Domain organization of the Escherichia coli RNA polymerase σ70 subunit

Journal of Molecular Biology

Volumn 263, Issue 5, 1996, Pages 637-647

  Severinova, Elena ^a,d   Severinov, Konstantin ^a   Fenyö, David ^a   Marr, Michael ^b   Brody, Edward N ^c   Roberts, Jeffrey W ^b   Chait, Brian T ^a   Darst, Seth A ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b Cornell University ^*  (United States)

^c UNIVERSITY AT BUFFALO   (United States)

^d INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

AsiA; E. coli RNA polymerase; Limited proteolysis; Sigma factor; Transcription

Indexed keywords

BACTERIAL ENZYME; RNA POLYMERASE; SIGMA FACTOR; TRYPSIN;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; ENZYME SUBUNIT; ESCHERICHIA COLI; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0030589041     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0604     Document Type: Article

References (43)

1. Beavis, R. C. & Chait, B. T. (1989). Factors affecting the ultraviolet laser desorption of proteins. Rapid Commun. Mass Spectrom. 3, 233-237.
2. Burgess, R. R., Erickson, B., Gentry, D., Gribskov, M., Hager, D., Lesley, S., Strickland, M. & Thompson, N. (1987). RNA Polymerase and the Regulation of Transcription (Reznikoff, W. S., Burgess, R. R., Dahlberg, J. E., Gross, C. A., Record, M. T. Jr & Wickens, M. P. eds), pp. 3-15, Elsevier Science Publishing Corp, New York.
3. N: bipartite functions. J. Mol. Biol. 248, 781-803.
4. Chamberlin, M. J., Merman, W. C., Wiggs, J. & Neff, N. (1979). A quantitative assay for bacterial RNA polymerases. J. Biol. Chem. 254, 10061-10069.
5. A factor. J. Bacterial. 172, 3257-3263.
6. D: overproduction, domain analysis and DNA-binding properties. J. Mol. Biol. 249, 743-753.
7. Chenchick, A., Beabealashvilli, R. & Mirzabekov, A. (1981). Topography of interaction of Escherichia coli RNA polymerase subunits with the lacUV5 promoter. FEBS Letters, 128, 46-50.
8. Chenchick, A., Beabealashvilli, R., Mirzabekov, A. D. & Shik, V. V. (1982). Contact between subunits of Escherichia coli RNA polymerase and the nucleotides of the lacUV5 promoter. Molekulyarnaya Biologiya, 16, 34-46.
9. Daniels, D., Zuber, P. & Losick, R. (1990). Two amino acids in an RNA polymerase σ factor involved in the recognition of adjacent base-pairs in the -10 region of a cognate promoter. Proc. Natl Acid. Sci. USA, 87, 8075-8079.
10. Dombroski, A. J., Walter, W. A., Record, M. T., Siegele, D. A. & Gross, C. A. (1992). Polypeptides containing highly conserved regions of transcription initiation factor sigma70 exhibit specificity of binding to promoter DNA. Cell, 70, 501-512.
11. Dombroski, A. J., Walter, W. A. & Gross, C. A. (1993). Amino-terminal amino acids modulate sigma-factor DNA-binding activity. Genes Dev. 7, 2446-2455.
12. Gardella, T., Moyle, T. & Susskind, M. M. (1989). A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. J. Mol. Biol. 206, 579-590.
13. Gribskov, M. & Burgess, R. R. (1983). Overexpression and purification of the sigma subunit of Escherichia coli RNA polymerase. Gene, 26, 109-118.
14. Hawley, D. K. & McClure, W. R. (1983). Compilation and analysis of Escherichia coli promoter DNA sequences. Nucl. Acids Res. 11, 2237-2255.
15. Helmann, J. D. & Chamberlin, M. J. (1988). Structure and function of bacterial sigma factors. Annu Rev. Biochem. 57, 839-872.
16. Hillenkamp, F., Karas, M., Beavis, R. C. & Chait, B. T. (1991). Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal. Chem. 63, 1193A-1203A.
17. Juang, Y.-L. & Helmann, J. D. (1994). A promoter melting region in the primary sigma factor of Bacillus subtilis: identification of functionally important aromatic amino acids. J. Mol. Biol. 235, 1470-1488.
18. Kashlev, M., Martin, E., Polyakov, A., Severinov, K., Nikiforov, V. & Goldfarb, A. (1993) Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme. Gene, 130, 9-14.
19. Keilty, S. & Rosenberg, M. (1987). Constituitive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262, 6389-6395.
20. Kumar, A., Malloch, R. A., Fujita, N., Smillie, D. A., Ishihama, A. & Hayward, R. S. (1993). The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter. J. Mol. Biol. 232, 406-418.
21. Kumar, A., Grimes, B., Fujita, N., Makino, K., Malloch, R. A., Hayward, R. S. & Ishihama, A. (1994). Role of the sigma 70 subunit of Escherichia coli RNA polymerase in transcription activation. J. Mol. Biol. 235, 405-413.
22. Lesley, S. A. & Burgess, R. R. (1989). Characterization of the Escherichia coli transcription factor sigma 70: localization of a region involved in the interaction with core RNA polymerase. Biochemistry, 28, 7728-7734.
23. 70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174, 3843-3849.
24. Losick, R. & Pero, J. (1981). Cascades of sigma factors. Cell, 25, 582-584.
25. Lowe, P. A., Hager, D. A. & Burgess, R. R. (1979). Purification and properties of the σ subunit of Escherichia coli DNA-dependent RNA polymerase. Biochemistry, 18, 1344-1352.
26. Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
27. McClure, W. R., Cech, C. L. & Johnston, D. E. (1978). A steady state assay for the RNA polymerase initiation reaction. J. Biol. Chem. 253, 8941-8948.
28. Mulvey, M. R. & Loewen, P. C. (1989). Nucleotide sequence of katF of Escherichia coli suggests that katF protein is a novel σ transcription factor. Nucl. Acids Res. 17, 9979-9991.
29. 70 protein. J. Bacteriol. 175, 85-93.
30. Polyakov, A., Severinova, E. & Darst, S. A. (1995). Three-dimensional structure of Escherichia coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell, 83, 365-373.
31. Ring, B. Z. & Roberts, J. W. (1994). Function of a nontranscribed DNA strand site in transcription elongation. Cell, 78, 317-324.
32. 70 in promoter-proximal pausing. Cell, 86, 485-493.
33. Roberts, C. W. & Roberts, J. W. (1996). Base-specific recognition of the non-template strand of promoter DNA by E. coli RNA polymerase. Cell, 86, 495-501.
34. A mutants defective in promoter melting. J. Bacteriol. 176, 5218-5224.
35. Severinov, K., Fenyö, D., Severinova, E., Mustaev, A., Chait, B. T., Goldfarb, A. & Darst, S. A. (1994). The sigma subunit conserved region 3 is part of "5′-face" of active center of Escherichia coli RNA polymerase. J. Biol. Chem. 269, 20,826-20,828.
36. Siegele, D. A., Hu, J. C., Walter, W. A. & Gross, C. A. (1989). Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 206, 591-603.
37. Stevens, A. (1977). Inhibition of DNA binding by an RNA polymerase inhibitor from T4 phage-infected Escherichia coli. Biochim. Biophys. Acta, 475, 193-196.
38. Studier, F. W., Rosenberg, A. H., Dunn, J. J. & Dubendorff, J. W. (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 185, 60-89.
39. Waldburger, C. & Susskind, M. M. (1994). Probing the informational content of Escherichia coli sigma70 region 2.3 by combinatorial cassette mutagenesis. J. Mol. Biol. 235, 1489-1500.
40. Waldburger, C., Gardella, T., Wong, R. & Susskind, M. M. (1990). Changes in conserved region 2 of Escherichia coli sigma 70 affecting promoter recognition. J. Mol. Biol. 215, 267-276.
41. Wilson, J. (1991). The use of monoclonal antibodies and limited proteolysis in elucidation of structure-function relationships in proteins. Methods Biochem. Anal. 35, 207-250.
42. Zhou, Y. N., Walter, W. A. & Gross, C. A. (1992). A mutant sigma 32 with a small deletion in conserved region 3 of sigma has reduced affinity for core RNA polymerase. J. Bacteriol. 174, 5005-5012.
43. Zuber, P., Healy, J., Carter, H. L., III, Cutting, S., Moran, C. P., Jr & Losick, R. (1989). Mutation changing the specificity of an RNA polymerase sigma factor. J. Mol. Biol. 206, 605-614.