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      Defining the proteolytic landscape during enterovirus infection

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Viruses cleave cellular proteins to remodel the host proteome. The study of these cleavages has revealed mechanisms of immune evasion, resource exploitation, and pathogenesis. However, the full extent of virus-induced proteolysis in infected cells is unknown, mainly because until recently the technology for a global view of proteolysis within cells was lacking. Here, we report the first comprehensive catalog of proteins cleaved upon enterovirus infection and identify the sites within proteins where the cleavages occur. We employed multiple strategies to confirm protein cleavages and assigned them to one of the two enteroviral proteases. Detailed characterization of one substrate, LSM14A, a p body protein with a role in antiviral immunity, showed that cleavage of this protein disrupts its antiviral function. This study yields a new depth of information about the host interface with a group of viruses that are both important biological tools and significant agents of disease.

          Author summary

          Enteroviruses are associated with a variety of human diseases, including gastroenteritis, the common cold, hand-foot-and-mouth disease, acute hemorrhagic conjunctivitis, and skin rash. In some cases, the infection can lead to myocarditis, encephalitis, progressive muscle weakness, and paralysis. Exactly how enteroviruses invade human tissues, defeat the host immune system, and alter normal cell biology is unknown. Understanding these cellular and molecular mechanisms will blaze the trail for the development of novel vaccine and therapeutic strategies. Here, we have applied a global N-terminomics approach to investigate how various enteroviruses recruit their proteases to remodel an infected cell, disarm host immunity, and create a favorable environment for their replication. This effort identified several new protease substrates, which we then confirmed by other experimental approaches. To our knowledge, this is the first systematic analysis of host proteins targeted for cleavage during enterovirus infection. The data generated in this study will serve as a valuable resource for the research community in the quest to uncover the molecular details of enterovirus cell biology and disease pathogenesis.

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          Most cited references47

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            clusterProfiler: an R package for comparing biological themes among gene clusters.

            Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.
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              STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

              Abstract Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein–protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein–protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ValidationRole: VisualizationRole: Writing – original draft
                Role: Validation
                Role: InvestigationRole: Methodology
                Role: InvestigationRole: Writing – review & editing
                Role: Methodology
                Role: InvestigationRole: Writing – review & editing
                Role: Formal analysis
                Role: Methodology
                Role: Formal analysisRole: SoftwareRole: Visualization
                Role: Funding acquisitionRole: Resources
                Role: Conceptualization
                Role: Formal analysisRole: SoftwareRole: Visualization
                Role: Data curationRole: Formal analysisRole: SoftwareRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                30 September 2020
                September 2020
                : 16
                : 9
                : e1008927
                Affiliations
                [1 ] Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, United States of America
                [2 ] Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States of America
                [3 ] National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, United States of America
                [4 ] The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
                [5 ] Laboratory of Brain Development and Repair, The Rockefeller University, New York, NY, United States of America
                [6 ] Department of Biology, Stanford University, Stanford, CA, United States of America
                [7 ] Proteomics Resource Center, The Rockefeller University, New York, NY, United States of America
                [8 ] Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States of America
                [9 ] Departments of Pediatrics and Biochemistry, University of Washington, Seattle, WA, United States of America
                [10 ] Institute for Systems Biology, Seattle, WA, United States of America
                University of California, Irvine, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0001-8505-7054
                http://orcid.org/0000-0001-9304-558X
                http://orcid.org/0000-0002-6527-6898
                http://orcid.org/0000-0003-1114-1426
                http://orcid.org/0000-0003-3012-2335
                http://orcid.org/0000-0002-2390-6572
                http://orcid.org/0000-0003-2685-2052
                http://orcid.org/0000-0001-5177-2068
                http://orcid.org/0000-0003-3087-8079
                Article
                PPATHOGENS-D-20-01061
                10.1371/journal.ppat.1008927
                7549765
                32997711
                22c9cc8b-d233-48bb-9599-6daa0d3dab4f
                © 2020 Saeed et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 20 May 2020
                : 24 August 2020
                Page count
                Figures: 7, Tables: 1, Pages: 28
                Funding
                This work was supported in part by the National Institutes of Health, NIAID grants R01 AI091707 (to C.M.R.), NCDIR grant 2P41GM109824-06 and R01 2R01GM112108-05 (to J.D.A.), and an Institut Mérieux grant (to M.S. and C.M.R.). M.F-T was supported by Novo Nordic Foundation, Swedish Medical Research Council, and Karolinska Institutet’s Strategic Research Program in Diabetes. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Medicine and Health Sciences
                Medical Conditions
                Infectious Diseases
                Viral Diseases
                Enterovirus Infection
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Proteases
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Proteases
                Research and analysis methods
                Biological cultures
                Cell lines
                HeLa cells
                Research and analysis methods
                Biological cultures
                Cell cultures
                Cultured tumor cells
                HeLa cells
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Rhabdoviruses
                Vesicular Stomatitis Virus
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Viral Pathogens
                Vesicular Stomatitis Virus
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Viral Pathogens
                Vesicular Stomatitis Virus
                Biology and Life Sciences
                Organisms
                Viruses
                Viral Pathogens
                Vesicular Stomatitis Virus
                Research and analysis methods
                Biological cultures
                Cell lines
                293T cells
                Biology and Life Sciences
                Molecular Biology
                Macromolecular Structure Analysis
                Protein Structure
                Protein Cleavage
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Structure
                Protein Cleavage
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Transfection
                Research and Analysis Methods
                Molecular Biology Techniques
                Transfection
                Custom metadata
                vor-update-to-uncorrected-proof
                2020-10-12
                All relevant data are within the manuscript and its Supporting Information files.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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