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      Vps11 and Vps18 of Vps-C membrane traffic complexes are E3 ubiquitin ligases and fine-tune signalling

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          Abstract

          In response to extracellular signals, many signalling proteins associated with the plasma membrane are sorted into endosomes. This involves endosomal fusion, which depends on the complexes HOPS and CORVET. Whether and how their subunits themselves modulate signal transduction is unknown. We show that Vps11 and Vps18 (Vps11/18), two common subunits of the HOPS/CORVET complexes, are E3 ubiquitin ligases. Upon overexpression of Vps11/Vps18, we find perturbations of ubiquitination in signal transduction pathways. We specifically demonstrate that Vps11/18 regulate several signalling factors and pathways, including Wnt, estrogen receptor α (ERα), and NFκB. For ERα, we demonstrate that the Vps11/18-mediated ubiquitination of the scaffold protein PELP1 impairs the activation of ERα by c-Src. Thus, proteins involved in membrane traffic, in addition to performing their well-described role in endosomal fusion, fine-tune signalling in several different ways, including through ubiquitination.

          Abstract

          Endosomal fusion depends on the HOPS and CORVET complexes but whether and how their subunits modulate signal transduction is not fully understood. Here, the authors show that the HOPS/CORVET subunits Vps11 and Vps18 are E3 ubiquitin ligases that are involved in the regulation of ERα signalling.

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          Systematic and quantitative assessment of the ubiquitin-modified proteome.

          Despite the diverse biological pathways known to be regulated by ubiquitylation, global identification of substrates that are targeted for ubiquitylation has remained a challenge. To globally characterize the human ubiquitin-modified proteome (ubiquitinome), we utilized a monoclonal antibody that recognizes diglycine (diGly)-containing isopeptides following trypsin digestion. We identify ~19,000 diGly-modified lysine residues within ~5000 proteins. Using quantitative proteomics we monitored temporal changes in diGly site abundance in response to both proteasomal and translational inhibition, indicating both a dependence on ongoing translation to observe alterations in site abundance and distinct dynamics of individual modified lysines in response to proteasome inhibition. Further, we demonstrate that quantitative diGly proteomics can be utilized to identify substrates for cullin-RING ubiquitin ligases. Interrogation of the ubiquitinome allows for not only a quantitative assessment of alterations in protein homeostasis fidelity, but also identification of substrates for individual ubiquitin pathway enzymes. Copyright © 2011 Elsevier Inc. All rights reserved.
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            miRpower: a web-tool to validate survival-associated miRNAs utilizing expression data from 2178 breast cancer patients.

            The proper validation of prognostic biomarkers is an important clinical issue in breast cancer research. MicroRNAs (miRNAs) have emerged as a new class of promising breast cancer biomarkers. In the present work, we developed an integrated online bioinformatic tool to validate the prognostic relevance of miRNAs in breast cancer.
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              Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics

              S.-E. Ong (2002)
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                Author and article information

                Contributors
                didier.picard@unige.ch
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                23 April 2019
                23 April 2019
                2019
                : 10
                : 1833
                Affiliations
                [1 ]ISNI 0000 0001 2322 4988, GRID grid.8591.5, Département de Biologie Cellulaire, , Université de Genève, Sciences III, ; 30 quai Ernest-Ansermet, 1211 Genève, Switzerland
                [2 ]ISNI 0000 0001 2322 4988, GRID grid.8591.5, Département de Génétique et Évolution, , Université de Genève, Sciences III, ; 30 quai Ernest-Ansermet, 1211 Genève, Switzerland
                [3 ]ISNI 0000 0004 0389 8485, GRID grid.55325.34, Present Address: Department of Molecular Microbiology, , Oslo University Hospital, ; 0372 Oslo, Norway
                Author information
                http://orcid.org/0000-0003-3533-0264
                http://orcid.org/0000-0003-1367-9692
                http://orcid.org/0000-0003-4722-5170
                http://orcid.org/0000-0001-8816-9668
                Article
                9800
                10.1038/s41467-019-09800-y
                6478910
                31015428
                dba659dd-1fe4-4fa6-aebb-4e236630b8af
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 14 May 2018
                : 2 April 2019
                Categories
                Article
                Custom metadata
                © The Author(s) 2019

                Uncategorized
                ubiquitin ligases,nuclear receptors,endosomes,ubiquitylation
                Uncategorized
                ubiquitin ligases, nuclear receptors, endosomes, ubiquitylation

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