Orthologous transcription factors in bacteria have different functions and regulate different genes

PLoS Computational Biology

Volumn 3, Issue 9, 2007, Pages 1739-1750

  Price, Morgan N ^a,b   Dehal, Paramvir S ^a,b   Arkin, Adam P ^a,b,c  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; ESCHERICHIA COLI; TRANSCRIPTION;

E. COLI; ESCHERICHIA COLI K12; EVOLUTIONARY HISTORY; EXPRESSION PATTERNS; GENE FAMILIES; ORTHOLOGS; PARALOGOUS GENES; REGULATED GENES; REGULATORY INTERACTIONS; REGULATORY RELATIONSHIPS;

TRANSCRIPTION FACTORS;

TRANSCRIPTION FACTOR;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENETICS; BACTERIAL GENOME; COMPLEX FORMATION; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC CONSERVATION; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; REGULATORY MECHANISM; SEQUENCE ANALYSIS; SHEWANELLA ONEIDENSIS; SIGNAL TRANSDUCTION; VIBRIO CHOLERAE;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SHEWANELLA ONEIDENSIS MR-1; VIBRIO CHOLERAE;

EID: 34848865681     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030175     Document Type: Article

References (53)

1. Guédon E, Jamet E, Renault P (2002) Gene regulation in Lactococcus lactis: The gap between predicted and characterized regulators. Antonie van Leeuwenhoek 82: 93-112.
2. Rajewsky N, Socci ND, Zapotocky M, Siggia ED (2002) The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res 12: 298-308.
3. Gelfand MS (2006) Evolution of transcriptional regulatory networks in microbial genomes. Curr Opin Struct Biol 16: 420-429.
4. Lozada-Chavez I, Janga SC, Collado-Vides J (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 34: 3434-3445.
5. Babu MM, Teichmann SA, Aravind L (2006) Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol 358: 614-633.
6. Fitch WM (2000) Homology: A personal view on some of the problems. Trends Genet 16: 227-231.
7. Ragan MA (2001) On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett 201: 187-191.
8. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102: 14332-14337.
9. Lerat E, Daubin V, Ochman H, Moran NA (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3: e130.
10. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (2005) The net of life: Reconstructing the microbial phylogenetic network. Genome Res 15: 954-959.
11. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, et al. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29: 22-28.
12. Ouzounis C (1999) Orthology: Another terminology muddle. Trends Genet 15: 445.
13. Koski LB, Golding GB (2001) The closest blast hit is often not the nearest neighbor. J Mol Evol 52: 540-542.
14. McGuire AM, Hughes JD, Church GM (2000) Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res 10: 744-757.
15. McCue LA, Thompson W, Carmack CS, Ryan MP, Liu JS, et al. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 29: 774-782.
16. Conlan S, Lawrence C, McCue LA (2005) Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes. Appl Environ Microbiol 71: 7442-7452.
17. Tan K, McCue LA, Stormo GD (2005) Making connections between novel transcription factors and their DNA motifs. Genome Res 15: 312-320.
18. McCue LA, Thompson W, Carmack CS, Lawrence CE (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res 12: 1523-1532.
19. Karp PD, Riley M, Saier M, Paulsen IT, Collado-Vides J, et al. (2002) The EcoCyc database. Nucleic Acids Res 30: 56-58.
20. Shen-Orr SS, Milo R, Magnan S, Alon U (2002) Network motifs in the transcription regulation network of Escherichia coli. Nat Genet 31: 64-68.
21. Makita Y, Nakao M, Ogasawara N, Nakai K (2004) DBTBS: Database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res 32: D75-D77.
22. Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, et al. (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res 34: D394-D397.
23. Rodionov DA, Mironov AA, Gelfand MS (2002) Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res 12: 1507-1516.
24. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: The universal protein knowledgebase. Nucleic Acids Res 32: D115-D119.
25. Alm EJ, Huang KH, Price MN, Koche RP, Keller K, et al. (2005) The MicrobesOnline Web site for comparative genomics. Genome Res 15: 1015-1022.
26. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
27. Howe K, Bateman A, Durbin R (2002) Quicktree: Building huge neighbour-joining trees of protein sequences. Bioinformatics 18: 1546-1547.
28. Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29: 153-159.
29. Gutiérrez-Ríos RM, Rosenblueth DA, Loza JA, Huerta AM, Glasner JD, et al. (2003) Regulatory network of Escherichia coli: Consistency between literature knowledge and microarray profiles. Genome Res 13: 2435-2443.
30. Price MN, Huang KH, Alm EJ, Arkin AP (2005) A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res 33: 880-892.
31. Dehal PS, Boore JL (2006) A phylogenomic gene cluster resource: The Phylogenetically Inferred Groups (PhIGs) database. BMC Bioinformatics 7: 201.
32. Gralnick JA, Brown CT, Newman DK (2005) Anaerobic regulation by an atypical Arc system in Shewanella oneidensis. Mol Microbiol 56: 1347-1357.
33. Maier TM, Myers CR (2001) Isolation and characterization of a Shewanella putrefaciens MR-1 electron transport regulator etrA mutant: Reassessment of the role of EtrA. J Bacteriol 183: 4918-4926.
34. McCarter LL (2001) Polar flagellar motility of the Vibrionaceae. Microbiol Mol Biol Rev 65: 445-462.
35. Aldridge P, Hughes KT (2002) Regulation of flagellar assembly. Curr Opin Microbiol 5: 160-165.
36. Price MN, Arkin AP, Alm EJ (2006) The life-cycle of operons. PLoS Genet 2: e96.
37. Gao H, Wang Y, Liu X, Yan T, Wu L, et al. (2004) Global transcriptome analysis of the heat shock response of Shewanella oneidensis. J Bacteriol 186: 7796-7803.
38. Robison K, McGuire AM, Church GM (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 284: 241-254.
39. Alkema WBL, Lenhard B, Wasserman WW (2004) Regulog analysis: Detection of conserved regulatory networks across bacteria: Application to Staphylococcus aureus. Genome Res 14: 1362-1373.
40. Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, et al. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5: e8.
41. Korbel JO, Jensen LJ, von Mering C, Bork P (2004) Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22: 911-917.
42. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
43. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
44. Mirkin BG, Fenner TI, Galperin MY, Koonin EV (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 3: 2.
45. Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13: 1589-1594.
46. Daubin V, Ochman H (2004) Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res 14: 1036-1042.
47. Moszer I, Jones LM, Moreira S, Fabry C, Danchin A (2002) SubtiList: The reference database for the Bacillus subtilis genome. Nucleic Acids Res 30: 62-65.
48. Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, et al. (2007) RegTransBase - A database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res 35: D407-D412.
49. Gollub J, Ball CA, Binkley G, Demeter J, Finkelstein DB, et al. (2003) The Stanford Microarray Database: Data access and quality assessment tools. Nucleic Acids Res 31: 94-96.
50. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, et al. (2005) NCBI GEO: Mining millions of expression profiles - Database and tools. Nucleic Acids Res 33: D562-D566.
51. Aichi M, Maeda S, Ichikawa K, Omata T (2004) Nitrite-responsive activation of the nitrate assimilation operon in cyanobacteria plays an essential role in up-regulation of nitrate assimilation activities under nitrate-limited growth conditions. J Bacteriol 186: 3224-3229.
52. Marczynski GT, Shapiro L (1992) Cell-cycle control of a cloned chromosomal origin of replication from Caulobacter crescentus. J Mol Biol 226: 959-977.
53. Peres CM, Harwood CS (2006) BadM is a transcriptional repressor and one of three regulators that control benzoyl coenzyme a reductase gene expression in Rhodopseudomonas palustris. J Bacteriol 188: 8662-8665.