rpoD

Summary

Gene Symbol: rpoD
Description: RNA polymerase, sigma 70 (sigma D) factor
Alias: ECK3057, JW3039, alt
Species: Escherichia coli str. K-12 substr. MG1655
Products:     rpoD

Top Publications

  1. Wade J, Castro Roa D, Grainger D, Hurd D, Busby S, Struhl K, et al. Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol. 2006;13:806-14 pubmed
    ..SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon. ..
  2. Brodolin K, Zenkin N, Mustaev A, Mamaeva D, Heumann H. The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat Struct Mol Biol. 2004;11:551-7 pubmed
    ..In addition, we suggest that the sigma(70) subunit in the elongation complex may provide a target for regulation of gene expression. ..
  3. Maeda H, Fujita N, Ishihama A. Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res. 2000;28:3497-503 pubmed
    ..Taken together with the intracellular sigma levels, we tried to estimate the number of each holoenzyme form in growing E. coli cells. ..
  4. Shultzaberger R, Chen Z, Lewis K, Schneider T. Anatomy of Escherichia coli sigma70 promoters. Nucleic Acids Res. 2007;35:771-88 pubmed
    ..Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the -35, so bending allows distal activators to reach the polymerase. ..
  5. Nickels B, Mukhopadhyay J, Garrity S, Ebright R, Hochschild A. The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nat Struct Mol Biol. 2004;11:544-50 pubmed
    ..Bioinformatic analysis suggests that promoter-proximal sigma(70)-dependent pauses may play a role in the regulation of many bacterial promoters. ..
  6. Ferguson A, Hughes A, Tufail U, Baumann C, Scott D, Hoggett J. Interaction of sigma 70 with Escherichia coli RNA polymerase core enzyme studied by surface plasmon resonance. FEBS Lett. 2000;481:281-4 pubmed
    ..9x10(-7) M, and the dissociation rate constant for release of sigma from core, in the absence of DNA or transcription, was 4x10(-3) s(-1), corresponding to a half-life of about 200 s. ..
  7. Schroeder L, deHaseth P. Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases. J Biol Chem. 2005;280:17422-9 pubmed
    ..A model is presented for how this mechanistic difference between the two RNA polymerase could explain our observations. ..
  8. Burgess R, Anthony L. How sigma docks to RNA polymerase and what sigma does. Curr Opin Microbiol. 2001;4:126-31 pubmed
    ..This region of beta' interacts with region 2.1-2.2 of sigma(70). Binding of this region of beta' to sigma(70) triggers a conformational change in sigma that allows it to bind to a -10 nontemplate promoter DNA strand oligonucleotide. ..
  9. Becker G, Hengge Aronis R. What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma(S). Mol Microbiol. 2001;39:1153-65 pubmed
    ..5 in sigmaS in transcription initiation. Moreover, we propose a consensus sequence for a sigmaS-selective promoter and discuss its emergence and functional properties from an evolutionary point of view. ..

More Information

Publications89

  1. Lonetto M, Gribskov M, Gross C. The sigma 70 family: sequence conservation and evolutionary relationships. J Bacteriol. 1992;174:3843-9 pubmed
  2. Kourennaia O, Tsujikawa L, deHaseth P. Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter DNA melting and -10 recognition. J Bacteriol. 2005;187:6762-9 pubmed
    ..4 on the activities of the two sigma factors are consistent with the pronounced differences between both the amino acid sequences in this region and the recognized promoter DNA sequences. ..
  3. Typas A, Becker G, Hengge R. The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase. Mol Microbiol. 2007;63:1296-306 pubmed
    ..it is known to recognize the same core promoter elements in vitro as the housekeeping sigma factor, sigma70 (RpoD)...
  4. Dombroski A, Johnson B, Lonetto M, Gross C. The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing. Proc Natl Acad Sci U S A. 1996;93:8858-62 pubmed
    ..Our data support the idea that sigma makes simultaneous, productive contacts at both the -10 and the -35 regions of the promoter and discerns the spacing between these conserved regions. ..
  5. Sclavi B, Zaychikov E, Rogozina A, Walther F, Buckle M, Heumann H. 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;102:4706-11 pubmed
    ..During the final isomerization step, the downstream double helix becomes embedded in the beta/beta' jaws, leading to a transcriptionally active complex. ..
  6. Brodolin K, Zenkin N, Severinov K. Remodeling of the sigma70 subunit non-template DNA strand contacts during the final step of transcription initiation. J Mol Biol. 2005;350:930-7 pubmed
    ..Establishment of downstream contacts leads to remodeling of upstream interactions between sigma70 and the -10 promoter element that might facilitate promoter escape and sigma release. ..
  7. Gill S, Weitzel S, von Hippel P. Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J Mol Biol. 1991;220:307-24 pubmed
    ..These results are used to begin to define the basic conformational states and interaction potentials of core polymerase in the various stages of the transcription cycle. ..
  8. Huerta A, Francino M, Morett E, Collado Vides J. Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes. PLoS Genet. 2006;2:e185 pubmed
  9. Zhi H, Jin D. Purification of highly-active and soluble Escherichia coli sigma 70 polypeptide overproduced at low temperature. Methods Enzymol. 2003;370:174-80 pubmed
  10. Huerta A, Collado Vides J. Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol. 2003;333:261-78 pubmed
    ..We suggest that transcriptional regulators as well as other functional promoters play an important role in keeping these latent signals suppressed. ..
  11. Malhotra A, Severinova E, Darst S. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell. 1996;87:127-36 pubmed
    ..The structure suggests one way in which DNA interactions may be inhibited in the absence of RNA polymerase and provides a framework for the interpretation of a large number of genetic and biochemical analyses. ..
  12. Sanderson A, Mitchell J, Minchin S, Busby S. Substitutions in the Escherichia coli RNA polymerase sigma70 factor that affect recognition of extended -10 elements at promoters. FEBS Lett. 2003;544:199-205 pubmed
    ..Our study shows that changes in these regions of the sigma(70) subunit can affect the recognition of different extended -10 element sequences. ..
  13. Wang H, Kaloper M, Benham C. SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes. Nucleic Acids Res. 2006;34:D373-8 pubmed
    ..SIDDBASE is available at www.gc.ucdavis.edu/benham/siddbase. ..
  14. Wang H, Noordewier M, Benham C. Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters. Genome Res. 2004;14:1575-84 pubmed
    ..We describe how these observations may illuminate specific mechanisms of regulation, and assist in the computational identification of promoter locations in prokaryotes. ..
  15. Gardella T, Moyle H, Susskind M. A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. J Mol Biol. 1989;206:579-90 pubmed
    ..In strains carrying both the mutant and wild-type sigma gene (rpoD), the mutant sigma causes a large increase in the activity of mutant P22 ant promoters with A.T or C...
  16. Niedziela Majka A, Heyduk T. Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting. J Biol Chem. 2005;280:38219-27 pubmed
  17. Young B, Gruber T, Gross C. Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting. Science. 2004;303:1382-4 pubmed
    ..Our results support the model that capture of nontemplate bases extruded from the DNA helix underlies the melting process. ..
  18. Burgess R, Travers A, Dunn J, Bautz E. Factor stimulating transcription by RNA polymerase. Nature. 1969;221:43-6 pubmed
  19. Kumar A, Malloch R, Fujita N, Smillie D, Ishihama A, Hayward R. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter. J Mol Biol. 1993;232:406-18 pubmed
  20. Mooney R, Landick R. Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev. 2003;17:2839-51 pubmed
    ..We report that tethering sigma70 to all RNAP molecules via genetic fusion of rpoD to rpoC (encoding sigma70 and RNAP's beta' subunit, respectively) yields viable Escherichia coli strains in which ..
  21. Andre E, Bastide L, Villain Guillot P, Latouche J, Rouby J, Leonetti J. A multiwell assay to isolate compounds inhibiting the assembly of the prokaryotic RNA polymerase. Assay Drug Dev Technol. 2004;2:629-35 pubmed
    ..We demonstrate the usefulness of the assay to screen for microbial RNA polymerase inhibitors as potential new drugs for the treatment of emerging antibiotic-resistant bacteria. ..
  22. Lehman I, Bessman M, Simms E, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem. 1958;233:163-70 pubmed
  23. Sarkar P, Switzer A, Peters C, Pogliano J, Wigneshweraraj S. Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli. Nucleic Acids Res. 2017;45:11131-11143 pubmed publisher
    ..The results imply that while synthetic transcriptional rewiring may confer bacteria with the intended desirable properties, such approaches may also collaterally allow them to acquire undesirable traits. ..
  24. Arthur T, Anthony L, Burgess R. Mutational analysis of beta '260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase. J Biol Chem. 2000;275:23113-9 pubmed
    ..A. (1999) Cell 98, 811-824), the region homologous to beta'(260-309) of Escherichia coli forms a coiled coil. Modeling of our mutations onto that coiled coil places the most defective mutations on one face of the coiled coil. ..
  25. Traviglia S, Datwyler S, Yan D, Ishihama A, Meares C. Targeted protein footprinting: where different transcription factors bind to RNA polymerase. Biochemistry. 1999;38:15774-8 pubmed
    ..GreA cuts a larger set of sites, whereas omega shows no overlap with the others, cutting only the beta' subunit at a unique location. ..
  26. Finn R, Orlova E, Gowen B, Buck M, van Heel M. Escherichia coli RNA polymerase core and holoenzyme structures. EMBO J. 2000;19:6833-44 pubmed
    ..All common RNA polymerase subunits (alpha(2), ss, ss') could be localized in both structures, thus suggesting the position of sigma(70) in the holoenzyme. ..
  27. Mooney R, Artsimovitch I, Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J Bacteriol. 1998;180:3265-75 pubmed
  28. Sullivan J, Bjornson K, Sowers L, deHaseth P. Spectroscopic determination of open complex formation at promoters for Escherichia coli RNA polymerase. Biochemistry. 1997;36:8005-12 pubmed
    ..The same substrates were also used to monitor the promoter re-annealing that ensues upon initiation of RNA synthesis. Similar rates for this process were observed for the two promoter variants employed in this study. ..
  29. Morichaud Z, Chaloin L, Brodolin K. Regions 1.2 and 3.2 of the RNA Polymerase σ Subunit Promote DNA Melting and Attenuate Action of the Antibiotic Lipiarmycin. J Mol Biol. 2016;428:463-76 pubmed publisher
    ..Our data suggested that template strand single-stranded DNA competes with Lpm for binding to RNAP and that σ(70) regions 1.2 and 3.2 attenuate Lpm action by promoting DNA duplex opening. ..
  30. Koroleva O, Busby S, Drutsa V. Effects of substitutions at position 180 in the Escherichia coli RNA polymerase ? 70 subunit. J Biosci. 2011;36:43-54 pubmed
  31. Nguyen L, Burgess R. Comparative analysis of the interactions of Escherichia coli sigma S and sigma 70 RNA polymerase holoenzyme with the stationary-phase-specific bolAp1 promoter. Biochemistry. 1997;36:1748-54 pubmed
    ..KMnO4 reactivity assays reveal that, at 37 degrees C, both holoenzymes produced similar but not identical patterns of reactivities. ..
  32. Glickman B. The role of DNA polymerase I in excision-repair. Basic Life Sci. 1975;5A:213-8 pubmed
    ..The ResAl strain, however, showed no ultraviolet stimulation of the incorporation of the density label. These observations indicate that DNA polymerase I plays a key role in the excision-repair process in E. coli. ..
  33. Burton Z, Burgess R, Lin J, Moore D, Holder S, Gross C. The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12. Nucleic Acids Res. 1981;9:2889-903 pubmed
    We have determined the nucleotide sequence of the rpoD gene which codes for the sigma subunit of RNA polymerase from E. coli K12...
  34. Barinova N, Kuznedelov K, Severinov K, Kulbachinskiy A. Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA. J Biol Chem. 2008;283:22482-9 pubmed publisher
  35. Szafranski P. On the evolution of the bacterial major sigma factors. J Mol Evol. 1992;34:465-7 pubmed
    ..It is proposed that major sigma factors may have originated by duplication and fusion of a DNA unit related to the ancestral gene for the whole sigma family. Coevolution of major sigma structures and complex promoters is suggested. ..
  36. Derbyshire V, Grindley N, Joyce C. The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction. EMBO J. 1991;10:17-24 pubmed
    ..The pH-dependence of the 3'-5' exonuclease reaction is consistent with a mechanism in which nucleophilic attack on the terminal phosphodiester bond is initiated by a hydroxide ion coordinated to one of the enzyme-bound metal ions. ..
  37. Abbotts J, Sengupta D, Zon G, Wilson S. Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis. J Biol Chem. 1988;263:15094-103 pubmed
    ..The results are consistent with a model in which termination occurs with several enzyme forms that are in equilibrium in an ordered catalytic mechanism. ..
  38. Sevostyanova A, Feklistov A, Barinova N, Heyduk E, Bass I, Klimasauskas S, et al. Specific recognition of the -10 promoter element by the free RNA polymerase sigma subunit. J Biol Chem. 2007;282:22033-9 pubmed
    ..Thus, the complex process of the -10 element recognition by RNA polymerase holoenzyme can be reduced to a simple system consisting of an isolated sigma subunit and a short aptamer oligonucleotide. ..
  39. Sharma U, Chatterji D. Differential mechanisms of binding of anti-sigma factors Escherichia coli Rsd and bacteriophage T4 AsiA to E. coli RNA polymerase lead to diverse physiological consequences. J Bacteriol. 2008;190:3434-43 pubmed publisher
    ..coli growth by AsiA expression is probably due to the ability of the AsiA protein to trap the holoenzyme RNA polymerase rather than its higher binding affinity to sigma(70). ..
  40. Huberman J, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. XXXV. A 3'-hydroxylribonucleotide binding site of Escherichia coli deoxyribonucleic acid polymerase. J Biol Chem. 1970;245:5326-34 pubmed
  41. Taylor W, Straus D, Grossman A, Burton Z, Gross C, Burgess R. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Cell. 1984;38:371-81 pubmed
    The rpoD gene encoding the sigma subunit of E. coli RNA polymerase is cotranscribed with rpsU and dnaG, encoding ribosomal protein S21 and DNA primase, respectively...
  42. Westblade L, Ilag L, Powell A, Kolb A, Robinson C, Busby S. Studies of the Escherichia coli Rsd-sigma70 complex. J Mol Biol. 2004;335:685-92 pubmed
    ..Alanine scanning and deletion mutagenesis were used to locate regions of sigma(70) that are required for the formation of the Rsd-sigma(70) complex. ..
  43. Waldburger C, Susskind M. Probing the informational content of Escherichia coli sigma 70 region 2.3 by combinatorial cassette mutagenesis. J Mol Biol. 1994;235:1489-500 pubmed
    ..In contrast, Thr429 is quite intolerant to substitution and is predicted to have an important role in sigma 70 function. ..
  44. Minnick D, Astatke M, Joyce C, Kunkel T. A thumb subdomain mutant of the large fragment of Escherichia coli DNA polymerase I with reduced DNA binding affinity, processivity, and frameshift fidelity. J Biol Chem. 1996;271:24954-61 pubmed
    ..The results are discussed in light of remarkably similar observations with T7 DNA polymerase in the presence or absence of thioredoxin, an accessory subunit that affects these same properties. ..
  45. Burgess R, Arthur T, Pietz B. Interaction of Escherichia coli sigma 70 with core RNA polymerase. Cold Spring Harb Symp Quant Biol. 1998;63:277-87 pubmed
  46. Sun L, Dove S, Panaghie G, deHaseth P, Hochschild A. An RNA polymerase mutant deficient in DNA melting facilitates study of activation mechanism: application to an artificial activator of transcription. J Mol Biol. 2004;343:1171-82 pubmed
    ..Our findings demonstrate that a melting-deficient RNAP mutant can be used to trap a normally unstable intermediate in transcription initiation, thus providing a novel tool for probing activation mechanism. ..
  47. Gross C, Blattner F, Taylor W, Lowe P, Burgess R. Isolation and characterization of transducing phage coding for sigma subunit of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 1979;76:5789-93 pubmed
    ..Phage containing the HindIII fragment complement both primase (dnaG) and sigma (rpoD) whereas those containing the Sac I fragment complement only sigma...
  48. Kontur W, Saecker R, Davis C, Capp M, Record M. Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subseq. Biochemistry. 2006;45:2161-77 pubmed
  49. Kim K, Lee Y. Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res. 2004;32:6057-68 pubmed
    ..Our data indicate that the switching of the utilization of both sigma factors and endoribonucleases in the biogenesis of 6S RNA would play an essential role in modulating its levels in E.coli. ..
  50. McMahan S, Burgess R. Mapping protease susceptibility sites on the Escherichia coli transcription factor sigma70. Biochemistry. 1999;38:12424-31 pubmed
    ..These results suggest that sigma70 undergoes significant conformational changes upon binding to core RNA polymerase and upon open promoter complex formation. ..
  51. Lee C, Cho S, Kim H, Kim M, Peterkofsky A, Seok Y. Potassium mediates Escherichia coli enzyme IIA(Ntr) -dependent regulation of sigma factor selectivity. Mol Microbiol. 2010;78:1468-83 pubmed publisher
    ..Taken together, the data suggest that EIIA(Ntr) controls sigma factor selectivity by regulating the intracellular K(+) level. ..
  52. Hatoum A, Roberts J. Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Mol Microbiol. 2008;68:17-28 pubmed publisher
    ..In addition to promoter-proximal RNAP trapping, we observed transcription-dependent DNA modifications spanning the tnaA and cspA leader regions up to 100 bp downstream of the transcription start site. ..
  53. Panchapakesan S, Unrau P. E. coli 6S RNA release from RNA polymerase requires ?70 ejection by scrunching and is orchestrated by a conserved RNA hairpin. RNA. 2012;18:2251-9 pubmed publisher
    ..Second, the formation of the hairpin accumulates RNA into a region of the polymerase complex previously associated with DNA scrunching, further destabilizing the 6S:pRNA:polymerase complex...
  54. Li Q, Lin H. The recognition and prediction of sigma70 promoters in Escherichia coli K-12. J Theor Biol. 2006;242:135-41 pubmed
    ..coli K-12 with 4639221bp. Results show that the 100% of the 683 experimentally verified sigma(70) promoters have been identified and some possible promoters are predicted. ..
  55. Gill S, Yager T, von Hippel P. Escherichia coli sigma 70 and NusA proteins. II. Physical properties and self-association states. J Mol Biol. 1991;220:325-33 pubmed
    ..coli core RNA polymerase in solution and as a component of the functional transcription complex. ..
  56. Łoziński T, Wierzchowski K. Mg2+-modulated KMnO4 reactivity of thymines in the open transcription complex reflects variation in the negative electrostatic potential along the separated DNA strands. Footprinting of Escherichia coli RNA polymerase complex at the lambdaP(R) promot. FEBS J. 2005;272:2838-53 pubmed
  57. Young B, Anthony L, Gruber T, Arthur T, Heyduk E, Lu C, et al. A coiled-coil from the RNA polymerase beta' subunit allosterically induces selective nontemplate strand binding by sigma(70). Cell. 2001;105:935-44 pubmed
    ..As the beta' 262--309 peptide can function with the previously crystallized portion of sigma(70), nontemplate recognition can be reconstituted with only 47 kDa, or 1/10 of holoenzyme. ..
  58. Yano R, Imai M, Yura T. The use of operon fusions in studies of the heat-shock response: effects of altered sigma 32 on heat-shock promoter function in Escherichia coli. Mol Gen Genet. 1987;207:24-8 pubmed
    ..In some instances, the response was significantly delayed. These results point to the usefulness of the lambda pF13-derivative phages for quantitative and systematic analysis of heat-shock response in E. coli. ..
  59. Lacour S, Leroy O, Kolb A, Landini P. Substitutions in region 2.4 of sigma70 allow recognition of the sigmaS-dependent aidB promoter. J Biol Chem. 2004;279:55255-61 pubmed
  60. Bar Nahum G, Epshtein V, Ruckenstein A, Rafikov R, Mustaev A, Nudler E. A ratchet mechanism of transcription elongation and its control. Cell. 2005;120:183-93 pubmed
    ..This balance is critical for cell viability since it determines the rate, processivity, and fidelity of transcription. ..
  61. Zhilina E, Miropolskaya N, Bass I, Brodolin K, Kulbachinskiy A. Characteristics of ?-dependent pausing by RNA polymerases from Escherichia coli and Thermus aquaticus. Biochemistry (Mosc). 2011;76:1098-106 pubmed publisher
  62. Ishihama A, Fujita N, Glass R. Subunit assembly and metabolic stability of E. coli RNA polymerase. Proteins. 1987;2:42-53 pubmed
    ..coli mutants with a defect in the assembly of RNA polymerase and the stationary-phase cells of a wild-type E. coli. The in vivo degradation of RNA polymerase was indicated to be initiated by alteration of the enzyme structure. ..
  63. Deutscher M, Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. XXIX. Hydrolysis of deoxyribonucleic acid from the 5' terminus by an exonuclease function of deoxyribonucleic acid polymerase. J Biol Chem. 1969;244:3029-37 pubmed
  64. Bonocora R, Caignan G, Woodrell C, Werner M, Hinton D. A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E.coli sigma70 to activate middle gene transcription. Mol Microbiol. 2008;69:331-43 pubmed publisher
    ..Our work supports accumulated evidence indicating that 'sigma appropriation' by MotA and AsiA uses a fundamentally different mechanism to activate transcription...
  65. Grainger D, Hurd D, Harrison M, Holdstock J, Busby S. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci U S A. 2005;102:17693-8 pubmed
  66. Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I, Severinov K, et al. Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element. EMBO J. 2007;26:955-64 pubmed
    ..2 acts as a core RNA polymerase-dependent allosteric switch that modulates non-template DNA strand recognition by sigma region 2 during transcription initiation and elongation. ..
  67. Watt R, Wang J, Leong M, Kung H, Cheah K, Liu D, et al. Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes. Nucleic Acids Res. 2007;35:e37 pubmed
    ..Our results show that E. coli has an organized and dynamic proteome, and demonstrate that this approach is applicable for tagging and (co-) localizing CDSs on a genome-wide scale. ..
  68. Nakamura Y, Osawa T, Yura T. Chromosomal location of a structural gene for the RNA polymerase sigma factor in Escherichia coli. Proc Natl Acad Sci U S A. 1977;74:1831-5 pubmed
    ..typhimurium. These results indicate that a structural gene for sigma (rpoD) is located at the metC-argG region, probably near the dnaG locus (66 min on the current genetic map of E. coli).
  69. Tolstova A, Dubrovin E, Koroleva O. [Investigation of the Dependence of Escherichia coli RNA Polymerase σ70-Subunit Structure on Ionic Strength by Molecular Dynamics Simulation Method]. Biofizika. 2015;60:1045-9 pubmed
    ..We suppose that this leads to the increase in polymerization rate. Simulation data do not confirm any hypothesis about a self-inhibition mechanism. ..
  70. Djordjevic M. Redefining Escherichia coli ?(70) promoter elements: -15 motif as a complement of the -10 motif. J Bacteriol. 2011;193:6305-14 pubmed publisher
  71. Osawa T, Yura T. Effects of reduced amount of RNA polymerase sigma factor on gene expression and growth of Escherichia coli: studies of the rpoD450 (amber) mutation. Mol Gen Genet. 1981;184:166-73 pubmed
    ..The expression of the groE operon, one of the major heat-inducible operons in E. coli is also studied in some detail. ..
  72. Zafar M, Shah I, Wolf R. Protein-protein interactions between sigma(70) region 4 of RNA polymerase and Escherichia coli SoxS, a transcription activator that functions by the prerecruitment mechanism: evidence for "off-DNA" and "on-DNA" interactions. J Mol Biol. 2010;401:13-32 pubmed publisher
    ..Moreover, SoxS is now the first example of an E. coli transcriptional activator that uses a single positive control surface to make specific protein-protein contacts with two different subunits of RNAP. ..
  73. Sirover M, Dube D, Loeb L. On the fidelity of DNA replication. Metal activation of Escherichia coli DNA polymerase I. J Biol Chem. 1979;254:107-11 pubmed
  74. Dombroski A, Walter W, Record M, Siegele D, Gross C. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell. 1992;70:501-12 pubmed
    ..Thus, we propose that sigma 70 is a sequence-specific DNA-binding protein that normally functions through an allosteric interaction with the core subunits of RNA polymerase. ..
  75. Heyneker H, Klenow H. Involvement of Escherichia coli DNA polymerase-I-associated 5' in equilibrium 3' exonuclease in excision-repair of UV-damaged DNA. Basic Life Sci. 1975;5A:219-23 pubmed
    ..coli. Evidence is presented that the polA107 mutation is located on that part of the DNA polymerase I gene coding for the small fragment on which 5' in equilibrium 3' exonucleolytic activity is found. ..
  76. Yuan A, Gregory B, Sharp J, McCleary K, Dove S, Hochschild A. Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor. Mol Microbiol. 2008;70:1136-51 pubmed publisher
    ..Our findings establish that the abilities of Rsd and AlgQ to interact with sigma(70) region 2 are important determinants of their in vitro and in vivo activities...
  77. Nagata Y, Mashimo K, Kawata M, Yamamoto K. The roles of Klenow processing and flap processing activities of DNA polymerase I in chromosome instability in Escherichia coli K12 strains. Genetics. 2002;160:13-23 pubmed
    ..We therefore proposed the model that the Klenow domain can process deletion and minus frameshift mismatch in the nascent DNA and that flap nuclease can process plus frameshift and duplication mismatch in the nascent DNA. ..
  78. Barnard A, Lloyd G, Green J, Busby S, Lee D. Location of the Escherichia coli RNA polymerase alpha subunit C-terminal domain at an FNR-dependent promoter: analysis using an artificial nuclease. FEBS Lett. 2004;558:13-8 pubmed
    ..coli transcription activator that is related to FNR. In complementary experiments, we show that the second alpha subunit C-terminal domain of RNA polymerase can be repositioned by upstream-bound CRP, but not by upstream-bound FNR. ..
  79. Bar Nahum G, Nudler E. Isolation and characterization of sigma(70)-retaining transcription elongation complexes from Escherichia coli. Cell. 2001;106:443-51 pubmed
    ..However, EC-sigma(70) has a substantially higher ability to support multiple rounds of transcription at certain promoters, suggesting its profound role in gene expression and regulation in bacteria. ..
  80. Uyemura D, Bambara R, Lehman I. On the processive mechanism of Escherichia coli DNA polymerase I. J Biol Chem. 1975;250:8577-84 pubmed