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Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
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2
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Katayama A, Fujita N, Ishihama A. Mapping of subunit-subunit contact surfaces on the beta' subunit of Escherichia coli RNA polymerase. J Biol Chem 2000; 275:3583-92. [PMID: 10652354 DOI: 10.1074/jbc.275.5.3583] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA polymerase core enzyme of Escherichia coli with the catalytic activity of RNA polymerization is assembled sequentially under the order: 2alpha --> alpha(2) --> alpha(2)beta --> alpha(2)betabeta'. The core enzyme gains the activities of promoter recognition and transcription initiation after binding the sigma subunit. The subunit-subunit contact surfaces of beta' subunit (1407 residues) were analyzed by testing complex formation between various beta' fragments and either the alpha(2)beta complex or the sigma(70) subunit. Results indicate that two regions, one central region between residues 515 and 842 and the other COOH-terminal proximal region downstream from residue 1141, are involved in binding the alpha(2)beta complex; and the NH(2)-terminal proximal region between residues 201 and 345 plays a major role in binding the sigma(70) subunit. However, both alpha(2)beta binding sites have weak activity of the sigma(70) subunit; likewise, the sigma(70) subunit-contact surface has weak binding activity of the alpha(2)beta complex. The sites involved in the catalytic function of RNA polymerization are all located within two spacer regions sandwiched between these three subunit-subunit contact surfaces.
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Affiliation(s)
- A Katayama
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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Ozoline ON, Murakami K, Negishi T, Fujita N, Ishihama A. Specific fluorescent labeling of two functional domains in RNA polymerase α subunit. Proteins 1998. [DOI: 10.1002/(sici)1097-0134(19980201)30:2<183::aid-prot8>3.0.co;2-o] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Larkin RM, Guilfoyle TJ. Reconstitution of yeast and Arabidopsis RNA polymerase alpha-like subunit heterodimers. J Biol Chem 1997; 272:12824-30. [PMID: 9139743 DOI: 10.1074/jbc.272.19.12824] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Two subunits of about 36-44 kDa and 13-19 kDa in the eukaryotic nuclear RNA polymerases share limited amino acid sequence similarity to the alpha subunit in Escherichia coli RNA polymerase. The alpha subunit in the prokaryotic enzyme has a stoichiometry of 2, but the stoichiometry of the alpha-like subunits in the eukaryotic enzymes is not entirely clear. To gain insight into the subunit stoichiometry and assembly pathway for eukaryotic RNA polymerases, in vitro reconstitution experiments have been carried out with recombinant alpha-like subunits from yeast and plant RNA polymerase II. The large and small alpha-like subunits from each species formed stable heterodimers in vitro, but neither the large or small alpha-like subunits formed stable homodimers. Furthermore, mixed heterodimers were formed between corresponding subunits of yeast and plants, but were not formed between corresponding subunits in different RNA polymerases from the same species. Our results suggest that RNA polymerase II alpha-like heterodimers may be the equivalent of alpha homodimers found in E. coli RNA polymerase.
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Affiliation(s)
- R M Larkin
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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Riftina F, DeFalco E, Krakow JS. Monoclonal antibodies as probes of the topological arrangement of the alpha subunits of Escherichia coli RNA polymerase. Biochemistry 1989; 28:3299-305. [PMID: 2472834 DOI: 10.1021/bi00434a027] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Three monoclonal anti-alpha antibodies were used to study the properties of the alpha subunit of Escherichia coli RNA polymerase. None of the monoclonal antibodies inhibited the d(A-T)n-directed synthesis of r(A-U)n. Reassembly of the RNA polymerase core was blocked by mAb 129C4 or mAb 126C6 while no effect was observed with mAb 124D1. The conversion of premature to mature core was partially inhibited by mAb 129C4 and almost totally inhibited by mAb 126C6. The data suggest that during the course of core assembly at least one of the alpha subunits undergoes conformational changes. The increase in affinity of mAb 126C6 for assembled alpha compared with free alpha also implies that alpha undergoes conformational changes during RNA polymerase assembly. Double antibody binding studies showed that the epitopes for mAb 124D1 and mAb 129C4 are available on only one of the alpha subunits in RNA polymerase. It would appear that the relevant domain on one of the alpha subunits in RNA polymerase is well exposed whereas this domain on the second alpha subunit is shielded by interaction with regions of the large beta and beta' subunits. The alpha domain in which the epitope for mAb 126C6 resides is not impeded by subunit interactions in the RNA polymerase. The data obtained also suggest that in the holoenzyme the sigma subunit may be positioned close to one of the alpha subunits, probably to the more exposed alpha. The alpha beta complex is the minimal stable subassembly since one of the alpha subunits dissociates from the alpha 2 beta complex following binding of any of the monoclonal antibodies studied.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- F Riftina
- Department of Biological Sciences, Hunter College of the City University of New York, New York 10021
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6
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Abstract
Escherichia coli RNA Polymerase is a multi-subunit enzyme that catalyzes RNA synthesis, using DNA as a template. The sigma subunit of this enzyme plays an important role in the recognition of promoter sites on DNA. Using DNase I footprinting, we have found that in the absence of the other subunits, sigma binds specifically to the bacteriophage lambda PR promoter DNA sequence. In the presence of the sigma subunit alone, a protective footprint encompassing the region between residue positions -41 and +17 was observed (where +1 is the transcription start site). The holoenzyme gave a footprint covering the same region. Thus not only does the sigma subunit interact with the DNA promoter site in the absence of the other components of RNA polymerase, but also the footprint of sigma is indistinguishable from that of the holoenzyme.
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Affiliation(s)
- U Ramesh
- Chemistry Department, University of California, Davis 95616
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7
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Giedroc DP, Coleman JE. Structural and functional differences between the two intrinsic zinc ions of Escherichia coli RNA polymerase. Biochemistry 1986; 25:4969-78. [PMID: 3094579 DOI: 10.1021/bi00365a037] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA-dependent RNA polymerase (RPase) from Escherichia coli contains 2 mol of intrinsic Zn(II)/mol of core enzyme (alpha 2 beta beta'). In techniques analogous to those employed with the Zn(II) metalloenzyme aspartate transcarbamoylase [Hunt, J. B., Neece, S. H., Schachman, H. K., & Ginsberg, A. (1984) J. Biol. Chem. 259, 14793-14803], we show that titration of core or holoRPase with 10 or 16 equiv, respectively, of the sulfhydryl reagent p-(hydroxymercuri)benzenesulfonate (PMPS) results in the facile release of 1 mol of Zn(II) [B-site Zn(II)] in a reaction totally reversible with the addition of excess thiol provided no metal chelator is present. If ethylenediaminetetraacetic acid (EDTA) is present, reversal of the PMPS-enzyme complex results in formation of a Zn1 RPase [A-site Zn(II)]. This enzyme retains full transcriptional activity relative to Zn2 RPase on both calf thymus (nonspecific) and T7 (sigma-dependent, specific) DNA templates. If the core enzyme-PMPS complex is incubated with a large excess of another metal such as Cd(II) followed by thiol treatment, a hybrid ZnACdB RPase is formed. Direct treatment of the enzyme with excess Cd(II) also gives rise to a hybrid ZnACdB RPase. Transcription by these enzymes is also comparable to that of the starting Zn2 enzyme. Isolation of in vivo synthesized Co2 RPase and Cd2 RPase and treatment of either enzyme with PMPS/EDTA results in formation of a CoA and CdA enzyme, respectively. Co(II)A and Cd(II)A enzymes show 123 and 76%, respectively, of the elongation rates on T7 DNA observed for the Zn(II) enzyme. Visible absorption spectroscopy of the Co2 enzyme exhibits four d-d transition bands positioned at 760 (epsilon = 800), 710 (epsilon = 900), 602 (epsilon = 1500), and 484 (epsilon = 4000) nm. In addition, two charge-transfer bands are found at 350 (epsilon = 9600) and 370 (epsilon = 9500) nm. Only the Co(II) ion bound at site A is associated with this unique set of intense d-d transitions. The positions and intensities of both the visible and charge-transfer bands of Co(II)A RPase approximate those shown by Co(II)-substituted metalloenzyme sites where the ligands are four S rather than mixed S,N or S,O sites.
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9
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Kumar SA. The structure and mechanism of action of bacterial DNA-dependent RNA polymerase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1981; 38:165-210. [PMID: 6170089 DOI: 10.1016/0079-6107(81)90013-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Fukuda R, Ishihama A, Saitoh T, Taketo M. Comparative studies of RNA polymerase subunits from various bacteria. MOLECULAR & GENERAL GENETICS : MGG 1977; 154:135-44. [PMID: 408600 DOI: 10.1007/bf00330829] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The molecular structure of RNA polymerases from Escherichia coli, Salmonella typhimurium, Salmonella anatum,serratia marcescens, Aerobacter aerogens, Proteus mirabilis and Bacillus subtilis were compared based on:i) inhibition of the enzyme activity by treatment with antibodies against E. coli RNA polymerase subunits;ii) analysis of antibody precipitates by sodium ododecyl sulfatepolyacrylamide gel electrophoresis; and iii) analysis of antibody precipitates by urea-isoelectrofocusing followed by sodium dodecyl sulfate-slab gel electrophoresis in the second dimension. All the bacterial RNA polymerases examined cross-react equally with anti-E. COLI HOLOPOLYMERASE BUT EXHIbit different extents of cross-reaction with antibodies against individual subunits. Except for B. subtilis RNA polymerase, the molecular weight and isoelectric point of the enzyme subunits are close to those of E. coli polymerase. However, minor difference were found at least within the resolution of the techniques employed:S. anatum polymerase has sigma subunit larger than E. coli sigma subunit; P. mirabilis enzyme has sigma subunit larger in size and more acidic in charge, and alpha subunit smaller and more basic than corresponding E. coli subunits. The electrophoretic map of B. subtilis enzyme subunits is completely different from that of E. coli enzyme.
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11
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Berge RK, Haarr L, Nygaard AP. Conversion of Escherichia coli RNA polymerase to a template independent enzyme. Nucleic Acids Res 1976; 3:1937-45. [PMID: 787928 PMCID: PMC343050 DOI: 10.1093/nar/3.8.1937] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Preparations of RNA polymerase (E.C.2.7.7.6) from uninfected Escherichia coli, T4 infected Escherichia coli, and Acinetobacter calcoaceticus when centrifuged in sucrose gradients in the absence of magnesium ions gave rise to five peaks, all of which were able to form polymers from ribonucleoside 5'-triphosphates in the absence of template or primer. All of the peaks obtained from the Escherichia coli enzyme appeared to contain the subunit alpha and beta and, in addition, polypeptides which appeared to be derived from the subunit beta.
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12
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Saitoh T, Ishihama A. Subunits of RNA polymerase in function and structure. VI. Sequence of the assembly in vitro of Escherichia coli RNA polymerase. J Mol Biol 1976; 104:621-35. [PMID: 781297 DOI: 10.1016/0022-2836(76)90125-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Kawai M, Ishihama A, Yura T. RNA polymerase mutants of Escherichia coli. III. A temperature-sensitive rifampicin-resistant mutant. MOLECULAR & GENERAL GENETICS : MGG 1976; 143:233-41. [PMID: 765757 DOI: 10.1007/bf00269399] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Temperature-sensitive mutants of Escherichia coli that are unable to grow at high temperature can be obtained among those selected for resistance to streptovaricin or rifampicin at low temperature (Yura et al., 1973). One of these mutants (KY5323) that was supposed to carry a single mutation affecting both rifampicin resistance and temperature sensitivity was further investigated. Using purified RNA polymerase preparations obtained from the mutant and the wild type, it was found that the activity for RNA chain elongation is more sensitive to heat treatment than that for RNA chain initiation or DNA binding, and that the mutant enzyme is significantly more labile than the wild-type enzyme with respect to RNA chain elongation, when heat treatment is carried out at high salt concentration. These results, taken together with those of the enzyme reconstitution experiments, strongly suggest that the beta subunit of the polymerase is directly involved in both RNA chain initiation and elongation reactions. Enzyme reconstitution experiments using isolated subunits derived from the mutant and the wild-type polymerases demonstrate that the alteration of beta subunit is primarily responsible for both rifampicin resistance and thermolability of the mutant enzyme. In addition, the results suggested the apparent alteration of both beta and alpha subunits in this mutant. Extensive transduction experiments provided genetic evidence that are consistent with the view that the strain KY5323 carries a second mutation affecting the beta subunit, beside the primary mutation affecting the beta subunit. The hypothetical beta subunit mutation seems to modify quantitatively the rifampicin resistance caused by the beta subunit mutation.
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Rognes A, Abraham KA. Substrate-binding ability of Escherichia coli ribonucleic acid polymerase in relation to its protein composition. Biochem J 1976; 153:55-62. [PMID: 769786 PMCID: PMC1172540 DOI: 10.1042/bj1530055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Interaction between Escherichia coli RNA polymerase and its substrates, the nucleoside triphosphates, was studied by gel-filtration and dialysis-rate-measurement techniques. 2. The holoenzyme bound variable amounts of ATP and GTP. There was no correlation between substrate-binding ability and enzyme activity of different enzyme preparations. 3. The core enzyme bound a maximum of 0.1 mol of ATP/mol of enzyme. The dissociation constant of this interaction was of the order of 1 X 10(-5)M. The core enzyme did not bind GTP. 4. A protein of mol.wt. 60000, which was eluted in the first fraction during phosphocellulose column chromatography of the holoenzyme, bound appreciable amounts of ATP. The dissociation constant of this interaction was of the order of 3 X 10(-5)-5 X 10(-6)M. 5. Evidence presented shows that this protein, and not the sigma factor, is responsible for the observed variation in the ATP-binding ability of the holoenzyme.
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15
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Nakamura Y, Yura T. Evidence for a positive regulation of RNA polymerase synthesis in Escherichia coli. J Mol Biol 1975; 97:621-42. [PMID: 1102717 DOI: 10.1016/s0022-2836(75)80063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Ito K, Iwakura Y, Ishihama A. Biosynthesis of RNA polymerase in Escherichia coli. III. Identification of intermediates in the assembly of RNA polymerase. J Mol Biol 1975; 96:257-71. [PMID: 1100844 DOI: 10.1016/0022-2836(75)90347-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Yarbrough LR, Hurwitz J. The Reversible Denaturation of Deoxyribonucleic Acid-dependent Ribonucleic Acid Polymerase of Escherichia coli. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(20)79740-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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18
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The Isolation of Subunits of Deoxyribonucleic Acid-dependent Ribonucleic Acid Polymerase of Escherichia coli. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(20)79741-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Fukuda R, Ishihama A. Subunits of RNA polymerase in function and structure; Maturation in vitro of core enzyme from Escherichia coli. J Mol Biol 1974; 87:523-40. [PMID: 4613838 DOI: 10.1016/0022-2836(74)90102-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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20
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Yarbrough LR, Wu CW. Role of Sulfhydryl Residues of Escherichia coli Ribonucleic Acid Polymerase in Template Recognition and Specific Initiation. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42485-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Iwakura Y, Ito K, Ishihama A. Biosynthesis of RNA polymerase in Escherichia coli. I. Control of RNA polymerase content at various growth rates. MOLECULAR & GENERAL GENETICS : MGG 1974; 133:1-23. [PMID: 4214991 DOI: 10.1007/bf00268673] [Citation(s) in RCA: 142] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Fukuda R, Iwakura Y, Ishihama A. Heterogeneity of RNA polymerase in Escherichia coli. I. A new holoenzyme containing a new sigma factor. J Mol Biol 1974; 83:353-67. [PMID: 4207198 DOI: 10.1016/0022-2836(74)90284-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Strniste GF, Smith DA. Induction of stable linkage between the deoxyribonucleic acid dependent ribonucleic acid polymerase and d(A-T)n-d(A-T)n by ultraviolet light. Biochemistry 1974; 13:485-93. [PMID: 4589312 DOI: 10.1021/bi00700a014] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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24
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Chamberlin MJ. 10. Bacterial DNA-Dependent RNA Polymerase. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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25
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Ito K, Ishihama A. Subunits of RNA polymerase in function and structure. 3. Accumulation of the intermediate alpha 2beta in the subunit assembly of Escherichia coli RNA polymerase by treatment with cyanate. J Mol Biol 1973; 79:115-25. [PMID: 4583368 DOI: 10.1016/0022-2836(73)90273-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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26
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Naito S, Ishihama A. Transcriptive complex: isolation by cesium sulfate-centrifugation. Biochem Biophys Res Commun 1973; 51:323-30. [PMID: 4571404 DOI: 10.1016/0006-291x(73)91260-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Iwakura Y, Ishihama A, Yura T. RNA polymerase mutants of Escherichia coli. Streptolydigin resistance and its relation to rifampicin resistance. MOLECULAR & GENERAL GENETICS : MGG 1973; 121:181-96. [PMID: 4571524 DOI: 10.1007/bf00277531] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Ishihama A, Ito K. Subunits of RNA polymerase in function and structure. II. Reconstitution of Escherichia coli RNA polymerase from isolated subunits. J Mol Biol 1972; 72:111-23. [PMID: 4567397 DOI: 10.1016/0022-2836(72)90073-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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