1
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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: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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] [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: 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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3
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Dicker K, Järvelin AI, Garcia-Moreno M, Castello A. The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity. Semin Cell Dev Biol 2021; 111:108-118. [PMID: 32921578 PMCID: PMC7482619 DOI: 10.1016/j.semcdb.2020.08.002] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022]
Abstract
RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the 'knowns' and 'unknowns' regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses.
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Affiliation(s)
- Kate Dicker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK; MRC-University of Glasgow Centre for Virus Research, University of Glasgow, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK.
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4
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Phillips MA, Harkiolaki M, Susano Pinto DM, Parton RM, Palanca A, Garcia-Moreno M, Kounatidis I, Sedat JW, Stuart DI, Castello A, Booth MJ, Davis I, Dobbie IM. CryoSIM: super-resolution 3D structured illumination cryogenic fluorescence microscopy for correlated ultrastructural imaging. Optica 2020; 7:802-812. [PMID: 34277893 PMCID: PMC8262592 DOI: 10.1364/optica.393203] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/27/2020] [Accepted: 06/05/2020] [Indexed: 05/19/2023]
Abstract
Rapid cryopreservation of biological specimens is the gold standard for visualizing cellular structures in their true structural context. However, current commercial cryo-fluorescence microscopes are limited to low resolutions. To fill this gap, we have developed cryoSIM, a microscope for 3D super-resolution fluorescence cryo-imaging for correlation with cryo-electron microscopy or cryo-soft X-ray tomography. We provide the full instructions for replicating the instrument mostly from off-the-shelf components and accessible, user-friendly, open-source Python control software. Therefore, cryoSIM democratizes the ability to detect molecules using super-resolution fluorescence imaging of cryopreserved specimens for correlation with their cellular ultrastructure.
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Affiliation(s)
- Michael A. Phillips
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
- STRUBI, Division of Structural Biology, Wellcome Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN,
UK
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - Maria Harkiolaki
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - David Miguel Susano Pinto
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Richard M. Parton
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Ana Palanca
- Department of Anatomy and Cell Biology, Faculty of Medicine, Universidad de Cantabria, CP39011 Santander,
Spain
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Ilias Kounatidis
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - John W. Sedat
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143,
USA
| | - David I. Stuart
- STRUBI, Division of Structural Biology, Wellcome Centre for Human Genetics, Old Road Campus, Roosevelt Drive, Oxford OX3 7BN,
UK
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE,
UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
| | - Martin J. Booth
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ,
UK
| | - Ilan Davis
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
- e-mail:
| | - Ian M. Dobbie
- Micron Advanced Bio-imaging Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
UK
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5
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Garcia-Moreno M, Noerenberg M, Ni S, Järvelin AI, González-Almela E, Lenz CE, Bach-Pages M, Cox V, Avolio R, Davis T, Hester S, Sohier TJM, Li B, Heikel G, Michlewski G, Sanz MA, Carrasco L, Ricci EP, Pelechano V, Davis I, Fischer B, Mohammed S, Castello A. System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection. Mol Cell 2019; 74:196-211.e11. [PMID: 30799147 PMCID: PMC6458987 DOI: 10.1016/j.molcel.2019.01.017] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/18/2018] [Accepted: 01/11/2019] [Indexed: 12/23/2022]
Abstract
The compendium of RNA-binding proteins (RBPs) has been greatly expanded by the development of RNA-interactome capture (RIC). However, it remained unknown if the complement of RBPs changes in response to environmental perturbations and whether these rearrangements are important. To answer these questions, we developed “comparative RIC” and applied it to cells challenged with an RNA virus called sindbis (SINV). Over 200 RBPs display differential interaction with RNA upon SINV infection. These alterations are mainly driven by the loss of cellular mRNAs and the emergence of viral RNA. RBPs stimulated by the infection redistribute to viral replication factories and regulate the capacity of the virus to infect. For example, ablation of XRN1 causes cells to be refractory to SINV, while GEMIN5 moonlights as a regulator of SINV gene expression. In summary, RNA availability controls RBP localization and function in SINV-infected cells. A quarter of the RBPome changes upon SINV infection Alterations in RBP activity are largely explained by changes in RNA availability Altered RBPs are crucial for viral infection efficacy GEMIN5 binds to the 5′ end of SINV RNAs and regulates viral gene expression
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Affiliation(s)
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Shuai Ni
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Esther González-Almela
- Centro de Biologia Molecular "Severo Ochoa," Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Caroline E Lenz
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Marcel Bach-Pages
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Victoria Cox
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Rosario Avolio
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Thomas Davis
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Svenja Hester
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Thibault J M Sohier
- Université de Lyon, ENSL, UCBL, CNRS, INSERM, LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Bingnan Li
- SciLifeLab, Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Gregory Heikel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3BF, UK; Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Gracjan Michlewski
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh EH9 3BF, UK; Division of Infection and Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK; Zhejiang University-University of Edinburgh Institute, Zhejiang University, 718 East Haizhou Road, Haining, Zhejiang 314400, People's Republic of China
| | - Miguel A Sanz
- Centro de Biologia Molecular "Severo Ochoa," Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Luis Carrasco
- Centro de Biologia Molecular "Severo Ochoa," Universidad Autonoma de Madrid, 28049 Madrid, Spain
| | - Emiliano P Ricci
- Université de Lyon, ENSL, UCBL, CNRS, INSERM, LBMC, 46 Allée d'Italie, 69007 Lyon, France
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK
| | - Bernd Fischer
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK.
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6
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Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. Wiley Interdiscip Rev RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
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Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
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7
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Garcia-Moreno M, Sanz MA, Carrasco L. A Viral mRNA Motif at the 3'-Untranslated Region that Confers Translatability in a Cell-Specific Manner. Implications for Virus Evolution. Sci Rep 2016; 6:19217. [PMID: 26755446 PMCID: PMC4709744 DOI: 10.1038/srep19217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/08/2015] [Indexed: 11/25/2022] Open
Abstract
Sindbis virus (SINV) mRNAs contain several motifs that participate in the regulation of their translation. We have discovered a motif at the 3′ untranslated region (UTR) of viral mRNAs, constituted by three repeated sequences, which is involved in the translation of both SINV genomic and subgenomic mRNAs in insect, but not in mammalian cells. These data illustrate for the first time that an element present at the 3′-UTR confers translatability to mRNAs from an animal virus in a cell-specific manner. Sequences located at the beginning of the 5′-UTR may also regulate SINV subgenomic mRNA translation in both cell lines in a context of infection. Moreover, a replicon derived from Sleeping disease virus, an alphavirus that have no known arthropod vector for transmission, is much more efficient in insect cells when the repeated sequences from SINV are inserted at its 3′-UTR, due to the enhanced translatability of its mRNAs. Thus, these findings provide a clue to understand, at the molecular level, the evolution of alphaviruses and their host range.
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Affiliation(s)
| | - Miguel Angel Sanz
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Luis Carrasco
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
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8
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Guridi A, Diederich AK, Aguila-Arcos S, Garcia-Moreno M, Blasi R, Broszat M, Schmieder W, Clauss-Lendzian E, Sakinc-Gueler T, Andrade R, Alkorta I, Meyer C, Landau U, Grohmann E. New antimicrobial contact catalyst killing antibiotic resistant clinical and waterborne pathogens. Mater Sci Eng C Mater Biol Appl 2015; 50:1-11. [PMID: 25746238 DOI: 10.1016/j.msec.2015.01.080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/21/2014] [Accepted: 01/24/2015] [Indexed: 12/19/2022]
Abstract
Microbial growth on medical and technical devices is a big health issue, particularly when microorganisms aggregate to form biofilms. Moreover, the occurrence of antibiotic-resistant bacteria in the clinical environment is dramatically growing, making treatment of bacterial infections very challenging. In search of an alternative, we studied a novel antimicrobial surface coating based on micro galvanic elements formed by silver and ruthenium with surface catalytic properties. The antimicrobial coating efficiently inhibited the growth of the nosocomial pathogens Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Enterococcus faecium as demonstrated by the growth inhibition on agar surface and in biofilms of antibiotic resistant clinical E. faecalis, E. faecium, and S. aureus isolates. It also strongly reduced the growth of Legionella in a drinking water pipeline and of Escherichia coli in urine. We postulate a mode of action of the antimicrobial material, which is independent of the release of silver ions. Thus, the novel antimicrobial coating could represent an alternative to combat microbial growth avoiding the toxic side effects of high levels of silver ions on eukaryotic cells.
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Affiliation(s)
- A Guridi
- Biophysics Unit (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - A-K Diederich
- University Medical Center Freiburg, Division of Infectious Diseases, Hugstetter Strasse 55, 79106 Freiburg, Germany; Biology II, Microbiology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - S Aguila-Arcos
- Biophysics Unit (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - M Garcia-Moreno
- Biophysics Unit (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - R Blasi
- University Medical Center Freiburg, Division of Infectious Diseases, Hugstetter Strasse 55, 79106 Freiburg, Germany; Biology II, Microbiology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - M Broszat
- University Medical Center Freiburg, Division of Infectious Diseases, Hugstetter Strasse 55, 79106 Freiburg, Germany; Biology II, Microbiology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - W Schmieder
- Biology II, Microbiology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - E Clauss-Lendzian
- Biology II, Microbiology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - T Sakinc-Gueler
- University Medical Center Freiburg, Division of Infectious Diseases, Hugstetter Strasse 55, 79106 Freiburg, Germany
| | - R Andrade
- Advanced Research Facilities (SGIker), University of the Basque Country, UPV/EHU, 48940 Leioa, Spain
| | - I Alkorta
- Biophysics Unit (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - C Meyer
- Largentec GmbH, Am Waldhaus 32, 14129 Berlin, Germany
| | - U Landau
- Largentec GmbH, Am Waldhaus 32, 14129 Berlin, Germany
| | - E Grohmann
- Biophysics Unit (CSIC, UPV/EHU), Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain; University Medical Center Freiburg, Division of Infectious Diseases, Hugstetter Strasse 55, 79106 Freiburg, Germany; Biology II, Microbiology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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9
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Garcia-Moreno M, Sanz MA, Carrasco L. Initiation codon selection is accomplished by a scanning mechanism without crucial initiation factors in Sindbis virus subgenomic mRNA. RNA 2015; 21:93-112. [PMID: 25404563 PMCID: PMC4274640 DOI: 10.1261/rna.047084.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 05/13/2023]
Abstract
Translation initiation of alphavirus subgenomic mRNA (sgmRNA) can occur in the absence of several initiation factors (eIFs) in infected cells; however, the precise translation mechanism is still poorly understood. In this study, we have examined the mechanism of initiation and AUG selection in Sindbis virus (SINV) sgmRNA. Our present findings suggest that sgmRNA is translated via a scanning mechanism, since the presence of a hairpin structure before the initiation codon hampers protein synthesis directed by this mRNA. In addition, translation is partially recovered when an in-frame AUG codon is placed upstream of this hairpin. This scanning process takes place without the participation of eIF4A and active eIF2. These results, combined with our findings through modifying the SINV sgmRNA leader sequence, do not support the possibility of a direct initiation from the start codon without previous scanning, or a shunting mechanism. Moreover, studies carried out with sgmRNAs containing two alternative AUG codons within a good context for translation reveal differences in AUG selection which are dependent on the cellular context and the phosphorylation state of eIF2α. Thus, initiation at the additional AUG is strictly dependent on active eIF2, whereas the genuine AUG codon can start translation following eIF2α inactivation. Collectively, our results suggest that SINV sgmRNA is translated by a scanning mechanism without the potential participation of crucial eIFs. A model is presented that explains the mechanism of initiation of mRNAs bearing two alternative initiation codons.
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Affiliation(s)
- Manuel Garcia-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C/Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
| | - Miguel Angel Sanz
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C/Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
| | - Luis Carrasco
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C/Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
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10
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Garcia-Moreno M, Sanz MA, Pelletier J, Carrasco L. Requirements for eIF4A and eIF2 during translation of Sindbis virus subgenomic mRNA in vertebrate and invertebrate host cells. Cell Microbiol 2012. [PMID: 23189929 DOI: 10.1111/cmi.12079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have examined the requirements for the initiation factors (eIFs) eIF4A and eIF2 to translate Sindbis virus (SV) subgenomic mRNA (sgmRNA) in the natural hosts of SV: vertebrate and arthropod cells. Notably, this viral mRNA does not utilize eIF4A in SV-infected mammalian cells. However, eIF4A is required to translate this mRNA in transfected cells. Therefore, SV sgmRNA exhibits a dual mechanism for translation with respect to the use of eIF4A. Interestingly, SV genomic mRNA requires eIF4A for translation during the early phase of infection. In sharp contrast to what is observed in mammalian cells, active eIF2 is necessary to translate SV sgmRNA in mosquito cells. However, eIF4A is not necessary for SV sgmRNA translation in this cell line. In the SV sgmRNA coding region, proximal to the initiation codon is a hairpin structure that confers eIF2 independence only in mammalian cells infected by SV. Strikingly, this structure does not provide independence for eIF4A neither in mammalian nor in mosquito cells. These findings provide the first evidence of different eIF requirements for translation of SV sgmRNA in vertebrate and invertebrate cells. These observations can help to understand the interaction of SV with its host cells.
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Affiliation(s)
- Manuel Garcia-Moreno
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/Nicolás Cabrera, 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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11
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Villalba JM, Barbero AJ, Diaz-Sierra R, Arribas E, Garcia-Meseguer MJ, Garcia-Sevilla F, Garcia-Moreno M, De Labra JAV, Varon R. Computerized evaluation of mean residence times in multicompartmental linear system and pharmacokinetics. J Comput Chem 2011; 32:915-31. [PMID: 20960438 DOI: 10.1002/jcc.21677] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 08/17/2010] [Accepted: 08/17/2010] [Indexed: 11/11/2022]
Abstract
Deriving mean residence times (MRTs) is an important task both in pharmacokinetics and in multicompartmental linear systems. Taking as starting point the analysis of MRTs in open or closed (Garcia-Meseguer et al., Bull Math Biol 2003, 65, 279) multicompartmental linear systems, we implement a versatile software, using the Visual Basic 6.0 language for MS-Windows, that is easy to use and with a user-friendly format for the input of data and the output of results. For any multicompartmental linear system of up to 512 compartments, whether closed or open, with traps or without traps and with zero input in one or more of the compartments, this software allows the user to obtain the symbolic expressions, in the most simplified form, and/or the numerical values of the MRTs in any of its compartments, in the entire system or in a part of the system. As far as we known from the literature, such a software has not been implemented before. The advantage of the present software is that it reduces on the work time needed and minimizes the human errors that are frequent in compartmental systems even those that are relatively staightforward. The software bioCelTer, along with instructions, can be downloaded from http://oretano.iele-ab.uclm.es/~fgarcia/bioCelTer/.
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Affiliation(s)
- J M Villalba
- Departamento de Ciencias Médicas, Facultad de Medicina, Universidad de Castilla-la Mancha, Albacete, Spain
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12
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Arribas E, Muñoz-Lopez A, Garcia-Meseguer MJ, Lopez-Najera A, Avalos L, Garcia-Molina F, Garcia-Moreno M, Varon R. Mean lifetime and first-passage time of the enzyme species involved in an enzyme reaction. Application to unstable enzyme systems. Bull Math Biol 2008; 70:1425-49. [PMID: 18506541 DOI: 10.1007/s11538-008-9307-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Accepted: 01/15/2008] [Indexed: 11/29/2022]
Abstract
Taking as starting point the complete analysis of mean residence times in linear compartmental systems performed by Garcia-Meseguer et al. (Bull. Math. Biol. 65:279-308, 2003) as well as the fact that enzyme systems, in which the interconversions between the different enzyme species involved are of first or pseudofirst order, act as linear compartmental systems, we hereby carry out a complete analysis of the mean lifetime that the enzyme molecules spend as part of the enzyme species, forms, or groups involved in an enzyme reaction mechanism. The formulas to evaluate these times are given as a function of the individual rate constants and the initial concentrations of the involved species at the onset of the reaction. We apply the results to unstable enzyme systems and support the results by using a concrete example of such systems. The practicality of obtaining the mean times and their possible application in a kinetic data analysis is discussed.
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Affiliation(s)
- E Arribas
- Applied Physics Department, University of Castilla-La Mancha, Albacete, Spain
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13
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Varon R, Garcia-Sevilla F, Garcia-Moreno M, Garcia-Canovas F, Peyro R, Duggleby RG. Computer program for the equations describing the steady state of enzyme reactions. Comput Appl Biosci 1997; 13:159-67. [PMID: 9146963 DOI: 10.1093/bioinformatics/13.2.159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
MOTIVATION The derivation of steady-state equations is frequently carried out in enzyme kinetic studies. Done manually, this becomes tedious and prone to human error. The computer programs now available which are able to accept reaction mechanisms of some complexity are focused only on the strict steady-state approach. RESULTS Here we present a computer program called REFERASS, with a short computation time and a user-friendly format for the input and output files, able to derive the strict steady-state equations and/or those corresponding to the usual assumption that one ore more of the reversible steps are in rapid equilibrium. This program handles enzyme-catalysed reactions with mechanisms involving up to 255 enzyme species connected by up to 255 reaction steps, subject to limits imposed by the memory and disk space available.
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Affiliation(s)
- R Varon
- Escuela Universitaria Politecnica, Universidad de Castilla-La Mancha, Albacete, Spain
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14
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Abstract
A general model of zymogen activation is proposed and explicit kinetic equations for the time courses of the various species and products involved are given. These equations are valid for the whole course of the reaction and therefore for both the transient phase and the steady state. This model is sufficiently general to include mechanisms possessing one or more steps of zymogen activation besides possible steps of inhibition (reversible or irreversible) or inactivation.
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Affiliation(s)
- B H Havsteen
- Biochemisches Institut, Universität zu Kiel, Germany
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