Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

A combination of structural approaches yields a complete atomic model of the highly biochemically characterized Escherichia coli RNA polymerase, enabling fuller exploitation of E. coli as a model for understanding transcription.

[1]  W. Lane,et al.  Molecular evolution of multisubunit RNA polymerases: sequence analysis. , 2010, Journal of molecular biology.

[2]  W. Lane,et al.  Molecular evolution of multisubunit RNA polymerases: structural analysis. , 2010, Journal of molecular biology.

[3]  R. Ebright,et al.  Three-dimensional EM structure of an intact activator-dependent transcription initiation complex , 2009, Proceedings of the National Academy of Sciences.

[4]  T. Pape,et al.  Organization of an Activator-Bound RNA Polymerase Holoenzyme , 2008, Molecular cell.

[5]  Stephen C Harvey,et al.  YUP.SCX: coaxing atomic models into medium resolution electron density maps. , 2008, Journal of structural biology.

[6]  Craig D. Kaplan,et al.  The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin. , 2008, Molecular cell.

[7]  J. Strathern,et al.  Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation. , 2008, Molecular cell.

[8]  Qing Jun Wang,et al.  Rapid isolation and identification of bacteriophage T4-encoded modifications of Escherichia coli RNA polymerase: a generic method to study bacteriophage/host interactions. , 2008, Journal of proteome research.

[9]  Serge X. Cohen,et al.  Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 , 2008, Nature Protocols.

[10]  G. Sheldrick.  A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[11]  Henning Urlaub,et al.  GraFix: sample preparation for single-particle electron cryomicroscopy , 2008, Nature Methods.

[12]  Enoch S. Huang,et al.  PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments , 2007, BMC Bioinformatics.

[13]  Tahir H. Tahirov,et al.  Structural basis for transcription elongation by bacterial RNA polymerase , 2007, Nature.

[14]  Jonathan Tennyson,et al.  Water vapour in the atmosphere of a transiting extrasolar planet , 2007, Nature.

[15]  Irina Artsimovitch,et al.  Structural basis for substrate loading in bacterial RNA polymerase , 2007, Nature.

[16]  Chao Yang,et al.  SPARX, a new environment for Cryo-EM image processing. , 2007, Journal of structural biology.

[17]  Craig D. Kaplan,et al.  Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis , 2006, Cell.

[18]  K. Severinov,et al.  Localization of the Escherichia coli RNA Polymerase β′ Subunit Residue Phosphorylated by Bacteriophage T7 Kinase Gp0.7 , 2006, Journal of bacteriology.

[19]  K. Murakami,et al.  Structure and function of lineage-specific sequence insertions in the bacterial RNA polymerase beta' subunit. , 2005, Journal of molecular biology.

[20]  Arkady Mustaev,et al.  A Ratchet Mechanism of Transcription Elongation and Its Control , 2005, Cell.

[21]  E. Geiduschek,et al.  The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[23]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[24]  David Baker,et al.  Protein structure prediction and analysis using the Robetta server , 2004, Nucleic Acids Res..

[25]  E. Koonin,et al.  Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. , 2004, Gene.

[26]  Jennifer L. Knight,et al.  Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. , 2004, Molecular cell.

[27]  A. Greenleaf,et al.  Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila , 2004, Molecular and General Genetics MGG.

[28]  William J. Rice,et al.  Structure and Function of the Transcription Elongation Factor GreB Bound to Bacterial RNA Polymerase , 2003, Cell.

[29]  K. Murakami,et al.  Co-overexpression of Escherichia coliRNA Polymerase Subunits Allows Isolation and Analysis of Mutant Enzymes Lacking Lineage-specific Sequence Insertions* , 2003, The Journal of Biological Chemistry.

[30]  Jimin Pei,et al.  PCMA: fast and accurate multiple sequence alignment based on profile consistency , 2003, Bioinform..

[31]  E. Koonin,et al.  Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases , 2003, BMC Structural Biology.

[32]  S. Nechaev,et al.  Mutations of Bacterial RNA Polymerase Leading to Resistance to Microcin J25* , 2002, The Journal of Biological Chemistry.

[33]  Francisco J Asturias,et al.  Structure of yeast RNA polymerase II in solution: implications for enzyme regulation and interaction with promoter DNA. , 2002, Structure.

[34]  S. Yokoyama,et al.  Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution , 2002, Nature.

[35]  K. Murakami,et al.  Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution , 2002, Science.

[36]  K. Murakami,et al.  Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex , 2002, Science.

[37]  Willy Wriggers,et al.  Conformational flexibility of bacterial RNA polymerase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[39]  R. Farías,et al.  Escherichia coli RNA Polymerase Is the Target of the Cyclopeptide Antibiotic Microcin J25 , 2001, Journal of bacteriology.

[40]  S. Darst,et al.  A Structural Model of Transcription Elongation , 2000 .

[41]  S. Darst,et al.  The anti-σ factor SpoIIAB forms a 2:1 complex with σ F, contacting multiple conserved regions of the σ factor 1 1 Edited by R. Ebright , 2000 .

[42]  K. Severinov,et al.  Direct localization of a beta-subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[43]  K. Severinov,et al.  Direct localization of a b -subunit domain on the three-dimensional structure of Escherichia coli RNA polymerase , 2000 .

[44]  W Chiu,et al.  EMAN: semiautomated software for high-resolution single-particle reconstructions. , 1999, Journal of structural biology.

[45]  K. Severinov,et al.  Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution , 1999, Cell.

[46]  K. Severinov,et al.  Mutations in and Monoclonal Antibody Binding to Evolutionary Hypervariable Region of Escherichia coli RNA Polymerase β′ Subunit Inhibit Transcript Cleavage and Transcript Elongation* , 1998, The Journal of Biological Chemistry.

[47]  K. Severinov,et al.  The Largest Subunits of RNA Polymerase from Gastric Helicobacters Are Tethered* , 1998, The Journal of Biological Chemistry.

[48]  S. Darst,et al.  Structure of the Escherichia coli RNA Polymerase α Subunit Amino-Terminal Domain , 1998 .

[49]  Irina Artsimovitch,et al.  Information Processing by RNA Polymerase: Recognition of Regulatory Signals during RNA Chain Elongation , 1998, Journal of bacteriology.

[50]  A. T. Basokur,et al.  Digital filter design using the hyperbolic tangent functions 1 , 1998 .

[51]  K. Severinov,et al.  Tethering of the Large Subunits of Escherichia coli RNA Polymerase* , 1997, The Journal of Biological Chemistry.

[52]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[53]  I. Rayment.  Reductive alkylation of lysine residues to alter crystallization properties of proteins. , 1997, Methods in enzymology.

[54]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[55]  S. Doublié.  Preparation of selenomethionyl proteins for phase determination. , 1997, Methods in enzymology.

[56]  Ivan Rayment,et al.  [12] Reductive alkylation of lysine residues to alter crystallization properties of proteins. , 1997, Methods in enzymology.

[57]  C. Gross,et al.  A structure/function analysis of Escherichia coli RNA polymerase. , 1996, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[58]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[59]  M. Karplus,et al.  Evaluation of comparative protein modeling by MODELLER , 1995, Proteins.

[60]  R. Landick,et al.  Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. , 1994, Genes & development.

[61]  K. Severinov,et al.  A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc. , 1994, The Journal of biological chemistry.

[62]  J. Frank,et al.  The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. , 1994, Ultramicroscopy.

[63]  R. Farías,et al.  Microcin 25, a novel antimicrobial peptide produced by Escherichia coli , 1992, Journal of bacteriology.

[64]  J. Luo,et al.  Characterization and epitope mapping of monoclonal antibodies directed against the beta' subunit of the Escherichia coli RNA polymerase. , 1992, The Journal of biological chemistry.

[65]  K. Severinov,et al.  Mapping of trypsin cleavage and antibody-binding sites and delineation of a dispensable domain in the beta subunit of Escherichia coli RNA polymerase. , 1991, The Journal of biological chemistry.

[66]  W A Hendrickson,et al.  Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three‐dimensional structure. , 1990, The EMBO journal.

[67]  L. Snyder,et al.  Escherichia coli mutations that prevent the action of the T4 unf/alc protein map in an RNA polymerase gene. , 1988, Genetics.

[68]  R. Young,et al.  Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[69]  M. Heel,et al.  Exact filters for general geometry three dimensional reconstruction , 1986 .

[70]  V. Nene,et al.  Genetic studies on the beta subunit of Escherichia coli RNA polymerase. VI. A redundant region in the beta polypeptide. , 1984, Molecular & general genetics : MGG.

[71]  W. O. Saxton,et al.  The correlation averaging of a regularly arranged bacterial cell envelope protein , 1982, Journal of microscopy.

[72]  L. Gold,et al.  A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[73]  W. Zillig,et al.  In vivo and in vitro phosphorylation of DNA-dependent RNA polymerase of Escherichia coli by bacteriophage-T7-induced protein kinase. , 1975, Proceedings of the National Academy of Sciences of the United States of America.