The structure and mechanism of action of bacterial DNA-dependent RNA polymerase

Sa, Kumar

doi:10.1016/0079-6107(81)90013-4

Progress in Biophysics and Molecular Biology

1981

DOI: 10.1016/0079-6107(81)90013-4

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The structure and mechanism of action of bacterial DNA-dependent RNA polymerase

Kumar Sa

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1983

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Cited by 44 publications

References 250 publications

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Genetically structured models for lac promoter–operator function in the chromosome and in multicopy plasmids: Lac promoter function

Lee

Bailey

1984

Biotech & Bioengineering

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A mathematical model based on molecular mechanisms for regulation of the lactose (lac) operon in Escherichia coli has been extended and applied to investigate the lac promoter function in the chromosome and in multicopy plasmids. The model simulates the influence of certain host cell mutations and also mutations in the lac promoter sequence in the chromosome in reasonable agreement with previous experimental measurements. The effect of the plasmid copy number and the cloning vector size on the promoter function of a cloned lac regulatory sequence in multicopy plasmids has also been examined. Model results indicate that the efficiency of the cloned lac promoter function is significantly decreased as the number of promoters per cloning vector and size of the vector are increased. The simulation results predict a maximum in the cloned gene transcription rate with respect to the plasmid copy number.

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Genetically structured models for lac promoter–operator function in the chromosome and in multicopy plasmids: Lac promoter function

Lee

Bailey

1984

Biotech & Bioengineering

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Comparative transcription of right- and left-handed poly[d(G-C)] by wheat germ RNA polymerase II.

Durand¹,

Job²,

Zarling³

et al. 1983

The EMBO Journal

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The template properties of left‐handed synthetic polymers, the Z* form of poly[d(G‐C)] and the Z form of poly[d(G‐m5C)], have been investigated using an eucaryotic RNA polymerase, the class II enzyme from wheat germ. Results from a comparative kinetic study of transcription using the polynucleotide substrates in the B and Z conformations are reported. Optimal conditions for enzyme activity compatible with the preservation of the desired template conformation were determined. On the basis of several criteria, both physical (c.d. spectra of the polymers, sedimentability of the Z* form) and biochemical, it was demonstrated that the left‐handed conformations of poly[d(G‐C)] and poly[d(G‐m5C)] serve as templates for wheat germ RNA polymerase II. The level of incorporation was less than that exhibited by the B form of poly[d(G‐C)], the relative activity being a function of the precise experimental conditions. Activity ratios (Z*/B or Z/B) ranged from 0.1 to 0.5. The effect of various incubation parameters, including pH, salt concentration, temperature, and the presence of dinucleoside monophosphate primers were investigated. The Km values for nucleoside triphosphate substrates were slightly smaller for the Z* form of poly[d(G‐C)] than for the B conformation. Titration of DNA (Z* or B) with enzyme and reciprocal experiments suggested that the reduced activity of left‐handed templates might derive from the availability of fewer and/or lower affinity sites for initiation and/or translocation on these templates. Specific antibodies raised against left‐handed DNA strongly inhibited the observed transcription of Z* and Z DNAs by wheat germ RNA polymerase II.

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Identification of a nucleic acid‐binding region within the largest subunit ofDrosophila melanogasterRNA polymerase II

1993

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The largest and the second-largest subunit of the multisubunit eukaryotic RNA polymerases are involved in interaction with the DNA template and the nascent RNA chain. Using Southwestern DNA-binding techniques and nitrocellulose filter binding assays of bacterially expressed fusion proteins, we have identified a region of the largest, 215-kDa, subunit of Drosophila RNA polymerase I1 that has the potential to bind nucleic acids nonspecifically. This nucleic acid-binding region is located between amino acid residues 309-384 and is highly conserved within the largest subunits of eukaryotic and bacterial RNA polymerases. A homology to a region of the DNAbinding cleft of Escherichia coli DNA polymerase I involved in binding of the newly synthesized DNA duplex provides indirect evidence that the nucleic acid-binding region of the largest subunit participates in interaction with double-stranded nucleic acids during transcription. The nonspecific DNA-binding behavior of the region is similar to that observed for the native enzyme in nitrocellulose filter binding assays and that of the separated largest subunit in Southwestern assays. A high content of basic amino acid residues is consistent with the electrostatic nature of nonspecific DNA binding by RNA polymerases.Keywords: fusion proteins; nucleic acid binding; RNA polymerase 11; Southwestern blotting Transcription of DNA into RNA is accomplished by DNA-dependent RNA polymerases. RNA synthesis involves recognition and binding of transcription factors and RNA polymerase to the promoter, initiation of RNA synthesis de novo, elongation of the RNA chain processively by movement of the enzyme along the DNA template, and finally termination and release of the nascent RNA chain. The first step in transcription initiation results in the formation of binary complexes. Two kinds of binary complexes can be observed for RNA polymerases. Nonspecific binary complexes are formed at all sites of the DNA template and are nonproductive. In contrast, specific complexes are formed at promoter sites leading to the initiation of RNA synthesis (Conaway & Conaway, 1991). In eukaryotes the formation of these specific preinitiation complexes involves the interaction of several general transcription initiation factors with promoter elements and the RNA polymerases (Sawadogo & Sentenac, ___.

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The structure and mechanism of action of bacterial DNA-dependent RNA polymerase

Cited by 44 publications

References 250 publications

Genetically structured models for lac promoter–operator function in the chromosome and in multicopy plasmids: Lac promoter function

Genetically structured models for lac promoter–operator function in the chromosome and in multicopy plasmids: Lac promoter function

Comparative transcription of right- and left-handed poly[d(G-C)] by wheat germ RNA polymerase II.

Identification of a nucleic acid‐binding region within the largest subunit ofDrosophila melanogasterRNA polymerase II

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