A mutation in region 1.1 of σ70 affects promoter DNA binding by Escherichia coli RNA polymerase holoenzyme

EMBO Journal

Volumn 18, Issue 3, 1999, Pages 709-716

  Bowers, Christina Wilson ^a   Dombroski, Alicia J ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

Initiation; RNA polymerase; Sigma; Transcription

Indexed keywords

ALANINE; BACTERIAL DNA; ISOLEUCINE; PROTEIN SUBUNIT; RNA POLYMERASE; SIGMA FACTOR;

AMINO ACID SUBSTITUTION; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE MUTATION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING;

AMINO ACID SUBSTITUTION; CATALYTIC DOMAIN; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; HOLOENZYMES; PHENOTYPE; POINT MUTATION; PROMOTER REGIONS (GENETICS); SIGMA FACTOR; SUPPRESSION, GENETIC; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0011981018     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.3.709     Document Type: Article

References (39)

1. 70 subunit from Escherichia coli RNA polymerase are modulated by an interaction with core enzyme. Biochemistry, 37, 3312-3320.
2. Daniels, D., Zuber, R. and Losick, R. (1990) Two amino acids in an RNA polymerase σ factor involved in recognition of adjacent base pairs in the -10 region of a cognate promoter. Proc. Natl Acad. Sci. USA, 87, 8075-8079.
3. Darst, S.A., Kubalek, E.W. and Kornberg, R.D. (1989) Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature, 340, 730-732.
4. deHaseth, P.L., Zupanic, M.L. and Record, M.T.,Jr (1998) RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol., 180, 3019-3025.
5. 70 exhibit specificity of binding to promoter DNA. Cell, 70, 501-512.
6. Dombroski, A.J., Walter, W.A. and Gross, C.A. (1993) Amino-terminal amino acids modulate σ-factor DNA-binding activity. Genes Dev., 7, 2446-2455.
7. 70 subunit of RNA polymerase with altered promoter specificity. J. Mol. Biol., 206, 579-590.
8. Gribskov, M. and Burgess, R.R. (1986) Sigma factors from E.coli, B.subtilis, phage SPO1 and phage T4 are homologous proteins. Nucleic Acids Res., 14, 6745-6763.
9. Gross, C.A., Lonetto, M. and Losick, R. (1992) Sigma factors. In McKnight, S.L. and Yamamoto, K.R. (eds). Transcriptional Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Vol. 1, pp. 129-176.
10. Hawley, D.K. and McClure, W.R. (1980) In vitro comparison of initiation properties of bacteriophage λ wild-type PR and x3 mutant promoters. Proc. Natl Acad. Sci. USA, 77, 6381-6385.
11. Helmann, J.D. and Chamberlin, M.J. (1988) Structure and function of bacterial sigma factors. Annu. Rev. Biochem., 57, 839-872.
12. Hinkle, D.C. and Chamberlin, M.J. (1972a) Studies of the binding of Escherichia coli RNA polymerase to DNA. I. The role of the sigma subunit in site selection. J. Mol. Biol., 70, 157-185.
13. Hinkle, D.C. and Chamberlin, M.J. (1972b) Studies of the binding of Escherichia coli RNA polymerase to DNA. II. Kinetics of the binding reaction. J. Mol. Biol., 70, 187-195.
14. Huang, X., Lopez de Saro, F.J. and Helmann, J.D. (1997) σ factor mutations affecting the sequence-selective interaction of RNA polymerase with -10 region single-stranded DNA. Nucleic Acids Res., 25, 2603-2609.
15. Juang, Y. and Helmann, J.D. (1994) A promoter melting region in the primary σ factor of Bacillus subtilis. J. Mol. Biol., 235, 1470-1488.
16. Jones, C.H. and Moran, C.P.,Jr (1992) Mutant σ factor blocks transition between promoter binding and initiation of transcription. Proc. Natl Acad. Sci. USA, 89, 1958-1962.
17. Kunkel, T.A., Roberts, J.D. and Zakour, R.A. (1987) Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol., 154, 367-382.
18. 70: localization of a region involved in the interaction with core RNA polymerase. Biochemistry, 28, 7728-7734.
19. 70 family: sequence conservation and evolutionary relationships. J. Bacteriol., 174, 3843-3849.
20. Losick, R. and Pero, J. (1981) Cascades of sigma factors. Cell, 25, 582-584.
21. Lowe, R. Hager, D.A. and Burgess, R.R. (1979) Purification and properties of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase. Biochemistry, 18, 1344-1352.
22. Marr, M.T. and Roberts, J.W. (1997) Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science, 276, 1258-1260.
23. 70 in an Escherichia coli RNA polymerase-lacUV5 open promoter complex. Biochemistry, 37, 7670-7675.
24. Polyakov, A., Severinova, E. and Darst, S.A. (1995) Three-dimensional structure of E.coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell, 83, 365-373.
25. 70), promoters and the kinetics of the steps of transcription initiation. In Neidhardt, F.C. (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. 2nd edn. Vol. 1, pp. 792-820.
26. 70 in promoter-proximal pausing. Cell, 86, 485-493.
27. Roberts, C.W. and Roberts, J.W. (1996) Base-specific recognition of the nontemplate strand of promoter DNA by E.coli RNA polymerase. Cell, 86, 495-501.
28. R promoter. J. Mol. Biol., 176, 495-521.
29. A mutants defective in promoter melting. J. Bacteriol., 176, 5218-5224.
30. Saucier, J. and Wang, J. (1972) Angular alteration of the DNA helix by E.coli RNA polymerase. Nature New Biol., 239, 167-170.
31. 70 subunit. J. Mol. Biol., 263, 637-647.
32. 70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol., 206, 591-603.
33. Stragier, P., Parsot, C. and Bouvier, J. (1985) Two functional domains conserved in major and alternate bacterial sigma factors. FEBS Lett., 187, 11-15.
34. Strauss, H.S., Burgess, R.R. and Record, M.T.,Jr (1980) Binding of Escherichia coli ribonucleic acid polymerase holoenzyme to a bacteriophage T7 promoter-containing fragment: evaluation of promoter binding constants as a function of solution conditions. Biochemistry, 19, 3504-3515.
35. Travers, A.A. and Burgess, R.R. (1969) Cyclic re-use of the RNA polymerase sigma factor. Nature, 222, 537-540.
36. 70 affecting promoter recognition. J. Mol. Biol., 215, 267-276.
37. 70 is required for efficient isomerization and intiation of transcription by Escherichia coli RNA polymerase. J. Mol. Biol., 267, 60-74.
38. Wu, Y.-H., Yarbrough, L.R. and Wu, C.-W. (1976) Conformational transition of Escherichia coli RNA polymerase induced by the interaction of σ subunit with core enzyme. Biochemistry, 15, 3254-3258.
39. Zuber, P., Healy, J., Carter, H.L.,III, Cutting, S., Moran, C.P.,Jr and Losick, R. (1989) Mutation changing the specificity of an RNA polymerase sigma factor. J. Mol. Biol., 206, 605-614.