RNA polymerase elongation factors

Annual Review of Microbiology

Volumn 62, Issue , 2008, Pages 211-233

  Roberts, Jeffrey W ^a   Shankar, Smita ^a   Filter, Joshua J ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Antiterminator; Pausing; Termination

Indexed keywords

CELL PROTEIN; ELONGATION FACTOR; PROTEIN GRE; PROTEIN NUSA; PROTEIN NUSG; RHO FACTOR; RIBONUCLEOPROTEIN; RNA POLYMERASE; TERMINATION FACTOR MFD; TRANSCRIPTION ELONGATION FACTOR; UNCLASSIFIED DRUG;

DNA DAMAGE; GENE EXPRESSION REGULATION; NONHUMAN; OPERON; PRIORITY JOURNAL; REGULATOR GENE; REVIEW; RNA TRANSCRIPTION; STOP CODON; TERMINAL SEQUENCE; TRANSCRIPTION REGULATION;

BACTERIA; BACTERIAL PROTEINS; BACTERIOPHAGE LAMBDA; BASE SEQUENCE; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; RNA, BACTERIAL; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS; VIRAL PROTEINS;

EID: 53849108160     PISSN: 00664227     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.micro.61.080706.093422     Document Type: Review

References (160)

1. Adelman JL, Jeong YJ, Liao JC, Patel G, Kim DE, et al. 2006. Mechanochemistry of transcription termination factor Rho. Mol. Cell 22:611-21
2. Adelman K, La Porta A, Santangelo TJ, Lis JT, Roberts JW, Wang MD. 2002. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc. Natl. Acad. Sci. USA 99:13538-43
3. Adhya S, Gottesman M, De Crombrugghe B. 1974. Release of polarity in Escherichia coli by gene N of phage lambda: termination and antitermination of transcription. Proc. Natl. Acad. Sri. USA 71:2534-38
4. Albrechtsen B, Squires CL, Li S, Squires C. 1990. Antitermination of characterized transcriptional terminators by the Escherichia coli rrnG leader region. J. Mol. Biol. 213:123-34
5. Artsimovitch I, Landick R. 2000. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA 97:7090-95
6. Artsimovitch I, Landick R. 2002. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell 109:193-203
7. Banik-Maiti S, King RA, Weisberg RA. 1997. The antiterminator RNA of phage HK022. J. Mol. Biol. 272:677-87
8. Barik S, Ghosh B, Whalen W, Lazinski D, Das A. 1987. An antitermination protein engages the elongating transcription apparatus at a promoter-proximal recognition site. Cell 50:885-99
9. Belogurov GA, Vassylyeva MN, Svetlov V, Klyuyev S, Grishin NV, et al. 2007. Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol. Cell 26:117-29
10. Beuth B, Pennell S, Arnvig KB, Martin SR, Taylor IA. 2005. Structure of a Mycobacterium tuberculosis NusA-RNA complex. EMBO J. 24:3576-87
11. Borukhov S, Lee J, Laptenko O. 2005. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol. Microbiol. 55:1315-24
12. Borukhov S, Polyakov A, Nikiforov V, Goldfarb A. 1992. GreA protein: a transcription elongation factor from Escherichia coli. Proc. Natl. Acad. Sci. USA 89:8899-902
13. Brodolin K, Zenkin N, Mustaev A, Mamaeva D, Heumann H. 2004. The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat. Struct. Mol. Biol. 11:551-57
14. Burns CM, Nowatzke WL, Richardson JP. 1999. Activation of Rho-dependent transcription termination by NusG. Dependence on terminator location and acceleration of RNA release. J. Biol. Chem. 274:5245-51
15. Burns CM, Richardson LV, Richardson JP. 1998. Combinatorial effects of NusA and NusG on transcription elongation and Rho-dependent termination in Escherichia coli. J. Mol. Biol. 278:307-16
16. Burova E, Hung SC, Chen J, Court DL, Zhou JG, et al. 1999. Escherichia coli nusG mutations that block transcription termination by coliphage HK022 Nun protein. Mol. Microbiol. 31:1783-93
17. Burova E, Hung SC, Sagitov V, Stitt BL, Gottesman ME. 1995. Escherichia coli NusG protein stimulates transcription elongation rates in vivo and in vitro. J. Bacteriol. 177:1388-92
18. Cardinale CJ, Washburn RS, Tadigotla VR, Brown LM, Gottesman ME, Nudler E. 2008. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 320:935-38
19. Chambers AL, Smith AJ, Savery NJ. 2003. A DNA translocation motif in the bacterial transcription-repair coupling factor, Mfd. Nucleic Acids Res. 31:6409-18
20. Chattopadhyay S, Garcia-Mena J, DeVito J, Wolska K, Das A. 1995. Bipartite function of a small RNA hairpin in transcription antitermination in bacteriophage lambda. Proc. Natl. Acad. Sci. USA 92:4061-65
21. Ciampi MS. 2006. Rho-dependent terminators and transcription termination. Microbiology 152:2515-28
22. Clerget M, Jin DJ, Weisberg RA. 1995. A zinc-binding region in the beta subunit of RNA polymerase is involved in antitermination of early transcription of phage HK022. J. Mol. Biol. 248:768-80
23. Condon C, Squires C, Squires CL. 1995. Control of rRNA transcription in Escherichia coli. Microbiol. Rev. 59:623-45
24. Das A, Wolska K. 1984. Transcription antitermination in vitro by lambda N gene product: requirement for a phage nut site and the products of host nusA, nusB, and nusE genes. Cell 38:165-73
25. Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, et al. 2006. Structural basis for bacterial transcription-coupled DNA repair. Cell 124:507-20
26. Dedrick RL, Kane CM, Chamberlin MJ. 1987. Purified RNA polymerase II recognizes specific termination sites during transcription in vitro. J. Biol. Chem. 262:9098-108
27. Deighan P, Hochschild A. 2007. The bacteriophage lambdaQ antiterminator protein regulates late gene expression as a stable component of the transcription elongation complex. Mol. Microbiol. 63:911-20
28. Faber C, Scharpf M, Becker T, Sticht H, Rosch P. 2001. The structure of the coliphage HK022 Nun protein-lambda-phage boxB RNA complex. Implications for the mechanism of transcription termination. J. Biol. Chem. 276:32064-70
29. Fisher RF, Yanofsky C. 1983. 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. 258:8146-50
30. Franklin NC. 1974. Altered reading of genetic signals fused to the N operon of bacteriophage lambda: genetic evidence for modification of polymerase by the protein product of the N gene. J. Mol. Biol. 89:33-48
31. Friedman DI, Baron LS. 1974. Genetic characterization of a bacterial locus involved in the activity of the N function of phage lambda. Virology 58:141-48
32. Friedman DI, Baumann M, Baron LS. 1976. Cooperative effects of bacterial mutations affecting lambda N gene expression. I. Isolation and characterization of a nusB mutant. Virology 73:119-27
33. Friedman DI, Schauer AT, Baumann MR, Baron LS, Adhya SL. 1981. Evidence that ribosomal protein S10 participates in control of transcription termination. Proc. Natl. Acad. Sci. USA 78:1115-18
34. Friedman DI, Wilgus GS, Mural RJ. 1973. Gene N regulator function of phage lambda immun21: evidence that a site of N action differs from a site of N recognition. J. Mol. Biol. 81:505-16
35. Galluppi GR, Richardson JP. 1980. ATP-induced changes in the binding of RNA synthesis termination protein Rho to RNA. J. Mol. Biol. 138:513-39
36. Gopal B, Haire LF, Gamblin SJ, Dodson EJ, Lane AN, et al. 2001. Crystal structure of the transcription elongation/antitermination factor NusA from Mycobacterium tuberculosis at 1.7 A resolution. J. Mol. Biol. 314:1087-95
37. Gottesman S. 2004. The small RNA regulators of Escherichia coli: roles and mechanisms. Annu. Rev. Microbiol. 58:303-28
38. Gowrishankar J, Harinarayanan R. 2004. Why is transcription coupled to translation in bacteria? Mol. Microbiol. 54:598-603
39. Grayhack EJ, Yang XJ, Lau LF, Roberts JW. 1985. Phage lambda gene Q antiterminator recognizes RNA polymerase near the promoter and accelerates it through a pause site. Cell 42:259-69
40. Greenblatt J, McLimont M, Hanly S. 1981. Termination of transcription by nusA gene protein of Escherichia coli. Nature 292:215-20
41. Gusarov I, Nudler E. 2001. Control of intrinsic transcription termination by N and NusA: the basic mechanisms. Cell 107:437-49
42. Hatoum A, Roberts J. 2008. Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Mol. Microbiol. 68:17-28
43. Henthorn KS, Friedman DI. 1996. Identification of functional regions of the Nun transcription termination protein of phage HK022 and the N antitermination protein of phage lambda using hybrid nun-N genes. J. Mol. Biol. 257:9-20
44. Herbert KM, La Porta A, Wong BJ, Mooney RA, Neuman KC, et al. 2006. Sequence-resolved detection of pausing by single RNA polymerase molecules. Cell 125:1083-94
45. Horwitz RJ, Li J, Greenblatt J. 1987. An elongation control particle containing the N gene transcriptional antitermination protein of bacteriophage lambda. Cell 51:631-41
46. Hsu LM, Vo NV, Chamberlin MJ. 1995. Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro. Proc. Natl. Acad. Sci. USA 92:11588-92
47. Huertas P, Aguilera A. 2003. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell 12:711-21
48. Hung SC, Gottesman ME. 1995. Phage HK022 Nun protein arrests transcription on phage lambda DNA in vitro and competes with the phage lambda N antitermination protein. J. Mol. Biol. 247:428-42
49. Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. 2006. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314:1144-47
50. Kim HC, Gottesman ME. 2004. Transcription termination by phage HK022 Nun is facilitated by COOH-terminal lysine residues. J. Biol. Chem. 279:13412-17
51. Kim HC, Washburn RS, Gottesman ME. 2006. Role of E. coli NusA in phage HK022 Nun-mediated transcription termination. J. Mol. Biol. 359:10-21
52. Kim HC, Zhou JG, Wilson HR, Mogilnitskiy G, Court DL, Gottesman ME. 2003. Phage HK022 Nun protein represses translation of phage lambda N (transcription termination/translation repression). Proc. Natl. Acad. Sci. USA 100:5308-12
53. King RA, Banik-Maiti S, Jin DJ, Weisberg RA. 1996. Transcripts that increase the processivity and elongation rate of RNA polymerase. Cell 87:893-903
54. King RA, Madsen PL, Weisberg RA. 2000. Constitutive expression of a transcription termination factor by a repressed prophage: promoters for transcribing the phage HK022 nun gene. J. Bacteriol. 182:456-62
55. King RA, Markov D, Sen R, Severinov K, Weisberg RA. 2004. A conserved zinc binding domain in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex. J. Mol. Biol. 342:1143-54
56. Komissarova N, Becker J, Solter S, Kireeva M, Kashlev M. 2002. Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell 10:1151-62
57. Komissarova N, Kashlev M. 1997. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272:15329-38
58. Korzheva N, Mustaev A, Kozlov M, Malhotra A, Nikiforov V, et al. 2000. A structural model of transcription elongation. Science 289:619-25
59. Landick R, Carey J, Yanofsky C. 1985. Ttanslation activates the paused transcription complex and restores transcription of the trp operon leader region. Proc. Natl. Acad. Sci. USA 82:4663-67
60. Landick R, Turnbough J, Yanofsky C. 1996. Transcription attenuation. In Escherichia coli and Salmonella: Cellular and Molecular Biology, ed. F Neidhardt, R Curtiss, JL Ingraham, ECC Lin, KB Low, et al., pp. 1263-86. Washington, DC: ASM Press
61. Laptenko O, Lee J, Lomakin I, Borukhov S. 2003. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J. 22:6322-34
62. Larson MH, Greenleaf WJ, Landick R, Block SM. 2008. Applied force reveals mechanistic and energetic details of transcription termination. Cell 132:971-82
63. Lau LF, Roberts JW. 1985. Rho-dependent transcription termination at lambda R1 requires upstream sequences. J. Biol. Chem. 260:574-84
64. Lau LF, Roberts JW, Wu R. 1983. RNA polymerase pausing and transcript release at the lambda tR1 terminator in vitro. J. Biol. Chem. 258:9391-97
65. Lazinski D, Grzadzielska E, Das A. 1989. Sequence-specific recognition of RNA hairpins by bacteriophage antiterminators requires a conserved arginine-rich motif. Cell 59:207-18
66. Lee DN, Phung L, Stewart J, Landick R. 1990. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J. Biol. Chem. 265:15145-53
67. Legault P, Li J, Mogridge J, Kay LE, Greenblatt J. 1998. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 93:289-99
68. Li J, Horwitz R, McCracken S, Greenblatt J. 1992. NusG, a new Escherichia coli elongation factor involved in transcriptional antitermination by the N protein of phage lambda. J. Biol. Chem. 267:6012-19
69. Li J, Mason SW, Greenblatt J. 1993. Elongation factor NusG interacts with termination factor Rho to regulate termination and antitermination of transcription. Genes Dev. 7:161-72
70. Li SC, Squires CL, Squires C. 1984. Antitermination of E. coli rRNA transcription is caused by a control region segment containing lambda nut-like sequences. Cell 38:851-60
71. Liu K, Hanna MM. 1995. NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes. Proc. Natl. Acad. Sci. USA 92:5012-16
72. Liu K, Zhang Y, Severinov K, Das A, Hanna MM. 1996. Role of Escherichia coli RNA polymerase alpha subunit in modulation of pausing, termination and antitermination by the transcription elongation factor NusA. EMBO J. 15:150-61
73. Lowery-Goldhammer C, Richardson JP. 1974. An RNA-dependent nucleoside triphosphate phosphohydrolase (ATPase) associated with Rho termination factor. Proc. Natl. Acad. Sci. USA 71:2003-7
74. Macdonald LE, Zhou Y, McAllister WT. 1993. Termination and slippage by bacteriophage T7 RNA polymerase. J. Mol. Biol. 232:1030-47
75. Mah TF, Li J, Davidson AR, Greenblatt J. 1999. Functional importance of regions in Escherichia coli elongation factor NusA that interact with RNA polymerase, the bacteriophage lambda N protein and RNA. Mol. Microbiol. 34:523-37
76. Marr MT, Datwyler SA, Meares CF, Roberts JW. 2001. Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins. Proc. Natl. Acad. Sci. USA 98:8972-78
77. Marr MT, Roberts JW. 2000. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol. Cell 6:1275-85
78. Martin FH, Tinoco I Jr. 1980. DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. Nucleic Acids Res. 8:2295-99
79. Mason SW, Li J, Gteenblatt J. 1992. Direct interaction between two Escherichia coli transcription antitermination factors, NusB and ribosomal protein S10. J. Mol. Biol. 223:55-66
80. Mason SW, Li J, Greenblatt J. 1992. Host factor requirements for processive antitermination of transcription and suppression of pausing by the N protein of bacteriophage lambda. J. Biol. Chem. 267:19418-26
81. McSwiggen JA, Bear DG, von Hippel PH. 1988. Interactions of Escherichia coli transcription termination factor Rho with RNA. I. Binding stoichiometries and free energies. J. Mol. Biol. 199:609-22
82. Mooney RA, Landick R. 2003. Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev. 17:2839-51
83. Morgan EA. 1980. Insertions of Tn 10 into an E. coli ribosomal RNA operon are incompletely polar. Cell 21:257-65
84. Morgan WD, Bear DG, Litchman BL, von Hippel PH. 1985. RNA sequence and secondary structure requirements for Rho-dependent transcription termination. Nucleic Acids Res. 13:3739-54
85. Morgan WD, Bear DG, von Hippel PH. 1983. Rho-dependent termination of transcription. II. Kinetics of mRNA elongation during transcription from the bacteriophage lambda PR promoter. J. Biol. Chem. 258:9565-74
86. Nehrke KW, Platt T. 1994. A quaternary transcription termination complex. Reciprocal stabilization by Rho factor and NusG protein. J. Mol. Biol. 243:830-39
87. Nehrke KW, Zalatan F, Platt T. 1993. NusG alters Rho-dependent termination of transcription in vitro independent of kinetic coupling. Gene Expr. 3:119-33
88. Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM. 2003. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115:437-47
89. Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A. 2004. The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nat. Struct. Mol. Biol. 11:544-50
90. Nickels BE, Roberts CW, Roberts JW, Hochschild A. 2006. RNA-mediated destabilization of the sigma(70) region 4/beta flap interaction facilitates engagement of RNA polymerase by the Q antiterminator. Mol. Cell 24:457-68
91. Nickels BE, Roberts CW, Sun H, Roberts JW, Hochschild A. 2002. The sigma(70) subunit of RNA polymerase is contacted by the (lambda)Q antiterminator during early elongation. Mol. Cell 10:611-22
92. Nodwell JR, Greenblatt J. 1993. Recognition of boxA antiterminator RNA by the E. coli antitermination factors NusB and ribosomal protein S10. Cell 72:261-68
93. Nudler E, Avetissova E, Markovtsov V, Goldfarb A. 1996. Transcription processivity: protein-DNA interactions holding together the elongation complex. Science 273:211-17
94. Nudler E, Gottesman ME. 2002. Transcription termination and antitermination in E. coli. Genes Cells 7:755-68
95. Nudler E, Mustaev A, Lukhtanov E, Goldfarb A. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89:33-41
96. Oberto J, Clerget M, Ditto M, Cam K, Weisberg RA. 1993. Antitermination of early transcription in phage HK022. Absence of a phage-encoded antitermination factor. J. Mol. Biol. 229:368-81
97. Olson ER, Flamm EL, Friedman DI. 1982. Analysis of nutR: a region of phage lambda required for antitermination of transcription. Cell 31:61-70
98. Opalka N, Chlenov M, Chacon P, Rice WJ, Wriggers W, Darst SA. 2003. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 114:335-45
99. Orlova M, Newlands J, Das A, Goldfarb A, Borukhov S. 1995. Intrinsic transcript cleavage activity of RNA polymerase. Proc. Natl. Acad. Sci. USA 92:4596-600
100. Park JS, Marr MT, Roberts JW. 2002. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109:757-67
101. Park JS, Roberts JW. 2006. Role of DNA bubble rewinding in enzymatic transcription termination. Proc. Natl. Acad. Sci. USA 103:4870-75
102. Pasman Z, von Hippel PH. 2000. Regulation of Rho-dependent transcription termination by NusG is specific to the Escherichia coli elongation complex. Biochemistry 39:5573-85
103. Patterson TA, Zhang Z, Baker T, Johnson LL, Friedman DI, Court DL. 1994. Bacteriophage lambda N-dependent transcription antitermination. Competition for an RNA site may regulate antitermination. J. Mol. Biol. 236:217-28
104. Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, et al. 2004. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118:311-22
105. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, et al. 2004. Regulation through the secondary channel-structural framework for ppGpp-DksA synergism during transcription. Cell 118:297-309
106. Rees WA, Weitzel SE, Das A, von Hippel PH. 1997. Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage lambda. J. Mol. Biol. 273:797-813
107. Rees WA, Weitzel SE, Yager TD, Das A, von Hippel PH. 1996. Bacteriophage lambda N protein alone can induce transcription antitermination in vitro. Proc. Natl. Acad. Sci. USA 93:342-46
108. Revyakin A, Liu C, Ebright RH, Strick TR. 2006. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314:1139-43
109. Richardson JP, Greenblatt J. 1996. Control of RNA chain elongation and termination. In Escherichia coli and Salmonella: Cellular and Molecular Biology, ed. FC Neidhardt, R Curtiss, JL Ingraham, ECC Lin, KB Low, et al., pp. 822-48. Washington, DC: ASM Press
110. Richardson JP, Grimley C, Lowery C. 1975. Transcription termination factor Rho activity is altered in Escherichia coli strains with suA gene mutations. Proc. Natl. Acad. Sci. USA 72:1725-28
111. Ring BZ, Yarnell WS, Roberts JW. 1996. Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing. Cell 86:485-93
112. Robert J, Sloan SB, Weisberg RA, Gottesman ME, Robledo R, Harbrecht D. 1987. The remarkable specificity of a new transcription termination factor suggests that the mechanisms of termination and antitermination are similar. Cell 51:483-92
113. Roberts JW. 1969. Termination factor for RNA synthesis. Nature 224:1168-74
114. Roberts JW, Yarnell W, Bartlett E, Guo J, Marr M, et al. 1998. Antitermination by bacteriophage lambda Q protein. Cold Spring Harb. Symp. Quant. Biol. 63:319-25
115. Robledo R, Atkinson BL, Gottesman ME. 1991. Escherichia coli mutations that block transcription termination by phage HK022 Nun protein. J. Mol. Biol. 220:613-19
116. Ryder AM, Roberts JW. 2003. Role of the nontemplate strand of the elongation bubble in intrinsic transcription termination. J. Mol. Biol. 334:205-13
117. Salstrom JS, Szybalski W. 1978. Coliphage lambdanutL-: a unique class of mutants defective in the site of gene N product utilization for antitermination of leftward transcription. J. Mol. Biol. 124:195-221
118. Santangelo TJ, Mooney RA, Landick R, Roberts JW. 2003. RNA polymerase mutations that impair conversion to a termination-resistant complex by Q antiterminator proteins. Genes Dev. 17:1281-92
119. Santangelo TJ, Roberts JW. 2004. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell 14:117-26
120. Schmidt MC, Chamberlin MJ. 1987. nusA protein of Escherichia coli is an efficient transcription termination factor for certain terminator sites. J. Mol. Biol. 195:809-18
121. Schwartz A, Margeat E, Rahmouni AR, Boudvillain M. 2007. Transcription termination factor Rho can displace streptavidin from biotinylated RNA. J. Biol. Chem. 282:31469-76
122. Selby CP, Sancar A. 1993. Molecular mechanism of transcription-repair coupling. Science 260:53-58
123. Sen R, King RA, Mzhavia N, Madsen PL, Weisberg RA. 2002. Sequence-specific interaction of nascent antiterminator RNA with the zinc-finger motif of Escherichia coli RNA polymerase. Mol. Microbiol. 46:215-22
124. Sen R, King RA, Weisberg RA. 2001. Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA. Mol. Cell 7:993-1001
125. Sevostyanova A, Svetlov V, Vassylyev DG, Artsimovitch I. 2008. The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex. Proc. Natl. Acad. Sci. USA 105:865-70
126. Shankar S, Hatoum A, Roberts JW. 2007. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol. Cell 27:914-27
127. Sigmund CD, Morgan EA. 1988. NusA protein affects transcriptional pausing and termination in vitro by binding to different sites on the transcription complex. Biochemistry 27:5622-27
128. Skordalakes E, Berger JM. 2006. Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell 127:553-64
129. Sloan SB, Weisberg RA. 1993. Use of a gene encoding a suppressor tRNA as a reporter of transcription: analyzing the action of the Nun protein of bacteriophage HK022. Proc. Natl. Acad. Sci. USA 90:9842-46
130. Smith AJ, Savery NJ. 2005. RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair. Nucleic Acids Res. 33:755-64
131. Smith AJ, Szczelkun MD, Savery NJ. 2007. Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase. Nucleic Acids Res. 35:1802-11
132. Sosunov V, Sosunova E, Mustaev A, Bass I, Nikiforov V, Goldfarb A. 2003. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22:2234-44
133. Squires CL, Greenblatt J, Li J, Condon C, Squires CL. 1993. Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components. Proc. Natl. Acad. Sci. USA 90:970-74
134. Stepanova E, Lee J, Ozerova M, Semenova E, Datsenko K, et al. 2007. Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro. J. Bacteriol. 189:8772-85
135. Straney DC, Crothers DM. 1987. A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter. J. Mol. Biol. 193:267-78
136. Stuart AC, Gottesman ME, Palmer AG 3rd. 2003. The N-terminus is unstructured, but not dynamically disordered, in the complex between HK022 Nun protein and lambda-phage BoxB RNA hairpin. FEBS Lett. 553:95-98
137. Sullivan SL, Ward DF, Gottesman ME. 1992. Effect of Escherichia coli nusG function on lambda N-mediated transcription antitermination. J. Bacteriol. 174:1339-44
138. Toulokhonov I, Artsimovitch I, Landick R. 2001. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science 292:730-33
139. Toulokhonov I, Zhang J, Palangat M, Landick R. 2007. A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol. Cell 27:406-19
140. Traviglia SL, Datwyler SA, Yan D, Ishihama A, Meares CF. 1999. Targeted protein footprinting: where different transcription factors bind to RNA polymerase. Biochemistry 38:15774-78
141. Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I. 2007. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448:157-62
142. Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R. 2007. Structural basis for substrate loading in bacterial RNA polymerase. Nature 448:163-68
143. Vieu E, Rahmouni AR. 2004. Dual role of boxB RNA motif in the mechanisms of termination/antitermination at the lambda tR1 terminator revealed in vivo. J. Mol. Biol. 339:1077-87
144. Vogel U, Jensen KF. 1997. NusA is required for ribosomal antitermination and for modulation of the transcription elongation rate of both antiterminated RNA and mRNA. J. Biol. Chem. 272:12265-71
145. Wagner LA, Weiss RB, Driscoll R, Dunn DS, Gesteland RF. 1990. Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli. Nucleic Acids Res. 18:3529-35
146. Washburn RS, Wang Y, Gottesman ME. 2003. Role of E. coli transcription-repair coupling factor Mfd in Nun-mediated transcription termination. J. Mol. Biol. 329:655-62
147. Watnick RS, Gottesman ME. 1998. Escherichia coli NusA is required for efficient RNA binding by phage HK022 nun protein. Proc. Natl. Acad. Sci. USA 95:1546-51
148. Watnick RS, Gottesman ME. 1999. Binding of transcription termination protein nun to nascent RNA and template DNA. Science 286:2337-39
149. Watnick RS, Herring SC, Palmer AG 3rd, Gottesman ME. 2000. The carboxyl terminus of phage HK022 Nun includes a novel zinc-binding motif and a tryptophan required for transcription termination. Genes Dev. 14:731-39
150. Weisberg RA, Gottesman ME. 1999. Processive antitermination. J. Bacteriol. 181:359-67
151. Whalen W, Ghosh B, Das A. 1988. NusA protein is necessary and sufficient in vitro for phage lambda N gene product to suppress a Rho-independent terminator placed downstream of nutL. Proc. Natl. Acad. Sci. USA 85:2494-98
152. Yang XJ, Hart CM, Grayhack EJ, Roberts JW. 1987. Transcription antitermination by phage lambda gene Q protein requires a DNA segment spanning the RNA start site. Genes Dev. 1:217-26
153. Yang XJ, Roberts JW. 1989. Gene Q antiterminator proteins of Escherichia coli phages 82 and lambda suppress pausing by RNA polymerase at a Rho-dependent terminator and at other sites. Proc. Natl. Acad. Sci. USA 86:5301-5
154. Yanofsky C. 2007. RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria. Rna 13:1141-54
155. Yarnell WS, Roberts JW. 1992. The phage lambda gene Q transcription antiterminator binds DNA in the late gene promoter as it modifies RNA polymerase. Cell 69:1181-89
156. Yarnell WS, Roberts JW. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284:611-15
157. Zalieckas JM, Wray LV Jr, Ferson AE, Fisher SH. 1998. Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons. Mol. Microbiol. 27:1031-38
158. Zenkin N, Yuzenkova Y, Severinov K. 2006. Transcript-assisted transcriptional proofreading. Science 313:518-20
159. Zheng C, Friedman DI. 1994. Reduced Rho-dependent transcription termination permits NusA-independent growth of Escherichia coli. Proc. Natl. Acad. Sci. USA 91:7543-47
160. Zhou Y, Navaroli DM, Enuameh MS, Martin CT. 2007. Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism. Proc. Natl. Acad. Sci. USA 104:10352-57