Complete, 12-subunit RNA polymerase II at 4.1-Å resolution: Implications for the initiation of transcription

The x-ray structure of complete RNA polymerase II from Saccharomyces cerevisiae has been determined, including a heterodimer of subunits Rpb4 and Rpb7 not present in previous “core” polymerase II structures. The heterodimer maintains the polymerase in the conformation of a transcribing complex, may bind RNA as it emerges from the enzyme, and is in a position to interact with general transcription factors and the Mediator of transcriptional regulation.

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

[2]  J. Barnett,et al.  Deletion of the RNA Polymerase Subunit RPB4 Acts as a Global, Not Stress-specific, Shut-off Switch for RNA Polymerase II Transcription at High Temperatures* , 2001, The Journal of Biological Chemistry.

[3]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[4]  R. Young,et al.  RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth , 1989, Molecular and cellular biology.

[5]  M. Choder,et al.  Rpb7 Can Interact with RNA Polymerase II and Support Transcription during Some Stresses Independently of Rpb4 , 1999, Molecular and Cellular Biology.

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

[7]  G. Jensen,et al.  Structure of wild‐type yeast RNA polymerase II and location of Rpb4 and Rpb7 , 1998, The EMBO journal.

[8]  D. Bushnell,et al.  Yeast RNA polymerase II transcription reconstituted with purified proteins. , 1997, Methods.

[9]  R. Young,et al.  Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. , 1991, The Journal of biological chemistry.

[10]  B. Pillai,et al.  Rpb4, a Non-essential Subunit of Core RNA Polymerase II ofSaccharomyces cerevisiae Is Important for Activated Transcription of a Subset of Genes* , 2001, The Journal of Biological Chemistry.

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

[12]  R. Young,et al.  A portion of RNA polymerase II molecules has a component essential for stress responses and stress survival , 1993, Molecular and cellular biology.

[13]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[14]  P. Thuriaux,et al.  An Rpb4/Rpb7-Like Complex in Yeast RNA Polymerase III Contains the Orthologue of Mammalian CGRP-RCP , 2003, Molecular and Cellular Biology.

[15]  R. Kornberg,et al.  Mediator of transcriptional regulation. , 2000, Annual review of biochemistry.

[16]  Huiqing Zhou,et al.  An hsRPB4/7-dependent yeast assay for trans-activation by the EWS oncogene , 2001, Oncogene.

[17]  R. Young,et al.  RPB7, one of two dissociable subunits of yeast RNA polymerase II, is essential for cell viability , 1993, Yeast.

[18]  C. Carles,et al.  A Novel Subunit of Yeast RNA Polymerase III Interacts with the TFIIB-Related Domain of TFIIIB70 , 2000, Molecular and Cellular Biology.

[19]  G. Varani,et al.  RNA recognition by RNP proteins during RNA processing. , 1998, Annual review of biophysics and biomolecular structure.

[20]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[21]  P. Cramer,et al.  Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution , 2001, Science.

[22]  Roger D Kornberg,et al.  Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. , 2002, Molecular cell.

[23]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

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

[25]  M. Hampsey,et al.  The RNA Polymerase II Machinery Structure Illuminates Function , 2002, Cell.

[26]  Phan T. Tran,et al.  Dissociable Rpb4-Rpb7 Subassembly of RNA Polymerase II Binds to Single-strand Nucleic Acid and Mediates a Post-recruitment Step in Transcription Initiation* , 2001, The Journal of Biological Chemistry.

[27]  Aaron J. Shatkin,et al.  The ends of the affair: Capping and polyadenylation , 2000, Nature Structural Biology.

[28]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

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

[30]  C. Carles,et al.  The A14–A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4–Rpb7 pol II subunits , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[31]  A. Furger,et al.  Integrating mRNA Processing with Transcription , 2002, Cell.

[32]  D. Bushnell,et al.  The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. , 1998, Genes & development.

[33]  N. Woychik,et al.  Multiple Mechanisms of Suppression Circumvent Transcription Defects in an RNA Polymerase Mutant , 2000, Molecular and Cellular Biology.

[34]  D. Bushnell,et al.  A Minimal Set of RNA Polymerase II Transcription Protein Interactions* , 1996, The Journal of Biological Chemistry.

[35]  F Werner,et al.  Structure of an archaeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex. , 2001, Molecular cell.

[36]  M. Kimura,et al.  Formation of a Carboxy-Terminal Domain Phosphatase (Fcp1)/TFIIF/RNA Polymerase II (pol II) Complex in Schizosaccharomyces pombe Involves Direct Interaction between Fcp1 and the Rpb4 Subunit of pol II , 2002, Molecular and Cellular Biology.

[37]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[38]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[39]  C. J. Jeong,et al.  Evidence that Gal11 protein is a target of the Gal4 activation domain in the mediator. , 2001, Biochemistry.

[40]  D. Bentley.  The mRNA assembly line: transcription and processing machines in the same factory. , 2002, Current opinion in cell biology.