NTP concentration effects on initial transcription by T7 RNAP indicate that translocation occurs through passive sliding and reveal that divergent promoters have distinct NTP concentration requirements for productive initiation

Journal of Molecular Biology

Volumn 281, Issue 5, 1998, Pages 777-792

  Guajardo, Richard ^a   Lopez, Pascal ^b   Dreyfus, Marc ^b   Sousa, Rui ^a  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

^b ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

NTP K(m); T7 RNA polymerase; Transcription; Transcriptional regulation; Translocation

Indexed keywords

DNA; RNA POLYMERASE;

ARTICLE; BACTERIOPHAGE T7; CHEMICAL BOND; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA SYNTHESIS; DNA TRANSCRIPTION; GENE TRANSLOCATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DEGRADATION;

UNIDENTIFIED BACTERIOPHAGE;

EID: 0032483305     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1988     Document Type: Article

References (45)

1. Bonner G., Patra D., Lafer E.M., Sousa R. Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure. EMBO J. 11:1992;3767-3775
2. Carpousis A.J., Stefano J.E., Gralla J.D. 5′Nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters. J. Mol. Biol. 157:1982;619-633
3. Carver T.E. Jr, Hochstrasser R.A., Millar D.P. Proofreading DNA; recognition of aberrant DNA termini by the Klenow fragment of DNA polymerase I. Proc. Natl Acad. Sci. USA. 91:1994;10670-10674
4. Donahaue J.P., Turnbough C.L. Jr. Nucleotide-specific transcriptional pausing in the pyrBI leader region of Escherichia coli K-12. J. Biol. Chem. 269:1994;18185-18191
5. Donlin M.J., Patel S.S., Johnson K.A. Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction. Biochemistry. 30:1991;538-546
6. Dunn J.J., Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166:1983;477-535
7. Eom S.H., Wang J., Steitz T.A. Structure of Taq polymerase with DNA at the polymerase active site. Nature. 382:1996;278-281
8. Gaal T., Bartlett M., Ross W., Turnbough C.L. Jr, Gourse R. NTP Concentration as a regulator of transcription initiation control of rRNA synthesis in bacteria. Science. 278:1997;2092-2097
9. Guajardo R., Sousa R. Model for the mechanism of polymerase translocation. J. Mol. Biol. 265:1997;8-19
10. Holstege F.C.P., Fiedler U., Timmers H.Th.M. Three transition in the RNA polymerase II transcription complex during initiation. EMBO J. 16:1997;7468-7480
11. Horton N., Lewis M., Lu P. E. coli lac repressor-lac operator interaction and the influence of allosteric activators. J. Mol. Biol. 265:1997;1-7
12. Hung S.C., Gottesman M.E. The NUN protein of bacteriophage HK022 unhibits translocation of Escherichia coli RNA polymerase without abolishing its catalytic activities. Genes Dev. 11:1997;2670-2678
13. Ikeda R.A., Richardson C.C. Interactions of the RNA polymerase of bacteriophage T7 with its promoter during binding and initiation of transcription. Proc. Natl Acad. Sci. USA. 83:1986;3614-3618
14. Jia Y., Patel S.S. Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase. Biochemistry. 36:1997;4223-4232
15. Jin D.J. Slippage synthesis at the galP2 promoter of Escherichia coli and its regulation by UTP concentration and cAMP·cAMP receptor protein. J. Biol. Chem. 269:1994;17221-17227
16. Johnson K.A. Conformational coupling in DNA polymerase fidelity. Annu. Rev. Biochem. 62:1993;685-713
17. Kammerer W., Deuschle U., Gentz R., Bujard H. Functional dissection of E. coli promoters information in the transcribed region is involved in late steps of the overall process. EMBO J. 5:1986;2995-3000
18. Komissarova N., Kashlev M. Transcriptional arrest Escherichia coli RNA polymerase translocates backward, leaving the 3′-end of the RNA intact and extruded. Proc. Natl Acad. Sci. USA. 94:1997;1755-1760
19. Krummel B., Chamberlin M.J. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry. 28:1989;7829-7842
20. Kubori T., Shimamoto N. A branched pathway in the early stage of transcription by Escherichia coli RNA polymerase. J. Mol. Biol. 256:1996;449-457
21. Kumar A., Patel S.S. Inhibition of T7 RNA polymerase transcription initiation and transition from initiation to elongation are inhibited by T7 lsyozyme via a ternary complex with RNA polymerase and promoter DNA. Biochemistry. 36:1997;13954-13962
22. Landick R. RNA polymerase slides home pause and termination site recognition. Cell. 88:1997;741-744
23. Landick R. RNA polymerase as a molecular motor. Cell. 93:1998;13-16
24. Lee J., Goldfarb A. Lac repressor acts by modifying the initial transcribing complex so that it cannot leave the promoter. Cell. 66:1991;793-798
25. Liu J., Turnbough C.L. Jr. Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at PyrC promoter in Escherichia coli. J. Bacteriol. 176:1994;2938-2945
26. Liu C., Heath L.S., Turnbough C.L. Jr. Regulation of pyrBI operon expression in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation. Genes Dev. 1994;2904-2912
27. Lopez P.J., Guillerez J., Sousa R., Dreyfus M. The low processivity of T7 RNA polymerase over the initially transcribed sequence can limit productive initiation in vivo. J. Mol. Biol. 269:1997;49-51
28. Lopez P.J., Guillerez J., Sousa R., Dreyfus M. On the Mechanism of inhibition of T7 RNA polymerase by lac repressor. J. Mol. Biol. 1998
29. Martin C.T., Muller D.K., Coleman J.E. Processivity in the early stages of transcription by T7 RNA polymerase. Biochemistry. 27:1988;5755-5762
30. McClure W.R., Chow Y. Kinetics and processivity of nucleic acid polymerases. Methods Enzymol. 64:1980;277-297
31. Milligan J.F., Groebe D.R., Witherell G.W., Uhlenbeck O.C. Nucl. Acids Res. 15:1987;8783-8798
32. Nudler E., Mustaev A., Lukhtanov E., Goldfarb A. The RNA-DNA hybrid maintains register of transcription by preventing backtracking of RNA polymerase. Cell. 89:1997;33-41
33. Qi F., Turnbough C.L. Jr. Regulation of codBA operon expression in E. coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching. J. Mol. Biol. 254:1995;552-565
34. Reeder T., Hawley D. Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism. Cell. 87:1996;767-777
35. Roberts J. Control of the Supply Line. Science. 278:1997;2073-2074
36. Saffman P.G., Delbruck M. Brownian motion in biological membranes. Proc. Natl Acad. Sci. USA. 72:1975;3111-3113
37. Schmidt M.C., Chamberlin M.J. Amplification and isolation of Escherichia coli nus A protein and studies of its effects on in vitro RNA chain elongation. Biochemistry. 23:1984;197-203
38. Sorensen K.I., Baker K.E., Kelln R.A., Neuhard J. Nucleotide pool-sensitive selection of the transcriptional start site in vivo at the S. typhinurium pyrC and pyrD promoters. J. Bacteriol. 175:1993;4137-4144
39. Sousa R., Padilla R. A mutant T7 RNA polymerase as a DNA Polymerase. EMBO J. 14:1995;4609-4621
40. Straney D.C., Crothers D.M. A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter. J. Mol. Biol. 193:1987;267-278
41. Tabor S., Richardson C.C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc. Natl Acad. Sci. USA. 82:1985;1074-1078
42. Villemain J., Guajardo R., Sousa R. The role of open complex instability in kinetic promoter selection by T7 RNA polymerase. J. Mol. Biol. 273:1997;958-977
43. von Hippel P.H., Bear D.G., Morgan W.D., McSwiggen J.A. Protein-nucleic acid interactions in transcription a molecular analysis. Annu. Rev. Biochem. 53:1984;389-446
44. Wilson H.R., Archer C.D., Liu J., Turnbough C.L. Jr. Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in E. coli. J. Bacteriol. 174:1992;514-524
45. Wilson H.R., von Hippel P.H. Stability of Escherichia coli transcription complexes near an intrinsic terminator. J. Mol. Biol. 244:1994;36-51