Research Topics
Genomes and Genes | rpoBSummaryGene Symbol: rpoB Description: RNA polymerase, beta subunit Alias: ECK3978, JW3950, ftsR, groN, mbrD?, nitB, rif, ron, sdgB, stl, stv, tabD, tabG Species: Top Publications
Research Grants
| Scientific Experts
|
Detail Information
Publications
Transcript cleavage factors from E. coliS Borukhov
Public Health Research Institute, New York, New York 10016
Cell 72:459-66. 1993..GreB rescued the arrested complexes via the transcript cleavage and restart pathway while GreA acted by an unknown mechanism, preventing the arrest only if added before the polymerase reached the arresting site...- Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzymeA Polyakov
Rockefeller University, New York, New York 10021, USA
Cell 83:365-73. 1995..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... - Cooperation between RNA polymerase molecules in transcription elongationVitaly Epshtein
Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
Science 300:801-5. 2003..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... - Wrapping of DNA around the E.coli RNA polymerase open promoter complexC Rivetti
Istituto di Scienze Biochimiche, Universita di Parma, 43100 Parma, Italy
EMBO J 18:4464-75. 1999..Based on these data, a model of the sigma(70).RP(o) conformation is proposed... - A ratchet mechanism of transcription elongation and its controlGil Bar-Nahum
Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
Cell 120:183-93. 2005..This balance is critical for cell viability since it determines the rate, processivity, and fidelity of transcription... - Transcription through the roadblocks: the role of RNA polymerase cooperationVitaly Epshtein
Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
EMBO J 22:4719-27. 2003..These results support a cooperation model of transcription whereby RNAP molecules behave as 'partners' helping one another to traverse intrinsic and extrinsic obstacles... - Crucial role of the RNA:DNA hybrid in the processivity of transcriptionI Sidorenkov
ABL Basic Research Program, National Cancer Institute Frederic Cancer Research and Development Center, Maryland 21702 1201, USA
Mol Cell 2:55-64. 1998..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... - Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpinsI Toulokhonov
Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
Science 292:730-3. 2001..These findings favor an allosteric model for regulation of transcript elongation... - Region 3.2 of the sigma subunit contributes to the binding of the 3'-initiating nucleotide in the RNA polymerase active center and facilitates promoter clearance during initiationAndrey Kulbachinskiy
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
J Biol Chem 281:18273-6. 2006..In summary, our data demonstrate an important role of sigma region 3.2 in the binding of initiating substrates in RNA polymerase active center and in the process of promoter clearance... - Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescaleChristopher D Herring
Department of Bioengineering, University of California, San Diego, California 92093, USA
Nat Genet 38:1406-12. 2006..The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts... - A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coliKim Sneppen
NORDITA, Nordic Institute for Theoretical Physics, Niels Bohr Institute, Blegdamsvej 17, DK 2100 Copenhagen, Denmark
J Mol Biol 346:399-409. 2005..The model provides a framework for using transcriptional interference to investigate various dynamic processes on DNA in vivo... - RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNAN Komissarova
Public Health Research Institute, New York, New York 10016, USA
J Biol Chem 272:15329-38. 1997..These oscillations of RNA polymerase can explain its apparent discontinuous advancement, which had been interpreted as indicating flexibility within the enzyme... - Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallographyS A Darst
The Rockefeller University, New York, New York, 10021, USA
J Struct Biol 124:115-22. 1998..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... - Coupling between transcription termination and RNA polymerase inchwormingE Nudler
Public Health Research Institute, New York, New York 10016, USA
Cell 81:351-7. 1995..The results indicate that straining and relaxation of RNA polymerase are steps in the termination mechanism... - Discontinuous mechanism of transcription elongationE Nudler
Public Health Research Institute, New York, NY 10016
Science 265:793-6. 1994..Thus, elongation proceeded in alternating laps of monotonous and inchworm-like movement with the flexible RNA polymerase configuration being subject to direct sequence control... - Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strengthL Rao
Department of Bacteriology, University of Wisconsin, Madison 53706
J Mol Biol 235:1421-35. 1994..A functional UP element is not absolutely essential for stimulation of rrnB P1 by the Fis protein... - Primary and secondary structure specificity of the cleavage of 'single-stranded' DNA by endonuclease Hinf IB Hofer
Nucleic Acids Res 10:2763-73. 1982..The results suggest that completely base-paired recognition sites are necessary for cleavage. Sequences surrounding the Hinf I pentanucleotides significantly modulate the reaction rates... - Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complexD Wang
Department of Biology, Washington University, St Louis, Missouri 63130, USA
Cell 81:341-50. 1995..We suggest pausing and termination could be alternative outcomes of a similar isomerization that depend on the strength of contacts to 3'-proximal RNA remaining after the jump... - Transcriptional and post-transcriptional control of ribosomal protein and ribonucleic acid polymerase genesR Little
J Bacteriol 147:25-35. 1981..the beta operon [which has the genetic organization: promoter (p beta), rplJ (L10), r;lL (L7/L12), attenuator, rpoB (beta), rpoC (beta'), terminator], the restriction caused a disproportionate increase between proximal and distal .. - Internal promoters of the rpoBC operon of Escherichia coliJ C Ma
Mol Gen Genet 184:548-50. 1981Four ribosomal protein genes, rplA, rplJ, rplK and rplL form an operon in E. coli together with the genes rpoB and rpoC which encode the beta and beta' subunits of RNA polymerase... - RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNALaura Tsujikawa
Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
Biochemistry 41:15334-41. 2002..These results are consistent with the residue at -11 being tightly bound in a hydrophobic pocket of the enzyme... - Increased RNA polymerase availability directs resources towards growth at the expense of maintenanceBertil Gummesson
Department of Cell and Molecular Biology, Gothenburg University, Goteborg, Sweden
EMBO J 28:2209-19. 2009..We conclude that ppGpp modulates the levels of free Esigma(70) and that this is an integral part of the alarmone's means of regulating a trade-off between growth and maintenance... - (p)ppGpp regulates type 1 fimbriation of Escherichia coli by modulating the expression of the site-specific recombinase FimBAnna Aberg
Department of Molecular Biology, Umea University, S 90187 Umea, Sweden
Mol Microbiol 60:1520-33. 2006..Our findings suggest that the (p)ppGpp-stimulated expression of type 1 fimbriae may be relevant during the interaction of pathogenic E. coli with the host... - Structural basis for bacterial transcription-coupled DNA repairAlexandra M Deaconescu
The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Cell 124:507-20. 2006..These data, along with a structural model for the interaction of TRCF with the transcription elongation complex, provide mechanistic insights into TRCF function... - RNA polymerase mutants defective in the initiation of transcription-coupled DNA repairA J Smith
Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk Bristol BS8 1TD, UK
Nucleic Acids Res 33:755-64. 2005.... - Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreBAndrey Kulbachinskiy
Public Health Research Institute, Newark, New Jersey, USA
Eur J Biochem 271:4921-31. 2004..We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme... - Association of RNA polymerase with transcribed regions in Escherichia coliJoseph T Wade
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 101:17777-82. 2004..These observations suggest that in vivo association of sigma(70) and NusA with elongating RNAP is regulated by growth conditions... - Minimal machinery of RNA polymerase holoenzyme sufficient for promoter meltingBrian A Young
Departments of Stomatology and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
Science 303:1382-4. 2004..Our results support the model that capture of nontemplate bases extruded from the DNA helix underlies the melting process... - Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosomeLilit Garibyan
Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
DNA Repair (Amst) 2:593-608. 2003Mutations in the rpoB gene of Escherichia coli result in resistance to the antibiotic rifampicin (Rif(r)) by altering the beta subunit of RNA polymerase... - Cytoplasmic RNA Polymerase in Escherichia coliN Shepherd
Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 0688, USA
J Bacteriol 183:2527-34. 2001..Together, these results suggest that most functional RNA polymerase is associated with the DNA and that little if any segregates into DNA-free minicells... - BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymeraseA Nussbaum-Shochat
Department of Molecular Biology, Hebrew University Hadassah Medical School, P O Box 12272, Jerusalem 91120, Israel
Proc Natl Acad Sci U S A 96:4336-41. 1999..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... - Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymeraseC S Garland
Laboratory of Cellular and Molecular Biology, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland 21224, USA
Biochemistry 38:3421-5. 1999..These studies show curvature to be a significant feature in the interaction between DNA template and RNA elongate even at the very beginning of transcription... - Spatial organization of transcription elongation complex in Escherichia coliE Nudler
Department of Biochemistry, New York University Medical Center, New York, NY 10016, USA
Science 281:424-8. 1998..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... - Determinants for Escherichia coli RNA polymerase assembly within the beta subunitY Wang
Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
J Mol Biol 270:648-62. 1997..We show that two regions of evolutionarily conserved sequence near the C terminus of beta (conserved regions H and I) are central to the assembly of RNAP and likely make subunit-subunit contacts with both alpha and beta'... - Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutationsTom M Conrad
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093 0332, USA
Genome Biol 10:R118. 2009.... - Characterization of the pleiotropic phenotypes of rifampin-resistant rpoB mutants of Escherichia coliD J Jin
Department of Bacteriology, University of Wisconsin, Madison 53706
J Bacteriol 171:5229-31. 1989We used our collection of 17 sequenced rifampin resistance alleles in rpoB to perform a systematic analysis of the phenotypes historically reported with this class of mutants, including growth phenotype, ability to support the growth of .. - Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structuresY d'Aubenton Carafa
C N R S Centre de Génétique Moleculaire, Laboratoire associé à l Université Pierre et Marie Curie, Gif sur Yvette, France
J Mol Biol 216:835-58. 1990..It also predicts with reasonable accuracy the in vitro termination efficiency of known rho-independent terminators, as well as predicting the existence of 35 as yet uncharacterized terminators... - Interaction between E. coli RNA polymerase and the tetR promoter from pSC101: homologies and differences with other E. coli promoter systems from close contact point studiesG Duval-Valentin
Nucleic Acids Res 14:1967-83. 1986.... - Functional importance of sequence in the stem-loop of a transcription terminatorS W Cheng
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109
Science 254:1205-7. 1991..These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure... - Protein-DNA cross-linking at the lac promoterM Buckle
Institut Pasteur, Unité de Physicochimie des Macromolécules Biologiques URA 1149 du CNRS, Paris, France
Nucleic Acids Res 19:833-40. 1991..These conclusions were derived from experiments performed using a generally applicable, non-interfering technique that reveals direct contacts between proteins and nucleic acids in nucleoprotein complexes... - Free RNA polymerase and modeling global transcription in Escherichia coliH Bremer
Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 0688, USA
Biochimie 85:597-609. 2003..0 and 2.5 doublings/h, respectively. The model accurately reflects a number of further experimental observations and suggests that the free RNA polymerase concentration increases with increasing growth rate... - A bacterial gene involved in transcription antitermination: regulation at a rho-independent terminator in the bgl operon of E. coliS Mahadevan
Cell 50:485-94. 1987..We propose that the bglC gene product mediates positive regulation of the bgl operon by functioning as an antiterminator at the rho-independent terminator located within the leader... - Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find themV Brendel
Department of Polymer Research, Weizmann Institute of Science, Rehovot, Israel
J Biomol Struct Dyn 3:705-23. 1986..A subset of the collection of sequence has been used to construct a computer algorithm to locate independent terminators by sequence analysis... - Genetic suppression of a dnaG mutation in Escherichia coliT Katayama
Institute for Virus Research, Kyoto University, Japan
J Bacteriol 171:1485-91. 1989..The other class of suppressor, sdgB, seemed to comprise mutant alleles in the rpoB gene coding for the beta subunit of RNA polymerase core enzyme... - Promoter recognition by Escherichia coli RNA polymerase. Role of the spacer DNA in functional complex formationD G Ayers
Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
J Mol Biol 207:749-56. 1989..As not all observations with the spacer length series of gapped and ungapped promoters can be interpreted in terms of an active role of the spacer DNA without additional assumptions, such a role must still be considered tentative... - Mutations affecting RNA polymerase associated with rifampicin resistance in Escherichia coliD H Ezekiel
Nature 220:276-7. 1968 - RNA synthesis in Escherichia coli after irradiation with ultraviolet lightH Michalke
J Mol Biol 41:1-23. 1969 - Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Deoxyribonuclease I footprinting of defined complexesB Krummel
Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720
J Mol Biol 225:239-50. 1992..We suggest that RNA chain elongation, like RNA chain initiation, may involve a saltatory process in which net translocation of the complex along the DNA occurs only after addition of a number of ribonucleotides to the RNA chain... - Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical propertiesB Krummel
Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720
J Mol Biol 225:221-37. 1992..The results raise important questions as to the actual mechanism of transcription elongation, and suggest that it is a much more complex process than previously assumed... - The Tn10-encoded tetR mRNA has heterogeneous 5' ends in vivo and in vitroU Gülland
Lehrstuhl fur Mikrobiologie, Friedrich Alexander Universitat Erlangen Nurnberg, Germany
Gene 114:97-101. 1992..In vivo transcription leads to longer reiteration products than in vitro transcription... - GreA protein: a transcription elongation factor from Escherichia coliS Borukhov
Department of Microbiology, Columbia University College of Physicians and Surgeons, New York, NY 10032
Proc Natl Acad Sci U S A 89:8899-902. 1992..Similar biochemical activities have been reported in eukaryotic RNA polymerases, indicating that transcript cleavage and restart of elongation may be a general transcriptional mechanism... - Bacterial mutants in which the gene N function of bacteriophage lambda is blocked have an altered RNA polymeraseC P Georgopoulos
Proc Natl Acad Sci U S A 68:2977-81. 1971Bacterial mutants have been isolated, called groN, that block phage development by interference with the action of the product of the phage N gene... - Spontaneous mutagenesis associated with nucleotide excision repair in Escherichia coliKimiko Hasegawa
Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630 0192, Japan
Genes Cells 13:459-69. 2008..in suppression of spontaneous mutations, and analyzed base substitutions occurring spontaneously within the rpoB gene in NER-proficient (wild-type), -deficient and -overproducing E. coli strains... - DNA strand specificity in promoter recognition by RNA polymeraseC S Park
Nucleic Acids Res 8:5895-912. 1980..These results provide insight into the molecular mechanism of promoter recognition and indicate that the interaction between RNA polymerase and DNA template is different at promoters and at non-specific sites... - RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)K Kvint
Department of Cell and Molecular Biology Microbiology, Goteborg University, Box 462, 405 30 Goteborg, Sweden
J Biol Chem 275:14795-8. 2000.... - A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificityT Gardella
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01605
J Mol Biol 206:579-90. 1989..These results suggest that this region of sigma 70 is directly involved in recognition of the -35 hexamer... - Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymeraseCaroline A Davis
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
Proc Natl Acad Sci U S A 104:7833-8. 2007.... - RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexesB Krummel
Department of Biochemistry, University of California, Berkeley 94720
Biochemistry 28:7829-42. 1989..Only after incorporation of 10 nucleotides is there significant movement of the enzyme away from the promoter region and a commitment to elongation... - UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linkerW Meng
Laboratory of Molecular Microbiology, Division of Genomic Medicine, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK
Nucleic Acids Res 29:4166-78. 2001..Our results suggest that the location of the UP element at rrnB P1 is crucial to its function and that the natural length of the alpha subunit linker is optimal for utilisation of the UP element at this promoter... - Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter meltingAnita Niedziela-Majka
Edward A Doisy Department of Biochemistry and Molecular Biology, St Louis University Medical School, St Louis, Missouri 63104, USA
J Biol Chem 280:38219-27. 2005.... - Characterization of Escherichia coli mutants with altered ploidyN J Trun
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
Res Microbiol 142:195-200. 1991..5 min; mbrC at 89.5 min; and mbrD at 90 min... - Diversity in the rates of transcript elongation by single RNA polymerase moleculesSimon F Tolić-Nørrelykke
Niels Bohr Institute, Blegdamsvej 17, DK 2100 Copenhagen, Denmark
J Biol Chem 279:3292-9. 2004..These differences may provide a parsimonious explanation for the complex transcription kinetics observed in bulk solution... - Participation of Rho-dependent transcription termination in oxidative stress sensitivity caused by an rpoB mutationNobuyuki Kawamura
Laboratory of Developmental Biochemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7 3 1, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
Genes Cells 10:477-87. 2005..termination Rho factor, suppressed the increased sensitivity to oxidative stress of the rifampicin-resistant rpoB mutation in Escherichia coli... - Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarraysDavid C Grainger
School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
J Bacteriol 186:6938-43. 2004..coli for MelR. This was confirmed by a transcriptomics experiment to analyze RNA in cells either with or without melR... - Growth phase-dependent modification of RNA polymerase in Escherichia coliM Ozaki
Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
Mol Gen Genet 230:17-23. 1991..We propose that modulation of RNA polymerase plays a role in the global switch of gene expression during the transition from exponential growth to stationary phase... - Rho-dependent termination of transcription. II. Kinetics of mRNA elongation during transcription from the bacteriophage lambda PR promoterW D Morgan
J Biol Chem 258:9565-74. 1983.... - Spacer mutations in the lac ps promoterJ E Stefano
Proc Natl Acad Sci U S A 79:1069-72. 1982..A model is suggested that proposes that three important promoter elements, the -10 region, the -35 region, and the spacer region, act simultaneously to facilitate open complex formation by RNA polymerase... - Structural analysis of ternary complexes of Escherichia coli RNA polymerase: ribonuclease footprinting of the nascent RNA in complexesS Milan
Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720 3202, USA
Biochemistry 38:218-25. 1999..Our results rule out the existence of a stable RNA-DNA hybrid in these ternary complexes of greater than 3 base pairs in length... - The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoterA J Bokal
Department of Bacteriology, University of Wisconsin Madison 53706
J Mol Biol 245:197-207. 1995.... - Nucleotide sequence of the proximal portion of the RNA polymerase beta subunit gene of Escherichia coliG Delcuve
Gene 11:367-73. 1980The nucleotide sequence of the 5'-proximal portion of the RNA polymerase beta subunit gene (rpoB) has been determined. From the nucleotide sequence it is possible to predict that NH2-terminal 390 amino acid residues of the protein... - Site-directed chemical modification for probing DNA-protein interactions. Osmium tetroxide modification of the -10 site of the lacUV5 promoter enhances open complex formationP T Chan
Department of Microbiology, University of Alabama, Birmingham 35294
J Biol Chem 264:21277-85. 1989..The latter result suggests that open complex formation appears to be enhanced due to promoter unpairing at the -10 (-12) adduct sites... - The pathway of E. coli RNA polymerase-promoter complex formation as visualized by footprintingB Hofer
Nucleic Acids Res 13:5995-6013. 1985..Only in the 'open' complex contacts were extended beyond the start site of transcription... - Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistanceD J Jin
Department of Bacteriology, University of Wisconsin, Madison 53706
J Mol Biol 202:45-58. 1988..Forty-two Rifr isolates with a variety of phenotypes were mapped to defined intervals within the rpoB gene using a set of deletions of the rpoB gene. The mutations were sequenced... - [Primary structure of Escherichia coli RNA-polymerase. Nucleotide sequence of gene rpoB and amino acid sequence of the beta-subunit]Iu A Ovchinnikov
Dokl Akad Nauk SSSR 253:994-8. 1980 - Ribosomal RNA operon anti-termination. Function of leader and spacer region box B-box A sequences and their conservation in diverse micro-organismsK L Berg
Department of Biological Sciences, Columbia University, New York, NY 10027
J Mol Biol 209:345-58. 1989..The frequent occurrence of this pattern suggested that the E. coli rrn anti-termination motif is widespread in nature and has been conserved in microbial evolution... - A multiwell assay to isolate compounds inhibiting the assembly of the prokaryotic RNA polymeraseEstelle Andre
CNRS UMR 5160 Faculté de Pharmacie, Montpellier, France
Assay Drug Dev Technol 2:629-35. 2004..We demonstrate the usefulness of the assay to screen for microbial RNA polymerase inhibitors as potential new drugs for the treatment of emerging antibiotic-resistant bacteria... - Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding proteinF Houman
Department of Molecular Biology and Microbiology, Tufts University Health Sciences Campus, Boston, Massachusetts 02111
Cell 62:1153-63. 1990..We propose that BglG prevents transcription termination by binding to nascent RNA and blocking formation of the terminator structure... - Studies of the binding of Escherichia coli RNA polymerase to DNA. I. The role of sigma subunit in site selectionD C Hinkle
J Mol Biol 70:157-85. 1972 - Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAPM M Barker
Department of Bacteriology, University of Wisconsin Madison, 1550 Linden Drive, Madison, WI, 53706, USA
J Mol Biol 305:689-702. 2001..Our data also place considerable constraints on models invoking hypothetical factors that might increase amino acid promoter activity in a ppGpp-dependent fashion... - [Mutagenesis of ion beam implantation and identification of two new rifampicin resistance determining sites in rpoB gene in Escherichia coli]Chuanxiao Xie
Key Laboratory of Ion Beam Bioengineering, Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, China
Wei Sheng Wu Xue Bao 43:732-9. 2003..5% (77/88) of the total mutation of base substitutions. Two new rif-determining sites had also been identified in rpoB gene in Escherichia coli. The first new site located in 1551... - Transcription frequency modulates the efficiency of an attenuator preceding the rpoBC RNA polymerase genes of Escherichia coli: possible autogenous controlK L Steward
Department of Microbiology and Immunology, Faculty of Medicine, University of Western Ontario, London, Canada
Nucleic Acids Res 20:4773-9. 1992..The implications for autogenous control of RNA polymerase synthesis are discussed... - Compilation and analysis of Escherichia coli promoter DNA sequencesD K Hawley
Nucleic Acids Res 11:2237-55. 1983..Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence... - DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcriptionF H Martin
Nucleic Acids Res 8:2295-9. 1980..It strongly supports the idea that instability of the DNA-RNA hybrid at the growing point of transcription plays a role in termination of transcription... - Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coliG Barry
Proc Natl Acad Sci U S A 77:3331-5. 1980..These hybrids were formed between RNA produced in vivo and specific DNA restriction fragments which span the rplL--rpoB intercistronic region... - Initiation by Escherichia coli RNA-polymerase: transformation of abortive to productive complexM A Grachev
FEBS Lett 115:23-6. 1980 - Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motifIndia Hook-Barnard
Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg 8, Room 2A 13, Bethesda, MD 20892 0830, USA
J Bacteriol 188:8352-9. 2006..coli RNA polymerase... - Coupling the distribution of RNA polymerase to global gene regulation and the dynamic structure of the bacterial nucleoid in Escherichia coliDing Jun Jin
Transcription Control Section, Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick, NIH, 1050 Boyles St, Frederick, MD 21702, USA
J Struct Biol 156:284-91. 2006..Thus, the distribution of RNAP, global gene regulation and the dynamic structure of the nucleoid are coupled in the bacterial cell... - Initial transcribed sequence mutations specifically affect promoter escape propertiesLilian M Hsu
Program in Biochemistry, Mount Holyoke College, South Hadley, Massachusetts 01075, USA
Biochemistry 45:8841-54. 2006..How the ITS might influence the course of early transcription is discussed within the structural context of an initial transcribing complex... - Relationship between the N function of bacteriophage lambda and host RNA polymeraseA Ghysen
J Mol Biol 65:259-72. 1972 - Increased A:T-->C:G mutations in the mutT strain upon 8-hydroxy-dGTP treatment: direct evidence for MutT involvement in the prevention of mutations by oxidized dGTPHiroyuki Kamiya
Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita ku, Sapporo 060 0812, Japan
J Biochem 136:359-62. 2004..coli cells, and mutations of a chromosomal gene were monitored. 8-OH-dGTP induced mutations of the rpoB gene, the degree of the mutation induction in the mutT strain being approximately 6-fold higher than that in the .. - Bicyclomycin sensitivity and resistance affect Rho factor-mediated transcription termination in the tna operon of Escherichia coliC Yanofsky
Department of Biological Sciences, Stanford University, California 94305 5020, USA
J Bacteriol 177:4451-6. 1995..complementation analyses suggest that five have mutations that affect rho, three have mutations that affect rpoB, and one has a mutation that affects a third locus, near rpoB...
Research Grants
- Bacterial RNAP Sigma Factor Structure and FunctionSeth A Darst; Fiscal Year: 2010..Bacterial strains resistant to rifampicin arise with appreciable frequency, compromising treatment. Insights into the mechanism of bacterial transcription can lead to new avenues for the development of antimicrobials. ..
- Bacterial RNAP Sigma Factor Structure and FunctionSeth Darst; Fiscal Year: 2007..subtilis Spx/alpha-C-terminal-domain complex. 4. Structurally characterize the sigmaF regulatory system (sigmaF/SpollAA/SpollAB/SpollE) controlling the initiation of sporulation in Bacillus. ..
- Transcription Elongation Control in E. coliEvgeny Nudler; Fiscal Year: 2006..It is further proposed to examine whether GreA/GreB transcript cleavage factors contribute to transcription fidelity in vivo. ..
- Upgrade of in-house X-ray diffraction equipmentSeth Darst; Fiscal Year: 2006....
- Regulation Of Transcription by 6S RNAKAREN WASSARMAN; Fiscal Year: 2007..How 6S RNA changes the transcriptional machinery and its activity, which will be addressed through biochemical approaches. ..
- Structure/Function of the Bacterial TRCFSeth Darst; Fiscal Year: 2007..3. Determine the structural basis for the specific transcription termination activity of TRCF through structural studies of an RNAP ternary elongation complex (RNAP/DNA/RNA) with TRCF. ..
- X-RAY CRYSTALLOGRAPHIC STUDIES OF TAQ RNA POLYMERASESeth Darst; Fiscal Year: 2007..Determine the crystal structure of RNAP with the transcription elongation factor GreA/B; 5. Determine the crystal structure of T. thermophilus sigma (E) holoenzyme. ..
- 6S RNA Regulation of TranscriptionKaren M Wassarman; Fiscal Year: 2010..Therefore, basic understanding of how this important RNA works as a global regulator, will facilitate understanding another level of regulation of gene expression that is likely to exist in all organisms. ..
- Structural Basis for Sporulation in BacillusSeth A Darst; Fiscal Year: 2010..4. Structurally characterize the ?F regulatory system (?F/SpollAA/SpollAB/SpollE) controlling the initiation of Bacillus sporulation. ..
- Bacterial RNAP Sigma Factor Structure and FunctionSeth A Darst; Fiscal Year: 2010..Bacterial strains resistant to rifampicin arise with appreciable frequency, compromising treatment. Insights into the mechanism of bacterial transcription can lead to new avenues for the development of antimicrobials. ..
- 6S RNA Regulation of TranscriptionKAREN WASSARMAN; Fiscal Year: 2009..Therefore, basic understanding of how this important RNA works as a global regulator, will facilitate understanding another level of regulation of gene expression that is likely to exist in all organisms. ..
- Structural Basis for Sporulation in BacillusSeth Darst; Fiscal Year: 2009..4. Structurally characterize the ?F regulatory system (?F/SpollAA/SpollAB/SpollE) controlling the initiation of Bacillus sporulation. ..
- Structural Basis for Sporulation in BacillusSeth Darst; Fiscal Year: 2007..4. Structurally characterize the ?F regulatory system (?F/SpollAA/SpollAB/SpollE) controlling the initiation of Bacillus sporulation. ..
- Structure & Function of Prokaryotic Transcript CleavageSergei Borukhov; Fiscal Year: 2005..abstract_text> ..
- E COLI RNA POLYMERASE SUBUNIT--STRUCTURE AND FUNCTIONSeth Darst; Fiscal Year: 2000..4) alpha Subunit. The domain architecture of the alpha subunit has been elucidated by others. We will undertake detailed structural studies of alpha subunit domains using the method of X-ray crystallography. ..
- STRUCTURE/FUNCTION OF E COLI TRANSCRIPT CLEAVAGE FACTORSSergei Borukhov; Fiscal Year: 2000..The resulting modified Gre proteins will be used to probe the interactions with RNA polymerase at different stages of transcription elongation. ..
- STRUCTURAL PARAMETERS OF E COLI RNA POLYMERASESeth Darst; Fiscal Year: 2001....
- Bacterial RNAP Sigma Factor Structure and FunctionSeth Darst; Fiscal Year: 2004..abstract_text> ..
- X-RAY CRYSTALLOGRAPHIC STUDIES OF TAQ RNA POLYMERASESeth Darst; Fiscal Year: 2003..6. Determine the structure of an active ternary elongation complex between taq core RNAP, DNA template, and RNA transcript. These studies will have a wide-ranging impact on studies of transciption. ..