1
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Bonnet C, Dian AL, Espie-Caullet T, Fabbri L, Lagadec L, Pivron T, Dutertre M, Luco R, Navickas A, Vagner S, Verga D, Uguen P. Post-transcriptional gene regulation: From mechanisms to RNA chemistry and therapeutics. Bull Cancer 2024; 111:782-790. [PMID: 38824069 DOI: 10.1016/j.bulcan.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 06/03/2024]
Abstract
A better understanding of the RNA biology and chemistry is necessary to then develop new RNA therapeutic strategies. This review is the synthesis of a series of conferences that took place during the 6th international course on post-transcriptional gene regulation at Institut Curie. This year, the course made a special focus on RNA chemistry.
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Affiliation(s)
- Clara Bonnet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Ana Luisa Dian
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Tristan Espie-Caullet
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucilla Fabbri
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Lucie Lagadec
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Thibaud Pivron
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Martin Dutertre
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Reini Luco
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Albertas Navickas
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Stephan Vagner
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, Inserm U1196, Chemistry and Modelling for the Biology of Cancer, Institut Curie, université Paris-Saclay, 91405 Orsay, France
| | - Patricia Uguen
- CNRS UMR3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France.
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2
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Lawrence SM. Human cytomegalovirus and neonatal infection. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100257. [PMID: 39070527 PMCID: PMC11276932 DOI: 10.1016/j.crmicr.2024.100257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024] Open
Abstract
Human cytomegalovirus is an ancient virus that has co-evolved with humans. It establishes a life-long infection in suspectable individuals for which there is no vaccination or cure. The virus can be transmitted to a developing fetus in seropositive pregnant women, and it is the leading cause of congenital infectious disease. While the majority of infected infants remain asymptomatic at birth, congenital cytomegalovirus infection can lead to substantial long-term neurodevelopmental impairments in survivors, resulting in considerable economic and social hardships. Recent discoveries regarding cytomegalovirus pathophysiology and viral replication cycles might enable the development of innovative diagnostics and therapeutics, including an effective vaccine. This Review will detail our understanding of human cytomegalovirus infection, with an in-depth discussion regarding the viral genome and transcriptome that contributes to its pathophysiology. The neonate's clinical course will also be highlighted, including maternal and neonatal testing, treatment recommendations, and long-term outcomes.
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Affiliation(s)
- Shelley M. Lawrence
- University of Utah, College of Medicine, Department of Pediatrics, Division of Neonatology, Salt Lake City, UT, USA
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3
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Murigneux E, Softic L, Aubé C, Grandi C, Judith D, Bruce J, Le Gall M, Guillonneau F, Schmitt A, Parissi V, Berlioz-Torrent C, Meertens L, Hansen MMK, Gallois-Montbrun S. Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly. Nat Commun 2024; 15:640. [PMID: 38245532 PMCID: PMC10799903 DOI: 10.1038/s41467-024-44958-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
Considerable progress has been made in understanding the molecular host-virus battlefield during SARS-CoV-2 infection. Nevertheless, the assembly and egress of newly formed virions are less understood. To identify host proteins involved in viral morphogenesis, we characterize the proteome of SARS-CoV-2 virions produced from A549-ACE2 and Calu-3 cells, isolated via ultracentrifugation on sucrose cushion or by ACE-2 affinity capture. Bioinformatic analysis unveils 92 SARS-CoV-2 virion-associated host factors, providing a valuable resource to better understand the molecular environment of virion production. We reveal that G3BP1 and G3BP2 (G3BP1/2), two major stress granule nucleators, are embedded within virions and unexpectedly favor virion production. Furthermore, we show that G3BP1/2 participate in the formation of cytoplasmic membrane vesicles, that are likely virion assembly sites, consistent with a proviral role of G3BP1/2 in SARS-CoV-2 dissemination. Altogether, these findings provide new insights into host factors required for SARS-CoV-2 assembly with potential implications for future therapeutic targeting.
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Affiliation(s)
- Emilie Murigneux
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Laurent Softic
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Corentin Aubé
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Carmen Grandi
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
| | - Delphine Judith
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Johanna Bruce
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Morgane Le Gall
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - François Guillonneau
- Proteom'IC facility, Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
- Institut de Cancérologie de l'Ouest (ICO), CRCi2NA-Inserm UMR 1307, CNRS UMR 6075, Nantes Université, Angers, France
| | - Alain Schmitt
- Université Paris Cité, CNRS, Inserm, Institut Cochin, F-75014, Paris, France
| | - Vincent Parissi
- Microbiologie Fondamentale et Pathogénicité Laboratory (MFP), UMR 5234, « Mobility of pathogenic genomes and chromatin dynamics » team (MobilVIR), CNRS-University of Bordeaux, DyNAVIR network, Bordeaux, France
| | | | - Laurent Meertens
- Université Paris Cité, Inserm U944, CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
| | - Maike M K Hansen
- Institute for Molecules and Materials, Radboud University, 6525, AJ, Nijmegen, the Netherlands
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4
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Castello A, Iselin L. Viral RNA Is a Hub for Critical Host-Virus Interactions. Subcell Biochem 2023; 106:365-385. [PMID: 38159234 DOI: 10.1007/978-3-031-40086-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
RNA is a central molecule in the life cycle of viruses, acting not only as messenger (m)RNA but also as a genome. Given these critical roles, it is not surprising that viral RNA is a hub for host-virus interactions. However, the interactome of viral RNAs remains largely unknown. This chapter discusses the importance of cellular RNA-binding proteins in virus infection and the emergent approaches developed to uncover and characterise them.
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Affiliation(s)
- Alfredo Castello
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Louisa Iselin
- MRC University of Glasgow Centre for Virus Research, Glasgow, UK
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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5
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Bhattarai K, Holcik M. Diverse roles of heterogeneous nuclear ribonucleoproteins in viral life cycle. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the host-virus interactions helps to decipher the viral replication strategies and pathogenesis. Viruses have limited genetic content and rely significantly on their host cell to establish a successful infection. Viruses depend on the host for a broad spectrum of cellular RNA-binding proteins (RBPs) throughout their life cycle. One of the major RBP families is the heterogeneous nuclear ribonucleoproteins (hnRNPs) family. hnRNPs are typically localized in the nucleus, where they are forming complexes with pre-mRNAs and contribute to many aspects of nucleic acid metabolism. hnRNPs contain RNA binding motifs and frequently function as RNA chaperones involved in pre-mRNA processing, RNA splicing, and export. Many hnRNPs shuttle between the nucleus and the cytoplasm and influence cytoplasmic processes such as mRNA stability, localization, and translation. The interactions between the hnRNPs and viral components are well-known. They are critical for processing viral nucleic acids and proteins and, therefore, impact the success of the viral infection. This review discusses the molecular mechanisms by which hnRNPs interact with and regulate each stage of the viral life cycle, such as replication, splicing, translation, and assembly of virus progeny. In addition, we expand on the role of hnRNPs in the antiviral response and as potential targets for antiviral drug research and development.
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6
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Balakrishnan K, Munusami P, Mohareer K, Priyakumar UD, Banerjee A, Luedde T, Mande SC, Münk C, Banerjee S. Staufen‐2 functions as a cofactor for enhanced Rev‐mediated nucleocytoplasmic trafficking of
HIV
‐1 genomic
RNA
via the
CRM1
pathway. FEBS J 2022; 289:6731-6751. [DOI: 10.1111/febs.16546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/21/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kannan Balakrishnan
- Department of Biochemistry, School of Life Sciences University of Hyderabad India
- Clinic for Gastroenterology, Hepatology, and Infectiology Medical Faculty, Heinrich Heine University Düsseldorf Germany
| | - Punnagai Munusami
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad India
- Department of Chemistry Arignar Anna Government Arts & Science College Karaikal Puducherry India
| | - Krishnaveni Mohareer
- Department of Biochemistry, School of Life Sciences University of Hyderabad India
| | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad India
| | - Atoshi Banerjee
- Nevada Institute of Personalized Medicine University of Nevada Las Vegas NV USA
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology, and Infectiology Medical Faculty, Heinrich Heine University Düsseldorf Germany
| | - Shekhar C. Mande
- National Centre for Cell Science Pune India
- Council of Scientific and Industrial Research New Delhi India
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology Medical Faculty, Heinrich Heine University Düsseldorf Germany
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences University of Hyderabad India
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7
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Host cytoskeletal vimentin serves as a structural organizer and an RNA-binding protein regulator to facilitate Zika viral replication. Proc Natl Acad Sci U S A 2022; 119:2113909119. [PMID: 35193960 PMCID: PMC8872754 DOI: 10.1073/pnas.2113909119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2022] [Indexed: 01/15/2023] Open
Abstract
We discovered a dual role of vimentin underlying Zika virus (ZIKV) replication. The vimentin network reorganizes to surround the replication complex. Depletion of vimentin resulted in drastic segregation of viral proteins and subsequent defective infection, indicating its function as an “organizer” that ensures the concentration of all necessary factors for high replication efficacy. With omics analysis, we prove that vimentin also functions as a “regulator” that dominates RNA-binding proteins during infection. These two roles complement one another to make an integrated view of vimentin in regulating ZIKV infection. Collectively, our study fills the long-term gap in our knowledge of the cellular function of intermediate filaments in addition to structural support and provides a potential target for ZIKV therapy. Emerging microbe infections, such as Zika virus (ZIKV), pose an increasing threat to human health. Investigations on ZIKV replication have revealed the construction of replication complexes (RCs), but the role of cytoskeleton in this process is largely unknown. Here, we investigated the function of cytoskeletal intermediate filament protein vimentin in the life cycle of ZIKV infection. Using advanced imaging techniques, we uncovered that vimentin filaments undergo drastic reorganization upon viral protein synthesis to form a perinuclear cage-like structure that embraces and concentrates RCs. Genetic removal of vimentin markedly disrupted the integrity of RCs and resulted in fragmented subcellular dispersion of viral proteins. This led to reduced viral genome replication, viral protein production, and release of infectious virions, without interrupting viral binding and entry. Furthermore, mass spectrometry and RNA-sequencing screens identified interactions and interplay between vimentin and hundreds of endoplasmic reticulum (ER)-resident RNA-binding proteins. Among them, the cytoplasmic-region of ribosome receptor binding protein 1, an ER transmembrane protein that directly binds viral RNA, interacted with and was regulated by vimentin, resulting in modulation of ZIKV replication. Together, the data in our work reveal a dual role for vimentin as a structural element for RC integrity and as an RNA-binding-regulating hub during ZIKV infection, thus unveiling a layer of interplay between Zika virus and host cell.
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8
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Iselin L, Palmalux N, Kamel W, Simmonds P, Mohammed S, Castello A. Uncovering viral RNA-host cell interactions on a proteome-wide scale. Trends Biochem Sci 2022; 47:23-38. [PMID: 34509361 PMCID: PMC9187521 DOI: 10.1016/j.tibs.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/14/2023]
Abstract
RNA viruses interact with a wide range of cellular RNA-binding proteins (RBPs) during their life cycle. The prevalence of these host-virus interactions has been highlighted by new methods that elucidate the composition of viral ribonucleoproteins (vRNPs). Applied to 11 viruses so far, these approaches have revealed hundreds of cellular RBPs that interact with viral (v)RNA in infected cells. However, consistency across methods is limited, raising questions about methodological considerations when designing and interpreting these studies. Here, we discuss these caveats and, through comparing available vRNA interactomes, describe RBPs that are consistently identified as vRNP components and outline their potential roles in infection. In summary, these novel approaches have uncovered a new universe of host-virus interactions holding great therapeutic potential.
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Affiliation(s)
- Louisa Iselin
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK; Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK; The Rosalind Franklin Institute, Oxfordshire, OX11 0FA, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK).
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9
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mRNA Trafficking in the Nervous System: A Key Mechanism of the Involvement of Activity-Regulated Cytoskeleton-Associated Protein (Arc) in Synaptic Plasticity. Neural Plast 2021; 2021:3468795. [PMID: 34603440 PMCID: PMC8486535 DOI: 10.1155/2021/3468795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Synaptic activity mediates information storage and memory consolidation in the brain and requires a fast de novo synthesis of mRNAs in the nucleus and proteins in synapses. Intracellular localization of a protein can be achieved by mRNA trafficking and localized translation. Activity-regulated cytoskeleton-associated protein (Arc) is a master regulator of synaptic plasticity and plays an important role in controlling large signaling networks implicated in learning, memory consolidation, and behavior. Transcription of the Arc gene may be induced by a short behavioral event, resulting in synaptic activation. Arc mRNA is exported into the cytoplasm and can be trafficked into the dendrite of an activated synapse where it is docked and translated. The structure of Arc is similar to the viral GAG (group-specific antigen) protein, and phylogenic analysis suggests that Arc may originate from the family of Ty3/Gypsy retrotransposons. Therefore, Arc might evolve through “domestication” of retroviruses. Arc can form a capsid-like structure that encapsulates a retrovirus-like sentence in the 3′-UTR (untranslated region) of Arc mRNA. Such complex can be loaded into extracellular vesicles and transported to other neurons or muscle cells carrying not only genetic information but also regulatory signals within neuronal networks. Therefore, Arc mRNA inter- and intramolecular trafficking is essential for the modulation of synaptic activity required for memory consolidation and cognitive functions. Recent studies with single-molecule imaging in live neurons confirmed and extended the role of Arc mRNA trafficking in synaptic plasticity.
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10
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Kamel W, Noerenberg M, Cerikan B, Chen H, Järvelin AI, Kammoun M, Lee JY, Shuai N, Garcia-Moreno M, Andrejeva A, Deery MJ, Johnson N, Neufeldt CJ, Cortese M, Knight ML, Lilley KS, Martinez J, Davis I, Bartenschlager R, Mohammed S, Castello A. Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell 2021; 81:2851-2867.e7. [PMID: 34118193 PMCID: PMC8142890 DOI: 10.1016/j.molcel.2021.05.023] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.
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Affiliation(s)
- Wael Kamel
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Marko Noerenberg
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Honglin Chen
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Mohamed Kammoun
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jeffrey Y Lee
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ni Shuai
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Michael J Deery
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Javier Martinez
- Center of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany; Division Virus-Associated Carcinogenesis, Germany Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK; Department of Chemistry, University of Oxford, Mansfield Road, OX1 3TA Oxford, UK; The Rosalind Franklin Institute, OX11 0FA Oxfordshire, UK.
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK.
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11
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Kamel W, Noerenberg M, Cerikan B, Chen H, Järvelin AI, Kammoun M, Lee JY, Shuai N, Garcia-Moreno M, Andrejeva A, Deery MJ, Johnson N, Neufeldt CJ, Cortese M, Knight ML, Lilley KS, Martinez J, Davis I, Bartenschlager R, Mohammed S, Castello A. Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell 2021; 81:2851-2867.e7. [PMID: 34118193 DOI: 10.1101/2020.11.25.398008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 05/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.
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Affiliation(s)
- Wael Kamel
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Marko Noerenberg
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Honglin Chen
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Mohamed Kammoun
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jeffrey Y Lee
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ni Shuai
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Michael J Deery
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Javier Martinez
- Center of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany; Division Virus-Associated Carcinogenesis, Germany Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK; Department of Chemistry, University of Oxford, Mansfield Road, OX1 3TA Oxford, UK; The Rosalind Franklin Institute, OX11 0FA Oxfordshire, UK.
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK.
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