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

References

• Archambault J, Friesen JD. Genetics of eukaryotic RNA polymerases I, II and III. Microbiol Rev 1993; 57:703 - 724
   PubMedGoogle Scholar
• Burgess RR, Anthony L. How sigma docks to RNA polymerase and what sigma does. Curr Opin Microbiol 2001; 4:126 - 131
   PubMed Web of Science ®Google Scholar
• 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 - 2147
   PubMed Web of Science ®Google Scholar
• Ishihama A. Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 2000; 54:499 - 518
   PubMed Web of Science ®Google Scholar
• Lonetto M, Gribskov M, Gross CA. The σ70 family: sequence conservation and evolutionary relationships. J Bacteriol 1992; 174:3843 - 3849
   PubMed Web of Science ®Google Scholar
• 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 - 1290
   PubMed Web of Science ®Google Scholar
• 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 - 719
   PubMed Web of Science ®Google Scholar
• Johnston EB, Lewis PJ, Griffith R. The interaction of Bacillus subtilis sigmaA with RNA polymerase. Protein Sci 2009; 18:2287 - 2297
   PubMed Web of Science ®Google Scholar
• Nickels BE, Garrity SJ, Mekler V, Minakhin L, Severinov K, Ebright RH, et al. The interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation. Proc Natl Acad Sci USA 2005; 102:4488 - 4493
   PubMed Web of Science ®Google Scholar
• Mooney RA, Artsimovitch I, Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J Bacteriol 1998; 180:3265 - 3275
   PubMed Web of Science ®Google Scholar
• Murakami KS, Darst SA. Bacterial RNA polymerases: the wholo story. Curr Opin Struct Biol 2003; 13:31 - 39
   PubMed Web of Science ®Google Scholar
• Goldman SR, Ebright RH, Nickels BE. Direct detection of abortive RNA transcripts in vivo. Science 2009; 324:927 - 928
   PubMed Web of Science ®Google Scholar
• Mooney RA, Darst SA, Landick R. Sigma and RNA polymerase: an on-again, off-again relationship?. Mol Cell 2005; 20:335 - 345
   Google Scholar
• Bar-Nahum G, Nudler E. Isolation and characterization of sigma-retaining transcription elongation complexes from Escherichia coli. Cell 2001; 106:443 - 451
   PubMed Web of Science ®Google Scholar
• 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 - 463
   PubMed Web of Science ®Google Scholar
• 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 - 468
   PubMed Web of Science ®Google Scholar
• Deighan P, Diez CM, Leibman M, Hochschild A, Nickels BE. The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase. Proc Natl Acad Sci USA 2008; 105:15305 - 15310
   PubMed Web of Science ®Google Scholar
• 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 - 148
   PubMed Web of Science ®Google Scholar
• 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 - 677
   PubMed Web of Science ®Google Scholar
• 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 - 881
   PubMed Web of Science ®Google Scholar
• 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 - 938
   PubMed Web of Science ®Google Scholar
• 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 - 1095
   PubMed Web of Science ®Google Scholar
• 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 - 13437
   PubMed Web of Science ®Google Scholar
• 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 - 324
   PubMed Web of Science ®Google Scholar
• Borukhov S, Lee J, Laptenko O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol Microbiol 2005; 55:1315
   PubMed Web of Science ®Google Scholar
• Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, et al. Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. Mol Cell 2005; 20:347 - 356
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Yang X, Lewis PJ. The interaction between RNA polymerase and the elongation factor NusA. RNA Biol 2010; 7
   Google Scholar
• 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 - 324
   PubMed Web of Science ®Google Scholar