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      Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes

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          Abstract

          Hsp90 is a molecular chaperone involved in the regulation and maturation of kinases and transcription factors. In Caenorhabditis elegans, it contributes to the development of fertility, maintenance of muscle structure, the regulation of heat-shock response and dauer state. To understand the consequences of Hsp90-depletion, we studied Hsp90 RNAi-treated nematodes by DNA microarrays and mass spectrometry. We find that upon development of phenotypes the levels of chaperones and Hsp90 cofactors are increased, while specific proteins related to the innate immune response are depleted. In microarrays, we further find many differentially expressed genes related to gonad and larval development. These genes form an expression cluster that is regulated independently from the immune response implying separate pathways of Hsp90-involvement. Using fluorescent reporter strains for the differentially expressed immune response genes skr-5, dod-24 and clec-60 we observe that their activity in intestinal tissues is influenced by Hsp90-depletion. Instead, effects on the development are evident in both gonad arms. After Hsp90-depletion, changes can be observed in early embryos and adults containing fluorescence-tagged versions of SEPA-1, CAV-1 or PUD-1, all of which are downregulated after Hsp90-depletion. Our observations identify molecular events for Hsp90-RNAi induced phenotypes during development and immune responses, which may help to separately investigate independent Hsp90-influenced processes that are relevant during the nematode’s life and development.

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          Most cited references55

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            The Gene Expression Omnibus Database.

            The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome-protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/.
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              Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition.

              HSP90 is a molecular chaperone that associates with numerous substrate proteins called clients. It plays many important roles in human biology and medicine, but determinants of client recognition by HSP90 have remained frustratingly elusive. We systematically and quantitatively surveyed most human kinases, transcription factors, and E3 ligases for interaction with HSP90 and its cochaperone CDC37. Unexpectedly, many more kinases than transcription factors bound HSP90. CDC37 interacted with kinases, but not with transcription factors or E3 ligases. HSP90::kinase interactions varied continuously over a 100-fold range and provided a platform to study client protein recognition. In wild-type clients, HSP90 did not bind particular sequence motifs, but rather associated with intrinsically unstable kinases. Stabilization of the kinase in either its active or inactive conformation with diverse small molecules decreased HSP90 association. Our results establish HSP90 client recognition as a combinatorial process: CDC37 provides recognition of the kinase family, whereas thermodynamic parameters determine client binding within the family. Copyright © 2012 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Writing – original draft
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Funding acquisitionRole: Supervision
                Role: ConceptualizationRole: InvestigationRole: Methodology
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SoftwareRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                27 October 2017
                2017
                : 12
                : 10
                : e0186386
                Affiliations
                [1 ] Center for Integrated Protein Science at the Technische Universität München, Department Chemie, Lichtenbergstr.Garching, Germany
                [2 ] Ruhr-University Bochum, Medizinisches Proteom-Center, Functional Proteomics, Universitätsstrasse, Bochum, Germany
                Université de Genève, SWITZERLAND
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-8952-9642
                Article
                PONE-D-17-07559
                10.1371/journal.pone.0186386
                5659845
                29078207
                66663f0a-16fe-49ff-81da-6fd99197694c
                © 2017 Eckl 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
                : 24 February 2017
                : 30 September 2017
                Page count
                Figures: 6, Tables: 1, Pages: 27
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: RI1873/1-3
                Award Recipient :
                The work was supported by P.U.R.E. (Protein Unit for Research in Europe, funded by the German federal state North Rhine-Westphalia). Klaus Richter is funded by the research grant DFG grant RI1873/1-3. This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the funding programme Open Access Publishing. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Immunology
                Immune Response
                Medicine and Health Sciences
                Immunology
                Immune Response
                Biology and life sciences
                Genetics
                Epigenetics
                RNA interference
                Biology and life sciences
                Genetics
                Gene expression
                RNA interference
                Biology and life sciences
                Genetics
                Genetic interference
                RNA interference
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                RNA interference
                Biology and Life Sciences
                Anatomy
                Digestive System
                Gastrointestinal Tract
                Medicine and Health Sciences
                Anatomy
                Digestive System
                Gastrointestinal Tract
                Research and Analysis Methods
                Bioassays and Physiological Analysis
                Microarrays
                Biology and Life Sciences
                Genetics
                Gene Identification and Analysis
                Genetic Networks
                Computer and Information Sciences
                Network Analysis
                Genetic Networks
                Biology and Life Sciences
                Developmental Biology
                Embryology
                Embryos
                Research and Analysis Methods
                Experimental Organism Systems
                Model Organisms
                Caenorhabditis Elegans
                Research and Analysis Methods
                Model Organisms
                Caenorhabditis Elegans
                Research and Analysis Methods
                Experimental Organism Systems
                Animal Models
                Caenorhabditis Elegans
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Nematoda
                Caenorhabditis
                Caenorhabditis Elegans
                Biology and Life Sciences
                Anatomy
                Reproductive System
                Genital Anatomy
                Gonads
                Medicine and Health Sciences
                Anatomy
                Reproductive System
                Genital Anatomy
                Gonads
                Custom metadata
                All relevant data are available from the Gene Expression Omnibus repository under series GSE105030 with the samples GSM2816664 to GSM2816669.

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                Uncategorized

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