Genomes and Genes
Gene Symbol: rpoB
Description: RNA polymerase, beta subunit
Alias: ECK3978, JW3950, ftsR, groN, mbrD?, nitB, rif, ron, sdgB, stl, stv, tabD, tabG
Species: Escherichia coli str. K-12 substr. MG1655
Publications104 found, 100 shown here
- 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. ..
- 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. ..
- 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. ..
- Boothroyd C, Malet R, Nene V, Glass R. Genetic studies on the beta subunit of Escherichia coli RNA polymerase. III. Analysis of low-level rifampicin-resistant mutants. Mol Gen Genet. 1983;190:523-6 pubmed..Continued expression of this unusual phenotype upon introduction of a high-level resistance allele is described in terms of DNA blockade. ..
- 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..In addition, the slower degradation and the ensuing accumulation of beta beta' subunits does not effect the rate of the beta beta' subunit synthesis. ..
- 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. ..
- Kashlev M, Lee J, Zalenskaya K, Nikiforov V, Goldfarb A. Blocking of the initiation-to-elongation transition by a transdominant RNA polymerase mutation. Science. 1990;248:1006-9 pubmed..The mutant polymerase inhibited transcription by blocking the access of the wild-type enzyme to promoters. ..
- Glass R, Honda A, Ishihama A. Genetic studies on the beta subunit of Escherichia coli RNA polymerase. IX. The role of the carboxy-terminus in enzyme assembly. Mol Gen Genet. 1986;203:492-5 pubmed..These studies permit, therefore, the localization of a region on the beta polypeptide involved in sigma binding. ..
- Georgopoulos C. Bacterial mutants in which the gene N function of bacteriophage lambda is blocked have an altered RNA polymerase. Proc Natl Acad Sci U S A. 1971;68:2977-81 pubmedBacterial mutants have been isolated, called groN, that block phage development by interference with the action of the product of the phage N gene...
- 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..and of their structural genes, yielding 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 ..
- 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. ..
- 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. ..
- Buyukuslu N, Trigwell S, Lim P, Fujita N, Ishihama A, Ralphs N, et al. Physical mapping of a collection of Mael-generating amber mutations in the beta gene of Escherichia coli RNA polymerase and the functional effect of internal deletions constructed through their manipulation. Genes Funct. 1997;1:119-29 pubmed..9-60 bp, are distributed almost along the entire length of the rpoB gene, the one exception being the interval 400-499. The lack of amber fragments for mutations within the 5' approx...
- 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
- 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
- Bruckner R, Matzura H. In vivo synthesis of a polycistronic messenger RNA for the ribosomal proteins L11, L1, L10 and L7/12 in Escherichia coli. Mol Gen Genet. 1981;183:277-82 pubmed..Smaller distinct mRNA species could also be detected by this technique. They originate from intercistronic transcription termination and re-initiation as well as from processing of the larger polycistronic mRNA. ..
- 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. ..
- 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. ..
- Crampton N, Bonass W, Kirkham J, Rivetti C, Thomson N. Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res. 2006;34:5416-25 pubmed..Interestingly, the distances between the two RNAP show that they are not always at closest approach after 'collision' has caused their arrest. ..
- Al Mamun A, Humayun M. Spontaneous mutagenesis is elevated in protease-defective cells. Mol Microbiol. 2009;71:629-39 pubmed publisher..In a rifampicin-sensitive to rifampicin-resistance assay that detects base substitution mutations in the essential rpoB gene, there is a modest, but appreciable increase in mutagenesis in Delta(clpP-clpX) cells relative to wild-type ..
- Carpousis A, Gralla J. Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation. J Mol Biol. 1985;183:165-77 pubmed..Subsequently, when a chain of ten bases, or slightly longer, is made, contacts with promoter DNA are irreversibly disrupted, sigma subunit is lost, and a "true" elongation complex is formed. ..
- Rowland G, Lim P, Glass R. In vivo cloning of a carboxy-terminal rpoB allele which confers altered transcriptional properties. Folia Microbiol (Praha). 1995;40:588-94 pubmed..Cloning of the allele was monitored by virtue of the fact that the deletion delta(rpoB)1570-1 resulted in an altered-size restriction fragment...
- Harinarayanan R, Gowrishankar J. Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J Mol Biol. 2003;332:31-46 pubmed..The former category of suppressors included rom(+), and mutations in rpoB(Q513L), pcnB, and polA, whereas the latter included a mutation in rho (R221C) and several non-null mutations (E74K, ..
- Geszvain K, Gruber T, Mooney R, Gross C, Landick R. A hydrophobic patch on the flap-tip helix of E.coli RNA polymerase mediates sigma(70) region 4 function. J Mol Biol. 2004;343:569-87 pubmed..Our studies failed to detect any role for sigma region 1.1 in establishing or maintaining the flap-sigma region 4 interaction, consistent with recent reports placing sigma region 1.1 in the downstream DNA channel. ..
- Tadigotla V, O Maoiléidigh D, Sengupta A, Epshtein V, Ebright R, Nudler E, et al. Thermodynamic and kinetic modeling of transcriptional pausing. Proc Natl Acad Sci U S A. 2006;103:4439-44 pubmed
- Xiao M, Zhu X, Xu H, Tang J, Liu R, Bi C, et al. A novel point mutation in RpoB improves osmotolerance and succinic acid production in Escherichia coli. BMC Biotechnol. 2017;17:10 pubmed publisher..point mutation leading to a single amino acid change (D654Y) within the β-subunit of DNA-dependent RNA polymerase (RpoB) significantly improved the osmotolerance of E. coli...
- Caruso M, Coppo A, Manzi A, Pulitzer J. Host--virus interactions in the control of T4 prereplicative transcription. I. tabC (rho) mutants. J Mol Biol. 1979;135:959-77 pubmed
- Jin D, Gross C. Three rpoBC mutations that suppress the termination defects of rho mutants also affect the functions of nusA mutants. Mol Gen Genet. 1989;216:269-75 pubmed..We find that two of the mutations are located in the 3' half of the rpoB gene encoding the beta subunit. The third mutation is in the rpoC gene, encoding the beta' subunit...
- Kajitani M, Fukuda R, Ishihama A. Autogenous and post-transcriptional regulation of Escherichia coli RNA polymerase synthesis in vitro. Mol Gen Genet. 1980;179:489-96 pubmed
- Xiong X, Reznikoff W. Transcriptional slippage during the transcription initiation process at a mutant lac promoter in vivo. J Mol Biol. 1993;231:569-80 pubmed..These results suggest that RNA polymerase interacts with the +10A promoter in a different manner from that for the majority of sigma 70 promoters. ..
- Nudler E, Goldfarb A, Kashlev M. Discontinuous mechanism of transcription elongation. Science. 1994;265:793-6 pubmed..Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control. ..
- Wang M, Schnitzer M, Yin H, Landick R, Gelles J, Block S. Force and velocity measured for single molecules of RNA polymerase. Science. 1998;282:902-7 pubmed..This contrasts with previous models that assumed force acts directly upon a single-base translocation step. ..
- 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. ..
- Barker M, Gaal T, Gourse R. 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;305:689-702 pubmed..Our data also place considerable constraints on models invoking hypothetical factors that might increase amino acid promoter activity in a ppGpp-dependent fashion. ..
- Furth J, Hurwitz J, Anders M. The role of deoxyribonucleic acid in ribonucleic acid synthesis. I. The purification and properties of ribonucleic acid polymerase. J Biol Chem. 1962;237:2611-9 pubmed
- Kamiya H, Ishiguro C, Harashima H. Increased A:T-->C:G mutations in the mutT strain upon 8-hydroxy-dGTP treatment: direct evidence for MutT involvement in the prevention of mutations by oxidized dGTP. J Biochem. 2004;136:359-62 pubmed..coli cells, and mutations of a chromosomal gene were monitored. 8-OH-dGTP induced mutations of the rpoB gene, the degree of the mutation induction in the mutT strain being approximately 6-fold higher than that in the ..
- 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. ..
- Weerasekera R, She Y, Markham K, Bai Y, Opalka N, Orlicky S, et al. Interactome and interface protocol (2IP): a novel strategy for high sensitivity topology mapping of protein complexes. Proteomics. 2007;7:3835-52 pubmed..This protocol requires low picomole sample quantities, can be applied to multisubunit protein complexes, and does not rely on specialized data mining software. ..
- Siebenlist U. RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter. Nature. 1979;279:651-2 pubmed
- Duval Valentin G, Ehrlich R. Interaction between E. coli RNA polymerase and the tetR promoter from pSC101: homologies and differences with other E. coli promoter systems from close contact point studies. Nucleic Acids Res. 1986;14:1967-83 pubmed
- Hofer B, Ruhe G, Koch A, Koster H. Primary and secondary structure specificity of the cleavage of 'single-stranded' DNA by endonuclease Hinf I. Nucleic Acids Res. 1982;10:2763-73 pubmed..The results suggest that completely base-paired recognition sites are necessary for cleavage. Sequences surrounding the Hinf I pentanucleotides significantly modulate the reaction rates. ..
- Hawley D, McClure W. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983;11:2237-55 pubmed..Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence. ..
- Nene V, Glass R. Genetic studies on the beta subunit of Escherichia coli RNA polymerase. IV. Structure-function correlates. Mol Gen Genet. 1984;194:166-72 pubmed..DNA-dependent RNA polymerase making use of nonsense suppression of amber mutations in the beta structural gene; rpoB. Translational mapping, together with the effect of known amino acid substitutions, has allowed us to locate sites ..
- Severinov K, Mooney R, Darst S, Landick R. Tethering of the large subunits of Escherichia coli RNA polymerase. J Biol Chem. 1997;272:24137-40 pubmedThe rpoB and rpoC genes of eubacteria and archaea, coding, respectively, for the beta and beta'-like subunits of DNA-dependent RNA polymerase, are organized in an operon with rpoB always preceding rpoC...
- Grainger D, Overton T, Reppas N, Wade J, Tamai E, Hobman J, et al. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol. 2004;186:6938-43 pubmed..coli for MelR. This was confirmed by a transcriptomics experiment to analyze RNA in cells either with or without melR. ..
- Errington L, Glass R, Hayward R, Scaife J. Structure and orientation of an RNA polymerase operon in Escherichia coli. Nature. 1974;249:519-22 pubmed
- Rao L, Ross W, Appleman J, Gaal T, Leirmo S, Schlax P, et al. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J Mol Biol. 1994;235:1421-35 pubmed..A functional UP element is not absolutely essential for stimulation of rrnB P1 by the Fis protein. ..
- 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. ..
- 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
- Kirkegaard K, Buc H, Spassky A, Wang J. Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes. Proc Natl Acad Sci U S A. 1983;80:2544-8 pubmed..One striking feature is that the midpoint of this transition for the tac promoter is 3 degrees C lower than the corresponding value for lac UV5, even though the sequence of the unpaired region in the two promoters is identical. ..
- Blatter E, Ross W, Tang H, Gourse R, Ebright R. Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell. 1994;78:889-96 pubmed..Our results suggest a model for the mechanism of involvement of alpha in transcription activation by promoter upstream elements and upstream-binding activator proteins. ..
- Schulz A, Mücke N, Langowski J, Rippe K. Scanning force microscopy of Escherichia coli RNA polymerase.sigma54 holoenzyme complexes with DNA in buffer and in air. J Mol Biol. 1998;283:821-36 pubmed..sigma54-DNA complexes at the promoter as compared to the contour length of the free DNA was 22 nm for the dried samples as opposed to only 6 nm for the undried samples imaged in buffer. This suggests an artefact of the drying process. ..
- 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
- Simpson R. The molecular topography of RNA polymerase-promoter interaction. Cell. 1979;18:277-85 pubmed..The sigma crosslink is close to the "Pribnow Box," which is centered about 10 bases upstream from the RNA start site, contains a striking homology between promoters and is the locus of many promoter mutations. ..
- Komissarova N, Kashlev M. Functional topography of nascent RNA in elongation intermediates of RNA polymerase. Proc Natl Acad Sci U S A. 1998;95:14699-704 pubmed..This result suggests that the transcript-RNAP interaction that is required for holding the EC together can be limited to the RNA region involved in the 8- to 10-nt RNA.DNA hybrid. ..
- Davis C, Capp M, Record M, Saecker R. The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 2005;102:285-90 pubmed..Based on this work, we propose that early wrapping interactions between upstream DNA and the polymerase exterior strongly affect the events that control entry and subsequent unwinding of the DNA start site in the jaws of polymerase. ..
- 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
- Wrande M, Roth J, Hughes D. Accumulation of mutants in "aging" bacterial colonies is due to growth under selection, not stress-induced mutagenesis. Proc Natl Acad Sci U S A. 2008;105:11863-8 pubmed publisher..In one prominent system, mutants resistant to rifampicin (Rif(R); rpoB; RNA polymerase) accumulate in cell populations that "age" on solid medium with little net growth...
- Rowley D, Wolf R. Molecular characterization of the Escherichia coli K-12 zwf gene encoding glucose 6-phosphate dehydrogenase. J Bacteriol. 1991;173:968-77 pubmed..The DNA segment between the -10 hexamer and the start point of transcription resembles the discriminator sequence of stable RNA genes, which has been implicated in stringent control and growth-rate-dependent regulation. ..
- Delcuve G, Downing W, Lewis H, Dennis P. Nucleotide sequence of the proximal portion of the RNA polymerase beta subunit gene of Escherichia coli. Gene. 1980;11:367-73 pubmedThe nucleotide sequence of the 5'-proximal portion of the RNA polymerase beta subunit gene (rpoB) has been determined. From the nucleotide sequence it is possible to predict that NH2-terminal 390 amino acid residues of the protein...
- Nene V, Glass R. Direct measurement of absolute suppressor efficiency. Biosci Rep. 1981;1:571-4 pubmed..The absolute efficiency of four different amber suppressors (Su1, Su2, Su3, and Su7) has been determined at two unique amber sites in the structural gene for the beta subunit of Escherichia coli RNA polymerase. ..
- Shepherd N, Dennis P, Bremer H. Cytoplasmic RNA Polymerase in Escherichia coli. J Bacteriol. 2001;183:2527-34 pubmed..Together, these results suggest that most functional RNA polymerase is associated with the DNA and that little if any segregates into DNA-free minicells. ..
- Xie C, Yao J, Pan R, Wu L, Yu Z. [Mutagenesis of ion beam implantation and identification of two new rifampicin resistance determining sites in rpoB gene in Escherichia coli]. Wei Sheng Wu Xue Bao. 2003;43:732-9 pubmed..5% (77/88) of the total mutation of base substitutions. Two new rif-determining sites had also been identified in rpoB gene in Escherichia coli. The first new site located in 1551...
- Lee J, Kashlev M, Borukhov S, Goldfarb A. A beta subunit mutation disrupting the catalytic function of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 1991;88:6018-22 pubmed..A model is proposed, attributing the multiple effect of the mutation to the malfunctioning of the RNAP active center. ..
- Jin D, Gross C. Characterization of the pleiotropic phenotypes of rifampin-resistant rpoB mutants of Escherichia coli. J Bacteriol. 1989;171:5229-31 pubmedWe used our collection of 17 sequenced rifampin resistance alleles in rpoB to perform a systematic analysis of the phenotypes historically reported with this class of mutants, including growth phenotype, ability to support the growth of ..
- Bokal A, Ross W, Gourse R. The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J Mol Biol. 1995;245:197-207 pubmed
- Davenport R, Wuite G, Landick R, Bustamante C. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science. 2000;287:2497-500 pubmed..The conformational metastability of RNA polymerase revealed by this single-molecule study of transcription has direct implications for the mechanisms of gene regulation in both bacteria and eukaryotes. ..
- Hook Barnard I, Johnson X, Hinton D. Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif. J Bacteriol. 2006;188:8352-9 pubmed..coli RNA polymerase. ..
- 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. ..
- Burgess R, Travers A, Dunn J, Bautz E. Factor stimulating transcription by RNA polymerase. Nature. 1969;221:43-6 pubmed
- Glass R, Nene V, Hunter M. Informational suppression as a tool for the investigation of gene structure and function. Biochem J. 1982;203:1-13 pubmed
- 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. ..
- Wang Y, Severinov K, Loizos N, Fenyo D, Heyduk E, Heyduk T, et al. Determinants for Escherichia coli RNA polymerase assembly within the beta subunit. J Mol Biol. 1997;270:648-62 pubmed..We show that two regions of evolutionarily conserved sequence near the C terminus of beta (conserved regions H and I) are central to the assembly of RNAP and likely make subunit-subunit contacts with both alpha and beta'. ..
- Kuznedelov K, Minakhin L, Niedziela Majka A, Dove S, Rogulja D, Nickels B, et al. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science. 2002;295:855-7 pubmed..Because the flexible flap is evolutionarily conserved, this domain may facilitate promoter recognition by specificity factors in eukaryotes as well. ..
- 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. ..
- 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. ..
- Sosunov V, Zorov S, Sosunova E, Nikolaev A, Zakeyeva I, Bass I, et al. The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase. Nucleic Acids Res. 2005;33:4202-11 pubmed
- 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. ..
- Tedin K, Bremer H. Toxic effects of high levels of ppGpp in Escherichia coli are relieved by rpoB mutations. J Biol Chem. 1992;267:2337-44 pubmed..Phage P1 transduction experiments showed that these mutants have mutations cotransducing with rpoB, the gene encoding the beta-subunit of RNA polymerase...
- Ezekiel D, Hutchins J. Mutations affecting RNA polymerase associated with rifampicin resistance in Escherichia coli. Nature. 1968;220:276-7 pubmed
- Kvint K, Farewell A, Nystrom T. RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s). J Biol Chem. 2000;275:14795-8 pubmed
- 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. ..
- 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. ..
- Uzan M, Danchin A. Correlation between the serine sensitivity and the derepressibility of the ilv genes in Escherichia coli relA- mutants. Mol Gen Genet. 1978;165:21-30 pubmed..Finally circumstancial evidence suggests that the one carbon metabolism may be involved in a process controlling isoleucine metabolism. ..
- Michalke H, Bremer H. RNA synthesis in Escherichia coli after irradiation with ultraviolet light. J Mol Biol. 1969;41:1-23 pubmed
- 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
- 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. ..
- 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. ..
- Harrison C, Turner D, Hinkle D. Laser crosslinking of E. coli RNA polymerase and T7 DNA. Nucleic Acids Res. 1982;10:2399-414 pubmed..coli RNA polymerase to T7 DNA under the conditions studied. The crosslinking yield depends on mercaptoethanol concentration, and is a linear function of laser intensity. The protein subunits crosslinked to DNA are beta, beta' and sigma. ..
- Murphy H, Cashel M. Isolation of RNA polymerase suppressors of a (p)ppGpp deficiency. Methods Enzymol. 2003;371:596-601 pubmed
- Vassylyeva M, Svetlov V, Dearborn A, Klyuyev S, Artsimovitch I, Vassylyev D. The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors. EMBO Rep. 2007;8:1038-43 pubmed..We show that substitutions of these residues and those in the GreB C-terminal domain cavity confer defects in GreB activity and binding to RNAP, and present a plausible model for the RNAP-GreB complex. ..
- 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..Using a terminally labeled DNA fragment covering the intercistronic region between rplL and rpoB as a probe, the structure of both in vivo and in vitro RNA were analyzed by S1 nuclease-mapping assays...