The transcriptional regulator pool of the marine bacterium Rhodopirellula baltica SH 1 T as revealed by whole genome comparisons

FEMS Microbiology Letters

Volumn 242, Issue 1, 2005, Pages 137-145

  Lombardot, Thierry ^a   Bauer, Margarete ^a   Teeling, Hanno ^a   Amann, Rudolf ^a   Glöckner, Frank Oliver ^a,b  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b JACOBS UNIVERSITY BREMEN   (Germany)

Author keywords

Comparison; Genome; Pirellula; Planctomycete; Regulation; Rhodopirellula

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIOPLANKTON; GENETIC CODE; GENOME ANALYSIS; GENOME SIZE; NONHUMAN; PRIORITY JOURNAL; RHODOPIRELLULA BALTICA; TRANSCRIPTION REGULATION;

ADAPTATION, PHYSIOLOGICAL; BACILLUS SUBTILIS; BACTERIA; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENES, REGULATOR; GENOME, BACTERIAL; PHYLOGENY; SIGMA FACTOR; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); PIRELLULA; PIRELLULA SP. 1; PLANCTOMYCETES; RHODOPIRELLULA; RHODOPIRELLULA BALTICA; UNCULTURED MARINE BACTERIUM;

EID: 11144317316     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsle.2004.10.049     Document Type: Article

References (44)

1. C.K. Stover, X.Q. Pham, A.L. Erwin, S.D. Mizoguchi, P. Warrener, M.J. Hickey, F.S. Brinkman, W.O. Hufnagle, D.J. Kowalik, M. Lagrou, R.L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L.L. Brody, S.N. Coulter, K.R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G.K. Wong, Z. Wu, I.T. Paulsen, J. Reizer, M.H. Saier, R.E. Hancock, S. Lory, and M.V. Olson Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen Nature 406 2000 959 964
2. T. Kaneko, Y. Nakamura, C.P. Wolk, T. Kuritz, S. Sasamoto, A. Watanabe, M. Iriguchi, A. Ishikawa, K. Kawashima, T. Kimura, Y. Kishida, M. Kohara, M. Matsumoto, A. Matsuno, A. Muraki, N. Nakazaki, S. Shimpo, M. Sugimoto, M. Takazawa, M. Yamada, M. Yasuda, and S. Tabata Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 DNA Res. 8 2001 205 213
3. S.D. Bentley, K.F. Chater, A.M. Cerdeno-Tarraga, G.L. Challis, N.R. Thomson, K.D. James, D.E. Harris, M.A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C.W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C.H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M.A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B.G. Barrell, J. Parkhill, and D.A. Hopwood Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) Nature 417 2002 141 147
4. I. Cases, V. de Lorenzo, and C.A. Ouzounis Transcription regulation and environmental adaptation in bacteria Trends Microbiol. 11 2003 248 253
5. F.O. Glöckner, M. Kube, M. Bauer, H. Teeling, T. Lombardot, W. Ludwig, D. Gade, A. Beck, K. Borzym, K. Heitmann, R. Rabus, H. Schlesner, R. Amann, and R. Reinhardt Complete genome sequence of the marine planctomycete Pirellula sp. strain 1 Proc. Natl. Acad. Sci. USA 100 2003 8298 8303
6. P.D. Franzmann, and V.B. Skerman Gemmata obscuriglobus, a new genus and species of the budding bacteria Antonie Van Leeuwenhoek 50 1984 261 268
7. H. Schlesner The development of media suitable for the microorganisms morphologically resembling Planctomyces spp., Pirellula spp., and other Planctomycetales from various aquatic habitats using dilute media System. Appl. Microbiol. 17 1994 135 145
8. J.A. Fuerst The planctomycetes: emerging models for microbial ecology, evolution and cell biology Microbiology 141 1995 1493 1506
9. M.K. Butler, J. Wang, R.I. Webb, and J.A. Fuerst Molecular and ultrastructural confirmation of classification of ATCC 35122 as a strain of Pirellula staleyi Int. J. Syst. Evol. Microbiol. 52 2002 1663 1667
10. J. Wang, C. Jenkins, R.I. Webb, and J.A. Fuerst Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater Appl. Environ. Microbiol. 68 2002 417 422
11. N. Ward, F.A. Rainey, E. Stackebrandt, and H. Schlesner Unraveling the extent of diversity within the order Planctomycetales Appl. Environ. Microbiol. 61 1995 2270 2275
12. C. Jenkins, and J.A. Fuerst Phylogenetic analysis of evolutionary relationships of the planctomycete division of the domain bacteria based on amino acid sequences of elongation factor Tu J. Mol. Evol. 52 2001 405 418
13. S. Gribaldo, and H. Philippe Ancient phylogenetic relationships Theor. Popul. Biol. 61 2002 391 408
14. C. Brochier, and H. Philippe A non-hyperthermophilic ancestor for bacteria Nature 417 2002 244
15. H. Teeling, T. Lombardot, M. Bauer, W. Ludwig, R.I. Amann, and F.O. Glöckner Reevaluation of the phylogenetic position of the Planctomycetes by means of concatenated ribosomal proteins, mRNA polymerase subunits and whole genome trees Int. J. Syst. Evol. Microbiol. 54 2004 791 801
16. M.R. Lindsay, R.I. Webb, and J.A. Fuerst Pirellulosomes: a new type of membrane-bounded cell compartment in planctomycete bacteria of the genus Pirellula Microbiology 143 1997 739 748
17. M.R. Lindsay, R.I. Webb, M. Strous, M.S. Jetten, M.K. Butler, R.J. Forde, and J.A. Fuerst Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell Arch. Microbiol. 175 2001 413 429
18. H. Schlesner, C. Rendsmann, B.J. Tindall, D. Gade, R. Rabus, S. Pfeiffer, and P. Hirsch Taxonomic heterogeneity within the Planctomycetales as derived by DNA-DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov., and emended description of the genus Pirellula Int. J. Syst. Evol. Microbiol. 54 2004 1567 1580
19. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, and G. Sherlock Gene ontology: tool for the unification of biology Nat. Genet. 25 2000 25 29
20. S.C. Rison, T.C. Hodgman, and J.M. Thornton Comparison of functional annotation schemes for genomes Funct. Integr. Genomics 1 2000 56 69
21. Karp, P.D. (2001) Many microbial genomes in Genbank do not conform to the genbank standard, ASM News 67
22. G. Stoesser, W. Baker, A. van den Broek, E. Camon, M. Garcia-Pastor, C. Kanz, T. Kulikova, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, N. Redaschi, P. Stoehr, M.A. Tuli, K. Tzouvara, and R. Vaughan The EMBL Nucleotide Sequence Database Nucl. Acids Res. 30 2002 21 26
23. F. Meyer, A. Goesmann, A.C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, and A. Puhler GenDB - an open source genome annotation system for prokaryote genomes Nucl. Acids Res. 31 2003 2187 2195
24. A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E.L. Sonnhammer, D.J. Studholme, C. Yeats, and S.R. Eddy The Pfam protein families database Nucl. Acids Res. 32 2004 D138 D141
25. N.J. Mulder, R. Apweiler, T.K. Attwood, A. Bairoch, D. Barrell, A. Bateman, D. Binns, M. Biswas, P. Bradley, P. Bork, P. Bucher, R.R. Copley, E. Courcelle, U. Das, R. Durbin, L. Falquet, W. Fleischmann, S. Griffiths-Jones, D. Haft, N. Harte, N. Hulo, D. Kahn, A. Kanapin, M. Krestyaninova, R. Lopez, I. Letunic, D. Lonsdale, V. Silventoinen, S.E. Orchard, M. Pagni, D. Peyruc, C.P. Ponting, J.D. Selengut, F. Servant, C.J. Sigrist, R. Vaughan, and E.M. Zdobnov The InterPro Database, 2003 brings increased coverage and new features Nucl. Acids Res. 31 2003 315 318
26. J.D. Helmann The extracytoplasmic function (ECF) sigma factors Adv. Microb. Physiol. 46 2002 47 110
27. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucl. Acids Res. 25 1997 3389 3402
28. R. Apweiler, A. Bairoch, C.H. Wu, W.C. Barker, B. Boeckmann, S. Ferro, E. Gasteiger, H. Huang, R. Lopez, M. Magrane, M.J. Martin, D.A. Natale, C. O'Donovan, N. Redaschi, and L.S. Yeh UniProt: the Universal Protein knowledgebase Nucl. Acids Res. 32 2004 D115 D119
29. R. Chenna, H. Sugawara, T. Koike, R. Lopez, T.J. Gibson, D.G. Higgins, and J.D. Thompson Multiple sequence alignment with the Clustal series of programs Nucl. Acids Res. 31 2003 3497 3500
30. J. Felsenstein PHYLIP - Phylogeny Inference Package Cladistics 5 1989 164 166
31. J. Xu, M.K. Bjursell, J. Himrod, S. Deng, L.K. Carmichael, H.C. Chiang, L.V. Hooper, and J.I. Gordon A genomic view of the human-Bacteroides thetaiotaomicron symbiosis Science 299 2003 2074 2076
32. D. Missiakas, and S. Raina The extracytoplasmic function sigma factors: role and regulation Mol. Microbiol. 28 1998 1059 1066
33. R. Manganelli, M.I. Voskuil, G.K. Schoolnik, E. Dubnau, M. Gomez, and I. Smith Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression Mol. Microbiol. 45 2002 365 374
34. M. Cao, and J.D. Helmann Regulation of the Bacillus subtilis bcrC bacitracin resistance gene by two extracytoplasmic function sigma factors J. Bacteriol. 184 2002 6123 6129
35. W. Li, C.E. Stevenson, N. Burton, P. Jakimowicz, M.S. Paget, M.J. Buttner, D.M. Lawson, and C. Kleanthous Identification and structure of the anti-sigma factor-binding domain of the disulphide-stress regulated sigma factor sigma(R) from Streptomyces coelicolor J. Mol. Biol. 323 2002 225 236
36. V. Braun, S. Mahren, and M. Ogierman Regulation of the FecI-type ECF sigma factor by transmembrane signalling Curr. Opin. Microbiol. 6 2003 173 180
37. P. Visca, L. Leoni, M.J. Wilson, and I.L. Lamont Iron transport and regulation, cell signalling and genomics: lessons from Escherichia coli and Pseudomonas Mol. Microbiol. 45 2002 1177 1190
38. M. Cao, L. Salzberg, C.S. Tsai, T. Mascher, C. Bonilla, T. Wang, R.W. Ye, L. Marquez-Magana, and J.D. Helmann Regulation of the Bacillus subtilis extracytoplasmic function protein sigma(Y) and its target promoters J. Bacteriol. 185 2003 4883 4890
39. K. Asai, H. Yamaguchi, C.M. Kang, K. Yoshida, Y. Fujita, and Y. Sadaie DNA microarray analysis of Bacillus subtilis sigma factors of extracytoplasmic function family FEMS Microbiol. Lett. 220 2003 155 160
40. X. Huang, K.L. Fredrick, and J.D. Helmann Promoter recognition by Bacillus subtilis sigmaW: autoregulation and partial overlap with the sigmaX regulon J. Bacteriol. 180 1998 3765 3770
41. D.J. Studholme, J.A. Fuerst, and A. Bateman Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica FEMS Microbiol. Lett. 236 2004 333 340
42. N.L. Ward, F.A. Rainey, B.P. Hedlund, J.T. Staley, W. Ludwig, and E. Stackebrandt Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny Int. J. Syst. Evol. Microbiol. 50 2000 1965 1972
43. D.J. Studholme, and R. Dixon In silico analysis of the sigma54-dependent enhancer-binding proteins in Pirellula species strain 1 FEMS Microbiol. Lett. 230 2004 215 225
44. E. Perez-Rueda, and J. Collado-Vides Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria J. Mol. Evol. 53 2001 172 179