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Betancurt-Anzola L, Martínez-Carranza M, Delarue M, Zatopek KM, Gardner AF, Sauguet L. Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases. Nat Commun 2023; 14:8306. [PMID: 38097591 PMCID: PMC10721889 DOI: 10.1038/s41467-023-44125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
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Affiliation(s)
- Leonardo Betancurt-Anzola
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
- New England Biolabs France, 5 Rue Henri Auguste Desbruères, 91000, Évry-Courcouronnes, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Kelly M Zatopek
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Andrew F Gardner
- New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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Pichard-Kostuch A, Da Cunha V, Oberto J, Sauguet L, Basta T. The universal Sua5/TsaC family evolved different mechanisms for the synthesis of a key tRNA modification. Front Microbiol 2023; 14:1204045. [PMID: 37415821 PMCID: PMC10321239 DOI: 10.3389/fmicb.2023.1204045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
TsaC/Sua5 family of enzymes catalyzes the first step in the synthesis of N6-threonyl-carbamoyl adenosine (t6A) one of few truly ubiquitous tRNA modifications important for translation accuracy. TsaC is a single domain protein while Sua5 proteins contains a TsaC-like domain and an additional SUA5 domain of unknown function. The emergence of these two proteins and their respective mechanisms for t6A synthesis remain poorly understood. Here, we performed phylogenetic and comparative sequence and structure analysis of TsaC and Sua5 proteins. We confirm that this family is ubiquitous but the co-occurrence of both variants in the same organism is rare and unstable. We further find that obligate symbionts are the only organisms lacking sua5 or tsaC genes. The data suggest that Sua5 was the ancestral version of the enzyme while TsaC arose via loss of the SUA5 domain that occurred multiple times in course of evolution. Multiple losses of one of the two variants in combination with horizontal gene transfers along a large range of phylogenetic distances explains the present day patchy distribution of Sua5 and TsaC. The loss of the SUA5 domain triggered adaptive mutations affecting the substrate binding in TsaC proteins. Finally, we identified atypical Sua5 proteins in Archaeoglobi archaea that seem to be in the process of losing the SUA5 domain through progressive gene erosion. Together, our study uncovers the evolutionary path for emergence of these homologous isofunctional enzymes and lays the groundwork for future experimental studies on the function of TsaC/Sua5 proteins in maintaining faithful translation.
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Affiliation(s)
- Adeline Pichard-Kostuch
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Violette Da Cunha
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jacques Oberto
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Tamara Basta
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
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3
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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4
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Madru C, Tekpinar AD, Rosario S, Czernecki D, Brûlé S, Sauguet L, Delarue M. Fast and efficient purification of SARS-CoV-2 RNA dependent RNA polymerase complex expressed in Escherichia coli. PLoS One 2021; 16:e0250610. [PMID: 33914787 PMCID: PMC8084133 DOI: 10.1371/journal.pone.0250610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/09/2021] [Indexed: 01/18/2023] Open
Abstract
To stop the COVID-19 pandemic due to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which caused more than 2.5 million deaths to date, new antiviral molecules are urgently needed. The replication of SARS-CoV-2 requires the RNA-dependent RNA polymerase (RdRp), making RdRp an excellent target for antiviral agents. RdRp is a multi-subunit complex composed of 3 viral proteins named nsp7, nsp8 and nsp12 that ensure the ~30 kb RNA genome’s transcription and replication. The main strategies employed so far for the overproduction of RdRp consist of expressing and purifying the three subunits separately before assembling the complex in vitro. However, nsp12 shows limited solubility in bacterial expression systems and is often produced in insect cells. Here, we describe an alternative strategy to co-express the full SARS-CoV-2 RdRp in E. coli, using a single plasmid. Characterization of the purified recombinant SARS-CoV-2 RdRp shows that it forms a complex with the expected (nsp7)(nsp8)2(nsp12) stoichiometry. RNA polymerization activity was measured using primer-extension assays showing that the purified enzyme is functional. The purification protocol can be achieved in one single day, surpassing in speed all other published protocols. Our construct is ideally suited for screening RdRp and its variants against very large chemical compounds libraries and has been made available to the scientific community through the Addgene plasmid depository (Addgene ID: 165451).
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Affiliation(s)
- Clément Madru
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
| | - Ayten Dizkirici Tekpinar
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- Department of Molecular Biology and Genetics, Faculty of Science, Van Yüzüncü Yıl University, Van, Turkey
| | - Sandrine Rosario
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
| | - Dariusz Czernecki
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- École Doctorale Complexité du Vivant, Sorbonne Université, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR, Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- * E-mail: (LS); (MD)
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur & CNRS UMR, Paris, France
- * E-mail: (LS); (MD)
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5
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Zatopek KM, Alpaslan E, Evans T, Sauguet L, Gardner A. Novel ribonucleotide discrimination in the RNA polymerase-like two-barrel catalytic core of Family D DNA polymerases. Nucleic Acids Res 2020; 48:12204-12218. [PMID: 33137176 PMCID: PMC7708050 DOI: 10.1093/nar/gkaa986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Family D DNA polymerase (PolD) is the essential replicative DNA polymerase for duplication of most archaeal genomes. PolD contains a unique two-barrel catalytic core absent from all other DNA polymerase families but found in RNA polymerases (RNAPs). While PolD has an ancestral RNA polymerase catalytic core, its active site has evolved the ability to discriminate against ribonucleotides. Until now, the mechanism evolved by PolD to prevent ribonucleotide incorporation was unknown. In all other DNA polymerase families, an active site steric gate residue prevents ribonucleotide incorporation. In this work, we identify two consensus active site acidic (a) and basic (b) motifs shared across the entire two-barrel nucleotide polymerase superfamily, and a nucleotide selectivity (s) motif specific to PolD versus RNAPs. A novel steric gate histidine residue (H931 in Thermococcus sp. 9°N PolD) in the PolD s-motif both prevents ribonucleotide incorporation and promotes efficient dNTP incorporation. Further, a PolD H931A steric gate mutant abolishes ribonucleotide discrimination and readily incorporates a variety of 2' modified nucleotides. Taken together, we construct the first putative nucleotide bound PolD active site model and provide structural and functional evidence for the emergence of DNA replication through the evolution of an ancestral RNAP two-barrel catalytic core.
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Affiliation(s)
| | - Ece Alpaslan
- New England Biolabs, 240 County Road Ipswich, MA 01938, USA
| | - Thomas C Evans
- New England Biolabs, 240 County Road Ipswich, MA 01938, USA
| | - Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France
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6
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Fourati Z, Sauguet L, Delarue M. Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Acta Crystallogr D Struct Biol 2020; 76:668-675. [PMID: 32627739 PMCID: PMC7336382 DOI: 10.1107/s205979832000772x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/05/2020] [Indexed: 11/21/2022] Open
Abstract
GLIC is a bacterial homologue of the pentameric ligand-gated ion channels (pLGICs) that mediate the fast chemical neurotransmission of nerve signalling in eukaryotes. Because the activation and allosteric modulation features are conserved among prokaryotic and eukaryotic pLGICs, GLIC is commonly used as a model to study the allosteric transition and structural pharmacology of pLGICs. It has previously been shown that GLIC is inhibited by some carboxylic acid derivatives. Here, experimental evidence for carboxylate binding to GLIC is provided by solving its X-ray structures with a series of monocarboxylate and dicarboxylate derivatives, and two carboxylate-binding sites are described: (i) the `intersubunit' site that partially overlaps the canonical pLGIC orthosteric site and (ii) the `intrasubunit' vestibular site, which is only occupied by a subset of the described derivatives. While the intersubunit site is widely conserved in all pLGICs, the intrasubunit site is only conserved in cationic eukaryotic pLGICs. This study sheds light on the importance of these two extracellular modulation sites as potential drug targets in pLGICs.
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Affiliation(s)
- Zaineb Fourati
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Ludovic Sauguet
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
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7
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Madru C, Henneke G, Raia P, Hugonneau-Beaufet I, Pehau-Arnaudet G, England P, Lindahl E, Delarue M, Carroni M, Sauguet L. Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun 2020; 11:1591. [PMID: 32221299 PMCID: PMC7101311 DOI: 10.1038/s41467-020-15392-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/05/2020] [Indexed: 11/09/2022] Open
Abstract
Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. In Eukarya and Archaea, the processivity of replicative DNAPs is greatly enhanced by its binding to the proliferative cell nuclear antigen (PCNA) that encircles the DNA. We determined the cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi at 3.77 Å. Using an integrative structural biology approach — combining cryo-EM, X-ray crystallography, protein–protein interaction measurements, and activity assays — we describe the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA. PolD recruits PCNA via a complex mechanism, which requires two different PIP-boxes. We infer that the second PIP-box, which is shared with the eukaryotic Polα replicative DNAP, plays a dual role in binding either PCNA or primase, and could be a master switch between an initiation and a processive phase during replication. Replicative DNA polymerases (DNAPs) have evolved the ability to copy the genome with high processivity and fidelity. Here, the authors present a cryo-EM structure of the DNA-bound PolD–PCNA complex from Pyrococcus abyssi to reveal the molecular basis for the interaction and cooperativity between a replicative DNAP and PCNA.
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Affiliation(s)
- Clément Madru
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | - Ghislaine Henneke
- CNRS, Ifremer, Université de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.,Sorbonne Université, École Doctorale Complexité du Vivant (ED515), Paris, France
| | - Inès Hugonneau-Beaufet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | | | - Patrick England
- Molecular Biophysics Platform, C2RT, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and CNRS UMR 3528, Paris, France.
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Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Rep 2019; 23:993-1004. [PMID: 29694907 DOI: 10.1016/j.celrep.2018.03.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/02/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022] Open
Abstract
Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics and drug development. Functional studies have implicated conserved sites of both potentiation and inhibition in pentameric ligand-gated ion channels, but a detailed structural mechanism for these bimodal effects is lacking. The prokaryotic model protein GLIC recapitulates anesthetic modulation of human ion channels, and it is accessible to structure determination in both apparent open and closed states. Here, we report ten X-ray structures and electrophysiological characterization of GLIC variants in the presence and absence of general anesthetics, including the surgical agent propofol. We show that general anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain. Our results support an integrated, multi-site mechanism for allosteric modulation, and they provide atomic details of both potentiation and inhibition by one of the most common general anesthetics.
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Affiliation(s)
- Zaineb Fourati
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Stephanie A Heusser
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Haidai Hu
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France; Sorbonne Universités, UPMC University Paris 6, 75005 Paris, France
| | - Reinis R Ruza
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, 11428 Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France.
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9
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Sauguet L. The Extended "Two-Barrel" Polymerases Superfamily: Structure, Function and Evolution. J Mol Biol 2019; 431:4167-4183. [PMID: 31103775 DOI: 10.1016/j.jmb.2019.05.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/14/2023]
Abstract
DNA and RNA polymerases (DNAP and RNAP) play central roles in genome replication, maintenance and repair, as well as in the expression of genes through their transcription. Multisubunit RNAPs carry out transcription and are represented, without exception, in all cellular life forms as well as in nucleo-cytoplasmic DNA viruses. Since their discovery, multisubunit RNAPs have been the focus of intense structural and functional studies revealing that they all share a well-conserved active-site region called the two-barrel catalytic core. The two-barrel core hosts the polymerase active site, which is located at the interface between two double-psi β-barrel domains that contribute distinct amino acid residues to the active site in an asymmetrical fashion. Recently, sequencing and structural studies have added a surprising variety of DNA and RNA to the two-barrel superfamily, including the archaeal replicative DNAP (PolD), which extends the family to DNA-dependent DNAPs involved in replication. While all these polymerases share a minimal core that must have been present in their common ancestor, the two-barrel polymerase superfamily now encompasses a remarkable diversity of enzymes, including DNA-dependent RNAPs, RNA-dependent RNAPs, and DNA-dependent DNAPs, which participate in critical biological processes such as DNA transcription, DNA replication, and gene silencing. The present review will discuss both common features and differences among the extended two-barrel polymerase superfamily, focusing on the newly discovered members. Comparing their structures provides insights into the molecular mechanisms evolved by the contemporary two-barrel polymerases to accomplish their different biological functions.
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Affiliation(s)
- Ludovic Sauguet
- Institut Pasteur, Unité de Dynamique Structurale des Macromolécules, 75015 Paris, France.
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10
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Raia P, Carroni M, Henry E, Pehau-Arnaudet G, Brûlé S, Béguin P, Henneke G, Lindahl E, Delarue M, Sauguet L. Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases. PLoS Biol 2019; 17:e3000122. [PMID: 30657780 PMCID: PMC6355029 DOI: 10.1371/journal.pbio.3000122] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/31/2019] [Accepted: 01/10/2019] [Indexed: 02/01/2023] Open
Abstract
PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.
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Affiliation(s)
- Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France
- Sorbonne Université, Ecole Doctorale Complexité du Vivant (ED515), Paris, France
| | - Marta Carroni
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Etienne Henry
- CNRS, IFREMER, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | | | - Sébastien Brûlé
- Molecular Biophysics Platform, Pasteur Institute, C2RT and CNRS UMR 3528, Paris, France
| | - Pierre Béguin
- Unit of Molecular Biology of Gene in Extremophiles, Pasteur Institute, Paris, France
| | - Ghislaine Henneke
- IFREMER, CNRS, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Erik Lindahl
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France
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11
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Raia P, Béguin P, Henneke G, Delarue M, Sauguet L. Secret From the ABYSS: Structures of the D-Family DNA Polymerase (POLD) Reveal that DNA Replication and DNA Transcription Share a Joint Evolutionary History in Archaea. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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12
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Howard RJ, Fourati Z, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Details of an Allosteric Mechanism for Bimodal Anesthetic Modulation of Pentameric Ligand-Gated Ion Channels. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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13
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Sauguet L, Raia P, Henneke G, Delarue M. Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography. Nat Commun 2016; 7:12227. [PMID: 27548043 PMCID: PMC4996933 DOI: 10.1038/ncomms12227] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023] Open
Abstract
Archaeal replicative DNA polymerase D (PolD) constitute an atypical class of DNA polymerases made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2), both with unknown structures. We have determined the crystal structures of Pyrococcus abyssi DP1 and DP2 at 2.5 and 2.2 Å resolution, respectively, revealing a catalytic core strikingly different from all other known DNA polymerases (DNAPs). Rather, the PolD DP2 catalytic core has the same ‘double-psi β-barrel' architecture seen in the RNA polymerase (RNAP) superfamily, which includes multi-subunit transcriptases of all domains of life, homodimeric RNA-silencing pathway RNAPs and atypical viral RNAPs. This finding bridges together, in non-viral world, DNA transcription and DNA replication within the same protein superfamily. This study documents further the complex evolutionary history of the DNA replication apparatus in different domains of life and proposes a classification of all extant DNAPs. The structures of many DNA polymerases is known, but PolD was a missing piece. Here, the authors report the crystal structure of this protein and use it to connect the DNA replication machinery with the transcription machinery in the same protein family.
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Affiliation(s)
- Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France
| | - Pierre Raia
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France.,Pierre and Marie Curie University, Paris 6, 75006 Paris, France
| | - Ghislaine Henneke
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,UBO, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, 75015 Paris, France
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14
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Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure 2016; 24:595-605. [DOI: 10.1016/j.str.2016.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 01/09/2023]
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15
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Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N. Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel. PLoS One 2016; 11:e0149795. [PMID: 26910105 PMCID: PMC4765991 DOI: 10.1371/journal.pone.0149795] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/04/2016] [Indexed: 12/15/2022] Open
Abstract
GLIC receptor is a bacterial pentameric ligand-gated ion channel whose action is inhibited by xenon. Xenon has been used in clinical practice as a potent gaseous anaesthetic for decades, but the molecular mechanism of interactions with its integral membrane receptor targets remains poorly understood. Here we characterize by X-ray crystallography the xenon-binding sites within both the open and "locally-closed" (inactive) conformations of GLIC. Major binding sites of xenon, which differ between the two conformations, were identified in three distinct regions that all belong to the trans-membrane domain of GLIC: 1) in an intra-subunit cavity, 2) at the interface between adjacent subunits, and 3) in the pore. The pore site is unique to the locally-closed form where the binding of xenon effectively seals the channel. A putative mechanism of the inhibition of GLIC by xenon is proposed, which might be extended to other pentameric cationic ligand-gated ion channels.
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Affiliation(s)
- Ludovic Sauguet
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Zeineb Fourati
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
| | - Thierry Prangé
- Laboratoire de cristallographie et RMN biologiques (UMR 8015 CNRS), Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules (UMR 3528 CNRS) Institut Pasteur, Paris, France
- * E-mail:
| | - Nathalie Colloc'h
- CNRS, UMR 6301, ISTCT CERVOxy group, GIP Cyceron, Caen, France
- UNICAEN, Normandie Univ., UMR 6301 ISTCT, Caen, France
- CEA, DSV/I2BM, UMR 6301 ISTCT, Caen, France
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16
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Ostrowski M, Porowinska D, Prochnicki T, Prevost M, Raynal B, Baron B, Sauguet L, Corringer PJ, Faure G. Neurotoxic phospholipase A2 from rattlesnake as a new ligand and new regulator of prokaryotic receptor GLIC (proton-gated ion channel from G. violaceus). Toxicon 2016; 116:63-71. [PMID: 26854368 DOI: 10.1016/j.toxicon.2016.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 11/26/2022]
Abstract
Neurotoxic phospholipases A2 (sPLA2) from snake venoms interact with various protein targets with high specificity and potency. They regulate function of multiple receptors or channels essential to life processes including neuronal or neuromuscular chemoelectric signal transduction. These toxic sPLA2 exhibit high pharmacological potential and determination of PLA2-receptor binding sites represents challenging part in the receptor-channel biochemistry and pharmacology. To investigate the mechanism of interaction of neurotoxic PLA2 with its neuronal receptor at the molecular level, we used as a model crotoxin, a heterodimeric sPLA2 from rattlesnake venom and proton-gated ion channel GLIC, a bacterial homolog of pentameric ligand-gated ion channels. The three-dimensional structures of both partners, crotoxin and GLIC have been solved by X-ray crystallography and production of full-length pentameric GLIC (with ECD and TM domains) is well established. In the present study, for the first time, we demonstrated physical and functional interaction of full-length purified and solubilized GLIC with CB, (PLA2 subunit of crotoxin). We identified GLIC as a new protein target of CB and CB as a new ligand of GLIC, and showed that this non covalent interaction (PLA2-GLIC) involves the extracellular domain of GLIC. We also determined a novel function of CB as an inhibitor of proton-gated ion channel activity. In agreement with conformational changes observed upon formation of the complex, CB appears to be negative allosteric modulator (NAM) of GLIC. Finally, we proposed a possible stoichiometric model for CB - GLIC interaction based on analytical ultracentrifugation.
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Affiliation(s)
- Maciej Ostrowski
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France; Department of Biochemistry, Nicolaus Copernicus University, Torun, Poland
| | - Dorota Porowinska
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France; Department of Biochemistry, Nicolaus Copernicus University, Torun, Poland
| | - Tomasz Prochnicki
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France
| | - Marie Prevost
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France
| | - Bertrand Raynal
- Institu Pasteur, Plate-Forme de Biophysique des Macromolecules et de leurs Interactions, 75015 Paris, France
| | - Bruno Baron
- Institu Pasteur, Plate-Forme de Biophysique des Macromolecules et de leurs Interactions, 75015 Paris, France
| | - Ludovic Sauguet
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France
| | - Grazyna Faure
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS-UMR 3571, 25, rue du Dr. Roux, F-75015 Paris, France.
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17
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Fourati Z, Sauguet L, Delarue M. Genuine open form of the pentameric ligand-gated ion channel GLIC. ACTA ACUST UNITED AC 2015; 71:454-60. [PMID: 25760595 DOI: 10.1107/s1399004714026698] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/04/2014] [Indexed: 12/22/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical neurotransmission of nerve signalling in the central and peripheral nervous systems. GLIC is a bacterial homologue of eukaryotic pLGIC, the X-ray structure of which has been determined in three different conformations. GLIC is thus widely used as a model to study the activation and the allosteric transition of this family of receptors. The recently solved high-resolution structure of GLIC (2.4 Å resolution) in the active state revealed two bound acetate molecules in the extracellular domain (ECD). Here, it is shown that these two acetates exactly overlap with known sites of pharmacological importance in pLGICs, and their potential influence on the structure of the open state is studied in detail. Firstly, experimental evidence is presented for the correct assignment of these acetate molecules by using the anomalous dispersion signal of bromoacetate. Secondly, the crystal structure of GLIC in the absence of acetate was solved and it is shown that acetate binding induces local conformational changes that occur in strategic sites of the ECD. It is expected that this acetate-free structure will be useful in future computational studies of the gating transition in GLIC and other pLGICs.
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Affiliation(s)
- Zaineb Fourati
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 25 Rue du Docteur Roux, 75015 Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 25 Rue du Docteur Roux, 75015 Paris, France
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 25 Rue du Docteur Roux, 75015 Paris, France
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18
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Ostrowski M, Prochnicki T, Prevost M, Sauguet L, Raynal B, Baron B, Corringer PJ, Faure G. 22. GLIC, a proton-gated ion channel from Gloeobacter violaceus as a new target for phospholipase A2. Toxicon 2014. [DOI: 10.1016/j.toxicon.2014.08.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Sauguet L, Poitevin F, Murail S, Van Renterghem C, Moraga-Cid G, Malherbe L, Thompson A, Corringer PJ, Baaden M, Delarue M. Structural Basis for Ion Permeation Mechanism in Pentameric Ligand-Gated Ion Channels. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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20
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Sauguet L, Howard R, Malherbe L, Lee US, Corringer PJ, Harris RA, Delarue M. X-Ray Structures of an Interfacial Potentiating Site for Alcohols and Anesthetics in a Pentameric Ligand-Gated Ion Channel. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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21
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Corringer PJ, Poitevin F, Prevost MS, Sauguet L, Delarue M, Changeux JP. Structure and pharmacology of pentameric receptor channels: from bacteria to brain. Structure 2012; 20:941-56. [PMID: 22681900 DOI: 10.1016/j.str.2012.05.003] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 05/16/2012] [Accepted: 05/17/2012] [Indexed: 01/21/2023]
Abstract
Orthologs of the pentameric receptor channels that mediate fast synaptic transmission in the central and peripheral nervous systems have been found in several bacterial species and in a single archaea genus. Recent X-ray structures of bacterial and invertebrate pentameric receptors point to a striking conservation of the structural features within the whole family, even between distant prokaryotic and eukaryotic members. These structural data reveal general principles of molecular organization that allow allosteric membrane proteins to mediate chemoelectric transduction. Notably, several conformations have been solved, including open and closed channels with distinct global tertiary and quaternary structure. The data reveal features of the ion channel architecture and of diverse categories of binding sites, such as those that bind orthosteric ligands, including neurotransmitters, and those that bind allosteric modulators, such as general anesthetics, ivermectin, or lipids. In this review, we summarize the most recent data, discuss insights into the mechanism of action in these systems, and elaborate on newly opened avenues for drug design.
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22
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Prevost MS, Sauguet L, Nury H, Van Renterghem C, Huon C, Poitevin F, Baaden M, Delarue M, Corringer PJ. A locally closed conformation of a bacterial pentameric proton-gated ion channel. Nat Struct Mol Biol 2012; 19:642-9. [PMID: 22580559 DOI: 10.1038/nsmb.2307] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 04/19/2012] [Indexed: 11/09/2022]
Abstract
Pentameric ligand-gated ion channels mediate signal transduction through conformational transitions between closed-pore and open-pore states. To stabilize a closed conformation of GLIC, a bacterial proton-gated homolog from Gloeobacter violaceus whose open structure is known, we separately generated either four cross-links or two single mutations. We found all six mutants to be in the same 'locally closed' conformation using X-ray crystallography, sharing most of the features of the open form but showing a locally closed pore as a result of a concerted bending of all of its M2 helices. The mutants adopt several variant conformations of the M2-M3 loop, and in all cases an interacting lipid that is observed in the open form disappears. A single cross-linked mutant is functional, according to electrophysiology, and the locally closed structure of this mutant indicates that it has an increased flexibility. Further cross-linking, accessibility and molecular dynamics data suggest that the locally closed form is a functionally relevant conformation that occurs during allosteric gating transitions.
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Prevost M, Sauguet L, Nury H, Van Renterghem C, Huon C, Poitevin F, Baaden M, Delarue M, Corringer PJ. Cysteine Crosslinking to Study Allosteric Transitions of a Bacterial Homolog of Pentameric Channel-Receptors. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Núñez-Ramírez R, Klinge S, Sauguet L, Melero R, Recuero-Checa MA, Kilkenny M, Perera RL, García-Alvarez B, Hall RJ, Nogales E, Pellegrini L, Llorca O. Flexible tethering of primase and DNA Pol α in the eukaryotic primosome. Nucleic Acids Res 2011; 39:8187-99. [PMID: 21715379 PMCID: PMC3185431 DOI: 10.1093/nar/gkr534] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The Pol α/primase complex or primosome is the primase/polymerase complex that initiates nucleic acid synthesis during eukaryotic replication. Within the primosome, the primase synthesizes short RNA primers that undergo limited extension by Pol α. The resulting RNA–DNA primers are utilized by Pol δ and Pol ε for processive elongation on the lagging and leading strands, respectively. Despite its importance, the mechanism of RNA–DNA primer synthesis remains poorly understood. Here, we describe a structural model of the yeast primosome based on electron microscopy and functional studies. The 3D architecture of the primosome reveals an asymmetric, dumbbell-shaped particle. The catalytic centers of primase and Pol α reside in separate lobes of high relative mobility. The flexible tethering of the primosome lobes increases the efficiency of primer transfer between primase and Pol α. The physical organization of the primosome suggests that a concerted mechanism of primer hand-off between primase and Pol α would involve coordinated movements of the primosome lobes. The first three-dimensional map of the eukaryotic primosome at 25 Å resolution provides an essential structural template for understanding initiation of eukaryotic replication.
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Affiliation(s)
- Rafael Núñez-Ramírez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Sebastian Klinge
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Ludovic Sauguet
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Roberto Melero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - María A. Recuero-Checa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Mairi Kilkenny
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Rajika L. Perera
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Begoña García-Alvarez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Richard J. Hall
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Eva Nogales
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
| | - Luca Pellegrini
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
- *To whom correspondence should be addressed. Tel: +34 918373112 (Ext. 4446); Fax: +34 915360432;
| | - Oscar Llorca
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK and University of California, 742 Stanley Hall, MS 3220, Berkeley, CA 94720-3220, USA
- *To whom correspondence should be addressed. Tel: +34 918373112 (Ext. 4446); Fax: +34 915360432;
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Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M. Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucleic Acids Res 2011; 39:4475-89. [PMID: 21296757 PMCID: PMC3105412 DOI: 10.1093/nar/gkr027] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which l-Phe is shown to be transferred from Phe-tRNAPhe to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.
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Affiliation(s)
- Ludovic Sauguet
- CEA, IBITECS, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France
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Kostov GK, Sauguet L, Ameduri B, Kaspar H, Zipplies T, Hintzer K. Radical copolymerization of vinylidene fluoride with 1-bromo-2,2-difluoroethylene. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/pola.24179] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Sauguet L, Klinge S, Perera RL, Maman JD, Pellegrini L. Shared active site architecture between the large subunit of eukaryotic primase and DNA photolyase. PLoS One 2010; 5:e10083. [PMID: 20404922 PMCID: PMC2852410 DOI: 10.1371/journal.pone.0010083] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 03/17/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND DNA synthesis during replication relies on RNA primers synthesised by the primase, a specialised DNA-dependent RNA polymerase that can initiate nucleic acid synthesis de novo. In archaeal and eukaryotic organisms, the primase is a heterodimeric enzyme resulting from the constitutive association of a small (PriS) and large (PriL) subunit. The ability of the primase to initiate synthesis of an RNA primer depends on a conserved Fe-S domain at the C-terminus of PriL (PriL-CTD). However, the critical role of the PriL-CTD in the catalytic mechanism of initiation is not understood. METHODOLOGY/PRINCIPAL FINDINGS Here we report the crystal structure of the yeast PriL-CTD at 1.55 A resolution. The structure reveals that the PriL-CTD folds in two largely independent alpha-helical domains joined at their interface by a [4Fe-4S] cluster. The larger N-terminal domain represents the most conserved portion of the PriL-CTD, whereas the smaller C-terminal domain is largely absent in archaeal PriL. Unexpectedly, the N-terminal domain reveals a striking structural similarity with the active site region of the DNA photolyase/cryptochrome family of flavoproteins. The region of similarity includes PriL-CTD residues that are known to be essential for initiation of RNA primer synthesis by the primase. CONCLUSION/SIGNIFICANCE Our study reports the first crystallographic model of the conserved Fe-S domain of the archaeal/eukaryotic primase. The structural comparison with a cryptochrome protein bound to flavin adenine dinucleotide and single-stranded DNA provides important insight into the mechanism of RNA primer synthesis by the primase.
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Affiliation(s)
- Ludovic Sauguet
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian Klinge
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rajika L. Perera
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Joseph D. Maman
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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Sauguet L, Ameduri B, Boutevin B. Fluorinated copolymers and terpolymers based on vinylidene fluoride and bearing sulfonic acid side-group. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/pola.21978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Sauguet L, Boyer C, Ameduri B, Boutevin B. Synthesis and Characterization of Poly(vinylidene fluoride)-g-poly(styrene) Graft Polymers Obtained by Atom Transfer Radical Polymerization of Styrene. Macromolecules 2006. [DOI: 10.1021/ma061554a] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Sauguet
- Laboratory of Macromolecular Chemistry, UMR-CNRS 5076, Institute Gerhardt, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 05, France
| | - C. Boyer
- Laboratory of Macromolecular Chemistry, UMR-CNRS 5076, Institute Gerhardt, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 05, France
| | - B. Ameduri
- Laboratory of Macromolecular Chemistry, UMR-CNRS 5076, Institute Gerhardt, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 05, France
| | - B. Boutevin
- Laboratory of Macromolecular Chemistry, UMR-CNRS 5076, Institute Gerhardt, Ecole Nationale Supérieure de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 05, France
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Sauguet L, Ameduri B, Boutevin B. Fluorinated, crosslinkable terpolymers based on vinylidene fluoride and bearing sulfonic acid side groups for fuel-cell membranes. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/pola.21551] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Guiot J, Néouze MA, Sauguet L, Améduri B, Boutevin B. Synthesis and copolymerization of fluorinated monomers bearing a reactive lateral group. XX. Copolymerization of vinylidene fluoride with 4-bromo-1,1,2-trifluorobut-1-ene. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/pola.20555] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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