The σ70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription

Nature Structural and Molecular Biology

Volumn 11, Issue 6, 2004, Pages 551-557

  Brodolin, Konstantin ^a,e   Zenkin, Nikolay ^a   Mustaev, Arkady ^b   Mamaeva, Daria ^c   Heumann, Hermann ^d  

^a INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

^b PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

^c ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^d MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^e INSTITUTE OF HUMAN GENETICS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HEPARIN; INITIATION FACTOR; POLYSACCHARIDE; RNA POLYMERASE; RNA POLYMERASE SIGMA 70; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BIOCHEMISTRY; COMPLEX FORMATION; CONSENSUS SEQUENCE; CONTROLLED STUDY; ENZYME INDUCTION; ENZYME SUBUNIT; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; LACTOSE OPERON; LACUV5 GENE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; REPRESSOR GENE; RNA STABILITY; RNA TRANSLATION; SYNTHESIS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

BASE SEQUENCE; DNA; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI PROTEINS; LAC OPERON; OPERATOR REGIONS (GENETICS); PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN SUBUNITS; SIGMA FACTOR; TRANSCRIPTION, GENETIC;

ANIMALIA; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 2542456496     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb768     Document Type: Article

References (43)

1. Young, B.A., Gruber, T.M. & Gross, C.A. Views of transcription initiation. Cell 109, 417-420 (2002).
2. 70 family, sequence conservation and evolutionary relationships. J. Bacteriol. 174, 3843-3849 (1992).
3. Hawley, D.K. & McClure, W.R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids. Res. 11, 2237-2255 (1983).
4. Travers, A. & Burgess, R. Cyclic re-use of the RNA polymerase σ factor. Nature 222, 537-540 (1969).
5. Hansen, U.M. & McClure, W.R. Role of the σ subunit of Escherichia coli RNA polymerase in initiation. II. Release of σ from ternary complexes. J. Biol. Chem. 255, 9564-9570 (1980).
6. Krummel, B. & Chamberlin, M.J. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry 28, 7829-7842 (1989).
7. Metzger, W., Schickor, P., Meier, T., Werel, W. & Heumann. H. Nucleation of RNA chain formation by Escherichia coli DNA-dependent RNA polymerase. J. Mol. Biol. 232, 35-49 (1993).
8. 70 in promoter-proximal pausing. Cell 186, 485-493 (1996).
9. 70-retaining transcription elongation complexes from Escherichia coli. Cell 106, 443-451 (2001).
10. 70 with RNA polymerase during transcription. Fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106, 453-463 (2001).
11. Murakami, K.S., Masuda, S. & Darst, S.A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296, 1280-1284 (2002).
12. Vassylyev, D.G. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417, 712-719 (2002).
13. Shimamoto, N., Kamigochi, T. & Utiyama, H. Release of the σ subunit of Escherichia coli DNA-dependent RNA polymerase depends mainly on time elapsed after the start of initiation, not on length of product RNA. J. Biol. Chem. 261, 11859-11865 (1986).
14. 70 subunit of RNA polymerase is contacted by the λQ antiterminator during early elongation. Mol. Cell 10, 611-622 (2002).
15. Brodolin, K. & Buckle, M. Differential melting of the transcription start site associated with changes in RNA polymerase-promoter contacts in open transcription complexes. J. Mol. Biol. 307, 25-30 (2001).
16. Brodolin, K., Mustaev, A., Severinov, K. & Nikiforov, V. Identification of RNA polymerase β′ subunit segment contacting the melted region of the lacUV5 promoter. J. Biol. Chem. 275, 3661-3666 (2000).
17. Severinov, K. et al. Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the β and β′ subunits of Escherichia coli RNA polymerase. J. Biol. Chem. 271, 27969-27974 (1996).
18. Pfeffer, S.R., Stahl, S.J. & Chamberlin, M.J. Binding of Escherichia coli RNA polymerase to T7 DNA. Displacement of holoenzyme from promoter complexes by heparin. J. Biol. Chem. 252, 5403-5407 (1977).
19. Cech, C.L. & McClure, W.R. Characterization of ribonucleic acid polymerase-T7 promoter binary complexes. Biochemistry 19, 2440-2447 (1980).
20. Fisher, R. & Blumenthal, T. Analysis of RNA polymerase by trypsin cleavage. Evidence for a specific association between subunits α and β involved in the closed to open complex transition. J. Biol. Chem. 255, 11056-11062 (1980).
21. Marr, M.T. & Roberts, J.W. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol. Cell 6, 1275-1285 (2000).
22. Carpousis, A.J. & Gralla, J.D. Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. J. Mol. Biol. 183, 165-177 (1985).
23. Borukhov, S., Sagitov, V. & Goldfarb, A. Transcript cleavage factors from E. coli. Cell 72, 459-466 (1993).
24. 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J. Mol. Biol. 220, 307-324 (1991).
25. 4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264, 8074-8081 (1989).
26. 70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 206, 591-603 (1989).
27. 70 affecting promoter recognition. J. Mol. Biol. 215, 267-276 (1990).
28. Juang, Y.-L. & Helmann, J.D. A promoter melting region in the primary σ factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. J. Mol. Biol. 235, 1470-1488 (1994).
29. Roberts, C.W. & Roberts, J.W. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell 86, 495-501 (1996).
30. Gilbert, W. & Maxam, A. The nucleotide sequence of the lac operator. Proc. Natl. Acad. Sci. USA 70, 3581-3584 (1973).
31. 70. Cell 105, 935-944 (2001).
32. 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nat. Struct. Mol. Biol. advance online publication, 2 May 2004 (doi:10.1038/nsmb757)
33. Karls et al. Pseudorevertants of a lac promoter mutation reveal overlapping nascent promoters. Nucleic Acids Res. 17, 3927-3949 (1989).
34. Ozoline, O.N., Deev, A.A., Arkhipova, M.V., Chasov, V.V. & Travers, A. Proximal transcribed regions of bacterial promoters have a non-random distribution of A/T tracts. Nucleic Acids Res. 27, 4768-4774 (1999).
35. Marr, M.T., Datwyler, S.A., Meares, C.F. & Roberts, J.W. Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins. Proc. Natl. Acad. Sci. USA 98, 8972-8978 (2001).
36. 70-dependent pausing at promoter-distal locations. Genes Dev. 17, 2839-2851 (2003).
37. Nugent, M.A. Heparin sequencing brings structure to the function of complex oligosaccharides. Proc. Natl. Acad. Sci. USA 97, 10301-10303 (2000).
38. Borukhov, S. et al. Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the β subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 266, 23921-23926 (1991).
39. Mooney, R.A. & Landick, R. RNA polymerase unveiled. Cell 98, 687-690 (1999).
40. Yarnell, W.S. & Roberts, J.W. The phage lambda gene Q transcription antiterminator binds DNA in the late gene promoter as it modifies RNA polymerase. Cell 69, 1181-1189 (1992).
41. Wassarman, K.M. & Storz, G. 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613-623 (2000).
42. Gribskov, M. & Burgess, R.R. Overexpression and purification of the σ subunit of Escherichia coli RNA polymerase. Gene 26, 109-118 (1983).
43. Keilty, S. & Rosenberg, M. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262, 6389-6395 (1987).