1932

Abstract

Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs), associate with the catalytic core RNA polymerase to guide it through the essential steps of initiation: promoter recognition and opening, and synthesis of the first few nucleotides of the transcript. Here we recount the key advances in σ biology, from their discovery 45 years ago to the most recent progress in understanding their structure and function at the atomic level. Recent data provide important structural insights into the mechanisms whereby σs initiate promoter opening. We discuss both the housekeeping σs, which govern transcription of the majority of cellular genes, and the alternative σs, which direct RNA polymerase to specialized operons in response to environmental and physiological cues. The review concludes with a genome-scale view of the extracytoplasmic function σs, the most abundant group of alternative σs.

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2014-09-08
2024-04-23
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Literature Cited

  1. Altan-Bonnet G, Libchaber A, Krichevsky O. 1.  2003. Bubble dynamics in double-stranded DNA. Phys. Rev. Lett. 90:13138101 [Google Scholar]
  2. Bae B, Davis E, Brown D, Campbell EA, Wigneshweraraj SR, Darst SA. 2.  2013. Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of σ70 domain 1.1. Proc. Natl. Acad. Sci. USA 110:4919772–77 [Google Scholar]
  3. Bao X, Nickels BE, Fan H. 3.  2012. Chlamydia trachomatis protein GrgA activates transcription by contacting the nonconserved region of σ66. Proc. Natl. Acad. Sci. USA 109:4216870–75 [Google Scholar]
  4. Bar-Nahum G, Nudler E. 4.  2001. Isolation and characterization of σ70-retaining transcription elongation complexes from Escherichia coli. Cell 106:4443–51 [Google Scholar]
  5. Barne KA, Bown JA, Busby SJW, Minchin SD. 5.  1997. Region 2.5 of the Escherichia coli RNA polymerase σ70 subunit is responsible for the recognition of the “extended-10” motif at promoters. EMBO J. 16:134034–40 [Google Scholar]
  6. Brodolin K, Zenkin N, Mustaev A, Mamaeva D, Heumann H. 6.  2004. The σ70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat. Struct. Mol. Biol. 11:6551–57 [Google Scholar]
  7. Browning DF, Busby SJW. 7.  2004. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2:157–65 [Google Scholar]
  8. Burgess RR, Travers AA. 8.  1970. Escherichia coli RNA polymerase: purification, subunit structure, and factor requirements. Fed. Proc. 29:31164–69 [Google Scholar]
  9. Burgess RR, Travers AA, Dunn JJ, Bautz EK. 9.  1969. Factor stimulating transcription by RNA polymerase. Nature 221:517543–46 [Google Scholar]
  10. Callaci S, Heyduk E, Heyduk T. 10.  1998. Conformational changes of Escherichia coli RNA polymerase σ70 factor induced by binding to the core enzyme. J. Biol. Chem. 273:4932995–3001 [Google Scholar]
  11. Callaci S, Heyduk E, Heyduk T. 11.  1999. Core RNA polymerase from E. coli induces a major change in the domain arrangement of the σ70 subunit. Mol. Cell 3:2229–38 [Google Scholar]
  12. Camarero JA, Shekhtman A, Campbell EA, Chlenov M, Gruber TM. 12.  et al. 2002. Autoregulation of a bacterial σ factor explored by using segmental isotopic labeling and NMR. Proc. Natl. Acad. Sci. USA 99:138536–41 [Google Scholar]
  13. Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH. 13.  2014. Structural basis for -10 promoter element melting by environmentally induced sigma factors. Nat. Struct. Mol. Biol 21:3269–76 doi: 10.1038/nsmb.2777 [Google Scholar]
  14. Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA. 14.  et al. 2002. Structure of the bacterial RNA polymerase promoter specificity σ subunit. Mol. Cell 9:3527–39 [Google Scholar]
  15. Campbell EA, Tupy JL, Gruber TM, Wang S, Sharp MM. 15.  et al. 2003. Crystal structure of Escherichia coli σE with the cytoplasmic domain of its anti-σ RseA. Mol. Cell 11:41067–78 [Google Scholar]
  16. Chen J, Darst SA, Thirumalai D. 16.  2010. Promoter melting triggered by bacterial RNA polymerase occurs in three steps. Proc. Natl. Acad. Sci. USA 107:2812523–28 [Google Scholar]
  17. Cowing DW, Gross CA. 17.  1989. Interaction of Escherichia coli RNA polymerase holoenzyme containing σ32 with heat shock promoters: DNase I footprinting and methylation protection. J. Mol. Biol. 210:3513–20 [Google Scholar]
  18. Cowing DW, Mecsas J, Record MT Jr, Gross CA. 18.  1989. Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the σ factor sigma 32 at the groE promoter. J. Mol. Biol. 210:3521–30 [Google Scholar]
  19. Darst SA. 19.  2001. Bacterial RNA polymerase. Curr. Opin. Struct. Biol. 11:2155–62 [Google Scholar]
  20. Darst SA, Feklistov A, Gross CA. 20.  Promoter melting by an alternative σ, one base at a time. Nat. Struct. Mol. Biol. 21:4350–51 [Google Scholar]
  21. deHaseth PL, Helmann JD. 21.  2005. Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol. Microbiol. 16:5817–24 [Google Scholar]
  22. deHaseth PL, Zupancic ML, Record MT Jr. 22.  1998. RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180:123019–25 [Google Scholar]
  23. Dickson RC, Abelson J, Barnes WM, Reznikoff WS. 23.  1975. Genetic regulation: the Lac control region. Science 187:417127–35 [Google Scholar]
  24. Dombroski AJ, Walter WA, Record MT Jr, Siegele DA, Gross CA. 24.  1992. Polypeptides containing highly conserved regions of transcription initiation factor σ70 exhibit specificity of binding to promoter DNA. Cell 70:3501–12 [Google Scholar]
  25. Dove SL, Darst SA, Hochschild A. 25.  2003. Region 4 of σ as a target for transcription regulation. Mol. Microbiol. 48:4863–74 [Google Scholar]
  26. Feklistov A. 26.  2013. RNA polymerase: in search of promoters. Ann. N. Y. Acad. Sci. 1293:25–32 [Google Scholar]
  27. Feklistov A, Barinova N, Sevostyanova A, Heyduk E, Bass I. 27.  et al. 2006. A basal promoter element recognized by free RNA polymerase σ subunit determines promoter recognition by RNA polymerase holoenzyme. Mol. Cell 23:197–107 [Google Scholar]
  28. Feklistov A, Darst SA. 28.  2011. Structural basis for promoter -10 element recognition by the bacterial RNA polymerase σ subunit. Cell 147:61257–69 [Google Scholar]
  29. Gribskov M, Burgess RR. 29.  1986. Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins. Nucleic Acids Res. 14:166745–63 [Google Scholar]
  30. Grossman AD, Erickson JW, Gross CA. 30.  1984. The htpR gene product of E. coli is a sigma factor for heat-shock promoters. Cell 38:2383–90 [Google Scholar]
  31. Haldenwang WG, Lang N, Losick R. 31.  1981. A sporulation-induced sigma-like regulatory protein from B. subtilis.. Cell 23:2615–24 [Google Scholar]
  32. Haldenwang WG, Losick R. 32.  1980. Novel RNA polymerase sigma factor from Bacillus subtilis. Proc. Natl. Acad. Sci. USA 77:127000–4 [Google Scholar]
  33. Haugen SP, Berkmen MB, Ross W, Gaal T, Ward C, Gourse RL. 33.  2006. rRNA Promoter regulation by nonoptimal binding of σ region 1.2: an additional recognition element for RNA polymerase. Cell 125:61069–82 [Google Scholar]
  34. Helmann JD, Chamberlin MJ. 34.  1988. Structure and function of bacterial sigma factors. Annu. Rev. Biochem. 57:839–72 [Google Scholar]
  35. Helmann JD, deHaseth PL. 35.  1999. Protein–nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners. Biochemistry 38:195959–67 [Google Scholar]
  36. Heyduk E. 36.  2006. A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting. J. Biol. Chem. 281:1812362–69 [Google Scholar]
  37. Hook-Barnard IG, Hinton DM. 37.  2007. Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters. Gene Regul. Syst. Biol. 1:275–93 [Google Scholar]
  38. Hsu LM. 38.  2002. Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta 1577:2191–207 [Google Scholar]
  39. Jain D, Nickels BE, Sun L, Hochschild A, Darst SA. 39.  2004. Structure of a ternary transcription activation complex. Mol. Cell 13:145–53 [Google Scholar]
  40. Juang YL, Helmann JD. 40.  1994. A promoter melting region in the primary σ factor of Bacillus subtilis: identification of functionally important aromatic amino acids. J. Mol. Biol. 235:51470–88 [Google Scholar]
  41. Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO. 41.  et al. 2005. Retention of transcription initiation factor σ70 in transcription elongation: single-molecule analysis. Mol. Cell 20:3347–56 [Google Scholar]
  42. Kapanidis AN, Strick T. 42.  2009. Biology, one molecule at a time. Trends Biochem. Sci. 34:5234–43 [Google Scholar]
  43. Kassavetis GA, Elliott T, Rabussay DP, Geiduschek EP. 43.  1983. Initiation of transcription at phage T4 late promoters with purified RNA polymerase. Cell 33:3887–97 [Google Scholar]
  44. Kassavetis GA, Geiduschek EP. 44.  1984. Defining a bacteriophage T4 late promoter: bacteriophage T4 gene 55 protein suffices for directing late promoter recognition. Proc. Natl. Acad. Sci. USA 81:165101–5 [Google Scholar]
  45. Khesin RB, Shemyakin MF, Gorlenko AM, Mindlin SZ, Ilyina TS. 45.  1969. Studies on the RNA polymerase in Escherichia coli K12 using the mutation affecting its activity. J. Mol. Biol. 42:3401–11 [Google Scholar]
  46. Koo B-M, Rhodius VA, Campbell EA, Gross CA. 46.  2009. Dissection of recognition determinants of Escherichia coli σ32 suggests a composite -10 region with an ‘extended -10’ motif and a core -10 element. Mol. Microbiol. 72:4815–29 [Google Scholar]
  47. Koo B-M, Rhodius VA, Campbell EA, Gross CA. 47.  2009. Mutational analysis of Escherichia coli σ28 and its target promoters reveals recognition of a composite -10 region, comprised of an ‘extended -10’ motif and a core -10 element. Mol. Microbiol. 72:4830–43 [Google Scholar]
  48. Koo B-M, Rhodius VA, Nonaka G, deHaseth PL, Gross CA. 48.  2009. Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition. Genes Dev 23:202426–36 [Google Scholar]
  49. Krakow JS, Daley K, Karstadt M. 49.  1969. Azotobacter vinelandii RNA polymerase. VII. Enzyme transitions during unprimed r[I-C] synthesis. Proc. Natl. Acad. Sci. USA 62:2432–37 [Google Scholar]
  50. Kulbachinskiy A, Mustaev A. 50.  2006. Region 3.2 of the subunit contributes to the binding of the 3′-initiating nucleotide in the RNA polymerase active center and facilitates promoter clearance during initiation. J. Biol. Chem. 281:2718273–76 [Google Scholar]
  51. Lane WJ, Darst SA. 51.  2006. The structural basis for promoter -35 element recognition by the group IV σ factors. PLoS Biol. 4:9e269 [Google Scholar]
  52. Lee HJ. 52.  2004. An unsubstituted C2 hydrogen of adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation. J. Biol. Chem. 279:1716899–902 [Google Scholar]
  53. Lee S, Bowman BR, Ueno Y, Wang S, Verdine GL. 53.  2008. Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine. J. Am. Chem. Soc. 130:3511570–71 [Google Scholar]
  54. Lim HM, Lee HJ, Roy S, Adhya S. 54.  2001. A “master” in base unpairing during isomerization of a promoter upon RNA polymerase binding. Proc. Natl. Acad. Sci. USA 98:2614849–52 [Google Scholar]
  55. Lonetto M, Gribskov M, Gross CA. 55.  1992. The σ70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174:123843–49 [Google Scholar]
  56. Lonetto MA, Brown KL, Rudd KE, Buttner MJ. 56.  1994. Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase σ factors involved in the regulation of extracytoplasmic functions. Proc. Natl. Acad. Sci. USA 91:167573–77 [Google Scholar]
  57. Losick R, Pero J. 57.  1981. Cascades of sigma factors. Cell 25:3582–84 [Google Scholar]
  58. Marr MT. 58.  1997. Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science 276:53161258–60 [Google Scholar]
  59. Mascher T, Hachmann A-B, Helmann JD. 59.  2007. Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function σ factors. J. Bacteriol. 189:196919–27 [Google Scholar]
  60. Mecsas J, Cowing DW, Gross CA. 60.  1991. Development of RNA polymerase-promoter contacts during open complex formation. J. Mol. Biol. 220:3585–97 [Google Scholar]
  61. Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A. 61.  et al. 2002. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108:5599–614 [Google Scholar]
  62. Minakhin L, Severinov K. 62.  2003. On the role of the Escherichia coli RNA polymerase σ70 region 4.2 and α-subunit C-terminal domains in promoter complex formation on the extended -10 galP1 promoter. J. Biol. Chem. 278:3229710–18 [Google Scholar]
  63. Mooney RA, Darst SA, Landick R. 63.  2005. Sigma and RNA polymerase: an on-again, off- again relationship?. Mol. Cell 20:3335–45 [Google Scholar]
  64. Mooney RA, Davis SE, Peters JM, Rowland JL, Ansari AZ, Landick R. 64.  2009. Regulator trafficking on bacterial transcription units in vivo. Mol. Cell 33:197–108 [Google Scholar]
  65. Moyle H, Waldburger C, Susskind MM. 65.  1991. Hierarchies of base pair preferences in the P22 ant promoter. J. Bacteriol. 173:61944–50 [Google Scholar]
  66. Mukhopadhyay J, Kapanidis AN, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH. 66.  2001. Translocation of σ70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106:4453–63 [Google Scholar]
  67. Murakami KS, Darst SA. 67.  2003. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13:131–39 [Google Scholar]
  68. Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA. 68.  2002. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296:55711285–90 [Google Scholar]
  69. Murakami KS, Masuda S, Darst SA. 69.  2002. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296:55711280–84 [Google Scholar]
  70. Nickels BE, Garrity SJ, Mekler V, Minakhin L, Severinov K. 70.  et al. 2005. The interaction between σ70 and the β-flap of Escherichia coli RNA polymerase inhibits extension of nascent RNA during early elongation. Proc. Natl. Acad. Sci. USA 102:124488–93 [Google Scholar]
  71. Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A. 71.  2004. The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nat. Struct. Mol. Biol. 11:6544–50 [Google Scholar]
  72. Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA. 72.  2006. Regulon and promoter analysis of the E. coli heat-shock factor, σ32, reveals a multifaceted cellular response to heat stress. Genes Dev. 20:131776–89 [Google Scholar]
  73. Perdue SA, Roberts JW. 73.  2011. σ70-dependent transcription pausing in Escherichia coli. J. Mol. Biol. 412:5782–92 [Google Scholar]
  74. Pribnow D. 74.  1975. Bacteriophage T7 early promoters: nucleotide sequences of two RNA polymerase binding sites. J. Mol. Biol. 99:3419–43 [Google Scholar]
  75. Protozanova E, Yakovchuk P, Frank-Kamenetskii MD. 75.  2004. Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342:3775–85 [Google Scholar]
  76. Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ. 76.  2005. Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo. Mol. Cell 20:3357–66 [Google Scholar]
  77. Reppas NB, Wade JT, Church GM, Struhl K. 77.  2006. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol. Cell 24:5747–57 [Google Scholar]
  78. Reznikoff WS, Siegele DA, Cowing DW, Gross CA. 78.  1985. The regulation of transcription initiation in bacteria. Annu. Rev. Genet. 19:355–87 [Google Scholar]
  79. Rhodius VA, Mutalik VK. 79.  2010. Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, σE. Proc. Natl. Acad. Sci. USA 107:72854–59 [Google Scholar]
  80. Rhodius VA, Mutalik VK, Gross CA. 80.  2012. Predicting the strength of UP-elements and full-length E. coli σE promoters. Nucleic Acids Res. 40:72907–24 [Google Scholar]
  81. Rhodius VA, Segall-Shapiro TH, Sharon BD, Ghodasara A, Orlova E. 81.  et al. 2013. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol. Syst. Biol. 9:702 [Google Scholar]
  82. Rhodius VA, Suh WC, Nonaka G, West J, Gross CA. 82.  2006. Conserved and variable functions of the σE stress response in related genomes. PLoS Biol. 4:1e2 [Google Scholar]
  83. Ring BZ, Yarnell WS, Roberts JW. 83.  1996. Function of E. coli RNA polymerase σ factor σ70 in promoter-proximal pausing. Cell 86:3485–93 [Google Scholar]
  84. Roberts CW, Roberts JW. 84.  1996. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell 86:3495–501 [Google Scholar]
  85. Roberts JW, Yarnell W, Bartlett E, Guo J, Marr M. 85.  et al. 1998. Antitermination by bacteriophage λ Q protein. Cold Spring Harb. Symp. Quant. Biol. 63:319–25 [Google Scholar]
  86. Roy S, Lim HM, Liu M, Adhya S. 86.  2004. Asynchronous basepair openings in transcription initiation: CRP enhances the rate-limiting step. EMBO J. 23:4869–75 [Google Scholar]
  87. Saecker RM, Record MT Jr, deHaseth PL. 87.  2011. Mechanism of bacterial transcription initiation: RNA polymerase—promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis. J. Mol. Biol. 412:5754–71 [Google Scholar]
  88. Sanderson A, Mitchell JE, Minchin SD, Busby SJW. 88.  2003. Substitutions in the Escherichia coli RNA polymerase σ70 factor that affect recognition of extended -10 elements at promoters. FEBS Lett. 544:1–3199–205 [Google Scholar]
  89. Savinkova LK, Baranova LV, Knorre VL, Salganik RI. 89.  1988. [Binding of RNA-polymerase from Escherichia coli with oligodeoxyribonucleotides homologous to transcribed and non-transcribed DNA stands in the “-10”-promoter region of bacterial genes]. Mol. Biol. (Mosk.). 22:3807–12 [Google Scholar]
  90. Schaller H, Gray C, Herrmann K. 90.  1975. Nucleotide sequence of an RNA polymerase binding site from the DNA of bacteriophage fd. Proc. Natl. Acad. Sci. USA 72:2737–41 [Google Scholar]
  91. Schwartz EC, Shekhtman A, Dutta K, Pratt MR, Cowburn D. 91.  et al. 2008. A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. Chem. Biol. 15:101091–103 [Google Scholar]
  92. Sen R, Nagai H, Hernandez VJ, Shimamoto N. 92.  1998. Reduction in abortive transcription from the λPR promoter by mutations in region 3 of the σ70 subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 273:169872–77 [Google Scholar]
  93. Severinov K, Fenyö D, Severinova E, Mustaev A, Chait BT. 93.  et al. 1994. The sigma subunit conserved region 3 is part of “5′-face” of active center of Escherichia coli RNA polymerase. J. Biol. Chem. 269:3320826–28 [Google Scholar]
  94. Severinova E, Severinov K, Fenyö D, Marr M, Brody EN. 94.  et al. 1996. Domain organization of the Escherichia coli RNA polymerase σ70 subunit. J. Mol. Biol. 263:5637–47 [Google Scholar]
  95. Sevostyanova A, Djordjevic M, Kuznedelov K, Naryshkina T, Gelfand MS. 95.  et al. 2007. Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage ϕYS40. J. Mol. Biol. 366:2420–35 [Google Scholar]
  96. Shimamoto N, Kamigochi T, Utiyama H. 96.  1986. Release of the σ subunit of Escherichia coli DNA-dependent RNA polymerase depends mainly on time elapsed after the start of initiation, not on length of product RNA. J. Biol. Chem. 261:2511859–65 [Google Scholar]
  97. Shorenstein RG, Losick R. 97.  1973. Purification and properties of the σ subunit of ribonucleic acid polymerase from vegetative Bacillus subtilis. J. Biol. Chem. 248:176163–69 [Google Scholar]
  98. Shultzaberger RK, Chen Z, Lewis KA, Schneider TD. 98.  2007. Anatomy of Escherichia coli 70 promoters. Nucleic Acids Res. 35:3771–88 [Google Scholar]
  99. Siegele DA, Hu JC, Gross CA. 99.  1988. Mutations in rpoD, the gene encoding the σ70 subunit of Escherichia coli RNA polymerase, that increase expression of the lac operon in the absence of CAP-cAMP. J. Mol. Biol. 203:129–37 [Google Scholar]
  100. Silverstone AE, Goman M, Scaife JG. 100.  1972. ALT: a new factor involved in the synthesis of RNA by Escherichia coli. Mol. Gen. Genet. 118:3223–34 [Google Scholar]
  101. Sorenson MK, Darst SA. 101.  2006. Disulfide cross-linking indicates that FlgM-bound and free σ28 adopt similar conformations. Proc. Natl. Acad. Sci. USA 103:4516722–27 [Google Scholar]
  102. Sorenson MK, Ray SS, Darst SA. 102.  2004. Crystal structure of the flagellar σ/anti-σ complex σ28/FlgM reveals an intact σ factor in an inactive conformation. Mol. Cell 14:1127–38 [Google Scholar]
  103. Staro A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T. 103.  2009. The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family. Mol. Microbiol. 74:3557–81 [Google Scholar]
  104. Stragier P, Parsot C, Bouvier J. 104.  1985. Two functional domains conserved in major and alternate bacterial sigma factors. FEBS Lett. 187:111–15 [Google Scholar]
  105. Talkington C, Pero J. 105.  1978. Promoter recognition by phage SP01-modified RNA polymerase. Proc. Natl. Acad. Sci. 75:31185–89 [Google Scholar]
  106. Travers AA, Buckland R, Goman M, Le Grice SS, Scaife JG. 106.  1978. A mutation affecting the sigma subunit of RNA polymerase changes transcriptional specificity. Nature 273:5661354–58 [Google Scholar]
  107. Travers AA, Burgess RR. 107.  1969. Cyclic re-use of the RNA polymerase sigma factor. Nature 222:5193537–40 [Google Scholar]
  108. Ulrich LE, Zhulin IB. 108.  2010. The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Nucleic Acids Res. 38:Suppl. 1D401–7 [Google Scholar]
  109. Vassylyev DG, Sekine S-I, Laptenko O, Lee J, Vassylyeva MN. 109.  et al. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417:6890712–19 [Google Scholar]
  110. Vuthoori S, Bowers CW, McCracken A, Dombroski AJ, Hinton DM. 110.  2001. Domain 1.1 of the σ70 subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes. J. Mol. Biol. 309:3561–72 [Google Scholar]
  111. Wade JT, Struhl K. 111.  2004. Association of RNA polymerase with transcribed regions in Escherichia coli. Proc. Natl. Acad. Sci. 101:5117777–82 [Google Scholar]
  112. Waldburger C, Gardella T, Wong R, Susskind MM. 112.  1990. Changes in conserved region 2 of Escherichia coli σ70 affecting promoter recognition. J. Mol. Biol. 215:2267–76 [Google Scholar]
  113. Wecke T, Halang P, Staroń A, Dufour YS, Donohue TJ, Mascher T. 113.  2012. Extracytoplasmic function σ factors of the widely distributed group ECF41 contain a fused regulatory domain. MicrobiologyOpen 1:2194–213 [Google Scholar]
  114. Williams KP, Kassavetis GA, Esch FS, Geiduschek EP. 114.  1987. Identification of the gene encoding an RNA polymerase-binding protein of bacteriophage T4. J. Virol. 61:2597–99 [Google Scholar]
  115. Williams KP, Kassavetis GA, Geiduschek EP. 115.  1987. Interactions of the bacteriophage T4 gene 55 product with Escherichia coli RNA polymerase: competition with Escherichia coli σ70 and release from late T4 transcription complexes following initiation. J. Biol. Chem. 262:2512365–71 [Google Scholar]
  116. Wilson C, Dombroski AJ. 116.  1997. Region 1 of σ70 is required for efficient isomerization and initiation of transcription by Escherichia coli RNA polymerase. J. Mol. Biol. 267:160–74 [Google Scholar]
  117. Wu CW, Yarbrough LR, Hillel Z, Wu FY. 117.  1975. Sigma cycle during in vitro transcription: demonstration by nanosecond fluorescence depolarization spectroscopy. Proc. Natl. Acad. Sci. USA 72:83019–23 [Google Scholar]
  118. Yi C, Chen B, Qi B, Zhang W, Jia G. 118.  et al. 2012. Duplex interrogation by a direct DNA repair protein in search of base damage. Nat. Struct. Mol. Biol. 19:7671–76 [Google Scholar]
  119. Young BA. 119.  2004. Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting. Science 303:56621382–84 [Google Scholar]
  120. Young BA, Anthony LC, Gruber TM, Arthur TM, Heyduk E. 120.  et al. 2001. A coiled-coil from the RNA polymerase β′ subunit allosterically induces selective nontemplate strand binding by σ70. Cell 105:7935–44 [Google Scholar]
  121. Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I. 121.  et al. 2007. Region 1.2 of the RNA polymerase σ subunit controls recognition of the -10 promoter element. EMBO J. 26:4955–64 [Google Scholar]
  122. Zhang Y, Feng Y, Chatterjee S, Tuske S, Ho MX. 122.  et al. 2012. Structural basis of transcription initiation. Science 338:61101076–80 [Google Scholar]
  123. Zuber P, Healy J, Carter HL, Cutting S, Moran CP, Losick R. 123.  1989. Mutation changing the specificity of an RNA polymerase sigma factor. J. Mol. Biol. 206:4605–14 [Google Scholar]
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