The interaction between bacterial transcription factors and RNA polymerase during the transition from initiation to elongation

Transcription

Volumn 1, Issue 2, 2010, Pages 66-69

  Yang, Xiao ^a   Lewis, Peter J ^a  

^a UNIVERSITY OF NEWCASTLE   (Australia)

Author keywords

Bacterial RNAP; Elongation; NusA; Sigma factors; Transcription initiation

Indexed keywords

BACTERIAL PROTEIN; DNA DIRECTED RNA POLYMERASE; ELONGATION FACTOR; ELONGATION FACTOR NUSA; RIBOSOME RNA; RNA POLYMERASE; RNA POLYMERASE BETA SUBUNIT; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSFER RNA; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BINDING AFFINITY; BINDING SITE; ENZYME STRUCTURE; NONHUMAN; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; RNA TRANSLATION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION;

BACTERIA (MICROORGANISMS);

EID: 79952263237     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.1.2.12791     Document Type: Article

References (30)

1. Archambault J, Friesen JD. Genetics of eukaryotic RNA polymerases I, II and III. Microbiol Rev 1993; 57:703-24.
2. Burgess RR, Anthony L. How sigma docks to RNA polymerase and what sigma does. Curr Opin Microbiol 2001; 4:126-31.
3. Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH, et al. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev 1999; 13:2134-47.
4. Ishihama A. Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 2000; 54:499-518.
5. 70 family: sequence conservation and evolutionary relationships. J Bacteriol 1992; 174:3843-9.
6. Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 2002; 296:1285-90.
7. Vassylyev DG, Sekine S, Laptenko O, Lee J, Vassylyeva MN, Borukhov S, et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 2002; 417:712-9.
8. Johnston EB, Lewis PJ, Griffith R. The interaction of Bacillus subtilis sigmaA with RNA polymerase. Protein Sci 2009; 18:2287-97.
9. 70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation. P Natl Acad Sci USA 2005; 102:4488-93.
10. Mooney RA, Artsimovitch I, Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J Bacteriol 1998; 180:3265-75.
11. Murakami KS, Darst SA. Bacterial RNA polymerases: the wholo story. Curr Opin Struct Biol 2003; 13:31-9.
12. Goldman SR, Ebright RH, Nickels BE. Direct detection of abortive RNA transcripts in vivo. Science 2009; 324:927-8.
13. Mooney RA, Darst SA, Landick R. Sigma and RNA polymerase: an on-again, off-again relationship? Mol Cell 2005; 20:335-45.
14. Bar-Nahum G, Nudler E. Isolation and characterization of sigma-retaining transcription elongation complexes from Escherichia coli. Cell 2001; 106:443-51.
15. Mukhopadhyay J, Kapanidis AN, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH. Translocation of sigma with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 2001; 106:453-63.
16. Nickels BE, Roberts CW, Roberts JW, Hochschild A. RNA-mediated destabilization of the sigma region 4/ beta flap interaction facilitates engagement of RNA polymerase by the Q antiterminator. Mol Cell 2006; 24:457-68.
17. Deighan P, Diez CM, Leibman M, Hochschild A, Nickels BE. The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase. P Natl Acad Sci USA 2008; 105:15305-10.
18. Friedman DI, Baron LS. Genetic characterization of a bacterial locus involved in the activity of the N function of phage lambda. Virology 1974; 58:141-8.
19. Gourse RL, Gaal T, Bartlett MS, Appleman JA, Ross W. rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli. Annu Rev Microbiol 1996; 50:645-77.
20. Schmidt MC, Chamberlin MJ. nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites. J Mol Biol 1987; 195:809-81.
21. Cardinale CJ, Washburn RS, Tadigotla VR, Brown LM, Gottesman ME, Nudler E. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 2008; 320:935-8.
22. Gopal B, Haire LF, Gamblin SJ, Dodson EJ, Lane AN, Papavinasasundaram KG, et al. Crystal structure of the transcription elongation/anti-termination factor NusA from Mycobacterium tuberculosis at 1.7 Å resolution. J Mol Biol 2001; 314:1087-95.
23. Shin DH, Nguyen HH, Jancarik J, Yokota H, Kim R, Kim SH. Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain. Biochemistry 2003; 42:13429-37.
24. Gill SC, Weitzel SE, von Hippel PH. Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J Mol Biol 1991; 220:307-24.
25. Borukhov S, Lee J, Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol Microbiol 2005; 55:1315.
26. 70 in transcription elongation: single-molecule analysis. Mol Cell 2005; 20:347-56.
27. Mooney RA, Davis SE, Peters JM, Rowland JL, Ansari AZ, Landick R. Regulator trafficking on bacterial transcription units in vivo. Mol Cell 2009; 33:97-108.
28. Yang X, Molimau S, Doherty GP, Johnston EB, Marles-Wright J, Rothnagel R, et al. The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA. EMBO Rep 2009; 10:997-1002.
29. Yang X, Lewis PJ. The interaction between RNA polymerase and the elongation factor NusA. RNA Biol 2010; 7.
30. Gill SC, Weitzel SE, von Hippel PH. Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J Mol Biol 1991; 220:307-24.