Genomes and Genes
Gene Symbol: rpoA
Description: RNA polymerase, alpha subunit
Alias: ECK3282, JW3257, pez, phs, sez
Species: Escherichia coli str. K-12 substr. MG1655
- 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. ..
- Munson L, Reznikoff W. Abortive initiation and long ribonucleic acid synthesis. Biochemistry. 1981;20:2081-5 pubmed..The correlation between the amount of abortive initiation and the half-time of long RNA production is discussed. ..
- Husnain S, Meng W, Busby S, Thomas M. Escherichia coli can tolerate insertions of up to 16 amino acids in the RNA polymerase alpha subunit inter-domain linker. Biochim Biophys Acta. 2004;1678:47-56 pubmed..coli, we utilised a recently described technique for the substitution of the chromosomal rpoA gene, encoding alpha, by mutant rpoA alleles...
- 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. ..
- Cowing D, Mecsas J, Record M, Gross C. Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter. J Mol Biol. 1989;210:521-30 pubmed..Finally, a process of local DNA denaturation (strand opening) leads to formation of the open complex (RPO). ..
- 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. ..
- Savery N, Lloyd G, Busby S, Thomas M, Ebright R, Gourse R. Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters. J Bacteriol. 2002;184:2273-80 pubmed..We also conclude that the relative contributions of individual residues within the 265 determinant depend on promoter sequence, and we discuss explanations for effects of substitutions in the 261 determinant. ..
- Krummel B, Chamberlin M. RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry. 1989;28:7829-42 pubmed..Only after incorporation of 10 nucleotides is there significant movement of the enzyme away from the promoter region and a commitment to 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. ..
- Ross W, Schneider D, Paul B, Mertens A, Gourse R. An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev. 2003;17:1293-307 pubmed..Previous data from the literature suggest that this same sigma-alphaCTD interaction also plays a role in transcription factor-mediated activation. ..
- Thomas M, Glass R. Escherichia coli rpoA mutation which impairs transcription of positively regulated systems. Mol Microbiol. 1991;5:2719-25 pubmed..in decreased expression of several positively regulated operons and has been mapped to within or very near the rpoA gene encoding the alpha subunit of RNA polymerase...
- Chen H, Tang H, Ebright R. Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription. Mol Cell. 2003;11:1621-33 pubmed....
- Mecsas J, Cowing D, Gross C. Development of RNA polymerase-promoter contacts during open complex formation. J Mol Biol. 1991;220:585-97 pubmed....
- Jeon Y, Negishi T, Shirakawa M, Yamazaki T, Fujita N, Ishihama A, et al. Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Science. 1995;270:1495-7 pubmed..Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface...
- Lee D, Wing H, Savery N, Busby S. Analysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C-terminal domain of the RNA polymerase alpha subunit: use of alanine scanning and suppression genetics. Mol Microbiol. 2000;37:1032-40 pubmed....
- Meng W, Savery N, Busby S, Thomas M. The Escherichia coli RNA polymerase alpha subunit linker: length requirements for transcription activation at CRP-dependent promoters. EMBO J. 2000;19:1555-66 pubmed..These observations have important implications for the architecture of transcription initiation complexes at CRP-dependent promoters. ..
- 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. ..
- 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. ..
- Lloyd G, Niu W, Tebbutt J, Ebright R, Busby S. Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters. Genes Dev. 2002;16:2557-65 pubmed....
- Gussin G, Olson C, Igarashi K, Ishihama A. Activation defects caused by mutations in Escherichia coli rpoA are promoter specific. J Bacteriol. 1992;174:5156-60 pubmed..The two alpha (rpoA) mutants, alpha-256 and alpha-235, have deletions of the C-terminal 73 and 94 amino acids, respectively...
- Wegrzyn G, Glass R, Thomas M. Involvement of the Escherichia coli RNA polymerase alpha subunit in transcriptional activation by the bacteriophage lambda CI and CII proteins. Gene. 1992;122:1-7 pubmed..Finally, we also provide genetic evidence for impaired transcription of the cI gene from the CI-activated promoter, pM in the rpoA341 background. ..
- Lee D, Busby S, Lloyd G. Exploitation of a chemical nuclease to investigate the location and orientation of the Escherichia coli RNA polymerase alpha subunit C-terminal domains at simple promoters that are activated by cyclic AMP receptor protein. J Biol Chem. 2003;278:52944-52 pubmed..Here we present data from experiments with simple Escherichia coli promoters that are activated by the cyclic AMP receptor protein. ..
- Grainger D, Belyaeva T, Lee D, Hyde E, Busby S. Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with the C-terminal domain of the RNA polymerase alpha subunit. Mol Microbiol. 2004;51:1311-20 pubmed..Finally, we used alanine scanning to identify determinants in the C-terminal domain of the RNA polymerase alpha subunit that are important for MelR-dependent activation of the melAB promoter. ..
- Benoff B, Yang H, Lawson C, Parkinson G, Liu J, Blatter E, et al. Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science. 2002;297:1562-6 pubmed..These findings are consistent with the proposal that activation involves a simple "recruitment" mechanism. ..
- Fujita N, Endo S, Ishihama A. Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase. Biochemistry. 2000;39:6243-9 pubmed....
- Kainz M, Gourse R. The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination. J Mol Biol. 1998;284:1379-90 pubmed..We conclude that the alphaCTD is a target for interactions with NusA that influence both termination and pausing, but in addition it participates in rho-dependent transcription termination in a NusA-independent manner. ..
- 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. ..
- 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. ..
- Schickor P, Metzger W, Werel W, Lederer H, Heumann H. Topography of intermediates in transcription initiation of E.coli. EMBO J. 1990;9:2215-20 pubmed..Our data suggest that only the DNA downstream of the promoter is involved in this unwinding process. ..
- 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. ..
- 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. ..
- Malan T, Kolb A, Buc H, McClure W. Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter. J Mol Biol. 1984;180:881-909 pubmed..DNA supercoiling enhanced the promoter strength of the lac wild-type and UV5 promoters. The combination of supercoiling and CRP-cAMP was necessary for optimal promoter strength for the lac wild-type promoter. ..
- 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. ..
- Kimura M, Ishihama A. Functional map of the alpha subunit of Escherichia coli RNA polymerase: amino acid substitution within the amino-terminal assembly domain. J Mol Biol. 1995;254:342-9 pubmed..Isolation of two mutants, alpha-K86A and alpha-V173A, both forming alpha 2 beta but not alpha 2 beta beta' complex, confirmed our previous conclusion that two separated regions participate in beta'-binding. ..
- Kovacic R. The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5. J Biol Chem. 1987;262:13654-61 pubmed..The 0 degree C footprints encompass both regions along with the spacer; the combination of these regions rather than an individual region may determine the character of the footprint and the magnitude of the binding constant. ..
- 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. ..
- Fujiki H, Zurek G. The subunits of DNA-dependent RNA polymerase from E. coli: I. Amino acid analysis and primary structure of the N-terminal regions. FEBS Lett. 1975;55:242-4 pubmed
- 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....
- 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. ..
- 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. ..
- 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. ..
- 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
- Kobayashi M, Nagata K, Ishihama A. Promoter selectivity of Escherichia coli RNA polymerase: effect of base substitutions in the promoter -35 region on promoter strength. Nucleic Acids Res. 1990;18:7367-72 pubmed..All these findings were confirmed by abortive initiation assays. ..
- 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. ..
- Zhang G, Darst S. Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain. Science. 1998;281:262-6 pubmed....
- Liu K, Hanna M. NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes. Proc Natl Acad Sci U S A. 1995;92:5012-6 pubmed..coli S100 cell extract. Peptide mapping localized the RNA interactions to the C-terminal domain of alpha. ..
- 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. ..
- Igarashi K, Hanamura A, Makino K, Aiba H, Mizuno T, Nakata A, et al. Functional map of the alpha subunit of Escherichia coli RNA polymerase: two modes of transcription activation by positive factors. Proc Natl Acad Sci U S A. 1991;88:8958-62 pubmed..Two different mechanisms are proposed for the positive control of transcription by activator proteins, one requiring the C-terminal domain of the alpha subunit, and the other not requiring it. ..
- Ozaki M, Fujita N, Wada A, Ishihama A. Promoter selectivity of the stationary-phase forms of Escherichia coli RNA polymerase and conversion in vitro of the S1 form enzyme into a log-phase enzyme-like form. Nucleic Acids Res. 1992;20:257-61 pubmed..These results may suggest that RNA polymerase is interconvertible between different forms with different promoter selectivity by interaction with a phosphorylated compound(s). ..
- 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. ..
- Tolić Nørrelykke S, Engh A, Landick R, Gelles J. Diversity in the rates of transcript elongation by single RNA polymerase molecules. J Biol Chem. 2004;279:3292-9 pubmed..These differences may provide a parsimonious explanation for the complex transcription kinetics observed in bulk solution. ..
- Borukhov S, Lee J. RNA polymerase structure and function at lac operon. C R Biol. 2005;328:576-87 pubmed..With structural information now available for RNAP and models of binary and ternary elongation complexes, the interaction between these factors and RNAP can be modeled, and possible molecular mechanisms of their action can be inferred. ..
- Artsimovitch I, Landick R. Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes Dev. 1998;12:3110-22 pubmed..Resistance of the paused complex to pyrophosphorolysis and its reversal by antisense oligonucleotides further suggest that interaction of the pause hairpin with RNA polymerase disengages the RNA 3' end from the active site. ..
- 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. ..
- 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. ..
- 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. ..
- Chan P, Sullivan J, Lebowitz J. Site-directed chemical modification for probing DNA-protein interactions. Osmium tetroxide modification of the -10 site of the lacUV5 promoter enhances open complex formation. J Biol Chem. 1989;264:21277-85 pubmed..The latter result suggests that open complex formation appears to be enhanced due to promoter unpairing at the -10 (-12) adduct sites. ..
- Darst S, Opalka N, Chacon P, Polyakov A, Richter C, Zhang G, et al. Conformational flexibility of bacterial RNA polymerase. Proc Natl Acad Sci U S A. 2002;99:4296-301 pubmed..This finding reveals, at least partially, the range of conformational flexibility of the RNAP, which is likely to have functional implications for the initiation of transcription, where the DNA template must be loaded into the channel. ..
- 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....
- Nussbaum Shochat A, Amster Choder O. BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 1999;96:4336-41 pubmed..The beta' subunit, produced in excess, prevented BglG activity as a transcriptional antiterminator. Possible roles of the interaction between BglG and the polymerase beta' subunit are discussed...
- Rowland G, Glass R. Conservation of RNA polymerase. Bioessays. 1990;12:343-6 pubmed
- Cabrera J, Jin D. Active transcription of rRNA operons is a driving force for the distribution of RNA polymerase in bacteria: effect of extrachromosomal copies of rrnB on the in vivo localization of RNA polymerase. J Bacteriol. 2006;188:4007-14 pubmed..These results demonstrate that active synthesis from rRNA promoters is a major driving force for the distribution of RNAP in bacteria. The implications of our results for the regulation of rRNA synthesis and cell growth are discussed. ..