Is it easy to stop RNA polymerase?

Cell Cycle

Volumn 5, Issue 4, 2006, Pages 399-404

  Artsimovitch, Irina ^a   Vassylyev, Dmitry G ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

Abortive initiation; Antibiotics; Catalytic center; Crystal structure; Rifamycin; RNA polymerase; Transcription

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL RNA; RIFAMYCIN; RNA POLYMERASE; TRANSCRIPTION FACTOR;

ANTIBIOTIC RESISTANCE; BACTERIAL CELL WALL; BACTERIUM ISOLATE; CELL DEATH; DRUG DESIGN; DRUG MECHANISM; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENZYME ACTIVITY; ENZYME INHIBITION; GENETIC TRANSCRIPTION; LEPROSY; MOLECULAR SIZE; NONHUMAN; PROKARYOTE; PROTEIN BINDING; REGULATORY MECHANISM; REVIEW; STRUCTURE ACTIVITY RELATION; TUBERCULOSIS;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 33645244284     PISSN: 15384101     EISSN: 15514005     Source Type: Journal    
DOI: 10.4161/cc.5.4.2466     Document Type: Review

References (41)

1. 70), promoters, and the kinetics of the steps of transcription initiation. In: Umbarger H, ed. Escherichia coli and Salmonella: Cellular and Molecular Biology. 2nd ed. Washington, DC: ASM Press, 1996:792-821.
2. Steitz TA, Steitz JA. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 1993; 90:6498-502.
3. Hsu LM. Promoter clearance and escape in prokaryotes. Biochim Biophys Acta 2002; 1577:191-207.
4. Nudler E, Gusarov I, Avetissova E, Kozlov M, Goldfarb A. Spatial organization of transcription elongation complex in Escherichia coli. Science 1998; 281:424-8.
5. Komissarova N, Kashlev M. Functional topography of nascent RNA in elongation intermediates of RNA polymerase. Proc Natl Acad Sci USA 1998; 95:14699-704.
6. Mooney RA, Darst SA, Landick R. Sigma and RNA polymerase: An on-again, off-again relationship? Mol Cell 2005; 20:335-45.
7. Richardson J, Greenblatt J. Control of RNA chain elongation and termination. In: Neidhardt F, Curtiss IIIrd R, Ingraham J, Lin E, Low K, Magasanik B, Reznikoff W, Riley M, Schaechter M, Umbarger H, eds. Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington, DC: ASM Press, 1996:822-48.
8. McClure WR, Cech CL. On the mechanism of rifampicin inhibition of RNA synthesis. J Biol Chem 1978; 253:8949-56.
9. Floss HG, Yu TW. Rifamycin-mode of action, resistance, and biosynthesis. Chem Rev 2005; 105:621-32.
10. Riva S, Silvestri LG. Rifamycins: A general view. Annu Rev Microbiol 1972; 26:199-224.
11. Rabussay D, Zillig W. A rifampicin resistent RNA-polymerase from E. coli altered in the beta-subunit. FEBS Lett 1969; 5:104-06.
12. Saito H, Tomioka H, Sato K, Emori M, Yamane T, Yamashita K, Hosoe K, Hidaka T. In vitro antimycobacterial activities of newly synthesized benzoxazinorifamycins. Antimicrob Agents Chemother 1991; 35:542-7.
13. Hudson A, Imamura T, Gutteridge W, Kanyok T, Nunn P. WHO Report, 2003.
14. Artsimovitch I, Vassylyeva MN, Svetlov D, Svetlov V, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Tahirov TH, Vassylyev DG. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell 2005; 122:351-63.
15. Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA. Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell 2001; 104:901-12.
16. Altmann CR, Solow-Codero DE, Chamberlin M. RNA cleavage and chain elongation by Escherichia coli DNA-dependent RNA polymerase in a binary enzyme:RNA complex. Proc Natl Acad Sci USA 1994; 91:3784-88.
17. Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA. Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase. EMBO J 2005; 24:674-82.
18. Kireeva ML, Komissarova N, Waugh DS, Kashlev M. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem 2000; 275:6530-6.
19. Nudler E, Mustaev A, Lukhtanov E, Goldfarb A. The RNA:DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 1997; 89:33-41.
20. Fisher RF, Yanofsky C. Mutations of the beta subunit of RNA polymerase alter both transcription pausing and transcription termination in the trp operon leader region in vitro. J Biol Chem 1983; 258:8146-50.
21. Jin DJ, Walter WA, Gross CA. Characterization of the termination phenotypes of rifampicin-resistant mutants. J Mol Biol 1988; 202:245-53.
22. McDowell JC, Roberts JW, Jin DJ, Gross C. Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science 1994; 266:822-25.
23. Zhou YN, Jin DJ. The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like "stringent" RNA polymerases in Escherichia coli. Proc Natl Acad Sci USA 1998; 95:2908-13.
24. Vo NV, Hsu LM, Kane CM, Chamberlin MJ. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape. Biochemistry 2003; 42:3798-811.
25. Vo NV, Hsu LM, Kane CM, Chamberlin MJ. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 2. Formation and characterization of two distinct classes of initial transcribing complexes. Biochemistry 2003; 42:3787-97.
26. Hsu LM, Vo NV, Kane CM, Chamberlin MJ. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 1. RNA chain initiation, abortive initiation, and promoter escape at three bacteriophage promoters. Biochemistry 2003; 42:3777-86.
27. Roberts J, Park JS. Mfd, the bacterial transcription repair coupling factor: Translocation, repair and termination. Curr Opin Microbiol 2004; 7:120-5.
28. Trautinger BW, Jaktaji RP, Rusakova E, Lloyd RG. RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 2005; 19:247-58.
29. Sen R, Nagai H, Shimamoto N. Polymerase arrest at the lambdaP(R) promoter during transcription initiation. J Biol Chem 2000; 275:10899-904.
30. Cheetham GM, Sieitz TA. Structure of a transcribing T7 RNA polymerase initiation complex. Science 1999; 286:2305-9.
31. Yin YW, Steitz TA. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 2002; 298:1387-95.
32. Tahirov TH, Temiakov D, Anikin M, Patlan V, McAllister WT, Vassylyev DG, Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature 2002; 420:43-50.
33. Cramer P. Multisubunit RNA polymerases. Curr Opin Struct Biol 2002; 12:89-97.
34. Temiakov D, Zenkin N, Vassylyeva MN, Perederina A, Tahirov TH, Kashkina E, Savkina M, Zorov S, Nikiforov V, Igarashi N, Matsugaki N, Wakatsuki S, Severinov K, Vassylyev DG. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 2005; 19:655-66.
35. Tuske S, Sarafianos SG, Wang X, Hudson B, Sineva E, Mukhopadhyay J, Birktoft JJ, Leroy O, Ismail S, Clark Jr AD, Dharia C, Napoli A, Laptenko O, Lee J, Borukhov S, Ebright RH, Arnold E. Inhibition of bacterial RNA polymerase by streptolydigin: Stabilization of a straight-bridge-helix active-center conformation. Cell 2005; 122:541-52.
36. Sarubbi E, Monti F, Corti E, Miele A, Selva E. Mode of action of the microbial metabolite GE23077, a novel potent and selective inhibitor of bacterial RNA polymerase. Eur J Biochem 2004; 271:3146-54.
37. Artsimovitch I, Chu C, Lynch AS, Landick R. A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 2003; 302:650-4.
38. Adelman K, Yuzenkova J, La Porta A, Zenkin N, Lee J, Lis JT, Borukhov S, Wang MD, Severinov K. Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25. Mol Cell 2004; 14:753-62.
39. Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol Cell 2004; 14:739-51.
40. Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S, Artsimovitch I. Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol 2005; 12:1086-93.
41. Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM. Force and velocity measured for single molecules of RNA polymerase. Science 1998; 282:902-7.