Gene Symbol: rpoC
Description: RNA polymerase, beta prime subunit
Alias: ECK3979, JW3951, tabB
Species: Escherichia coli str. K-12 substr. MG1655
Products:     rpoC

Top Publications

  1. Polyakov A, Severinova E, Darst S. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell. 1995;83:365-73 pubmed
    ..coli holoenzyme recognizes promoter sites on double-stranded DNA, while both E. coli core and yeast RNAPII are elongating forms of the polymerase and are incapable of promoter recognition. ..
  2. Sidorenkov I, Komissarova N, Kashlev M. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol Cell. 1998;2:55-64 pubmed
    ..Our data show that a hybrid at least 9 nt long, formed between the template DNA and 3'-proximal RNA transcript, is necessary for the high processivity of EC during RNA chain elongation. ..
  3. Darst S, Polyakov A, Richter C, Zhang G. Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography. J Struct Biol. 1998;124:115-22 pubmed
    ..This structure, combined with a new 19-A resolution structure determined by cryo-electron microscopy of helical crystals of E. coli core RNAP embedded in vitreous ice, leads to a model for the organization of the RNAP subunits. ..
  4. Rivetti C, Guthold M, Bustamante C. Wrapping of DNA around the E.coli RNA polymerase open promoter complex. EMBO J. 1999;18:4464-75 pubmed
    ..Based on these data, a model of the sigma(70).RP(o) conformation is proposed. ..
  5. Epshtein V, Nudler E. Cooperation between RNA polymerase molecules in transcription elongation. Science. 2003;300:801-5 pubmed
    ..Such cooperation between RNAP molecules links the rate of elongation to the rate of initiation and explains why elongation is still fast and processive in vivo even without anti-arrest factors. ..
  6. Sneppen K, Dodd I, Shearwin K, Palmer A, Schubert R, Callen B, et al. A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli. J Mol Biol. 2005;346:399-409 pubmed
    ..The model provides a framework for using transcriptional interference to investigate various dynamic processes on DNA in vivo. ..
  7. 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. ..
  8. Komissarova N, Kashlev M. RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA. J Biol Chem. 1997;272:15329-38 pubmed
    ..These oscillations of RNA polymerase can explain its apparent discontinuous advancement, which had been interpreted as indicating flexibility within the enzyme. ..
  9. Epshtein V, Toulmé F, Rahmouni A, Borukhov S, Nudler E. Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J. 2003;22:4719-27 pubmed
    ..These results support a cooperation model of transcription whereby RNAP molecules behave as 'partners' helping one another to traverse intrinsic and extrinsic obstacles. ..

More Information

Publications104 found, 100 shown here

  1. Herring C, Raghunathan A, Honisch C, Patel T, Applebee M, Joyce A, et al. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet. 2006;38:1406-12 pubmed
    ..The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts. ..
  2. 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
  3. Borukhov S, Polyakov A, Nikiforov V, Goldfarb A. GreA protein: a transcription elongation factor from Escherichia coli. Proc Natl Acad Sci U S A. 1992;89:8899-902 pubmed
    ..Similar biochemical activities have been reported in eukaryotic RNA polymerases, indicating that transcript cleavage and restart of elongation may be a general transcriptional mechanism. ..
  4. Leirmo S, Gourse R. Factor-independent activation of Escherichia coli rRNA transcription. I. Kinetic analysis of the roles of the upstream activator region and supercoiling on transcription of the rrnB P1 promoter in vitro. J Mol Biol. 1991;220:555-68 pubmed
    ..In the accompanying paper, a variety of chemical and enzymatic probes are used to characterize RPinit and RPo both with and without the UAR. ..
  5. Mahadevan S, Wright A. A bacterial gene involved in transcription antitermination: regulation at a rho-independent terminator in the bgl operon of E. coli. Cell. 1987;50:485-94 pubmed
    ..We propose that the bglC gene product mediates positive regulation of the bgl operon by functioning as an antiterminator at the rho-independent terminator located within the leader. ..
  6. 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. ..
  7. McKee R, Glass R. Deletion mapping of Escherichia coli RNA polymerase genes. Biochem Soc Trans. 1980;8:731-2 pubmed
  8. Brodolin K, Studitsky V, Mirzabekov A. Conformational changes in E. coli RNA polymerase during promoter recognition. Nucleic Acids Res. 1993;21:5748-53 pubmed
    ..In presence of lac repressor before or after formation of the RPO cross-linking pattern is similar with that of RPI (RPC) complex. ..
  9. Murakami K, Kimura M, Owens J, Meares C, Ishihama A. The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Proc Natl Acad Sci U S A. 1997;94:1709-14 pubmed
    ..The results clearly indicated that the two alpha subunits bind in tandem to two helix turns of the rrnBP1 UP element, and that the beta'-associated alpha subunit is bound to the promoter-distal region. ..
  10. Markov D, Christie G, Sauer B, Calendar R, Park T, Young R, et al. P2 growth restriction on an rpoC mutant is suppressed by alleles of the Rz1 homolog lysC. J Bacteriol. 2004;186:4628-37 pubmed
  11. Maurer S, Fritz J, Muskhelishvili G, Travers A. RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex. EMBO J. 2006;25:3784-90 pubmed
    ..We suggest that the architecture of the ternary complex provides a general paradigm for the facilitation of direct, but weak, interactions between polymerase and an activator. ..
  12. Swapna G, Chakraborty A, Kumari V, Sen R, Nagaraja V. Mutations in ?' subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance. Mol Microbiol. 2011;80:1169-85 pubmed publisher
  13. Steward K, Linn T. Transcription frequency modulates the efficiency of an attenuator preceding the rpoBC RNA polymerase genes of Escherichia coli: possible autogenous control. Nucleic Acids Res. 1992;20:4773-9 pubmed
    ..The implications for autogenous control of RNA polymerase synthesis are discussed. ..
  14. Buckle M, Geiselmann J, Kolb A, Buc H. Protein-DNA cross-linking at the lac promoter. Nucleic Acids Res. 1991;19:833-40 pubmed
    ..These conclusions were derived from experiments performed using a generally applicable, non-interfering technique that reveals direct contacts between proteins and nucleic acids in nucleoprotein complexes. ..
  15. Fredrick K, Helmann J. RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates. Proc Natl Acad Sci U S A. 1997;94:4982-7 pubmed
    ..Thus, sigmaA appears to recognize the -10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, sigma also localizes the transcription start site. ..
  16. Sen R, King R, Mzhavia N, Madsen P, Weisberg R. Sequence-specific interaction of nascent antiterminator RNA with the zinc-finger motif of Escherichia coli RNA polymerase. Mol Microbiol. 2002;46:215-22 pubmed
  17. Kulbachinskiy A, Feklistov A, Krasheninnikov I, Goldfarb A, Nikiforov V. Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. Eur J Biochem. 2004;271:4921-31 pubmed
    ..We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme. ..
  18. Szalewska Palasz A, Johansson L, Bernardo L, Skarfstad E, Stec E, Brannstrom K, et al. Properties of RNA polymerase bypass mutants: implications for the role of ppGpp and its co-factor DksA in controlling transcription dependent on sigma54. J Biol Chem. 2007;282:18046-56 pubmed
  19. Ross W, Ernst A, Gourse R. Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove. Genes Dev. 2001;15:491-506 pubmed
    ..These studies greatly improve the resolution of our picture of the promoter-RNAP interaction. ..
  20. Sukhodolets M, Garges S. Interaction of Escherichia coli RNA polymerase with the ribosomal protein S1 and the Sm-like ATPase Hfq. Biochemistry. 2003;42:8022-34 pubmed publisher
    ..The limited sequence homology between Hfq and known ATP-utilizing enzymes suggests a new class of ATPases...
  21. Cabrera J, Jin D. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues. Mol Microbiol. 2003;50:1493-505 pubmed
    ..coli under different physiological conditions, we constructed a functional rpoC-gfp gene fusion on the chromosome...
  22. Dennis P, Nene V, Glass R. Autogenous posttranscriptional regulation of RNA polymerase beta and beta' subunit synthesis in Escherichia coli. J Bacteriol. 1985;161:803-6 pubmed
    ..P. Dennis, Proc. Natl. Acad. Sci. U.S.A. 74:5416-5420, 1977). ..
  23. Ma J, Newman A, Hayward R. Internal promoters of the rpoBC operon of Escherichia coli. Mol Gen Genet. 1981;184:548-50 pubmed
    Four ribosomal protein genes, rplA, rplJ, rplK and rplL form an operon in E. coli together with the genes rpoB and rpoC which encode the beta and beta' subunits of RNA polymerase...
  24. Suh W, Ross W, Record M. Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site. Science. 1993;259:358-61 pubmed
    ..These results provide a structural basis for the requirement for uptake of Mg2+ in the formation of RPo2 from RPo1, as deduced from kinetic studies at this promoter. ..
  25. Sakata Sogawa K, Shimamoto N. RNA polymerase can track a DNA groove during promoter search. Proc Natl Acad Sci U S A. 2004;101:14731-5 pubmed
    ..These results confirm our previous observations of longitudinal movement of RNA polymerase along fixed, extended DNA and, moreover, imply that groove tracking facilitates scanning of DNA sequences. ..
  26. Wigneshweraraj S, Burrows P, Severinov K, Buck M. Stable DNA opening within open promoter complexes is mediated by the RNA polymerase beta'-jaw domain. J Biol Chem. 2005;280:36176-84 pubmed
    ..Clearly, regulated communication between the mobile modules of the RNAP and the functional domain(s) of the sigma subunit is required for stable DNA opening. ..
  27. 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
  28. Kolb K, Hein P, Landick R. Antisense oligonucleotide-stimulated transcriptional pausing reveals RNA exit channel specificity of RNA polymerase and mechanistic contributions of NusA and RfaH. J Biol Chem. 2014;289:1151-63 pubmed publisher
    ..Effects of RfaH, which suppresses oligo-stabilization of pausing, were competitive with antisense oligonucleotide concentration, suggesting that RfaH and exit channel duplexes compete via opposing effects on RNAP clamp conformation...
  29. Newlands J, Ross W, Gosink K, Gourse R. Factor-independent activation of Escherichia coli rRNA transcription. II. characterization of complexes of rrnB P1 promoters containing or lacking the upstream activator region with Escherichia coli RNA polymerase. J Mol Biol. 1991;220:569-83 pubmed
  30. Ovchinnikov Y, Monastyrskaya G, Gubanov V, Guryev S, Chertov OYu -, Modyanov N, et al. The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit. Eur J Biochem. 1981;116:621-9 pubmed
    ..a continuous nucleotide sequence (4714 base pairs) that embraces the entire rpoB gene, the initial part of the rpoC gene and the intercistronic region, together with the total amino acid sequence of the beta subunit, comprising ..
  31. An G, Friesen J. Characterization of promoter-cloning plasmids: analysis of operon structure in the rif region of Escherichia coli and isolation of an enhanced internal promoter mutant. J Bacteriol. 1980;144:904-16 pubmed
    ..and rpoB, the gene for ribonucleic acid polymerase subunit beta; (iv) transcription terminated immediately after rpoC, the gene for ribonucleic acid polymerase subunit beta'; (v) a gene coding for unknown protein U, which is located ..
  32. Chan C, Landick R. Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin. J Mol Biol. 1993;233:25-42 pubmed
    ..We suggest that electrostatic interaction between the pause hairpin and RNA polymerase, rather than disruption of an RNA:DNA heteroduplex, delays elongation at the his leader pause site. ..
  33. Garland C, Tarien E, Nirmala R, Clark P, Rifkind J, Eichhorn G. Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymerase. Biochemistry. 1999;38:3421-5 pubmed
    ..These studies show curvature to be a significant feature in the interaction between DNA template and RNA elongate even at the very beginning of transcription. ..
  34. Gregory B, Deighan P, Hochschild A. An artificial activator that contacts a normally occluded surface of the RNA polymerase holoenzyme. J Mol Biol. 2005;353:497-506 pubmed
    ..Our results thus demonstrate that changes in the accessibility of a normally occluded surface of the RNAP holoenzyme can modulate the activity of a gene-specific regulator of transcription. ..
  35. Davis C, Bingman C, Landick R, Record M, Saecker R. 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;104:7833-8 pubmed
  36. Kalyaeva E, Sever I, Nikiforov V, Danilevskaya O. A mutation suppressing the overproduction of RNA polymerase beta beta' subunits in the RpoC1 strain of Escherichia coli. Mol Gen Genet. 1980;178:669-74 pubmed
  37. Greenblatt J, Li J, Condon C, Squires C. Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components. Proc Natl Acad Sci U S A. 1993;90:970-4 pubmed
    ..The DNA template requirements were the same as those previously established in vivo; transcription of a wild-type boxA sequence is both necessary and sufficient to promote RNA polymerase modification into a terminator-resistant form. ..
  38. Nudler E, Gusarov I, Avetissova E, Kozlov M, Goldfarb A. Spatial organization of transcription elongation complex in Escherichia coli. Science. 1998;281:424-8 pubmed
    ..The results explain how RNA in the integrated unit RBS-HBS-DBS may stabilize the ternary complex, whereas a hairpin in RNA result in its dissociation. ..
  39. Zaychikov E, Denissova L, Guckenberger R, Heumann H. Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA. Nucleic Acids Res. 1999;27:3645-52 pubmed
    ..We suggest that the periodicity of the bending angle reflects periodic changes of the conformation of the halted complexes that might have relevance for the translocation mechanism. ..
  40. Azam T, Hiraga S, Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells. 2000;5:613-26 pubmed
    ..coli could be classified into two groups. One group proteins was distributed uniformly within the nucleoid, but the other group of proteins showed an irregular distribution, forming immuno-stained spots or clumps. ..
  41. Adelman K, La Porta A, Santangelo T, Lis J, Roberts J, Wang M. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc Natl Acad Sci U S A. 2002;99:13538-43 pubmed
    ..This elongation behavior is compared with that of a mutant RNA polymerase that pauses more frequently and elongates more slowly than wild type. ..
  42. Hsu L, Cobb I, Ozmore J, Khoo M, Nahm G, Xia L, et al. Initial transcribed sequence mutations specifically affect promoter escape properties. Biochemistry. 2006;45:8841-54 pubmed
    ..How the ITS might influence the course of early transcription is discussed within the structural context of an initial transcribing complex. ..
  43. Severinova E, Severinov K. Localization of the Escherichia coli RNA polymerase beta' subunit residue phosphorylated by bacteriophage T7 kinase Gp0.7. J Bacteriol. 2006;188:3470-6 pubmed publisher
  44. Houman F, Diaz Torres M, Wright A. Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein. Cell. 1990;62:1153-63 pubmed
    ..We propose that BglG prevents transcription termination by binding to nascent RNA and blocking formation of the terminator structure. ..
  45. Boni I, Borodin A. [Rare initiation codons are regulators of expression of the rpoC gene]. Bioorg Khim. 1990;16:1134-7 pubmed
    Translation of the rpoC genes in Escherichia coli and Salmonella typhimurium is known to start from the GUG codon. Now, using toeprint analysis we have shown UUG to be the initiation codon of the Pseudomonas putida rpoC gene...
  46. Fukuda R, Nagasawa Fujimori H. Mechanism of the rifampicin induction of RNA polymerase beta and beta' subunit synthesis in Escherichia coli. J Biol Chem. 1983;258:2720-8 pubmed
    ..However, no clear indication has been obtained of possible enhancement of the transcription initiation by rifampicin from the putative promoter. ..
  47. Nene V, Glass R. Properties of a collection of Escherichia coli RNA polymerase mutants. Biochem Soc Trans. 1980;8:732-3 pubmed
  48. Zaychikov E, Martin E, Denissova L, Kozlov M, Markovtsov V, Kashlev M, et al. Mapping of catalytic residues in the RNA polymerase active center. Science. 1996;273:107-9 pubmed
    ..The mutant RNAP is catalytically inactive but can bind promoters and form an open complex. The mutant fails to support Fe2+-induced cleavage of DNA or protein. Thus, the NAD-FDGD motif is involved in chelation of the active center Mg2+. ..
  49. 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. ..
  50. Mulligan M, Brosius J, McClure W. Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J Biol Chem. 1985;260:3529-38 pubmed
    ..The choice of start point for transcription is affected by spacer length. Transcription from all the promoters was stimulated at moderate concentrations of salt (less than 150 mM) and persisted at high salt concentrations (300 mM). ..
  51. Arthur T, Burgess R. Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta' subunit. J Biol Chem. 1998;273:31381-7 pubmed
    ..We were able to more precisely map the interaction domain to amino acid residues 260-309 of beta' using nickel nitrilotriacetic acid co-immobilization assays. ..
  52. Lew C, Gralla J. Nucleotide-dependent isomerization of Escherichia coli RNA polymerase. Biochemistry. 2004;43:12660-6 pubmed
    ..It is proposed that complete polymerase isomerization can require nucleotide binding, which can assist formation of the active site that engages the transcription start site. ..
  53. Abbondanzieri E, Greenleaf W, Shaevitz J, Landick R, Block S. Direct observation of base-pair stepping by RNA polymerase. Nature. 2005;438:460-5 pubmed
    ..Global fits were inconsistent with a model for movement incorporating a power stroke tightly coupled to pyrophosphate release, but consistent with a brownian ratchet model incorporating a secondary NTP binding site. ..
  54. Bratton B, Mooney R, Weisshaar J. Spatial distribution and diffusive motion of RNA polymerase in live Escherichia coli. J Bacteriol. 2011;193:5138-46 pubmed publisher
    ..There is significant cell-to-cell heterogeneity in both DRNAP and fmobile. ..
  55. Cheng S, Lynch E, Leason K, Court D, Shapiro B, Friedman D. Functional importance of sequence in the stem-loop of a transcription terminator. Science. 1991;254:1205-7 pubmed
    ..These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure. ..
  56. Michalke H, Bremer H. RNA synthesis in Escherichia coli after irradiation with ultraviolet light. J Mol Biol. 1969;41:1-23 pubmed
  57. Buckle M, Pemberton I, Jacquet M, Buc H. The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase. J Mol Biol. 1999;285:955-64 pubmed
    ..Sigma thus appears as the principal partner acting during promoter recognition, a strongly coupled process involving two major intermediates only. ..
  58. Bremer H, Dennis P, Ehrenberg M. Free RNA polymerase and modeling global transcription in Escherichia coli. Biochimie. 2003;85:597-609 pubmed
    ..0 and 2.5 doublings/h, respectively. The model accurately reflects a number of further experimental observations and suggests that the free RNA polymerase concentration increases with increasing growth rate. ..
  59. Siebenlist U. RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter. Nature. 1979;279:651-2 pubmed
  60. Rowland G, Glass R. Conservation of RNA polymerase. Bioessays. 1990;12:343-6 pubmed
  61. Mosteller R, Yanofsky C. Transcription of the tryptophan operon in Escherichia coli: rifampicin as an inhibitor of initiation. J Mol Biol. 1970;48:525-31 pubmed
  62. Hansen U, McClure W. Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. J Biol Chem. 1980;255:9564-70 pubmed
    ..Models to explain the cause of sigma release are discussed. ..
  63. Jin D, Cabrera J. Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coli. J Struct Biol. 2006;156:284-91 pubmed
    ..Thus, the distribution of RNAP, global gene regulation and the dynamic structure of the nucleoid are coupled in the bacterial cell. ..
  64. Linn T, Goman M, Scaife J. Lambda transducing bacteriophage carrying deletions of the argCBH-rpoBC region of the Escherichia coli chromosome. J Bacteriol. 1979;140:479-89 pubmed
    ..We thus extend and confirm knowledge of the organization of this part of the chromosome. The new phages are useful tools for studying the genes for the bacterial transcription and translation machinery. ..
  65. Bass I, Gorlenko Z, Danilevskaya O, Dmitriev A, Kalyaeva E, Mindlin S, et al. Variations in the rate of synthesis of beta and beta' RNA polymerase polypeptides under the influence of certain factors. Mol Gen Genet. 1977;154:101-10 pubmed
  66. 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. ..
  67. Ray P, Hall R, Finn R, Chen S, Patwardhan A, Buck M, et al. Conformational changes of Escherichia coli sigma54-RNA-polymerase upon closed-promoter complex formation. J Mol Biol. 2005;354:201-5 pubmed
    ..The binding of DNA leads to significant conformational changes in the enzyme's catalytic subunits, apparently a necessity for the initiation of enhancer-dependent promoter-specific transcription. ..
  68. Ederth J, Mooney R, Isaksson L, Landick R. Functional interplay between the jaw domain of bacterial RNA polymerase and allele-specific residues in the product RNA-binding pocket. J Mol Biol. 2006;356:1163-79 pubmed
    ..We suggest that the counteracting effects on pausing of the alterations in the jaw and the product RNA binding site may be mediated either by effects on translocation or via allosteric communication to the RNAP active site. ..
  69. d Aubenton Carafa Y, Brody E, Thermes C. Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J Mol Biol. 1990;216:835-58 pubmed
    ..It also predicts with reasonable accuracy the in vitro termination efficiency of known rho-independent terminators, as well as predicting the existence of 35 as yet uncharacterized terminators. ..
  70. Burgess R, Travers A, Dunn J, Bautz E. Factor stimulating transcription by RNA polymerase. Nature. 1969;221:43-6 pubmed
  71. 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. ..
  72. 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. ..
  73. Szoke P, Allen T, deHaseth P. Promoter recognition by Escherichia coli RNA polymerase: effects of base substitutions in the -10 and -35 regions. Biochemistry. 1987;26:6188-94 pubmed
    ..4) The extent to which a particular base change affects the kinetic parameters depends on the sequence of the promoter into which it is introduced. ..
  74. Harley C, Reynolds R. Analysis of E. coli promoter sequences. Nucleic Acids Res. 1987;15:2343-61 pubmed
    ..This compilation and analysis should be useful for studies of promoter structure and function and for programs which identify potential promoter sequences. ..
  75. Milan S, D Ari L, Chamberlin M. Structural analysis of ternary complexes of Escherichia coli RNA polymerase: ribonuclease footprinting of the nascent RNA in complexes. Biochemistry. 1999;38:218-25 pubmed
    ..Our results rule out the existence of a stable RNA-DNA hybrid in these ternary complexes of greater than 3 base pairs in length. ..
  76. Heyduk E, Baichoo N, Heyduk T. Interaction of the alpha-subunit of Escherichia coli RNA polymerase with DNA: rigid body nature of the protein-DNA contact. J Biol Chem. 2001;276:44598-603 pubmed
  77. Kul bachinskiĭ A, Ershova G, Korzheva N, Brodolin K, Nikiforov V. [Mutations in beta'-subunit of the Escherichia coli RNA-polymerase influence interaction with downstream duplex DNA in the elongation complex]. Genetika. 2002;38:1422-7 pubmed
    ..The mutations reduced stability of both promoter and elongation complexes, probably because they altered the contacts between RNAP and the downstream duplex DNA. ..
  78. Shaevitz J, Abbondanzieri E, Landick R, Block S. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature. 2003;426:684-7 pubmed
    ..Inosine triphosphate increased the frequency of backtracking pauses, whereas the accessory proteins GreA and GreB, which stimulate the cleavage of nascent RNA, decreased the duration of such pauses. ..
  79. Mosrin Huaman C, Turnbough C, Rahmouni A. Translocation of Escherichia coli RNA polymerase against a protein roadblock in vivo highlights a passive sliding mechanism for transcript elongation. Mol Microbiol. 2004;51:1471-81 pubmed
    ..They also suggest that fluctuations in the intracellular NTP pools may play a key role in gene regulation at the transcript elongation level. ..
  80. Kruse T, Blagoev B, Løbner Olesen A, Wachi M, Sasaki K, Iwai N, et al. Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli. Genes Dev. 2006;20:113-24 pubmed
    ..Thus, our results raise the possibility that the MreB-RNAP interaction is functionally important for chromosome segregation. ..
  81. Wang D, Meier T, Chan C, Feng G, Lee D, Landick R. Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell. 1995;81:341-50 pubmed
    ..We suggest pausing and termination could be alternative outcomes of a similar isomerization that depend on the strength of contacts to 3'-proximal RNA remaining after the jump. ..
  82. Nechaev S, Severinov K. Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein. J Mol Biol. 1999;289:815-26 pubmed
    ..gp55-dependent phage T4 late promoter transcription is also resistant to gp2. From these results, we conclude that the interaction of the sigma70region 4 with the -35 consensus promoter element is the primary target of gp2 inhibition. ..
  83. Krummel B, Chamberlin M. Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical properties. J Mol Biol. 1992;225:221-37 pubmed
    ..The results raise important questions as to the actual mechanism of transcription elongation, and suggest that it is a much more complex process than previously assumed. ..
  84. Kasas S, Thomson N, Smith B, Hansma H, Zhu X, Guthold M, et al. Escherichia coli RNA polymerase activity observed using atomic force microscopy. Biochemistry. 1997;36:461-8 pubmed
  85. Luo J, Sharif K, Jin R, Fujita N, Ishihama A, Krakow J. Molecular anatomy of the beta' subunit of the E. coli RNA polymerase: identification of regions involved in polymerase assembly. Genes Cells. 1996;1:819-27 pubmed
    ..The region between amino acids 201 and 477 on beta' may be directly or indirectly involved in the interaction between the beta' subunit and the sigma subunit. ..
  86. Gülland U, Hillen W. The Tn10-encoded tetR mRNA has heterogeneous 5' ends in vivo and in vitro. Gene. 1992;114:97-101 pubmed
    ..In vivo transcription leads to longer reiteration products than in vitro transcription. ..
  87. 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
    ..These results suggest that this region of sigma 70 is directly involved in recognition of the -35 hexamer. ..
  88. Sever I, Kalyaeva E, Danilevskaya O, Gorlenko Z. Decreased degradation of beta beta' RNA polymerase subunits and abnormal proteins in a mutant E. coli. Mol Gen Genet. 1982;188:494-8 pubmed
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