In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon

Bioinformatics

Volumn 19, Issue 17, 2003, Pages 2225-2236

  Erill, Ivan ^a   Escribano, Marcos ^a   Campoy, Susana ^a   Barbé, Jordi ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; COMPARATIVE GENE MAPPING; COMPUTER ANALYSIS; COMPUTER PROGRAM; DATA ANALYSIS; FEASIBILITY STUDY; GENE CONTROL; GENE SEQUENCE; GENETIC ANALYSIS; GRAM NEGATIVE BACTERIUM; INTERNET; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; REGULON;

BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; NEGIBACTERIA; PROTEOBACTERIA;

EID: 0344464768     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg303     Document Type: Article

References (54)

1. Achenbach,L.A., Carey,J. and Madigan,M.T. (2001) Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments. Appl. Environ. Microbiol., 67, 2922-2926.
2. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Bailey,T.L. and Elkan,C. (1995) The value of prior knowledge in discovering motifs with MEME. Proceedings of the 3rd International Conference of the Intelligence Systems in Molecular Biology. AAAI Press, Menlo Park, CA, pp. 21-29.
4. Benítez-Bellón,E., Moreno-Hagellsieb,G. and Collado-Vides,J. (2002) Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA. Genome Biol., 3, research0013.1-0013.16.
5. Benson,N.R., Wong,R.M.-Y. and McClelland,M. (2000) Analysis of the SOS response in Salmonella enterica serovar typhimurium using RNA fingerprinting by arbitrarily primed PCR. J. Bacteriol., 182, 3490-3497.
6. Berg,O.G. (1988) Selection of DNA binding sites by regulatory proteins: the LexA protein and the arginine repressor use different strategies for functional specificity. Nucleic Acids Res., 16, 5089-5105.
7. Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins, statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
8. Corpet,F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
9. Courcelle,J., Khodursky,A., Peter,B., Brown,P.O. and Hanawalt,P.C. (2001) Comparative gene expression profiles following UV exposure in wild type and SOS deficient Escherichia coli. Genetics, 158, 41-64.
10. Dayhoff,M., Schwartz,R.M. and Orcutt,B.C. (1978) A model of evolutionary change in proteins. In Dayhoff,M. (ed.), Atlas of Protein Sequence and Structure, vol. 5. National Biomedical Research Foundation, Silver Spring, MD, pp. 345-352.
11. Eisen,J.A. (1995) The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol., 41, 1105-1123.
12. Felsenstein,J. (1989) PHYLIP: phylogeny inference package (version 3.2). Cladistics, 5, 164-166.
13. Feng,D.F., Cho,G. and Doolittle,R.F. (1997) Determining divergence times with a protein clock: update and reevaluation. Proc. Natl Acad. Sci. USA, 94, 13028-13033.
14. Fernandez de Henestrosa,A.R., Cuñé,J., Erill,I., Magnuson,J.K. and Barbé,J. (2002) A green nonsulfur bacterium, Dehalococcoides ethenogenes, with the LexA binding sequence found in gram-positive organisms. J. Bacteriol., 184, 6073-6080.
15. Fernandez de Henestrosa,A.R., Ogi,T., Aoyagi,S., Chafin,D., Hayes,J.J., Ohmori,H. and Woodgate,R. (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol., 35, 1560-1572.
16. Fox,G.E., Stackebrandt,E., Hespel,R.B., Gibson,J., Maniloff,J., Dyer,T.A., Wolfe,R.S., Balch,W.E., Tanner,R.S., Magrum,L.J. et al. (1980) The Phylogeny of Procaryotes. Science, 209, 457-463.
17. Fukushima,M., Kakinuma,K. and Kawaguchi,R. (2002) Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J. Clin. Microbiol., 40, 2779-2785.
18. Garriga,X., Calero,S. and Barbé,J. (1992) Nucleotide sequence analysis and comparison of the lexA genes from Salmonella typhimurium, Erwinia carotovora, Pseudomonas aeruginosa and Pseudomonas putida. Mol. Gen. Genet., 236, 125-134.
19. Gelfand,M.S., Koonin,E.V. and Mironov,A.A. (2000a) Prediction of transcription regulatory sites in Archaea by a comparative-genomic approach. Nucleic Acids Res., 28, 695-705.
20. Gelfand,M.S., Novichkov,P.S., Novichkova,E.S. and Mironov,A.A. (2000b) Comparative analysis of regulatory patterns in bacterial genomes. Brief. Bioinfor., 1, 357-371.
21. Gupta,R.S. (2000) The natural evolutionary relationships among prokaryotes. Crit. Rev. Microbiol., 26, 111-131.
22. Henikoff,S. and Henikoff,J.G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10519.
23. Khil,P.P. and Camerini-Otero,R.D. (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol., 44, 89-105.
24. Ko,K.S., Lee,H.K., Park,M.Y., Lee,K.H., Yun,Y.J., Woo,S.Y., Miyamoto,H. and Kook,Y.H. (2002) Application of RNA polymerase beta-subunit gene (rpoB) sequences for the molecular differentiation of Legionella species. J. Clin. Microbiol., 40, 2653-2658.
25. Koch,W.H. and Woodgate,R. (1998) The SOS response. In Nickoloff,J.A. and Hoekstra,M.F. (eds), DNA Damage and Repair: DNA Repair in Prokaryotes and Lower Eukaryotes. Humana Press, Totowa, New Jersey, pp. 107-134.
26. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wooton,J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
27. Lawrence,C.E., Reilly,A.A. (1990) An EM algorithm for the identification and characterization of common sites in unaligned biopolymers sequence. Proteins, 7, 41-51.
28. Lewis,L.K., Harlow,G.R., Gregg-Jolly,L.A. and Mount,D.W. (1994) Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli. J. Mol. Biol., 241, 507-523.
29. Little,J.W. (1984) Autodigestion of lexA and phage repressors. Proc. Natl Acad. Sci. USA, 81, 1375-1379.
30. Lloyd,A.T. and Sharp,P.M. (1993) Evolution of the recA gene and the molecular phylogeny of bacteria. J. Mol. Evol., 37, 399-407.
31. Ludwig,W., Weizenegger,M., Betzl,D., Leidel,E., Lenz,T., Ludvigsen,A., Mollenhoff,D., Wenzig,P. and Schleifer,K.H. (1990) Complete nucleotide sequences of seven eubacterial genes coding for the elongation factor Tu: functional, structural and phylogenetic evaluations. Arch. Microbiol., 153, 241-247.
32. Makarova,K.S., Mironov,A.A. and Gelfand,M.S. (2001) Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol., 2, research0013.1-0013.8.
33. McCue,L.A., Thompson,W., Carmack,C.S., Ryan,M.P., Liu,J.S., Derbyshire,V. and Lawrence,C.E. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res., 29, 774-782.
34. McGuire,A.M., Hughes,J.D. and Church,G.M. (2000) Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res., 10, 744-757.
35. Nomenclature Committee (1985) IUB nomenclature for incompletely specified bases in nucleic acid sequences recommendations 1984. Eur. J. Biochem., 150, 1-5.
36. Ochman,H. and Wilson,A.C. (1987) Evolution in bacteria: evidence for a universal rate in cellular genomes. J. Mol. Evol., 26, 74-86.
37. Page,R.D.M. (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comp. Appl. Biosci., 12, 357-358.
38. Pitulle,C., Strehse,C., Brown,J.W. and Breitschwerdt,E.B. (2002) Investigation of the phylogenetic relationships within the genus Bartonella based on comparative sequence analysis of the rnpB gene, 16S rDNA and 23S rDNA. Int. J. Sist. Evol. Microbiol., 52, 2075-2080.
39. Radman,M. (1974) Phenomenology of an inducible muta-genic DNA repair pathway in Escherichia coli: SOS repair hypothesis. In Prakash,L. et al. (eds) Molecular and Environmental Aspects of Mutagenesis Springfield, IL, 128-142.
40. Rajewsky,N., Socci,N., Zapotocky,M. and Siggia,E.D. (2002) The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res., 12, 298-308.
41. Rodionov,D.A., Mironov,A.A. and Gelfand,M.S. (2001) Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria. FEMS Microbiol. Lett., 205, 305-314.
42. Roy,S., Sahu,A. and Adhya,S. (2002) Evolution of DNA binding motifs and operators. Gene, 285, 169-173.
43. Snel,B., Bork,P. and Huynen,M.A. (1999) Genome phylogeny based on gene content. Nat. Genet., 21, 108-110.
44. Stormo,G.D. and Hartzell,G.W. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-1187.
45. Tan,K., Moreno-Hagelsieb,G., Collado-Vides,J. and Stormo,G.D. (2001) A Comparative Genomics Approach to Prediction of New Members of Regulons. Genome Res., 11, 566-584.
46. Tapias,A., Fernández,S., Alonso,J.C. and Barbé,J. (2002) Rhodobacter sphaeroides LexA has dual activity: optimising and repressing recA gene transcription. Nucleic Acids Res., 30, 1539-1546.
47. Tekaia,F., Lazcano,A. and Dujon,B. (1999) The genomic tree as revealed from whole proteome comparisons. Genome Res., 9, 550-557.
48. van Helden,J., André,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeastgenes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
49. Walker,G.C. (1984) Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev., 48, 60-93.
50. Winterling,K.W., Chafin,D., Hayes,J.J. Sun,J., Levine,A.S., Yasbin,R.E. and Woodgate,R. (1998) The Bacillus subtilis DinR binding site: redefinition of the consensus sequence. J. Bacteriol., 180, 2201-2211.
51. Woese,C.R. (1998) The universal ancestor. Proc. Natl Acad. Sci. USA, 95, 6854-6859.
52. Woese,C.R. and Fox,G.E. (1977) Phylogenetic Structure of the Prokaryotic Domains: The Primary Kingdoms. Proc. Natl Acad. Sci. USA, 74, 5088-5090.
53. Xie,G., Bonner,C.A., Brettin,T., Gottardo,R., Keyhani,N.O. and Jensen,R.A. (2003) Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cianobacteria. Genome Biol., 4, R14.
54. Zuckerkandl,E. (1975) The appearance of new structures and functions in proteins during evolution. J. Mol. Evol., 7, 1-57.