The DNA-binding domain as a functional indicator: The case of the AraC/XylS family of transcription factors

Genetica

Volumn 133, Issue 1, 2008, Pages 65-76

  Ibarra, J Antonio ^a,b   Pérez Rueda, Ernesto ^a   Segovia, Lorenzo ^a   Puente, J Luis ^a  

^a INSTITUTO DE BIOTECNOLOGÍA   (Mexico)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

AraC XylS family; DNA binding domain; Functional genomics; Phylogenomics; Transcriptional regulators

Indexed keywords

ARAC PROTEIN;

ARTICLE; BACTERIAL GENOME; CHEMISTRY; ESCHERICHIA COLI K 12; ESCHERICHIA COLI O157; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PATHOGENICITY; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; PSEUDOMONAS SYRINGAE; VIRULENCE;

ARAC TRANSCRIPTION FACTOR; ESCHERICHIA COLI K12; ESCHERICHIA COLI O157; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; MULTIGENE FAMILY; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS SYRINGAE; VIRULENCE;

BACTERIA (MICROORGANISMS);

EID: 41549144323     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10709-007-9185-y     Document Type: Article

References (45)

1. Avison MB (2004) Comparative genomics: digging for data. Methods Mol Biol 266:47-69
2. Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL. Nucleic Acids Res 28:45-48
3. Barbosa TM, Levy SB (2000) Differential expression of over 60 chromosomal genes in Escherichia coli by constituve expression of MarA. J Bacteriol 182:3467-3474
4. Bateman A, Coin L, Durbin R et al (2004) The Pfam Protein Families Database. Nucleic Acids Res 1(Database issue): D138-D141
5. Blattner FR, Plunkett G 3rd, Bloch CA et al (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474
6. Brune I, Brinkrolf K, Kalinowski J, Puhler A et al (2005) The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics 6:86
7. Brunker P, Hils M, Altenbuchner J et al (1998) The mannitol utilization genes of Pseudomonas fluorescens are regulated by an activator: cloning, nucleotide sequence and expression of the mtlR gene. Gene 215:19-27
8. Buell CR, Joardar V, Lindeberg M et al (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 100:10181-10196
9. Daubin V, Gouy M, Perriere G (2002) A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12:1080-1090
10. Egan SM (2002) Growing repertoire of AraC/XylS activators. J Bacteriol 184:5529-5532
11. Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8:163-167
12. Eisen JA, Fraser CM (2003) Phylogenomics: intersection of evolution and genomics. Science 300:1706-1707
13. Eisen JA, Hanawalt PC (1999) A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res 435:171-213
14. Gadelle D, Filee J, Buhler C et al (2003) Phylogenomics of type II DNA topoisomerases. Bioessays 25:232-242
15. Gallegos MT, Schleif R, Bairoch A et al (1997) Arac/XylS family of transcriptional regulators. Microbiol Mol Biol Rev 61:393-410
16. Gomez-Duarte OG, Kaper JB (1995) A plasmid-encoded regulatory region activates chromosomal eaeA expression in enteropathogenic Escherichia coli. Infect Immun 63:1767-1776
17. Gough J, Karplus K, Hughey R et al (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313:903-919
18. Griffith KL, Becker SM, Wolf RJ (2005) Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon. Mol Microbiol 56:1103-1117
19. Heinrichs DE, Poole K (1996) PchR, a regulator of ferripyochelin receptor gene (fptA) expression in Pseudomonas aeruginosa, functions both as an activator and as a repressor. J Bacteriol 178:2586-2592
20. Hentschel U, Steinert M, Hacker J (2000) Common molecular mechanism of symbiosis and pathogenesis. Trends Microbiol 8:226-231
21. Kaper JB, Nataro JP, Mobley HLT (2004) Pathogenic Escherichia coli. Nat Revs 2:123-140
22. Kwon HJ, Bennik MH, Demple B et al (2000) Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Nat Struct Biol 7:424-430
23. Lindler LE, Plana GV, Burland V et al (1998) Complete DNA Sequence and Detailed Analysis of the Yersinia pestis KIM5 Plasmid Encoding Murine Toxin and Capsular Antigen. Infect Immun 66:5731-5742
24. Makita Y, Nakao M, Ogasawara N et al (2004) DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res 32: D75-D77
25. Martin RG, Gillette WK, Rosner JL (2000) The ykgA gene of Escherichia coli. Mol Microbiol 37:978-979
26. Martin RG, Rosner JL (2001) The AraC transcriptional activators. Curr Opin Microbiol 4:132-137
27. Martinez-Bueno M, Molina-Henares AJ, Pareja E et al (2004) BacTregulators: a database of transcriptional regulators in bacteria and archaea. Bioinformatics 20:2787-2791
28. Moreno-Campuzano S, Chandra JS, Perez-Rueda E (2006) Identification and analysis of DNA-binding Transcription Factors in Bacillus subtilis and other Firmicutes- A genomic approach BMC Genomics 7:147
29. Munson GP, Holcomb LG, Scott JR (2001) Novel group of virulence activators within the AraC family that are not restricted to upstream binding sites. Infect Immun 69:186-193
30. Ochman H, Moran NA (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1098
31. Perez-Rueda E, Collado-Vides J (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res 28:1838-1847
32. Perez-Rueda E, Collado-Vides J, Segovia L (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28:341-350
33. Pomposiello PJ, Bennik MHJ, Demple B (2001) Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate. J Bacteriol 183:3890-3902
34. Porter ME, Smith SG, Dorman CJ (1998) Two highly related regulatory proteins, Shigella flexneri VirF and enterotoxigenic Escherichia coli Rns, have common and distinct regulatory properties. FEMS Microbiol Lett 162:303-309
35. Reimmann C, Serino L, Beyeler M et al (1998) Dihydroaeruginoic acid synthetase and pyochelin synthetase, products of the pchEF genes, are induced by extracellular pyochelin in Pseudomonas aeruginosa. Microbiology 144:3135-3148
36. Rhee S, Martin RG, Rosner JL et al (1998) A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci USA 95:10413-10418
37. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstruction phylogenetic trees. Mol Biol Evol 4:406-425
38. Sicheritz-Ponten T, Andersson SG (2001) A phylogenomic approach to microbial evolution. Nucleic Acids Res 29:545-552
39. Singh A, Gupta R, Vishwakarma RA et al (2005) Requirement of the mymA operon for appropriate cell wall ultrastructure and persistence of Mycobacterium tuberculosis in the spleens of guinea pigs. J Bacteriol 187:4173-4186
40. Singh A, Jain S, Gupta S et al (2003) mymA operon of Mycobacterium tuberculosis: its regulation and importance in the cell envelope. FEMS Microbiol Lett 227:53-63
41. Sonnhammer EL, Eddy SR, Birney E et al (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26:320-322
42. Thompson JD, Gibson TJ, Plewniak F et al (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
43. Titball RW, Howells AM, Oyston PC et al (1997) Expression of the Yersinia pestis capsular antigen (F1 antigen) on the surface of an aroA mutant of Salmonella typhimurium induces high levels of protection against plague. Infect Immun 65:1926-1930
44. Tobe T, Schoolnik GK, Sohel I et al (1996) Cloning and characterization of bfpTVW, genes required for the transcriptional activation of bfpA in enteropathogenic Escherichia coli. Mol Microbiol 21:963-975
45. Zhang L, Chaudhuri RR, Constantinidou C et al (2004) Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157:H7. J Bacteriol 72:7282-7293