1
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proc Natl Acad Sci U S A 2024; 121:e2318527121. [PMID: 39190355 PMCID: PMC11388330 DOI: 10.1073/pnas.2318527121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and, more importantly, a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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2
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Muscat S, Martino G, Manigrasso J, Marcia M, De Vivo M. On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules. J Chem Theory Comput 2024. [PMID: 39150960 DOI: 10.1021/acs.jctc.4c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
RNA molecules play a vital role in biological processes within the cell, with significant implications for science and medicine. Notably, the biological functions exerted by specific RNA molecules are often linked to the RNA conformational ensemble. However, the experimental characterization of such three-dimensional RNA structures is challenged by the structural heterogeneity of RNA and by its multiple dynamic interactions with binding partners such as small molecules, proteins, and metal ions. Consequently, our current understanding of the structure-function relationship of RNA molecules is still limited. In this context, we highlight molecular dynamics (MD) simulations as a powerful tool to complement experimental efforts on RNAs. Despite the recognized limitations of current force fields for RNA MD simulations, examining the dynamics of selected RNAs has provided valuable functional insights into their structures.
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Affiliation(s)
- Stefano Muscat
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Gianfranco Martino
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Jacopo Manigrasso
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Sweden
| | - Marco Marcia
- European Molecular Biology Laboratory Grenoble, 71 Avenue des Martyrs, 38042 Grenoble, France
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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3
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Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion-dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. eLife 2024; 13:RP99960. [PMID: 39141555 PMCID: PMC11325842 DOI: 10.7554/elife.99960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice UniversityHoustonUnited States
| | - Grace Zhou
- Department of Biosciences, Rice UniversityHoustonUnited States
| | - Yang Gao
- Department of Biosciences, Rice UniversityHoustonUnited States
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4
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Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592236. [PMID: 38746211 PMCID: PMC11092635 DOI: 10.1101/2024.05.02.592236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Grace Zhou
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
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5
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Zhang D, Xu S, Luo Z, Lin Z. MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions. Nat Commun 2024; 15:5140. [PMID: 38886375 PMCID: PMC11183143 DOI: 10.1038/s41467-024-49490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Holliday junction resolution is a crucial process in homologous recombination and DNA double-strand break repair. Complete Holliday junction resolution requires two stepwise incisions across the center of the junction, but the precise mechanism of metal ion-catalyzed Holliday junction cleavage remains elusive. Here, we perform a metal ion-triggered catalysis in crystals to investigate the mechanism of Holliday junction cleavage by MOC1. We capture the structures of MOC1 in complex with a nicked Holliday junction at various catalytic states, including the ground state, the one-metal ion binding state, and the two-metal ion binding state. Moreover, we also identify a third metal ion that may aid in the nucleophilic attack on the scissile phosphate. Further structural and biochemical analyses reveal a metal ion-mediated allosteric regulation between the two active sites, contributing to the enhancement of the second strand cleavage following the first strand cleavage, as well as the precise symmetric cleavage across the Holliday junction. Our work provides insights into the mechanism of metal ion-catalyzed Holliday junction resolution by MOC1, with implications for understanding how cells preserve genome integrity during the Holliday junction resolution phase.
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Affiliation(s)
- Danping Zhang
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Shenjie Xu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, 215123, China
| | - Zhipu Luo
- MOE Key Laboratory of Geriatric Diseases and Immunology, Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, 215123, China.
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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6
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Aupič J, Borišek J, Fica SM, Galej WP, Magistrato A. Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome. Nat Commun 2023; 14:8482. [PMID: 38123540 PMCID: PMC10733407 DOI: 10.1038/s41467-023-44174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Cleavage and formation of phosphodiester bonds in nucleic acids is accomplished by large cellular machineries composed of both protein and RNA. Long thought to rely on a two-metal-ion mechanism for catalysis, structure comparisons revealed many contain highly spatially conserved second-shell monovalent cations, whose precise function remains elusive. A recent high-resolution structure of the spliceosome, essential for pre-mRNA splicing in eukaryotes, revealed a potassium ion in the active site. Here, we employ biased quantum mechanics/ molecular mechanics molecular dynamics to elucidate the function of this monovalent ion in splicing. We discover that the K+ ion regulates the kinetics and thermodynamics of the first splicing step by rigidifying the active site and stabilizing the substrate in the pre- and post-catalytic state via formation of key hydrogen bonds. Our work supports a direct role for the K+ ion during catalysis and provides a mechanistic hypothesis likely shared by other nucleic acid processing enzymes.
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Affiliation(s)
- Jana Aupič
- National Research Council of Italy (CNR)-Materials Foundry (IOM) c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Jure Borišek
- Theory department, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Alessandra Magistrato
- National Research Council of Italy (CNR)-Materials Foundry (IOM) c/o International School for Advanced Studies (SISSA), Trieste, Italy.
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7
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559052. [PMID: 37790421 PMCID: PMC10543002 DOI: 10.1101/2023.09.22.559052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structure indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/bridge helix (BH) interactions induce conformational changes that could propel translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the hyperactive Rpb1 T834P bridge helix mutant reveals rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston MA 02115 USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260 USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
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8
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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9
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Chang C, Zhou G, Gao Y. In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:034702. [PMID: 37333512 PMCID: PMC10275647 DOI: 10.1063/4.0000187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 06/20/2023]
Abstract
DNA polymerases are the enzymatic catalysts that synthesize DNA during DNA replication and repair. Kinetic studies and x-ray crystallography have uncovered the overall kinetic pathway and led to a two-metal-ion dependent catalytic mechanism. Diffusion-based time-resolved crystallography has permitted the visualization of the catalytic reaction at atomic resolution and made it possible to capture transient events and metal ion binding that have eluded static polymerase structures. This review discusses past static structures and recent time-resolved structures that emphasize the crucial importance of primer alignment and different metal ions binding during catalysis and substrate discrimination.
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Affiliation(s)
| | | | - Yang Gao
- Author to whom correspondence should be addressed:. Tel.: +1 (713) 348-2619
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10
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Kitagawa Y, Liao Z, Morikawa K, Oda M. Metal-binding and folding thermodynamics of Escherichia coli ribonuclease HI related to its catalytic function. Biophys Chem 2023; 295:106961. [PMID: 36736006 DOI: 10.1016/j.bpc.2023.106961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
Abstract
Escherichia coli ribonuclease HI (RNH) hydrolyzes the RNA strands of RNA/DNA hybrids in the presence of Mg2+ at the highest level, relative to other metal ions. The Mg2+ binding affinity was 8.39 × 103 M-1, which was lower than those of other metal ions. The low-affinity binder can express the maximum catalytic activity of RNH. The stability of RNH increased with increasing metal ion concentration, except for Zn2+. The thermodynamic origin for enhancing the stability of RNH with Mg2+ was more favorable entropy compared to those with other metal ions, indicating that Mg2+ binding changes the RNH structure while maintaining flexibility. Upon H124A mutation, the metal ion binding affinities decreased for Mn2+ and Zn2+ to a relatively large extent. The present thermodynamic analyses provide information on the structural dynamics of RNH with metal ion exchangeable binding, which can reasonably explain the metal-ion-dependent catalytic activity.
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Affiliation(s)
- Yumi Kitagawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Zengwei Liao
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan; Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kosuke Morikawa
- Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamo Hangi-cho, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan.
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11
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Unarta IC, Goonetilleke EC, Wang D, Huang X. Nucleotide addition and cleavage by RNA polymerase II: Coordination of two catalytic reactions using a single active site. J Biol Chem 2022; 299:102844. [PMID: 36581202 PMCID: PMC9860460 DOI: 10.1016/j.jbc.2022.102844] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
RNA polymerase II (Pol II) incorporates complementary ribonucleotides into the growing RNA chain one at a time via the nucleotide addition cycle. The nucleotide addition cycle, however, is prone to misincorporation of noncomplementary nucleotides. Thus, to ensure transcriptional fidelity, Pol II backtracks and then cleaves the misincorporated nucleotides. These two reverse reactions, nucleotide addition and cleavage, are catalyzed in the same active site of Pol II, which is different from DNA polymerases or other endonucleases. Recently, substantial progress has been made to understand how Pol II effectively performs its dual role in the same active site. Our review highlights these recent studies and provides an overall model of the catalytic mechanisms of Pol II. In particular, RNA extension follows the two-metal-ion mechanism, and several Pol II residues play important roles to facilitate the catalysis. In sharp contrast, the cleavage reaction is independent of any Pol II residues. Interestingly, Pol II relies on its residues to recognize the misincorporated nucleotides during the backtracking process, prior to cleavage. In this way, Pol II efficiently compartmentalizes its two distinct catalytic functions using the same active site. Lastly, we also discuss a new perspective on the potential third Mg2+ in the nucleotide addition and intrinsic cleavage reactions.
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Affiliation(s)
- Ilona Christy Unarta
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eshani C Goonetilleke
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Dong Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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12
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Pang J, Guo Q, Lu Z. The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H. Front Microbiol 2022; 13:1034811. [PMID: 36478866 PMCID: PMC9719913 DOI: 10.3389/fmicb.2022.1034811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2023] Open
Abstract
Ribonucleoside monophosphates are inevitably misincorporated into the DNA genome inside cells, and they need to be excised to avoid chromosome instability. Ribonucleases H (RNases H) are enzymes that specifically hydrolyze the RNA strand of RNA/DNA hybrids or the RNA moiety from DNA containing a stretch of RNA, they therefore are required for DNA integrity. Extensive studies have drawn a mostly clear picture of the mechanisms of RNase H catalysis, but some questions are still lacking definitive answers. This review summarizes three alternative models of RNase H catalysis. The two-metal model is prevalent, but a three-metal model suggests the involvement of a third cation in catalysis. Apparently, the mechanisms underlying metal-dependent hydrolyzation are more complicated than initially thought. We also discuss the metal choices of RNases H and analyze how chemically similar cations function differently. Substrate and cleavage-site specificities vary among RNases H, and this is explicated in detail. An intriguing phenomenon is that organisms have diverse RNase H combinations, which may provide important hints to how rnh genes were transferred during evolution. Whether RNase H is essential for cellular growth, a key question in the study of in vivo functions, is also discussed. This article may aid in understanding the mechanisms underlying RNase H and in developing potentially promising applications of it.
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Affiliation(s)
| | | | - Zheng Lu
- Department of Biology, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, Shantou, China
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13
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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14
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Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P. Nat Commun 2022; 13:5120. [PMID: 36045135 PMCID: PMC9433436 DOI: 10.1038/s41467-022-32843-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022] Open
Abstract
Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the conformational changes that occur during binding are poorly understood. Here, we show that pairing between the 5′ leader and 3′RCCA extending the acceptor stem of ptRNA inhibits ES* formation. Cryo-electron microscopy single particle analysis reveals a dynamic enzyme that becomes ordered upon formation of ES* in which extended acceptor stem pairing is unwound. Comparisons of structures with alternative ptRNAs reveals that once unwinding is completed RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences at its cleavage site. Our study reveals active site interactions and conformational changes that drive molecular recognition by RNase P and lays the foundation for understanding how binding interactions are linked to helix unwinding and catalysis. Ribonuclease P efficiently processes all tRNA precursors despite sequence variation at the site of cleavage. Here, authors use high-throughput enzymology and cryoEM to reveal conformational changes that drive recognition by bacterial RNase P.
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15
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Yang X, Saha S, Yang W, Neuman KC, Pommier Y. Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β. Nat Commun 2022; 13:4656. [PMID: 35945419 PMCID: PMC9363430 DOI: 10.1038/s41467-022-32221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
In metazoans, topoisomerase 3β (TOP3B) regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal aging. As a Type IA topoisomerase, TOP3B acts by general acid-base catalysis to break and rejoin single-stranded DNA. Passage of a second DNA strand through the transient break permits dissipation of hypernegative DNA supercoiling and catenation/knotting. Additionally, hsTOP3B was recently demonstrated as the human RNA topoisomerase, required for normal neurodevelopment and proposed to be a potential anti-viral target upon RNA virus infection. Here we elucidate the biochemical mechanisms of human TOP3B. We delineate the roles of divalent metal ions, and of a conserved Lysine residue (K10) in the differential catalysis of DNA and RNA. We also demonstrate that three regulatory factors fine-tune the catalytic performance of TOP3B: the TOP3B C-terminal tail, its protein partner TDRD3, and the sequence of its DNA/RNA substrates.
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Affiliation(s)
- Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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16
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Visualizing the three-metal-ion-dependent cleavage of a mutagenic nucleotide. Proc Natl Acad Sci U S A 2022; 119:e2207180119. [PMID: 35737831 PMCID: PMC9245661 DOI: 10.1073/pnas.2207180119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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17
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Jamsen JA, Shock DD, Wilson SH. Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints. Nat Commun 2022; 13:3193. [PMID: 35680862 PMCID: PMC9184648 DOI: 10.1038/s41467-022-30141-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/19/2022] [Indexed: 12/26/2022] Open
Abstract
Efficient and accurate DNA synthesis is enabled by DNA polymerase fidelity checkpoints that promote insertion of the right instead of wrong nucleotide. Erroneous X-family polymerase (pol) λ nucleotide insertion leads to genomic instability in double strand break and base-excision repair. Here, time-lapse crystallography captures intermediate catalytic states of pol λ undergoing right and wrong natural nucleotide insertion. The revealed nucleotide sensing mechanism responds to base pair geometry through active site deformation to regulate global polymerase-substrate complex alignment in support of distinct optimal (right) or suboptimal (wrong) reaction pathways. An induced fit during wrong but not right insertion, and associated metal, substrate, side chain and pyrophosphate reaction dynamics modulated nucleotide insertion. A third active site metal hastened right but not wrong insertion and was not essential for DNA synthesis. The previously hidden fidelity checkpoints uncovered reveal fundamental strategies of polymerase DNA repair synthesis in genomic instability. DNA polymerase (pol) λ performs DNA synthesis in base excision and double strand break repair. How pol λ accomplishes nucleotide insertion that can lead to mutagenesis and genomic instability was unclear. Here the authors employ time-lapse crystallography to reveal hidden polymerase checkpoints that enable right and wrong natural nucleotide insertion by pol λ.
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Affiliation(s)
- Joonas A Jamsen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
| | - David D Shock
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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18
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Nakamura T, Yamagata Y. Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc Natl Acad Sci U S A 2022; 119:e2203118119. [PMID: 35594391 PMCID: PMC9173781 DOI: 10.1073/pnas.2203118119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/09/2022] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli MutT prevents mutations by hydrolyzing mutagenic 8-oxo-2'-deoxyguanosine 5'-triphosphate (8-oxo-dGTP) in the presence of Mg2+ or Mn2+ ions. MutT is one of the most studied enzymes in the nucleoside diphosphate-linked moiety X (Nudix) hydrolase superfamily, which is widely distributed in living organisms. However, the catalytic mechanisms of most Nudix hydrolases, including two- or three-metal-ion mechanisms, are still unclear because these mechanisms are proposed using the structures mimicking the reaction states, such as substrate analog complexes. Here, we visualized the hydrolytic reaction process of MutT by time-resolved X-ray crystallography using a biological substrate, 8-oxo-dGTP, and an active metal ion, Mn2+. The reaction was initiated by soaking MutT crystals in a MnCl2 solution and stopped by freezing the crystals at various time points. In total, five types of intermediate structures were refined by investigating the time course of the electron densities in the active site as well as the anomalous signal intensities of Mn2+ ions. The structures and electron densities show that three Mn2+ ions bind to the Nudix motif of MutT and align the substrate 8-oxo-dGTP for catalysis. Accompanied by the coordination of the three Mn2+ ions, a water molecule, bound to a catalytic base, forms a binuclear Mn2+ center for nucleophilic substitution at the β-phosphorus of 8-oxo-dGTP. The reaction condition using Mg2+ also captured a structure in complex with three Mg2+ ions. This study provides the structural details essential for understanding the three-metal-ion mechanism of Nudix hydrolases and proposes that some of the Nudix hydrolases share this mechanism.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto, 862-8678, Japan
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19
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In crystallo observation of three metal ion promoted DNA polymerase misincorporation. Nat Commun 2022; 13:2346. [PMID: 35487947 PMCID: PMC9054841 DOI: 10.1038/s41467-022-30005-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/11/2022] [Indexed: 11/11/2022] Open
Abstract
Error-free replication of DNA is essential for life. Despite the proofreading capability of several polymerases, intrinsic polymerase fidelity is in general much higher than what base-pairing energies can provide. Although researchers have investigated this long-standing question with kinetics, structural determination, and computational simulations, the structural factors that dictate polymerase fidelity are not fully resolved. Time-resolved crystallography has elucidated correct nucleotide incorporation and established a three-metal-ion-dependent catalytic mechanism for polymerases. Using X-ray time-resolved crystallography, we visualize the complete DNA misincorporation process catalyzed by DNA polymerase η. The resulting molecular snapshots suggest primer 3´-OH alignment mediated by A-site metal ion binding is the key step in substrate discrimination. Moreover, we observe that C-site metal ion binding preceded the nucleotidyl transfer reaction and demonstrate that the C-site metal ion is strictly required for misincorporation. Our results highlight the essential but separate roles of the three metal ions in DNA synthesis. By observing DNA polymerase misincorporation with time-resolved crystallography, the authors visualize three-metal ion dependent polymerase catalysis and identify A-site metal-mediated primer alignment as a key step in nucleotide discrimination.
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20
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Jones SP, Goossen C, Lewis SD, Delaney AM, Gleghorn ML. Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes. J Struct Biol X 2022; 6:100066. [PMID: 35340590 PMCID: PMC8943300 DOI: 10.1016/j.yjsbx.2022.100066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/16/2022] Open
Abstract
RNases are varied in the RNA structures and sequences they target for cleavage and are an important type of enzyme in cells. Despite the numerous examples of RNases known, and of those with determined three-dimensional structures, relatively few examples exist with the RNase bound to intact cognate RNA substrate prior to cleavage. To better understand RNase structure and sequence specificity for RNA targets, in vitro methods used to assemble these enzyme complexes trapped in a pre-cleaved state have been developed for a number of different RNases. We have surveyed the Protein Data Bank for such structures and in this review detail methodologies that have successfully been used and relate them to the corresponding structures. We also offer ideas and suggestions for future method development. Many strategies within this review can be used in combination with X-ray crystallography, as well as cryo-EM, and other structure-solving techniques. Our hope is that this review will be used as a guide to resolve future yet-to-be-determined RNase-substrate complex structures.
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Affiliation(s)
- Seth P. Jones
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Christian Goossen
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, Lothrop St, Pittsburgh, PA 15261, United States
| | - Sean D. Lewis
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
- Mayo Clinic, 200 1st St SW, Rochester, MN 5590, United States
| | - Annie M. Delaney
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
| | - Michael L. Gleghorn
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, United States
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21
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Rossetto D, Mansy SS. Metals Are Integral to Life as We Know It. Front Cell Dev Biol 2022; 10:864830. [PMID: 35309928 PMCID: PMC8930831 DOI: 10.3389/fcell.2022.864830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Investigations of biology and the origins of life regularly focus on the components of the central dogma and thus the elements that compose nucleic acids and peptides. Less attention is given to the inorganic components of a biological cell, which are required for biological polymers to function. The Earth was and continues to be rich in metals, and so investigations of the emergence and evolution of life must account for the role that metal ions play. Evolution is shaped by what is present, and not all elements of the periodic table are equally accessible. The presence of metals, the solubility of their ions, and their intrinsic reactivity all impacted the composition of the cells that emerged. Geological and bioinformatic analyses clearly show that the suite of accessible metal ions changed over the history of the Earth; however, such analyses tend to be interpreted in comparison to average oceanic conditions, which do not represent well the many niche environments present on the Earth. While there is still debate concerning the sequence of events that led to extant biology, what is clear is that life as we know it requires metals, and that past and current metal-dependent events remain, at least partially, imprinted in the chemistry of the cell.
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Affiliation(s)
| | - Sheref S Mansy
- D-CIBIO, University of Trento, Povo, Italy
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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22
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Alpha-hydroxytropolones are noncompetitive inhibitors of human RNase H1 that bind to the active site and modulate substrate binding. J Biol Chem 2022; 298:101790. [PMID: 35247386 PMCID: PMC9034292 DOI: 10.1016/j.jbc.2022.101790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 11/23/2022] Open
Abstract
The ribonucleases H (RNases H) of HIV and hepatitis B virus are type 1 RNases H that are promising drug targets because inhibiting their activity blocks viral replication. Eukaryotic ribonuclease H1 (RNase H1) is an essential protein and a probable off-target enzyme for viral RNase H inhibitors. α-hydroxytropolones (αHTs) are a class of anti-RNase H inhibitors that can inhibit the HIV, hepatitis B virus, and human RNases H1; however, it is unclear how these inhibitors could be developed to distinguish between these enzymes. To accelerate the development of selective RNase H inhibitors, we performed biochemical and kinetic studies on the human enzyme, which was recombinantly expressed in Escherichia coli. Size-exclusion chromatography showed that free RNase H1 is monomeric and forms a 2:1 complex with a substrate of 12 bp. FRET heteroduplex cleavage assays were used to test inhibition of RNase H1 in steady-state kinetics by two structurally diverse αHTs, 110 and 404. We determined that turnover rate was reduced, but inhibition was not competitive with substrate, despite inhibitor binding to the active site. Given the compounds’ reversible binding to the active site, we concluded that traditional noncompetitive and mixed inhibition mechanisms are unlikely. Instead, we propose a model in which, by binding to the active site, αHTs stabilize an inactive enzyme–substrate–inhibitor complex. This new model clarifies the mechanism of action of αHTs against RNase H1 and will aid the development of RNase H inhibitors selective for the viral enzymes.
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23
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Liao Z, Oyama T, Kitagawa Y, Katayanagi K, Morikawa K, Oda M. Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography. Acta Crystallogr D Struct Biol 2022; 78:390-398. [PMID: 35234152 PMCID: PMC8900815 DOI: 10.1107/s2059798322000870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
The ribonuclease (RNase) H family of enzymes catalyze the specific cleavage of RNA strands of RNA/DNA hybrid duplexes and play an important role in DNA replication and repair. Since the first report of the crystal structure of RNase HI, its catalytic mechanisms, which require metal ions, have been discussed based on numerous structural and functional analyses, including X-ray crystallography. In contrast, the function of the conserved histidine residue (His124 in Escherichia coli) in the flexible loop around the active site remains poorly understood, although an important role was suggested by NMR analyses. Here, novel high-resolution X-ray crystal structures of E. coli RNase HI are described, with a particular focus on the interactions of divalent cations with His124 oriented towards the active site. The enzyme-Mg2+ complex contains two metal ions in the active site, one of which has previously been observed. The second ion lies alongside the first and binds to His124 in an octahedral coordination scheme. In the enzyme-Zn2+ complex a single metal ion was found to bind to the active site, showing a tetrahedral coordination geometry with the surrounding atoms, including His124. These results provide structural evidence that His124 plays a crucial role in the catalytic activity of RNase HI by interacting weakly and transiently with metal ions in the catalytic center.
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Affiliation(s)
- Zengwei Liao
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Yumi Kitagawa
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Katsuo Katayanagi
- Graduate School of Intergrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Kosuke Morikawa
- Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
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24
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Lee H, Cho H, Kim J, Lee S, Yoo J, Park D, Lee G. RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids. Nucleic Acids Res 2022; 50:1801-1814. [PMID: 34788459 PMCID: PMC8886854 DOI: 10.1093/nar/gkab1064] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022] Open
Abstract
RNase H is involved in fundamental cellular processes and is responsible for removing the short stretch of RNA from Okazaki fragments and the long stretch of RNA from R-loops. Defects in RNase H lead to embryo lethality in mice and Aicardi-Goutieres syndrome in humans, suggesting the importance of RNase H. To date, RNase H is known to be a non-sequence-specific endonuclease, but it is not known whether it performs other functions on the structural variants of RNA:DNA hybrids. Here, we used Escherichia coli RNase H as a model, and examined its catalytic mechanism and its substrate recognition modes, using single-molecule FRET. We discovered that RNase H acts as a processive exoribonuclease on the 3' DNA overhang side but as a distributive non-sequence-specific endonuclease on the 5' DNA overhang side of RNA:DNA hybrids or on blunt-ended hybrids. The high affinity of previously unidentified double-stranded (ds) and single-stranded (ss) DNA junctions flanking RNA:DNA hybrids may help RNase H find the hybrid substrates in long genomic DNA. Our study provides new insights into the multifunctionality of RNase H, elucidating unprecedented roles of junctions and ssDNA overhang on RNA:DNA hybrids.
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Affiliation(s)
- Hyunjee Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - HyeokJin Cho
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jooyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Sua Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungmin Yoo
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Daeho Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Single-Molecule Biology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
- Cell Mechanobiology Laboratory, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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25
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Becskei A, Rahaman S. The life and death of RNA across temperatures. Comput Struct Biotechnol J 2022; 20:4325-4336. [PMID: 36051884 PMCID: PMC9411577 DOI: 10.1016/j.csbj.2022.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans. We illustrate the temperature dependence of RNA metabolism with examples from the synthesis to the degradation of mRNAs, and review recently emerged questions. Are cells exposed to greater temperature variations and gradients than previously surmised? How do cells reconcile the conflicting thermal stability requirements of primary and tertiary structures of RNAs? To what extent do enzymes contribute to the temperature compensation of the reaction rates in mRNA turnover by lowering the energy barrier of the catalyzed reactions? We conclude with the ecological, forensic applications of the temperature-dependence of RNA degradation and the biotechnological aspects of mRNA vaccine production.
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26
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Manigrasso J, De Vivo M, Palermo G. Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis. ACS Catal 2021; 11:8786-8797. [PMID: 35145762 DOI: 10.1021/acscatal.1c01825] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent in crystallo reaction intermediates have detailed how nucleic acid hydrolysis occurs in the RNA ribonuclease H1 (RNase H1), a fundamental metalloenzyme involved in maintaining the human genome. At odds with the previous characterization, these in crystallo structures unexpectedly captured multiple metal ions (K+ and Mg2+) transiently bound in the vicinity of the two-metal-ion active site. Using multi-microsecond all-atom molecular dynamics and free-energy simulations, we investigated the functional implications of the dynamic exchange of multiple K+ and Mg2+ ions at the RNase H1 reaction center. We found that such ions are timely positioned at non-overlapping locations near the active site, at different stages of catalysis, being crucial for both reactants' alignment and leaving group departure. We also found that this cation trafficking is tightly regulated by variations of the solution's ionic strength and is aided by two conserved second-shell residues, E188 and K196, suggesting a mechanism for the cations' recruitment during catalysis. These results indicate that controlled trafficking of multi-cation dynamics, opportunely prompted by second-shell residues, is functionally essential to the complex enzymatic machinery of the RNase H1. These findings revise the current knowledge on the RNase H1 catalysis and open new catalytic possibilities for other similar metalloenzymes including, but not limited to, CRISPR-Cas9, group II intron ribozyme and the human spliceosome.
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Affiliation(s)
- Jacopo Manigrasso
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, 16163, Italy.,Department of Bioengineering, University of California Riverside, Riverside, CA 52512, United States
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, CA 52512, United States.,Department of Chemistry, University of California Riverside, Riverside, CA 52512, United States
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27
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Chen Y, Khazina E, Izaurralde E, Weichenrieder O. Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex. Nucleic Acids Res 2021; 49:6489-6510. [PMID: 34038562 PMCID: PMC8216464 DOI: 10.1093/nar/gkab414] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/07/2023] Open
Abstract
The CCR4 and CAF1 deadenylases physically interact to form the CCR4-CAF1 complex and function as the catalytic core of the larger CCR4-NOT complex. Together, they are responsible for the eventual removal of the 3′-poly(A) tail from essentially all cellular mRNAs and consequently play a central role in the posttranscriptional regulation of gene expression. The individual properties of CCR4 and CAF1, however, and their respective contributions in different organisms and cellular environments are incompletely understood. Here, we determined the crystal structure of a human CCR4-CAF1 complex and characterized its enzymatic and substrate recognition properties. The structure reveals specific molecular details affecting RNA binding and hydrolysis, and confirms the CCR4 nuclease domain to be tethered flexibly with a considerable distance between both enzyme active sites. CCR4 and CAF1 sense nucleotide identity on both sides of the 3′-terminal phosphate, efficiently differentiating between single and consecutive non-A residues. In comparison to CCR4, CAF1 emerges as a surprisingly tunable enzyme, highly sensitive to pH, magnesium and zinc ions, and possibly allowing distinct reaction geometries. Our results support a picture of CAF1 as a primordial deadenylase, which gets assisted by CCR4 for better efficiency and by the assembled NOT proteins for selective mRNA targeting and regulation.
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Affiliation(s)
- Ying Chen
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, D-72076 Tübingen, Germany
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28
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Dürr SL, Bohuszewicz O, Berta D, Suardiaz R, Jambrina PG, Peter C, Shao Y, Rosta E. The Role of Conserved Residues in the DEDDh Motif: the Proton-Transfer Mechanism of HIV-1 RNase H. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Simon L. Dürr
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Olga Bohuszewicz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | - Dénes Berta
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
| | - Reynier Suardiaz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | | | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
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29
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Borišek J, Magistrato A. An Expanded Two-Zn2+-Ion Motif Orchestrates Pre-mRNA Maturation in the 3′-End Processing Endonuclease Machinery. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Alessandra Magistrato
- CNR-IOM-Democritos National Simulation Center c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy
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30
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Ando T, Jongruja N, Okumura N, Morikawa K, Kanaya S, Takao T. Identification of the ternary complex of ribonuclease HI:RNA/DNA hybrid:metal ions by ESI mass spectrometry. J Biol Chem 2021; 296:100462. [PMID: 33639158 PMCID: PMC8042393 DOI: 10.1016/j.jbc.2021.100462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/14/2021] [Accepted: 02/23/2021] [Indexed: 12/17/2022] Open
Abstract
Ribonuclease HI, an endoribonuclease, catalyzes the hydrolysis of the RNA strand of an RNA/DNA hybrid and requires divalent metal ions for its enzymatic activity. However, the mechanistic details of the activity of ribonuclease HI and its interaction with divalent metal ions remain unclear. In this study, we performed real-time monitoring of the enzyme–substrate complex in the presence of divalent metal ions (Mn2+ or Zn2+) using electrospray ionization–mass spectrometry (ESI-MS). The findings provide clear evidence that the enzymatic activity of the ternary complex requires the binding of two divalent metal ions. The Zn2+ ions bind to both the enzyme itself and the enzyme:substrate complex more strongly than Mn2+ ions, and gives, in part, the ternary complex, [RNase HI:nicked RNA/DNA hybrid:2Zn2+], suggesting that the ternary complex is retained, even after the hydrolysis of the substrate. The collective results presented herein shed new light on the essential role of divalent metal ions in the activity of ribonuclease HI and demonstrate how Zn2+ ions confer inhibitory properties on the activity of this enzyme by forming a highly stable complex with the substrate.
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Affiliation(s)
- Tomoshige Ando
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Nobuaki Okumura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kosuke Morikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Osaka, Japan.
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31
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Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tanmoy Pal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Luke Xie
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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32
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Casalino L, Nierzwicki Ł, Jinek M, Palermo G. Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics. ACS Catal 2020; 10:13596-13605. [PMID: 33520346 PMCID: PMC7842700 DOI: 10.1021/acscatal.0c03566] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum-classical molecular dynamics (MD) and free energy methods are used to disclose the two-metal-dependent mechanism of phosphodiester bond cleavage in CRISPR-Cas9. Ab initio MD reveals a conformational rearrangement of the Mg2+-bound RuvC active site, which entails the relocation of H983 to act as a general base. Then, the DNA cleavage proceeds through a concerted associative pathway fundamentally assisted by the joint dynamics of the two Mg2+ ions. This clarifies previous controversial experimental evidence, which could not fully establish the catalytic role of the conserved H983 and the metal cluster conformation. The comparison with other two-metal-dependent enzymes supports the identified mechanism and suggests a common catalytic strategy for genome editing and recombination. Overall, the non-target DNA cleavage catalysis described here resolves a fundamental open question in the CRISPR-Cas9 biology and provides valuable insights for improving the catalytic efficiency and the metal-dependent function of the Cas9 enzyme, which are at the basis of the development of genome editing tools.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
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33
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González de Cózar JM, Carretero-Junquera M, Ciesielski GL, Miettinen SM, Varjosalo M, Kaguni LS, Dufour E, Jacobs HT. A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1. J Biochem 2020; 168:515-533. [PMID: 32589740 PMCID: PMC7657459 DOI: 10.1093/jb/mvaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 11/14/2022] Open
Abstract
In eukaryotes, ribonuclease H1 (RNase H1) is involved in the processing and removal of RNA/DNA hybrids in both nuclear and mitochondrial DNA. The enzyme comprises a C-terminal catalytic domain and an N-terminal hybrid-binding domain (HBD), separated by a linker of variable length, 115 amino acids in Drosophila melanogaster (Dm). Molecular modelling predicted this extended linker to fold into a structure similar to the conserved HBD. Based on a deletion series, both the catalytic domain and the conserved HBD were required for high-affinity binding to heteroduplex substrates, while loss of the novel HBD led to an ∼90% drop in Kcat with a decreased KM, and a large increase in the stability of the RNA/DNA hybrid-enzyme complex, supporting a bipartite-binding model in which the second HBD facilitates processivity. Shotgun proteomics following in vivo cross-linking identified single-stranded DNA-binding proteins from both nuclear and mitochondrial compartments, respectively RpA-70 and mtSSB, as prominent interaction partners of Dm RNase H1. However, we were not able to document direct and stable interactions with mtSSB when the proteins were co-overexpressed in S2 cells, and functional interactions between them in vitro were minor.
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Affiliation(s)
| | | | - Grzegorz L Ciesielski
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - Sini M Miettinen
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Laurie S Kaguni
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Dufour
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
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34
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Berta D, Buigues PJ, Badaoui M, Rosta E. Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H + and Mg 2+ ions in enzyme reactions. Curr Opin Struct Biol 2020; 61:198-206. [PMID: 32065923 DOI: 10.1016/j.sbi.2020.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022]
Abstract
Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details of the proton transfers coupled to the phosphate cleavage is one of the key challenges in QM/MM calculations of these and other enzyme catalyzed reactions. The lack of experimental information offers both an opportunity for computations as well as often unresolved controversies. We discuss the example of small GTPases including the important human Ras protein. The high dimensionality and chemical complexity of these reactions demand carefully chosen computational techniques both in terms of the underlying quantum chemical theory and the sampling of the conformational ensemble. We also point out the important role of Mg2+ ions, and recent advances in their transient involvement in the catalytic mechanisms.
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Affiliation(s)
- Dénes Berta
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Pedro J Buigues
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Magd Badaoui
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom.
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35
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Donati E, Genna V, De Vivo M. Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases. J Am Chem Soc 2020; 142:2823-2834. [PMID: 31939291 PMCID: PMC7993637 DOI: 10.1021/jacs.9b10656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Enzymes of the 5′ structure-specific
nuclease family are crucial for DNA repair, replication, and recombination.
One such enzyme is the human exonuclease 1 (hExo1) metalloenzyme,
which cleaves DNA strands, acting primarily as a processive 5′-3′
exonuclease and secondarily as a 5′-flap endonuclease. Recently,
in crystallo reaction intermediates have elucidated how hExo1 exerts
hydrolysis of DNA phosphodiester bonds. These hExo1 structures show
a third metal ion intermittently bound close to the two-metal-ion
active site, to which recessed ends or 5′-flap substrates bind.
Evidence of this third ion has been observed in several nucleic-acid-processing
metalloenzymes. However, there is still debate over what triggers
the (un)binding of this transient third ion during catalysis and whether
this ion has a catalytic function. Using extended molecular dynamics
and enhanced sampling free-energy simulations, we observed that the
carboxyl side chain of Glu89 (located along the arch motif in hExo1)
flips frequently from the reactant state to the product state. The
conformational flipping of Glu89 allows one metal ion to be recruited
from the bulk and promptly positioned near the catalytic center. This
is in line with the structural evidence. Additionally, our simulations
show that the third metal ion assists the departure, through the mobile
arch, of the nucleotide monophosphate product from the catalytic site.
Structural comparisons of nuclease enzymes suggest that this Glu(Asp)-mediated
mechanism for third ion recruitment and nucleic acid hydrolysis may
be shared by other 5′ structure-specific nucleases.
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Affiliation(s)
- Elisa Donati
- Laboratory of Molecular Modelling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy
| | - Vito Genna
- Laboratory of Molecular Modelling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy
| | - Marco De Vivo
- Laboratory of Molecular Modelling & Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 Genoa , Italy
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36
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Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol Cell 2019; 76:44-56.e3. [PMID: 31444105 DOI: 10.1016/j.molcel.2019.06.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/16/2019] [Accepted: 06/27/2019] [Indexed: 02/01/2023]
Abstract
Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.
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37
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Hyjek M, Figiel M, Nowotny M. RNases H: Structure and mechanism. DNA Repair (Amst) 2019; 84:102672. [PMID: 31371183 DOI: 10.1016/j.dnarep.2019.102672] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022]
Abstract
RNases H are a family of endonucleases that hydrolyze RNA residues in various nucleic acids. These enzymes are present in all branches of life, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements. RNases H are divided into two main classes (RNases H1 and H2 or type 1 and type 2 enzymes) with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. Additionally, a third class is found in some Archaea and bacteria. Besides distinct cellular functions specific for each type of RNases H, this family of proteins is generally involved in the maintenance of genome stability with overlapping and cooperative role in removal of R-loops thus preventing their accumulation. Extensive biochemical and structural studies of RNases H provided not only a comprehensive and complete picture of their mechanism but also revealed key basic principles of nucleic acid recognition and processing. RNase H1 is present in prokaryotes and eukaryotes and cleaves RNA in RNA/DNA hybrids. Its main function is hybrid removal, notably in the context of R-loops. RNase H2, which is also present in all branches of life, can play a similar role but it also has a specialized function in the cleavage of single ribonucleotides embedded in the DNA. RNase H3 is present in Archaea and bacteria and is closely related to RNase H2 in sequence and structure but has RNase H1-like biochemical properties. This review summarizes the mechanisms of substrate recognition and enzymatic cleavage by different classes of RNases H with particular insights into structural features of nucleic acid binding, specificity towards RNA and/or DNA strands and catalysis.
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Affiliation(s)
- Malwina Hyjek
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Marcin Nowotny
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
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38
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Genna V, Marcia M, De Vivo M. A Transient and Flexible Cation-π Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases. J Am Chem Soc 2019; 141:10770-10776. [PMID: 31251587 DOI: 10.1021/jacs.9b03663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metal-dependent DNA and RNA nucleases are enzymes that cleave nucleic acids with great efficiency and precision. These enzyme-mediated hydrolytic reactions are fundamental for the replication, repair, and storage of genetic information within the cell. Here, extensive classical and quantum-based free-energy molecular simulations show that a cation-π interaction is transiently formed in situ at the metal core of Bacteriophage-λ Exonuclease (Exo-λ), during catalysis. This noncovalent interaction (Lys131-Tyr154) triggers nucleophile activation for nucleotide excision. Then, our simulations also show the oscillatory dynamics and swinging of the newly formed cation-π dyad, whose conformational change may favor proton release from the cationic Lys131 to the bulk solution, thus restoring the precatalytic protonation state in Exo-λ. Altogether, we report on the novel mechanistic character of cation-π interactions for catalysis. Structural and bioinformatic analyses support that flexible orientation and transient formation of mobile cation-π interactions may represent a common catalytic strategy to promote nucleic acid hydrolysis in DNA and RNA nucleases.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble , 71 Avenue des Martyrs , Grenoble 38042 , France
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery , Istituto Italiano di Tecnologia , Via Morego 30 , 16163 , Genoa , Italy
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39
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Su Y, Ghodke PP, Egli M, Li L, Wang Y, Guengerich FP. Human DNA polymerase η has reverse transcriptase activity in cellular environments. J Biol Chem 2019; 294:6073-6081. [PMID: 30842261 DOI: 10.1074/jbc.ra119.007925] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Indexed: 12/24/2022] Open
Abstract
Classical DNA and RNA polymerase (pol) enzymes have defined roles with their respective substrates, but several pols have been found to have multiple functions. We reported previously that purified human DNA pol η (hpol η) can incorporate both deoxyribonucleoside triphosphates (dNTPs) and ribonucleoside triphosphates (rNTPs) and can use both DNA and RNA as substrates. X-ray crystal structures revealed that two pol η residues, Phe-18 and Tyr-92, behave as steric gates to influence sugar selectivity. However, the physiological relevance of these phenomena has not been established. Here, we show that purified hpol η adds rNTPs to DNA primers at physiological rNTP concentrations and in the presence of competing dNTPs. When two rATPs were inserted opposite a cyclobutane pyrimidine dimer, the substrate was less efficiently cleaved by human RNase H2. Human XP-V fibroblast extracts, devoid of hpol η, could not add rNTPs to a DNA primer, but the expression of transfected hpol η in the cells restored this ability. XP-V cell extracts did not add dNTPs to DNA primers hybridized to RNA, but could when hpol η was expressed in the cells. HEK293T cell extracts could add dNTPs to DNA primers hybridized to RNA, but lost this ability if hpol η was deleted. Interestingly, a similar phenomenon was not observed when other translesion synthesis (TLS) DNA polymerases-hpol ι, κ, or ζ-were individually deleted. These results suggest that hpol η is one of the major reverse transcriptases involved in physiological processes in human cells.
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Affiliation(s)
- Yan Su
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Pratibha P Ghodke
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Martin Egli
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Lin Li
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146.
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40
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Ka Man Tse C, Xu J, Xu L, Sheong FK, Wang S, Chow HY, Gao X, Li X, Cheung PPH, Wang D, Zhang Y, Huang X. Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate. Nat Catal 2019; 2:228-235. [PMID: 31179024 PMCID: PMC6548511 DOI: 10.1038/s41929-019-0227-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
RNA polymerase II (Pol II) utilises the same active site for polymerization and intrinsic cleavage. Pol II proofreads the nascent transcript by its intrinsic nuclease activity to maintain high transcriptional fidelity critical for cell growth and viability. The detailed catalytic mechanism of intrinsic cleavage remains unknown. Here, we combined ab initio quantum mechanics/molecular mechanics studies and biochemical cleavage assays to show that Pol II utilises downstream phosphate oxygen to activate the attacking nucleophile in hydrolysis, while the newly formed 3'-end is protonated through active-site water without a defined general acid. Experimentally, alteration of downstream phosphate oxygen either by 2'-5' sugar linkage or stereo-specific thio-substitution of phosphate oxygen drastically reduced cleavage rate. We showed by N7-modification that guanine nucleobase does not directly involve as acid-base catalyst. Our proposed mechanism provides important insights into the understanding of intrinsic transcriptional cleavage reaction, an essential step of transcriptional fidelity control.
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Affiliation(s)
- Carmen Ka Man Tse
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Jun Xu
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Liang Xu
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry, Sun Yat-Sen University, Guangzhou, China
| | - Fu Kit Sheong
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shenglong Wang
- Department of Chemistry, New York University, New York, New York 10003 United States
| | - Hoi Yee Chow
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Centre (CBRC), CEMSE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Hong Kong
| | - Peter Pak-Hang Cheung
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Dong Wang
- Department of Cellular and Molecular Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003 United States
- NYU-ECNU Centre for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xuhui Huang
- Department of Chemistry, Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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41
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Tsai M. Catalytic mechanism of DNA polymerases-Two metal ions or three? Protein Sci 2019; 28:288-291. [PMID: 30368961 PMCID: PMC6319748 DOI: 10.1002/pro.3542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Ming‐Daw Tsai
- Institute of Biological Chemistry, Academia SinicaTaipei115Taiwan
- Institute of Biochemical Sciences, National Taiwan UniversityTaipei106Taiwan
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