Region 1 of σ70 is required for efficient isomerization and initiation of transcription by Escherichia coli RNA polymerase

Journal of Molecular Biology

Volumn 267, Issue 1, 1997, Pages 60-74

  Wilson, Christina ^a   Dombroski, Alicia J ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

Isomerization; Region 1; Transcription initiation; 70

Indexed keywords

POLYPEPTIDE; RNA POLYMERASE; SIGMA FACTOR; DNA DIRECTED RNA POLYMERASE; RNA POLYMERASE SIGMA 70;

AMINO TERMINAL SEQUENCE; ARTICLE; DNA BINDING; ENZYME SUBUNIT; ESCHERICHIA COLI; ISOMERISM; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION INITIATION; AMINO ACID SEQUENCE; CHEMISTRY; ENZYMOLOGY; GENETIC TRANSCRIPTION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY;

ESCHERICHIA COLI; PROKARYOTA;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ISOMERISM; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, AMINO ACID; SIGMA FACTOR; TRANSCRIPTION, GENETIC;

EID: 0031581917     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0875     Document Type: Article

References (45)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment research tool. J. Mol. Biol. 215:1990;403-410.
2. Bernard S. L., Meares C. F. The σ subunit of RNA polymerase contacts the leading ends of transcripts 9-13 bases long on the λ P R promoter but not on T7 A1. Biochemistry. 25:1986;5914-5919.
3. Buckle M., Geiselman J., Kolb A., Buc H. Protein-DNA cross-linking at the lac promoter. Nucl. Acids Res. 19:1991;833-840.
4. 32. J. Bacteriol. 170:1988;3479-3484.
5. 2+binding and its structural consequences at the transcription start site. Biochemistry. 34:1995;15624-15632.
6. Daniels D., Zuber R., Losick R. 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. 87:1990;8075-8079.
7. DeHaseth P. L., Helmann J. D. Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol. Microbiol. 16:1995;817-824.
8. 70exhibit specificity of binding to promoter DNA. Cell. 70:1992;501-512.
9. Dombroski A. J., Walter W. A., Gross C. A. Amino-terminal amino acids modulate σ-factor DNA-binding activity. Genes Dev. 7:1993;2446-2455.
10. 70subunit of RNA polymerase with altered promoter specificity. J. Mol. Biol. 206:1989;579-590.
11. Gribskov M., Burgess R. R. Sigma factors from E. coli, B. subtilis, phage SPO1, and phage T4 are homologous proteins. Nucl. Acids Res. 14:1986;6745-6763.
12. Gross C. A., Lonetto M., Losick R. Sigma factors. Transcriptional Regulation. 1992;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
13. Rand ×3 mutant promoters. Proc. Natl Acad. Sci. USA. 77:1980;6381-6385.
14. Helmann J. D., Chamberlin M. J. Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57:1988;839-872.
15. Hinkle D. C., Chamberlin M. The role of sigma subunit in template site selection by E. coli RNA polymerase. Cold Spring Harbor Symp. Quant. Biol. 35:1970;65-72.
16. Hsu L. M. Quantitative parameters for promoter clearance. Methods Enzymol. 273:1996;59-71.
17. Hu J. C., Gross C. A. Mutations in rpoD that increase expression of genes in the mal regulon of Escherichia coli k-12. J. Mol. Biol. 203:1988;15-27.
18. Jones C. H., Moran C. P., Jr. Mutant σ factor blocks transition between promoter binding and initiation of transcription. Proc. Natl Acad. Sci. USA. 89:1992;1958-1962.
19. Efrom Bacillus subtilis. J Bacteriol. 174:1992;6815-6821.
20. Juang Y., Helmann J. D. A promoter melting region in the primary σ factor of Bacillus subtilis. J. Mol. Bio. 235:1994;1470-1488.
21. 70: localization of a region involved in the interaction with core RNA polymerase. Biochemistry. 28:1989;7728-7734.
22. 70family: sequence conservation and evolutionary relationships. J. Bacteriol. 174:1992;3843-3849.
23. Losick R., Pero J. Cascades of sigma factors. Cell. 25:1981;582-584.
24. McClure W. R. Rate-limiting steps in RNA chain initiation. Proc. Natl Acad. Sci. USA. 77:1980;5634-5638.
25. Meissner P. S., Sisk W. P., Berman M. L. Bacteriophage λ cloning system for the construction of directional cDNA libraries. Proc. Natl Acad. Sci. USA. 84:1987;4171.
26. Melancon P., Burgess R. R., Record M. T., Jr. Nitrocellulose filter binding studies of the interactions of E. coli RNA polymerase holoenzyme with deoxyribonucleic acid restriction fragments: evidence for multiple classes of non-promoter interactions, some of which display promoter-like properties. Biochemistry. 21:1982;4318-4331.
27. 54(sigma N). Mol. Microbiol. 10:1993;903-909.
28. Newlands J. T., Ross W., Gosink K. K., Gourse R. L. Factor-independent activation of Escherichia coli rRNA Transcription. J. Mol. Bio. 220:1991;569-583.
29. 70), promoters, and the kinetics of the steps of transcription initiation. Neidhardt F. C. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. 1996;ASM Press, Washington DC.
30. Rpromoter by salt concentration. Biochemistry. 24:1985;4721-4726.
31. Rpromoter. J. Mol. Biol. 176:1984;495-521.
32. Amutants defective in promoter melting. J. Bacteriol. 176:1994;5218-5224.
33. 54. Cell. 62:1990;945-954.
34. Saucier J., Wang J. Angular alteration of the DNA helix by E. coli RNA polymerase. Nat. New Biol. 239:1972;167-170.
35. 70subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 206:1989;591-603.
36. Simpson R. B. The molecular topography of RNA polymerase-promoter interaction. Cell. 18:1979;277-285.
37. Stragier P., Parsot C., Bouvier J. Two functional domains conserved in major and alternate bacterial sigma factors. FEBS Letters. 187:1985;11-15.
38. 2+. Biochemistry. 31:1992;7815-7825.
39. Rtranscription start site. Science. 259:1993;358-361.
40. d18 DNA containing promoters for λ genes and for rrnB, tufB, rplK, A, rplJ,L , and rpoB, C genes. Gene. 6:1979;331-365.
41. Travers A. A., Burgess R. R. Cyclic re-use of the RNA polymerase sigma factor. Nature. 222:1969;537-540.
42. 70region 2.3 by combinatorial cassette mutagenesis. J. Mol. Biol. 235:1994;1489-1500.
43. 70affecting promoter recognition. J. Mol. Biol. 215:1990;267-276.
44. 54in setting the rate and temperature dependence of promoter melting in vivo. J. Biol. Chem. 267:1992;24762-24768.
45. Zuber P., Healy J., Carter H. L., III, Cutting S., Moran C. P., Jr, Losick R. Mutation changing the specificity of an RNA polymerase sigma factor. J. Mol. Biol. 206:1989;605-614.