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Abstract
Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.
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Affiliation(s)
- Sara Osman
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;,
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2
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Pahl A, Lutz C, Hechler T. Amatoxins as RNA Polymerase II Inhibiting Antibody–Drug Conjugate (ADC) Payloads. CYTOTOXIC PAYLOADS FOR ANTIBODY – DRUG CONJUGATES 2019. [DOI: 10.1039/9781788012898-00398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Amatoxins are a group of natural toxins which occur in the death cap mushroom (Amanita phalloides). They work by inhibiting RNA polymerase II, which results in apoptosis. RNA-polymerase II inhibition is a novel mechanism of action in cancer therapy and offers the possibility of breaking through drug resistance or destroying dormant tumour cells, which could produce major clinical advances. Amanitin, as the most potent member of this toxin family, has been made accessible for cancer therapy by developing it as a payload for antibody–drug conjugates (ADCs). This chapter describes the discovery and chemistry of the amatoxins, and the development of the amanitin-ADC technology.
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Affiliation(s)
- Andreas Pahl
- Heidelberg Pharma Schriesheimer Str. 101 68526 Ladenburg Germany
| | - Christian Lutz
- Heidelberg Pharma Schriesheimer Str. 101 68526 Ladenburg Germany
| | - Torsten Hechler
- Heidelberg Pharma Schriesheimer Str. 101 68526 Ladenburg Germany
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3
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Heinecke CL, Ackerson CJ. Preparation of gold nanocluster bioconjugates for electron microscopy. Methods Mol Biol 2013; 950:293-311. [PMID: 23086882 DOI: 10.1007/978-1-62703-137-0_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this chapter, we describe types of gold nanoparticle-biomolecule conjugates and their use in electron microscopy. Included are two detailed protocols for labeling an IgG antibody with gold monolayer protected clusters. The first approach is a direct bonding approach that utilizes the ligand place exchange reaction. The second approach describes NHS-EDC coupling of Au(144)(pMBA)(60) with IgG. Also included are various characterization techniques for determining labeling efficiency.
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4
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Martinez-Rucobo FW, Cramer P. Structural basis of transcription elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:9-19. [PMID: 22982352 DOI: 10.1016/j.bbagrm.2012.09.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 01/13/2023]
Abstract
For transcription elongation, all cellular RNA polymerases form a stable elongation complex (EC) with the DNA template and the RNA transcript. Since the millennium, a wealth of structural information and complementary functional studies provided a detailed three-dimensional picture of the EC and many of its functional states. Here we summarize these studies that elucidated EC structure and maintenance, nucleotide selection and addition, translocation, elongation inhibition, pausing and proofreading, backtracking, arrest and reactivation, processivity, DNA lesion-induced stalling, lesion bypass, and transcriptional mutagenesis. In the future, additional structural and functional studies of elongation factors that control the EC and their possible allosteric modes of action should result in a more complete understanding of the dynamic molecular mechanisms underlying transcription elongation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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5
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Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro. Proc Natl Acad Sci U S A 2012; 109:1931-6. [PMID: 22308335 DOI: 10.1073/pnas.1109994109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATPases and histone chaperones facilitate RNA polymerase II (pol II) elongation on chromatin. In vivo, the coordinated action of these enzymes is necessary to permit pol II passage through a nucleosome while restoring histone density afterward. We have developed a biochemical system recapitulating this basic process. Transcription through a nucleosome in vitro requires the ATPase remodels structure of chromatin (RSC) and the histone chaperone nucleosome assembly protein 1 (NAP1). In the presence of NAP1, RSC generates a hexasome. Despite the propensity of RSC to evict histones, NAP1 reprograms the reaction such that the hexasome is retained on the template during multiple rounds of transcription. This work has implications toward understanding the mechanism of pol II elongation on chromatin.
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6
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Sander B, Golas MM. Visualization of bionanostructures using transmission electron microscopical techniques. Microsc Res Tech 2010; 74:642-63. [DOI: 10.1002/jemt.20963] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Accepted: 10/01/2010] [Indexed: 11/10/2022]
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7
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Sexton JZ, Ackerson CJ. Determination of Rigidity of Protein Bound Au(144) Clusters by Electron Cryomicroscopy. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2010; 114:16037-16042. [PMID: 21116473 PMCID: PMC2992337 DOI: 10.1021/jp101970x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A method for estimating the positional displacement of protein bound gold nanoparticles is presented and used to estimate the rigidity of linkage of Au(144) nanoparticles bound to a tetrameric model protein. We observe a distribution of displacement values where most Au(144) clusters are immobilized to within 3Å relative to the protein center of mass. The shape of the distribution suggests two physical processes of thermal motion and protein deformation. The application of this and similar rigid gold nanoparticle/protein conjugates in high resolution single particle electron cryo-microscopy is discussed.
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Affiliation(s)
- Jonathan Z. Sexton
- Department of Structural Biology, 299 Campus Drive West, Stanford, CA 94305
- Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC
| | - Christopher J. Ackerson
- Department of Structural Biology, 299 Campus Drive West, Stanford, CA 94305
- Department of Chemistry, Colorado State University, Fort Collins, CO 80521
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8
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Brueckner F, Armache KJ, Cheung A, Damsma GE, Kettenberger H, Lehmann E, Sydow J, Cramer P. Structure-function studies of the RNA polymerase II elongation complex. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:112-20. [PMID: 19171965 PMCID: PMC2631633 DOI: 10.1107/s0907444908039875] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 11/26/2008] [Indexed: 11/23/2022]
Abstract
RNA polymerase II (Pol II) is the eukaryotic enzyme that is responsible for transcribing all protein-coding genes into messenger RNA (mRNA). The mRNA-transcription cycle can be divided into three stages: initiation, elongation and termination. During elongation, Pol II moves along a DNA template and synthesizes a complementary RNA chain in a processive manner. X-ray structural analysis has proved to be a potent tool for elucidating the mechanism of Pol II elongation. Crystallographic snapshots of different functional states of the Pol II elongation complex (EC) have elucidated mechanistic details of nucleotide addition and Pol II translocation. Further structural studies in combination with in vitro transcription experiments led to a mechanistic understanding of various additional features of the EC, including its inhibition by the fungal toxin alpha-amanitin, the tunability of the active site by the elongation factor TFIIS, the recognition of DNA lesions and the use of RNA as a template.
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Affiliation(s)
- Florian Brueckner
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Karim-Jean Armache
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Alan Cheung
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Gerke E. Damsma
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Hubert Kettenberger
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Elisabeth Lehmann
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jasmin Sydow
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Patrick Cramer
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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9
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Cramer P, Armache KJ, Baumli S, Benkert S, Brueckner F, Buchen C, Damsma GE, Dengl S, Geiger SR, Jasiak AJ, Jawhari A, Jennebach S, Kamenski T, Kettenberger H, Kuhn CD, Lehmann E, Leike K, Sydow JF, Vannini A. Structure of eukaryotic RNA polymerases. Annu Rev Biophys 2008; 37:337-52. [PMID: 18573085 DOI: 10.1146/annurev.biophys.37.032807.130008] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The eukaryotic RNA polymerases Pol I, Pol II, and Pol III are the central multiprotein machines that synthesize ribosomal, messenger, and transfer RNA, respectively. Here we provide a catalog of available structural information for these three enzymes. Most structural data have been accumulated for Pol II and its functional complexes. These studies have provided insights into many aspects of the transcription mechanism, including initiation at promoter DNA, elongation of the mRNA chain, tunability of the polymerase active site, which supports RNA synthesis and cleavage, and the response of Pol II to DNA lesions. Detailed structural studies of Pol I and Pol III were reported recently and showed that the active center region and core enzymes are similar to Pol II and that strong structural differences on the surfaces account for gene class-specific functions.
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Affiliation(s)
- P Cramer
- Gene Center Munich and Center for Integrated Protein Science CIPSM, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
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10
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Abstract
This year's Nobel laureate in chemistry is Roger Kornberg. Patrick Cramer gives a personal account of how the Kornberg laboratory determined the structure of the RNA polymerase II core enzyme.
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Affiliation(s)
- Patrick Cramer
- Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.
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11
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Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 2005; 3:e405. [PMID: 16279839 PMCID: PMC1283537 DOI: 10.1371/journal.pbio.0030405] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 09/27/2005] [Indexed: 12/11/2022] Open
Abstract
Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or “linear motif” (e.g., SH3 binding to PxxP). Many domains are known, though comparatively few linear motifs have been discovered. Their short length (three to eight residues), and the fact that they often reside in disordered regions in proteins makes them difficult to detect through sequence comparison or experiment. Nevertheless, each new motif provides critical molecular details of how interaction networks are constructed, and can explain how one protein is able to bind to very different partners. Here we show that binding motifs can be detected using data from genome-scale interaction studies, and thus avoid the normally slow discovery process. Our approach based on motif over-representation in non-homologous sequences, rediscovers known motifs and predicts dozens of others. Direct binding experiments reveal that two predicted motifs are indeed protein-binding modules: a DxxDxxxD protein phosphatase 1 binding motif with a KD of 22 μM and a VxxxRxYS motif that binds Translin with a KD of 43 μM. We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes. Many protein interactions are mediated by short amino acid motifs. The authors describe a new approach to identify these interaction motifs and experimentally validate some of their binding predictions.
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Affiliation(s)
- Victor Neduva
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rune Linding
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - Toby J Gibson
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joe Lewis
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Serrano
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert B Russell
- 1European Molecular Biology Laboratory, Heidelberg, Germany
- 2European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, United Kingdom
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12
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Miyata T, Suzuki H, Oyama T, Mayanagi K, Ishino Y, Morikawa K. Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis. Proc Natl Acad Sci U S A 2005; 102:13795-800. [PMID: 16169902 PMCID: PMC1236569 DOI: 10.1073/pnas.0506447102] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ring-shaped sliding clamps and clamp loader ATPases are essential factors for rapid and accurate DNA replication. The clamp ring is opened and resealed at the primer-template junctions by the ATP-fueled clamp loader function. The processivity of the DNA polymerase is conferred by its attachment to the clamp loaded onto the DNA. In eukarya and archaea, the replication factor C (RFC) and the proliferating cell nuclear antigen (PCNA) play crucial roles as the clamp loader and the clamp, respectively. Here, we report the electron microscopic structure of an archaeal RFC-PCNA-DNA complex at 12-A resolution. This complex exhibits excellent fitting of each atomic structure of RFC, PCNA, and the primed DNA. The PCNA ring retains an open conformation by extensive interactions with RFC, with a distorted spring washer-like conformation. The complex appears to represent the intermediate, where the PCNA ring is kept open before ATP hydrolysis by RFC.
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Affiliation(s)
- Tomoko Miyata
- Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
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13
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Kettenberger H, Armache KJ, Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 2005; 16:955-65. [PMID: 15610738 DOI: 10.1016/j.molcel.2004.11.040] [Citation(s) in RCA: 343] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2004] [Revised: 11/19/2004] [Accepted: 11/23/2004] [Indexed: 01/22/2023]
Abstract
The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.
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Affiliation(s)
- Hubert Kettenberger
- Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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14
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Aloy P, Böttcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB. Structure-Based Assembly of Protein Complexes in Yeast. Science 2004; 303:2026-9. [PMID: 15044803 DOI: 10.1126/science.1092645] [Citation(s) in RCA: 271] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Images of entire cells are preceding atomic structures of the separate molecular machines that they contain. The resulting gap in knowledge can be partly bridged by protein-protein interactions, bioinformatics, and electron microscopy. Here we use interactions of known three-dimensional structure to model a large set of yeast complexes, which we also screen by electron microscopy. For 54 of 102 complexes, we obtain at least partial models of interacting subunits. For 29, including the exosome, the chaperonin containing TCP-1, a 3'-messenger RNA degradation complex, and RNA polymerase II, the process suggests atomic details not easily seen by homology, involving the combination of two or more known structures. We also consider interactions between complexes (cross-talk) and use these to construct a structure-based network of molecular machines in the cell.
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Affiliation(s)
- Patrick Aloy
- European Molecular Biology Laboratory, Structural and Computational Biology Programme, 1, 69117 Heidelberg, Germany
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15
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King RA, Sen R, Weisberg RA. Using a lac repressor roadblock to analyze the E. coli transcription elongation complex. Methods Enzymol 2004; 371:207-18. [PMID: 14712702 DOI: 10.1016/s0076-6879(03)71015-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Affiliation(s)
- Rodney A King
- Laboratory of Molecular Genetics, NICHD, NIH, Building 6B, Room 3B-308, Bethesda, Maryland 20892, USA
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16
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, 81377 Munich, Germany
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17
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Abstract
The elongation of transcripts by RNA polymerase II (RNAPII) is subject to regulation and requires the services of a host of accessory proteins. Although the biochemical mechanisms underlying elongation and its regulation remain obscure, recent progress sets the stage for rapid advancement in our understanding of this phase of transcription. High-resolution crystal structures will allow focused analyses of RNAPII in all its functional states. Several recent studies suggest specific roles for the C-terminal heptad repeats of the largest subunit of RNAPII in elongation. Proteomic approaches are being used to identify new transcription-elongation factors and to define interactions between elongation factors and RNAPII. Finally, a combination of genetic analysis and the localization of factors on transcribed chromatin is being used to confirm a role for factors in elongation.
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Affiliation(s)
- Grant A Hartzog
- Department of MCD Biology, University of California, Santa Cruz, California 95064, USA.
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18
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Gnatt A. Elongation by RNA polymerase II: structure-function relationship. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:175-90. [PMID: 12213651 DOI: 10.1016/s0167-4781(02)00451-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
RNA polymerase II is the eukaryotic enzyme that transcribes all the mRNA in the cell. Complex mechanisms of transcription and its regulation underlie basic functions including differentiation and morphogenesis. Recent evidence indicates the process of RNA chain elongation as a key step in transcription control. Elongation was therefore expected and found to be linked to human diseases. For these reasons, major efforts in determining the structures of RNA polymerases from yeast and bacteria, at rest and as active enzymes, were undertaken. These studies have revealed much information regarding the processes involved in transcription. Eukaryotic RNA polymerases and their homologous bacterial counterparts are flexible enzymes with domains that separate DNA and RNA, prevent the escape of nucleic acids during transcription, allow for extended pausing or "arrest" during elongation, allow for translocation of the DNA and more. Structural studies of RNA polymerases are described below within the context of the process of transcription elongation, its regulation and function.
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Affiliation(s)
- Averell Gnatt
- Department of Pharmacology and Experimental Therapeutics and Department of Pathology, University of Maryland Baltimore, 655 West Baltimore St., Baltimore, MD 21201, USA.
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Bischler N, Brino L, Carles C, Riva M, Tschochner H, Mallouh V, Schultz P. Localization of the yeast RNA polymerase I-specific subunits. EMBO J 2002; 21:4136-44. [PMID: 12145213 PMCID: PMC126139 DOI: 10.1093/emboj/cdf392] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The spatial distribution of four subunits specifically associated to the yeast DNA-dependent RNA polymerase I (RNA pol I) was studied by electron microscopy. A structural model of the native enzyme was determined by cryo-electron microscopy from isolated molecules and was compared with the atomic structure of RNA pol II Delta 4/7, which lacks the specific polypeptides. The two models were aligned and a difference map revealed four additional protein densities present in RNA pol I, which were characterized by immunolabelling. A protruding protein density named stalk was found to contain the RNA pol I-specific subunits A43 and A14. The docking with the atomic structure showed that the stalk protruded from the structure at the same site as the C-terminal domain (CTD) of the largest subunit of RNA pol II. Subunit A49 was placed on top of the clamp whereas subunit A34.5 bound at the entrance of the DNA binding cleft, where it could contact the downstream DNA. The location of the RNA pol I-specific subunits is correlated with their biological activity.
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Affiliation(s)
- Nicolas Bischler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP163, F-67404 Illkirch Cedex, France
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20
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Prescott EM, Proudfoot NJ. Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci U S A 2002; 99:8796-801. [PMID: 12077310 PMCID: PMC124378 DOI: 10.1073/pnas.132270899] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcriptional interference between genes and the regulatory elements of simple eukaryotes such as Saccharomyces cerevisiae is an unavoidable consequence of their compressed genetic arrangement. We have shown previously that with the tandem arranged genes GAL10 and GAL7, inefficient transcriptional termination of the upstream gene inhibits initiation of transcription on the downstream gene. We now show that transcriptional interference can occur also with S. cerevisiae RNA polymerase II genes arranged convergently. We demonstrate that when the GAL10 and GAL7 genes are rearranged in a convergent orientation, transcriptional initiation occurs at full levels. However, as soon as the two transcripts begin to overlap, elongation is restricted, resulting in a severe reduction in steady-state mRNA accumulation. This effect is observed only in cis arrangement, arguing against RNA-interference effects acting on the potential generation of antisense transcripts. These data reinforce the necessity of separating adjacent RNA polymerase II transcription units by efficient termination signals.
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Affiliation(s)
- Elizabeth M Prescott
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
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21
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Saecker RM, Tsodikov OV, McQuade KL, Schlax PE, Capp MW, Record MT. Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates. J Mol Biol 2002; 319:649-71. [PMID: 12054861 DOI: 10.1016/s0022-2836(02)00293-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The kinetics of interaction of Esigma(70) RNA polymerase (R) with the lambdaP(R) promoter (P) were investigated by filter binding over a broad range of temperatures (7.3-42 degrees C) and concentrations of RNA polymerase (1-123 nM) in large excess over promoter DNA. Under all conditions examined, the kinetics of formation of competitor-resistant complexes (I(2), RP(o)) are single-exponential with first order rate constant beta(CR). Interpretation of the polymerase concentration dependence of beta(CR) in terms of the three step mechanism of open complex formation yields the equilibrium constant K(1) for formation of the first kinetically significant intermediate (I(1)) and the forward rate constant (k(2)) for the conformational change converting I(1) to the second kinetically significant intermediate I(2): R + P-->(K(1))<--I(1)(k(2))-->I(2). Use of rapid quench mixing allows K(1) and k(2) to be individually determined over the entire temperature range investigated, previously not possible at this promoter using manual mixing. Given the large (>60 bp) interface formed in I(1), its relatively small binding constant K(1) at 37 degrees C at this [salt] (approximately 6 x 10(6) M(-1)) strongly argues that binding free energy is used to drive large-scale structural changes in polymerase and/or promoter DNA or other coupled processes. Evidence for coupling of protein folding is provided by the large and negative activation heat capacity of k(a)[DeltaC(o,++)(a)= -1.5(+/-0.2)kcal K(-1)], now shown to originate directly from formation of I(1) [DeltaC(o)(1)= -1.4(+/-0.3)kcal K(-1)] rather than from the formation of I(2) as previously proposed. The isomerization I(1)-->I(2) exhibits relatively slow kinetics and has a very large temperature-independent Arrhenius activation energy [E(act)(2)= 34(+/-2)kcal]. This kinetic signature suggests that formation of the transition state (I(1)-I(2)++ involves large conformational changes dominated by changes in the exposure of polar and/or charged surface to water. Structural and biochemical data lead to the following hypotheses to interpret these results. We propose that formation of I(1) involves coupled folding of unstructured regions of polymerase (beta, beta' and sigma(70)) and bending of promoter DNA (in the -10 region). We propose that interactions with region 2 of sigma(70) and possibly domain 1 of beta induce a kink at the -11/-12 base pairs of the lambdaP(R) promoter which places the downstream DNA (-5 to +20) in the jaws of the beta and beta' subunits of polymerase in I(1). These early interactions of beta and beta' with the DNA downstream of position -5 trigger jaw closing (with coupled folding) and subsequent steps of DNA opening.
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Affiliation(s)
- Ruth M Saecker
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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22
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Affiliation(s)
- J Soppa
- Institute for Microbiology, Biocentre Niederursel, J. W. Goethe University Frankfurt, D-60439 Frankfurt, Germany
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23
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Langelier MF, Trinh V, Coulombe B. [Focus on RNA polymerase II]. Med Sci (Paris) 2002; 18:210-216. [PMID: 27713596 DOI: 10.1051/medsci/2002182210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marie-France Langelier
- Laboratoire de transcription génique, Institut de recherches cliniques de Montréal, 110, avenue des Pins ouest, Montréal (Québec) H2W 1R7, Canada
| | - Vincent Trinh
- Laboratoire de transcription génique, Institut de recherches cliniques de Montréal, 110, avenue des Pins ouest, Montréal (Québec) H2W 1R7, Canada
| | - Benoit Coulombe
- Laboratoire de transcription génique, Institut de recherches cliniques de Montréal, 110, avenue des Pins ouest, Montréal (Québec) H2W 1R7, Canada
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24
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Abstract
Recently determined high-resolution structures of eukaryotic transcription factors have illuminated the enzymatic mechanism underlying transcription. Progress has been made in characterising protein-protein interactions between negative cofactors and general transcription factors, and between transrepression domains and corepressors. Structures of sequence-specific transcription factors have revealed further versatility in the mode of interaction with DNA and several have provided new insights into the molecular basis of human disease.
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Affiliation(s)
- Alan J Warren
- MRC Laboratory of Molecular Biology, Hills Road, CB22QH, Cambridge, UK
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25
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Abstract
Transcription of the genetic information in all cells is carried out by multisubunit RNA polymerases (RNAPs). Comparison of the crystal structures of a bacterial and a eukaryotic RNAP reveals a conserved core that comprises the active site and a multifunctional clamp. Together with a further structure of eukaryotic RNAP bound to DNA and RNA, these results elucidate many aspects of the transcription mechanism, including initiation, elongation, nucleotide addition, processivity and proofreading.
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany.
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26
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Abstract
Electron crystallography as a structural determination technique has grown dramatically in use over recent years. Improvements in microscopes, equipment, practical techniques, computation facilities and image processing methods are reflected in the increasing number of near-atomic resolution structures that have been published. In this review we shall summarize the techniques involved in structure determination of soluble proteins using electron crystallography. Many soluble protein structures have been investigated in this manner over the past two decades. Here we present several examples where a variety of approaches have been used to gradually increase the information obtained.
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Affiliation(s)
- M J Ellis
- Center for Structural Biochemistry, Karolinska Institutet, Novum, S-141 57, Huddinge, Sweden
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27
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Affiliation(s)
- E P Geiduschek
- Division of Biology and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA.
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28
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Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 2001; 292:1876-82. [PMID: 11313499 DOI: 10.1126/science.1059495] [Citation(s) in RCA: 712] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.
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MESH Headings
- Base Pairing
- Base Sequence
- Binding Sites
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- Metals/metabolism
- Models, Genetic
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA, Fungal/biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Transcription, Genetic
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Affiliation(s)
- A L Gnatt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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29
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MESH Headings
- Binding Sites
- Crystallization
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- Gene Expression Regulation, Fungal
- Promoter Regions, Genetic
- Protein Conformation
- Protein Folding
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Subunits
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA, Fungal/biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/enzymology
- Saccharomyces cerevisiae/genetics
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- A Klug
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
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30
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Spangler L, Wang X, Conaway JW, Conaway RC, Dvir A. TFIIH action in transcription initiation and promoter escape requires distinct regions of downstream promoter DNA. Proc Natl Acad Sci U S A 2001; 98:5544-9. [PMID: 11331764 PMCID: PMC33249 DOI: 10.1073/pnas.101004498] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2001] [Indexed: 11/18/2022] Open
Abstract
TFIIH is a multifunctional RNA polymerase II general initiation factor that includes two DNA helicases encoded by the Xeroderma pigmentosum complementation group B (XPB) and D (XPD) genes and a cyclin-dependent protein kinase encoded by the CDK7 gene. Previous studies have shown that the TFIIH XPB DNA helicase plays critical roles not only in transcription initiation, where it catalyzes ATP-dependent formation of the open complex, but also in efficient promoter escape, where it suppresses arrest of very early RNA polymerase II elongation intermediates. In this report, we present evidence that ATP-dependent TFIIH action in transcription initiation and promoter escape requires distinct regions of the DNA template; these regions are well separated from the promoter region unwound by the XPB DNA helicase and extend, respectively, approximately 23-39 and approximately 39-50 bp downstream from the transcriptional start site. Taken together, our findings bring to light a role for promoter DNA in TFIIH action and are consistent with the model that TFIIH translocates along promoter DNA ahead of the RNA polymerase II elongation complex until polymerase has escaped the promoter.
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Affiliation(s)
- L Spangler
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
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31
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Harrington KJ, Laughlin RB, Liang S. Balanced branching in transcription termination. Proc Natl Acad Sci U S A 2001; 98:5019-24. [PMID: 11309513 PMCID: PMC33156 DOI: 10.1073/pnas.240431598] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255, 809-812 and von Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244, 36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.
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Affiliation(s)
- K J Harrington
- Department of Physics, Stanford University, Stanford, CA 94305, USA
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32
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Dvir A, Conaway JW, Conaway RC. Mechanism of transcription initiation and promoter escape by RNA polymerase II. Curr Opin Genet Dev 2001; 11:209-14. [PMID: 11250146 DOI: 10.1016/s0959-437x(00)00181-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently, key advances in biochemical and structural studies of RNA polymerase II (pol II) and the basal transcriptional machinery have shed considerable light on the basic mechanisms underlying the initiation stage of eukaryotic mRNA synthesis. The development of methods for obtaining crystal structures of pol II and its complexes has revolutionized transcriptional studies and holds promise that aspects of initiation will soon be understood at atomic resolution; crosslinking studies have revealed intriguing features of the topology of the pol II initiation complex and provided working models for dynamic steps of initiation; and mechanistic studies have identified promoter escape as a critical step during initiation and brought to light novel roles for the general initiation factors TFIIE, TFIIF, and TFIIH in this process.
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Affiliation(s)
- A Dvir
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309, USA
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33
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Abstract
The recently determined crystal structure of a bacterial core RNA polymerase (RNAP) provides the first glimpse of this family of evolutionarily conserved cellular RNAPs. Using the structure as a framework, a consistent picture of protein-nucleic acid interactions in transcription complexes has been accumulated from cross-linking experiments. The molecule can be viewed as a molecular machine, with distinct structural features hypothesized to perform specific functions. Comparison with the alpha-carbon backbone of a eukaryotic RNAP reveals close structural similarity.
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Affiliation(s)
- S A Darst
- The Rockefeller University, Box 224, 1230 York Avenue, New York, NY 10021, USA.
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34
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Abstract
Our understanding of the elaborate mechanism of gene transcription initiation in eukaryotes has been widened by recent structural information on some of the key components of the complex preinitiation transcriptional machinery. The high-resolution structures of both bacterial and eukaryotic polymerases are technical landmarks of great biological significance that have given us the first molecular insight into the mechanism of this large enzyme. While new atomic structures of different domains of general transcription factors, such as the double bromodomain of TAF250, have become available by means of X-ray crystallography and NMR studies, more global pictures of multisubunit transcription complexes, such as TFIID, TFIIH or the yeast mediator, have now been obtained by electron microscopy and image-reconstruction techniques. A combination of methodologies may prove essential for a complete structural description of the initial steps in the expression of eukaryotic genes.
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Affiliation(s)
- E Nogales
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California at Berkeley, 94720-3200, USA.
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35
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Ebright RH. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 2000; 304:687-98. [PMID: 11124018 DOI: 10.1006/jmbi.2000.4309] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial RNA polymerase and eukaryotic RNA polymerase II exhibit striking structural similarities, including similarities in overall structure, relative positions of subunits, relative positions of functional determinants, and structures and folding topologies of subunits. These structural similarities are paralleled by similarities in mechanisms of interaction with DNA.
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Affiliation(s)
- R H Ebright
- Howard Hughes Medical Institute, Waksman Institute and Department of Chemistry Rutgers University, Piscataway, NJ 08854, USA.
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36
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Hemming SA, Jansma DB, Macgregor PF, Goryachev A, Friesen JD, Edwards AM. RNA polymerase II subunit Rpb9 regulates transcription elongation in vivo. J Biol Chem 2000; 275:35506-11. [PMID: 10938084 DOI: 10.1074/jbc.m004721200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase II lacking the Rpb9 subunit uses alternate transcription initiation sites in vitro and in vivo and is unable to respond to the transcription elongation factor TFIIS in vitro. Here, we show that RPB9 has a synthetic phenotype with the TFIIS gene. Disruption of RPB9 in yeast also resulted in sensitivity to 6-azauracil, which is a phenotype linked to defects in transcription elongation. Expression of the TFIIS gene on a high-copy plasmid partially suppressed the 6-azauracil sensitivity of Deltarpb9 cells. We set out to determine the relevant cellular role of yeast Rpb9 by assessing the ability of 20 different site-directed and deletion mutants of RPB9 to complement the initiation and elongation defects of Deltarpb9 cells in vivo. Rpb9 is composed of two zinc ribbons. The N-terminal zinc ribbon restored the wild-type pattern of initiation start sites, but was unable to complement the growth defects associated with defects in elongation. Most of the site-directed mutants complemented the elongation-specific growth phenotypes and reconstituted the normal pattern of transcription initiation sites. The anti-correlation between the growth defects of cells disrupted for RPB9 and the selection of transcription start sites suggests that this is not the primary cellular role for Rpb9. Genome-wide transcription profiling of Deltarpb9 cells revealed only a few changes, predominantly in genes related to metabolism.
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Affiliation(s)
- S A Hemming
- Banting and Best Department of Medical Research, University of Toronto, Charles H. Best Institute, Toronto, Ontario M5G 1L6, Canada
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37
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Douziech M, Coin F, Chipoulet JM, Arai Y, Ohkuma Y, Egly JM, Coulombe B. Mechanism of promoter melting by the xeroderma pigmentosum complementation group B helicase of transcription factor IIH revealed by protein-DNA photo-cross-linking. Mol Cell Biol 2000; 20:8168-77. [PMID: 11027286 PMCID: PMC86426 DOI: 10.1128/mcb.20.21.8168-8177.2000] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The p89/xeroderma pigmentosum complementation group B (XPB) ATPase-helicase of transcription factor IIH (TFIIH) is essential for promoter melting prior to transcription initiation by RNA polymerase II (RNAPII). By studying the topological organization of the initiation complex using site-specific protein-DNA photo-cross-linking, we have shown that p89/XPB makes promoter contacts both upstream and downstream of the initiation site. The upstream contact, which is in the region where promoter melting occurs (positions -9 to +2), requires tight DNA wrapping around RNAPII. The addition of hydrolyzable ATP tethers the template strand at positions -5 and +1 to RNAPII subunits. A mutation in p89/XPB found in a xeroderma pigmentosum patient impairs the ability of TFIIH to associate correctly with the complex and thereby melt promoter DNA. A model for open complex formation is proposed.
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Affiliation(s)
- M Douziech
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
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38
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Chang WH, Kornberg RD. Electron crystal structure of the transcription factor and DNA repair complex, core TFIIH. Cell 2000; 102:609-13. [PMID: 11007479 DOI: 10.1016/s0092-8674(00)00083-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Core TFIIH from yeast, made up of five subunits required both for RNA polymerase II transcription and nucleotide excision DNA repair, formed 2D crystals on charged lipid layers. Diffraction from electron micrographs of the crystals in negative stain extended to about 13 angstrom resolution, and 3D reconstruction revealed several discrete densities whose volumes corresponded well with those of individual TFIIH subunits. The structure is based on a ring of three subunits, Tfb1, Tfb2, and Tfb3, to which are appended several functional moieties: Rad3, bridged to Tfb1 by SsI1; SsI2, known to interact with Tfb2; and Kin28, known to interact with Tfb3.
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Affiliation(s)
- W H Chang
- Department of Structural Biology, Stanford University School of Medicine, California 94305, USA
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39
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Naryshkin N, Revyakin A, Kim Y, Mekler V, Ebright RH. Structural organization of the RNA polymerase-promoter open complex. Cell 2000; 101:601-11. [PMID: 10892647 DOI: 10.1016/s0092-8674(00)80872-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have used systematic site-specific protein-DNA photocrosslinking to define interactions between bacterial RNA polymerase (RNAP) and promoter DNA in the catalytically competent RNAP-promoter open complex (RPo). We have mapped more than 100 distinct crosslinks between individual segments of RNAP subunits and individual phosphates of promoter DNA. The results provide a comprehensive description of protein-DNA interactions in RPo, permit construction of a detailed model for the structure of RPo, and permit analysis of effects of a transcriptional activator on the structure of RPo.
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Affiliation(s)
- N Naryshkin
- Howard Hughes Medical Institute, Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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40
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Kireeva ML, Komissarova N, Kashlev M. Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity. J Mol Biol 2000; 299:325-35. [PMID: 10860741 DOI: 10.1006/jmbi.2000.3755] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An eight nucleotide RNA:DNA hybrid at the 3' end of the transcript is required for the stability of the elongation complex (EC) of RNA polymerase II. A non-template DNA strand is not needed for the stability of the EC, which contains this minimal hybrid. Here, we apply a recently developed method for promoter-independent assembly of functional EC of RNA polymerase II from synthetic RNA and DNA oligonucleotides to study the minimal composition of the nucleic acid array required for stability of the complex with RNA longer than eight nucleotides. We found that upon RNA extension beyond 14-16 nt in the course of transcription, non-template DNA becomes essential for maintaining a stable EC. Our data suggest that the overextended RNA:DNA hybrid formed in the absence the non-template DNA acts as a negative regulator of EC stability. The dissociation of the EC correlates with the backsliding of the polymerase along the overextended hybrid. The dual role of the hybrid provides a mechanism for the control of a correct nucleic acid architecture in the EC and of RNA polymerase II processivity.
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MESH Headings
- Animals
- Base Pair Mismatch/genetics
- Base Pairing/genetics
- Base Sequence
- Binding Sites
- Catalysis
- DNA/chemistry
- DNA/genetics
- DNA/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/metabolism
- Enzyme Stability
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Heteroduplexes/chemistry
- Nucleic Acid Heteroduplexes/genetics
- Nucleic Acid Heteroduplexes/metabolism
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/metabolism
- Potassium Permanganate/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- RNA/biosynthesis
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Polymerase II/antagonists & inhibitors
- RNA Polymerase II/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/metabolism
- Templates, Genetic
- Transcription, Genetic/genetics
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Affiliation(s)
- M L Kireeva
- ABL-Basic Research Program, NCI - Frederick Cancer Research and Development Center, Bldg. 539, Room 222, Frederick, MD, 21702-1201, USA
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41
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Abstract
Several papers published within the last year utilize innovative techniques for characterizing intermediates in RNA polymerase II transcription. Structural studies of polymerase and its associated factors provide a detailed picture of the transcription machinery, and studies of transcription complex assembly both in vitro and in vivo provide insights into the mechanism of gene expression. A high resolution picture of the transcription complex is likely to be available within the foreseeable future. The challenge is to determine the roles of individual proteins within this surprisingly large molecular machine.
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Affiliation(s)
- S Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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42
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Geiduschek EP, Bartlett MS. Engines of gene expression. NATURE STRUCTURAL BIOLOGY 2000; 7:437-9. [PMID: 10881183 DOI: 10.1038/75820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Cramer P, Bushnell DA, Fu J, Gnatt AL, Maier-Davis B, Thompson NE, Burgess RR, Edwards AM, David PR, Kornberg RD. Architecture of RNA polymerase II and implications for the transcription mechanism. Science 2000; 288:640-9. [PMID: 10784442 DOI: 10.1126/science.288.5466.640] [Citation(s) in RCA: 417] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A backbone model of a 10-subunit yeast RNA polymerase II has been derived from x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits exhibit a high degree of identity with the corresponding human proteins, and 9 of the 10 subunits are conserved among the three eukaryotic RNA polymerases I, II, and III. Notable features of the model include a pair of jaws, formed by subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and Rpb6, may be locked in the closed position by RNA, accounting for the great stability of transcribing complexes. A pore in the protein complex beneath the active center may allow entry of substrates for polymerization and exit of the transcript during proofreading and passage through pause sites in the DNA.
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MESH Headings
- Amino Acid Motifs
- Binding Sites
- Catalytic Domain
- Crystallization
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- Enzyme Stability
- Escherichia coli/enzymology
- Humans
- Models, Molecular
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Secondary
- RNA Polymerase II/chemistry
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Thermus/enzymology
- Transcription Factors/chemistry
- Transcription Factors/metabolism
- Transcription Factors, General
- Transcription, Genetic
- Transcriptional Elongation Factors
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Affiliation(s)
- P Cramer
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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44
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MESH Headings
- Binding Sites
- Catalytic Domain
- Crystallization
- Crystallography, X-Ray
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- Models, Molecular
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/enzymology
- Templates, Genetic
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- J W Conaway
- Howard Hughes Medical Institute, Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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45
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Kireeva ML, Komissarova N, Waugh DS, Kashlev M. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J Biol Chem 2000; 275:6530-6. [PMID: 10692458 DOI: 10.1074/jbc.275.9.6530] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sliding clamp model of transcription processivity, based on extensive studies of Escherichia coli RNA polymerase, suggests that formation of a stable elongation complex requires two distinct nucleic acid components: an 8-9-nt transcript-template hybrid, and a DNA duplex immediately downstream from the hybrid. Here, we address the minimal composition of the processive elongation complex in the eukaryotes by developing a method for promoter-independent assembly of functional elongation complex of S. cerevisiae RNA polymerase II from synthetic DNA and RNA oligonucleotides. We show that only one of the nucleic acid components, the 8-nt RNA:DNA hybrid, is necessary for the formation of a stable elongation complex with RNA polymerase II. The double-strand DNA upstream and downstream of the hybrid does not affect stability of the elongation complex. This finding reveals a significant difference in processivity determinants of RNA polymerase II and E. coli RNA polymerase. In addition, using the imperfect RNA:DNA hybrid disturbed by the mismatches in the RNA, we show that nontemplate DNA strand may reduce the elongation complex stability via the reduction of the RNA:DNA hybrid length. The structure of a "minimal stable" elongation complex suggests a key role of the RNA:DNA hybrid in RNA polymerase II processivity.
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Affiliation(s)
- M L Kireeva
- Advanced BioScience Laboratories, Inc.-Basic Research Program, NCI-Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, Maryland 21702-1201, USA
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46
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47
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48
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Paper Alert. Structure 1999. [DOI: 10.1016/s0969-2126(00)80034-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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49
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Fu J, Gnatt AL, Bushnell DA, Jensen GJ, Thompson NE, Burgess RR, David PR, Kornberg RD. Yeast RNA polymerase II at 5 A resolution. Cell 1999; 98:799-810. [PMID: 10499797 DOI: 10.1016/s0092-8674(00)81514-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Appropriate treatment of X-ray diffraction from an unoriented 18-heavy atom cluster derivative of a yeast RNA polymerase II crystal gave significant phase information to 5 A resolution. The validity of the phases was shown by close similarity of a 6 A electron density map to a 16 A molecular envelope of the polymerase from electron crystallography. Comparison of the 6 A X-ray map with results of electron crystallography of a paused transcription elongation complex suggests functional roles for two mobile protein domains: the tip of a flexible arm forms a downstream DNA clamp; and a hinged domain may serve as an RNA clamp, enclosing the transcript from about 8-18 residues upstream of the 3'-end in a tunnel.
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Affiliation(s)
- J Fu
- Department of Structural Biology, Stanford University School of Medicine, Fairchild Science Center, California 94305, USA
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Affiliation(s)
- R A Mooney
- Department of Bacteriology, University of Wisconsin, Madison 53706, USA
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