NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.

Multi-subunit RNA polymerases bind nucleotide triphosphate (NTP) substrates in the pretranslocated state and carry the dNMP-NTP base pair into the active site for phosphoryl transfer. NTP-driven translocation requires that NTP substrates enter the main-enzyme channel before loading into the active site. Based on this model, a new view of fidelity and efficiency of RNA synthesis is proposed. The model predicts that, during processive elongation, NTP-driven translocation is coupled to a protein conformational change that allows pyrophosphate release: coupling the end of one bond-addition cycle to substrate loading and translocation for the next. We present a detailed model of the RNA polymerase II elongation complex based on 2 low-affinity NTP binding sites located in the main-enzyme channel. This model posits that NTP substrates, elongation factors, and the conserved Rpb2 subunit fork loop 2 cooperate to regulate opening of the downstream transcription bubble.

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

[2]  J. Arnold,et al.  Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective☆ , 2004, Virus Research.

[3]  Michelle D. Wang,et al.  Molecular mechanism of transcription inhibition by peptide antibiotic Microcin J25. , 2004, Molecular cell.

[4]  R. Landick.  Active-Site Dynamics in RNA Polymerases , 2004, Cell.

[5]  Chunfen Zhang,et al.  Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism. , 2004, Journal of molecular biology.

[6]  Patrick Cramer,et al.  Structural basis of transcription: α-Amanitin–RNA polymerase II cocrystal at 2.8 Å resolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Michael Feig,et al.  Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. , 2005, Molecular cell.

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

[9]  Smita S. Patel,et al.  Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. , 1991, Biochemistry.

[10]  P. Cramer,et al.  Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution , 2001, Science.

[11]  W. Wooster,et al.  Crystal structure of , 2005 .

[12]  Sean J. Johnson,et al.  Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[13]  G. Montelione,et al.  Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. , 2003, Journal of the American Chemical Society.

[14]  George Oster,et al.  Ratchets, power strokes, and molecular motors , 2002 .

[15]  Christophe Benoist,et al.  Structural Basis for the Transition from Initiation to Elongation Transcription in T 7 RNA Polymerase , 2022 .

[16]  R. Sousa.  On models and methods for studying polymerase translocation. , 2003, Methods in enzymology.

[17]  H. Handa,et al.  Assay of transient state kinetics of RNA polymerase II elongation. , 2003, Methods in enzymology.

[18]  Ulf Göransson,et al.  Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone. , 2003, Journal of the American Chemical Society.

[19]  Thomas A. Steitz,et al.  Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase , 2002, Science.

[20]  D. Erie,et al.  Downstream DNA Sequence Effects on Transcription Elongation , 2003, Journal of Biological Chemistry.

[21]  Zachary F. Burton,et al.  Human RNA Polymerase II Elongation in Slow Motion: Role of the TFIIF RAP74 α1 Helix in Nucleoside Triphosphate-Driven Translocation , 2005, Molecular and Cellular Biology.

[22]  P. Cramer,et al.  Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. , 2004, Molecular cell.

[23]  George Oster,et al.  Brownian ratchets: Darwin's motors , 2002, Nature.

[24]  Thomas A Steitz,et al.  The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase , 2004, Cell.

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

[26]  M. Kashlev,et al.  The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex* , 2000, The Journal of Biological Chemistry.

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

[28]  Sean J. Johnson,et al.  Structures of Mismatch Replication Errors Observed in a DNA Polymerase , 2004, Cell.

[29]  D. Erie,et al.  Allosteric Binding of Nucleoside Triphosphates to RNA Polymerase Regulates Transcription Elongation , 2001, Cell.

[30]  J. Arnold,et al.  Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg2+. , 2004, Biochemistry.

[31]  D. Bushnell,et al.  Structural Basis of Transcription Nucleotide Selection by Rotation in the RNA Polymerase II Active Center , 2004, Cell.

[32]  K. Johnson,et al.  Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates. , 1995, Methods in enzymology.

[33]  R. Sousa.  Machinations of a Maxwellian Demon , 2005, Cell.

[34]  B. Chait,et al.  Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail. , 2003, Journal of the American Chemical Society.

[35]  D. Bushnell,et al.  Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II , 2004, Science.

[36]  Hiroshi Handa,et al.  NTP-driven Translocation by Human RNA Polymerase II* , 2003, The Journal of Biological Chemistry.

[37]  Kenneth A. Johnson,et al.  1 Transient-State Kinetic Analysis of Enzyme Reaction Pathways , 1992 .

[38]  J. Arnold,et al.  Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn2+. , 2004, Biochemistry.

[39]  Honggao Yan,et al.  Combinatorial Control of Human RNA Polymerase II (RNAP II) Pausing and Transcript Cleavage by Transcription Factor IIF, Hepatitis δ Antigen, and Stimulatory Factor II* , 2003, Journal of Biological Chemistry.

[40]  R. Sousa,et al.  A model for the mechanism of polymerase translocation. , 1997, Journal of molecular biology.

[41]  M. Levitt,et al.  Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Shigeyuki Yokoyama,et al.  Structural Basis for Substrate Selection by T7 RNA Polymerase , 2004, Cell.

[43]  Y. Nedialkov,et al.  α-Amanitin Blocks Translocation by Human RNA Polymerase II* , 2004, Journal of Biological Chemistry.