Development of software facilities to characterize regulatory binding motifs and application to streptococcaceae

Journal of Molecular Microbiology and Biotechnology

Volumn 14, Issue 1-3, 2007, Pages 67-73

  Pons, Nicolas ^a   Batto, Jean Michel ^a   Ehrlich, Stanislav Dusko ^a   Renault, Pierre ^a  

^a CEMAGREF   (France)

Author keywords

Comparative genomics; Database; Regulatory motifs; Regulatory network; Streptococcaceae

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; GENETIC ANALYSIS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN MOTIF; STREPTOCOCCACEAE;

AMINO ACID MOTIFS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOMICS; LACTOCOCCUS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SOFTWARE; STREPTOCOCCACEAE; STREPTOCOCCUS; USER-COMPUTER INTERFACE;

STREPTOCOCCACEAE;

EID: 35648996383     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000106084     Document Type: Article

References (31)

1. Alkema WB, Lenhard B, Wasserman WW: Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res 2004;14:1362-1373.
2. Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 1994;2:28-36.
3. Barriere C, Veiga-da-Cunha M, Pons N, Guedon E, van Hijum SA, Kok J, Kuipers OP, Ehrlich DS, Renault P: Fructose utilization in Lactococcus lactis as a model for low-GC Gram-positive bacteria: its regulator, signal, and DNA-binding site. J Bacteriol 2005;187:3752-3761.
4. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P: Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 2004;22:1554-1558.
5. Bulyk ML, Huang X, Choo Y, Church GM: Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci USA 2001;98:7158-7163.
6. Dsouza M, Larsen N, Overbeek R: Searching for patterns in genomic data. Trends Genet 1997;13:497-498.
7. Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004;5:113.
8. Facklam R: What happened to the streptococci: overview of taxonomic and nomenclature changes. Clin Microbiol Rev 2002;15:613-630.
9. Grundy FJ, Henkin TM: Regulation of gene expression by effectors that bind to RNA. Curr Opin Microbiol 2004;7:126-131.
10. Guedon E, Jamet E, Renault P: Gene regulation in Lactococcus lactis: the gap between predicted and characterized regulators. Antonie Van Leeuwenhoek 2002;82:93-112.
11. Guedon E, Sperandio B, Pons N, Ehrlich SD, Renault P: Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes. Microbiology 2005;151:3895-3909.
12. Hols P, Hancy F, Fontaine L, Grossiord B, Prozzi D, Leblond-Bourget N, Decaris B, Bolotin A, Delorme C, Dusko Ehrlich S, Guedon E, Monnet V, Renault P, Kleerebezem M: New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics. FEMS Microbiol Rev 2005;29:435-463.
13. Koonin EV: Systemic determinants of gene evolution and function. Mol Syst Biol 2005;1:2005.2021.
14. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002;298:799-804.
15. Mao L, Mackenzie C, Roh JH, Eraso JM, Kaplan S, Resat H: Combining microarray and genomic data to predict DNA binding motifs. Microbiology 2005;151:3197-3213.
16. Martinez-Antonio A and Collado-Vides J: Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 2003;6:482-489.
17. McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE: Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 2001;29:774-782.
18. McGuire AM, Hughes JD, Church GM: Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res 2000;10:744-757.
19. Meng X, Brodsky MH, Wolfe SA: A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol 2005;23:988-994.
20. Moreno MS, Schneider BL, Maile RR, Weyler W, Saier MH Jr: Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses. Mol Microbiol 2001;39:1366-1381.
21. Mwangi MM, Siggia ED: Genome wide identification of regulatory motifs in Bacillus subtilis. BMC Bioinformatics 2003;4:18.
22. Perez-Rueda E, Collado-Vides J: The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res 2000;28:1838-1847.
23. Reznikoff WS, Siegele DA, Cowing DW, Gross CA: The regulation of transcription initiation in bacteria. Annu Rev Genet 1985;19:355-387.
24. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS: Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 2004; 32: 3340-3353.
25. Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P: High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 2002;20:831-835.
26. Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A, Martinez-Flores I, Jimenez-Jacinto V, Bonavides-Martinez C, Segura-Salazar J, Martinez-Antonio A, Collado-Vides J: RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res 2006;34:D394-D397.
27. Schell MA: Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 1993;47:597-626.
28. Schneider TD, Stephens RM: Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 1990;18:6097-6100.
29. Sperandio B, Polard P, Ehrlich DS, Renault P, Guedon E: Sulfur amino acid metabolism and its control in Lactococcus lactis IL1403. J Bacteriol 2005;187:3762-3778.
30. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
31. Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ: Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res 2006;34:1947-1958.