Functional determinants of transcription factors in Escherichia coli: Protein families and binding sites

Trends in Genetics

Volumn 19, Issue 2, 2003, Pages 75-79

  Babu, M Madan ^a   Teichmann, Sarah A ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; BINDING SITE; DNA BINDING; DNA STRUCTURE; ESCHERICHIA COLI; GENE CONTROL; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; REVIEW;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0037303198     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-9525(02)00039-2     Document Type: Short Survey

References (21)

1. Salgado H., et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29:2001;72-74.
2. Shen-Orr S.S., et al. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31:2002;64-68.
3. Perez-Rueda E., Collado-Vides J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28:2000;1838-1847.
4. Gough J., Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res. 30:2002;268-272.
5. Karplus K., et al. Hidden Markov models for detecting remote protein homologies. Bioinformatics. 14:1998;846-856.
6. Murzin A.G., et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
7. Bateman A., et al. The Pfam protein families database. Nucleic Acids Res. 30:2002;276-280.
8. Morett E., Segovia L. The sigma 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 175:1993;6067-6074.
9. Aravind L., Koonin E.V. DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27:1999;4658-4670.
10. Prag G., et al. Structural principles of prokaryotic gene regulatory proteins and the evolution of repressors and gene activators. Mol. Microbiol. 26:1997;619-620.
11. Perez-Rueda E., et al. Genomic position analyses and the transcription machinery. J. Mol. Biol. 275:1998;165-170.
12. Collado-Vides J., et al. Control site location and transcriptional regulation in Escherichia coli. Microbiol. Rev. 55:1991;371-394.
13. Dai X., Rothman-Denes L.B. DNA structure and transcription. Curr. Opin. Microbiol. 2:1999;126-130.
14. Lobell R.B., Schleif R.F. DNA looping and unlooping by AraC protein. Science. 250:1990;528-532.
15. Travers A., Muskhelishvili G. DNA microloops and microdomains: a general mechanism for transcription activation by torsional transmission. J. Mol. Biol. 279:1998;1027-1043.
16. Pemberton I.K., et al. FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter. J. Mol. Biol. 318:2002;651-663.
17. Rhee K.Y., et al. Leucine-responsive regulatory protein-DNA interactions in the leader region of the ilvGMEDA operon of Escherichia coli. J. Biol. Chem. 271:1996;26499-26507.
18. Rojo F. Repression of transcription initiation in bacteria. J. Bacteriol. 181:1999;2987-2991.
19. Hochschild A., Dove S.L. Protein-protein contacts that activate and repress prokaryotic transcription. Cell. 92:1998;597-600.
20. Rhodius V.A., Busby S.J. Positive activation of gene expression. Curr. Opin. Microbiol. 1:1998;152-159.
21. Muller-Hill B. Some repressors of bacterial transcription. Curr. Opin. Microbiol. 1:1998;145-151.