1
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Aouadi W, Najburg V, Legendre R, Varet H, Kergoat L, Tangy F, Larrous F, Komarova AV, Bourhy H. Comparative analysis of rabies pathogenic and vaccine strains detection by RIG-I-like receptors. Microbes Infect 2024; 26:105321. [PMID: 38461968 DOI: 10.1016/j.micinf.2024.105321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/25/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Rabies virus (RABV) is a lethal neurotropic virus that causes 60,000 human deaths every year globally. RABV infection is characterized by the suppression of the interferon (IFN)-mediated antiviral response. However, molecular mechanisms leading to RABV sensing by RIG-I-like receptors (RLR) that initiates IFN signaling currently remain elusive. Here, we showed that RABV RNAs are primarily recognized by the RIG-I RLR, resulting in an IFN response in the infected cells, but this response varied according to the type of RABV used. Pathogenic RABV strain RNAs, Tha, were poorly detected in the cytosol by RIG-I and therefore caused a weak antiviral response. However, we revealed a strong IFN activity triggered by the attenuated RABV vaccine strain RNAs, SAD, mediated by RIG-I. We characterized two major 5' copy-back defective interfering (5'cb DI) genomes generated during SAD replication. Furthermore, we identified an interaction between 5'cb DI genomes, and RIG-I correlated with a high stimulation of the type I IFN signaling. This study indicates that wild-type RABV RNAs poorly activate the RIG-I pathway, while the presence of 5'cb DIs in the live-attenuated vaccine strain serves as an intrinsic adjuvant that strengthens its efficiency by enhancing RIG-I detection thus strongly stimulates the IFN response.
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Affiliation(s)
- Wahiba Aouadi
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France
| | - Valérie Najburg
- Institut Pasteur, Université Paris Cité, Vaccines-innovation Laboratory, 75015 Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Hub Bioinformatics, and Biostatistics, 75015 Paris, France
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Hub Bioinformatics, and Biostatistics, 75015 Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France
| | - Frédéric Tangy
- Institut Pasteur, Université Paris Cité, Vaccines-innovation Laboratory, 75015 Paris, France
| | - Florence Larrous
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France
| | - Anastassia V Komarova
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity Laboratory, 75015 Paris, France.
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, 75015 Paris, France.
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2
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Vera-Peralta H, Najburg V, Combredet C, Douché T, Gianetto QG, Matondo M, Tangy F, Mura M, Komarova AV. Applying Reverse Genetics to Study Measles Virus Interactions with the Host. Methods Mol Biol 2024; 2808:89-103. [PMID: 38743364 DOI: 10.1007/978-1-0716-3870-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The study of virus-host interactions is essential to achieve a comprehensive understanding of the viral replication process. The commonly used methods are yeast two-hybrid approach and transient expression of a single tagged viral protein in host cells followed by affinity purification of interacting cellular proteins and mass spectrometry analysis (AP-MS). However, by these approaches, virus-host protein-protein interactions are detected in the absence of a real infection, not always correctly compartmentalized, and for the yeast two-hybrid approach performed in a heterologous system. Thus, some of the detected protein-protein interactions may be artificial. Here we describe a new strategy based on recombinant viruses expressing tagged viral proteins to capture both direct and indirect protein partners during the infection (AP-MS in viral context). This way, virus-host protein-protein interacting co-complexes can be purified directly from infected cells for further characterization.
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Affiliation(s)
- Heidy Vera-Peralta
- Institut Pasteur, Université Paris Cité, Innovation Lab: Vaccines, Paris, France
- Institut de recherche biomédicale des armées, Immunopathologie, Bretigny-sur-Orge, France
| | - Valerie Najburg
- Institut Pasteur, Université Paris Cité, Innovation Lab: Vaccines, Paris, France
| | - Chantal Combredet
- Institut Pasteur, Université Paris Cité, Innovation Lab: Vaccines, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology, CNRS, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology, CNRS, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics Hub, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology, CNRS, Paris, France
| | | | - Marie Mura
- Institut Pasteur, Université Paris Cité, Innovation Lab: Vaccines, Paris, France
- Institut de recherche biomédicale des armées, Immunopathologie, Bretigny-sur-Orge, France
| | - Anastassia V Komarova
- Institut Pasteur, Université Paris Cité, Interactomics, RNA and Immunity Laboratory, Paris, France.
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3
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Collados Rodríguez M, Maillard P, Journeaux A, Komarova AV, Najburg V, David RYS, Helynck O, Guo M, Zhong J, Baize S, Tangy F, Jacob Y, Munier-Lehmann H, Meurs EF. Novel Antiviral Molecules against Ebola Virus Infection. Int J Mol Sci 2023; 24:14791. [PMID: 37834238 PMCID: PMC10573436 DOI: 10.3390/ijms241914791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Infection with Ebola virus (EBOV) is responsible for hemorrhagic fever in humans with a high mortality rate. Combined efforts of prevention and therapeutic intervention are required to tackle highly variable RNA viruses, whose infections often lead to outbreaks. Here, we have screened the 2P2I3D chemical library using a nanoluciferase-based protein complementation assay (NPCA) and isolated two compounds that disrupt the interaction of the EBOV protein fragment VP35IID with the N-terminus of the dsRNA-binding proteins PKR and PACT, involved in IFN response and/or intrinsic immunity, respectively. The two compounds inhibited EBOV infection in cell culture as well as infection by measles virus (MV) independently of IFN induction. Consequently, we propose that the compounds are antiviral by restoring intrinsic immunity driven by PACT. Given that PACT is highly conserved across mammals, our data support further testing of the compounds in other species, as well as against other negative-sense RNA viruses.
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Affiliation(s)
- Mila Collados Rodríguez
- School of Infection & Immunity (SII), College of Medical, Veterinary and Life Sciences (MVLS), Sir Michael Stoker Building, MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow G61 1QH, UK
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| | - Patrick Maillard
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
| | - Alexandra Journeaux
- Unit of Biology of Emerging Viral Infections, Institut Pasteur, 69007 Lyon, France; (A.J.); (S.B.)
| | - Anastassia V. Komarova
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, 75015 Paris, France;
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Raul-Yusef Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Blizard Institute—Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Olivier Helynck
- Unité de Chimie et Biocatalyse, CNRS, UMR 3523, Institut Pasteur, Université de Paris, 75015 Paris, France; (O.H.); (H.M.-L.)
| | - Mingzhe Guo
- CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200023, China; (M.G.); (J.Z.)
| | - Jin Zhong
- CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Shanghai Institute of Immunity and Infection, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai 200023, China; (M.G.); (J.Z.)
| | - Sylvain Baize
- Unit of Biology of Emerging Viral Infections, Institut Pasteur, 69007 Lyon, France; (A.J.); (S.B.)
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, 75015 Paris, France; (V.N.); (R.-Y.S.D.); (F.T.)
- Université Paris Cité, 75013 Paris, France;
| | - Yves Jacob
- Université Paris Cité, 75013 Paris, France;
- Unité Génétique Moléculaire des Virus à ARN, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France
| | - Hélène Munier-Lehmann
- Unité de Chimie et Biocatalyse, CNRS, UMR 3523, Institut Pasteur, Université de Paris, 75015 Paris, France; (O.H.); (H.M.-L.)
| | - Eliane F. Meurs
- Unité Hépacivirus et Immunité Innée, CNRS, UMR 3569, Département de Virologie, Institut Pasteur, 75015 Paris, France; (P.M.); (E.F.M.)
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4
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Khalfi P, Suspène R, Raymond KA, Caval V, Caignard G, Berry N, Thiers V, Combredet C, Rufie C, Rigaud S, Ghozlane A, Volant S, Komarova AV, Tangy F, Vartanian JP. Antagonism of ALAS1 by the Measles Virus V protein contributes to degradation of the mitochondrial network and promotes interferon response. PLoS Pathog 2023; 19:e1011170. [PMID: 36802406 PMCID: PMC9983871 DOI: 10.1371/journal.ppat.1011170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 03/03/2023] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Viruses have evolved countless mechanisms to subvert and impair the host innate immune response. Measles virus (MeV), an enveloped, non-segmented, negative-strand RNA virus, alters the interferon response through different mechanisms, yet no viral protein has been described as directly targeting mitochondria. Among the crucial mitochondrial enzymes, 5'-aminolevulinate synthase (ALAS) is an enzyme that catalyzes the first step in heme biosynthesis, generating 5'-aminolevulinate from glycine and succinyl-CoA. In this work, we demonstrate that MeV impairs the mitochondrial network through the V protein, which antagonizes the mitochondrial enzyme ALAS1 and sequesters it to the cytosol. This re-localization of ALAS1 leads to a decrease in mitochondrial volume and impairment of its metabolic potential, a phenomenon not observed in MeV deficient for the V gene. This perturbation of the mitochondrial dynamics demonstrated both in culture and in infected IFNAR-/- hCD46 transgenic mice, causes the release of mitochondrial double-stranded DNA (mtDNA) in the cytosol. By performing subcellular fractionation post infection, we demonstrate that the most significant source of DNA in the cytosol is of mitochondrial origin. Released mtDNA is then recognized and transcribed by the DNA-dependent RNA polymerase III. The resulting double-stranded RNA intermediates will be captured by RIG-I, ultimately initiating type I interferon production. Deep sequencing analysis of cytosolic mtDNA editing divulged an APOBEC3A signature, primarily analyzed in the 5'TpCpG context. Finally, in a negative feedback loop, APOBEC3A an interferon inducible enzyme will orchestrate the catabolism of mitochondrial DNA, decrease cellular inflammation, and dampen the innate immune response.
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Affiliation(s)
- Pierre Khalfi
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Kyle A. Raymond
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Vincent Caval
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | | | - Noémie Berry
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
- UMR1161 Virologie, ANSES-INRAE-ENVA, Maisons-Alfort, France
| | - Valérie Thiers
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Chantal Combredet
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Claude Rufie
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Stéphane Rigaud
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Amine Ghozlane
- Bioinformatics and Biostatistics HUB, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics HUB, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Anastassia V. Komarova
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Frédéric Tangy
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- * E-mail:
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5
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Kozachenko VE, Arsenina OI, Makhortova PI, Popova AV, Popova NV, Komarova AV. [The use of distal occlusion correctors during treatment on an individual lingual bracket system in adult patients]. Stomatologiia (Mosk) 2023; 102:53-58. [PMID: 37622302 DOI: 10.17116/stomat202310204153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
A case of treatment of a 35-year-old patient with a retroposition of the lower jaw, distal occlusion of the posterior teeth, deep incisal overlap, narrowing of the deformity of the dentoalveolar arches, protrusion of the lower incisors, crowded position of the teeth, mismatch between the incisor lines, absence due to extraction of tooth 3.6, with impacted dystopic tooth 3.8 is presented. Fixed individual orthodontic appliances of the WIN («DW Lingual Systems GmbH» Germany) were used. It was found that the use of the Herbst apparatus in combination with the WIN lingual bracket system in adult patients helps to achieve optimal functional and aesthetic results. The use of a distal bite correction device is an additional support for the mesialization of the molars of the lower jaw.
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Affiliation(s)
- V E Kozachenko
- Central Research Institute of Dentistry and Maxillofacial Surgery», Moscow, Russia
| | - O I Arsenina
- Central Research Institute of Dentistry and Maxillofacial Surgery», Moscow, Russia
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - P I Makhortova
- Central Research Institute of Dentistry and Maxillofacial Surgery», Moscow, Russia
- Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - A V Popova
- Central Research Institute of Dentistry and Maxillofacial Surgery», Moscow, Russia
| | - N V Popova
- Central Research Institute of Dentistry and Maxillofacial Surgery», Moscow, Russia
- Burnasyan Federal Medical Biophysical Center of Federal Medical Biological Agency, Moscow, Russia
| | - A V Komarova
- Central Research Institute of Dentistry and Maxillofacial Surgery», Moscow, Russia
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6
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Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV. Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. iScience 2022; 25:104599. [PMID: 35789859 PMCID: PMC9250025 DOI: 10.1016/j.isci.2022.104599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/01/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Pattern recognition receptors (PRRs) protect against microbial invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. Although microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation remains overlooked. Here, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by different RNA viruses. In each infection, several RNAs transcribed by RNA polymerase III (Pol3) specifically engaged RLRs, particularly the family of Y RNAs. Sensing of Y RNAs was dependent on their mimicking of viral secondary structure and their 5'-triphosphate extremity. Further, we found that HIV-1 triggered a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, inducing a transcriptome-wide change of cellular RNA 5'-triphosphorylation that licenses Y RNA immunogenicity. Overall, our work uncovers the contribution of endogenous RNAs to antiviral immunity and demonstrates the importance of this pathway in HIV-1 infection.
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Affiliation(s)
- Nicolas Vabret
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valérie Najburg
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ramya Gopal
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher McClain
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics at the Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sreekumar Balan
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yannis Rahou
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Guillaume Beauclair
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Maxime Chazal
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Hugo Varet
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Raul Y. Sanchez David
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Lise Chauveau
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nolwenn Jouvenet
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Extra-mural Member, Parker Institute of Cancer Immunotherapy, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Physiology, Biophysics, & Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anastassia V. Komarova
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
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7
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Znaidia M, Demeret C, van der Werf S, Komarova AV. Characterization of SARS-CoV-2 Evasion: Interferon Pathway and Therapeutic Options. Viruses 2022; 14:v14061247. [PMID: 35746718 PMCID: PMC9231409 DOI: 10.3390/v14061247] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 12/17/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. SARS-CoV-2 is characterized by an important capacity to circumvent the innate immune response. The early interferon (IFN) response is necessary to establish a robust antiviral state. However, this response is weak and delayed in COVID-19 patients, along with massive pro-inflammatory cytokine production. This dysregulated innate immune response contributes to pathogenicity and in some individuals leads to a critical state. Characterizing the interplay between viral factors and host innate immunity is crucial to better understand how to manage the disease. Moreover, the constant emergence of new SARS-CoV-2 variants challenges the efficacy of existing vaccines. Thus, to control this virus and readjust the antiviral therapy currently used to treat COVID-19, studies should constantly be re-evaluated to further decipher the mechanisms leading to SARS-CoV-2 pathogenesis. Regarding the role of the IFN response in SARS-CoV-2 infection, in this review we summarize the mechanisms by which SARS-CoV-2 evades innate immune recognition. More specifically, we explain how this virus inhibits IFN signaling pathways (IFN-I/IFN-III) and controls interferon-stimulated gene (ISG) expression. We also discuss the development and use of IFNs and potential drugs controlling the innate immune response to SARS-CoV-2, helping to clear the infection.
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8
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Di Gioacchino A, Legendre R, Rahou Y, Najburg V, Charneau P, Greenbaum BD, Tangy F, van der Werf S, Cocco S, Komarova AV. sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. RNA 2022; 28:277-289. [PMID: 34937774 PMCID: PMC8848934 DOI: 10.1261/rna.078969.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M > ORF3a > N>ORF6 > ORF7a > ORF8 > S > E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.
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Affiliation(s)
- Andrea Di Gioacchino
- Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015, Paris, France
| | - Yannis Rahou
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
| | - Valérie Najburg
- Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
| | - Pierre Charneau
- Institut Pasteur, Pasteur-TheraVectys joined unit, 75015, Paris, France
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10065, USA
- Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York 10065, USA
| | - Frédéric Tangy
- Institut Pasteur, Université de Paris, Laboratory of Innovative Vaccines, 75015, Paris, France
| | - Sylvie van der Werf
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
| | - Simona Cocco
- Sorbonne Université, Université de Paris, Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, 75005, Paris, France
| | - Anastassia V Komarova
- Institut Pasteur, Université de Paris, CNRS UMR3569, Génétique Moléculaire des Virus à ARN, F-75015 Paris, France
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9
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Di Gioacchino A, Šulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. Mol Biol Evol 2021; 38:2428-2445. [PMID: 33555346 PMCID: PMC7928797 DOI: 10.1093/molbev/msab036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We characterize CpG content by a CpG force that accounts for statistical constraints acting on the genome at the nucleotidic and amino acid levels. The CpG force, as the CpG content, is overall low compared with other pathogenic betacoronaviruses; however, it widely fluctuates along the genome, with a particularly low value, comparable with the circulating seasonal HKU1, in the spike coding region and a greater value, comparable with SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3'UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the zinc finger antiviral protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias, and the pressure to lower CpG content.
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Affiliation(s)
- Andrea Di Gioacchino
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Anastassia V Komarova
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rémi Monasson
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
| | - Simona Cocco
- Laboratoire de Physique de l’Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
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10
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Meignié A, Combredet C, Santolini M, Kovács IA, Douché T, Gianetto QG, Eun H, Matondo M, Jacob Y, Grailhe R, Tangy F, Komarova AV. Proteomic Analysis Uncovers Measles Virus Protein C Interaction With p65-iASPP Protein Complex. Mol Cell Proteomics 2021; 20:100049. [PMID: 33515806 PMCID: PMC7950213 DOI: 10.1016/j.mcpro.2021.100049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses manipulate the central machineries of host cells to their advantage. They prevent host cell antiviral responses to create a favorable environment for their survival and propagation. Measles virus (MV) encodes two nonstructural proteins MV-V and MV-C known to counteract the host interferon response and to regulate cell death pathways. Several molecular mechanisms underlining MV-V regulation of innate immunity and cell death pathways have been proposed, whereas MV-C host-interacting proteins are less studied. We suggest that some cellular factors that are controlled by MV-C protein during viral replication could be components of innate immunity and the cell death pathways. To determine which host factors are targeted by MV-C, we captured both direct and indirect host-interacting proteins of MV-C protein. For this, we used a strategy based on recombinant viruses expressing tagged viral proteins followed by affinity purification and a bottom-up mass spectrometry analysis. From the list of host proteins specifically interacting with MV-C protein in different cell lines, we selected the host targets that belong to immunity and cell death pathways for further validation. Direct protein interaction partners of MV-C were determined by applying protein complementation assay and the bioluminescence resonance energy transfer approach. As a result, we found that MV-C protein specifically interacts with p65–iASPP protein complex that controls both cell death and innate immunity pathways and evaluated the significance of these host factors on virus replication. Measles virus controls immune response and cell death pathways to achieve replication. Host proteins interaction network with measles virulence factor C protein. Cellular p65–iASPP complex is targeted by measles virus C protein.
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Affiliation(s)
- Alice Meignié
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Chantal Combredet
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Marc Santolini
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France; Network Science Institute and Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - István A Kovács
- Network Science Institute and Department of Physics, Northeastern University, Boston, Massachusetts, USA; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA; Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Thibaut Douché
- Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France
| | - Quentin Giai Gianetto
- Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France; Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, CNRS USR 3756, Paris, France
| | - Hyeju Eun
- Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Mariette Matondo
- Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France
| | - Yves Jacob
- Laboratory of Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France.
| | - Anastassia V Komarova
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France; Laboratory of Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR-3569, Paris, France.
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11
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Di Gioacchino A, Šulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The heterogeneous landscape and early evolution of pathogen-associated CpG dinucleotides in SARS-CoV-2. bioRxiv 2020. [PMID: 32511407 DOI: 10.1101/2020.05.06.074039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We find that the CpG content, which we characterize by a force parameter that accounts for statistical constraints acting on the genome at the nucleotidic and amino-acid levels, is, on average, low compared to other pathogenic betacoronaviruses. However, the CpG force widely fluctuates along the genome, with a particularly low value, comparable to the circulating seasonal HKU1, in the spike coding region and a greater value, comparable to SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3'UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the Zinc finger Anti-viral Protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias and the pressure to lower CpG content.
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12
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Di Gioacchino A, Šulc P, Komarova AV, Greenbaum BD, Monasson R, Cocco S. The Heterogeneous Landscape and Early Evolution of Pathogen-Associated CpG Dinucleotides in SARS-CoV-2. SSRN 2020:3611280. [PMID: 32714120 PMCID: PMC7366803 DOI: 10.2139/ssrn.3611280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 05/27/2020] [Indexed: 11/15/2022]
Abstract
SARS-CoV-2 infection can lead to acute respiratory syndrome in patients, which can be due in part to dysregulated immune signalling. We analyze here the occurrences of CpG dinucleotides, which are putative pathogen-associated molecular patterns, along the viral sequence. Carrying out a comparative analysis with other ssRNA viruses and within the Coronaviridae family, we find the CpG content of SARS-CoV-2, while low compared to other betacoronaviruses, widely fluctuates along its primary sequence. While the CpG relative abundance and its associated CpG force parameter are low for the spike protein (S) and comparable to circulating seasonal coronaviruses such as HKU1, they are much greater and comparable to SARS and MERS for the 3'-end of the viral genome. In particular, the nucleocapsid protein (N), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3'UTRs of all subgenomic RNA, has high CpG content. We speculate this dual nature of CpG content can confer to SARS-CoV-2 high ability to both enter the host and trigger pattern recognition receptors (PRRs) in different contexts. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic. Using a new application of selective forces on dinucleotides to estimate context driven mutational processes, we find that synonymous mutations seem driven both by the viral codon bias and by the high value of the CpG force in the N protein, leading to a loss in CpG content. Sequence motifs preceding these CpG-loss-associated loci match recently identified binding patterns of the Zinc Finger anti-viral Protein (ZAP) protein. Funding: This work was partially supported by the ANR19 Decrypted CE30-0021-01 grants. B.G. was supported by National Institutes of Health grants 7R01AI081848-04, 1R01CA240924-01, a Stand Up to Cancer - Lustgarten Foundation Convergence Dream Team Grant, and The Pershing Square Sohn Prize - Mark Foundation Fellow supported by funding from The Mark Foundation for Cancer Research.
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Affiliation(s)
- Andrea Di Gioacchino
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
| | - Anastassia V Komarova
- Molecular Genetics of RNA viruses, Department of Virology, Institut Pasteur, CNRS UMR-3569, 75015 Paris, France
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue New York, NY 10065
| | - Rémi Monasson
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Simona Cocco
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, F-75005 Paris, France
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13
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Arsenina OI, Komarova AV, Popova NV, Popova AV, Egorova DO. [Elimination of discoordination of the masticatory muscles work in patients with muscular-articular dysfunction of the temporomandibular joint by using «elastocorrector» appliance]. Stomatologiia (Mosk) 2020; 99:61-65. [PMID: 32441078 DOI: 10.17116/stomat20209902161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of the study was to analyze the effectiveness of elastocorrective therapy in the complex treatment of patients with musculo-articular dysfunction of TMJ. Patients (n=237) underwent a comprehensive examination, including: 1) analysis of control and diagnostic plaster models of the jaws; 2) clinical examination; 3) X-ray examination: panoramic X-ray and TRG in lateral projection, computed tomography (CT) of the temporomandibular joint or X-ray zonography of the temporomandibular joint, and magnetic resonance tomography (MRI) of the temporomandibular joint, 4) electromyography of the chewing muscles, 5) T-Scan occlusion computer analysis; 6) stabilometry. After clinical, X-ray examination and data analysis of functional research methods, an algorithm for diagnostic and therapeutic measures was developed. All patients were prescribed the use of elastocorrector: at night during sleep and during the day for 1.5-2 hours. As a result of the use of elastocorrector in patients with muscle-articular dysfunction of the TMJ the position of the mandible was normalized and the spatial ratio of TMJ elements was optimized, the masticatory muscles function and bioelectric activity was normalized and the overload of muscles of mastication during functional movements is eliminated. «Elastocorrector» appliance can be used in patients with TMJ musculo-articular dysfunction both for orthodontic treatment (to eliminate chewing muscle hypertonus, compression of intra-articular structures, premature occlusive contacts) and to prepare for further treatment (orthopedic, therapeutic, etc.).
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Affiliation(s)
- O I Arsenina
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia.,Russian Peoples Friendship University, Moscow, Russia
| | - A V Komarova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - N V Popova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - A V Popova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - D O Egorova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
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14
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Pagliuso A, Tham TN, Allemand E, Robertin S, Dupuy B, Bertrand Q, Bécavin C, Koutero M, Najburg V, Nahori MA, Tangy F, Stavru F, Bessonov S, Dessen A, Muchardt C, Lebreton A, Komarova AV, Cossart P. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling. Cell Host Microbe 2019; 26:823-835.e11. [PMID: 31761719 PMCID: PMC6907008 DOI: 10.1016/j.chom.2019.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/21/2019] [Accepted: 10/07/2019] [Indexed: 01/20/2023]
Abstract
RNA-binding proteins (RBPs) perform key cellular activities by controlling the function of bound RNAs. The widely held assumption that RBPs are strictly intracellular has been challenged by the discovery of secreted RBPs. However, extracellular RBPs have been described in eukaryotes, while secreted bacterial RBPs have not been reported. Here, we show that the bacterial pathogen Listeria monocytogenes secretes a small RBP that we named Zea. We show that Zea binds a subset of L. monocytogenes RNAs, causing their accumulation in the extracellular medium. Furthermore, during L. monocytogenes infection, Zea binds RIG-I, the non-self-RNA innate immunity sensor, potentiating interferon-β production. Mouse infection studies reveal that Zea affects L. monocytogenes virulence. Together, our results unveil that bacterial RNAs can be present extracellularly in association with RBPs, acting as “social RNAs” to trigger a host response during infection. L. monocytogenes secretes an RNA-binding protein, Zea Zea binds and protects L. monocytogenes RNA, resulting in extracellular RNA accumulation During infection, Zea binds RIG-I and modulates RIG-I-dependent IFN response Zea plays a role in L. monocytogenes virulence in mice
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Affiliation(s)
- Alessandro Pagliuso
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France.
| | - To Nam Tham
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Eric Allemand
- Unité de régulation épigénétique, Institut Pasteur, UMR3738 CNRS, Paris, France
| | - Stevens Robertin
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, Université de Paris, Paris, France
| | - Quentin Bertrand
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, Grenoble, France
| | - Christophe Bécavin
- Hub de bioinformatique et biostatistique - Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Unité mixte de Service et Recherche 3756 Institut Pasteur - Centre National de la Recherche Scientifique, Paris 75015, France
| | - Mikael Koutero
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris 75015, France; CNRS UMR-3569, Paris, France
| | - Marie-Anne Nahori
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris 75015, France; CNRS UMR-3569, Paris, France
| | - Fabrizia Stavru
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France
| | - Sergey Bessonov
- Department I of Internal Medicine, University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Andréa Dessen
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Bacterial Pathogenesis Group, Grenoble, France; Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas, SP, Brazil
| | - Christian Muchardt
- Unité de régulation épigénétique, Institut Pasteur, UMR3738 CNRS, Paris, France
| | - Alice Lebreton
- Équipe Infection et Devenir de l'ARN, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université Paris, Paris 75005, France; INRA, IBENS, 75005 Paris, France
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris 75015, France; CNRS UMR-3569, Paris, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris, France; U604 Inserm, Paris, France; USC2020 INRA, Paris, France.
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15
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Sanchez David RY, Combredet C, Najburg V, Millot GA, Beauclair G, Schwikowski B, Léger T, Camadro JM, Jacob Y, Bellalou J, Jouvenet N, Tangy F, Komarova AV. LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses. Sci Signal 2019; 12:eaar3993. [PMID: 31575732 DOI: 10.1126/scisignal.aar3993] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) RIG-I, MDA5, and LGP2 stimulate inflammatory and antiviral responses by sensing nonself RNA molecules produced during viral replication. Here, we investigated how LGP2 regulates the RIG-I- and MDA5-dependent induction of type I interferon (IFN) signaling and showed that LGP2 interacted with different components of the RNA-silencing machinery. We identified a direct protein-protein interaction between LGP2 and the IFN-inducible, double-stranded RNA binding protein PACT. The LGP2-PACT interaction was mediated by the regulatory C-terminal domain of LGP2 and was necessary for inhibiting RIG-I-dependent responses and for amplifying MDA5-dependent responses. We described a point mutation within LGP2 that disrupted the LGP2-PACT interaction and led to the loss of LGP2-mediated regulation of RIG-I and MDA5 signaling. These results suggest a model in which the LGP2-PACT interaction regulates the inflammatory responses mediated by RIG-I and MDA5 and enables the cellular RNA-silencing machinery to coordinate with the innate immune response.
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Affiliation(s)
- Raul Y Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Ecole doctorale B3MI/Paris7, Paris, France
| | - Chantal Combredet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Gael A Millot
- Hub de Bioinformatique et Biostatistique-C3BI, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Guillaume Beauclair
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Benno Schwikowski
- Systems Biology Laboratory and USR 3756, Institut Pasteur and CNRS, Paris, France
| | - Thibaut Léger
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jean-Michel Camadro
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
- Mitochondria, Metals, and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Université Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Yves Jacob
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
| | - Jacques Bellalou
- Platform of Recombinant Proteins in Prokaryotic Cells, Institut Pasteur, 75015, CNRS UMR 3528, Paris, France
| | - Nolwenn Jouvenet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
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16
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Beauclair G, Mura M, Combredet C, Tangy F, Jouvenet N, Komarova AV. DI-tector: defective interfering viral genomes' detector for next-generation sequencing data. RNA 2018; 24:1285-1296. [PMID: 30012569 PMCID: PMC6140465 DOI: 10.1261/rna.066910.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/10/2018] [Indexed: 05/14/2023]
Abstract
Defective interfering (DI) genomes, or defective viral genomes (DVGs), are truncated viral genomes generated during replication of most viruses, including live viral vaccines. Among these, "panhandle" or copy-back (cb) and "hairpin" or snap-back (sb) DI genomes are generated during RNA virus replication. 5' cb/sb DI genomes are highly relevant for viral pathogenesis since they harbor immunostimulatory properties that increase virus recognition by the innate immune system of the host. We have developed DI-tector, a user-friendly and freely available program that identifies and characterizes cb/sb genomes from next-generation sequencing (NGS) data. DI-tector confirmed the presence of 5' cb genomes in cells infected with measles virus (MV). DI-tector also identified a novel 5' cb genome, as well as a variety of 3' cb/sb genomes whose existence had not previously been detected by conventional approaches in MV-infected cells. The presence of these novel cb/sb genomes was confirmed by RT-qPCR and RT-PCR, validating the ability of DI-tector to reveal the landscape of DI genome population in infected cell samples. Performance assessment using different experimental and simulated data sets revealed the robust specificity and sensitivity of DI-tector. We propose DI-tector as a universal tool for the unbiased detection of DI viral genomes, including 5' cb/sb DI genomes, in NGS data.
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Affiliation(s)
- Guillaume Beauclair
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France
- CNRS UMR-3569, Paris, 75015, France
| | - Marie Mura
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France
- CNRS UMR-3569, Paris, 75015, France
- Unité des Biothérapies anti-infectieuses et Immunologie, Institut de Recherche Biomédicale des Armées BP73, Brétigny-sur-Orge, 91223, France
| | - Chantal Combredet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France
- CNRS UMR-3569, Paris, 75015, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France
- CNRS UMR-3569, Paris, 75015, France
| | - Nolwenn Jouvenet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France
- CNRS UMR-3569, Paris, 75015, France
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Paris, 75015, France
- CNRS UMR-3569, Paris, 75015, France
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17
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Chazal M, Beauclair G, Gracias S, Najburg V, Simon-Lorière E, Tangy F, Komarova AV, Jouvenet N. RIG-I Recognizes the 5' Region of Dengue and Zika Virus Genomes. Cell Rep 2018; 24:320-328. [PMID: 29996094 DOI: 10.1016/j.celrep.2018.06.047] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/21/2018] [Accepted: 06/08/2018] [Indexed: 12/24/2022] Open
Abstract
The flavivirus genus comprises major human pathogens, such as Dengue (DENV) and Zika (ZIKV) viruses. RIG-I and MDA5 are key cytoplasmic pathogen recognition receptors that are implicated in detecting viral RNAs. Here, we show that RNAs that co-purified with RIG-I during DENV infection are immuno-stimulatory, whereas RNAs bound to MDA5 are not. An affinity purification method combined with next-generation sequencing (NGS) revealed that the 5' region of the DENV genome is recognized by RIG-I. No DENV RNA was bound to MDA5. In vitro production of fragments of the DENV genome confirmed the NGS data and revealed that the 5' end of the genome, when bearing 5'-triphosphates, is the RIG-I ligand. The 5' region of the ZIKV genome is also a RIG-I agonist. We propose that RIG-I binds to the highly structured and conserved 5' region of flavivirus nascent transcripts before capping and that this mechanism leads to interferon secretion by infected cells.
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Affiliation(s)
- Maxime Chazal
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France; Unité de Génétique Fonctionnelle des Maladies Infectieuses, Institut Pasteur, Paris 75015, France; CNRS UMR2000 Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris 75015, France
| | - Guillaume Beauclair
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Ségolène Gracias
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Valérie Najburg
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Etienne Simon-Lorière
- Unité de Génétique Fonctionnelle des Maladies Infectieuses, Institut Pasteur, Paris 75015, France; CNRS UMR2000 Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris 75015, France
| | - Frédéric Tangy
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Anastassia V Komarova
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France.
| | - Nolwenn Jouvenet
- Unité Génomique Virale et Vaccination, Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France.
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Sanchez David RY, Combredet C, Sismeiro O, Dillies MA, Jagla B, Coppée JY, Mura M, Guerbois Galla M, Despres P, Tangy F, Komarova AV. Comparative analysis of viral RNA signatures on different RIG-I-like receptors. eLife 2016; 5:e11275. [PMID: 27011352 PMCID: PMC4841775 DOI: 10.7554/elife.11275] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/24/2016] [Indexed: 12/17/2022] Open
Abstract
The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules. Two viruses with negative- and positive-sense RNA genome were used: measles (MV) and chikungunya (CHIKV). NGS analysis revealed that distinct regions of MV genome were specifically recognized by distinct RLRs: RIG-I recognized defective interfering genomes, whereas MDA5 and LGP2 specifically bound MV nucleoprotein-coding region. During CHIKV infection, RIG-I associated specifically to the 3' untranslated region of viral genome. This study provides the first comparative view of the viral RNA ligands for RIG-I, MDA5 and LGP2 in the presence of infection.
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Affiliation(s)
- Raul Y Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Ecole doctorale, Biochimie, Biothérapies, Biologie Moléculaire et Infectiologie (B3MI), Université Paris Diderot - Paris 7, Paris, France
| | - Chantal Combredet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Odile Sismeiro
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Marie-Agnès Dillies
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Bernd Jagla
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Marie Mura
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Unité Interactions Hôte-Agents Pathogens, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | | | - Philippe Despres
- Technology Platform CYROI, University of Reunion Island, Saint-Clotilde, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
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19
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Arsenina OI, Popova NV, Komarova AV, Popova AV, Pogabalo IV, Ivanova YA. [EMG functional changes in masticatory muscles by elastopositioner use in patients with TMJ dysfunction]. Stomatologiia (Mosk) 2015; 94:41-44. [PMID: 26271702 DOI: 10.17116/stomat201594341-44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The analysis of the results of EMG studies in patients with TMJ dysfunction was carried out before and after use of elastpositioner "Corrector". The study revealed significant functional disturbances of the masticatory muscles, which were corrected after applying elastpositioner: there was a trend to decreased activity of masseter and temporal muscles, especially in the stagе of rest.
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Affiliation(s)
- O I Arsenina
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - N V Popova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - A V Komarova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - A V Popova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - I V Pogabalo
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
| | - Yu A Ivanova
- Central Research Institute of Dentistry and Maxillofacial Surgery, Moscow, Russia
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20
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Arsenina OI, Popova NV, Popova AV, Komarova AV. [Use of elastopositioner for treatment of masticator muscles discoordination in patients with TMJ dysfunction]. Stomatologiia (Mosk) 2014; 93:57-64. [PMID: 25588343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The paper presents the analysis of functional changes in patients with TMJ-dysfunction before and after the use of elastopositioner. Analysis has shown that at the initial stages the device provide relief from pain and masticatory muscles hypertension, reduced the bioelectric activity of the muscles. Normalization of the lower jaw movements when opening and closing the mouth and reduction of noise events in TMJ were also noted.
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Affiliation(s)
| | - N V Popova
- FGBU TsNIIS i ChLKh Minzdrava Rossii, Moskva
| | - A V Popova
- FGBU TsNIIS i ChLKh Minzdrava Rossii, Moskva
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21
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Komarova AV, Combredet C, Sismeiro O, Dillies MA, Jagla B, Sanchez David RY, Vabret N, Coppée JY, Vidalain PO, Tangy F. Identification of RNA partners of viral proteins in infected cells. RNA Biol 2013; 10:944-56. [PMID: 23595062 PMCID: PMC4111734 DOI: 10.4161/rna.24453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 12/20/2022] Open
Abstract
RNA viruses exhibit small-sized genomes encoding few proteins, but still establish complex networks of protein-protein and RNA-protein interactions within a cell to achieve efficient replication and spreading. Deciphering these interactions is essential to reach a comprehensive understanding of the viral infection process. To study RNA-protein complexes directly in infected cells, we developed a new approach based on recombinant viruses expressing tagged viral proteins that were purified together with their specific RNA partners. High-throughput sequencing was then used to identify these RNA molecules. As a proof of principle, this method was applied to measles virus nucleoprotein (MV-N). It revealed that in addition to full-length genomes, MV-N specifically interacted with a unique population of 5' copy-back defective interfering RNA genomes that we characterized. Such RNA molecules were able to induce strong activation of interferon-stimulated response element promoter preferentially via the cytoplasmic pattern recognition receptor RIG-I protein, demonstrating their biological functionality. Thus, this method provides a new platform to explore biologically active RNA-protein networks that viruses establish within infected cells.
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Affiliation(s)
- Anastassia V. Komarova
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| | - Chantal Combredet
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| | - Odile Sismeiro
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | - Marie-Agnès Dillies
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | - Bernd Jagla
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | | | - Nicolas Vabret
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
| | - Jean-Yves Coppée
- Plateforme Transcriptome et Epigénome – Génopole; Institut Pasteur; Paris, France
| | | | - Frédéric Tangy
- Unité de Génomique virale et Vaccination; Institut Pasteur; CNRS URA-3015; Paris, France
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22
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Komarova AV, Combredet C, Meyniel-Schicklin L, Chapelle M, Caignard G, Camadro JM, Lotteau V, Vidalain PO, Tangy F. Proteomic analysis of virus-host interactions in an infectious context using recombinant viruses. Mol Cell Proteomics 2011; 10:M110.007443. [PMID: 21911578 DOI: 10.1074/mcp.m110.007443] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
RNA viruses exhibit small-sized genomes encoding few proteins, but still establish complex networks of interactions with host cell components to achieve replication and spreading. Ideally, these virus-host protein interactions should be mapped directly in infected cell culture, but such a high standard is often difficult to reach when using conventional approaches. We thus developed a new strategy based on recombinant viruses expressing tagged viral proteins to capture both direct and indirect physical binding partners during infection. As a proof of concept, we engineered a recombinant measles virus (MV) expressing one of its virulence factors, the MV-V protein, with a One-STrEP amino-terminal tag. This allowed virus-host protein complex analysis directly from infected cells by combining modified tandem affinity chromatography and mass spectrometry analysis. Using this approach, we established a prosperous list of 245 cellular proteins interacting either directly or indirectly with MV-V, and including four of the nine already known partners of this viral factor. These interactions were highly specific of MV-V because they were not recovered when the nucleoprotein MV-N, instead of MV-V, was tagged. Besides key components of the antiviral response, cellular proteins from mitochondria, ribosomes, endoplasmic reticulum, protein phosphatase 2A, and histone deacetylase complex were identified for the first time as prominent targets of MV-V and the critical role of the later protein family in MV replication was addressed. Most interestingly, MV-V showed some preferential attachment to essential proteins in the human interactome network, as assessed by centrality and interconnectivity measures. Furthermore, the list of MV-V interactors also showed a massive enrichment for well-known targets of other viruses. Altogether, this clearly supports our approach based on reverse genetics of viruses combined with high-throughput proteomics to probe the interaction network that viruses establish in infected cells.
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Affiliation(s)
- Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS URA 3015, Paris, France
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23
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Komarova AV, Real E, Borman AM, Brocard M, England P, Tordo N, Hershey JW, Kean KM, Jacob Y. Rabies virus matrix protein interplay with eIF3, new insights into rabies virus pathogenesis. Nucleic Acids Res 2007; 35:1522-32. [PMID: 17287294 PMCID: PMC1865048 DOI: 10.1093/nar/gkl1127] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Viral proteins are frequently multifunctional to accommodate the high density of information encoded in viral genomes. Matrix (M) protein of negative-stranded RNA viruses such as Rhabdoviridae is one such example. Its primary function is virus assembly/budding but it is also involved in the switch from viral transcription to replication and the concomitant down regulation of host gene expression. In this study we undertook a search for potential rabies virus (RV) M protein's cellular partners. In a yeast two-hybrid screen the eIF3h subunit was identified as an M-interacting cellular factor, and the interaction was validated by co-immunoprecipitation and surface plasmon resonance assays. Upon expression in mammalian cell cultures, RV M protein was localized in early small ribosomal subunit fractions. Further, M protein added in trans inhibited in vitro translation on mRNA encompassing classical (Kozak-like) 5′-UTRs. Interestingly, translation of hepatitis C virus IRES-containing mRNA, which recruits eIF3 via a different noncanonical mechanism, was unaffected. Together, the data suggest that, as a complement to its functions in virus assembly/budding and regulation of viral transcription, RV M protein plays a role in inhibiting translation in virus-infected cells through a protein–protein interaction with the cellular translation machinery.
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Affiliation(s)
- Anastassia V. Komarova
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Eléonore Real
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Andrew M. Borman
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Michèle Brocard
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Patrick England
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Noël Tordo
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - John W.B. Hershey
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Katherine M. Kean
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
| | - Yves Jacob
- Unité de la Régulation de la Traduction Eucaryote et Virale, CNRS URA 1966, Unité de Génétique Papillomavirus et Cancer Humain, Plate-forme de Biophysique des Macromolecules et de leurs interactions, Unité Postulante des Stratégies Antivirales, Institute Pasteur, 75015 Paris, France and Department of Biochemistry and Molecular Medicine. School of Medicine. University of California Davis, Davis, CA 95616, USA
- *To whom the correspondence should be addressed. 01 45 68 87 5301 45 68 89 66 Correspondence may also be addressed to Katherine M. Kean
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Komarova AV, Brocard M, Kean KM. The case for mRNA 5' and 3' end cross talk during translation in a eukaryotic cell. Prog Nucleic Acid Res Mol Biol 2007; 81:331-67. [PMID: 16891176 DOI: 10.1016/s0079-6603(06)81009-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Anastassia V Komarova
- Unité Postulante Régulation de la Traduction Eucaryote et Virale, Institut Pasteur, CNRS URA 1966, 75724 Paris cedex 15, France
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25
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Brocard M, Paulous S, Komarova AV, Deveaux V, Kean KM. Evidence that PTB does not stimulate HCV IRES-driven translation. Virus Genes 2006; 35:5-15. [PMID: 17039407 DOI: 10.1007/s11262-006-0038-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 08/29/2006] [Indexed: 02/05/2023]
Abstract
It is now well established that Hepatitis C Virus (HCV) translation is driven by an Internal Ribosome Entry Site (IRES) resulting in cap-independent translation. Such a mechanism usually occurs with the help of IRES Associated Factors (ITAFs). Moreover, an important translational feature is likely conserved from the model of classical mRNA circularisation (5'-3' cross-talk), involving the HCV RNA highly structured 3' extremity called the 3'X region. This could bind several cellular factors and modulate the translation efficacy, at least in Rabbit Reticulocyte Lysate (RRL). In particular, polypyrimidine-binding proteins have been proposed to be potential HCV ITAFs, such as Polypyrimidine Tract Binding protein (PTB). However, contradictions still exist as to the role of PTB: its ability to bind both the HCV IRES and the 3'X region leads to the hypothesis that it could positively modulate IRES-driven translation in the presence of the X structure. Results of translational and PTB-binding studies of X mutant sequences led us to discredit PTB as protagonist of 3'X region stimulation on HCV IRES-driven translation. Moreover, competition assays of X RNA in trans on IRES-driven translation demonstrate the involvement of at least two stimulating factors and led to the conclusion that this mechanism is more complex than initially thought. Although we did not identify these factors, it is no longer doubtful that there is effectively a stimulating functional interaction between the HCV IRES and the 3'X region in RRL.
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Affiliation(s)
- Michèle Brocard
- Unité Postulante Régulation de la Traduction Eucaryote et Virale, URA CNRS 1966, Institut Pasteur, 25 rue du Dr. Roux-75724, Paris cedex 15, France.
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Komarova AV, Chufistova LS, Aseev LV, Boni IV. [An Escherichia coli strain producing a leaderless mRNA from the chromosomal lac promoter]. Bioorg Khim 2005; 31:557-60. [PMID: 16245700 DOI: 10.1007/s11171-005-0069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A special Escherichia coli strain capable of producing a leaderless lacZ mRNA from the chromosomal lac promoter was constructed to study the mechanism of leaderless mRNA translation. The translation efficiency of this noncanonical mRNA is very low in comparison with the canonical cellular templates, but it increases by one order of magnitude in the presence of chromosomal mutations in the genes encoding the ribosomal S1 and S2 proteins. The new strain possesses obvious advantages over the commonly used plasmid constructs (first of all, due to the constant dosage of lacZ gene in the cell) and opens possibilities for investigation of the specific conditions for leaderless mRNA translation in vivo using molecular genetic approaches.
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Komarova AV, Tchufistova LS, Dreyfus M, Boni IV. AU-rich sequences within 5' untranslated leaders enhance translation and stabilize mRNA in Escherichia coli. J Bacteriol 2005; 187:1344-9. [PMID: 15687198 PMCID: PMC545611 DOI: 10.1128/jb.187.4.1344-1349.2005] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 11/05/2004] [Indexed: 11/20/2022] Open
Abstract
We have shown previously that when the Escherichia coli chromosomal lacZ gene is put under the control of an extended Shine-Dalgarno (SD) sequence (10 or 6 nucleotides in length), the translation efficiency can be highly variable, depending on the presence of AU-rich targets for ribosomal protein S1 in the mRNA leader. Here, the same strains have been used to examine the question of how strong ribosome binding to extended SD sequences affects the stability of lacZ mRNAs translated with different efficiencies. The steady-state concentration of the lacZ transcripts has been found to vary over a broad range, directly correlating with translation efficiency but not with the SD duplex stability. The observed strain-to-strain variations in lacZ mRNA level became far less marked in the presence of the rne-1 mutation, which partially inactivates RNase E. Together, the results show that (i) an SD sequence, even one that is very long, cannot stabilize the lacZ mRNA in E. coli if translation is inefficient; (ii) inefficiently translated lacZ transcripts are sensitive to RNase E; and (iii) AU-rich elements inserted upstream of a long SD sequence enhance translation and stabilize mRNA, despite the fact that they constitute potential RNase E sites. These data strongly support the idea that the lacZ mRNA in E. coli can be stabilized only by translating, and not by stalling, ribosomes.
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Affiliation(s)
- Anastassia V Komarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Tchufistova LS, Komarova AV, Boni IV. A key role for the mRNA leader structure in translational control of ribosomal protein S1 synthesis in gamma-proteobacteria. Nucleic Acids Res 2003; 31:6996-7002. [PMID: 14627832 PMCID: PMC290253 DOI: 10.1093/nar/gkg883] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2003] [Revised: 09/16/2003] [Accepted: 10/07/2003] [Indexed: 11/13/2022] Open
Abstract
The translation initiation region (TIR) of the Escherichia coli rpsA mRNA coding for ribosomal protein S1 is characterized by a remarkable efficiency in driving protein synthesis despite the absence of the canonical Shine-Dalgarno element, and by a strong and specific autogenous repression in the presence of free S1 in trans. The efficient and autoregulated E.coli rpsA TIR comprises not less than 90 nt upstream of the translation start and can be unambiguously folded into three irregular hairpins (HI, HII and HIII) separated by A/U-rich single-stranded regions (ss1 and ss2). Phylogenetic comparison revealed that this specific fold is highly conserved in the gamma-subdivision of proteobacteria (but not in other subdivisions), except for the Pseudomonas group. To test phylogenetic predictions experimentally, we have generated rpsA'-'lacZ translational fusions by inserting the rpsA TIRs from various gamma-proteobacteria in-frame with the E.coli chromosomal lacZ gene. Measurements of their translation efficiency and negative regulation by excess protein S1 in trans have shown that only those rpsA TIRs which share the structural features with that of E.coli can govern efficient and regulated translation. We conclude that the E.coli-like mechanism for controlling the efficiency of protein S1 synthesis evolved after divergence of Pseudomona.
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Affiliation(s)
- Ludmila S Tchufistova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Nikitina EA, Komarova AV, Golubkova EV, Tret'iakova IV, Mamon LA. [Semidominant effect of the l(1)ts403 (sbr10) mutation on nondisjunction of sex chromosomes in meiosis in Drosophila melanogaster females exposed to heat]. Genetika 2003; 39:341-348. [PMID: 12722633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The sbr gene of Drosophila melanogaster belongs to the NXF (nuclear export factor) family responsible for the mRNA transport from nucleus to cytoplasm. We have shown that in the heat-exposed (37 degrees C, 1 h) females, the l(1)ts403 (sbr10) mutation leads, in particular, to the high-frequency nondisjunction and loss of sex chromosomes in meiosis. For this trait, the incomplete dominance of the sbr10 mutation is observed. At the same time, the sbr10 mutation is recessive for many other traits of the heat-exposed flies: reduced viability, low fertility, impaired synthesis of the heat shock proteins, etc. The females heterozygous for the null allele (Df(1)vL4, a deletion eliminating gene srb) do not differ from females homozygous for the wild-type allele in frequency of the heat shock-induced nondisjunction and loss of sex chromosomes in meiosis. Because of this, the sbr10 mutation can be assigned to the gain-of-function alleles (those gaining the dominance function). Expression of the mutant sbr10 allele against the background of the wild-type allele suggests that in the heat shock-exposed females, the heat-modified product of this ts allele has a strong effect on sex chromosome disjunction in meiosis.
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Affiliation(s)
- E A Nikitina
- St. Petersburg State University, Department of Genetics and Breeding, St. Petersburg, 199034 Russia
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Komarova AV, Tchufistova LS, Supina EV, Boni IV. Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 2002; 8:1137-1147. [PMID: 12358433 PMCID: PMC1370328 DOI: 10.1017/s1355838202029990] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
There are two major components of Escherichia coli ribosomes directly involved in selection and binding of mRNA during initiation of protein synthesis-the highly conserved 3' end of 16S rRNA (aSD) complementary to the Shine-Dalgarno (SD) domain of mRNA, and the ribosomal protein S1. A contribution of the SD-aSD and S1-mRNA interactions to translation yield in vivo has been evaluated in a genetic system developed to compare efficiencies of various ribosome-binding sites (RBS) in driving beta-galactosidase synthesis from the single-copy (chromosomal) lacZ gene. The in vivo experiments have been supplemented by in vitro toeprinting and gel-mobility shift assays. A shortening of a potential SD-aSD duplex from 10 to 8 and to 6 bp increased the beta-galactosidase yield (four- and sixfold, respectively) suggesting that an extended SD-aSD duplex adversely affects translation, most likely due to its redundant stability causing ribosome stalling at the initiation step. Translation yields were significantly increased upon insertion of the A/U-rich S1 binding targets upstream of the SD region, but the longest SD remained relatively less efficient. In contrast to complete 30S ribosomes, the S1-depleted 30S particles have been able to form an extended SD-aSD duplex, but not the true ternary initiation complex. Taken together, the in vivo and in vitro data allow us to conclude that S1 plays two roles in translation initiation: It forms an essential part of the mRNA-binding track even when mRNA bears a long SD sequence, and through the binding to the 5' untranslated region, it can ensure a substantial enhancing effect on translation.
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Affiliation(s)
- Anastassia V Komarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow
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Komarova AV, Chufistova LS, Supina EV, Boni IV. [Extensive complementarity of the Shine-Dalgarno region and 3'-terminal sequence of 16S ribosomal RNA is inefficient for translation in vivo]. Bioorg Khim 2001; 27:282-90. [PMID: 11558262 DOI: 10.1023/a:1011356520576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Translation initiation in Escherichia coli involves as a rule complementary interactions between a Shine-Dalgarno (SD) sequence upstream of the initiation codon and a highly conserved 3'-end sequence of 16S rRNA (anti-SD). The translation efficiency is believed to be directly affected by the affinity of the ribosome to the mRNA initiation region. Earlier, high-affinity RNA ligands to E. coli ribosomes were selected by the SELEX approach, with the ligands containing an extended SD-sequence well represented. In this work, we examined the ability of artificial ribosome binding sites (RBSs) containing such an extended (10-nt) SD-sequence (superSD) to drive translation in vivo, as well as its ability to form the translation initiation complex in vitro. Toe print experiments showed the formation of a ternary initiation complex on mRNA comprising superSD. Moreover, they proved the formation of an extended SD-duplex in the binary 30S-mRNA complex. Nevertheless, the superSD appeared to be inefficient in translation in vivo. We believe that the initiation complex involving a superSD-element is too stable to be functional; it may impede the transition from initiation to elongation, thus disrupting the transcription-translation coupling and inhibiting the formation of polysomes.
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Affiliation(s)
- A V Komarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997 Russia
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Mamon LA, Komarova AV, Bondarenko LV, Barabanova LV, Tikhomirova MM. [Development of thermotolerance in Drosophila melanogaster line l(1) ts403 with a defect in heat shock protein synthesis]. Genetika 1998; 34:920-928. [PMID: 9749333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
To elucidate the role of heat shock proteins (HSP) in the formation of resistance to extreme factors and in the development of organismic and cell response to these factors, thermotolerance in a Drosophila melanogaster line with defective HSP synthesis was studied with regard to several criteria: (1) survival of adult-females; (2) damage to egg chambers in ovarioles; (3) dynamics of oviposition; (4) frequency of loss and nondisjunction of sex chromosomes in meiosis of females exposed to a heat shock (HS). According to all these criteria, the l(l)ts403 females were more sensitive to a HS 37 degrees C, the exposure at 37 degrees C for 1 h (HS37) than the females of the wild-type line Canton S. Only the data on the first three aforementioned parameters were indicative of thermotolerance development. In files exposed to HS35 followed by HS37, a decrease in nondisjunction and loss of sex chromosomes in the 3- and 4-day ovipositions was observed as compared to the flies exposed to HS37 only. This can be explained by the differences in oviposition dynamics and, consequently, in the realization rate of the oogenesis stages in these two experimental variants. The pleiotropic effect of the l(l)ts403 mutation that led to a disturbance in HSP gene expression at the posttranscriptional level and to an increase in the frequency of sex chromosome nondisjunction in the meiosis of females exposed to HS37 suggests that these processes were connected. As no thermotolerance was revealed by studying the sex chromosome nondisjunction, but thermotolerance was found by estimating the other parameters, we suggest that the product of the gene studied is involved in a signal system operating at a stage that precedes the HS-induced changes in the translation and division apparatuses of a cell.
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Affiliation(s)
- L A Mamon
- Department of Genetics and Breeding, St. Petersburg State University, Russia
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Topnikov VE, Komarova AV. [Relations between the biochemical and chemical oxygen demand during the biological treatment of sewage]. Gig Sanit 1985:68-70. [PMID: 4085818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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