rpoD

Summary

Gene Symbol: rpoD
Description: RNA polymerase, sigma 70 (sigma D) factor
Alias: ECK3057, JW3039, alt
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. ncbi rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase
    Shanil P Haugen
    Department of Bacteriology, University of Wisconsin Madison, 420 Henry Mall, 53706, USA
    Cell 125:1069-82. 2006
  2. pmc Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element
    Nikolay Zenkin
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
    EMBO J 26:955-64. 2007
  3. pmc Fine structure of the promoter-sigma region 1.2 interaction
    Shanil P Haugen
    Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 105:3292-7. 2008
  4. pmc The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase
    India G 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, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 106:737-42. 2009
  5. pmc Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation
    Nataliya Miropolskaya
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
    J Biol Chem 287:23779-89. 2012
  6. ncbi Both regions 4.1 and 4.2 of E. coli sigma(70) are together required for binding to bacteriophage T4 AsiA in vivo
    Umender K Sharma
    AstraZeneca R and D, Bellary Road, Hebbal, Bangalore, India Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Gene 376:133-43. 2006
  7. pmc The sigma 70 family: sequence conservation and evolutionary relationships
    M Lonetto
    Department of Bacteriology, University of Wisconsin, Madison 53706
    J Bacteriol 174:3843-9. 1992
  8. ncbi Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex
    S C Gill
    Department of Chemistry, University of Oregon, Eugene 97403
    J Mol Biol 220:307-24. 1991
  9. ncbi A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity
    T Gardella
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01605
    J Mol Biol 206:579-90. 1989
  10. ncbi Factor stimulating transcription by RNA polymerase
    R R Burgess
    Nature 221:43-6. 1969

Research Grants

Scientific Experts

Detail Information

Publications138 found, 100 shown here

  1. ncbi rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase
    Shanil P Haugen
    Department of Bacteriology, University of Wisconsin Madison, 420 Henry Mall, 53706, USA
    Cell 125:1069-82. 2006
    ..2-discriminator interaction, rRNA promoters create the short-lived complex required for specific responses to the RNAP binding factors ppGpp and DksA, ultimately accounting for regulation of ribosome synthesis...
  2. pmc Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element
    Nikolay Zenkin
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
    EMBO J 26:955-64. 2007
    ..2 acts as a core RNA polymerase-dependent allosteric switch that modulates non-template DNA strand recognition by sigma region 2 during transcription initiation and elongation...
  3. pmc Fine structure of the promoter-sigma region 1.2 interaction
    Shanil P Haugen
    Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
    Proc Natl Acad Sci U S A 105:3292-7. 2008
    ..2. Our results refine models of RNAP-DNA interactions in the promoter complex that are crucial for regulation of transcription initiation...
  4. pmc The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase
    India G 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, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 106:737-42. 2009
    ..We speculate that the spacer can influence the trajectory or flexibility of DNA as it enters the RNAP channel and that region 1.1 acts as a "gatekeeper" to monitor channel entry...
  5. pmc Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation
    Nataliya Miropolskaya
    Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
    J Biol Chem 287:23779-89. 2012
    ..1 and 1.2 affecting promoter complex stability and region 1.2 involved in DNA melting during initiation...
  6. ncbi Both regions 4.1 and 4.2 of E. coli sigma(70) are together required for binding to bacteriophage T4 AsiA in vivo
    Umender K Sharma
    AstraZeneca R and D, Bellary Road, Hebbal, Bangalore, India Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Gene 376:133-43. 2006
    ..1 and 4.2 fragments together also did not show any interaction with AsiA. The results presented here suggest that binding of AsiA to sigma(70), in vivo, requires the presence of both sub-domains of region 4 of sigma(70)...
  7. pmc The sigma 70 family: sequence conservation and evolutionary relationships
    M Lonetto
    Department of Bacteriology, University of Wisconsin, Madison 53706
    J Bacteriol 174:3843-9. 1992
  8. ncbi Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex
    S C Gill
    Department of Chemistry, University of Oregon, Eugene 97403
    J Mol Biol 220:307-24. 1991
    ..These results are used to begin to define the basic conformational states and interaction potentials of core polymerase in the various stages of the transcription cycle...
  9. ncbi A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity
    T Gardella
    Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester 01605
    J Mol Biol 206:579-90. 1989
    ..In strains carrying both the mutant and wild-type sigma gene (rpoD), the mutant sigma causes a large increase in the activity of mutant P22 ant promoters with A.T or C...
  10. ncbi Factor stimulating transcription by RNA polymerase
    R R Burgess
    Nature 221:43-6. 1969
  11. pmc The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing
    A J Dombroski
    Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston 77030, USA
    Proc Natl Acad Sci U S A 93:8858-62. 1996
    ..Our data support the idea that sigma makes simultaneous, productive contacts at both the -10 and the -35 regions of the promoter and discerns the spacing between these conserved regions...
  12. pmc Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase
    H Maeda
    National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka 411 8540, Japan
    Nucleic Acids Res 28:3497-503. 2000
    ..Taken together with the intracellular sigma levels, we tried to estimate the number of each holoenzyme form in growing E. coli cells...
  13. ncbi Interaction of sigma 70 with Escherichia coli RNA polymerase core enzyme studied by surface plasmon resonance
    A L Ferguson
    Department of Biology, University of York, P O Box 373, Heslington, YO10 5YW, York, UK
    FEBS Lett 481:281-4. 2000
    ..9x10(-7) M, and the dissociation rate constant for release of sigma from core, in the absence of DNA or transcription, was 4x10(-3) s(-1), corresponding to a half-life of about 200 s...
  14. ncbi What makes an Escherichia coli promoter sigma(S) dependent? Role of the -13/-14 nucleotide promoter positions and region 2.5 of sigma(S)
    G Becker
    Institut für Biologie Mikrobiologie, Freie Universitat Berlin, Königin Luise Str 12 16, 14195 Berlin, Germany
    Mol Microbiol 39:1153-65. 2001
    ..5 in sigmaS in transcription initiation. Moreover, we propose a consensus sequence for a sigmaS-selective promoter and discuss its emergence and functional properties from an evolutionary point of view...
  15. ncbi How sigma docks to RNA polymerase and what sigma does
    R R Burgess
    McArdle Laboratory for Cancer Research, University of Wisconsin Madison, 1400 University Avenue, Madison, WI 53706, USA
    Curr Opin Microbiol 4:126-31. 2001
    ..This region of beta' interacts with region 2.1-2.2 of sigma(70). Binding of this region of beta' to sigma(70) triggers a conformational change in sigma that allows it to bind to a -10 nontemplate promoter DNA strand oligonucleotide...
  16. ncbi Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals
    Araceli M Huerta
    Program of Computational Genomics, Nitrogen Fixation Center, UNAM, Cuernavaca, AP 565 A, Morelos 62100, Mexico
    J Mol Biol 333:261-78. 2003
    ..We suggest that transcriptional regulators as well as other functional promoters play an important role in keeping these latent signals suppressed...
  17. ncbi Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting
    Brian 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...
  18. ncbi The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter
    Bryce E Nickels
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 11:544-50. 2004
    ..Bioinformatic analysis suggests that promoter-proximal sigma(70)-dependent pauses may play a role in the regulation of many bacterial promoters...
  19. ncbi The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription
    Konstantin Brodolin
    Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 2, Moscow 123182, Russia
    Nat Struct Mol Biol 11:551-7. 2004
    ..In addition, we suggest that the sigma(70) subunit in the elongation complex may provide a target for regulation of gene expression...
  20. pmc Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters
    Huiquan Wang
    UC Davis Genome Center, University of California, Davis, California 95616, USA
    Genome Res 14:1575-84. 2004
    ..We describe how these observations may illuminate specific mechanisms of regulation, and assist in the computational identification of promoter locations in prokaryotes...
  21. ncbi A multiwell assay to isolate compounds inhibiting the assembly of the prokaryotic RNA polymerase
    Estelle 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...
  22. ncbi Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases
    Lisa A Schroeder
    Center for RNA Molecular Biology and Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106 4973, USA
    J Biol Chem 280:17422-9. 2005
    ..A model is presented for how this mechanistic difference between the two RNA polymerase could explain our observations...
  23. ncbi Remodeling of the sigma70 subunit non-template DNA strand contacts during the final step of transcription initiation
    Konstantin Brodolin
    Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq 2, Moscow 123182, Russia
    J Mol Biol 350:930-7. 2005
    ..Establishment of downstream contacts leads to remodeling of upstream interactions between sigma70 and the -10 promoter element that might facilitate promoter escape and sigma release...
  24. pmc Mutational analysis of Escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter DNA melting and -10 recognition
    Olga V Kourennaia
    Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 4973, USA
    J Bacteriol 187:6762-9. 2005
    ..4 on the activities of the two sigma factors are consistent with the pronounced differences between both the amino acid sequences in this region and the recognized promoter DNA sequences...
  25. pmc SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes
    Huiquan Wang
    UC Davis Genome Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
    Nucleic Acids Res 34:D373-8. 2006
    ..SIDDBASE is available at www.gc.ucdavis.edu/benham/siddbase...
  26. ncbi Extensive functional overlap between sigma factors in Escherichia coli
    Joseph T Wade
    Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, Massachusetts 02115, USA
    Nat Struct Mol Biol 13:806-14. 2006
    ..SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon...
  27. pmc Selection for unequal densities of sigma70 promoter-like signals in different regions of large bacterial genomes
    Araceli M Huerta
    Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Mexico
    PLoS Genet 2:e185. 2006
    ....
  28. pmc Anatomy of Escherichia coli sigma70 promoters
    Ryan K Shultzaberger
    Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, PO Box B, Building 469, Room 144, Frederick, MD 21702 1201, USA
    Nucleic Acids Res 35:771-88. 2007
    ..Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the -35, so bending allows distal activators to reach the polymerase...
  29. ncbi The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase
    Athanasios Typas
    Institut fur Biologie, Mikrobiologie, Freie Universitat Berlin, Königin Luise Str 12 16, 14195 Berlin, Germany
    Mol Microbiol 63:1296-306. 2007
    ..it is known to recognize the same core promoter elements in vitro as the housekeeping sigma factor, sigma70 (RpoD)...
  30. ncbi The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "extended minus 10" promoter
    A Kumar
    Institute of Cell and Molecular Biology, University of Edinburgh, Scotland, U K
    J Mol Biol 232:406-18. 1993
    ....
  31. ncbi Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase
    A Malhotra
    Rockefeller University, New York, New York 10021, USA
    Cell 87:127-36. 1996
    ..The structure suggests one way in which DNA interactions may be inhibited in the absence of RNA polymerase and provides a framework for the interpretation of a large number of genetic and biochemical analyses...
  32. ncbi Isolation and characterization of mutations in region 1.2 of Escherichia coli sigma70
    N E Baldwin
    Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, 6431 Fannin JFB 1 765, Houston, TX 77030, USA
    Mol Microbiol 42:427-37. 2001
    ..2 during transcription initiation. In this study, we show that mutations in region 1.2 can affect promoter binding, open complex and initiated complex formation and the transition from abortive transcription to elongation...
  33. ncbi Substitutions in the Escherichia coli RNA polymerase sigma70 factor that affect recognition of extended -10 elements at promoters
    Andrew Sanderson
    School of Biosciences, The University of Birmingham, UK
    FEBS Lett 544:199-205. 2003
    ..Our study shows that changes in these regions of the sigma(70) subunit can affect the recognition of different extended -10 element sequences...
  34. pmc Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations
    Rachel Anne Mooney
    Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
    Genes Dev 17:2839-51. 2003
    ..We report that tethering sigma70 to all RNAP molecules via genetic fusion of rpoD to rpoC (encoding sigma70 and RNAP's beta' subunit, respectively) yields viable Escherichia coli strains in which ..
  35. ncbi Purification of highly-active and soluble Escherichia coli sigma 70 polypeptide overproduced at low temperature
    Huijun Zhi
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bldg 37, Rm 5144, Bethesda, Maryland 20892, USA
    Methods Enzymol 370:174-80. 2003
  36. pmc Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter
    Bianca Sclavi
    Max Planck Institute of Biochemistry, Am Klopferspitz 18a, D82152 Martinsried bei Munchen, Germany
    Proc Natl Acad Sci U S A 102:4706-11. 2005
    ..During the final isomerization step, the downstream double helix becomes embedded in the beta/beta' jaws, leading to a transcriptionally active complex...
  37. 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
    ....
  38. pmc The DnaK chaperone modulates the heat shock response of Escherichia coli by binding to the sigma 32 transcription factor
    K Liberek
    Department of Cellular, Viral and Molecular Biology, University of Utah Medical Center, Salt Lake City 84132
    Proc Natl Acad Sci U S A 89:3516-20. 1992
    ..Consistent with the fact that dnaK756 mutant bacteria overexpress heat shock proteins at all temperatures, purified DnaK756 mutant protein did not appreciably bind to sigma 32...
  39. ncbi Growth phase-dependent modification of RNA polymerase in Escherichia coli
    M 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...
  40. pmc Use of the polymerase chain reaction for physical mapping of Escherichia coli genes
    J Versalovic
    Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas
    J Bacteriol 173:5253-5. 1991
  41. ncbi Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase
    D A Siegele
    Department of Bacteriology, University of Wisconsin, Madison 53706
    J Mol Biol 206:591-603. 1989
    We have systematically assayed the in vivo promoter recognition properties of 13 mutations in rpoD, the gene that encodes the sigma 70 subunit of Escherichia coli RNA polymerase holoenzyme, using transcriptional fusions to 37 mutant and ..
  42. ncbi Genetic requirements for hyper-recombination by very short patch mismatch repair: involvement of Escherichia coli DNA polymerase I
    S Dzidic
    Institut Jacques Monod, Paris, France
    Mol Gen Genet 217:254-6. 1989
    ..The absence of endonuclease activities involved in the repair of base-loss sites, Nth, Nfo and Xth, does not affect VSP repair. Implications for the mechanism of the VSP repair are discussed...
  43. ncbi The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12
    Z F Burton
    Cell 32:335-49. 1983
    The sigma subunit of E. coli RNA polymerase is encoded by the rpoD gene...
  44. pmc The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12
    Z Burton
    Nucleic Acids Res 9:2889-903. 1981
    We have determined the nucleotide sequence of the rpoD gene which codes for the sigma subunit of RNA polymerase from E. coli K12...
  45. ncbi How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides
    M Astatke
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520, USA
    J Mol Biol 278:147-65. 1998
    ....
  46. pmc Interactions of Escherichia coli sigma(70) within the transcription elongation complex
    S S Daube
    Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA
    Proc Natl Acad Sci U S A 96:8390-5. 1999
    ....
  47. pmc Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase
    M Jishage
    National Institute of Genetics, Department of Molecular Genetics, Mishima, Shizuoka 411 8540, Japan
    J Bacteriol 183:2952-6. 2001
    ....
  48. pmc The roles of Klenow processing and flap processing activities of DNA polymerase I in chromosome instability in Escherichia coli K12 strains
    Yuki Nagata
    Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980 8578, Japan
    Genetics 160:13-23. 2002
    ..We therefore proposed the model that the Klenow domain can process deletion and minus frameshift mismatch in the nascent DNA and that flap nuclease can process plus frameshift and duplication mismatch in the nascent DNA...
  49. ncbi Free RNA polymerase and modeling global transcription in Escherichia coli
    H 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...
  50. ncbi Translocation of Escherichia coli RNA polymerase against a protein roadblock in vivo highlights a passive sliding mechanism for transcript elongation
    Christine Mosrin-Huaman
    Centre de Biophysique Moleculaire, CNRS, rue Charles Sadron, 45071 Orleans Cedex 2, France
    Mol Microbiol 51:1471-81. 2004
    ..They also suggest that fluctuations in the intracellular NTP pools may play a key role in gene regulation at the transcript elongation level...
  51. ncbi An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo
    Brian D Gregory
    Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
    Mol Microbiol 56:1208-19. 2005
    ..Our results demonstrate the utility of this altered-specificity system for genetically dissecting sigma(70) and its interactions with transcription regulators...
  52. pmc RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex
    Sebastian Maurer
    International University Bremen, Bremen, Germany
    EMBO J 25:3784-90. 2006
    ..We suggest that the architecture of the ternary complex provides a general paradigm for the facilitation of direct, but weak, interactions between polymerase and an activator...
  53. pmc A sigma-core interaction of the RNA polymerase holoenzyme that enhances promoter escape
    Mark Leibman
    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
    EMBO J 26:1579-90. 2007
    ..We also demonstrate that removal of the sigma(70) NCR results in a severe growth defect; we suggest that its importance for growth may reflect its role in promoter escape...
  54. pmc Regulator trafficking on bacterial transcription units in vivo
    Rachel A Mooney
    Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
    Mol Cell 33:97-108. 2009
    ..However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation...
  55. doi Potassium mediates Escherichia coli enzyme IIA(Ntr) -dependent regulation of sigma factor selectivity
    Chang Ro Lee
    Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151 742, Republic of Korea
    Mol Microbiol 78:1468-83. 2010
    ..Taken together, the data suggest that EIIA(Ntr) controls sigma factor selectivity by regulating the intracellular K(+) level...
  56. pmc Characterization of twenty-six new heat shock genes of Escherichia coli
    S E Chuang
    Laboratory of Genetics, University of Wisconsin Madison 53706
    J Bacteriol 175:5242-52. 1993
    ..Possible assignments of some of the hsl genes to known proteins are discussed...
  57. pmc Chromosomal location of a structural gene for the RNA polymerase sigma factor in Escherichia coli
    Y Nakamura
    Proc Natl Acad Sci U S A 74:1831-5. 1977
    ..typhimurium. These results indicate that a structural gene for sigma (rpoD) is located at the metC-argG region, probably near the dnaG locus (66 min on the current genetic map of E. coli).
  58. pmc Isolation and characterization of transducing phage coding for sigma subunit of Escherichia coli RNA polymerase
    C A Gross
    Proc Natl Acad Sci U S A 76:5789-93. 1979
    ..Phage containing the HindIII fragment complement both primase (dnaG) and sigma (rpoD) whereas those containing the Sac I fragment complement only sigma...
  59. ncbi Hyperproduction of the sigma subunit of RNA polymerase in a mutant of Escherichia coli
    Y Nakamura
    Mol Gen Genet 141:97-111. 1975
    ..The possible involvement of the core polymerase in determining the rate of synthesis of sigma subunit is discussed...
  60. ncbi Escherichia coli sigma 70 and NusA proteins. II. Physical properties and self-association states
    S C Gill
    Institute of Molecular Biology, University of Oregon, Eugene 97403
    J Mol Biol 220:325-33. 1991
    ..coli core RNA polymerase in solution and as a component of the functional transcription complex...
  61. pmc The 3'-5' exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction
    V Derbyshire
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510
    EMBO J 10:17-24. 1991
    ..The pH-dependence of the 3'-5' exonuclease reaction is consistent with a mechanism in which nucleophilic attack on the terminal phosphodiester bond is initiated by a hydroxide ion coordinated to one of the enzyme-bound metal ions...
  62. ncbi Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity
    R D Kuchta
    Department of Chemistry, Pennsylvania State University, University Park 16802
    Biochemistry 27:6716-25. 1988
    ....
  63. ncbi Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase
    W E Taylor
    Cell 38:371-81. 1984
    The rpoD gene encoding the sigma subunit of E. coli RNA polymerase is cotranscribed with rpsU and dnaG, encoding ribosomal protein S21 and DNA primase, respectively...
  64. ncbi Promoter selectivity control of Escherichia coli RNA polymerase by ionic strength: differential recognition of osmoregulated promoters by E sigma D and E sigma S holoenzymes
    Q Ding
    Department of Molecular Genetics, National Institute of Genetics, Shizuoka, Japan
    Mol Microbiol 16:649-56. 1995
    ....
  65. pmc Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions
    M Jishage
    Department of Molecular Genetics, National Institute of Genetics, Mishima, Japan
    J Bacteriol 178:5447-51. 1996
    ..Western immunoblot analysis, the intracellular levels of two principal sigma subunits, sigma 70 (sigma D, the rpoD gene product) and sigma 38 (sigma S, the rpoS gene product), and of two minor sigma subunits, sigma 54 (sigma N, ..
  66. ncbi Biochemical and mutational studies of the 5'-3' exonuclease of DNA polymerase I of Escherichia coli
    Y Xu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    J Mol Biol 268:284-302. 1997
    ..This finding is discussed in relation to structural and mutational data for related 5' nucleases...
  67. pmc Function-based selection and characterization of base-pair polymorphisms in a promoter of Escherichia coli RNA polymerase-sigma(70)
    J Xu
    Department of Biological Sciences, State University of New York at Buffalo, 14260 1300, USA
    J Bacteriol 183:2866-73. 2001
    ....
  68. 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
    ....
  69. pmc EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
    Weidong Tian
    Center of Excellence in Bioinformatics, University at Buffalo, The State University of New York, 901 Washington Street, Buffalo, NY 14203 1199, USA
    Nucleic Acids Res 32:6226-39. 2004
    ..Applied to Escherichia coli genome, EFICAz assigns more detailed enzymatic function than KEGG, and generates numerous novel predictions...
  70. 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...
  71. ncbi Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB
    Andrey 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...
  72. pmc Altering the interaction between sigma70 and RNA polymerase generates complexes with distinct transcription-elongation properties
    Yvonne Berghöfer-Hochheimer
    Department of Microbiology and Immunology and Stomatology, Genentech Hall, 600 16th Street, University of California, San Francisco, CA 94143, USA
    Proc Natl Acad Sci U S A 102:1157-62. 2005
    ..These states, in turn, may affect the conformational states adopted by the elongating enzyme, thereby physically and functionally imprinting RNA polymerase...
  73. pmc DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping
    Minsang Shin
    Genome Research Center for Enteropathogenic Bacteria and Research Institute of Vibrio Infection, Department of Microbiology, Chonnam National University Medical School, Kwangju 501 746, South Korea
    Genes Dev 19:2388-98. 2005
    ..Expression of this class of genes by Esigma38 in the stationary phase is not due to its promoter specificity but to the architecture of the promoter . Esigma38 complex...
  74. ncbi The recognition and prediction of sigma70 promoters in Escherichia coli K-12
    Qian Zhong Li
    Department of Physics, Laboratory of Theoretical Biophysics, College of Sciences and Technology, Inner Mongolia University, Hohhot 010021, China
    J Theor Biol 242:135-41. 2006
    ..coli K-12 with 4639221bp. Results show that the 100% of the 683 experimentally verified sigma(70) promoters have been identified and some possible promoters are predicted...
  75. pmc Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments
    Wayne S Kontur
    Department of Chemistry, University of Wisconsin Madison, 1101 University Ave, Madison, WI 53706 1322, USA
    J Mol Biol 376:1034-47. 2008
    ..The division of the large positive enthalpy change between the late steps of the mechanism suggests that an additional unstable intermediate (I(3)) may exist between I(2) and RP(o)...
  76. pmc A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E.coli sigma70 to activate middle gene transcription
    Richard P Bonocora
    Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, NIDDK, National Institutes of Health, Bethesda, MD, USA
    Mol Microbiol 69:331-43. 2008
    ..Our work supports accumulated evidence indicating that 'sigma appropriation' by MotA and AsiA uses a fundamentally different mechanism to activate transcription...
  77. pmc The secret to 6S: regulating RNA polymerase by ribo-sequestration
    Kimberly B Decker
    Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Microbiol 73:137-40. 2009
    ..Several residues that interact with 6S RNA are ones previously known to interact with protein activators of Esigma(70). Their work adds 6S RNA to the growing list of factors that can regulate Esigma(70) by interacting with region 4...
  78. pmc Increased RNA polymerase availability directs resources towards growth at the expense of maintenance
    Bertil 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...
  79. ncbi Effects of substitutions at position 180 in the Escherichia coli RNA polymerase σ 70 subunit
    Olga N Koroleva
    Chemical Faculty, Lomonosov Moscow State University, 119992 Moscow, Russia
    J Biosci 36:43-54. 2011
    ....
  80. ncbi Metal binding to DNA polymerase I, its large fragment, and two 3',5'-exonuclease mutants of the large fragment
    G P Mullen
    Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
    J Biol Chem 265:14327-34. 1990
    ..The essential divalent metal activator of the polymerase reaction requires the presence of the dNTP substrate for tight metal binding indicating that the bound substrate coordinates the metal.(ABSTRACT TRUNCATED AT 400 WORDS)..
  81. ncbi Mechanisms of error discrimination by Escherichia coli DNA polymerase I
    W S El-Deiry
    Department of Medicine, University of Miami School of Medicine, Florida 33101
    Biochemistry 27:546-53. 1988
    ..The mutagenic metal ion Mn2+ was found to affect error discrimination by both the polymerase and 3'- and 5'-exonuclease activities of DNA polymerase I.(ABSTRACT TRUNCATED AT 250 WORDS)..
  82. ncbi ALT: a new factor involved in the synthesis of RNA by Escherichia coli
    A E Silverstone
    Mol Gen Genet 118:223-34. 1972
  83. ncbi Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12
    J R Lupski
    Mol Gen Genet 195:391-401. 1984
    The regulatory regions for the rpsU-dnaG-rpoD macromolecular synthesis operon have been fused to a structural gene whose product is readily assayed (the Cmr structural gene coding for chloramphenicol acetyl transferase, CAT)...
  84. ncbi Regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon and the initiation of DNA replication in Escherichia coli K-12
    J R Lupski
    Mol Gen Genet 189:48-57. 1983
    ..This places the order on the E. coli genetic map at 66 min in the clockwise direction as rpsU-dnaG-rpoD which are all contained in a single macromolecular synthesis operon...
  85. ncbi A new mutation rpoD800, affecting the sigma subunit of E. coli RNA polymerase is allelic to two other sigma mutants
    H Liebke
    Mol Gen Genet 177:277-82. 1980
    ..locus affected by rpoD800 is shown to be allelic to the locus affected by the spontaneous mutants ts285 and alt-1. All three mutations result in altered sigma and in altered growth at high temperature...

Research Grants2

  1. X-Ray Crystallographic Studies of N4 RNA Polymerases
    Katsuhiko Murakami; Fiscal Year: 2008
    ..These studies will provide insights into the mechanism of transcription of the T7 bacteriophage-like single-subunit RNAP family, and specifically those enzymes in the family that require accessory factors. ..
  2. Structure & Function of Prokaryotic Transcript Cleavage
    Sergei Borukhov; Fiscal Year: 2005
    ..abstract_text> ..