A ratchet mechanism of transcription elongation and its control

Cell

Volumn 120, Issue 2, 2005, Pages 183-193

  Bar Nahum, Gil ^a   Epshtein, Vitaly ^a   Ruckenstein, Andrei E ^b   Rafikov, Ruslan ^a   Mustaev, Arkady ^c   Nudler, Evgeny ^a  

^a NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHODIESTERASE; RNA POLYMERASE;

ARTICLE; CELL VIABILITY; CHEMICAL BOND; ESCHERICHIA COLI; GENE TRANSLOCATION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI;

EID: 12944324227     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2004.11.045     Document Type: Article

References (46)

1. Artsimovitch I., Landick R. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA. 97:2000;7090-7095
2. Bar-Nahum G., Nudler E. Isolation and characterization of sigma(70)-retaining transcription elongation complexes from Escherichia coli. Cell. 106:2001;443-451
3. Burova E., Hung S.C., Sagitov V., Stitt B.L., Gottesman M.E. Escherichia coli NusG protein stimulates transcription elongation rates in vivo and in vitro. J. Bacteriol. 177:1995;1388-1392
4. Condon C., Squires C., Squires C.L. Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59:1995;623-645
5. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase II at 2.8 angstrom resolution Science. 292:2001;1863-1876
6. Epshtein V., Mustaev A., Markovtsov V., Bereshchenko O., Nikiforov V., Goldfarb A. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol. Cell. 10:2002;623-634
7. Foster J.E., Holmes S.F., Erie D.A. Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell. 106:2001;243-252
8. Fromant M., Blanquet S., Plateau P. Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction. Anal. Biochem. 224:1999;347-353
9. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription. an RNA polymerase II elongation complex at 3.3 Å resolution Science. 292:2001;1876-1882
10. Guajardo R., Sousa R. A model for the mechanism of polymerase translocation. J. Mol. Biol. 265:1997;8-19
11. Gusarov I., Nudler E. The mechanism of intrinsic transcription termination. Mol. Cell. 3:1999;495-504
12. Gusarov I., Nudler E. Control of intrinsic transcription termination by N and NusA. The basic mechanisms Cell. 107:2001;437-449
13. Holmes S.F., Erie D.A. Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion. J. Biol. Chem. 278:2003;35597-35608
14. Kettenberger H., Armache K.J., Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell. 114:2003;347-357
15. Komissarova N., Kashlev M. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272:1997;15329-15338
16. Korzheva N., Mustaev A., Kozlov M., Malhotra A., Nikiforov V., Goldfarb A., Darst S.A. A structural model of transcription elongation. Science. 289:2000;619-625
17. Landick R., Turnbough J.R., Yanofsky C. Transcription attenuation. Neidhardt F.C. Escherichia coli and Salmonella typhimurium. 1996;1263-1286 American Society for Microbiology, Washington
18. Laptenko O., Lee J., Lomakin I., Borukhov S. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J. 22:2003;6322-6334
19. McDowell J.C., Roberts J.W., Jin D.J., Gross C. Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science. 266:1994;822-825
20. Mustaev A., Zaychikov E., Grachev M., Kozlov M., Severinov K., Epshtein V., Korzheva N., Bereshchenko O., Markovtsov V., Lukhtanov E., et al. Strategies and methods of cross-linking of RNA polymerase active center. Methods Enzymol. 371:2003;191-206
21. Nedialkov Y.A., Gong X.Q., Hovde S.L., Yamaguchi Y., Handa H., Geiger J.H., Yan H., Burton Z.F. NTP-driven translocation by human RNA polymerase II. J. Biol. Chem. 278:2003;18303-18312
22. Neuman K.C., Abbondanzieri E.A., Landick R., Gelles J., Block S.M. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell. 115:2003;437-447
23. Nudler E. Transcription elongation. structural basis and mechanisms J. Mol. Biol. 288:1999;1-12
24. Nudler E., Gottesman M.E. Transcription termination and anti-termination in E. coli. Genes Cells. 7:2002;755-768
25. Nudler E., Gusarov I. Analysis of the intrinsic transcription termination mechanism and its control. Methods Enzymol. 371:2003;369-382
26. Nudler E., Mustaev A., Lukhtanov E., Goldfarb A. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell. 89:1997;33-41
27. Nudler E., Gusarov I., Bar-Nahum G. Methods of walking with the RNA polymerase. Methods Enzymol. 371:2003;160-169
28. Opalka N., Chlenov M., Chacon P., Rice W.J., Wriggers W., Darst S.A. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell. 114:2003;335-345
29. Orlova M., Newlands J., Das A., Goldfarb A., Borukhov S. Intrinsic transcript cleavage activity of RNA polymerase. Proc. Natl. Acad. Sci. USA. 92:1995;4596-4600
30. Reines D., Conaway J.W., Conaway R.C. Mechanism and regulation of transcriptional elongation by RNA polymerase II. Curr. Opin. Cell Biol. 11:1999;342-346
31. Roberts J.W., Yarnell W., Bartlett E., Guo J., Marr M., Ko D.C., Sun H., Roberts C.W. Antitermination by bacteriophage lambda Q protein. Cold Spring Harb. Symp. Quant. Biol. 63:1998;319-325
32. Schmidt M.C., Chamberlin M.J. Amplification and isolation of Escherichia coli nusA protein and studies of its effects on in vitro RNA chain elongation. Biochemistry. 23:1984;197-203
33. Sosunova E., Sosunov V., Kozlov M., Nikiforov V., Goldfarb A., Mustaev A. Donation of catalytic residues to RNA polymerase active center by transcription factor Gre. Proc. Natl. Acad. Sci. USA. 100:2003;15469-15474
34. Sousa R. A new level of regulation in transcription elongation? Trends Biochem. Sci. 26:2001;695-697
35. Temiakov D., Patlan V., Anikin M., McAllister W.T., Yokoyama S., Vassylyev D.G. Structural basis for substrate selection by t7 RNA polymerase. Cell. 116:2004;381-391
36. Toulokhonov I., Landick R. The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination. Mol. Cell. 12:2003;1125-1136
37. Toulokhonov I., Artsimovitch I., Landick R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science. 292:2001;730-733
38. Uptain S.M., Kane C.M., Chamberlin M.J. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66:1997;117-172
39. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature. 417:2002;712-719
40. Vogel U., Jensen K.F. Effects of ppGpp on rate of transcription elongation in isoleucine-starved Escherichia coli. J. Biol. Chem. 269:1994;16236-16241
41. von Hippel P.H. An integrated model of the transcription complex in elongation, termination, and editing. Science. 281:1998;660-665
42. Wada T., Takagi T., Yamaguchi Y., Ferdous A., Imai T., Hirose S., Sugimoto S., Yano K., Hartzog G.A., Winston F., et al. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12:1998;343-356
43. Yin Y.W., Steitz T.A. The structural mechanism of translocation and helicase activity in t7 RNA polymerase. Cell. 116:2004;393-404
44. Zakharova N., Bass I., Arsenieva E., Nikiforov V., Severinov K. Mutations in and monoclonal antibody binding to evolutionary hypervariable region of Escherichia coli RNA polymerase beta′ subunit inhibit transcript cleavage and transcript elongation. J. Biol. Chem. 273:1998;24912-24920
45. Zaychikov E., Martin E., Denissova L., Kozlov M., Markovtsov V., Kashlev M., Heumann H., Nikiforov V., Goldfarb A., Mustaev A. Mapping of catalytic residues in the RNA polymerase active center. Science. 273:1996;107-109
46. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell. 98:1999;811-824