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Vollenweider HJ. Visual biochemistry: new insight into structure and function of the genome. METHODS OF BIOCHEMICAL ANALYSIS 2006; 28:201-65. [PMID: 6178943 DOI: 10.1002/9780470110485.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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2
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Klaus S, Vogel F, Gautschi J, Stålhammar-Carlemalm M, Meyer J. DNA of the Streptomyces phage SH10: binding sites for Escherichia coli RNA polymerase and denaturation map. MOLECULAR & GENERAL GENETICS : MGG 1983; 189:21-6. [PMID: 6343784 DOI: 10.1007/bf00326050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Escherichia coli RNA polymerase bound to Streptomyces phage SH10 DNA was visualized by electron microscopy. Six specific binding sites were observed at map units 53, 85, 93, 97, 98, and 99 on the physical map of the 48 kb long genome. Electron microscopy of partially denatured SH10 DNA revealed a characteristic melting pattern of A + T-rich regions around map units 1, 3, 48, 52, and 99. A comparison of the denaturation map with the RNA polymerase binding sites indicates that three binding sites are located in the most A + T-rich regions, two in other early melting regions and one in a segment of higher DNA helix stability.
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Melançon P, Burgess RR, Record MT. Nitrocellulose filter binding studies of the interactions of Escherichia coli RNA polymerase holoenzyme with deoxyribonucleic acid restriction fragments: evidence for multiple classes of nonpromoter interactions, some of which display promoter-like properties. Biochemistry 1982; 21:4318-31. [PMID: 6289878 DOI: 10.1021/bi00261a022] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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4
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Lavialle C, Reuveni Y, Thoren M, Salzman N. Molecular interaction between simian virus 40 DNA and Escherichia coli RNA polymerase. Mapping of the initiation sites on supercoiled and linear DNA. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68227-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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5
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Coetzee WF, Pretorius GH. Interaction of escherichia coli RNA polymerase with the genome of Proteus mirabilis phage 5006M. Virology 1982; 117:11-8. [PMID: 7039087 DOI: 10.1016/0042-6822(82)90502-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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6
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Vogel F, Scherneck S. A comparison of the phage T4 gene 32 protein and Escherichia coli RNA polymerase binding sites on hamster papovavirus DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 696:102-6. [PMID: 6282329 DOI: 10.1016/0167-4781(82)90015-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Phage T4 gene 32 protein and Escherichia coli RNA polymerase were bound to hamster papovavirus DNA. The binding regions were identified by electron microscopy employing a protein-free spreading technique. After gene 32 protein treatment four denaturation regions could be mapped, at 0.04-0.12, 0.30-0.36, 0.50-0.60 and 0.75-0.90 DNA map units, respectively, using the unique BamHI cleavage site as zero point. Eight RNA polymerase binding sites can be found which are localized at positions 0.05; 0.11; 0.18; 0.31; 0.57; 0.66; 0.76 and 0.82. A comparison of the RNA polymerase binding sites with the gene 32 protein denaturation pattern reveals a correspondence of six of eight polymerase binding sites with (A+T)-rich regions within the hamster papovavirus genome.
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Morelli G, Buhk HJ, Fisseau C, Lother H, Yoshinaga K, Messer W. Promoters in the region of the E. coli replication origin. MOLECULAR & GENERAL GENETICS : MGG 1981; 184:255-9. [PMID: 6276695 DOI: 10.1007/bf00272913] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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9
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Lurz R, Danbara H, Rückert B, Timmis KN. Plasmid replication functions. VII. Electron microscopic localization of RNA polymerase binding sites in the replication control region of plasmid R6-5. MOLECULAR & GENERAL GENETICS : MGG 1981; 183:490-6. [PMID: 7038379 DOI: 10.1007/bf00268770] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
RNA polymerase binding sites on the R6-5 miniplasmid derivative, plasmid pKT401, were mapped by electron microscopy of DNA:RNA polymerase complexes formed with both circular-supercoiled and restriction endonuclease-linearized plasmid DNA molecules. Of eight specific binding sites on pKT401 that were identified, three were found to be in the P-6 fragment of the plasmid replication region, three in the Tn3 element, and two in other parts of the plasmid molecule. Binding sites 1 and 3 in the P-6 fragment are most probably the promoters of the copB and copA/incA plasmid replication control genes, respectively, whereas site 2 in this fragment appears to be the promoter of the essential replication gene, repA. The location of these promoters in relation to the site of action of the plasmid replication control elements, copT, and the origin of replication, oriV, suggests that replication control may be effected by regulation of transcription events initiated at site 2, or of the activity of transcripts initiated from this site, i.e., by regulation of the expression of the repA gene or another function dependent upon these events.
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In vitro transcription of the yeast alcohol dehydrogenase I gene by homologous RNA polymerase B (II). Selective initiation and discontinuous elongation on a supercoiled template. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68549-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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11
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Ballario P, Buongiorno-Nardelli M, Carnevali F, Di Mauro E, Pedone F. Selective in vitro transcription by purified yeast RNA polymerase II on cloned 2 micron DNA. Nucleic Acids Res 1981; 9:3959-78. [PMID: 7029462 PMCID: PMC327408 DOI: 10.1093/nar/9.16.3959] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The in vitro transcription properties of purified yeast RNA polymerase II have been analyzed on prokaryotic plasmids (pBR322 and pBR313) and chimaeric plasmids bearing yeast 2 micron sequences (BTYP 1, BTYH 2 and BTYH 3). Conditions for selective transcription of the 2 micron DNA sequences in chimaeric plasmids have been determined. pBR322 and pBR313 are not transcribed by the purified RNA polymerase II when not bearing eukaryotic inserts. We show that the agarose gel electrophoretic analysis of ternary transcription complexes allows the localization of nascent RNA chains. The RNA produced has been visualized by electron microscopy (nascent RNA hybridization loops) and by gel electrophoretic analysis. All the observed properties are shared by RNA polymerase II purified by a conventional method (1) and by a rapid alternative procedure described herein. The peculiar properties of a partially purified form of RNA polymerase II are reported.
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12
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Crepin M, Triadou P, Lelong JC, Gros F. Identification of transcription initiation sites for bacterial RNA polymerase and eukaryotic RNA polymerase B on the 5' end of the mouse beta-Globin gene. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 118:371-7. [PMID: 7285930 DOI: 10.1111/j.1432-1033.1981.tb06412.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Using a recombinant phage containing the mouse beta-Globin gene with lambda gtWES bacteriophage DNA, transcription initiation sites for Escherichia coli RNA polymerase and calf thymus RNA polymerase B were mapped at the 5' and 3' ends of the mouse beta-Globin gene. The bacterial enzyme was capable of initiating RNA synthesis at the 3' end site located at about 700 residues from the 3' end of the beta-Globin restriction enzyme map. Initiation at this site was more efficient than initiation at the known early lambda promotors (PL, PR). Calf thymus RNA polymerase B initiated transcription at the same sites as the bacterial enzyme but in this case maximum efficiency was at the 5' end site as compared to the 3' end site. Initiation of transcription occurs in the region of the d(T-A-T-A-A) sequence. Initiation efficiency at the 5' end site, as probed by the maximum rate of transcription, was shown to depend partly upon the presence of the adjacent sequences upstream and downstream of the 5' initiation site.
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Triadou P, Lelong JC, Gros F, Crépin M. Modulation of the initiation of mouse beta-globin transcription by non-histone proteins purified from mouse erythropoietic Friend cells. Biochem Biophys Res Commun 1981; 101:45-54. [PMID: 7284007 DOI: 10.1016/s0006-291x(81)80008-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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14
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Soloski MJ, Holowczak JA. Characterization of supercoiled nucleoprotein complexes released from detergent-treated vaccinia virions. J Virol 1981; 37:770-83. [PMID: 7218437 PMCID: PMC171065 DOI: 10.1128/jvi.37.2.770-783.1981] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Treatment of vaccinia virions with 1% sodium dodecyl sulfate in the absence of reducing agents resulted in the release of subviral particles termed "subnucleoids," which contained viral DNA in combination with four polypeptides with molecular weights of 90,000, 68,000, 58,000 and 10,000. Biochemical and electron microscopic studies showed that viral DNA in combination with these polypeptides was maintained in a superhelical configuration. When subnucleoids were "fixed" with glutaraldehyde and formaldehyde and then examined by electron microscopy, spherical particles were observed, in which the supercoiled DNA was folded into globular structures that were 20 to 60 nm in diameter and were interconnected by DNA-protein fibers resembling the nucleosome structures described for eucaryotic chromatin.
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Chandrasekaran E, Mendicino A, Garver F, Mendicino J. Structures of sialylated O-glycosidically and N-glycosidically linked oligosaccharides in a monoclonal immunoglobulin light chain. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69839-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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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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17
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Jakobovits EB, Saragosti S, Yaniv M, Aloni Y. Escherichia coli RNA polymerase in vitro mimics simian virus 40 in vivo transcription when the template is viral nucleoprotein. Proc Natl Acad Sci U S A 1980; 77:6556-60. [PMID: 6256744 PMCID: PMC350324 DOI: 10.1073/pnas.77.11.6556] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have used a low-salt detergent-free extraction procedure on cells infected with simian virus 40 to obtain viral nucleoprotein late after infection. Addition of EScherichia coli RNA polymerase and ribonucleotide triphosphates to the viral minichromosomes permitted transcription of RNA from viral templates. This synthesis was initiated predominantly within a fragment of DNA spanning 0.67 to 0.76 map unit on the genome. The synthesis from this region proceeded primarily along the "late" strand in a clockwise direction. These results were in contrast to the synthesis obtained with naked viral DNA in which initiation occurred on other regions of the genome and from which transcription proceeded counterclockwise along the early strand. These findings indicate that the nucleoprotein template or factors tightly associated with it may be responsible for site(s) and strand selection in transcription of simian virus 40.
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Saragosti S, Croissant O, Yaniv M. Localization of the binding sites of prokaryotic and eukaryotic RNA polymerases on simian virus 40 DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 106:25-31. [PMID: 6280998 DOI: 10.1111/j.1432-1033.1980.tb05993.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The binding sites of calf thymus RNA polymerase (B) II, wheat germ RNA polymerase B and of the Escherichia coli RNA polymerase were mapped on the simian virus 40 genome by observation of enzyme-linear DNA complexes by electron microscopy. Three to four major sites and several minor sites are observed for each enzyme; common binding sites for the three enzymes are found in positions 0.17, 0.53 and 0.90 of the viral physical map. Initiation complexes with these enzymes can be stabilized with specific ribodinucleotides and a single ribonucleoside triphosphate. Whereas ApA and ATP greatly enhances the binding of the E. coli enzyme at position 0.17, they stabilize the binding of the eukaryotic enzyme at many sites, some of them located in close proximity of the origin of replication.
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19
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Dandolo L, Blangy D. Transcription of polyoma DNA by Escherichia coli RNA polymerase: influence of ionic strength on promoter selection. J Virol 1980; 33:927-35. [PMID: 6245276 PMCID: PMC288625 DOI: 10.1128/jvi.33.3.927-935.1980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The influence of ionic strength on transcription of polyoma DNA by Escherichia coli RNA polymerase was investigated. At 0.15 M KCl, transcription was highly symmetrical and, due to the lack of reinitiation, a limited extent of RNA synthesis was observed. When the concentration of KCl was raised to 0.45 M, the affinity of the enzyme for its template, as well as its apparent affinity for ribonucleoside triphosphates, was reduced. Under optimal conditions, the rate and extent of RNA synthesis at 0.45 M KCl were greater than at 0.15 M KCl, and transcription was mostly asymmetric. Binding and initiation sites at both ionic strengths were identified; at 0.15 M KCl, transcription was initiated from two major sites, located at 0.99 and 0.06 map unit, whereas at 0.45 M KCl, a unique initiation site, at 0.99 map unit, was selected by RNA polymerase.
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20
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Kadesch TR, Williams RC, Chamberlin MJ. Electron microscopic studies of the binding of Escherichia coli RNA polymerase to DNA. I. Characterization of the non-specific interactions of holoenzyme with a restriction fragment of bacteriophage T7 DNA. J Mol Biol 1980; 136:65-78. [PMID: 6988595 DOI: 10.1016/0022-2836(80)90366-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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21
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Vollenweider HJ, Fiandt M, Szybalski W. A relationship between DNA helix stability and recognition sites for RNA polymerase. Science 1979; 205:508-11. [PMID: 377494 DOI: 10.1126/science.377494] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The RNA polymerase binding sites on the DNA of (i) the aroE-trkA-spc segment of the Escherichia coli genome, (ii) transposon Tn3, (iii) plasmid ColE1, and (iv) coliphage lambda were mapped by electron microscopy, with the use of the BAC technique; these maps were compared with the maps of the early-melting regions for the same genomes. The results indicate that in all these cases the binding sites for the E. coli RNA polymerase lie preferentially in the early melting regions of DNA. These data indicate that helix stability may be an important feature of the multipartite nature of the promoter structure.
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22
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Saragosti S, Lescure B, Yaniv M. Comparative study of calf thymus and wheat germ RNA polymerase II: stability of initiation complexes and elongation rates. Biochem Biophys Res Commun 1979; 88:1077-84. [PMID: 223568 DOI: 10.1016/0006-291x(79)91518-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Calame KL, Yamada Y, Shanblatt SH, Nakada D. Location of promoter sites on plasmid NTP1 which contains the ampicillin resistance transposon Tn1701. J Mol Biol 1979; 127:397-409. [PMID: 372545 DOI: 10.1016/0022-2836(79)90229-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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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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25
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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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26
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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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27
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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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28
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Cherny DI, Aleksandrov AA, Zarudnaya MI, Kosaganov YN, Lazurkin YS, Beabealashvilli RS, Svochkina LP. Investigation of the binding of Escherichia coli RNA polymerase to DNA from bacteriophages T2 and T7 by kinetic formaldehyde method and electron microscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 79:309-17. [PMID: 334547 DOI: 10.1111/j.1432-1033.1977.tb11811.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The complexes of T2 DNA with RNA polymerase of Escherichia coli were studied by two methods: kinetic formaldehyde method with preliminary fixation of complexes with low formaldehyde concentrations, and electron microscopy. For electron-microscopic investigations the effect of different conditions of formaldehyde fixation for DNA-RNA-polymerase complexes was studied and optimal fixation conditions were found. The suggested fixation method for DNA-RNA-polymerase complexes allows investigation of RNA polymerase molecule distribution on DNA in a wide range of conditions (ionic strength of the solution, weight ration of enzyme to DNA etc.). The comparison of the concentration of RNA polymerase molecules bound to DNA, determined by electron microscopy, and the concentration of defects in DNA as determined by the kinetic formaldehyde method, showed their coincidence. The electron-microscopic procedure was used to make maps of RNA polymerase distribution on T7 DNA. A correlation between the binding regions of the enzyme and the genetic map of early DNA T7 region was found.
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29
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Crémisi C, Chestier A, Dauguet C, Yaniv M. Transcription of SV 40 nucleoprotein complexes in vitro. Biochem Biophys Res Commun 1977; 78:74-82. [PMID: 199173 DOI: 10.1016/0006-291x(77)91223-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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