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PMID: 18521075 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

Advances in bacterial promoter recognition and its control by factors that do not bind DNA.

Nature reviews. Microbiology ·Vol. 6 ·No. 7 ·2008-07-00 ·Pages 507-19

Haugen SP, Ross W, Gourse RL

Abstract

Early work identified two promoter regions, the -10 and -35 elements, that interact sequence specifically with bacterial RNA polymerase (RNAP). However, we now know that several additional promoter elements contact RNAP and influence transcription initiation. Furthermore, our picture of promoter control has evolved beyond one in which regulation results solely from activators and repressors that bind to DNA sequences near the RNAP binding site: many important transcription factors bind directly to RNAP without binding to DNA. These factors can target promoters by affecting specific kinetic steps on the pathway to open complex formation, thereby regulating RNA output from specific promoters.

MeSH Terms
Bacterial Proteins/metabolism DNA/metabolism DNA-Directed RNA Polymerases/metabolism Gene Expression Regulation, Bacterial Promoter Regions, Genetic/genetics Transcription Factors/metabolism Transcription, Genetic
Chemicals
Bacterial Proteins Transcription Factors DNA DNA-Directed RNA Polymerases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Haugen Shanil P
Department of Bacteriology, University of Wisconsin- Madison, 1550 Linden Drive, Madison, Wisconsin 53706, USA.
Ross Wilma
Gourse Richard L
References (147)
147 references, click to expand
  1. An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4.
    Genes Dev. 2003 May 15;17(10):1293-307 PMID: 12756230
  2. pH-dependent conformational switch activates the inhibitor of transcription elongation.
    EMBO J. 2006 May 17;25(10):2131-41 PMID: 16628221
  3. Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates.
    J Mol Biol. 2002 Jun 7;319(3):649-71 PMID: 12054861
  4. Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase.
    J Mol Biol. 2007 Mar 2;366(4):1243-57 PMID: 17207814
  5. Structural organization of the RNA polymerase-promoter open complex.
    Cell. 2000 Jun 9;101(6):601-11 PMID: 10892647
  6. Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70.
    Mol Microbiol. 2008 Mar;67(6):1242-56 PMID: 18208528
  7. Regulation of carAB expression in Escherichia coli occurs in part through UTP-sensitive reiterative transcription.
    J Bacteriol. 1998 Feb;180(3):705-13 PMID: 9457878
  8. Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.
    Genes Dev. 2005 Oct 1;19(19):2378-87 PMID: 16204187
  9. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP.
    Cell. 2004 Aug 6;118(3):311-22 PMID: 15294157
  10. Spx-RNA polymerase interaction and global transcriptional control during oxidative stress.
    J Bacteriol. 2004 Apr;186(7):1911-8 PMID: 15028674
  11. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition.
    Mol Microbiol. 2000 Aug;37(4):687-95 PMID: 10972792
  12. Strand opening-deficient Escherichia coli RNA polymerase facilitates investigation of closed complexes with promoter DNA: effects of DNA sequence and temperature.
    J Biol Chem. 2007 Jul 20;282(29):21319-26 PMID: 17507375
  13. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli.
    J Bacteriol. 2006 Aug;188(16):5775-82 PMID: 16885445
  14. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.
    Mol Cell. 2006 Dec 8;24(5):747-757 PMID: 17157257
  15. Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site.
    Science. 1993 Jan 15;259(5093):358-61 PMID: 8420002
  16. Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding.
    Cell. 1994 Sep 9;78(5):889-96 PMID: 8087855
  17. Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription.
    Cell. 2004 Aug 6;118(3):297-309 PMID: 15294156
  18. Structural basis for transcription elongation by bacterial RNA polymerase.
    Nature. 2007 Jul 12;448(7150):157-62 PMID: 17581590
  19. Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus.
    J Bacteriol. 2006 Oct;188(20):7111-22 PMID: 17015650
  20. Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo.
    Mol Cell. 2005 Nov 11;20(3):357-66 PMID: 16285918
  21. Characterization of transcriptional initiation from promoters P1 and P2 of the pyrBI operon of Escherichia coli K12.
    J Biol Chem. 1990 Nov 5;265(31):19091-9 PMID: 1699940
  22. The Escherichia coli Fis promoter is regulated by changes in the levels of its transcription initiation nucleotide CTP.
    J Biol Chem. 2004 Dec 3;279(49):50818-28 PMID: 15385561
  23. Nucleotide-dependent isomerization of Escherichia coli RNA polymerase.
    Biochemistry. 2004 Oct 5;43(39):12660-6 PMID: 15449955
  24. Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA.
    Cell. 2001 Aug 24;106(4):453-63 PMID: 11525731
  25. Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase.
    Cell. 1996 Aug 9;86(3):495-501 PMID: 8756731
  26. Crl stimulates RpoS activity during stationary phase.
    Mol Microbiol. 1998 Sep;29(5):1225-36 PMID: 9767590
  27. Anti-sigma factors.
    Curr Opin Microbiol. 1999 Apr;2(2):135-41 PMID: 10322161
  28. Adenines at -11, -9 and -8 play a key role in the binding of Bacillus subtilis Esigma(A) RNA polymerase to -10 region single-stranded DNA.
    Nucleic Acids Res. 1999 Dec 1;27(23):4541-6 PMID: 10556308
  29. A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding.
    Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14849-52 PMID: 11734629
  30. A sigma-core interaction of the RNA polymerase holoenzyme that enhances promoter escape.
    EMBO J. 2007 Mar 21;26(6):1579-90 PMID: 17332752
  31. Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA.
    J Biol Chem. 2006 Jun 2;281(22):15238-48 PMID: 16597620
  32. A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.
    Mol Cell. 2006 Jul 7;23(1):97-107 PMID: 16798040
  33. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase.
    Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):285-90 PMID: 15626761
  34. Binding of the initiation factor sigma(70) to core RNA polymerase is a multistep process.
    Mol Cell. 2001 Jul;8(1):21-31 PMID: 11511357
  35. A coiled-coil from the RNA polymerase beta' subunit allosterically induces selective nontemplate strand binding by sigma(70).
    Cell. 2001 Jun 29;105(7):935-44 PMID: 11439189
  36. An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation.
    EMBO J. 2004 Nov 10;23(22):4473-83 PMID: 15496987
  37. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel.
    Mol Cell. 2004 Jun 18;14(6):739-51 PMID: 15200952
  38. The regulation of bacterial transcription initiation.
    Nat Rev Microbiol. 2004 Jan;2(1):57-65 PMID: 15035009
  39. Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.
    J Mol Biol. 2008 Mar 21;377(2):551-64 PMID: 18272182
  40. Regulation of RNA polymerase through the secondary channel.
    Cell. 2004 Aug 6;118(3):281-4 PMID: 15294154
  41. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase.
    Science. 1993 Nov 26;262(5138):1407-13 PMID: 8248780
  42. rRNA transcription in Escherichia coli.
    Annu Rev Genet. 2004;38:749-70 PMID: 15568992
  43. Structural basis for transcription regulation by alarmone ppGpp.
    Cell. 2004 Apr 30;117(3):299-310 PMID: 15109491
  44. An inactive open complex mediated by an UP element at Escherichia coli promoters.
    Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7202-7 PMID: 10377392
  45. ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms.
    Mol Microbiol. 2008 Feb;67(3):619-32 PMID: 18086212
  46. Exploitation of a chemical nuclease to investigate the location and orientation of the Escherichia coli RNA polymerase alpha subunit C-terminal domains at simple promoters that are activated by cyclic AMP receptor protein.
    J Biol Chem. 2003 Dec 26;278(52):52944-52 PMID: 14530288
  47. The study of guanosine 5'-diphosphate 3'-diphosphate-mediated transcription regulation in vitro using a coupled transcription-translation system.
    J Biol Chem. 2000 Mar 10;275(10):6783-9 PMID: 10702235
  48. Crl facilitates RNA polymerase holoenzyme formation.
    J Bacteriol. 2006 Nov;188(22):7966-70 PMID: 16980472
  49. Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly.
    Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):892-7 PMID: 11158566
  50. Effect of mutations in the "extended -10" motif of three Bacillus subtilis sigmaA-RNA polymerase-dependent promoters.
    J Mol Biol. 1999 Feb 26;286(3):683-93 PMID: 10024443
  51. Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments.
    J Mol Biol. 2008 Feb 29;376(4):1034-47 PMID: 18191943
  52. Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners.
    Biochemistry. 1999 May 11;38(19):5959-67 PMID: 10320321
  53. Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.
    J Bacteriol. 2002 May;184(9):2500-20 PMID: 11948165
  54. Bacterial RNA polymerases: the wholo story.
    Curr Opin Struct Biol. 2003 Feb;13(1):31-9 PMID: 12581657
  55. 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 U S A. 2005 Mar 22;102(12):4488-93 PMID: 15761057
  56. The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription.
    Mol Microbiol. 2006 May;60(3):749-64 PMID: 16629675
  57. The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants.
    Biochem J. 2004 Oct 15;383(Pt 2):371-82 PMID: 15250823
  58. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution.
    Science. 2002 May 17;296(5571):1280-4 PMID: 12016306
  59. Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli.
    J Bacteriol. 1992 Jan;174(2):514-24 PMID: 1345912
  60. General pathway for turning on promoters transcribed by RNA polymerases containing alternative sigma factors.
    J Bacteriol. 2006 Jul;188(13):4589-91 PMID: 16788165
  61. Release of the sigma 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. 1986 Sep 5;261(25):11859-65 PMID: 2427513
  62. Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove.
    Genes Dev. 2001 Mar 1;15(5):491-506 PMID: 11238372
  63. Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter.
    Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4706-11 PMID: 15738402
  64. Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting.
    Science. 2004 Feb 27;303(5662):1382-4 PMID: 14988563
  65. ppGpp: a global regulator in Escherichia coli.
    Trends Microbiol. 2005 May;13(5):236-42 PMID: 15866041
  66. Transcription profiling of the stringent response in Escherichia coli.
    J Bacteriol. 2008 Feb;190(3):1084-96 PMID: 18039766
  67. Different roles for basic and aromatic amino acids in conserved region 2 of Escherichia coli sigma(70) in the nucleation and maintenance of the single-stranded DNA bubble in open RNA polymerase-promoter complexes.
    J Biol Chem. 2001 Aug 24;276(34):31891-6 PMID: 11443133
  68. Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein-DNA interactions and growth rate in osmotically stressed Escherichia coli K-12.
    J Mol Recognit. 2004 Sep-Oct;17(5):488-96 PMID: 15362109
  69. Identification of the bacterial alarmone guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in plants.
    Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4320-4 PMID: 15010537
  70. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.
    Science. 2002 May 17;296(5571):1285-90 PMID: 12016307
  71. Look, no hands! Unconventional transcriptional activators in bacteria.
    Trends Microbiol. 2007 Dec;15(12):530-7 PMID: 17997097
  72. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme.
    Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4554-9 PMID: 15070756
  73. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.
    Science. 2006 Nov 17;314(5802):1144-7 PMID: 17110578
  74. Structural basis of transcription activation: the CAP-alpha CTD-DNA complex.
    Science. 2002 Aug 30;297(5586):1562-6 PMID: 12202833
  75. Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif.
    J Bacteriol. 2006 Dec;188(24):8352-9 PMID: 17012380
  76. Identification and analysis of 'extended -10' promoters in Escherichia coli.
    Nucleic Acids Res. 2003 Aug 15;31(16):4689-95 PMID: 12907708
  77. Structure of the bacterial RNA polymerase promoter specificity sigma subunit.
    Mol Cell. 2002 Mar;9(3):527-39 PMID: 11931761
  78. The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like "stringent" RNA polymerases in Escherichia coli.
    Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2908-13 PMID: 9501189
  79. Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase.
    J Biol Chem. 2004 May 7;279(19):19540-50 PMID: 14978043
  80. Promoter selectivity of Escherichia coli RNA polymerase: omega factor is responsible for the ppGpp sensitivity.
    Nucleic Acids Res. 1989 Nov 11;17(21):8755-65 PMID: 2685748
  81. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching.
    Science. 2006 Nov 17;314(5802):1139-43 PMID: 17110577
  82. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
    Cell. 2004 Nov 12;119(4):481-9 PMID: 15537538
  83. Redox-sensitive transcriptional control by a thiol/disulphide switch in the global regulator, Spx.
    Mol Microbiol. 2005 Jan;55(2):498-510 PMID: 15659166
  84. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution.
    Nature. 2002 Jun 13;417(6890):712-9 PMID: 12000971
  85. Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide.
    Science. 1997 May 23;276(5316):1258-60 PMID: 9157885
  86. Potassium glutamate as a transcriptional inhibitor during bacterial osmoregulation.
    EMBO J. 2006 Apr 5;25(7):1515-21 PMID: 16541105
  87. Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro.
    J Bacteriol. 2007 Dec;189(24):8772-85 PMID: 17766423
  88. Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli.
    J Bacteriol. 2007 Jul;189(14):5193-202 PMID: 17496080
  89. The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase.
    J Mol Biol. 1999 Jan 22;285(3):955-64 PMID: 9918716
  90. RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA.
    Biochemistry. 2002 Dec 24;41(51):15334-41 PMID: 12484772
  91. 6S RNA: a small RNA regulator of transcription.
    Curr Opin Microbiol. 2007 Apr;10(2):164-8 PMID: 17383220
  92. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters.
    EMBO J. 1997 Jul 1;16(13):4034-40 PMID: 9233812
  93. DksA potentiates direct activation of amino acid promoters by ppGpp.
    Proc Natl Acad Sci U S A. 2005 May 31;102(22):7823-8 PMID: 15899978
  94. NTP-entry routes in multi-subunit RNA polymerases.
    Trends Biochem Sci. 2005 Dec;30(12):651-4 PMID: 16243529
  95. Structure of a ternary transcription activation complex.
    Mol Cell. 2004 Jan 16;13(1):45-53 PMID: 14731393
  96. Escherichia coli promoter opening and -10 recognition: mutational analysis of sigma70.
    EMBO J. 2000 Mar 1;19(5):1130-7 PMID: 10698953
  97. Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase.
    Proc Natl Acad Sci U S A. 2007 May 8;104(19):7833-8 PMID: 17470797
  98. rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase.
    Cell. 2006 Jun 16;125(6):1069-82 PMID: 16777598
  99. Guanosine 3',5'-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli.
    Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2374-9 PMID: 16467149
  100. Sigma and RNA polymerase: an on-again, off-again relationship?
    Mol Cell. 2005 Nov 11;20(3):335-45 PMID: 16285916
  101. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria.
    Science. 1997 Dec 19;278(5346):2092-7 PMID: 9405339
  102. Isolation and characterization of sigma(70)-retaining transcription elongation complexes from Escherichia coli.
    Cell. 2001 Aug 24;106(4):443-51 PMID: 11525730
  103. (p)ppGpp: still magical?
    Annu Rev Microbiol. 2008;62:35-51 PMID: 18454629
  104. Promoter recognition by Escherichia coli RNA polymerase: effects of the UP element on open complex formation and promoter clearance.
    Biochemistry. 1998 Dec 22;37(51):18074-80 PMID: 9922176
  105. The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized.
    Genes Dev. 1999 Nov 15;13(22):3015-26 PMID: 10580008
  106. DNA determinants of promoter selectivity in Escherichia coli.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:477-81 PMID: 6345065
  107. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.
    Cell. 2002 Mar 8;108(5):599-614 PMID: 11893332
  108. Visualization and quantitative analysis of complex formation between E. coli RNA polymerase and an rRNA promoter in vitro.
    Nucleic Acids Res. 1988 Oct 25;16(20):9789-809 PMID: 3054811
  109. Induction of expression of hfq by DksA is essential for Shigella flexneri virulence.
    Mol Microbiol. 2006 Oct;62(2):469-79 PMID: 17020583
  110. Structural kinetics of transcription activation at the malT promoter of Escherichia coli by UV laser footprinting.
    Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9022-7 PMID: 9256428
  111. Regulation of upp expression in Escherichia coli by UTP-sensitive selection of transcriptional start sites coupled with UTP-dependent reiterative transcription.
    J Bacteriol. 1997 Nov;179(21):6665-73 PMID: 9352914
  112. Fine structure of the promoter-sigma region 1.2 interaction.
    Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3292-7 PMID: 18287032
  113. The TRTGn motif stabilizes the transcription initiation open complex.
    J Mol Biol. 2002 Sep 20;322(3):521-32 PMID: 12225746
  114. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro.
    J Mol Biol. 2001 Jan 26;305(4):673-88 PMID: 11162084
  115. Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase.
    EMBO J. 2003 Dec 1;22(23):6322-34 PMID: 14633991
  116. Crl activates transcription initiation of RpoS-regulated genes involved in the multicellular behavior of Salmonella enterica serovar Typhimurium.
    J Bacteriol. 2006 Jun;188(11):3983-94 PMID: 16707690
  117. T4 AsiA blocks DNA recognition by remodeling sigma70 region 4.
    EMBO J. 2004 Aug 4;23(15):2952-62 PMID: 15257291
  118. ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes.
    Mol Microbiol. 2006 Jul;61(1):194-205 PMID: 16824105
  119. A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria.
    Mol Cell. 2007 Sep 7;27(5):793-805 PMID: 17803943
  120. A structural model of transcription elongation.
    Science. 2000 Jul 28;289(5479):619-25 PMID: 10915625
  121. Views of transcription initiation.
    Cell. 2002 May 17;109(4):417-20 PMID: 12086598
  122. Catabolite activator protein: DNA binding and transcription activation.
    Curr Opin Struct Biol. 2004 Feb;14(1):10-20 PMID: 15102444
  123. Regulation of pyrBI operon expression in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation.
    Genes Dev. 1994 Dec 1;8(23):2904-12 PMID: 7527789
  124. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.
    Cell. 1999 Sep 17;98(6):811-24 PMID: 10499798
  125. Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association.
    Proc Natl Acad Sci U S A. 2005 Jan 11;102(2):291-6 PMID: 15626760
  126. Promoter sequence for stringent control of bacterial ribonucleic acid synthesis.
    J Bacteriol. 1980 Feb;141(2):973-6 PMID: 6154042
  127. Stationary phase reorganisation of the Escherichia coli transcription machinery by Crl protein, a fine-tuner of sigmas activity and levels.
    EMBO J. 2007 Mar 21;26(6):1569-78 PMID: 17332743
  128. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
    Cell. 2003 Aug 8;114(3):335-45 PMID: 12914698
  129. LexA represses CTXphi transcription by blocking access of the alpha C-terminal domain of RNA polymerase to promoter DNA.
    J Biol Chem. 2006 Dec 22;281(51):39407-12 PMID: 17046810
  130. Control of rRNA expression by small molecules is dynamic and nonredundant.
    Mol Cell. 2003 Jul;12(1):125-34 PMID: 12887898
  131. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.
    Science. 2001 Jun 8;292(5523):1863-76 PMID: 11313498
  132. DNA-bend modulation in a repressor-to-activator switching mechanism.
    Nature. 1995 Mar 23;374(6520):371-5 PMID: 7885478
  133. Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription.
    Mol Cell. 2003 Jun;11(6):1621-33 PMID: 12820974
  134. Interrelated effects of DNA supercoiling, ppGpp, and low salt on melting within the Escherichia coli ribosomal RNA rrnB P1 promoter.
    Mol Microbiol. 1992 Aug;6(16):2243-51 PMID: 1406265
  135. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase.
    Science. 2006 Dec 8;314(5805):1601-3 PMID: 17158328
  136. A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting.
    J Biol Chem. 2006 May 5;281(18):12362-9 PMID: 16531399
  137. 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. 2004 Apr 23;279(17):16899-902 PMID: 14990576
  138. Characterization of the closed complex intermediate formed during transcription initiation by Escherichia coli RNA polymerase.
    J Biol Chem. 1998 Sep 4;273(36):23549-57 PMID: 9722594
  139. Physiological effects of Crl in Salmonella are modulated by sigmaS level and promoter specificity.
    J Bacteriol. 2007 Apr;189(8):2976-87 PMID: 17293430
  140. Regulation of the fimB promoter: a case of differential regulation by ppGpp and DksA in vivo.
    Mol Microbiol. 2008 Mar;67(6):1223-41 PMID: 18284577
  141. The X-ray crystal structure of RNA polymerase from Archaea.
    Nature. 2008 Feb 14;451(7180):851-4 PMID: 18235446
  142. Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. coli RNA polymerase.
    Biochemistry. 2000 Oct 10;39(40):12274-83 PMID: 11015206
  143. Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching.
    J Mol Biol. 1995 Dec 8;254(4):552-65 PMID: 7500333
  144. Repression and activation of promoter-bound RNA polymerase activity by Gal repressor.
    J Mol Biol. 1997 Sep 26;272(3):293-300 PMID: 9325090
  145. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP.
    J Mol Biol. 2001 Jan 26;305(4):689-702 PMID: 11162085
  146. Cyclic re-use of the RNA polymerase sigma factor.
    Nature. 1969 May 10;222(5193):537-40 PMID: 5781654
  147. Stationary phase gene regulation: what makes an Escherichia coli promoter sigmaS-selective?
    Curr Opin Microbiol. 2002 Dec;5(6):591-5 PMID: 12457703
Article Info
Journal
Nature reviews. Microbiology
Abbr.
Nat Rev Microbiol
ISSN
1740-1534
Published
2008-07-00
Epub
2008-00-03
Pages
507-19
Language
English
Region
England
NLM ID
101190261
PMCID
PMC3700611
Subset
IM
Grants
NIGMS NIH HHS · R37 GM037048 · United States
NIGMS NIH HHS · R37 GM37048 · United States
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