A Tale of Good Fortune in the Era of DNA

Literature Cited

1. 1. 

   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. PNAS 71:2534–38
   [Google Scholar]
2. 2. 

   Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA 2015. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. eLife 4:e08504
   [Google Scholar]
3. 3. 

   Bird JG, Strobel EJ, Roberts JW 2016. A universal transcription pause sequence is an element of initiation factor σ70-dependent pausing. Nucleic Acids Res 44:6732–40
   [Google Scholar]
4. 4. 

   Blattner FR, Dahlberg JE. 1972. RNA synthesis startpoints in bacteriophage λ: Are the promoter and operator transcribed. Nat. New Biol. 237:227–32
   [Google Scholar]
5. 5. 

   Brennan CA, Dombroski AJ, Platt T 1987. Transcription termination factor rho is an RNA-DNA helicase. Cell 48:945–52
   [Google Scholar]
6. 6. 

   Burgess RR, Travers AA, Dunn JJ, Bautz EK 1969. Factor stimulating transcription by RNA polymerase. Nature 221:43–46
   [Google Scholar]
7. 7. 

   Capecchi MR, Gussin GN. 1965. Suppression in vitro: identification of a serine-sRNA as a “nonsense” suppressor. Science 149:417–22
   [Google Scholar]
8. 8. 

   Craig NL, Roberts JW. 1980. E. coli recA protein-directed cleavage of phage λ repressor requires polynucleotide. Nature 283:26–30
   [Google Scholar]
9. 9. 

   Crick FH, Barnett L, Brenner S, Watts-Tobin RJ 1961. General nature of the genetic code for proteins. Nature 192:1227–32
   [Google Scholar]
10. 10. 

    Deighan P, Diez CM, Leibman M, Hochschild A, Nickels BE 2008. The bacteriophage λ Q antiterminator protein contacts the β-flap domain of RNA polymerase. PNAS 105:15305–10
    [Google Scholar]
11. 11. 

    Franklin NC. 1974. Altered reading of genetic signals fused to the N operon of bacteriophage λ: genetic evidence for modification of polymerase by the protein product of the N gene. J. Mol. Biol. 89:33–48
    [Google Scholar]
12. 12. 

    Friedman DI, Olson ER, Georgopoulos C, Tilly K, Herskowitz I, Banuett F 1984. Interactions of bacteriophage and host macromolecules in the growth of bacteriophage λ. Microbiol. Rev. 48:299–325
    [Google Scholar]
13. 13. 

    Friedman DI, Wilgus GS, Mural RJ 1973. Gene N regulator function of phage λimmun21: evidence that a site of N action differs from a site of N recognition. J. Mol. Biol. 81:505–16
    [Google Scholar]
14. 14. 

    Goff CG. 1974. Chemical structure of a modification of the Escherichia coli ribonucleic acid polymerase α polypeptides induced by bacteriophage T₄ infection. J. Biol. Chem. 249:6181–90
    [Google Scholar]
15. 15. 

    Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A 2015. The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo. eLife 4:e10514
    [Google Scholar]
16. 16. 

    Grayhack EJ, Roberts JW. 1982. The phage λ Q gene product: activity of a transcription antiterminator in vitro. Cell 30:637–48
    [Google Scholar]
17. 17. 

    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
    [Google Scholar]
18. 18. 

    Greenblatt J, Nodwell JR, Mason SW 1993. Transcriptional antitermination. Nature 364:401–6
    [Google Scholar]
19. 19. 

    Greenblatt J, Schleif R. 1971. Arabinose C protein: regulation of the arabinose operon in vitro. Nat. New Biol. 233:166–70
    [Google Scholar]
20. 20. 

    Hart CM, Roberts JW. 1994. Deletion analysis of the lambda tR1 termination region: effect of sequences near the transcript release sites, and the minimum length of rho-dependent transcripts. J. Mol. Biol. 237:255–65
    [Google Scholar]
21. 21. 

    Hatoum A, Roberts J. 2008. Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Mol. Microbiol. 68:17–28
    [Google Scholar]
22. 22. 

    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
    [Google Scholar]
23. 23. 

    Herskowitz I, Signer ER. 1970. A site essential for expression of all late genes in bacteriophage λ. J. Mol. Biol. 47:545–56
    [Google Scholar]
24. 24. 

    Horvitz HR. 1974. Control by bacteriophage T4 of two sequential phosphorylations of the alpha subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 90:727–38
    [Google Scholar]
25. 25. 

    Jacob F, Monod J. 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3:318–56
    [Google Scholar]
26. 26. 

    Kainz M, Roberts J. 1992. Structure of transcription elongation complexes in vivo. Science 255:838–41
    [Google Scholar]
27. 27. 

    Krupp F, Said N, Huang YH, Loll B, Burger J et al. 2019. Structural basis for the action of an all-purpose transcription anti-termination factor. Mol. Cell 74:143–57.e5
    [Google Scholar]
28. 28. 

    Larson MH, Greenleaf WJ, Landick R, Block SM 2008. Applied force reveals mechanistic and energetic details of transcription termination. Cell 132:971–82
    [Google Scholar]
29. 29. 

    Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D et al. 2014. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science 344:1042–47
    [Google Scholar]
30. 30. 

    Lau LF, Roberts JW, Wu R 1983. RNA polymerase pausing and transcript release at the λt_R1 terminator in vitro. J. Biol. Chem. 258:9391–97
    [Google Scholar]
31. 31. 

    Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A et al. 2018. Mechanism for the regulated control of bacterial transcription termination by a universal adaptor protein. Mol. Cell 71:911–22.e4
    [Google Scholar]
32. 32. 

    Lin LL, Little JW. 1989. Autodigestion and RecA-dependent cleavage of Ind⁻ mutant LexA proteins. J. Mol. Biol. 210:439–52
    [Google Scholar]
33. 33. 

    Little JW, Edmiston SH, Pacelli LZ, Mount DW 1980. Cleavage of the Escherichia coli lexA protein by the recA protease. PNAS 77:3225–29
    [Google Scholar]
34. 34. 

    Lowery-Goldhammer C, Richardson JP. 1974. An RNA-dependent nucleoside triphosphate phosphohydrolase (ATPase) associated with rho termination factor. PNAS 71:2003–7
    [Google Scholar]
35. 35. 

    Lwoff A, Siminovitch L, Kjeldgaard N 1950. Induction de la production de bactériophages chez une bactérie lysogène. Ann. Inst. Pasteur 79:815–59
    [Google Scholar]
36. 36. 

    Mooney RA, Landick R. 2003. Tethering σ⁷⁰ to RNA polymerase reveals high in vivo activity of σ factors and σ⁷⁰-dependent pausing at promoter-distal locations. Genes Dev 17:2839–51
    [Google Scholar]
37. 37. 

    Nickels BE, Roberts CW, Roberts JW, Hochschild A 2006. RNA-mediated destabilization of the σ⁷⁰ region 4/β flap interaction facilitates engagement of RNA polymerase by the Q antiterminator. Mol. Cell 24:457–68
    [Google Scholar]
38. 38. 

    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
    [Google Scholar]
39. 39. 

    Park JS, Roberts JW. 2006. Role of DNA bubble rewinding in enzymatic transcription termination. PNAS 103:4870–75
    [Google Scholar]
40. 40. 

    Peters JM, Mooney RA, Grass JA, Jessen ED, Tran F, Landick R 2012. Rho and NusG suppress pervasive antisense transcription in Escherichia coli. Genes Dev 26:2621–33
    [Google Scholar]
41. 41. 

    Phizicky EM, Roberts JW. 1981. Induction of SOS functions: regulation of proteolytic activity of E. coli RecA protein by interaction with DNA and nucleoside triphosphate. Cell 25:259–67
    [Google Scholar]
42. 42. 

    Radman M. 1975. SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci 5A:355–67
    [Google Scholar]
43. 43. 

    Richardson JP, Grimley C, Lowery C 1975. Transcription termination factor rho activity is altered in Escherichia coli with suA gene mutations. PNAS 72:1725–28
    [Google Scholar]
44. 44. 

    Ring BZ, Roberts JW. 1994. Function of a nontranscribed DNA strand site in transcription elongation. Cell 78:317–24
    [Google Scholar]
45. 45. 

    Ring BZ, Yarnell WS, Roberts JW 1996. Function of E. coli RNA polymerase σ factor σ⁷⁰ in promoter-proximal pausing. Cell 86:485–93
    [Google Scholar]
46. 46. 

    Roberts CW, Roberts JW. 1996. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell 86:495–501
    [Google Scholar]
47. 47. 

    Roberts JW. 1969. Promoter mutation in vitro. Nature 223:480–82
    [Google Scholar]
48. 48. 

    Roberts JW. 1969. Termination factor for RNA synthesis. Nature 224:1168–74
    [Google Scholar]
49. 49. 

    Roberts JW. 2019. Mechanisms of bacterial transcription termination. J. Mol. Biol. 431:4030–39
    [Google Scholar]
50. 50. 

    Roberts JW, Devoret R. 1983. Lysogenic induction. Lambda II RW Hendrix, JW Roberts, RW Stahl, RA Weisberg 123–44 Cold Spring Harbor, NY: Cold Spring Harb. Lab.
    [Google Scholar]
51. 51. 

    Roberts JW, Roberts CW. 1975. Proteolytic cleavage of bacteriophage lambda repressor in induction. PNAS 72:147–51
    [Google Scholar]
52. 52. 

    Roberts JW, Roberts CW, Craig NL 1978. Escherichia coli recA gene product inactivates phage λ repressor. PNAS 75:4714–18
    [Google Scholar]
53. 53. 

    Roberts JW, Roberts CW, Mount DW 1977. Inactivation and proteolytic cleavage of phage λ repressor in vitro in an ATP-dependent reaction. PNAS 74:2283–87
    [Google Scholar]
54. 54. 

    Roberts JW, Steitz JE. 1967. The reconstitution of infective bacteriophage R17. PNAS 58:1416–21
    [Google Scholar]
55. 55. 

    Santangelo TJ, Roberts JW. 2004. Forward translocation is the natural pathway of RNA release at an intrinsic terminator. Mol. Cell 14:117–26
    [Google Scholar]
56. 56. 

    Sassanfar M, Roberts JW. 1990. Nature of the SOS-inducing signal in Escherichia coli: the involvement of DNA replication. J. Mol. Biol. 212:79–96
    [Google Scholar]
57. 57. 

    Selby CP, Sancar A. 1993. Molecular mechanism of transcription-repair coupling. Science 260:53–58
    [Google Scholar]
58. 58. 

    Shankar S, Hatoum A, Roberts JW 2007. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol. Cell 27:914–27
    [Google Scholar]
59. 59. 

    Shi J, Gao X, Tian T, Yu Z, Gao B et al. 2019. Structural basis of Q-dependent transcription antitermination. Nat. Commun. 10:2925
    [Google Scholar]
60. 60. 

    Skordalakes E, Berger JM. 2006. Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell 127:553–64
    [Google Scholar]
61. 61. 

    Strobel EJ, Roberts JW. 2015. Two transcription pause elements underlie a σ⁷⁰-dependent pause cycle. PNAS 112:E4374–80
    [Google Scholar]
62. 62. 

    Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR et al. 2014. Interactions between RNA polymerase and the “core recognition element” counteract pausing. Science 344:1285–89
    [Google Scholar]
63. 63. 

    Watson JD, Hopkins NH, Roberts JW, Steitz JA, Weiner AM 1987. Molecular Biology of the Gene Menlo Park, CA: Benjamin Cummings. , 4th ed..
64. 64. 

    Witkin EM. 1967. The radiation sensitivity of Escherichia coli B: a hypothesis relating filament formation and prophage induction. PNAS 57:1275–79
    [Google Scholar]
65. 65. 

    Yang XJ, Goliger JA, Roberts JW 1989. Specificity and mechanism of antitermination by Q proteins of bacteriophages λ and 82. J. Mol. Biol. 210:453–60
    [Google Scholar]
66. 66. 

    Yang XJ, Roberts JW. 1989. Gene Q antiterminator proteins of Escherichia coli phages 82 and λ suppress pausing by RNA polymerase at a ρ-dependent terminator and at other sites. PNAS 86:5301–5
    [Google Scholar]
67. 67. 

    Yarnell WS, Roberts JW. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284:611–15
    [Google Scholar]
68. 68. 

    Yin Z, Kaelber JT, Ebright RH 2019. Structural basis of Q-dependent antitermination. PNAS 116:18384–90
    [Google Scholar]
69. 69. 

    Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98:811–24
    [Google Scholar]
70. 70. 

    Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX et al. 2012. Structural basis of transcription initiation. Science 338:1076–80
    [Google Scholar]