Gain of UBE2D1 Facilitates Hepatocellular Carcinoma
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The Effect of Temperature Adaptation on the Ubiquitin–Proteasome Pathway in Notothenioid Fishes Anne E
© 2017. Published by The Company of Biologists Ltd | Journal of Experimental Biology (2017) 220, 369-378 doi:10.1242/jeb.145946 RESEARCH ARTICLE The effect of temperature adaptation on the ubiquitin–proteasome pathway in notothenioid fishes Anne E. Todgham1,*, Timothy A. Crombie2 and Gretchen E. Hofmann3 ABSTRACT proliferation to compensate for the effects of low temperature on ’ There is an accumulating body of evidence suggesting that the sub- aerobic metabolism (Johnston, 1989; O Brien et al., 2003; zero Antarctic marine environment places physiological constraints Guderley, 2004). Recently, there has been an accumulating body – on protein homeostasis. Levels of ubiquitin (Ub)-conjugated proteins, of literature to suggest that protein homeostasis the maintenance of – 20S proteasome activity and mRNA expression of many proteins a functional protein pool has been highly impacted by evolution involved in both the Ub tagging of damaged proteins as well as the under these cold and stable conditions. different complexes of the 26S proteasome were measured to Maintaining protein homeostasis is a fundamental physiological examine whether there is thermal compensation of the Ub– process, reflecting a dynamic balance in synthetic and degradation proteasome pathway in Antarctic fishes to better understand the processes. There are numerous lines of evidence to suggest efficiency of the protein degradation machinery in polar species. Both temperature compensation of protein synthesis in Antarctic Antarctic (Trematomus bernacchii, Pagothenia borchgrevinki)and invertebrates (Whiteley et al., 1996; Marsh et al., 2001; Robertson non-Antarctic (Notothenia angustata, Bovichtus variegatus) et al., 2001; Fraser et al., 2002) and fish (Storch et al., 2005). In notothenioids were included in this study to investigate the zoarcid fishes, it has been demonstrated that Antarctic eelpouts mechanisms of cold adaptation of this pathway in polar species. -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
UBE2E1 (Ubch6) [Untagged] E2 – Ubiquitin Conjugating Enzyme
UBE2E1 (UbcH6) [untagged] E2 – Ubiquitin Conjugating Enzyme Alternate Names: UbcH6, UbcH6, Ubiquitin conjugating enzyme UbcH6 Cat. No. 62-0019-100 Quantity: 100 µg Lot. No. 1462 Storage: -70˚C FOR RESEARCH USE ONLY NOT FOR USE IN HUMANS CERTIFICATE OF ANALYSIS Page 1 of 2 Background Physical Characteristics The enzymes of the ubiquitylation Species: human Protein Sequence: pathway play a pivotal role in a num- GPLGSPGIPGSTRAAAM SDDDSRAST ber of cellular processes including Source: E. coli expression SSSSSSSSNQQTEKETNTPKKKESKVSMSKN regulated and targeted proteasomal SKLLSTSAKRIQKELADITLDPPPNCSAGP degradation of substrate proteins. Quantity: 100 μg KGDNIYEWRSTILGPPGSVYEGGVFFLDIT FTPEYPFKPPKVTFRTRIYHCNINSQGVI Three classes of enzymes are in- Concentration: 1 mg/ml CLDILKDNWSPALTISKVLLSICSLLTDCNPAD volved in the process of ubiquitylation; PLVGSIATQYMTNRAEHDRMARQWTKRYAT activating enzymes (E1s), conjugating Formulation: 50 mM HEPES pH 7.5, enzymes (E2s) and protein ligases 150 mM sodium chloride, 2 mM The residues underlined remain after cleavage and removal (E3s). UBE2E1 is a member of the E2 dithiothreitol, 10% glycerol of the purification tag. ubiquitin-conjugating enzyme family UBE2E1 (regular text): Start bold italics (amino acid and cloning of the human gene was Molecular Weight: ~23 kDa residues 1-193) Accession number: AAH09139 first described by Nuber et al. (1996). UBE2E1 shares 74% sequence ho- Purity: >98% by InstantBlue™ SDS-PAGE mology with UBE2D1 and contains an Stability/Storage: 12 months at -70˚C; N-terminal extension of approximately aliquot as required 40 amino acids. A tumour suppressor candidate, tumour-suppressing sub- chromosomal transferable fragment Quality Assurance cDNA (TSSC5) is located in the re- gion of human chromosome 11p15.5 Purity: Protein Identification: linked with Beckwith-Wiedemann syn- 4-12% gradient SDS-PAGE Confirmed by mass spectrometry. -
UBE2B Sirna Set I Sirna Duplexes Targeted Against Three Exon Regions
Catalog # Aliquot Size U211-911-05 3 x 5 nmol U211-911-20 3 x 20 nmol U211-911-50 3 x 50 nmol UBE2B siRNA Set I siRNA duplexes targeted against three exon regions Catalog # U211-911 Lot # Z2109-16 Specificity Formulation UBE2B siRNAs are designed to specifically knock-down The siRNAs are supplied as a lyophilized powder and human UBE2B expression. shipped at room temperature. Product Description Reconstitution Protocol UBE2B siRNA is a pool of three individual synthetic siRNA Briefly centrifuge the tubes (maximum RCF 4,000g) to duplexes designed to knock-down human UBE2B mRNA collect lyophilized siRNA at the bottom of the tube. expression. Each siRNA is 19-25 bases in length. The gene Resuspend the siRNA in 50 µl of DEPC-treated water accession number is NM_003337. (supplied by researcher), which results in a 1x stock solution (10 µM). Gently pipet the solution 3-5 times to mix Gene Aliases and avoid the introduction of bubbles. Optional: aliquot E2-17kDa; HHR6B; HR6B; RAD6B; UBC2 1x stock solutions for storage. Storage and Stability Related Products The lyophilized powder is stable for at least 4 weeks at room temperature. It is recommended that the Product Name Catalog Number lyophilized and resuspended siRNAs are stored at or UBE2A Protein U210-30H below -20oC. After resuspension, siRNA stock solutions ≥2 UBE2B Protein U211-30H µM can undergo up to 50 freeze-thaw cycles without UBE2C Protein U212-30H significant degradation. For long-term storage, it is UBE2D1 (UBCH5A) U213-30H recommended that the siRNA is stored at -70oC. For most Protein favorable performance, avoid repeated handling and UBE2D2 (UBC4) Protein U214-30H multiple freeze/thaw cycles. -
The X-Linked Intellectual Disability Gene Product and E3 Ubiquitin Ligase KLHL15 Degrades Doublecortin Proteins to Constrain Neuronal Dendritogenesis
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.02.324285; this version posted October 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. KLHL15 degrades doublecortin proteins The X-linked intellectual disability gene product and E3 ubiquitin ligase KLHL15 degrades doublecortin proteins to constrain neuronal dendritogenesis Jianing Song1,2, Ronald A. Merrill1,2, Andrew Y. Usachev1, and Stefan Strack1* From the 1Department of Neuroscience and Pharmacology and the Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242 2 These authors contributed equally to the work. *To whom correspondence should be addressed: Stefan Strack: Dept. of Neuroscience and Pharmacology, The University of Iowa, Iowa City, IA 52242; [email protected]; Tel. (319) 384-4439; Fax. (319) 335-8930 Running Title: KLHL15 degrades doublecortin proteins Keywords: Kelch-like 15, KLHL15, E3 ubiquitin ligase, protein phosphatase 2A, signal transduction, doublecortin, doublecortin-like kinases, microtubule-associated protein, ubiquitination, proteasomal degradation, protein turnover, neurite outgrowth, dendritic complexity, pulse-chase, HaloTag ______________________________________________________________________________ ABSTRACT doublecortin (DCX), also an X-linked disease gene, and doublecortin-like kinases 1 and 2 Proper brain development and function (DCLK1/2) as bona fide KLHL15 interactors requires finely controlled mechanisms -
UBE2C Is Upregulated by Estrogen and Promotes Epithelial–Mesenchymal Transition Via P53 in Endometrial Cancer
Published OnlineFirst October 29, 2019; DOI: 10.1158/1541-7786.MCR-19-0561 MOLECULAR CANCER RESEARCH | CANCER GENES AND NETWORKS UBE2C Is Upregulated by Estrogen and Promotes Epithelial–Mesenchymal Transition via p53 in Endometrial Cancer Yan Liu1, Rong Zhao1, Shuqi Chi1, Wei Zhang1, Chengyu Xiao1, Xing Zhou1, Yingchao Zhao2, and Hongbo Wang1 ABSTRACT ◥ Ubiquitin-conjugating enzyme E2C (UBE2C) plays important inhibited endometrial cancer cell proliferation, migration, invasion, roles in tumor progression; nevertheless, its function in endometrial and epithelial–mesenchymal transition (EMT), whereas UBE2C cancer remains unclear. This study elucidated the impact of UBE2C overexpression exerted the opposite effects. UBE2C downregulation on endometrial cancer and its underlying mechanism. Human increased p53 and its downstream p21 expression, with p53 over- endometrial cancer and normal endometrial tissues were acquired expression reversing the EMT-promoting effects of UBE2C. UBE2C from patients at Wuhan Union Hospital and UBE2C expression was enhanced p53 ubiquitination to facilitate its degradation in endo- detected by Western blotting and qRT-PCR. Endometrial cancer metrial cancer cells. Estradiol (E2) induced UBE2C expression via cells were transfected with a UBE2C overexpression plasmid or estrogen receptor a, which binds directly to the UBE2C promoter UBE2C-specific short hairpin RNA (shRNA) to up- or downregu- element. Silencing of UBE2C inhibited E2-promoted migration, late UBE2C expression, respectively. CCK8 and transwell assays -
Characterization of the Cellular Network of Ubiquitin Conjugating and Ligating Enzymes Ewa Katarzyna Blaszczak
Characterization of the cellular network of ubiquitin conjugating and ligating enzymes Ewa Katarzyna Blaszczak To cite this version: Ewa Katarzyna Blaszczak. Characterization of the cellular network of ubiquitin conjugating and ligating enzymes. Cellular Biology. Université Rennes 1, 2015. English. NNT : 2015REN1S116. tel-01547616 HAL Id: tel-01547616 https://tel.archives-ouvertes.fr/tel-01547616 Submitted on 27 Jun 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. ANNÉE 2015 THÈSE / UNIVERSITÉ DE RENNES 1 sous le sceau de l’Université Européenne de Bretagne pour le grade de DOCTEUR DE L’UNIVERSITÉ DE RENNES 1 Mention : BIOLOGIE École doctorale Vie-Agro-Santé présentée par Ewa Katarzyna Blaszczak Préparée à l’unité de recherche UMR 6290, IGDR Institut de Génétique et Développement de Rennes Université Rennes 1 Thèse soutenue à Rennes le 26.06.2015 Characterization of devant le jury composé de : Aude ECHALIER-GLAZER the cellular network Maître de conférence University of Leicester / rapporteur of ubiquitin Lionel PINTARD Directeur de recherche -
The MALDI TOF E2/E3 Ligase Assay As an Universal Tool for Drug Discovery in the Ubiquitin Pathway
bioRxiv preprint doi: https://doi.org/10.1101/224600; this version posted November 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. The MALDI TOF E2/E3 ligase assay as an universal tool for drug discovery in the ubiquitin pathway Virginia De Cesare*1, Clare Johnson2, Victoria Barlow2, James Hastie2 Axel Knebel1 and 5 Matthias Trost*1,3 1MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK; 2MRC Protein Phosphorylation and Ubiquitylation Unit Reagents and Services, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK; . 3Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, 10 NE2 1HH, UK *To whom correspondence should be addressed: Virginia De Cesare ([email protected]) Matthias Trost ([email protected]) 15 Contact information: V.D.C.: MRC PPU, University of Dundee, Dow St, Dundee, DD1 5EH, Phone: +44 1382 20 85822 M.T.: Newcastle University, Institute for Cell and Molecular Biosciences, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, Phone: +44 191 2087009 Key words: Ubiquitin, E3 ligase, E2 enzyme, MALDI TOF, mass spectrometry, drug 25 discovery, high-throughput, assay, MDM2, HOIP, ITCH 1 bioRxiv preprint doi: https://doi.org/10.1101/224600; this version posted November 29, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
S41467-019-12388-Y.Pdf
ARTICLE https://doi.org/10.1038/s41467-019-12388-y OPEN A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases Leo Kiss1,4, Jingwei Zeng 1,4, Claire F. Dickson1,2, Donna L. Mallery1, Ji-Chun Yang 1, Stephen H. McLaughlin 1, Andreas Boland1,3, David Neuhaus1,5 & Leo C. James1,5* 1234567890():,; The cytosolic antibody receptor TRIM21 possesses unique ubiquitination activity that drives broad-spectrum anti-pathogen targeting and underpins the protein depletion technology Trim-Away. This activity is dependent on formation of self-anchored, K63-linked ubiquitin chains by the heterodimeric E2 enzyme Ube2N/Ube2V2. Here we reveal how TRIM21 facilitates ubiquitin transfer and differentiates this E2 from other closely related enzymes. A tri-ionic motif provides optimally distributed anchor points that allow TRIM21 to wrap an Ube2N~Ub complex around its RING domain, locking the closed conformation and promoting ubiquitin discharge. Mutation of these anchor points inhibits ubiquitination with Ube2N/ Ube2V2, viral neutralization and immune signalling. We show that the same mechanism is employed by the anti-HIV restriction factor TRIM5 and identify spatially conserved ionic anchor points in other Ube2N-recruiting RING E3s. The tri-ionic motif is exclusively required for Ube2N but not Ube2D1 activity and provides a generic E2-specific catalysis mechanism for RING E3s. 1 Medical Research Council Laboratory of Molecular Biology, Cambridge, UK. 2Present address: University of New South Wales, Sydney, NSW, Australia. 3Present address: Department of Molecular Biology, Science III, University of Geneva, Geneva, Switzerland. 4These authors contributed equally: Leo Kiss, Jingwei Zeng. 5These authors jointly supervised: David Neuhaus, Leo C. -
Uncovering New Mechanisms of Cdc34 and Cullin-Ring Activity
UNLV Theses, Dissertations, Professional Papers, and Capstones 12-15-2019 Uncovering New Mechanisms of Cdc34 and Cullin-Ring Activity Spencer Hill Follow this and additional works at: https://digitalscholarship.unlv.edu/thesesdissertations Part of the Biochemistry Commons Repository Citation Hill, Spencer, "Uncovering New Mechanisms of Cdc34 and Cullin-Ring Activity" (2019). UNLV Theses, Dissertations, Professional Papers, and Capstones. 3808. http://dx.doi.org/10.34917/18608668 This Dissertation is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself. This Dissertation has been accepted for inclusion in UNLV Theses, Dissertations, Professional Papers, and Capstones by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. UNCOVERING NEW MECHANISMS OF CDC34 AND CULLIN-RING ACTIVITY By Spencer Wayne Hill Bachelor of Science in Biochemistry University of Nevada, Las Vegas 2013 A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy - Chemistry Department of Chemistry and Biochemistry College of Sciences The Graduate College University of Nevada, Las Vegas December 2019 Dissertation Approval The Graduate College The University of Nevada, Las Vegas November 1st, 2019 This dissertation prepared by Spencer Wayne Hill entitled Uncovering New Mechanisms of Cdc34 and Cullin-Ring Activity is approved in partial fulfillment of the requirements for the degree of Doctor of Philosophy - Chemistry Department of Chemistry and Biochemistry Gary Kleiger, Ph.D. -
Comparative Analysis of the Ubiquitin-Proteasome System in Homo Sapiens and Saccharomyces Cerevisiae
Comparative Analysis of the Ubiquitin-proteasome system in Homo sapiens and Saccharomyces cerevisiae Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Hartmut Scheel aus Rheinbach Köln, 2005 Berichterstatter: Prof. Dr. R. Jürgen Dohmen Prof. Dr. Thomas Langer Dr. Kay Hofmann Tag der mündlichen Prüfung: 18.07.2005 Zusammenfassung I Zusammenfassung Das Ubiquitin-Proteasom System (UPS) stellt den wichtigsten Abbauweg für intrazelluläre Proteine in eukaryotischen Zellen dar. Das abzubauende Protein wird zunächst über eine Enzym-Kaskade mit einer kovalent gebundenen Ubiquitinkette markiert. Anschließend wird das konjugierte Substrat vom Proteasom erkannt und proteolytisch gespalten. Ubiquitin besitzt eine Reihe von Homologen, die ebenfalls posttranslational an Proteine gekoppelt werden können, wie z.B. SUMO und NEDD8. Die hierbei verwendeten Aktivierungs- und Konjugations-Kaskaden sind vollständig analog zu der des Ubiquitin- Systems. Es ist charakteristisch für das UPS, daß sich die Vielzahl der daran beteiligten Proteine aus nur wenigen Proteinfamilien rekrutiert, die durch gemeinsame, funktionale Homologiedomänen gekennzeichnet sind. Einige dieser funktionalen Domänen sind auch in den Modifikations-Systemen der Ubiquitin-Homologen zu finden, jedoch verfügen diese Systeme zusätzlich über spezifische Domänentypen. Homologiedomänen lassen sich als mathematische Modelle in Form von Domänen- deskriptoren (Profile) beschreiben. Diese Deskriptoren können wiederum dazu verwendet werden, mit Hilfe geeigneter Verfahren eine gegebene Proteinsequenz auf das Vorliegen von entsprechenden Homologiedomänen zu untersuchen. Da die im UPS involvierten Homologie- domänen fast ausschließlich auf dieses System und seine Analoga beschränkt sind, können domänen-spezifische Profile zur Katalogisierung der UPS-relevanten Proteine einer Spezies verwendet werden. Auf dieser Basis können dann die entsprechenden UPS-Repertoires verschiedener Spezies miteinander verglichen werden. -
Protein Folding and Quality Control in the ER
Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Protein Folding and Quality Control in the ER Kazutaka Araki and Kazuhiro Nagata Laboratory of Molecular and Cellular Biology, Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Kita-ku, Kyoto 803-8555, Japan Correspondence: [email protected] The endoplasmic reticulum (ER) uses an elaborate surveillance system called the ER quality control (ERQC) system. The ERQC facilitates folding and modification of secretory and mem- brane proteins and eliminates terminally misfolded polypeptides through ER-associated degradation (ERAD) or autophagic degradation. This mechanism of ER protein surveillance is closely linked to redox and calcium homeostasis in the ER, whose balance is presumed to be regulated by a specific cellular compartment. The potential to modulate proteostasis and metabolism with chemical compounds or targeted siRNAs may offer an ideal option for the treatment of disease. he endoplasmic reticulum (ER) serves as a complex in the ER membrane (Johnson and Tprotein-folding factory where elaborate Van Waes 1999; Saraogi and Shan 2011). After quality and quantity control systems monitor arriving at the translocon, translation resumes an efficient and accurate production of secretory in a process called cotranslational translocation and membrane proteins, and constantly main- (Hegde and Kang 2008; Zimmermann et al. tain proper physiological homeostasis in the 2010). Numerous ER-resident chaperones and ER including redox state and calcium balance. enzymes aid in structural and conformational In this article, we present an overview the recent maturation necessary for proper protein fold- progress on the ER quality control system, ing, including signal-peptide cleavage, N-linked mainly focusing on the mammalian system.