1998; ). Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacter xylinum: genetic organization and occurrence of conserved domains in isoenzymes. J Bacteriol 180, 4416–4425.
    [Google Scholar]
  56. Tommassen, J., Filloux, A., Bally, M., Murgier, M. & Lazdunski, A. ( 1992; ). Protein secretion in Pseudomonas aeruginosa. FEMS Microbiol Rev 103, 73-90.[CrossRef]
    [Google Scholar]
  57. Turner, L. R., Lara, J. C., Nunn, D. N. & Lory, S. ( 1993; ). Mutations in the consensus ATP-binding sites of XcpR and PilB eliminate extracellular protein secretion and pilus biogenesis in Pseudomonas aeruginosa. J Bacteriol 175, 4962-4969.
    [Google Scholar]
  58. Uphoff, T. S. & Welch, R. A. ( 1990; ). Nucleotide sequencing of the Proteus mirabilis calcium-independent hemolysin genes (hpmA and hpmB) reveals sequence similarity with the Serratia marcescens hemolysin genes (shlA and shlB). J Bacteriol 172, 1206-1216.
    [Google Scholar]
  59. Wang, Y. D., Zhao, S. & Hill, C. W. ( 1998; ). Rhs elements comprise three subfamilies which diverged prior to acquisition by Escherichia coli. J Bacteriol 180, 4102-4110.
    [Google Scholar]
  60. Ward, M. J. & Zusman, D. R. ( 1999; ). Motility in Myxococcus xanthus and its role in developmental aggregation. Curr Opin Microbiol 2, 624-629.[CrossRef]
    [Google Scholar]
  61. Wheeler, R. T. & Shapiro, L. ( 1997; ). Bacterial chromosome segregation: is there a mitotic apparatus? Cell 88, 577-579.[CrossRef]
    [Google Scholar]
  62. Willems, R. J., van der Heide, H. G. & Mooi, F. R. ( 1992; ). Characterization of a Bordetella pertussis fimbrial gene cluster which is located directly downstream of the filamentous haemagglutinin gene. Mol Microbiol 6, 2661-2671.[CrossRef]
    [Google Scholar]
  63. Willems, R. J., Geuijen, C., van der Heide, H. G., Renauld, G., Bertin, P., van den Akker, W. M., Locht, C. & Mooi, F. R. ( 1994; ). Mutational analysis of the Bordetella pertussis fim/fha gene cluster: identification of a gene with sequence similarities to haemolysin accessory genes involved in export of FHA. Mol Microbiol 11, 337-347.[CrossRef]
    [Google Scholar]
  64. Williams, S. G., Varcoe, L. T., Attridge, S. R. & Manning, P. A. ( 1996; ). Vibrio cholerae Hcp, a secreted protein coregulated with HlyA. Infect Immun 64, 283-289.
    [Google Scholar]
  65. Wu, H., Kato, J., Kuroda, A., Ikeda, T., Takiguchi, N. & Ohtake, H. ( 2000; ). Identification and characterization of two chemotactic transducers for inorganic phosphate in Pseudomonas aeruginosa. J Bacteriol 182, 3400-3404.[CrossRef]
    [Google Scholar]
  66. Yahr, T. L., Goranson, J. & Frank, D. W. ( 1996; ). Exoenzyme S of PseudomoNas aeruginosa is secreted by a type III pathway. Mol Microbiol 22, 991-1003.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-146-10-2351
Loading
/content/journal/micro/10.1099/00221287-146-10-2351
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error