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da Silva Lameira C, Münßinger S, Yang L, Eikmanns BJ, Bellinzoni M. Corynebacterium glutamicum pyruvate:quinone oxidoreductase: an enigmatic metabolic enzyme with unusual structural features. FEBS J 2024; 291:4501-4521. [PMID: 39080980 DOI: 10.1111/febs.17232] [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: 04/02/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 10/17/2024]
Abstract
Pyruvate:quinone oxidoreductase (PQO) is a flavin-containing peripheral membrane enzyme catalyzing the decarboxylation of pyruvate to acetate and CO2 with quinone as an electron acceptor. Here, we investigate PQO activity in Corynebacterium glutamicum, examine purified PQO, and describe the crystal structure of the native enzyme and a truncated version. The specific PQO activity was highest in stationary phase cells grown in complex medium, lower in cells grown in complex medium containing glucose or acetate, and lowest in cells grown in minimal acetate-medium. A similar pattern with about 30-fold higher specific PQO activities was observed in C. glutamicum with plasmid-bound pqo expression under the control of the tac promoter, indicating that the differences in PQO activity are likely due to post-transcriptional control. Continuous cultivation of C. glutamicum at dilution rates between 0.05 and 0.4 h-1 revealed a negative correlation between PQO activity and growth rate. Kinetic analysis of PQO enzymes purified from cells grown in complex or in minimal acetate-medium revealed substantial differences in specific activity (72.3 vs. 11.9 U·mg protein-1) and turnover number (kcat: 440 vs. 78 s-1, respectively), suggesting post-translational modifications affecting PQO activity. Structural analysis of PQO revealed a homotetrameric arrangement very similar to the Escherichia coli pyruvate oxidase PoxB except for the C-terminal membrane binding domain, which exhibited a conformation markedly different from its PoxB counterpart. A truncated PQO variant lacking 17 C-terminal amino acids showed higher affinity to pyruvate and was independent of detergent activation, highlighting the importance of the C-terminus for enzyme activation and lipid binding.
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Affiliation(s)
| | - Sini Münßinger
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Germany
| | - Lu Yang
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, Paris, France
| | - Bernhard J Eikmanns
- Institute of Molecular Biology and Biotechnology of Prokaryotes, University of Ulm, Germany
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, Paris, France
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2
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Vernuccio R, León AM, Poojari CS, Buchrieser J, Selverian C, Jaleta Y, Meola A, Guivel-Benhassine F, Porrot F, Haouz A, Chevreuil M, Raynal B, Mercer J, Simon-Loriere E, Chandran K, Schwartz O, Hub JS, Guardado-Calvo P. MECHANISMS OF TECOVIRIMAT ANTIVIRAL ACTIVITY AND POXVIRUS RESISTANCE. RESEARCH SQUARE 2024:rs.3.rs-5002222. [PMID: 39399667 PMCID: PMC11469519 DOI: 10.21203/rs.3.rs-5002222/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Mpox is a zoonotic disease endemic in central and west Africa. However, since 2022, human-adapted mpox virus (MPXV) strains are causing large outbreaks spreading outside these regions, leading the World Health Organization to declare public health emergency twice. Tecovirimat, the most widely used drug to treat these infections, blocks viral egress through a poorly understood mechanism. Tecovirimat-resistant strains, all with mutations in the viral phospholipase F13, pose public health concerns. Herein, we report the structure of an F13 homodimer, both alone and in complex with tecovirimat. We demonstrate that tecovirimat acts as a molecular glue, inducing the dimerization of the phospholipase. F13 escape mutations in MPXV clinical isolates are at the dimer interface and prevent drug-induced dimerization in solution and cells. These findings, which decipher tecovirimat's mode of action, will allow better monitoring of poxvirus outbreaks and pave the way for developing more potent and resilient therapeutics.
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Affiliation(s)
- Riccardo Vernuccio
- G5 Structural Biology of Infectious Diseases, Institut Pasteur, Université Paris Cité, Paris, France
| | - Alejandro Martínez León
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Chetan S. Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Julian Buchrieser
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Christopher Selverian
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yakin Jaleta
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Annalisa Meola
- G5 Structural Biology of Infectious Diseases, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Françoise Porrot
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Ahmed Haouz
- Cristallography Platform-C2RT, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Maelenn Chevreuil
- Plate-forme de Biophysique Moleculaire-C2RT, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moleculaire-C2RT, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Jason Mercer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Etienne Simon-Loriere
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Université Paris Cité, Paris, France
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Olivier Schwartz
- Virus & Immunity Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 3569, Paris, France
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany
| | - Pablo Guardado-Calvo
- G5 Structural Biology of Infectious Diseases, Institut Pasteur, Université Paris Cité, Paris, France
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3
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Dejoux A, Zhu Q, Ganneau C, Goff ORL, Godon O, Lemaitre J, Relouzat F, Huetz F, Sokal A, Vandenberghe A, Pecalvel C, Hunault L, Derenne T, Gillis CM, Iannascoli B, Wang Y, Rose T, Mertens C, Nicaise-Roland P, England P, Mahévas M, de Chaisemartin L, Le Grand R, Letscher H, Saul F, Pissis C, Haouz A, Reber LL, Chappert P, Jönsson F, Ebo DG, Millot GA, Bay S, Chollet-Martin S, Gouel-Chéron A, Bruhns P. Rocuronium-specific antibodies drive perioperative anaphylaxis but can also function as reversal agents in preclinical models. Sci Transl Med 2024; 16:eado4463. [PMID: 39259810 DOI: 10.1126/scitranslmed.ado4463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/06/2024] [Accepted: 08/05/2024] [Indexed: 09/13/2024]
Abstract
Neuromuscular blocking agents (NMBAs) relax skeletal muscles to facilitate surgeries and ease intubation but can lead to adverse reactions, including complications because of postoperative residual neuromuscular blockade (rNMB) and, in rare cases, anaphylaxis. Both adverse reactions vary between types of NMBAs, with rocuronium, a widely used nondepolarizing NMBA, inducing one of the longest rNMB durations and highest anaphylaxis incidences. rNMB induced by rocuronium can be reversed by the synthetic γ-cyclodextrin sugammadex. However, in rare cases, sugammadex can provoke anaphylaxis. Thus, additional therapeutic options are needed. Rocuronium-induced anaphylaxis is proposed to rely on preexisting rocuronium-binding antibodies. To understand the pathogenesis of rocuronium-induced anaphylaxis and to identify potential therapeutics, we investigated the memory B cell antibody repertoire of patients with suspected hypersensitivity to rocuronium. We identified polyclonal antibody repertoires with a high diversity among V(D)J genes without evidence of clonal groups. When recombinantly expressed, these antibodies demonstrated specificity and low affinity for rocuronium without cross-reactivity for other NMBAs. Moreover, when these antibodies were expressed as human immunoglobulin E (IgE), they triggered human mast cell activation and passive systemic anaphylaxis in transgenic mice, although their affinities were insufficient to serve as reversal agents. Rocuronium-specific, high-affinity antibodies were thus isolated from rocuronium-immunized mice. The highest-affinity antibody was able to reverse rocuronium-induced neuromuscular blockade in nonhuman primates with kinetics comparable to that of sugammadex. Together, these data support the hypothesis that antibodies cause anaphylactic reactions to rocuronium and pave the way for improved diagnostics and neuromuscular blockade reversal agents.
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Affiliation(s)
- Alice Dejoux
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Qianqian Zhu
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- Université Paris-Saclay, INSERM, Inflammation Microbiome Immunosurveillance, 91400 Orsay, France
| | - Christelle Ganneau
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Chimie des Biomolécules, 75015 Paris, France
| | - Odile Richard-Le Goff
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
| | - Ophélie Godon
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
| | - Julien Lemaitre
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases, 92260 Fontenay-aux-Roses and 94250 Le Kremlin-Bicêtre, France
| | - Francis Relouzat
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases, 92260 Fontenay-aux-Roses and 94250 Le Kremlin-Bicêtre, France
| | - François Huetz
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
| | - Aurélien Sokal
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, 94000 Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale, Université Paris-Est Créteil, 94000 Créteil, France
- Service de Médecine interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris Cité, 92110 Clichy, France
| | - Alexis Vandenberghe
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, 94000 Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale, Université Paris-Est Créteil, 94000 Créteil, France
| | - Cyprien Pecalvel
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, 31000 Toulouse, France
| | - Lise Hunault
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Thomas Derenne
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Caitlin M Gillis
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
| | - Bruno Iannascoli
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
| | - Yidan Wang
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
| | - Thierry Rose
- Institut Pasteur, Université Paris Cité, INSERM UMR1224, Biologie Cellulaire des Lymphocytes, Ligue Nationale Contre le Cancer, Équipe Labellisée Ligue 2018, 75015 Paris, France
| | - Christel Mertens
- Faculty of Medicine and Health Science, Department of Immunology-Allergology-Rheumatology, Antwerp University Hospital and the Infla-Med Center of Excellence, University of Antwerp, Antwerp, Belgium; Department of Immunology and Allergology, AZ Jan Palfijn Ghent, 9000 Ghent, Belgium
| | - Pascale Nicaise-Roland
- Service d'immunologie Biologique, DMU BIOGEM, Hôpital Bichat, APHP, 75018, Paris, France
| | - Patrick England
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Molecular Biophysics Core Facility, 75015 Paris, France
| | - Matthieu Mahévas
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, 94000 Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale, Université Paris-Est Créteil, 94000 Créteil, France
| | - Luc de Chaisemartin
- Université Paris-Saclay, INSERM, Inflammation Microbiome Immunosurveillance, 91400 Orsay, France
- Service d'immunologie Biologique, DMU BIOGEM, Hôpital Bichat, APHP, 75018, Paris, France
| | - Roger Le Grand
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases, 92260 Fontenay-aux-Roses and 94250 Le Kremlin-Bicêtre, France
| | - Hélène Letscher
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Autoimmune, Hematological and Bacterial Diseases, 92260 Fontenay-aux-Roses and 94250 Le Kremlin-Bicêtre, France
| | - Frederick Saul
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Plate-forme Cristallographie-C2RT, 75015 Paris, France
| | - Cédric Pissis
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Plate-forme Cristallographie-C2RT, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Plate-forme Cristallographie-C2RT, 75015 Paris, France
| | - Laurent L Reber
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse III, 31000 Toulouse, France
| | - Pascal Chappert
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, 94000 Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale, Université Paris-Est Créteil, 94000 Créteil, France
| | - Friederike Jönsson
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- CNRS, F-75015 Paris, France
| | - Didier G Ebo
- Faculty of Medicine and Health Science, Department of Immunology-Allergology-Rheumatology, Antwerp University Hospital and the Infla-Med Center of Excellence, University of Antwerp, Antwerp, Belgium; Department of Immunology and Allergology, AZ Jan Palfijn Ghent, 9000 Ghent, Belgium
| | - Gaël A Millot
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Sylvie Bay
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Chimie des Biomolécules, 75015 Paris, France
| | - Sylvie Chollet-Martin
- Université Paris-Saclay, INSERM, Inflammation Microbiome Immunosurveillance, 91400 Orsay, France
- Service d'immunologie Biologique, DMU BIOGEM, Hôpital Bichat, APHP, 75018, Paris, France
| | - Aurélie Gouel-Chéron
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- Anaesthesiology and Critical Care Medicine Department, DMU Parabol, Bichat-Claude Bernard Hospital, AP-HP, 75018 Paris, France
- Université Paris Cité, 75010 Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université Paris Cité, INSERM UMR1222, Antibodies in Therapy and Pathology, 75015 Paris, France
- INSERM 1152, DHU FIRE, Labex Inflamex, Université Paris Diderot Paris 7, 75018 Paris, France
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4
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Planchais C, Fernández I, Chalopin B, Bruel T, Rosenbaum P, Beretta M, Dimitrov JD, Conquet L, Donati F, Prot M, Porrot F, Planas D, Staropoli I, Guivel-Benhassine F, Baquero E, van der Werf S, Haouz A, Simon-Lorière E, Montagutelli X, Maillère B, Rey FA, Guardado-Calvo P, Nozach H, Schwartz O, Mouquet H. Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2. iScience 2024; 27:110354. [PMID: 39071888 PMCID: PMC11277385 DOI: 10.1016/j.isci.2024.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024] Open
Abstract
Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.
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Affiliation(s)
- Cyril Planchais
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Timothée Bruel
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Pierre Rosenbaum
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Maxime Beretta
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
| | - Françoise Porrot
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Delphine Planas
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Isabelle Staropoli
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Florence Guivel-Benhassine
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Eduard Baquero
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Sylvie van der Werf
- CNRS UMR3569, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Cristallography Platform-C2RT, 75015 Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Félix A. Rey
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Olivier Schwartz
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
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5
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Henderikx RJM, Mann D, Domanska A, Dong J, Shahzad S, Lak B, Filopoulou A, Ludig D, Grininger M, Momoh J, Laanto E, Oksanen HM, Bisikalo K, Williams PA, Butcher SJ, Peters PJ, Beulen BWAMM. VitroJet: new features and case studies. Acta Crystallogr D Struct Biol 2024; 80:232-246. [PMID: 38488730 PMCID: PMC10994172 DOI: 10.1107/s2059798324001852] [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: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Single-particle cryo-electron microscopy has become a widely adopted method in structural biology due to many recent technological advances in microscopes, detectors and image processing. Before being able to inspect a biological sample in an electron microscope, it needs to be deposited in a thin layer on a grid and rapidly frozen. The VitroJet was designed with this aim, as well as avoiding the delicate manual handling and transfer steps that occur during the conventional grid-preparation process. Since its creation, numerous technical developments have resulted in a device that is now widely utilized in multiple laboratories worldwide. It features plasma treatment, low-volume sample deposition through pin printing, optical ice-thickness measurement and cryofixation of pre-clipped Autogrids through jet vitrification. This paper presents recent technical improvements to the VitroJet and the benefits that it brings to the cryo-EM workflow. A wide variety of applications are shown: membrane proteins, nucleosomes, fatty-acid synthase, Tobacco mosaic virus, lipid nanoparticles, tick-borne encephalitis viruses and bacteriophages. These case studies illustrate the advancement of the VitroJet into an instrument that enables accurate control and reproducibility, demonstrating its suitability for time-efficient cryo-EM structure determination.
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Affiliation(s)
- Rene J. M. Henderikx
- CryoSol-World, Weert, The Netherlands
- Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
| | - Daniel Mann
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing (IBI-6): Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Aušra Domanska
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Life Science Institute–Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Jing Dong
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Saba Shahzad
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing (IBI-6): Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Behnam Lak
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Life Science Institute–Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Aikaterini Filopoulou
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing (IBI-6): Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Damian Ludig
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jeffrey Momoh
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging, RWTH Aachen University, Aachen, Germany
| | - Elina Laanto
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Hanna M. Oksanen
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kyrylo Bisikalo
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Life Science Institute–Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Pamela A. Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Sarah J. Butcher
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Life Science Institute–Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Peter J. Peters
- Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, The Netherlands
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6
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Nat Commun 2024; 15:331. [PMID: 38184686 PMCID: PMC10771500 DOI: 10.1038/s41467-023-44606-z] [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: 07/20/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015, Paris, France.
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7
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Bitencourt-Ferreira G, Villarreal MA, Quiroga R, Biziukova N, Poroikov V, Tarasova O, de Azevedo Junior WF. Exploring Scoring Function Space: Developing Computational Models for Drug Discovery. Curr Med Chem 2024; 31:2361-2377. [PMID: 36944627 DOI: 10.2174/0929867330666230321103731] [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: 06/23/2022] [Revised: 12/15/2022] [Accepted: 12/29/2022] [Indexed: 03/23/2023]
Abstract
BACKGROUND The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHODS We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.
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Affiliation(s)
| | - Marcos A Villarreal
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Rodrigo Quiroga
- CONICET-Departamento de Matemática y Física, Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Nadezhda Biziukova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Olga Tarasova
- Institute of Biomedical Chemistry, Pogodinskaya Str., 10/8, Moscow, 119121, Russia
| | - Walter F de Azevedo Junior
- Pontifical Catholic University of Rio Grande do Sul - PUCRS, Porto Alegre-RS, Brazil
- Specialization Program in Bioinformatics, The Pontifical Catholic University of Rio Grande do Sul (PUCRS), Av. Ipiranga, 6681 Porto Alegre / RS 90619-900, Brazil
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8
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Mori M, Villa S, Chiarelli LR, Meneghetti F, Bellinzoni M. Structural Study of a New MbtI-Inhibitor Complex: Towards an Optimized Model for Structure-Based Drug Discovery. Pharmaceuticals (Basel) 2023; 16:1559. [PMID: 38004425 PMCID: PMC10675255 DOI: 10.3390/ph16111559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
MbtI from Mycobacterium tuberculosis (Mtb) is a Mg2+-dependent salicylate synthase, belonging to the chorismate-utilizing enzyme (CUE) family. As a fundamental player in iron acquisition, MbtI promotes the survival and pathogenicity of Mtb in the infected host. Hence, it has emerged in the last decade as an innovative, potential target for the anti-virulence therapy of tuberculosis. In this context, 5-phenylfuran-2-carboxylic acids have been identified as potent MbtI inhibitors. The first co-crystal structure of MbtI in complex with a member of this class was described in 2020, showing the enzyme adopting an open configuration. Due to the high mobility of the loop adjacent to the binding pocket, large portions of the amino acid chain were not defined in the electron density map, hindering computational efforts aimed at structure-driven ligand optimization. Herein, we report a new, high-resolution co-crystal structure of MbtI with a furan-based derivative, in which the closed configuration of the enzyme allowed tracing the entirety of the active site pocket in the presence of the bound inhibitor. Moreover, we describe a new crystal structure of MbtI in open conformation and in complex with the known inhibitor methyl-AMT, suggesting that in vitro potency is not related to the observed enzyme conformation. These findings will prove fundamental to enhance the potency of this series via rational structure-based drug-design approaches.
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Affiliation(s)
- Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Laurent R. Chiarelli
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via A. Ferrata 9, 27100 Pavia, Italy;
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy; (M.M.); (S.V.); (F.M.)
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015 Paris, France
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9
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela MM, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel AM. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. Nat Microbiol 2023; 8:1896-1910. [PMID: 37679597 PMCID: PMC10522489 DOI: 10.1038/s41564-023-01473-0] [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: 12/27/2022] [Accepted: 08/11/2023] [Indexed: 09/09/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic Actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis. These bacteria have multi-layered cell walls composed of the mycolyl-arabinogalactan-peptidoglycan complex and a polar growth mode, thus requiring tight coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the coiled-coil protein Wag31. Here, using C. glutamicum, we report the discovery of two divisome members: a gephyrin-like repurposed molybdotransferase (Glp) and its membrane receptor (GlpR). Our results show how cell cycle progression requires interplay between Glp/GlpR, FtsZ and Wag31, showcasing a crucial crosstalk between the divisome and elongasome machineries that might be targeted for anti-mycobacterial drug discovery. Further, our work reveals that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis, similar to the gephyrin/GlyR system that mediates synaptic signalling in higher eukaryotes through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- Mariano Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Julienne Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Adrià Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
- Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daniela Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Azalia Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Quentin Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Mathildeb Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Maria Magdalena Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Ahmed Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, Lyon, France
| | - Pedro M Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
| | - Anne Marie Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France.
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10
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Zinke M, Lejeune M, Mechaly A, Bardiaux B, Boneca IG, Delepelaire P, Izadi-Pruneyre N. Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.11.552980. [PMID: 37609138 PMCID: PMC10441417 DOI: 10.1101/2023.08.11.552980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Active nutrient uptake is fundamental for survival and pathogenicity of Gram-negative bacteria, which operate a multi-protein Ton system to transport essential nutrients like metals and vitamins. This system harnesses the proton motive force at the inner membrane to energize the import through the outer membrane, but the mechanism of energy transfer remains enigmatic. Here, we study the periplasmic domain of ExbD, a crucial component of the proton channel of the Ton system. We show that this domain is a dynamic dimer switching between two conformations representing the proton channel's open and closed states. By in vivo phenotypic assays we demonstrate that this conformational switch is essential for the nutrient uptake by bacteria. The open state of ExbD triggers a disorder to order transition of TonB, enabling TonB to supply energy to the nutrient transporter. We also reveal the anchoring role of the peptidoglycan layer in this mechanism. Herein, we propose a mechanistic model for the Ton system, emphasizing ExbD duality and the pivotal catalytic role of peptidoglycan. Sequence analysis suggests that this mechanism is conserved in other systems energizing gliding motility and membrane integrity. Our study fills important gaps in understanding bacterial motor mechanism and proposes novel antibacterial strategies.
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Affiliation(s)
- Maximilian Zinke
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, F-75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne F-75015, Paris, France
| | - Philippe Delepelaire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université Paris Cité, UMR7099 CNRS, F-75005, Paris, France
- Institut de Biologie Physico-Chimique, F-75005, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, F-75015 Paris, France
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11
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Yang L, Wagner T, Mechaly A, Boyko A, Bruch EM, Megrian D, Gubellini F, Alzari PM, Bellinzoni M. High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun 2023; 14:4851. [PMID: 37563123 PMCID: PMC10415282 DOI: 10.1038/s41467-023-40253-6] [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: 02/23/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.
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Affiliation(s)
- Lu Yang
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Wuhan Institute of Biological Products Co. Ltd., Wuhan, 430207, PR China
| | - Tristan Wagner
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, D-28359, Bremen, Germany
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plateforme de Cristallographie, F-75015, Paris, France
| | - Alexandra Boyko
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- BostonGene, Yerevan, Armenia
| | - Eduardo M Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
- Sanofi, In vitro Biology, Integrated Drug Discovery, 350 Water St, Cambridge, MA, 02141, USA
| | - Daniela Megrian
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Francesca Gubellini
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Pedro M Alzari
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75015, Paris, France.
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12
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Gedeon A, Ayoub N, Brûlé S, Raynal B, Karimova G, Gelin M, Mechaly A, Haouz A, Labesse G, Munier‐Lehmann H. Insight into the role of the Bateman domain at the molecular and physiological levels through engineered IMP dehydrogenases. Protein Sci 2023; 32:e4703. [PMID: 37338125 PMCID: PMC10357500 DOI: 10.1002/pro.4703] [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: 03/03/2023] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
Inosine 5'-monophosphate (IMP) dehydrogenase (IMPDH) is an ubiquitous enzyme that catalyzes the NAD+ -dependent oxidation of inosine 5'-monophosphate into xanthosine 5'-monophosphate. This enzyme is formed of two distinct domains, a core domain where the catalytic reaction occurs, and a less-conserved Bateman domain. Our previous studies gave rise to the classification of bacterial IMPDHs into two classes, according to their oligomeric and kinetic properties. MgATP is a common effector but cause to different effects when it binds within the Bateman domain: it is either an allosteric activator for Class I IMPDHs or a modulator of the oligomeric state for Class II IMPDHs. To get insight into the role of the Bateman domain in the dissimilar properties of the two classes, deleted variants of the Bateman domain and chimeras issued from the interchange of the Bateman domain between the three selected IMPDHs have been generated and characterized using an integrative structural biology approach. Biochemical, biophysical, structural, and physiological studies of these variants unveil the Bateman domain as being the carrier of the molecular behaviors of both classes.
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Affiliation(s)
- Antoine Gedeon
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Unité de Microbiologie Structurale, CNRS UMR3525ParisFrance
| | - Nour Ayoub
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
| | - Sébastien Brûlé
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Bertrand Raynal
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Biophysique Moléculaire, C2RT, CNRS UMR3528ParisFrance
| | - Gouzel Karimova
- Institut Pasteur, Université Paris Cité, Unité de Biochimie des Interactions Macromoléculaires, CNRS UMR3528ParisFrance
| | - Muriel Gelin
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plate‐Forme de Cristallographie, C2RT, CNRS UMR3528ParisFrance
| | - Gilles Labesse
- Centre de Biologie StructuraleUniversité Montpellier, INSERM, CNRSMontpellierFrance
| | - Hélène Munier‐Lehmann
- Institut Pasteur, Université Paris Cité, Unité de Chimie et Biocatalyse, CNRS UMR3523ParisFrance
- Present address:
Institut Pasteur, Université Paris Cité, Plate‐Forme de Criblage Chémogénomique et Biologique, CNRS UMR3523ParisFrance
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13
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Fernández I, Dynesen LT, Coquin Y, Pederzoli R, Brun D, Haouz A, Gessain A, Rey FA, Buseyne F, Backovic M. The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells. Nat Commun 2023; 14:1262. [PMID: 36878926 PMCID: PMC9988990 DOI: 10.1038/s41467-023-36923-0] [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: 09/30/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
The surface envelope glycoprotein (Env) of all retroviruses mediates virus binding to cells and fusion of the viral and cellular membranes. A structure-function relationship for the HIV Env that belongs to the Orthoretrovirus subfamily has been well established. Structural information is however largely missing for the Env of Foamy viruses (FVs), the second retroviral subfamily. In this work we present the X-ray structure of the receptor binding domain (RBD) of a simian FV Env at 2.57 Å resolution, revealing two subdomains and an unprecedented fold. We have generated a model for the organization of the RBDs within the trimeric Env, which indicates that the upper subdomains form a cage-like structure at the apex of the Env, and identified residues K342, R343, R359 and R369 in the lower subdomain as key players for the interaction of the RBD and viral particles with heparan sulfate.
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Affiliation(s)
- Ignacio Fernández
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Lasse Toftdal Dynesen
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Riccardo Pederzoli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Delphine Brun
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, Plateforme de cristallographie-C2RT, CNRS UMR 3528, 75015, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Félix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'Épidémiologie et Physiopathologie des Virus Oncogènes, 75015, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015, Paris, France.
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14
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Hellert J, Aebischer A, Haouz A, Guardado-Calvo P, Reiche S, Beer M, Rey FA. Structure, function, and evolution of the Orthobunyavirus membrane fusion glycoprotein. Cell Rep 2023; 42:112142. [PMID: 36827185 DOI: 10.1016/j.celrep.2023.112142] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/29/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
La Crosse virus, responsible for pediatric encephalitis in the United States, and Schmallenberg virus, a highly teratogenic veterinary virus in Europe, belong to the large Orthobunyavirus genus of zoonotic arthropod-borne pathogens distributed worldwide. Viruses in this under-studied genus cause CNS infections or fever with debilitating arthralgia/myalgia syndromes, with no effective treatment. The main surface antigen, glycoprotein Gc (∼1,000 residues), has a variable N-terminal half (GcS) targeted by the patients' antibody response and a conserved C-terminal moiety (GcF) responsible for membrane fusion during cell entry. Here, we report the X-ray structure of post-fusion La Crosse and Schmallenberg virus GcF, revealing the molecular determinants for hairpin formation and trimerization required to drive membrane fusion. We further experimentally confirm the role of residues in the fusion loops and in a vestigial endoplasmic reticulum (ER) translocation sequence at the GcS-GcF junction. The resulting knowledge provides essential molecular underpinnings for future development of potential therapeutic treatments and vaccines.
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Affiliation(s)
- Jan Hellert
- Structural Virology Unit, Institut Pasteur - Université Paris-Cité, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015 Paris, France; Centre for Structural Systems Biology (CSSB), Leibniz-Institut für Virologie (LIV), Notkestraße 85, 22607 Hamburg, Germany
| | - Andrea Aebischer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany; Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany
| | - Ahmed Haouz
- Crystallography Platform C2RT, Institut Pasteur, CNRS UMR 3528, 25-28 rue du Dr. Roux, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Structural Virology Unit, Institut Pasteur - Université Paris-Cité, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015 Paris, France
| | - Sven Reiche
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald, Germany.
| | - Félix A Rey
- Structural Virology Unit, Institut Pasteur - Université Paris-Cité, CNRS UMR 3569, 25-28 rue du Dr. Roux, 75015 Paris, France.
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15
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Dazzoni R, Li Y, López-Castilla A, Brier S, Mechaly A, Cordier F, Haouz A, Nilges M, Francetic O, Bardiaux B, Izadi-Pruneyre N. Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system. Structure 2023; 31:152-165.e7. [PMID: 36586404 DOI: 10.1016/j.str.2022.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/31/2022]
Abstract
Type II secretion systems (T2SSs) allow diderm bacteria to secrete hydrolytic enzymes, adhesins, or toxins important for growth and virulence. To promote secretion of folded proteins, T2SSs assemble periplasmic filaments called pseudopili or endopili at an inner membrane subcomplex, the assembly platform (AP). Here, we combined biophysical approaches, nuclear magnetic resonance (NMR) and X-ray crystallography, to study the Klebsiella AP components PulL and PulM. We determined the structure and associations of their periplasmic domains and describe the structure of the heterodimer formed by their ferredoxin-like domains. We show how structural complementarity and plasticity favor their association during the secretion process. Cysteine scanning and crosslinking data provided additional constraints to build a structural model of the PulL-PulM assembly in the cellular context. Our structural and functional insights, together with the relative cellular abundance of its components, support the role of AP as a dynamic hub that orchestrates pilus polymerization.
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Affiliation(s)
- Régine Dazzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Yuanyuan Li
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Aracelys López-Castilla
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Sébastien Brier
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, 75015 Paris, France
| | - Florence Cordier
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, 75015 Paris, France
| | - Michael Nilges
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, 75015 Paris.
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, 75015 Paris.
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16
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Martinez M, Petit J, Leyva A, Sogues A, Megrian D, Rodriguez A, Gaday Q, Ben Assaya M, Portela M, Haouz A, Ducret A, Grangeasse C, Alzari PM, Durán R, Wehenkel A. Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526586. [PMID: 36778425 PMCID: PMC9915583 DOI: 10.1101/2023.02.01.526586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The order Corynebacteriales includes major industrial and pathogenic actinobacteria such as Corynebacterium glutamicum or Mycobacterium tuberculosis . Their elaborate multi-layered cell wall, composed primarily of the mycolyl-arabinogalactan-peptidoglycan complex, and their polar growth mode impose a stringent coordination between the septal divisome, organized around the tubulin-like protein FtsZ, and the polar elongasome, assembled around the tropomyosin-like protein Wag31. Here, we report the identification of two new divisome members, a gephyrin-like repurposed molybdotransferase (GLP) and its membrane receptor (GLPR). We show that the interplay between the GLPR/GLP module, FtsZ and Wag31 is crucial for orchestrating cell cycle progression. Our results provide a detailed molecular understanding of the crosstalk between two essential machineries, the divisome and elongasome, and reveal that Corynebacteriales have evolved a protein scaffold to control cell division and morphogenesis similar to the gephyrin/GlyR system that in higher eukaryotes mediates synaptic signaling through network organization of membrane receptors and the microtubule cytoskeleton.
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Affiliation(s)
- M. Martinez
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - J. Petit
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - D. Megrian
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Rodriguez
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Q. Gaday
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Ben Assaya
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - M. Portela
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Haouz
- Plate-forme de cristallographie, C2RT-Institut Pasteur, CNRS, UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - A. Ducret
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - C. Grangeasse
- Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France
| | - P. M. Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
| | - R. Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - A. Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, F-75015 Paris, France
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17
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Covaleda-Cortés G, Mechaly A, Brissac T, Baehre H, Devaux L, England P, Raynal B, Hoos S, Gominet M, Firon A, Trieu-Cuot P, Kaminski PA. The c-di-AMP-binding protein CbpB modulates the level of ppGpp alarmone in Streptococcus agalactiae. FEBS J 2023. [PMID: 36629470 DOI: 10.1111/febs.16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Cyclic di-AMP is an essential signalling molecule in Gram-positive bacteria. This second messenger regulates the osmotic pressure of the cell by interacting directly with the regulatory domains, either RCK_C or CBS domains, of several potassium and osmolyte uptake membrane protein systems. Cyclic di-AMP also targets stand-alone CBS domain proteins such as DarB in Bacillus subtilis and CbpB in Listeria monocytogenes. We show here that the CbpB protein of Group B Streptococcus binds c-di-AMP with a very high affinity. Crystal structures of CbpB reveal the determinants of binding specificity and significant conformational changes occurring upon c-di-AMP binding. Deletion of the cbpB gene alters bacterial growth in low potassium conditions most likely due to a decrease in the amount of ppGpp caused by a loss of interaction between CbpB and Rel, the GTP/GDP pyrophosphokinase.
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Affiliation(s)
- Giovanni Covaleda-Cortés
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
| | - Ariel Mechaly
- CNRS-UMR 3528, Crystallography Platform, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, France
| | - Terry Brissac
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
| | - Heike Baehre
- Research Core Unit Metabolomics, Hannover Medical School, Germany
| | - Laura Devaux
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
| | - Patrick England
- CNRS UMR 3528, Molecular Biophysics Platform, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, France
| | - Bertrand Raynal
- CNRS UMR 3528, Molecular Biophysics Platform, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, France
| | - Sylviane Hoos
- CNRS UMR 3528, Molecular Biophysics Platform, Center for Technological Resources and Research, Institut Pasteur, Université Paris Cité, France
| | - Myriam Gominet
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
| | - Arnaud Firon
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
| | - Patrick Trieu-Cuot
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
| | - Pierre Alexandre Kaminski
- Unité Biologie des Bactéries Pathogènes à Gram-positif, CNRS UMR 6047, Institut Pasteur, Université Paris Cité, France
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18
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Genera M, Colcombet-Cazenave B, Croitoru A, Raynal B, Mechaly A, Caillet J, Haouz A, Wolff N, Caillet-Saguy C. Interactions of the protein tyrosine phosphatase PTPN3 with viral and cellular partners through its PDZ domain: insights into structural determinants and phosphatase activity. Front Mol Biosci 2023; 10:1192621. [PMID: 37200868 PMCID: PMC10185773 DOI: 10.3389/fmolb.2023.1192621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023] Open
Abstract
The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a phosphatase containing a PDZ (PSD-95/Dlg/ZO-1) domain that has been found to play both tumor-suppressive and tumor-promoting roles in various cancers, despite limited knowledge of its cellular partners and signaling functions. Notably, the high-risk genital human papillomavirus (HPV) types 16 and 18 and the hepatitis B virus (HBV) target the PDZ domain of PTPN3 through PDZ-binding motifs (PBMs) in their E6 and HBc proteins respectively. This study focuses on the interactions between the PTPN3 PDZ domain (PTPN3-PDZ) and PBMs of viral and cellular protein partners. We solved the X-ray structures of complexes between PTPN3-PDZ and PBMs of E6 of HPV18 and the tumor necrosis factor-alpha converting enzyme (TACE). We provide new insights into key structural determinants of PBM recognition by PTPN3 by screening the selectivity of PTPN3-PDZ recognition of PBMs, and by comparing the PDZome binding profiles of PTPN3-recognized PBMs and the interactome of PTPN3-PDZ. The PDZ domain of PTPN3 was known to auto-inhibit the protein's phosphatase activity. We discovered that the linker connecting the PDZ and phosphatase domains is involved in this inhibition, and that the binding of PBMs does not impact this catalytic regulation. Overall, the study sheds light on the interactions and structural determinants of PTPN3 with its cellular and viral partners, as well as on the inhibitory role of its PDZ domain on its phosphatase activity.
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Affiliation(s)
- Mariano Genera
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
- Sorbonne Université, Complexité du Vivant, F-75005, Paris, France
| | - Baptiste Colcombet-Cazenave
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
- Sorbonne Université, Complexité du Vivant, F-75005, Paris, France
| | - Anastasia Croitoru
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform-C2RT, CNRS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, Institut Pasteur, Université Paris Cité, Paris, France
| | - Joël Caillet
- CNRS, Institut de Biologie Physico-Chimique, Université Paris Cité, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nicolas Wolff
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
| | - Célia Caillet-Saguy
- Institut Pasteur, Université Paris Cité, Channel Receptors Unit, Paris, France
- *Correspondence: Célia Caillet-Saguy,
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19
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FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales. Proc Natl Acad Sci U S A 2022; 119:e2214599119. [PMID: 36469781 PMCID: PMC9897464 DOI: 10.1073/pnas.2214599119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bacterial cell wall is a multi-layered mesh, whose major component is peptidoglycan (PG), a sugar polymer cross-linked by short peptide stems. During cell division, a careful balance of PG synthesis and degradation, precisely coordinated both in time and space, is necessary to prevent uncontrolled destruction of the cell wall. In Corynebacteriales, the D,L endopeptidase RipA has emerged as a major PG hydrolase for cell separation, and RipA defaults have major implications for virulence of the human pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. However, the precise mechanisms by which RipA mediates cell separation remain elusive. Here we report phylogenetic, biochemical, and structural analysis of the Corynebacterium glutamicum homologue of RipA, Cg1735. The crystal structures of full-length Cg1735 in two different crystal forms revealed the C-terminal NlpC/P60 catalytic domain obtruded by its N-terminal conserved coiled-coil domain, which locks the enzyme in an autoinhibited state. We show that this autoinhibition is relieved by the extracellular core domain of the transmembrane septal protein Cg1604. The crystal structure of Cg1604 revealed a (β/α) protein with an overall topology similar to that of receiver domains from response regulator proteins. The atomic model of the Cg1735-Cg1604 complex, based on bioinformatical and mutational analysis, indicates that a conserved, distal-membrane helical insertion in Cg1604 is responsible for Cg1735 activation. The reported data provide important insights into how intracellular cell division signal(s), yet to be identified, control PG hydrolysis during RipA-mediated cell separation in Corynebacteriales.
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20
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5-(4-Nitrophenyl)furan-2-carboxylic Acid. MOLBANK 2022. [DOI: 10.3390/m1515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ever-evolving research in the field of antitubercular agents has led to the identification of several new potential drug classes. Among them, 5-phenyl-furan-2-carboxylic acids have emerged as innovative potential therapeutics, targeting iron acquisition in mycobacterial species. In our efforts to characterize the molecular interactions between these compounds and their protein target (MbtI from M. tuberculosis) by means of co-crystallization experiments, we unexpectedly obtained the structure of 5-(4-nitrophenyl)furan-2-carboxylic acid (1). Herein, we describe the preparation of the compound and its analysis by 1H NMR, 13C NMR, HRMS, and SC-XRD.
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21
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Aleshin VA, Bunik VI, Bruch EM, Bellinzoni M. Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase. Int J Mol Sci 2022; 23:ijms231911306. [PMID: 36232607 PMCID: PMC9570180 DOI: 10.3390/ijms231911306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Glutamate dehydrogenase (GDH) plays a key role in the metabolism of glutamate, an important compound at a cross-road of carbon and nitrogen metabolism and a relevant neurotransmitter. Despite being one of the first discovered allosteric enzymes, GDH still poses challenges for structural characterization of its allosteric sites. Only the structures with ADP, and at low (3.5 Å) resolution, are available for mammalian GDH complexes with allosteric activators. Here, we aim at deciphering a structural basis for the GDH allosteric activation using bovine GDH as a model. For the first time, we report a mammalian GDH structure in a ternary complex with the activators leucine and ADP, co-crystallized with potassium ion, resolved to 2.45 Å. An improved 2.4-angstrom resolution of the GDH complex with ADP is also presented. The ternary complex with leucine and ADP differs from the binary complex with ADP by the conformation of GDH C-terminus, involved in the leucine binding and subunit interactions. The potassium site, identified in this work, may mediate interactions between the leucine and ADP binding sites. Our data provide novel insights into the mechanisms of GDH activation by leucine and ADP, linked to the enzyme regulation by (de)acetylation.
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Affiliation(s)
- Vasily A. Aleshin
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Victoria I. Bunik
- Department of Biokinetics, A. N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
| | - Eduardo M. Bruch
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
| | - Marco Bellinzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Microbiologie Structurale, F-75724 Paris, France
- Correspondence: (V.I.B.); (M.B.); Tel.: +7-495-9394484 (V.I.B.); +33-1-45688608 (M.B.)
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22
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Léger C, Pitard I, Sadi M, Carvalho N, Brier S, Mechaly A, Raoux-Barbot D, Davi M, Hoos S, Weber P, Vachette P, Durand D, Haouz A, Guijarro JI, Ladant D, Chenal A. Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium. BMC Biol 2022; 20:176. [PMID: 35945584 PMCID: PMC9361521 DOI: 10.1186/s12915-022-01381-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Calmodulin (CaM) is an evolutionarily conserved eukaryotic multifunctional protein that functions as the major sensor of intracellular calcium signaling. Its calcium-modulated function regulates the activity of numerous effector proteins involved in a variety of physiological processes in diverse organs, from proliferation and apoptosis, to memory and immune responses. Due to the pleiotropic roles of CaM in normal and pathological cell functions, CaM antagonists are needed for fundamental studies as well as for potential therapeutic applications. Calmidazolium (CDZ) is a potent small molecule antagonist of CaM and one the most widely used inhibitors of CaM in cell biology. Yet, CDZ, as all other CaM antagonists described thus far, also affects additional cellular targets and its lack of selectivity hinders its application for dissecting calcium/CaM signaling. A better understanding of CaM:CDZ interaction is key to design analogs with improved selectivity. Here, we report a molecular characterization of CaM:CDZ complexes using an integrative structural biology approach combining SEC-SAXS, X-ray crystallography, HDX-MS, and NMR. RESULTS We provide evidence that binding of a single molecule of CDZ induces an open-to-closed conformational reorientation of the two domains of CaM and results in a strong stabilization of its structural elements associated with a reduction of protein dynamics over a large time range. These CDZ-triggered CaM changes mimic those induced by CaM-binding peptides derived from physiological protein targets, despite their distinct chemical natures. CaM residues in close contact with CDZ and involved in the stabilization of the CaM:CDZ complex have been identified. CONCLUSION Our results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists. Calmidazolium is a potent and widely used inhibitor of calmodulin, a major mediator of calcium-signaling in eukaryotic cells. Structural characterization of calmidazolium-binding to calmodulin reveals that it triggers open-to-closed conformational changes similar to those induced by calmodulin-binding peptides derived from enzyme targets. These results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists.
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Affiliation(s)
- Corentin Léger
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Irène Pitard
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Mirko Sadi
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
- Université Paris Cité, Paris, France
| | - Nicolas Carvalho
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
- Université Paris Cité, Paris, France
| | - Sébastien Brier
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Ariel Mechaly
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Dorothée Raoux-Barbot
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Maryline Davi
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Patrick Weber
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - J Iñaki Guijarro
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Daniel Ladant
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.
| | - Alexandre Chenal
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.
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23
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Walter P, Mechaly A, Bous J, Haouz A, England P, Lai‐Kee‐Him J, Ancelin A, Hoos S, Baron B, Trapani S, Bron P, Labesse G, Munier‐Lehmann H. Structural basis for the allosteric inhibition of UMP kinase from Gram‐positive bacteria, a promising antibacterial target. FEBS J 2022; 289:4869-4887. [DOI: 10.1111/febs.16393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Patrick Walter
- Unité de Chimie et Biocatalyse Département de Biologie Structurale et Chimie Institut Pasteur CNRS UMR3523 Paris France
| | - Ariel Mechaly
- Plate‐Forme de Cristallographie C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Julien Bous
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Ahmed Haouz
- Plate‐Forme de Cristallographie C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Patrick England
- Plate‐Forme de Biophysique Moléculaire C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Joséphine Lai‐Kee‐Him
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Aurélie Ancelin
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Sylviane Hoos
- Plate‐Forme de Biophysique Moléculaire C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Bruno Baron
- Plate‐Forme de Biophysique Moléculaire C2RT Institut Pasteur CNRS UMR3528 Paris France
| | - Stefano Trapani
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Patrick Bron
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS) Univ Montpellier INSERM CNRS Montpellier France
| | - Hélène Munier‐Lehmann
- Unité de Chimie et Biocatalyse Département de Biologie Structurale et Chimie Institut Pasteur CNRS UMR3523 Paris France
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24
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Through Diffusion Measurements of Molecules to a Numerical Model for Protein Crystallization in Viscous Polyethylene Glycol Solution. CRYSTALS 2022. [DOI: 10.3390/cryst12070881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein crystallography has become a popular method for biochemists, but obtaining high-quality protein crystals for precise structural analysis and larger ones for neutron analysis requires further technical progress. Many studies have noted the importance of solvent viscosity for the probability of crystal nucleation and for mass transportation; therefore, in this paper, we have reported on experimental results and simulation studies regarding the use of viscous polyethylene glycol (PEG) solvents for protein crystals. We investigated the diffusion rates of proteins, peptides, and small molecules in viscous PEG solvents using fluorescence correlation spectroscopy. In high-molecular-weight PEG solutions (molecular weights: 10,000 and 20,000), solute diffusion showed deviations, with a faster diffusion than that estimated by the Stokes–Einstein equation. We showed that the extent of the deviation depends on the difference between the molecular sizes of the solute and PEG solvent, and succeeded in creating equations to predict diffusion coefficients in viscous PEG solutions. Using these equations, we have developed a new numerical model of 1D diffusion processes of proteins and precipitants in a counter-diffusion chamber during crystallization processes. Examples of the application of anomalous diffusion in counter-diffusion crystallization are shown by the growth of lysozyme crystals.
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25
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Zhu Y, Alvarez F, Wolff N, Mechaly A, Brûlé S, Neitthoffer B, Etienne-Manneville S, Haouz A, Boëda B, Caillet-Saguy C. Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins. Front Microbiol 2022; 13:829094. [PMID: 35283834 PMCID: PMC8909127 DOI: 10.3389/fmicb.2022.829094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022] Open
Abstract
The C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein E contains a PBM (PDZ-binding motif) targeting PDZ (PSD-95/Dlg/ZO-1) domains, which is identical to the PBM of SARS-CoV. The latter is involved in the pathogenicity of the virus. Recently, we identified 10 human PDZ-containing proteins showing significant interactions with SARS-CoV-2 protein E PBM. We selected several of them involved in cellular junctions and cell polarity (TJP1, PARD3, MLLT4, and LNX2) and MPP5/PALS1 previously shown to interact with SARS-CoV E PBM. Targeting cellular junctions and polarity components is a common strategy by viruses to hijack cell machinery to their advantage. In this study, we showed that these host PDZ domains TJP1, PARD3, MLLT4, LNX2, and MPP5/PALS1 interact in a PBM-dependent manner in vitro and colocalize with the full-length E protein in cellulo, sequestrating the PDZ domains to the Golgi compartment. We solved three crystal structures of complexes between human LNX2, MLLT4, and MPP5 PDZs and SARS-CoV-2 E PBM highlighting its binding preferences for several cellular targets. Finally, we showed different affinities for the PDZ domains with the original SARS-CoV-2 C-terminal sequence containing the PBM and the one of the beta variant that contains a mutation close to the PBM. The acquired mutations in the E protein localized near the PBM might have important effects both on the structure and the ion-channel activity of the E protein and on the host machinery targeted by the variants during the infection.
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Affiliation(s)
- Yanlei Zhu
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Flavio Alvarez
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Nicolas Wolff
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Benoit Neitthoffer
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Célia Caillet-Saguy
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
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26
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Takahashi DT, Gadelle D, Agama K, Kiselev E, Zhang H, Yab E, Petrella S, Forterre P, Pommier Y, Mayer C. Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states. Nat Commun 2022; 13:59. [PMID: 35013228 PMCID: PMC8748870 DOI: 10.1038/s41467-021-27686-7] [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: 04/14/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic topoisomerases I (TOP1) are ubiquitous enzymes removing DNA torsional stress. However, there is little data concerning the three-dimensional structure of TOP1 in the absence of DNA, nor how the DNA molecule can enter/exit its closed conformation. Here, we solved the structure of thermostable archaeal Caldiarchaeum subterraneum CsTOP1 in an apo-form. The enzyme displays an open conformation resulting from one substantial rotation between the capping (CAP) and the catalytic (CAT) modules. The junction between these two modules is a five-residue loop, the hinge, whose flexibility permits the opening/closing of the enzyme and the entry of DNA. We identified a highly conserved tyrosine near the hinge as mediating the transition from the open to closed conformation upon DNA binding. Directed mutagenesis confirmed the importance of the hinge flexibility, and linked the enzyme dynamics with sensitivity to camptothecin, a TOP1 inhibitor targeting the TOP1 enzyme catalytic site in the closed conformation. Topoisomerase I (TOP1) relaxes both positive and negative supercoils by nicking DNA and after rotation of the broken DNA strand closes the nick. Here, the authors present the DNA free crystal structure of TOP1 from the hyperthermophilic archaeon Caldiarchaeum subterraneum in the open form and discuss the mechanism of how DNA enters the catalytic site of TOP1.
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Affiliation(s)
- Diane T Takahashi
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France. .,Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France. .,Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, BP 10413, F-67412, Illkirch, France.
| | - Danièle Gadelle
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Evgeny Kiselev
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Emilie Yab
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Stephanie Petrella
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France
| | - Patrick Forterre
- Institut de Biologie Integrative de la Cellule, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, Cedex, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA.
| | - Claudine Mayer
- Institut Pasteur, Université de Paris, CNRS UMR 3528, Unité de Microbiologie Structurale, F-75015, Paris, France.,Université de Paris, F-75013, Paris, France.,ICube-UMR7357, CSTB, Centre de Recherche en Biomédecine de Strasbourg, 67084, Strasbourg, France
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27
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Mishra AK, Hellert J, Freitas N, Guardado-Calvo P, Haouz A, Fels JM, Maurer DP, Abelson DM, Bornholdt ZA, Walker LM, Chandran K, Cosset FL, McLellan JS, Rey FA. Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies. Science 2022; 375:104-109. [PMID: 34793197 PMCID: PMC9771711 DOI: 10.1126/science.abl6502] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is the most widespread tick-borne zoonotic virus, with a 30% case fatality rate in humans. Structural information is lacking in regard to the CCHFV membrane fusion glycoprotein Gc—the main target of the host neutralizing antibody response—as well as antibody–mediated neutralization mechanisms. We describe the structure of prefusion Gc bound to the antigen-binding fragments (Fabs) of two neutralizing antibodies that display synergy when combined, as well as the structure of trimeric, postfusion Gc. The structures show the two Fabs acting in concert to block membrane fusion, with one targeting the fusion loops and the other blocking Gc trimer formation. The structures also revealed the neutralization mechanism of previously reported antibodies against CCHFV, providing the molecular underpinnings essential for developing CCHFV–specific medical countermeasures for epidemic preparedness.
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Affiliation(s)
- Akaash K. Mishra
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA 78712
| | - Jan Hellert
- Structural Virology Unit, Institut Pasteur, CNRS UMR 3569, 25-28 rue du Docteur Roux, Cedex 15, Paris, France 75724
| | - Natalia Freitas
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, Lyon, France 69007
| | - Pablo Guardado-Calvo
- Structural Virology Unit, Institut Pasteur, CNRS UMR 3569, 25-28 rue du Docteur Roux, Cedex 15, Paris, France 75724
| | - Ahmed Haouz
- Crystallography Platform C2RT, Institut Pasteur, CNRS UMR 3528, 25-28 rue du Docteur Roux, Cedex 15, Paris, France 75724
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA 10461
| | | | | | | | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA 10461
| | - François-Loïc Cosset
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, Lyon, France 69007
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA 78712,Correspondence: (J.S.M.); (F.A.R)
| | - Felix A. Rey
- Structural Virology Unit, Institut Pasteur, CNRS UMR 3569, 25-28 rue du Docteur Roux, Cedex 15, Paris, France 75724,Correspondence: (J.S.M.); (F.A.R)
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28
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Fagnen C, Bannwarth L, Oubella I, Zuniga D, Haouz A, Forest E, Scala R, Bendahhou S, De Zorzi R, Perahia D, Vénien-Bryan C. Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain. Int J Mol Sci 2021; 23:335. [PMID: 35008764 PMCID: PMC8745282 DOI: 10.3390/ijms23010335] [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: 11/16/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological processes. In pancreatic β-cells, K-ATP channels composed of Kir6.2 and SUR1 play a key role in coupling blood glucose and insulin secretion. A tryptophan residue located at the cytosolic end of the transmembrane helix is highly conserved in eukaryote and prokaryote Kir channels. Any mutation on this amino acid causes a gain of function and neonatal diabetes mellitus. In this study, we have investigated the effect of mutation on this highly conserved residue on a KirBac channel (prokaryotic homolog of mammalian Kir6.2). We provide the crystal structure of the mutant KirBac3.1 W46R (equivalent to W68R in Kir6.2) and its conformational flexibility properties using HDX-MS. In addition, the detailed dynamical view of the mutant during the gating was investigated using the in silico method. Finally, functional assays have been performed. A comparison of important structural determinants for the gating mechanism between the wild type KirBac and the mutant W46R suggests interesting structural and dynamical clues and a mechanism of action of the mutation that leads to the gain of function.
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Affiliation(s)
- Charline Fagnen
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Ludovic Bannwarth
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Iman Oubella
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Dania Zuniga
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Ahmed Haouz
- Institut Pasteur, C2RT-Plate-Forme de Cristallographie CNRS-UMR3528, 75724 Paris, France;
| | - Eric Forest
- CNRS, IBS, CEA, University Grenoble Alpes, 38044 Grenoble, France;
| | - Rosa Scala
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Saïd Bendahhou
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy;
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Catherine Vénien-Bryan
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
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29
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Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex. Proc Natl Acad Sci U S A 2021; 118:2112107118. [PMID: 34819376 DOI: 10.1073/pnas.2112107118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high-molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an odhA gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.
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30
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Czernecki D, Hu H, Romoli F, Delarue M. Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8. Nucleic Acids Res 2021; 49:11974-11985. [PMID: 34751404 PMCID: PMC8599892 DOI: 10.1093/nar/gkab955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France.,Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Haidai Hu
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Filippo Romoli
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
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31
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Transfer of a Rational Crystal Contact Engineering Strategy between Diverse Alcohol Dehydrogenases. CRYSTALS 2021. [DOI: 10.3390/cryst11080975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein crystallization can serve as a purification step in biotechnological processes but is often limited by the non-crystallizability of proteins. Enabling or improving crystallization is mostly achieved by high-throughput screening of crystallization conditions and, more recently, by rational crystal contact engineering. Two selected rational crystal contact mutations, Q126K and T102E, were transferred from the alcohol dehydrogenases of Lactobacillus brevis (LbADH) to Lactobacillus kefir (LkADH). Proteins were expressed in E. coli and batch protein crystallization was performed in stirred crystallizers. Highly similar crystal packing of LkADH wild type compared to LbADH, which is necessary for the transfer of crystal contact engineering strategies, was achieved by aligning purification tag and crystallization conditions, as shown by X-ray diffraction. After comparing the crystal sizes after crystallization of LkADH mutants with the wild type, the mean protein crystal size of LkADH mutants was reduced by 40–70% in length with a concomitant increase in the total amount of crystals (higher number of nucleation events). Applying this measure to the LkADH variants studied results in an order of crystallizability T102E > Q126K > LkADH wild type, which corresponds to the results with LbADH mutants and shows, for the first time, the successful transfer of crystal contact engineering strategies.
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32
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Czernecki D, Bonhomme F, Kaminski PA, Delarue M. Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA. Nat Commun 2021; 12:4710. [PMID: 34354070 PMCID: PMC8342488 DOI: 10.1038/s41467-021-25064-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, Paris, France
| | - Frédéric Bonhomme
- Unit of Epigenetic Chemical Biology, CNRS UMR 3523, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Pierre-Alexandre Kaminski
- Unit of Biology of Pathogenic Gram-Positive Bacteria, CNRS UMR 2001, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, Paris, France.
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33
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Pende N, Sogues A, Megrian D, Sartori-Rupp A, England P, Palabikyan H, Rittmann SKMR, Graña M, Wehenkel AM, Alzari PM, Gribaldo S. SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system. Nat Commun 2021; 12:3214. [PMID: 34088904 PMCID: PMC8178401 DOI: 10.1038/s41467-021-23099-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Most archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.
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Affiliation(s)
- Nika Pende
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France
| | - Adrià Sogues
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Daniela Megrian
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France
- École Doctorale Complexité du vivant, Sorbonne University, Paris, France
| | | | - Patrick England
- Plate-forme de biophysique moléculaire, C2RT-Institut Pasteur, CNRS, UMR 3528, Paris, France
| | - Hayk Palabikyan
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Wien, Austria
| | - Martín Graña
- Bioinformatics Unit, Institut Pasteur of Montevideo, Montevideo, Uruguay
| | - Anne Marie Wehenkel
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France.
| | - Pedro M Alzari
- Structural Microbiology Unit, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France.
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How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA. Nat Commun 2021; 12:2420. [PMID: 33893297 PMCID: PMC8065100 DOI: 10.1038/s41467-021-22626-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.
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35
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Kato R, Hiraki M, Yamada Y, Tanabe M, Senda T. A fully automated crystallization apparatus for small protein quantities. Acta Crystallogr F Struct Biol Commun 2021; 77:29-36. [PMID: 33439153 PMCID: PMC7805554 DOI: 10.1107/s2053230x20015514] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/23/2020] [Indexed: 12/05/2022] Open
Abstract
In 2003, a fully automated protein crystallization and monitoring system (PXS) was developed to support the structural genomics projects that were initiated in the early 2000s. In PXS, crystallization plates were automatically set up using the vapor-diffusion method, transferred to incubators and automatically observed according to a pre-set schedule. The captured images of each crystallization drop could be monitored through the internet using a web browser. While the screening throughput of PXS was very high, the demands of users have gradually changed over the ensuing years. To study difficult proteins, it has become important to screen crystallization conditions using small amounts of proteins. Moreover, membrane proteins have become one of the main targets for X-ray crystallography. Therefore, to meet the evolving demands of users, PXS was upgraded to PXS2. In PXS2, the minimum volume of the dispenser is reduced to 0.1 µl to minimize the amount of sample, and the resolution of the captured images is increased to five million pixels in order to observe small crystallization drops in detail. In addition to the 20°C incubators, a 4°C incubator was installed in PXS2 because crystallization results may vary with temperature. To support membrane-protein crystallization, PXS2 includes a procedure for the bicelle method. In addition, the system supports a lipidic cubic phase (LCP) method that uses a film sandwich plate and that was specifically designed for PXS2. These improvements expand the applicability of PXS2, reducing the bottleneck of X-ray protein crystallography.
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Affiliation(s)
- Ryuichi Kato
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Masahiko Hiraki
- Institute of Particle and Nuclear Studies, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Yusuke Yamada
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Mikio Tanabe
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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36
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Nemecz D, Ostrowski M, Ravatin M, Saul F, Faure G. Crystal Structure of Isoform CBd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of CB for Interaction with Protein Targets. Molecules 2020; 25:molecules25225290. [PMID: 33202772 PMCID: PMC7696373 DOI: 10.3390/molecules25225290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
Crotoxin, from the venom of the South American rattlesnake Crotalus durissus terrificus, is a potent heterodimeric presynaptic β-neurotoxin that exists in individual snake venom as a mixture of isoforms of a basic phospholipase A2 (PLA2) subunit (CBa2, CBb, CBc, and CBd) and acidic subunit (CA1-4). Specific natural mutations in CB isoforms are implicated in functional differences between crotoxin isoforms. The three-dimensional structure of two individual CB isoforms (CBa2, CBc), and one isoform in a crotoxin (CA2CBb) complex, have been previously reported. This study concerns CBd, which by interaction with various protein targets exhibits many physiological or pharmacological functions. It binds with high affinity to presynaptic receptors showing neurotoxicity, but also interacts with human coagulation factor Xa (hFXa), exhibiting anticoagulant effect, and acts as a positive allosteric modulator and corrector of mutated chloride channel, cystic fibrosis transmembrane conductance regulator (CFTR), implicated in cystic fibrosis. Thus, CBd represents a novel family of agents that have potential in identifying new drug leads related to anticoagulant and anti-cystic fibrosis function. We determined here the X-ray structure of CBd and compare it with the three other natural isoforms of CB. The structural role of specific amino acid variations between CB isoforms are analyzed and the structural framework of CB for interaction with protein targets is described.
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Affiliation(s)
- Dorota Nemecz
- Institut Pasteur, Récepteurs-Canaux, CNRS UMR 3571, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France; (D.N.); (M.O.); (M.R.)
- Biochemistry Department, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Maciej Ostrowski
- Institut Pasteur, Récepteurs-Canaux, CNRS UMR 3571, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France; (D.N.); (M.O.); (M.R.)
- Biochemistry Department, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Marc Ravatin
- Institut Pasteur, Récepteurs-Canaux, CNRS UMR 3571, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France; (D.N.); (M.O.); (M.R.)
- Sanofi R&D, Integrated Drug Discovery-High Content Biology, 94400 Vitry-sur-Seine, France
| | - Frederick Saul
- Institut Pasteur, Plateforme de Cristallographie-C2RT, CNRS UMR 3528, 75015 Paris, France;
| | - Grazyna Faure
- Institut Pasteur, Récepteurs-Canaux, CNRS UMR 3571, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France; (D.N.); (M.O.); (M.R.)
- Correspondence: ; Tel.: +33-14-568-86-86; Fax: +33-14-568-88-36
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37
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Zhu Y, Delhommel F, Cordier F, Lüchow S, Mechaly A, Colcombet-Cazenave B, Girault V, Pepermans E, Bahloul A, Gautier C, Brûlé S, Raynal B, Hoos S, Haouz A, Caillet-Saguy C, Ivarsson Y, Wolff N. Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners. J Mol Biol 2020; 432:5920-5937. [PMID: 32971111 DOI: 10.1016/j.jmb.2020.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022]
Abstract
Hearing is a mechanical and neurochemical process, which occurs in the hair cells of inner ear that converts the sound vibrations into electrical signals transmitted to the brain. The multi-PDZ scaffolding protein whirlin plays a critical role in the formation and function of stereocilia exposed at the surface of hair cells. In this article, we reported seven stereociliary proteins that encode PDZ binding motifs (PBM) and interact with whirlin PDZ3, where four of them are first reported. We solved the atomic resolution structures of complexes between whirlin PDZ3 and the PBMs of myosin 15a, CASK, harmonin a1 and taperin. Interestingly, the PBM of CASK and taperin are rare non-canonical PBM, which are not localized at the extreme C terminus. This large capacity to accommodate various partners could be related to the distinct functions of whirlin at different stages of the hair cell development.
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Affiliation(s)
- Yanlei Zhu
- Unité Récepteurs-Canaux, Institut Pasteur, 75015 Paris, France; Complexité du Vivant, Sorbonne Université, 75005 Paris, France
| | - Florent Delhommel
- Unité Récepteurs-Canaux, Institut Pasteur, 75015 Paris, France; Complexité du Vivant, Sorbonne Université, 75005 Paris, France
| | | | | | - Ariel Mechaly
- Plateforme de Cristallographie, Institut Pasteur, Paris, France
| | - Baptiste Colcombet-Cazenave
- Unité Récepteurs-Canaux, Institut Pasteur, 75015 Paris, France; Complexité du Vivant, Sorbonne Université, 75005 Paris, France
| | | | - Elise Pepermans
- Complexité du Vivant, Sorbonne Université, 75005 Paris, France; Unité de génétique et physiologie de l'audition, Institut Pasteur, 75015 Paris, France
| | - Amel Bahloul
- Unité de génétique et physiologie de l'audition, Institut Pasteur, 75015 Paris, France
| | - Candice Gautier
- Istituto Pasteur - Fondazione C. Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Sébastien Brûlé
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Bertrand Raynal
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Ahmed Haouz
- Plateforme de Cristallographie, Institut Pasteur, Paris, France
| | | | - Ylva Ivarsson
- Department of Chemistry-BMC, Uppsala University, Sweden
| | - Nicolas Wolff
- Unité Récepteurs-Canaux, Institut Pasteur, 75015 Paris, France.
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38
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Vollmer B, Pražák V, Vasishtan D, Jefferys EE, Hernandez-Duran A, Vallbracht M, Klupp BG, Mettenleiter TC, Backovic M, Rey FA, Topf M, Grünewald K. The prefusion structure of herpes simplex virus glycoprotein B. SCIENCE ADVANCES 2020; 6:eabc1726. [PMID: 32978151 PMCID: PMC7518877 DOI: 10.1126/sciadv.abc1726] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/12/2020] [Indexed: 05/03/2023]
Abstract
Cell entry of enveloped viruses requires specialized viral proteins that mediate fusion with the host membrane by substantial structural rearrangements from a metastable pre- to a stable postfusion conformation. This metastability renders the herpes simplex virus 1 (HSV-1) fusion glycoprotein B (gB) highly unstable such that it readily converts into the postfusion form, thereby precluding structural elucidation of the pharmacologically relevant prefusion conformation. By identification of conserved sequence signatures and molecular dynamics simulations, we devised a mutation that stabilized this form. Functionally locking gB allowed the structural determination of its membrane-embedded prefusion conformation at sub-nanometer resolution and enabled the unambiguous fit of all ectodomains. The resulting pseudo-atomic model reveals a notable conservation of conformational domain rearrangements during fusion between HSV-1 gB and the vesicular stomatitis virus glycoprotein G, despite their very distant phylogeny. In combination with our comparative sequence-structure analysis, these findings suggest common fusogenic domain rearrangements in all class III viral fusion proteins.
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Affiliation(s)
- B Vollmer
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
- Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - V Pražák
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - D Vasishtan
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - E E Jefferys
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - M Vallbracht
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - B G Klupp
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - T C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - M Backovic
- Institut Pasteur, Structural Virology Unit, Department of Virology, Paris, France
| | - F A Rey
- Institut Pasteur, Structural Virology Unit, Department of Virology, Paris, France
| | - M Topf
- Institute of Structural and Molecular Biology, Birkbeck, London, UK
| | - K Grünewald
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK.
- Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
- Department of Chemistry, MIN Faculty, Universität Hamburg, Hamburg, Germany
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39
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Medits I, Vaney M, Rouvinski A, Rey M, Chamot‐Rooke J, Rey FA, Heinz FX, Stiasny K. Extensive flavivirus E trimer breathing accompanies stem zippering of the post-fusion hairpin. EMBO Rep 2020; 21:e50069. [PMID: 32484292 PMCID: PMC7403712 DOI: 10.15252/embr.202050069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/23/2022] Open
Abstract
Flaviviruses enter cells by fusion with endosomal membranes through a rearrangement of the envelope protein E, a class II membrane fusion protein, into fusogenic trimers. The rod-like E subunits bend into "hairpins" to bring the fusion loops next to the C-terminal transmembrane (TM) anchors, with the TM-proximal "stem" element zippering the E trimer to force apposition of the membranes. The structure of the complete class II trimeric hairpin is known for phleboviruses but not for flaviviruses, for which the stem is only partially resolved. Here, we performed comparative analyses of E-protein trimers from the tick-borne encephalitis flavivirus with sequential stem truncations. Our thermostability and antibody-binding data suggest that the stem "zipper" ends at a characteristic flavivirus conserved sequence (CS) that cloaks the fusion loops, with the downstream segment not contributing to trimer stability. We further identified a highly dynamic behavior of E trimers C-terminally truncated upstream the CS, which, unlike fully stem-zippered trimers, undergo rapid deuterium exchange at the trimer interface. These results thus identify important "breathing" intermediates in the E-protein-driven membrane fusion process.
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Affiliation(s)
- Iris Medits
- Center for VirologyMedical University of ViennaViennaAustria
| | | | - Alexander Rouvinski
- Unité de Virologie StructuraleInstitut PasteurCNRS UMR 3569 VirologieParisFrance
- Present address:
Department of Microbiology and Molecular GeneticsInstitute for Medical Research Israel‐CanadaThe Kuvin Center for the Study of Infectious and Tropical DiseasesThe Hebrew University of JerusalemJerusalemIsrael
| | - Martial Rey
- Unité de Spectrométrie de Masse pour la BiologieInstitut PasteurCNRS USR 2000ParisFrance
| | - Julia Chamot‐Rooke
- Unité de Spectrométrie de Masse pour la BiologieInstitut PasteurCNRS USR 2000ParisFrance
| | - Felix A Rey
- Unité de Virologie StructuraleInstitut PasteurCNRS UMR 3569 VirologieParisFrance
| | - Franz X Heinz
- Center for VirologyMedical University of ViennaViennaAustria
| | - Karin Stiasny
- Center for VirologyMedical University of ViennaViennaAustria
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40
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Mori M, Stelitano G, Gelain A, Pini E, Chiarelli LR, Sammartino JC, Poli G, Tuccinardi T, Beretta G, Porta A, Bellinzoni M, Villa S, Meneghetti F. Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design. J Med Chem 2020; 63:7066-7080. [PMID: 32530281 PMCID: PMC8008425 DOI: 10.1021/acs.jmedchem.0c00373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
Mg2+-dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis
of siderophores. Because iron is essential for the survival and pathogenicity
of the microorganism, this protein constitutes an attractive target
for antitubercular therapy, also considering the absence of homologous
enzymes in mammals. An extension of the structure–activity
relationships of our furan-based candidates allowed us to disclose
the most potent competitive inhibitor known to date (10, Ki = 4 μM), which also proved
effective on mycobacterial cultures. By structural studies, we characterized
its unexpected Mg2+-independent binding mode. We also investigated
the role of the Mg2+ cofactor in catalysis, analyzing the
first crystal structure of the MbtI–Mg2+–salicylate
ternary complex. Overall, these results pave the way for the development
of novel antituberculars through the rational design of improved MbtI
inhibitors.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - José C Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy
| | - Alessio Porta
- Dipartimento di Chimica, Università degli Studi di Pavia, via T. Taramelli 12, 27100 Pavia, Italy
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75015 Paris, France
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
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