rpoA

Summary

Gene Symbol: rpoA
Description: RNA polymerase, alpha subunit
Alias: ECK3282, JW3257, pez, phs, sez
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. ncbi 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 initiation
    Andrey Kulbachinskiy
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
    J Biol Chem 281:18273-6. 2006
  2. ncbi Development of RNA polymerase-promoter contacts during open complex formation
    J Mecsas
    Department of Bacteriology, University of Wisconsin Madison 53706
    J Mol Biol 220:585-97. 1991
  3. ncbi Escherichia coli rpoA mutation which impairs transcription of positively regulated systems
    M S Thomas
    Department of Biochemistry, University of Nottingham Medical School, Queen s Medical Centre, UK
    Mol Microbiol 5:2719-25. 1991
  4. pmc Topography of intermediates in transcription initiation of E.coli
    P Schickor
    Max Planck Institute of Biochemistry, Martinsried, FRG
    EMBO J 9:2215-20. 1990
  5. ncbi RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes
    B Krummel
    Department of Biochemistry, University of California, Berkeley 94720
    Biochemistry 28:7829-42. 1989
  6. ncbi Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter
    D W Cowing
    Department of Bacteriology, University of Wisconsin Madison 53706
    J Mol Biol 210:521-30. 1989
  7. ncbi The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5
    R T Kovacic
    Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
    J Biol Chem 262:13654-61. 1987
  8. ncbi Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter
    T P Malan
    J Mol Biol 180:881-909. 1984
  9. ncbi Abortive initiation and long ribonucleic acid synthesis
    L M Munson
    Biochemistry 20:2081-5. 1981
  10. ncbi Functional map of the alpha subunit of Escherichia coli RNA polymerase: amino acid substitution within the amino-terminal assembly domain
    M Kimura
    Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
    J Mol Biol 254:342-9. 1995

Research Grants

Scientific Experts

  • A V Kulbachinskiy
  • E Nudler
  • Innokenti Toulokhonov
  • Frederique Braun
  • Ding Jun Jin
  • Lilian M Hsu
  • Martin Pelchat
  • Kim Sneppen
  • S A Darst
  • Oleg Laptenko
  • David C Grainger
  • Bianca Sclavi
  • Nigel J Savery
  • N Fujita
  • Sergei Borukhov
  • Vitaly Epshtein
  • Richard H Ebright
  • Stephen J W Busby
  • Mark S Thomas
  • Georgina S Lloyd
  • David J Lee
  • Valentina Rippa
  • David A Schneider
  • Grzegorz Wegrzyn
  • A Ishihama
  • W Ross
  • M S Thomas
  • Sara Cellai
  • Thomas Kruse
  • India Hook-Barnard
  • Jyothi Bhat
  • R L Gourse
  • Anita Niedziela-Majka
  • Gil Bar-Nahum
  • Estelle Andre
  • Anne M L Barnard
  • Seyyed I Husnain
  • Joseph T Wade
  • Wilma Ross
  • Joshua W Shaevitz
  • Richard L Gourse
  • Maxim V Sukhodolets
  • Leonid Minakhin
  • Agnieszka Szalewska-Pałasz
  • Hao Chen
  • Barbara Kedzierska
  • Anna Herman-Antosiewicz
  • Magdalena Gabig
  • Y H Jeon
  • Laura Tsujikawa
  • Akira Katayama
  • Brian Benoff
  • N Komissarova
  • C Zou
  • Nunzianna Doti
  • Angela Duilio
  • Benedetta Di Palo
  • M Buckle
  • Angela Amoresano
  • D J Lee
  • Claudia Cirulli
  • P S Fritsch
  • W Meng
  • S J Busby
  • C S Garland
  • E Zaychikov
  • C Rivetti
  • I N Olekhnovich
  • A Nussbaum-Shochat
  • Ekaterine Kortkhonjia
  • Nikolai Naryshkin
  • M Kimura
  • Nicola Vannini
  • R E Glass
  • Laura Mangiarotti
  • Claudio Rivetti
  • Noritaka Iwai
  • Sarah Lamb
  • Dhiman Sarkar
  • Suresh M Solapure
  • M N Harish
  • Kumi Sasaki
  • Anders Løbner-Olesen
  • Xanthia B Johnson
  • A Schulz
  • Rajendra Rane
  • M D Wang
  • Blagoy Blagoev
  • Darren Plant
  • Raman K Roy

Detail Information

Publications113 found, 100 shown here

  1. ncbi 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 initiation
    Andrey 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...
  2. ncbi Development of RNA polymerase-promoter contacts during open complex formation
    J Mecsas
    Department of Bacteriology, University of Wisconsin Madison 53706
    J Mol Biol 220:585-97. 1991
    ....
  3. ncbi Escherichia coli rpoA mutation which impairs transcription of positively regulated systems
    M S Thomas
    Department of Biochemistry, University of Nottingham Medical School, Queen s Medical Centre, UK
    Mol Microbiol 5:2719-25. 1991
    ..in decreased expression of several positively regulated operons and has been mapped to within or very near the rpoA gene encoding the alpha subunit of RNA polymerase...
  4. pmc Topography of intermediates in transcription initiation of E.coli
    P Schickor
    Max Planck Institute of Biochemistry, Martinsried, FRG
    EMBO J 9:2215-20. 1990
    ..Our data suggest that only the DNA downstream of the promoter is involved in this unwinding process...
  5. ncbi RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes
    B 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...
  6. ncbi Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter
    D W Cowing
    Department of Bacteriology, University of Wisconsin Madison 53706
    J Mol Biol 210:521-30. 1989
    ..Finally, a process of local DNA denaturation (strand opening) leads to formation of the open complex (RPO)...
  7. ncbi The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5
    R T Kovacic
    Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
    J Biol Chem 262:13654-61. 1987
    ..The 0 degree C footprints encompass both regions along with the spacer; the combination of these regions rather than an individual region may determine the character of the footprint and the magnitude of the binding constant...
  8. ncbi Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter
    T P Malan
    J Mol Biol 180:881-909. 1984
    ..DNA supercoiling enhanced the promoter strength of the lac wild-type and UV5 promoters. The combination of supercoiling and CRP-cAMP was necessary for optimal promoter strength for the lac wild-type promoter...
  9. ncbi Abortive initiation and long ribonucleic acid synthesis
    L M Munson
    Biochemistry 20:2081-5. 1981
    ..The correlation between the amount of abortive initiation and the half-time of long RNA production is discussed...
  10. ncbi Functional map of the alpha subunit of Escherichia coli RNA polymerase: amino acid substitution within the amino-terminal assembly domain
    M Kimura
    Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
    J Mol Biol 254:342-9. 1995
    ..Isolation of two mutants, alpha-K86A and alpha-V173A, both forming alpha 2 beta but not alpha 2 beta beta' complex, confirmed our previous conclusion that two separated regions participate in beta'-binding...
  11. ncbi Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding
    E E Blatter
    Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08855
    Cell 78:889-96. 1994
    ..Our results suggest a model for the mechanism of involvement of alpha in transcription activation by promoter upstream elements and upstream-binding activator proteins...
  12. ncbi Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme
    A 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...
  13. pmc The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element
    K Murakami
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
    Proc Natl Acad Sci U S A 94:1709-14. 1997
    ..The results clearly indicated that the two alpha subunits bind in tandem to two helix turns of the rrnBP1 UP element, and that the beta'-associated alpha subunit is bound to the promoter-distal region...
  14. ncbi RNA polymerase switches between inactivated and activated states By translocating back and forth along the DNA and the RNA
    N 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...
  15. ncbi Crucial role of the RNA:DNA hybrid in the processivity of transcription
    I 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...
  16. ncbi The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for efficient rho-dependent transcription termination
    M Kainz
    Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI, 53706, USA
    J Mol Biol 284:1379-90. 1998
    ..We conclude that the alphaCTD is a target for interactions with NusA that influence both termination and pausing, but in addition it participates in rho-dependent transcription termination in a NusA-independent manner...
  17. pmc Wrapping of DNA around the E.coli RNA polymerase open promoter complex
    C 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...
  18. pmc The Escherichia coli RNA polymerase alpha subunit linker: length requirements for transcription activation at CRP-dependent promoters
    W Meng
    Division of Molecular and Genetic Medicine, University of Sheffield Medical School, Sheffield S10 2RX, UK
    EMBO J 19:1555-66. 2000
    ..These observations have important implications for the architecture of transcription initiation complexes at CRP-dependent promoters...
  19. pmc Fine structure of E. coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove
    W Ross
    Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genes Dev 15:491-506. 2001
    ..These studies greatly improve the resolution of our picture of the promoter-RNAP interaction...
  20. pmc Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters
    Nigel J Savery
    Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, United Kingdom
    J Bacteriol 184:2273-80. 2002
    ..We also conclude that the relative contributions of individual residues within the 265 determinant depend on promoter sequence, and we discuss explanations for effects of substitutions in the 261 determinant...
  21. ncbi Structural basis of transcription activation: the CAP-alpha CTD-DNA complex
    Brian Benoff
    Waksman Institute and Department of Chemistry, Howard Hughes Medical Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 297:1562-6. 2002
    ..There are no large-scale conformational changes in CAP and alphaCTD, and the interface between CAP and alphaCTD is small. These findings are consistent with the proposal that activation involves a simple "recruitment" mechanism...
  22. pmc Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters
    Georgina S Lloyd
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    Genes Dev 16:2557-65. 2002
    ....
  23. ncbi Cooperation between RNA polymerase molecules in transcription elongation
    Vitaly 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...
  24. pmc An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4
    Wilma Ross
    Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genes Dev 17:1293-307. 2003
    ..Previous data from the literature suggest that this same sigma-alphaCTD interaction also plays a role in transcription factor-mediated activation...
  25. ncbi Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription
    Hao Chen
    Waksman Institute, Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA
    Mol Cell 11:1621-33. 2003
    ....
  26. pmc Transcription through the roadblocks: the role of RNA polymerase cooperation
    Vitaly 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...
  27. ncbi Exploitation of a chemical nuclease to investigate the location and orientation of the Escherichia coli RNA polymerase alpha subunit C-terminal domains at simple promoters that are activated by cyclic AMP receptor protein
    David J Lee
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
    J Biol Chem 278:52944-52. 2003
    ..Here we present data from experiments with simple Escherichia coli promoters that are activated by the cyclic AMP receptor protein...
  28. ncbi Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with the C-terminal domain of the RNA polymerase alpha subunit
    David C Grainger
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 51:1311-20. 2004
    ..Finally, we used alanine scanning to identify determinants in the C-terminal domain of the RNA polymerase alpha subunit that are important for MelR-dependent activation of the melAB promoter...
  29. ncbi A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli
    Kim 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...
  30. ncbi A ratchet mechanism of transcription elongation and its control
    Gil 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...
  31. ncbi Involvement of the Escherichia coli RNA polymerase alpha subunit in transcriptional activation by the bacteriophage lambda CI and CII proteins
    G Wegrzyn
    Department of Biochemistry, University of Nottingham Medical School, Queen s Medical Centre, UK
    Gene 122:1-7. 1992
    ..Finally, we also provide genetic evidence for impaired transcription of the cI gene from the CI-activated promoter, pM in the rpoA341 background...
  32. pmc Activation defects caused by mutations in Escherichia coli rpoA are promoter specific
    G N Gussin
    Biology Department, University of Iowa, Iowa City 52242
    J Bacteriol 174:5156-60. 1992
    ..The two alpha (rpoA) mutants, alpha-256 and alpha-235, have deletions of the C-terminal 73 and 94 amino acids, respectively...
  33. ncbi Solution structure of the activator contact domain of the RNA polymerase alpha subunit
    Y H Jeon
    Institute for Protein Research, Osaka University, Japan
    Science 270:1495-7. 1995
    ..Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface...
  34. ncbi Structural requirements for the interdomain linker of alpha subunit of Escherichia coli RNA polymerase
    N Fujita
    Department of Molecular Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411 8540, Japan
    Biochemistry 39:6243-9. 2000
    ....
  35. ncbi Analysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C-terminal domain of the RNA polymerase alpha subunit: use of alanine scanning and suppression genetics
    D J Lee
    School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Mol Microbiol 37:1032-40. 2000
    ....
  36. ncbi Escherichia coli can tolerate insertions of up to 16 amino acids in the RNA polymerase alpha subunit inter-domain linker
    Seyyed I Husnain
    Division of Genomic Medicine, School of Medicine and Biomedical Sciences, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, UK
    Biochim Biophys Acta 1678:47-56. 2004
    ..coli, we utilised a recently described technique for the substitution of the chromosomal rpoA gene, encoding alpha, by mutant rpoA alleles...
  37. ncbi Insights into Escherichia coli RNA polymerase structure from a combination of x-ray and electron crystallography
    S 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...
  38. pmc Changes in Escherichia coli rRNA promoter activity correlate with changes in initiating nucleoside triphosphate and guanosine 5' diphosphate 3'-diphosphate concentrations after induction of feedback control of ribosome synthesis
    David A Schneider
    Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Bacteriol 185:6185-91. 2003
    ..In contrast, we observed no change in the level of DNA supercoiling under the feedback conditions examined...
  39. ncbi Transcription analyses with heteroduplex trp attenuator templates indicate that the transcript stem and loop structure serves as the termination signal
    T Ryan
    J Biol Chem 258:4690-3. 1983
    ..This result strongly supports a model in which the formation of a stem and loop structure in the nascent RNA transcript is the signal for transcriptional termination...
  40. pmc DNA strand specificity in promoter recognition by RNA polymerase
    C 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...
  41. ncbi Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin
    C L Chan
    Department of Biology, Washington University, St Louis, MO 63130
    J Mol Biol 233:25-42. 1993
    ..We suggest that electrostatic interaction between the pause hairpin and RNA polymerase, rather than disruption of an RNA:DNA heteroduplex, delays elongation at the his leader pause site...
  42. pmc Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
    Joshua W Shaevitz
    Department of Physics, Stanford University, Stanford, California 94305, USA
    Nature 426:684-7. 2003
    ..Inosine triphosphate increased the frequency of backtracking pauses, whereas the accessory proteins GreA and GreB, which stimulate the cleavage of nascent RNA, decreased the duration of such pauses...
  43. ncbi High-throughput screening of RNA polymerase inhibitors using a fluorescent UTP analog
    Jyothi Bhat
    AstraZeneca India Pvt Ltd, Hebbal, Bangalore, India
    J Biomol Screen 11:968-76. 2006
    ..Activity of hits selected for the hit-to-lead optimization was also confirmed against Mycobacterium bovis RNAP which has >99% sequence identity with Mycobacterium tuberculosis RNAP subunits...
  44. pmc Functional map of the alpha subunit of Escherichia coli RNA polymerase: two modes of transcription activation by positive factors
    K Igarashi
    National Institute of Genetics, Department of Molecular Genetics, Shizuoka, Japan
    Proc Natl Acad Sci U S A 88:8958-62. 1991
    ..Two different mechanisms are proposed for the positive control of transcription by activator proteins, one requiring the C-terminal domain of the alpha subunit, and the other not requiring it...
  45. ncbi Transcription of the tryptophan operon in Escherichia coli: rifampicin as an inhibitor of initiation
    R D Mosteller
    J Mol Biol 48:525-31. 1970
  46. ncbi DNA sequence of the promoter region for the alpha ribosomal protein operon in Escherichia coli
    L E Post
    J Biol Chem 255:4653-59. 1980
    ..S13 gene is a part of the alpha operon and the gene order is promoter (P alpha), rpsM (S13), rpsK (S11), rpsD(S4), rpoA(alpha), and rplQ(L17). The DNA sequence extending 650 bases before S13 gene was determined...
  47. ncbi Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter
    A J Carpousis
    Biochemistry 19:3245-53. 1980
    ..Production of a long RNA transcript is then essentially an escape from this cycling reaction. The drug rifampicin, which drastically inhibits escape to produce RNA, limits, but dose not prevent, the cycling reaction...
  48. ncbi The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter
    A J Bokal
    Department of Bacteriology, University of Wisconsin Madison 53706
    J Mol Biol 245:197-207. 1995
    ....
  49. pmc Conformational changes in E. coli RNA polymerase during promoter recognition
    K L Brodolin
    W A Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
    Nucleic Acids Res 21:5748-53. 1993
    ..In presence of lac repressor before or after formation of the RPO cross-linking pattern is similar with that of RPI (RPC) complex...
  50. ncbi The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase
    E Nudler
    Public Health Research Institute, New York, New York 10016, USA
    Cell 89:33-41. 1997
    ..Thus, the 3'-proximal RNA-DNA hybrid plays the dual role of keeping the active site in register with the template and sensing the helix-destabilizing mismatches in RNA, launching correction through backtracking and cleavage...
  51. pmc RNA polymerase sigma factor determines start-site selection but is not required for upstream promoter element activation on heteroduplex (bubble) templates
    K Fredrick
    Section of Microbiology, Cornell University, Ithaca, NY 14853 8101, USA
    Proc Natl Acad Sci U S A 94:4982-7. 1997
    ..Thus, sigmaA appears to recognize the -10 region even in a single-stranded state. We propose that in addition to its described roles in promoter recognition and start-site melting, sigma also localizes the transcription start site...
  52. ncbi Force and velocity measured for single molecules of RNA polymerase
    M D Wang
    Department of Molecular Biology and Princeton Materials Institute, Princeton University, Princeton, NJ 08544, USA
    Science 282:902-7. 1998
    ..This contrasts with previous models that assumed force acts directly upon a single-base translocation step...
  53. ncbi Systematic search for zinc-binding proteins in Escherichia coli
    Akira Katayama
    National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka, Japan
    Eur J Biochem 269:2403-13. 2002
    ..coli increased up to more than 30 species (or more than 3% of about 1000 proteins expressed under laboratory culture conditions). The specificity and affinity of zinc-binding were analysed for some of the zinc-binding proteins...
  54. ncbi The cell surface protein Ag43 facilitates phage infection of Escherichia coli in the presence of bile salts and carbohydrates
    Magdalena Gabig
    Department of Molecular Biology, University of Gdansk, Kładki 24, 80 822 Gdansk, Poland
    Microbiology 148:1533-42. 2002
    ..that the promoter for the agn43 gene was more active in the rpoA341 mutant than in the otherwise isogenic rpoA(+) strain...
  55. ncbi Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting
    Anita 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
    ....
  56. pmc Actin homolog MreB and RNA polymerase interact and are both required for chromosome segregation in Escherichia coli
    Thomas Kruse
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, DK 5230 Odense M, Denmark
    Genes Dev 20:113-24. 2006
    ..Thus, our results raise the possibility that the MreB-RNAP interaction is functionally important for chromosome segregation...
  57. ncbi Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli
    L E Post
    J Biol Chem 254:10604-6. 1979
    ..This short distance supports the idea that some post-transcriptional regulation determines the differential synthesis of alpha and ribosomal proteins...
  58. ncbi Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein
    F 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...
  59. ncbi Functional importance of sequence in the stem-loop of a transcription terminator
    S 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...
  60. pmc Protein-DNA cross-linking at the lac promoter
    M 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...
  61. ncbi Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography
    S A Darst
    Department of Cell Biology, Beckman Laboratories, Stanford, California 94305
    Nature 340:730-2. 1989
    ..In the light of functional similarities between these two enzymes, together with other evidence, this probably identifies the active-site region of RNA polymerase...
  62. pmc phs Locus of Escherichia coli, a mutation causing pleiotropic lesions in metabolism, is an rpoA allele
    G C Rowland
    J Bacteriol 164:972-5. 1985
    The phs mutation, which causes a pleiotropic growth defect, has been mapped and shown to be an allele of rpoA, the gene for the alpha subunit of RNA polymerase...
  63. ncbi A bacterial gene involved in transcription antitermination: regulation at a rho-independent terminator in the bgl operon of E. coli
    S 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...
  64. ncbi Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter
    M E Mulligan
    J Biol Chem 260:3529-38. 1985
    ..The choice of start point for transcription is affected by spacer length. Transcription from all the promoters was stimulated at moderate concentrations of salt (less than 150 mM) and persisted at high salt concentrations (300 mM)...
  65. ncbi Studies of the binding of Escherichia coli RNA polymerase to DNA. I. The role of sigma subunit in site selection
    D C Hinkle
    J Mol Biol 70:157-85. 1972
  66. ncbi RNA synthesis in Escherichia coli after irradiation with ultraviolet light
    H Michalke
    J Mol Biol 41:1-23. 1969
  67. pmc Compilation and analysis of Escherichia coli promoter DNA sequences
    D 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...
  68. ncbi Genetic studies of the phs locus of Escherichia coli, a mutation causing pleiotropic lesions in metabolism and pH homeostasis
    G C Rowland
    FEBS Lett 173:295-300. 1984
    In Escherichia coli a pleiotropic mutation, phs, has been reported to affect Na+-linked metabolic functions and pH homeostasis. The phs mutation was previously mapped by its proximity to a met marker, presumed to be metB at 89 min...
  69. pmc NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes
    K Liu
    Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
    Proc Natl Acad Sci U S A 92:5012-6. 1995
    ..coli S100 cell extract. Peptide mapping localized the RNA interactions to the C-terminal domain of alpha...
  70. ncbi Coupling between transcription termination and RNA polymerase inchworming
    E 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...
  71. ncbi Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength
    L 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...
  72. pmc Ribosomal RNA antitermination in vitro: requirement for Nus factors and one or more unidentified cellular components
    C L Squires
    Department of Biological Sciences, Columbia University, New York, NY 10027
    Proc Natl Acad Sci U S A 90:970-4. 1993
    ..The DNA template requirements were the same as those previously established in vivo; transcription of a wild-type boxA sequence is both necessary and sufficient to promote RNA polymerase modification into a terminator-resistant form...
  73. pmc Compilation of E. coli mRNA promoter sequences
    S Lisser
    Department of Molecular Genetics, Hebrew University Hadassah Medical School, Jerusalem, Israel
    Nucleic Acids Res 21:1507-16. 1993
    ..We comment on the reliability of the sequence databanks and analyze the conservation of known promoter features in the current compilation. This database is available by E-mail...
  74. pmc Determinants of RNA polymerase alpha subunit for interaction with beta, beta', and sigma subunits: hydroxyl-radical protein footprinting
    T Heyduk
    Department of Biochemistry and Molecular Biology, St Louis University Medical School, MO 63104, USA
    Proc Natl Acad Sci U S A 93:10162-6. 1996
    ..e., 50% protection). We propose that only one of the two alpha protomers of RNAP interacts with beta and that only one of the two alpha protomers of RNAP interacts with beta'...
  75. ncbi A nested set of C-terminal deletions of the alpha subunit of Escherichia coli RNA polymerase define regions concerned with assembly, proteolysis, stabilization and transcriptional activation in vivo
    C Zou
    Department of Biochemistry, Queen s Medical Centre, Nottingham, UK
    Genes Cells 2:81-94. 1997
    ..One particular C-terminal alpha mutant, rpoA341, impairs the response of Escherichia coli RNA polymerase to several activators, including MelR...
  76. ncbi Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain
    Y H Jeon
    Institute for Protein Research, Osaka University, Suita, Japan
    J Mol Biol 267:953-62. 1997
    ..The dynamics data also revealed that the residues in the contact site for DNA and transcription factors exhibited higher mobility than other secondary structural elements...
  77. ncbi The effect of a nested set of C-terminal substituted deletions on the function of the alpha subunit of Escherichia coli RNA polymerase
    M S Thomas
    Division of Genetics, School of Clinical Laboratory Sciences, Queen s Medical Centre, Nottingham University, U K
    Int J Biochem Cell Biol 29:1475-83. 1997
    A genetic screen was devised to obtain plasmid-borne rpoA alleles exhibiting partial or no complementation of the chromosomal Escherichia coli rpoA341 allele responsible for a pleiotropic phenotype...
  78. ncbi Spatial organization of transcription elongation complex in Escherichia coli
    E 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...
  79. ncbi The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase
    M Buckle
    Unité de Physicochimie des Macromolécules Biologiques UMR 1773 du CNRS, Institut Pasteur, 25 rue du Dr Roux, Paris Cedex, 75724
    J Mol Biol 285:955-64. 1999
    ..Sigma thus appears as the principal partner acting during promoter recognition, a strongly coupled process involving two major intermediates only...
  80. ncbi Curvature of dinucleotide poised for formation of trinucleotide in transcription with Escherichia coli RNA polymerase
    C 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...
  81. pmc BglG, the transcriptional antiterminator of the bgl system, interacts with the beta' subunit of the Escherichia coli RNA polymerase
    A 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...
  82. pmc Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA
    E Zaychikov
    Max Planck Institut fur Biochemie, Am Klopferspitz 18a, D82152 Martinsried, Germany
    Nucleic Acids Res 27:3645-52. 1999
    ..We suggest that the periodicity of the bending angle reflects periodic changes of the conformation of the halted complexes that might have relevance for the translocation mechanism...
  83. pmc Role of the RNA polymerase alpha subunits in MetR-dependent activation of metE and metH: important residues in the C-terminal domain and orientation requirements within RNA polymerase
    P S Fritsch
    Molecular Biology Graduate Program, The University of Iowa, Iowa City, Iowa 52242, USA
    J Bacteriol 182:5539-50. 2000
    ..We propose that the different alphaCTD requirements at these two promoters are due to a combination of the difference in the location of the activation site and limits on the rotational flexibility of the alphaCTD...
  84. ncbi RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA
    Laura 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...
  85. ncbi Toxicity of the bacteriophage lambda cII gene product to Escherichia coli arises from inhibition of host cell DNA replication
    Barbara Kedzierska
    Department of Molecular Biology, University of Gdansk, Kladki 24, 80 822 Gdansk, Poland
    Virology 313:622-8. 2003
    ..Moreover, inhibition of cell growth, caused by both wild-type and mutant CII proteins in either rpoA(+) or rpoA341 hosts, could be relieved by overexpression of the E. coli dnaB and dnaC genes...
  86. ncbi Location of the Escherichia coli RNA polymerase alpha subunit C-terminal domain at an FNR-dependent promoter: analysis using an artificial nuclease
    Anne M L Barnard
    School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
    FEBS Lett 558:13-8. 2004
    ..coli transcription activator that is related to FNR. In complementary experiments, we show that the second alpha subunit C-terminal domain of RNA polymerase can be repositioned by upstream-bound CRP, but not by upstream-bound FNR...
  87. pmc Association of RNA polymerase with transcribed regions in Escherichia coli
    Joseph 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...
  88. pmc Escherichia coli RNA polymerase recognition of a sigma70-dependent promoter requiring a -35 DNA element and an extended -10 TGn motif
    India 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...
  89. pmc GreA protein: a transcription elongation factor from Escherichia coli
    S 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...
  90. ncbi Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical properties
    B 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...
  91. pmc Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase
    K Igarashi
    Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
    Nucleic Acids Res 18:5945-8. 1990
    The rpoA gene of Escherichia coli encodes the alpha subunit of the DNA-dependent RNA polymerase...
  92. ncbi Interaction of RNA polymerase with lacUV5 promoter DNA during mRNA initiation and elongation. Footprinting, methylation, and rifampicin-sensitivity changes accompanying transcription initiation
    A J Carpousis
    J Mol Biol 183:165-77. 1985
    ..Subsequently, when a chain of ten bases, or slightly longer, is made, contacts with promoter DNA are irreversibly disrupted, sigma subunit is lost, and a "true" elongation complex is formed...
  93. ncbi Ribosomal RNA operon anti-termination. Function of leader and spacer region box B-box A sequences and their conservation in diverse micro-organisms
    K 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...
  94. ncbi Terminators of transcription with RNA polymerase from Escherichia coli: what they look like and how to find them
    V 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...
  95. ncbi Unstable mutations caused by regional tandem multiplications in the gene for ribosomal protein S4 show thermosensitivity in Escherichia coli
    J Schnier
    Mol Gen Genet 199:265-70. 1985
    ..We postulate that the two mutant genes that contain regional multiplications possibly take an intra-strands secondary structure, which is cleaved to regenerate the wild-type sequence, probably during DNA replication...
  96. ncbi Initiation by Escherichia coli RNA-polymerase: transformation of abortive to productive complex
    M A Grachev
    FEBS Lett 115:23-6. 1980
  97. pmc DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription
    F 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...
  98. pmc Primary and secondary structure specificity of the cleavage of 'single-stranded' DNA by endonuclease Hinf I
    B 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...
  99. ncbi The alpha subunit of RNA polymerase and transcription antitermination
    A T Schauer
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109 0620, USA
    Mol Microbiol 21:839-51. 1996
    ..A deletion of the 3' terminus of rpoA, resulting in the expression of an alpha subunit missing the CTD, also enhances N-mediated antitermination and, ..

Research Grants6

  1. STRUCTURAL PARAMETERS OF E COLI RNA POLYMERASE
    Seth Darst; Fiscal Year: 2001
    ....
  2. Structure & Function of Prokaryotic Transcript Cleavage
    Sergei Borukhov; Fiscal Year: 2005
    ..abstract_text> ..
  3. Upgrade of in-house X-ray diffraction equipment
    Seth Darst; Fiscal Year: 2006
    ..unreadable] [unreadable]..
  4. Structure/Function of the Bacterial TRCF
    Seth Darst; Fiscal Year: 2008
    ..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. ..
  5. X-RAY CRYSTALLOGRAPHIC STUDIES OF TAQ RNA POLYMERASE
    Seth Darst; Fiscal Year: 2008
    ..Determine the crystal structure of RNAP with the transcription elongation factor GreA/B; 5. Determine the crystal structure of T. thermophilus sigma (E) holoenzyme. ..
  6. Structural Basis for Sporulation in Bacillus
    Seth A Darst; Fiscal Year: 2010
    ..4. Structurally characterize the ?F regulatory system (?F/SpollAA/SpollAB/SpollE) controlling the initiation of Bacillus sporulation. ..