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Cardarelli M, Pomponi M, Risuleo G, Di Mauro E. Agrobacterium tumefaciens RNA polymerase: a new purification procedure and a study of the stable binding sites on homologous deoxyribonucleic acid. Biochemistry 1981; 20:6097-102. [PMID: 7306497 DOI: 10.1021/bi00524a028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA polymerase (RNA nucleotidyltransferase, EC 2.7.7.6) of Agrobacterium tumefaciens has been purified according to a fast and efficient procedure. The method involves only two chromatographic steps and yields a highly active enzyme. The RNA polymerase was studied with respect to the ability to bind its homologous genome. A. tumefaciens deoxyribonucleic acid (DNA) binds the enzyme even when fragmented at undergenic size (300 base pairs). The general binding is unspecific and very labile at low concentrations of heparin (0.66 micrograms/mL). The number and distribution of the stable binding sites, class A sites [Hinkle, D., & Chamberlin, M. J. (1972) J. Mol. Biol. 70, 157-185], have been calculated from the heparin-induced dissociation kinetics of binary complexes formed between the enzyme and DNA fragments of various sizes. A total of 3.5 x 10(3) class A sites (forming binary complexes with a half-life of 16.6 min) are present on A. tumefaciens genome, a large number of which show a distribution of 800-1000 base pairs. The rest have a more widely spaced distribution. The interactions between Escherichia coli RNA polymerase and the A. tumefaciens template have also been examined, and it has been observed that E. coli holoenzyme forms stable complexes with a shorter half-life and recognizes a lower number of class A sites on A. tumefaciens genome.
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Cooke R, Durand R, Teissere M, Penon P, Ricard J. Characterisation of heparin-resistant complex formation and RNA synthesis by wheat germ RNA polymerases I, II and III, in vitro on cauliflower mosaic virus DNA. Biochem Biophys Res Commun 1981; 98:36-42. [PMID: 6163430 DOI: 10.1016/0006-291x(81)91866-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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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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Di Mauro E, Ballario P, Pedone F. Escherichia coli ribonucleic acid polymerase binding to the deoxyribonucleic acid of the echinoid Paracentrotus lividus: properties of the complexes and distribution of stable binding sites. Biochemistry 1980; 19:1392-6. [PMID: 6992863 DOI: 10.1021/bi00548a020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe the properties of the complexes that form between Escherichia coli RNA polymerase and Paracentrotus lividus DNA: dissociation kinetics, temperature dependence of the complex formation, resistance to heparin, and range of RNA polymerase-DNA weight/weight ratios that give rise to the stable binding events. The amount and distribution of the sites that form stable binding [class A sites as defined by Hinkle & Chamberlin [Hinkle, D., & Chamberlin, M. J. (1972) J. Mol. Biol. 70, 157]] with E. coli RNA polymerase were determined by the analysis of the dissociation of complexes formed by the enzyme on DNA fragments of various length. The P. lividus appears to form 3.1 X 10(5) stable (t1/2 greater than or equal to 15 min) complexes per haploid genome; the great majority of these complexes shows a short-range distribution (1000-2000 base pairs). The observed attributes of the stable binding sites of P. lividus DNA for E. coli RNA polymerase (amount, distribution, and quantitative ability to start in vitro RNA chains) point to the conclusion that E. coli and sea urchin DNA are nearly indistinguishable by the criteria adopted. The behavior of the sea urchin stable binding sites for the E. coli enzyme is not consistent with the expected behavior of the in vivo promoters.
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Dynan WS, Burgess RR. In vitro transcription by wheat germ ribonucleic acid polymerase II: effects of heparin and role of template integrity. Biochemistry 1979; 18:4581-8. [PMID: 387073 DOI: 10.1021/bi00588a019] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Double-stranded deoxyribonucleic acid (DNA) from bacteriophage lambda is a good template for wheat germ DNA-dependent ribonucleic acid (RNA) polymerase II. We delineated conditions for obtaining maximum polymerase activity using as template both the relatively intact DNA extracted from the the lambda phage and DNA into which single-strand nicks have been introduced by deoxyribonuclease (DNase) I digestion. The deliberate introduction of nicks produces a modest increase in transcription. The NaCl and MgCl2 optima are broader with the nicked template, so that higher concentrations of these salts are needed before polymerase activity begins to decline. Heparin inhibits initiation but not elongation by wheat germ polymerase. Polymerase can be protected against heparin inhibition by forming binary complexes with the template. The formation of these complexes is reduced at low temperature. The complexes, once formed, decay in the presence of heparin with a half-life of 10--20 min. The number of complexes is highly dependent on the degree of nicking of the template, suggesting that single-strand nicks are the predominant type of site where these heparin-resistant complexes are formed. Our data do not allow us to decide whether or not the presence of nicks plays as decisive a role in the absence of heparin.
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Davison B, Leighton T, Rabinowitz J. Purification of Bacillus subtilis RNA polymerase with heparin-agarose. In vitro transcription of phi 29 DNA. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86833-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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DiMauro E, Ballario P, Pedone F. Transcription in sea urchin. The role of non-histone chromosomal proteins in preventing unproductive binding of RNA polymerase to template. CELL DIFFERENTIATION 1979; 8:291-304. [PMID: 389435 DOI: 10.1016/0045-6039(79)90005-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Pays E, Donaldson D, Gilmour RS. Specificity of chromatin transcription in vitro. Anomalies due to RNA-dependent RNA synthesis. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 562:112-30. [PMID: 373804 DOI: 10.1016/0005-2787(79)90131-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the presence of Mn2+, globin mRNA can be transcribed into a partial RNA copy by Escherichia coli RNA polymerase. This process also occurs when the mRNA is transcribed together with chromatin. A fraction, at least, of the newly synthesized RNA copy (anti-globin RNA) can serve as a template for the synthesis of globin sequences of the same polarity as the original mRNA. This process is sufficient to explain the specific synthesis of a subset of the globin RNA on mouse foetal liver chromatin. It also accounts for the synthesis of double-stranded RNA sequence by E. coli RNA polymerase, on chromatin as well as on pure mRNA. Results are presented suggesting that the poly(A) tract of the mRNA could be preferentially transcribed. In the presence of Mg2+, the RNA-dependent transcription is strongly inhibited, as well as the synthesis of double-stranded RNA. Under these conditions, the transcription on chromatin appears to be largely DNA dependent, and the synthesis of globin sequences is completely asymmetric. Spermine (0.3 mM) seems to improve the specificity of transcription. The transcription of chromatin in vitro is thus largely dependent on the nature of the divalent cation present in the in the incubation mixture.
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Monjardino J, James A. In vitro transcription of polyoma DNA. Biochem Biophys Res Commun 1978; 84:618-25. [PMID: 214082 DOI: 10.1016/0006-291x(78)90750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Horowitz M, Laub O, Bratosin S, Aloni Y. Splicing of SV40 late mRNA is a post-transcriptional process. Nature 1978; 275:558-9. [PMID: 211442 DOI: 10.1038/275558a0] [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: 12/13/2022]
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Lescure B, Chestier A, Yaniv M. Transcription of polyoma virus DNA in vitro. II. Transcription of superhelical and linear polyoma DNA by RNA polymerase II. J Mol Biol 1978; 124:73-85. [PMID: 213607 DOI: 10.1016/0022-2836(78)90148-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Lescure B, Dauguet C, Yaniv M. Transcription of polyoma virus DNA in vitro. III. Localization of calf thymus RNA polymerase II binding sites. J Mol Biol 1978; 124:87-96. [PMID: 213608 DOI: 10.1016/0022-2836(78)90149-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Pedone F, Ballario P, Di Mauro E. Homologous RNA polymerase binding to Escherichia coli DNA: a study of the distribution of stable binding sites. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 87:445-51. [PMID: 354932 DOI: 10.1111/j.1432-1033.1978.tb12394.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The number and the distribution of the sites of Escherichia coli DNA that form stable complexes with the homologous RNA polymerase (class A sites according to Hinkle and Chamberlin [3]) have been investigated. Almost all the DNA can bind RNA polymerase, even when fragmented at short (undergenic) size; this general non-promoter-specific binding is highly labile and is not temperature-dependent. The range of RNA polymerase/DNA ratios that give rise to the stable temperature-dependent complexes was examined. The amount and the distribution of class A complexes were studied analysing the dissociation of complexes formed by RNA polymerase on DNA fragments of various length. The E. coli genome appears to form 3.8 X 10(3) stable complexes; the majority of these complexes shows a short-range distribution (800-1200 base pairs). The rest is more widely spaced (1200-6000 base pairs).
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Koller T, Kübler O, Portmann R, Sogo JM. High resolution physical mapping of specific binding sites of Escherichia coli RNA polymerase on the DNA of bacteriophage T7 . J Mol Biol 1978; 120:121-31. [PMID: 347089 DOI: 10.1016/0022-2836(78)90298-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Pfeffer SR, Stahl SJ, Chamberlin MJ. Binding of Escherichia coli RNA polymerase to T7 DNA. Displacement of holoenzyme from promoter complexes by heparin. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(19)63363-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
The rate of in vitro transcription of the rRNA genes of E. coli is more than 20 fold higher than the averaged transcription rate of other genome segments of the same size. This "preferential transcription" of rRNA genes reflects a high efficiency of their promoters in chain initiation. We show that the high initiation rate at rRNA promoters results from a high rate of RNA polymerase binding to these promoters as measured by the formation of heparin-resistant RNA polymerase-DNA complexes. The results indicate that the preferential binding of RNA polymerase to rRNA promoters is mainly due to their large binding capacity rather than to a high rate constant of polymerase binding to a single binding site. The polymerase binding capcity of rRNA promoters was estimated from the number of rRNA chains initiated by heparin-resistant complexes under conditions of template saturation and from the number of rRNA transcription units participating in the binding reaction. At least 30 RNA polymerase molecules were found to be protected from heparin per rRNA transcription unit. The rest of the genome (99.4%; possibly sufficient to encode 4000 nonribosomal RNA species) protects under these conditions 2000 enzyme molecules. These results suggest that a high multiplicity of RNA polymerase binding may be responsible for the high efficiency of rRNA promoters. The validity of this hypothesis is discussed.
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Long E, Crippa M. DNA-dependent RNA polymerase C from Xenopus laevis ovaries: formation of stable heparin-resistant DNA-binding complexes. FEBS Lett 1976; 72:67-70. [PMID: 1001472 DOI: 10.1016/0014-5793(76)80814-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Fábry M, Sümegi J, Venetianer P. Purification and properties of the RNA polymerase of an extremely thermophilic bacterium: Thermus aquaticus T2. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 435:228-35. [PMID: 949494 DOI: 10.1016/0005-2787(76)90104-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA polymerase of the extremely thermophilic bacterium Thermus aquaticus T 2 has been purified to homogeneity. The apparent molecular weights of the subunits of the enzyme are : 165 000, 130000, 92 000 and 44 000. The in vitro temperature optimum of enzyme activity is around 65 degrees C. The enzyme has a preference towards the homologous template and is strongly inhibited by KCI. Rifampicin inhibits the enzyme only to 50% even at very high concentrations. Heparin inhibits it completely, but only at higher molar excess than in the case of the Escherichia coli enzyme. The enzyme can form heparin-resistant complexes at elevated temperatures on the homologous template, but not on E. coli DNA.
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Chan JY, Loor RM, Wang TY. Transcription in vitro of Ehrlich ascites tumor DNA and chromatin by purified homologous RNA polymerase II (or B). Arch Biochem Biophys 1976; 173:564-76. [PMID: 1275509 DOI: 10.1016/0003-9861(76)90293-9] [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: 12/26/2022]
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Abstract
A regulatory mutant of the Adh (alcohol dehydrogenase) gene was induced by ethyl methanesulfonate. The mutation reduces the ability of the gene to complete for the limited gene activating factor. The mutant shows full activity in the homozygote but only one-half the activity of the progenitor gene in heterozygotes where it is competing with another allele for the limited factor. Evidence is presented for multiple regulatory sites in both the Adh and Adh2 loci.
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Ferencz A, Seifart KH. Comparative effect of heparin on RNA synthesis of isolated rat-liver nucleoli and purified RNA polymerase A. EUROPEAN JOURNAL OF BIOCHEMISTRY 1975; 53:605-13. [PMID: 1095373 DOI: 10.1111/j.1432-1033.1975.tb04104.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The polyanion heparin has been employed to study the interaction of rat liver DNA-dependent RNA polymerase A and its template under various conditions. Heparin very efficiently inhibits polymerase molecules, which are not bound to DNA or are associated with the template in a loose, i.e. non-specific fashion. Purified nucleoli, isloated from rat liver nuclei, contain RNA polymerase A in abundant quantities of which only a portion is bound in a transcriptional complex. Excess enzyme, which is contained in the nucleolus in a quasi free form, can be transferred to an exogenously added template and can be completely inhibited by the prior addition of heparin. The enzyme contained in a transcriptional complex, however, initiated in vivo and completing these RNA chains in vitro, is fully resistant to heparin. In contrast to these results it has been found that RNA polymerase A extracted from nuclei and purified by various chromatographic steps does not form heparin-resistant complexes, even after the enzyme has been bound to the DNA template. Moreover it has been found that purified RNA polymerase A transcribes truly native DNA extremely poorly, indicating that the enzyme is highly deficient in the act of initiation on duplex DNA. It is therefore questionable whether the interaction of the purified enzyme and isolated DNA represents binding to true initiation complexes as is observed in the intact nucleolus.
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Squires CL, Lee FD, Yanofsky C. Interaction of the trp repressor and RNA polymerase with the trp operon. J Mol Biol 1975; 92:93-111. [PMID: 1097702 DOI: 10.1016/0022-2836(75)90093-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Richardson JP. Initiation of transcription by Escherichia coli RNA polymerase from supercoiled and non-supercoiled bacteriophage PM2 DNA. J Mol Biol 1975; 91:477-87. [PMID: 1097698 DOI: 10.1016/0022-2836(75)90274-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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26
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Peters GG, Hayward RS. Dinucleotide sequences in the regions of T7 DNA coding for termination of early transcription. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 48:199-208. [PMID: 4614973 DOI: 10.1111/j.1432-1033.1974.tb03757.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Portmann R, Sogo JM, Koller T, Zillig W. Binding sites of E. coli RNA polymerase on T7 DNA as determined by electron microscopy. FEBS Lett 1974; 45:64-7. [PMID: 4606271 DOI: 10.1016/0014-5793(74)80811-2] [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: 01/11/2023]
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Giacomoni PU, Le Talaer JY, Le Pecq JB. Escherichia coli RNA-polymerase binding sites on DNA are only 14 base pairs long and are located between sequences that are very rich in AplusT. Proc Natl Acad Sci U S A 1974; 71:3091-5. [PMID: 4528552 PMCID: PMC388627 DOI: 10.1073/pnas.71.8.3091] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
E. coli DNA-dependent RNA-polymerase binding sites on DNAs of T5, T7, and lambda coliphages have been isolated according to three different methods in order to analyze the binding sites themselves as well as the nearest neighboring regions. It is shown that the binding sites are regions that are rather rich in G+C, are about 14 base pairs long and are located between DNA sequences highly enriched in A+T. The biological implications of this result are discussed.
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Udvardy A, Sumegi J, Venetianer P. Tight binding of RNA polymerase to rDNA genes in E. coli. Nature 1974; 249:548-50. [PMID: 4599763 DOI: 10.1038/249548a0] [Citation(s) in RCA: 4] [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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Bordier C, Dubochet J. Electron microscopic localization of the binding sites of Escherichia coli RNA polymerase in the early promoter region of T7 DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 44:617-24. [PMID: 4600365 DOI: 10.1111/j.1432-1033.1974.tb03519.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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