Defining the Human Deubiquitinating Enzyme Interaction Landscape
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TL;DR: A global proteomic analysis of Dubs and their associated protein complexes provided the first glimpse into the Dub interaction landscape, places previously unstudied Dubs within putative biological pathways, and identifies previously unknown interactions and protein complexes involved in this increasingly important arm of the ubiquitin-proteasome pathway.
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About: This article is published in Cell. The article was published on 23 Jul 2009. and is currently open access. The article focuses on the topics: Deubiquitinating enzyme & Interactome.
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Citations
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity.
Danielle L. Swaney,Dana J. Ramms,Zhiyong Wang,Jisoo Park,Yusuke Goto,Margaret Soucheray,Neil E. Bhola,Kyumin Kim,Fan Zheng,Yan Zeng,Michael J. McGregor,Kari A. Herrington,Rachel A. O'Keefe,Nan Jin,Nathan K. VanLandingham,Helene Foussard,John Von Dollen,Mehdi Bouhaddou,David Jimenez-Morales,Kirsten Obernier,Jason F. Kreisberg,Min-Kyu Kim,Daniel Johnson,Natalia Jura,Jennifer R. Grandis,J. Silvio Gutkind,Trey Ideker,Nevan J. Krogan +27 more
TL;DR: In this article, a framework for elucidating tumor genetic complexity through multidimensional protein-protein interaction maps and applying it to enhancing our understanding of head and neck squamous cell was proposed.
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Stress-induced lncRNA LASTR fosters cancer cell fitness by regulating the activity of the U4/U6 recycling factor SART3
Linde De Troyer,Peihua Zhao,Tibor J. Pastor,Maria Francesca Baietti,Jasmine Barra,Roberto Vendramin,Rüveyda Dok,Benoit Lechat,Paul Najm,Delphi Van Haver,Francis Impens,Eleonora Leucci,Anna Sablina +12 more
TL;DR: It is found that the stress-induced long non-coding RNA, LINC02657 or LASTR (lncRNA associated with SART3 regulation of splicing), is upregulated in hypoxic breast cancer and is essential for the growth of LAS TR-positive triple-negative breast tumors.
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Proteolysis of Rad17 by Cdh1/APC regulates checkpoint termination and recovery from genotoxic stress.
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TL;DR: An assay to identify fast‐turnover proteins induced by various types of genotoxic stress led to the identification of Rad17 as a protein exhibiting a distinctive pattern of upregulation followed by subsequent degradation after exposure to UV radiation in human primary cells.
Ubiquitin-Specific Protease 4 Is an Endogenous Negative Regulator of Metabolic Dysfunctions in Nonalcoholic Fatty Liver Disease in Mice.
Yichao Zhao,Fang Wang,Lingchen Gao,Longwei Xu,Renyang Tong,Nan Lin,Yuanyuan Su,Yang Yan,Yu Gao,Jie He,Ling-Cong Kong,Ancai Yuan,Ying Zhuge,Jun Pu +13 more
TL;DR: Evidence is provided that USP4 functions as a pivotal suppressor in NAFLD and related metabolic disorders.
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E3-Independent Constitutive Monoubiquitination Complements Histone Methyltransferase Activity of SETDB1
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TL;DR: This work demonstrates that SETDB1, a major histone H3K9 methyltransferase is monoubiquitinated at the evolutionarily conserved lysine-867 in its SET-Insertion domain and highlights an E3-independent mechanism for monoubiqueitination and reveals mechanistic details ofSETDB1's enzymatic activity and the functional significance of its SET -Insertion.
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TL;DR: The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery.
BioGRID: a general repository for interaction datasets
Chris Stark,Bobby-Joe Breitkreutz,Teresa Reguly,Lorrie Boucher,Ashton Breitkreutz,Mike Tyers +5 more
TL;DR: BioGRID is a freely accessible database of physical and genetic interactions that includes >116 000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens.
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Nevan J. Krogan,Gerard Cagney,Gerard Cagney,Haiyuan Yu,Gouqing Zhong,Xinghua Guo,Alexandr Ignatchenko,Joyce Li,Shuye Pu,Nira Datta,Aaron Tikuisis,Thanuja Punna,José M. Peregrín-Alvarez,Michael Shales,Xin Zhang,Michael Davey,Mark D. Robinson,Alberto Paccanaro,James E. Bray,Anthony Sheung,Bryan Beattie,Dawn Richards,Veronica Canadien,Atanas Iliev Lalev,Frank Mena,Peter D Wong,Andrei Starostine,Myra M. Canete,James Vlasblom,Samuel Wu,Chris Orsi,Sean R. Collins,Shamanta Chandran,Robin Haw,Jennifer J. Rilstone,Kiran Gandi,Natalie J. Thompson,Gabe Musso,Peter St Onge,Shaun Ghanny,Mandy H. Y. Lam,Gareth Butland,Amin M. Altaf-Ul,Shigehiko Kanaya,Ali Shilatifard,Erin K. O'Shea,Jonathan S. Weissman,C. James Ingles,Timothy P. Hughes,John Parkinson,Mark Gerstein,Shoshana J. Wodak,Andrew Emili,Jack Greenblatt +53 more
TL;DR: T tandem affinity purification was used to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae to identify protein–protein interactions, which will help future studies on individual proteins as well as functional genomics and systems biology.
A Genomic and Functional Inventory of Deubiquitinating Enzymes
Sebastian M.B. Nijman,Mark P.A. Luna-Vargas,Arno Velds,Thijn R. Brummelkamp,Annette M.G. Dirac,Titia K. Sixma,René Bernards +6 more
TL;DR: An inventory of the deubiquitinating enzymes encoded in the human genome is presented and the literature concerning these enzymes is reviewed, with particular emphasis on their function, specificity, and the regulation of their activity.
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One step at a time: endoplasmic reticulum-associated degradation
TL;DR: The current understanding of each step during ERAD, with emphasis on the factors that catalyse distinct activities is summarized, to highlight the importance of this pathway.
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