Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factor GreA and GreB

Genes to Cells

Volumn 6, Issue 5, 2001, Pages 389-401

  Sen, Ranjan ^a,b   Nagai, Hiroki ^a,c   Shimamoto, Nobuo ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; BACTERIAL RNA; ELONGATION FACTOR; HOLOENZYME; RNA POLYMERASE;

ARTICLE; COMPLEX FORMATION; CONCENTRATION (PARAMETERS); CONFORMATION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE SWITCHING; MODEL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA CLEAVAGE; RNA SYNTHESIS; RNA TRANSLATION; SYNTHESIS; TRANSCRIPTION INITIATION;

BASE SEQUENCE; BINDING SITES; DNA-DIRECTED RNA POLYMERASES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, GENETIC; MUTATION; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; RNA-BINDING PROTEINS; TEMPLATES, GENETIC; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0035000838     PISSN: 13569597     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2443.2001.00436.x     Document Type: Article

References (34)

1. Arndt, K.M. & Chamberlin, M.J. (1990) RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes. J. Mol. Biol. 213, 79-108.
2. Borukhov, S. & Goldfarb, A. (1996) Purification and assay of Escherichia coli transcript cleavage factors GreA and GreB. Meth. Enzymol. 274, 315-326.
3. Borukhov, S., Polyakov, A., Nikiforov, V. & Goldfarb, A. (1992) GreA protein: a transcription elongation factor from Escherichia coll Proc. Natl. Acad. Sci. USA 89, 8899-8902.
4. Borukhov, S., Sagitov, V. & Goldfarb, A. (1993) Transcript cleavage factors from E. coli. Cell 72, 459-466.
5. Carpousis, A.J. & Gralla, J.D. (1980) Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lacUV5 promoter. Biochemistry 19, 3245-3253.
6. Craig, M.L., Tsodikov, O.V, McQuade, K.L., et al. (1998) DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol. 283, 741-756.
7. Ellinger, T., Behnke, D, Bujard, H. & Gralla, J.D (1994) Stalling of Escherichia coli RNA polymerase in the +6 to +12 region in vivo is associated with tight binding to consensus promoter elements. J. Mol. Biol. 239, 455-465.
8. Erie, DA., Hajeiseyedjavadi, O., Young, M. & von Hippel, P.H. (1992) Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science 262, 867-873.
9. Feng, G.H., Lee, DN., Wang, D, Chan, C.L. & Landick, R. (1994) GreA induced transcript cleavage in transcription complexes containing Escherichia coli RNA polymerase is controlled by multiple factors, including nascent transcript location and structure. J. Biol. Chem. 269, 22282-22294.
10. Hamamoto, Y., Hirashima, S., Natori, S., Yamamoto, N. & Kobayashi, N. (1988) Augmentation and stable expression of a novel transcription factor SII in CD4-positive cells on infection with human immunodeficiency virus type-1 (HIV-1). Biochem. Biophys. Res. Commun. 155, 1364-1352.
11. Heinemann, M. & Wagner, R. (1997) Guanosine 3′,5′-bis (diphosphate) (ppGpp)-dependent inhibition of transcription from stringently controlled Escherichia coli promoters can be explained by an altered initiation pathway that traps RNA polymerase. Eur. J. Biochem. 247, 990-999.
12. Hsu, L.M., Vo, N.V. & Chamberlin, M.J. (1995) Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro. Proc. Natl. Acad. Sci. USA 92, 11588-11592.
13. Izban, M.G. & Luse, D.S. (1992) The RNA polymerase II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII. Genes Dev. 6, 1342-1356.
14. Kammerer, W, Deuschle, U, Gentz, R. & Bujard, H. (1986) Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. EMBO J. 5, 2995-3000.
15. Komissarova, N. & Kashlev, M. (1997) Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94, 1755-1760.
16. Koulich, D, Orlova, M., Malhotra, A., Sali, A., Darst, S. & Borukhov, S. (1997) Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. J. Biol. Chem. 272, 7201-7210.
17. Krummel, B. & Chamberlin, M.J. (1992) Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical properties. J. Mol. Biol. 225, 221-237.
18. Kubori, T. & Shimamoto, N. (1996) A branched pathway in the early stage of transcription by Escherichia coli RNA polymerase. J. Mol. Biol. 256, 449-457.
19. Kubori, T. & Shimamoto, N. (1997) Physical interference between Escherichia coli RNA polymerase molecules transcribing in tandem enhances abortive synthesis and misincorporation. Nucl. Acids Res. 25, 2640-2647.
20. Lee, D.N., Feng, G. & Landick, R. (1994) GreA-induced transcript cleavage is accompanied by reverse translocation to a different transcription complex conformation. J. Biol. Chem. 269, 22295-22303.
21. Menendez, M., Kolb, A. & Buc, H. (1987) A new target for CRP activation at the malT promoter. EMBO J. 6, 4227-4234.
22. Metzger, W., Schickor, P., Meier, T., Werel, W. & Heumann, H. (1993) Nucleation of RNA chain formation by Escherichia coli DNA-dependent RNA polymerase. J. Mol. Biol. 232, 35-49.
23. Nudler, E., Mutaev, A., Lukhtanov, E. & Goldfarb, A. (1997) The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89, 33-41.
24. Orlova, M., Newlands, J., Das, A., Goldfarb, A. & Borukhov, S. (1995) Intrinsic cleavage activity of RNA polymerase. Proc. Natl. Acad. Sc. USA 92, 4596-4600.
25. Pfeffer, S.R., Stahl, S.J. & Chamberlin, M.J. (1977) Binding of Escherichia coli RNA polymerase to T7 DNA. Displacement of holoenzyme from promoter complexes by heparin. J. Biol. Chem. 252, 5403-5407.
26. Reines, D, Chamberlin, M.J. & Kane, C.M. (1989) Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro. J. Biol. Chem. 264, 10799-10809.
27. 70 subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 273, 9872-9877.
28. R promoter during transcription initiation. J. Biol. Chem. 275, 10899-10904.
29. Shimamoto, N., Wu, F.Y.H. & Wu, C.W. (1981) Mechanism of RNA chain initiation 3. Molecular pulse-labeling study of ribonucleic acid synthesis on T7 deoxyribonucleic acid template. Biochemistry 20, 4745-4755.
30. Sparkowski, J. & Das, A. (1990) The nucleotide sequence of greA, a suppressor gene that restores growth of an Escherichia coli RNA polymerase mutant at high temperature. Nucl. Acids Res. 18, 6443.
31. Sparkowski, J. & Das, A. (1991) Location of a new gene, greA, on the Escherichia coli chromosome. J. Bacteriol. 173, 5256-5257.
32. Surratt, C.K., Milan, S.C. & Chamberlin, M.J. (1991) Spontaneous cleavage of RNA in Ternary complexes of Escherichia coli RNA polymerase and its significance for the mechanism of transcription. Proc. Natl. Acad. Sci. USA 88, 7983-7987.
33. Tagami, H. & Aiba, H. (1998) A common role of CRP in transcription activation: CRP acts transiently to stimulate events leading to open complex formation at a diverse set of promoters. EMBO J. 17, 1759-1767.
34. Tagami, H. & Aiba, H. (1999) An inactive open complex mediated by an UP element at Escherichia coli promoters. Proc. Natl. Acad. Sci. USA 96, 7202-7207.