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Wan Afifudeen CL, Aziz A, Wong LL, Takahashi K, Toda T, Abd Wahid ME, Cha TS. Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage. PHYTOCHEMISTRY 2021; 192:112936. [PMID: 34509143 DOI: 10.1016/j.phytochem.2021.112936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/26/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
The non-model microalga Messastrum gracile SE-MC4 is a potential species for biodiesel production. However, low biomass productivity hinders it from passing the life cycle assessment for biodiesel production. Therefore, the current study was aimed at uncovering the differences in the transcriptome profiles of the microalgae at early exponential and early stationary growth phases and dissecting the roles of specific differential expressed genes (DEGs) involved in cell division during M. gracile cultivation. The transcriptome analysis revealed that the photosynthetic integral membrane protein genes such as photosynthetic antenna protein were severely down-regulated during the stationary growth phase. In addition, the signaling pathways involving transcription, glyoxylate metabolism and carbon metabolism were also down-regulated during stationary growth phase. Current findings suggested that the coordination between photosynthetic integral membrane protein genes, signaling through transcription and carbon metabolism classified as prominent strategies during exponential growth stage. These findings can be applied in genetic improvement of M. gracile for biodiesel application.
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Affiliation(s)
- C L Wan Afifudeen
- Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Ahmad Aziz
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Li Lian Wong
- Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Tatsuki Toda
- Faculty of Science and Engineering, Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, 192-8577, Japan.
| | - Mohd Effendy Abd Wahid
- Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
| | - Thye San Cha
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Satreps-Cosmos Laboratory, Central Laboratory Complex, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
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2
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Villa-Hernández S, Bermejo R. Replisome-Cohesin Interfacing: A Molecular Perspective. Bioessays 2018; 40:e1800109. [PMID: 30106480 DOI: 10.1002/bies.201800109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/23/2018] [Indexed: 12/27/2022]
Abstract
Cohesion is established in S-phase through the action of key replisome factors as replication forks engage cohesin molecules. By holding sister chromatids together, cohesion critically assists both an equal segregation of the duplicated genetic material and an efficient repair of DNA breaks. Nonetheless, the molecular events leading the entrapment of nascent chromatids by cohesin during replication are only beginning to be understood. The authors describe here the essential structural features of the cohesin complex in connection to its ability to associate DNA molecules and review the current knowledge on the architectural-functional organization of the eukaryotic replisome, significantly advanced by recent biochemical and structural studies. In light of this novel insight, the authors discuss the mechanisms proposed to assist interfacing of replisomes with chromatin-bound cohesin complexes and elaborate on models for nascent chromatids entrapment by cohesin in the environment of the replication fork.
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Affiliation(s)
- Sara Villa-Hernández
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
| | - Rodrigo Bermejo
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 928040 Madrid, Spain
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3
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Schulz S, Gietl A, Smollett K, Tinnefeld P, Werner F, Grohmann D. TFE and Spt4/5 open and close the RNA polymerase clamp during the transcription cycle. Proc Natl Acad Sci U S A 2016; 113:E1816-25. [PMID: 26979960 PMCID: PMC4822635 DOI: 10.1073/pnas.1515817113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription is an intrinsically dynamic process and requires the coordinated interplay of RNA polymerases (RNAPs) with nucleic acids and transcription factors. Classical structural biology techniques have revealed detailed snapshots of a subset of conformational states of the RNAP as they exist in crystals. A detailed view of the conformational space sampled by the RNAP and the molecular mechanisms of the basal transcription factors E (TFE) and Spt4/5 through conformational constraints has remained elusive. We monitored the conformational changes of the flexible clamp of the RNAP by combining a fluorescently labeled recombinant 12-subunit RNAP system with single-molecule FRET measurements. We measured and compared the distances across the DNA binding channel of the archaeal RNAP. Our results show that the transition of the closed to the open initiation complex, which occurs concomitant with DNA melting, is coordinated with an opening of the RNAP clamp that is stimulated by TFE. We show that the clamp in elongation complexes is modulated by the nontemplate strand and by the processivity factor Spt4/5, both of which stimulate transcription processivity. Taken together, our results reveal an intricate network of interactions within transcription complexes between RNAP, transcription factors, and nucleic acids that allosterically modulate the RNAP during the transcription cycle.
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Affiliation(s)
- Sarah Schulz
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Katherine Smollett
- RNA Polymerase Laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, 38106 Braunschweig, Germany; Laboratory for Emerging Nanometrology (LENA), Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Finn Werner
- RNA Polymerase Laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom;
| | - Dina Grohmann
- Physikalische und Theoretische Chemie-NanoBioSciences, Technische Universität Braunschweig, 38106 Braunschweig, Germany;
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4
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López-Blanco JR, Chacón P. Structural modeling from electron microscopy data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- José Ramón López-Blanco
- Department of Biological Physical Chemistry; Rocasolano Physical Chemistry Institute, CSIC; Madrid Spain
| | - Pablo Chacón
- Department of Biological Physical Chemistry; Rocasolano Physical Chemistry Institute, CSIC; Madrid Spain
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5
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Hybrid electron microscopy-FRET imaging localizes the dynamical C-terminus of Tfg2 in RNA polymerase II-TFIIF with nanometer precision. J Struct Biol 2013; 184:52-62. [PMID: 23732819 DOI: 10.1016/j.jsb.2013.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 05/06/2013] [Accepted: 05/21/2013] [Indexed: 01/23/2023]
Abstract
TFIIF-a general transcription factor comprising two conserved subunits can associate with RNA polymerase II (RNAPII) tightly to regulate the synthesis of messenger RNA in eukaryotes. Herein, a hybrid method that combines electron microscopy (EM) and Förster resonance energy transfer (FRET) is described and used to localize the C-terminus of the second TFIIF subunit (Tfg2) in the architecture of RNAPII-TFIIF. In the first stage, a poly-histidine tag appended to the Tfg2 C-terminus was labeled with nickel-NTA nanogold and a seven-step single particle EM protocol was devised to obtain the region accessible by the nanogold in 3D, suggesting the Tfg2 C-terminus is proximal to the clamp of RNAPII. Next, the C-termini of the Rpb2 and the Rpb4 subunits of RNAPII, adjacent to the clamp, were selected for placing FRET satellites to enable the nano-positioning (NP) analysis, by which the localization precision was improved such that the Tfg2 C-terminus was found to dwell on the clamp ridge but could move to the clamp top during transcription. Because the tag receptive to the EM or FRET probes can be readily introduced to any protein subunit, this hybrid approach is generally applicable to complement cryo-EM study of many protein complexes to nanometer precision.
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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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7
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Cai G, Chaban YL, Imasaki T, Kovacs JA, Calero G, Penczek PA, Takagi Y, Asturias FJ. Interaction of the mediator head module with RNA polymerase II. Structure 2012; 20:899-910. [PMID: 22579255 DOI: 10.1016/j.str.2012.02.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/24/2012] [Accepted: 02/28/2012] [Indexed: 02/09/2023]
Abstract
Mediator, a large (21 polypeptides, MW ∼1 MDa) complex conserved throughout eukaryotes, plays an essential role in control of gene expression by conveying regulatory signals that influence the activity of the preinitiation complex. However, the precise mode of interaction between Mediator and RNA polymerase II (RNAPII), and the mechanism of regulation by Mediator remain elusive. We used cryo-electron microscopy and reconstituted in vitro transcription assays to characterize a transcriptionally-active complex including the Mediator Head module and components of a minimum preinitiation complex (RNAPII, TFIIF, TFIIB, TBP, and promoter DNA). Our results reveal how the Head interacts with RNAPII, affecting its conformation and function.
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Affiliation(s)
- Gang Cai
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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8
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Dahan N, Choder M. The eukaryotic transcriptional machinery regulates mRNA translation and decay in the cytoplasm. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:169-73. [PMID: 22982191 DOI: 10.1016/j.bbagrm.2012.08.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/28/2012] [Accepted: 08/29/2012] [Indexed: 11/29/2022]
Abstract
In eukaryotes, nuclear mRNA synthesis is physically separated from its cytoplasmic translation and degradation. Recent unexpected findings have revealed that, despite this separation, the transcriptional machinery can remotely control the cytoplasmic stages. Key to this coupling is the capacity of the transcriptional machinery to "imprint" the transcript with factors that escort it to the cytoplasm and regulate its localization, translation and decay. Some of these factors are known transcriptional regulators that also function in mRNA decay and are hence named "synthegradases". Imprinting can be carried out and/or regulated by RNA polymerase II or by promoter cis- and trans-acting elements. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Nili Dahan
- Department of Molecular Microbiology, Technion-Israel Institute of Technology, Haifa, Israel
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9
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Fernández-Tornero C, Böttcher B, Rashid UJ, Steuerwald U, Flörchinger B, Devos DP, Lindner D, Müller CW. Conformational flexibility of RNA polymerase III during transcriptional elongation. EMBO J 2010; 29:3762-72. [PMID: 20967027 DOI: 10.1038/emboj.2010.266] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 09/27/2010] [Indexed: 01/21/2023] Open
Abstract
RNA polymerase (Pol) III is responsible for the transcription of genes encoding small RNAs, including tRNA, 5S rRNA and U6 RNA. Here, we report the electron cryomicroscopy structures of yeast Pol III at 9.9 Å resolution and its elongation complex at 16.5 Å resolution. Particle sub-classification reveals prominent EM densities for the two Pol III-specific subcomplexes, C31/C82/C34 and C37/C53, that can be interpreted using homology models. While the winged-helix-containing C31/C82/C34 subcomplex initiates transcription from one side of the DNA-binding cleft, the C37/C53 subcomplex accesses the transcription bubble from the opposite side of this cleft. The transcribing Pol III enzyme structure not only shows the complete incoming DNA duplex, but also reveals the exit path of newly synthesized RNA. During transcriptional elongation, the Pol III-specific subcomplexes tightly enclose the incoming DNA duplex, which likely increases processivity and provides structural insights into the conformational switch between Pol III-mediated initiation and elongation.
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Affiliation(s)
- Carlos Fernández-Tornero
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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10
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Opalka N, Brown J, Lane WJ, Twist KAF, Landick R, Asturias FJ, Darst SA. Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol 2010; 8. [PMID: 20856905 PMCID: PMC2939025 DOI: 10.1371/journal.pbio.1000483] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 08/04/2010] [Indexed: 11/25/2022] Open
Abstract
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. The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program. Transcription, or the synthesis of RNA from DNA, is one of the most important processes in the cell. The central enzyme of transcription is the DNA-dependent RNA polymerase (RNAP), a large, macromolecular assembly consisting of at least five subunits. Historically, much of our fundamental information on the process of transcription has come from genetic and biochemical studies of RNAP from the model bacterium Escherichia coli. More recently, major breakthroughs in our understanding of the mechanism of action of RNAP have come from high resolution crystal structures of various bacterial, archaebacterial, and eukaryotic enzymes. However, all of our high-resolution bacterial RNAP structures are of enzymes from the thermophiles Thermus aquaticus or T. thermophilus, organisms with poorly characterized transcription systems. It has thus far proven impossible to obtain a high-resolution structure of E. coli RNAP, which has made it difficult to relate the large collection of genetic and biochemical data on RNAP function directly to the available structural information. Here, we used a combination of approaches—high-resolution X-ray crystallography of E. coli RNAP fragments, ab initio structure prediction, homology modeling, and single-particle cryo-electron microscopy—to generate complete atomic models of E. coli RNAP. Our detailed and comprehensive structural models provide the heretofore missing structural framework for understanding the function of the highly characterized E. coli RNAP.
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Affiliation(s)
- Natacha Opalka
- The Rockefeller University, New York, New York, United States of America
| | - Jesse Brown
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - William J. Lane
- Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts, United States of America
| | | | - Robert Landick
- Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Francisco J. Asturias
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (FJA); (SAD)
| | - Seth A. Darst
- The Rockefeller University, New York, New York, United States of America
- * E-mail: (FJA); (SAD)
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11
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Kelly DF, Dukovski D, Walz T. Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy. J Mol Biol 2010; 400:675-81. [PMID: 20562026 DOI: 10.1016/j.jmb.2010.05.045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/11/2010] [Accepted: 05/18/2010] [Indexed: 11/24/2022]
Abstract
Affinity Grids are electron microscopy (EM) grids with a pre-deposited lipid monolayer containing functionalized nickel-nitrilotriacetic acid lipids. Affinity Grids can be used to prepare His-tagged proteins for single-particle EM from impure solutions or even directly from cell extracts. Here, we introduce the concept of His-tagged adaptor molecules, which eliminate the need for the target protein or complex to be His-tagged. The use of His-tagged protein A as adaptor molecule allows Affinity Grids to be used for the preparation of virtually any protein or complex provided that a specific antibody is available or can be raised against the target protein. The principle is that the Affinity Grid is coated with a specific antibody that is recruited to the grid by His-tagged protein A. The antibody-decorated Affinity Grid can then be used to isolate the target protein directly from a cell extract. We first established this approach by preparing negatively stained specimens of both native ribosomal complexes and ribosomal complexes carrying different purification tags directly from HEK-293T cell extract. We then used the His-tagged protein A/antibody strategy to isolate RNA polymerase II, still bound to native DNA, from HEK-293T cell extract, allowing us to calculate a 25-A-resolution density map by single-particle cryo-EM.
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Affiliation(s)
- Deborah F Kelly
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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12
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Zernike phase plate cryoelectron microscopy facilitates single particle analysis of unstained asymmetric protein complexes. Structure 2010; 18:17-27. [PMID: 20152149 DOI: 10.1016/j.str.2009.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 11/25/2009] [Accepted: 12/02/2009] [Indexed: 10/20/2022]
Abstract
Single particle reconstruction from cryoelectron microscopy images, though emerging as a powerful means in structural biology, is faced with challenges as applied to asymmetric proteins smaller than megadaltons due to low contrast. Zernike phase plate can improve the contrast by restoring the microscope contrast transfer function. Here, by exploiting simulated Zernike and conventional defocused cryoelectron microscope images with noise characteristics comparable to those of experimental data, we quantified the efficiencies of the steps in single particle analysis of ice-embedded RNA polymerase II (500 kDa), transferrin receptor complex (290 kDa), and T7 RNA polymerase lysozyme (100 kDa). Our results show Zernike phase plate imaging is more effective as to particle identification and also sorting of orientations, conformations, and compositions. Moreover, our analysis on image alignment indicates that Zernike phase plate can, in principle, reduce the number of particles required to attain near atomic resolution by 10-100 fold for proteins between 100 kDa and 500 kDa.
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13
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Cai G, Imasaki T, Takagi Y, Asturias FJ. Mediator structural conservation and implications for the regulation mechanism. Structure 2009; 17:559-67. [PMID: 19368889 DOI: 10.1016/j.str.2009.01.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 01/29/2009] [Accepted: 01/30/2009] [Indexed: 11/27/2022]
Abstract
Mediator, the multisubunit complex that plays an essential role in the regulation of transcription initiation in all eukaryotes, was isolated using an affinity purification protocol that yields pure material suitable for structural analysis. Conformational sorting of yeast Mediator single-particle images characterized the inherent flexibility of the complex and made possible calculation of a cryo-EM reconstruction. Comparison of free and RNA polymerase II (RNAPII) -associated yeast Mediator reconstructions demonstrates that intrinsic flexibility allows structural modules to reorganize and establish a complex network of contacts with RNAPII. We demonstrate that, despite very low sequence homology, the structures of human and yeast Mediators are surprisingly similar and the structural rearrangement that enables interaction of yeast Mediator with RNAPII parallels the structural rearrangement triggered by interaction of human Mediator with a nuclear receptor. This suggests that the topology and structural dynamics of Mediator constitute important elements of a conserved regulation mechanism.
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Affiliation(s)
- Gang Cai
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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14
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Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc 2009; 3:1941-74. [PMID: 19180078 DOI: 10.1038/nprot.2008.156] [Citation(s) in RCA: 353] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist.
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Affiliation(s)
- Tanvir R Shaikh
- Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
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15
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Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis. Proc Natl Acad Sci U S A 2008; 106:127-32. [PMID: 19109435 DOI: 10.1073/pnas.0811689106] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A simple genetic tag-based labeling method that permits specific attachment of a fluorescence probe near the C terminus of virtually any subunit of a protein complex is implemented. Its immediate application to yeast RNA polymerase II (pol II) enables us to test various hypotheses of RNA exit channel by using fluorescence resonance energy transfer (FRET) analysis. The donor dye is labeled on a site near subunit Rpb3 or Rpb4, and the acceptor dye is attached to the 5' end of RNA transcript in the pol II elongation complex. Both in-gel and single-molecule FRET analysis show that the growing RNA is leading toward Rpb4, not Rpb3, supporting the notion that RNA exits through the proposed channel 1. Distance constraints derived from our FRET results, in conjunction with triangulation, reveal the exit track of RNA transcript on core pol II by identifying amino acids in the vicinity of the 5' end of RNA and show that the extending RNA forms contacts with the Rpb7 subunit. The significance of RNA exit route in promoter escape and that in cotranscriptional mRNA processing is discussed.
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16
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Structure of a RSC-nucleosome complex and insights into chromatin remodeling. Nat Struct Mol Biol 2008; 15:1272-7. [PMID: 19029894 DOI: 10.1038/nsmb.1524] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2008] [Accepted: 10/31/2008] [Indexed: 12/21/2022]
Abstract
ATP-dependent chromatin-remodeling complexes, such as RSC, can reposition, evict or restructure nucleosomes. A structure of a RSC-nucleosome complex with a nucleosome determined by cryo-EM shows the nucleosome bound in a central RSC cavity. Extensive interaction of RSC with histones and DNA seems to destabilize the nucleosome and lead to an overall ATP-independent rearrangement of its structure. Nucleosomal DNA appears disordered and largely free to bulge out into solution as required for remodeling, but the structure of the RSC-nucleosome complex indicates that RSC is unlikely to displace the octamer from the nucleosome to which it is bound. Consideration of the RSC-nucleosome structure and published biochemical information suggests that ATP-dependent DNA translocation by RSC may result in the eviction of histone octamers from adjacent nucleosomes.
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17
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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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19
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Kostek SA, Grob P, De Carlo S, Lipscomb JS, Garczarek F, Nogales E. Molecular architecture and conformational flexibility of human RNA polymerase II. Structure 2007; 14:1691-700. [PMID: 17098194 DOI: 10.1016/j.str.2006.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 09/14/2006] [Accepted: 09/19/2006] [Indexed: 11/25/2022]
Abstract
Transcription by RNA polymerase II (RNAPII) is a central process in eukaryotic gene regulation. While atomic details exist for the yeast RNAPII, characterization of the human complex lags behind, mostly due to the inability to obtain large quantities of purified material. Although the complexes have the same protein composition and high sequence similarity, understanding of transcription and of transcription-coupled DNA repair (TCR) in humans will require the use of human proteins in structural studies. We have used cryo-electron microscopy, image reconstruction, and variance analysis to characterize the structure and dynamics of human RNAPII (hRNAPII). Our studies show that hRNAPII in solution parallels the conformational flexibility of the yeast structures crystallized in different states but also illustrate a more extensive conformational range with potential biological significance. This hRNAPII study will serve as a structural platform to build up higher-order transcription and TCR complexes and to gain information that may be unique to the human RNAPII system.
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Affiliation(s)
- Seth A Kostek
- Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, California 94720, USA
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20
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Takagi Y, Calero G, Komori H, Brown JA, Ehrensberger AH, Hudmon A, Asturias F, Kornberg RD. Head module control of mediator interactions. Mol Cell 2006; 23:355-64. [PMID: 16885025 DOI: 10.1016/j.molcel.2006.06.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2006] [Revised: 05/22/2006] [Accepted: 06/07/2006] [Indexed: 10/24/2022]
Abstract
Yeast Mediator proteins interacting with Med17(Srb4) have been expressed at a high level with the use of recombinant baculoviruses and recovered in homogeneous form as a seven subunit, 223 kDa complex. Electron microscopy and single-particle analysis identify this complex as the Mediator head module. The recombinant head module complements "headless" Mediator for the initiation of transcription in vitro. The module interacts with an RNA polymerase II-TFIIF complex, but not with the polymerase or TFIIF alone. This interaction is lost in the presence of a DNA template and associated RNA transcript, recapitulating the release of Mediator that occurs upon the initiation of transcription. Disruption of the head module in a temperature-sensitive mutant in vivo leads to the release of middle and tail modules from a transcriptionally active promoter. The head module evidently controls Mediator-RNA polymerase II and Mediator-promoter interactions.
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Affiliation(s)
- Yuichiro Takagi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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21
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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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22
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Yang C, Ng EG, Penczek PA. Unified 3-D structure and projection orientation refinement using quasi-Newton algorithm. J Struct Biol 2005; 149:53-64. [PMID: 15629657 DOI: 10.1016/j.jsb.2004.08.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 08/26/2004] [Indexed: 11/18/2022]
Abstract
We describe an algorithm for simultaneous refinement of a three-dimensional (3-D) density map and of the orientation parameters of two-dimensional (2-D) projections that are used to reconstruct this map. The application is in electron microscopy, where the 3-D structure of a protein has to be determined from a set of 2-D projections collected at random but initially unknown angles. The design of the algorithm is based on the assumption that initial low resolution approximation of the density map and reasonable guesses for orientation parameters are available. Thus, the algorithm is applicable in final stages of the structure refinement, when the quality of the results is of main concern. We define the objective function to be minimized in real space and solve the resulting nonlinear optimization problem using a Quasi-Newton algorithm. We calculate analytical derivatives with respect to density distribution and the finite difference approximations of derivatives with respect to orientation parameters. We demonstrate that calculation of derivatives is robust with respect to noise in the data. This is due to the fact that noise is annihilated by the back-projection operations. Our algorithm is distinguished from other orientation refinement methods (i) by the simultaneous update of the density map and orientation parameters resulting in a highly efficient computational scheme and (ii) by the high quality of the results produced by a direct minimization of the discrepancy between the 2-D data and the projected views of the reconstructed 3-D structure. We demonstrate the speed and accuracy of our method by using simulated data.
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Affiliation(s)
- Chao Yang
- Lawrence Berkeley National Laboratory, Computational Research Division, Berkeley, CA 94720, USA
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23
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24
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Abstract
New structural studies of RNA polymerase II (Pol II) complexes mark the beginning of a detailed mechanistic analysis of the eukaryotic mRNA transcription cycle. Crystallographic models of the complete Pol II, together with new biochemical and electron microscopic data, give insights into transcription initiation. The first X-ray analysis of a Pol II complex with a transcription factor, the elongation factor TFIIS, supports the idea that the polymerase has a 'tunable' active site that switches between mRNA synthesis and cleavage. The new studies also show that domains of transcription factors can enter polymerase openings, to modulate function during transcription.
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
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25
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Chen HT, Hahn S. Mapping the Location of TFIIB within the RNA Polymerase II Transcription Preinitiation Complex. Cell 2004; 119:169-80. [PMID: 15479635 DOI: 10.1016/j.cell.2004.09.028] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 09/03/2004] [Accepted: 09/09/2004] [Indexed: 10/26/2022]
Abstract
Biochemical probes positioned on the surface of the general transcription factor TFIIB were used to probe the architecture of the RNA polymerase II (Pol II) transcription preinitiation complex (PIC). In PICs, the TFIIB linker and core domains are positioned over the central cleft and wall of Pol II. This positioning is not observed in the smaller Pol II-TFIIB complex. These results lead to a new model for the structure of the PIC, which agrees with most previously documented protein-DNA interactions within Pol II and archaea PICs. Specific interaction of the TFIIB core domain with Pol II positions and orients the promoter DNA over the Pol II central cleft, and TBP-DNA bending leads to bending of the promoter around the surface of Pol II. The TFIIF subunit Tfg1 was found in close proximity to the TFIIB B finger, linker, and core domains, suggesting that these two factors closely cooperate during initiation.
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Affiliation(s)
- Hung-Ta Chen
- Fred Hutchinson Cancer Research Center and Howard Hughes Medical Institute, 1100 Fairview Avenue North, Seattle, WA 98109 USA
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26
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Abstract
Recent X-ray and cryo-electron microscopy studies have provided information about the basal eukaryotic transcription machinery and about Mediator, the complex involved in transcription regulation during initiation. On the basis of this structural information, a model describing the minimal transcription complex and its interaction with Mediator has been proposed. The model provides insight into the possible mechanisms of transcription initiation and regulation.
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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27
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Affiliation(s)
- Patrick Cramer
- Institute of Biochemistry and Gene Center, University of Munich, 81377 Munich, Germany
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28
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Chung WH, Craighead JL, Chang WH, Ezeokonkwo C, Bareket-Samish A, Kornberg RD, Asturias FJ. RNA Polymerase II/TFIIF Structure and Conserved Organization of the Initiation Complex. Mol Cell 2003; 12:1003-13. [PMID: 14580350 DOI: 10.1016/s1097-2765(03)00387-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The structure of an RNA polymerase II/general transcription factor TFIIF complex was determined by cryo-electron microscopy and single particle analysis. Density due to TFIIF was not concentrated in one area but rather was widely distributed across the surface of the polymerase. The largest subunit of TFIIF interacted with the dissociable Rpb4/Rpb7 polymerase subunit complex and with the mobile "clamp." The distribution of the second largest subunit of TFIIF was very similar to that previously reported for the sigma subunit in the bacterial RNA polymerase holoenzyme, consisting of a series of globular domains extending along the polymerase active site cleft. This result indicates that the second TFIIF subunit is a true structural homolog of the bacterial sigma factor and reveals an important similarity of the transcription initiation mechanism between bacteria and eukaryotes. The structure of the RNAPII/TFIIF complex suggests a model for the organization of a minimal transcription initiation complex.
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Affiliation(s)
- Wen-Hsiang Chung
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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29
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Abstract
Long recognized as a target of regulation in prokaryotes, transcript elongation has recently become the focus of many investigators interested in eukaryotic gene expression. The growth of this area has been fueled by the availability of new methods and molecular structures, expanding sequence databases and an appreciation for the exquisite coordination required among different processes in the nucleus. Our article collates new information on regulatory accessory factors, as well as their ultimate target, RNA polymerase, in the nucleus of eukaryotic cells. How this regulation influences the biology of the organism is quite profound, and from single cell to multicellular eukaryotes significant similarities exist in the molecular responses to extracellular signals during transcript elongation. The most advanced genetic knowledge in this area comes from Saccharomyces cerevisiae, but the biochemistry and cell biology results from other organisms are also highlighted.
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Affiliation(s)
- Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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30
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Mitsuzawa H, Kanda E, Ishihama A. Rpb7 subunit of RNA polymerase II interacts with an RNA-binding protein involved in processing of transcripts. Nucleic Acids Res 2003; 31:4696-701. [PMID: 12907709 PMCID: PMC169969 DOI: 10.1093/nar/gkg688] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2003] [Revised: 06/17/2003] [Accepted: 06/27/2003] [Indexed: 11/14/2022] Open
Abstract
Rpb4-Rpb7, a dissociable subcomplex of RNA polymerase II (pol II), is required for transcription initiation. To understand the role of Rpb7 in transcription initiation or other processes in transcription, we carried out a two-hybrid screen for proteins that interact with Rpb7 of the fission yeast Schizosaccharomyces pombe. The screen identified the S.pombe homolog of the Saccharomyces cerevisiae Nrd1, an RNA-binding protein implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by pol II. The S.pombe protein, named Seb1 for seven binding, was essential for cell viability, and bound directly to Rpb7 in vitro. Saccharomyces cerevisiae Rpb7 also interacted with Nrd1, indicating that the interaction is conserved in evolution. Glu166 and/or Asp167 of S.pombe Rpb7, residues near the C-terminus of the 172 amino acid protein, were found to be important for its interaction with Seb1. Our results suggest that Rpb7 may function to anchor a processing factor to the pol II apparatus, thereby coupling RNA processing to transcription. The role for Rpb7 is consistent with its location in the pol II complex determined by recent structural studies.
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Affiliation(s)
- Hiroshi Mitsuzawa
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
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31
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Abstract
PURPOSE OF REVIEW Structural biology is one of the most informative disciplines available to biochemical research. It unites technologies that can reveal high-resolution (often atomic) details of the inner workings of biochemical systems. These insights are crucial for an understanding of basic life processes, such as the reaction mechanism of a drug-converting enzyme, signal transduction from one protein to another, activation of a metabolic pathway by a gene effector, action modes of drugs, or the consequences of a mutation on the function of an enzyme. Structural biology is also vital for characterizing the molecular basis of many diseases and often provides a starting platform for the development of specifically tuned therapies, for example by designing drugs that bind to particular targets in order to affect their functionality. An overview of the main techniques as well as some selected case studies are presented. RECENT FINDINGS Recent advances in the three major structure determination techniques (X-ray crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy) have made it possible to obtain three-dimensional structural information on larger systems, at higher resolution and with much less effort than in the past. Because these techniques often provide complementary information, combining them is particularly powerful for gaining comprehensive insights into complex systems, as illustrated by the recent structure determinations of the low-density lipoprotein receptor and the ribosome. SUMMARY Structural biology is no longer exclusive to a few dedicated specialists. Many of its techniques are now easily accessible and can be used as tools in general life science research.
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Affiliation(s)
- Mischa Machius
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.
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32
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De Carlo S, Carles C, Riva M, Schultz P. Cryo-negative staining reveals conformational flexibility within yeast RNA polymerase I. J Mol Biol 2003; 329:891-902. [PMID: 12798680 DOI: 10.1016/s0022-2836(03)00510-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The structure of the yeast DNA-dependent RNA polymerase I (RNA Pol I), prepared by cryo-negative staining, was studied by electron microscopy. A structural model of the enzyme at a resolution of 1.8 nm was determined from the analysis of isolated molecules and showed an excellent fit with the atomic structure of the RNA Pol II Delta4/7. The high signal-to-noise ratio (SNR) of the stained molecular images revealed a conformational flexibility within the image data set that could be recovered in three-dimensions after implementation of a novel strategy to sort the "open" and "closed" conformations in our heterogeneous data set. This conformational change mapped in the "wall/flap" domain of the second largest subunit (beta-like) and allows a better accessibility of the DNA-binding groove. This displacement of the wall/flap domain could play an important role in the transition between initiation and elongation state of the enzyme. Moreover, a protrusion was apparent in the cryo-negatively stained model, which was absent in the atomic structure and was not detected in previous 3D models of RNA Pol I. This structure could, however, be detected in unstained views of the enzyme obtained from frozen hydrated 2D crystals, indicating that this novel feature is not induced by the staining process. Unexpectedly, negatively charged molybdenum compounds were found to accumulate within the DNA-binding groove, which is best explained by the highly positive electrostatic potential of this region of the molecule, thus, suggesting that the stain distribution reflects the overall surface charge of the molecule.
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Affiliation(s)
- Sacha De Carlo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP163, F-67404 Illkirch Cedex, C.U. de Strasbourg, France.
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33
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Armache KJ, Kettenberger H, Cramer P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc Natl Acad Sci U S A 2003; 100:6964-8. [PMID: 12746495 PMCID: PMC165813 DOI: 10.1073/pnas.1030608100] [Citation(s) in RCA: 203] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2003] [Indexed: 12/17/2022] Open
Abstract
RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core and the two-subunit Rpb4/7 complex that is required for transcription initiation. Previous structures of the Pol II core revealed a "clamp," which binds the DNA template strand via three "switch regions," and a flexible "linker" to the C-terminal repeat domain (CTD). Here we derived a model of the complete Pol II by fitting structures of the core and Rpb4/7 to a 4.2-A crystallographic electron density map. Rpb4/7 protrudes from the polymerase "upstream face," on which initiation factors assemble for promoter DNA loading. Rpb7 forms a wedge between the clamp and the linker, restricting the clamp to a closed position. The wedge allosterically prevents entry of the promoter DNA duplex into the active center cleft and induces in two switch regions a conformation poised for template-strand binding. Interaction of Rpb4/7 with the linker explains Rpb4-mediated recruitment of the CTD phosphatase to the CTD during Pol II recycling. The core-Rpb7 interaction and some functions of Rpb4/7 are apparently conserved in all eukaryotic and archaeal RNA polymerases but not in the bacterial enzyme.
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Affiliation(s)
- Karim-Jean Armache
- Institute of Biochemistry and Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
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34
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Affiliation(s)
- Francisco J Asturias
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, CB227, La Jolla, CA 92037, USA.
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35
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Bushnell DA, Kornberg RD. Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription. Proc Natl Acad Sci U S A 2003; 100:6969-73. [PMID: 12746498 PMCID: PMC165814 DOI: 10.1073/pnas.1130601100] [Citation(s) in RCA: 225] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2003] [Indexed: 01/22/2023] Open
Abstract
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.
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Affiliation(s)
- David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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36
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Tan Q, Prysak MH, Woychik NA. Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol Cell Biol 2003; 23:3329-38. [PMID: 12697831 PMCID: PMC153193 DOI: 10.1128/mcb.23.9.3329-3338.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Revised: 10/16/2002] [Accepted: 01/17/2003] [Indexed: 11/20/2022] Open
Abstract
We have identified a conditional mutation in the shared Rpb6 subunit, assembled in RNA polymerases I, II, and III, that illuminated a new role that is independent of its assembly function. RNA polymerase II and III activities were significantly reduced in mutant cells before and after the shift to nonpermissive temperature. In contrast, RNA polymerase I was marginally affected. Although the Rpb6 mutant strain contained two mutations (P75S and Q100R), the majority of growth and transcription defects originated from substitution of an amino acid nearly identical in all eukaryotic counterparts as well as bacterial omega subunits (Q100R). Purification of mutant RNA polymerase II revealed that two subunits, Rpb4 and Rpb7, are selectively lost in mutant cells. Rpb4 and Rpb7 are present at substoichiometric levels, form a dissociable subcomplex, are required for RNA polymerase II activity at high temperatures, and have been implicated in the regulation of enzyme activity. Interaction experiments support a direct association between the Rpb6 and Rpb4 subunits, indicating that Rpb6 is one point of contact between the Rpb4/Rpb7 subcomplex and RNA polymerase II. The association of Rpb4/Rpb7 with Rpb6 suggests that analogous subunits of each RNA polymerase impart class-specific functions through a conserved core subunit.
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Affiliation(s)
- Qian Tan
- Department of Molecular Genetics, Microbiology and Immunology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854-5635, USA
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37
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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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38
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Current Awareness on Yeast. Yeast 2003. [DOI: 10.1002/yea.940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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39
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Frank J. A cold look at transcription. Structure 2002; 10:1156-7. [PMID: 12220487 DOI: 10.1016/s0969-2126(02)00836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, Empire State Plaza, Albany, NY 12201, USA
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40
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Davis JA, Takagi Y, Kornberg RD, Asturias FA. Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol Cell 2002; 10:409-15. [PMID: 12191485 DOI: 10.1016/s1097-2765(02)00598-1] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The holoenzyme formed by RNA polymerase II (RNAPII) and the Mediator complex is the target of transcriptional regulators in vivo. A three-dimensional structure of the yeast holoenzyme has been generated from electron microscopic images of single holoenzyme particles. Extensive changes in Mediator conformation required for interaction with RNAPII have been modeled by correlating the polymerase-bound and free Mediator structures. Determination of the precise orientation of the RNAPII in the holoenzyme indicates that Mediator contacts are centered on the RNAPII Rpb3/Rpb11 heterodimer, the eukaryotic homolog of the alpha(2) homodimer involved in transcription regulation in prokaryotes. Implications for the possible mechanism of transcription regulation by Mediator are discussed.
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Affiliation(s)
- Joshua A Davis
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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