DOCSLIB.ORG

Structural and Functional Characterization of the RING-Like Protein RTF2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Structural and Functional Characterization of the RING-Like Protein RTF2 Structural and functional characterization of the RING-like protein RTF2 by Andrew Zhai A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Graduate Department of Biochemistry University of Toronto Copyright © 2020 by Andrew Zhai Abstract Structural and functional characterization of the RING-like protein RTF2 Andrew Zhai Doctor of Philosophy Graduate Department of Biochemistry University of Toronto 2020 RING and RING-like domains represent the functional component on the vast majority of E3 ligases. With over 600 known members, the family of RING E3 ligases promote the direct transfer of ubiquitin from an E2 onto a substrate, acting as the key mediators of specificity during the reaction. However, beyond acting as a simple scaffold for E2-binding, many RING and RING-like domains have been found to play a more active role by inducing conformational selectivity in the otherwise flexible E2~ubiquitin conjugate. With their central role in the ubiquitination reaction, it is no surprise that RING and RING-like domains exhibit a wide array of regulatory mechanisms that govern their activity, including the ability to function in different oligomeric states. Specifically, while some function as monomers, many RING and RING-like E3 ligases are dependent on dimerization for their activity. This thesis explores the structure and function of a poorly characterized, evolutionarily conserved RING-like protein RTF2. In the first chapter, I examine the crystal structure of human RTF2 revealing two conserved RING-like domains: an N-terminal U-box-like domain associated with a SP-RING domain in an arrangement I describe as an intra-chain heterodimer. I then move on to describe a role for RTF2 in pre-mRNA splicing and begin to explore its interactome using proximity-dependent biotin identification (BioID). In the third chapter, I identify conserved functional elements on both RING-like domains and ii demonstrate the importance of these residues for RTF2-dependent splicing, possibly by facilitating E2 recruitment. Together, these results reveal a novel RING-like structural mode and provide a foundation for further work examining the mechanism underlying RTF2 function and its role in pre-mRNA splicing. iii Acknowledgments Of course, I extend my most immediate gratitude to my supervisor Gil Privé for his years of mentorship and allowing me the privilege of conducting research in his lab. Graduate school has been equal parts rewarding and challenging, but his guidance allowed me to emerge mostly intact. The lessons I have learned while under his tutelage are ones that I will remember throughout my life. I have also been fortunate enough to count two incredible scientists, Frank Sicheri and Brian Raught, as my committee members. They deserve thanks for their continuous support and advice during the completion of this thesis. I have always left our meetings with a renewed sense of enthusiasm and clarity due to their invaluable input. On top of this I also wish to thank Brian as well as Étienne Coyaud for their role as collaborators. Their patience in working with structural biologists on proteomics projects knows no bounds. Likewise, I would like to extend my gratitude towards Ben Blencowe and Sandy Pan for their collaboration on the RNA-seq and alternative splicing analysis portion of this thesis. I would also like to express my gratitude for Nana Lee and her unwavering dedication to my professional development. I wish to thank all past and present members of the Privé lab. While writing has mostly been an isolated experience, they ensured that my time at the bench was filled with lively discussion. In particular I owe much of the work presented here to Liyan Qiu who initiated the RTF2 project and conducted the crystallography and structure determination. I also thank Neil Pomroy for keeping the lab in check and making sure I didn’t break thousands of dollars’ worth of equipment. To Amie, Jess, Kyle, and the extended Anglo-Canadian Zinc Consortium: thank you for giving me life outside of the lab. Your friendship is something that I lean on. The endless jokes about crystallography didn’t make sense to me at first but I’ve learned to accept them. There are not enough words to express the appreciation I have for my parents as well as my grandparents. It is due to the sacrifices they’ve made that I have been able to pursue a fulfilling education in science. My mom, whose hard work and dedication I try to emulate in my own life, iv and my dad, who is to this day the most intelligent person I know. Whatever accomplishments I have are because of them. Finally, to my best friend and partner Rebecca. Every day I thank my lucky stars that I am able to share my life with you. Life after graduate school will bring even more adventures and obstacles, but with you I welcome the challenge with open arms. Also, thanks to my two unlicensed emotional support animals: Levi (left) and Trudy (right) v Table of Contents Chapter 1: Introduction ................................................................................................................. 1 1.1 The discovery of ubiquitin biology ........................................................................................... 2 1.2 Introduction to the ubiquitin system ....................................................................................... 3 1.3 Core components of the ubiquitination cascade ..................................................................... 5 1.3.1 Ubiquitin and ubiquitin-like modifiers .................................................................................................. 6 1.3.2 E1: ubiquitin activating enzymes ......................................................................................................... 10 1.3.3 E2-ubiquitin conjugating enzyme ........................................................................................................ 11 1.3.4 E3 – ubiquitin protein ligases .............................................................................................................. 13 1.4 The RING family of E3 ligases ............................................................................................... 16 1.4.1 Multi-subunit RING E3 ligases ........................................................................................................... 16 1.4.2 RBR E3 ligases .................................................................................................................................... 19 1.4.3 Simple RING E3 ligases ...................................................................................................................... 20 1.5 The RING domain ................................................................................................................... 23 1.5.1 History of the RING domain: From DNA binding to ubiquitin ligase ................................................ 23 1.5.2 Structure of the RING domain ............................................................................................................. 25 1.5.3 U-box and SP-RING domains ............................................................................................................. 27 1.5.4 E2 activation by RING-like E3 ligases ................................................................................................ 30 1.5.5 Oligomerization of RING and RING-like domains ............................................................................. 35 1.6 Introduction to pre-mRNA splicing ....................................................................................... 38 1.6.1 Mechanisms of alternative splicing ..................................................................................................... 42 1.6.2 Emerging roles for RING and RING-like E3 ligases in splicing ......................................................... 44 1.7 RTF2: An uncharacterized RING-like protein ..................................................................... 47 1.7.1 Cellular functions of RTF2 .................................................................................................................. 47 1.7.2 RTF2 is a core essential gene............................................................................................................... 48 1.8 Thesis rationale and overview ................................................................................................ 49 Chapter 2: Crystal structure of RTF2 ......................................................................................... 52 2.1 Abstract .................................................................................................................................... 53 2.2 Introduction ............................................................................................................................. 53 vi 2.3 Materials and methods ............................................................................................................ 56 2.3.1 Cloning, protein expression, and purification ...................................................................................... 56 2.3.2 Crystallization and structure determination ......................................................................................... 56 2.4 Results ....................................................................................................................................... 57 2.4.1 Structure of the RTF2 RING-like domains .........................................................................................
Load more

Recommended publications
  • The HECT Domain Ubiquitin Ligase HUWE1 Targets Unassembled Soluble Proteins for Degradation
    OPEN Citation: Cell Discovery (2016) 2, 16040; doi:10.1038/celldisc.2016.40 ARTICLE www.nature.com/celldisc The HECT domain ubiquitin ligase HUWE1 targets unassembled soluble proteins for degradation Yue Xu1, D Eric Anderson2, Yihong Ye1 1Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; 2Advanced Mass Spectrometry Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA In eukaryotes, many proteins function in multi-subunit complexes that require proper assembly. To maintain complex stoichiometry, cells use the endoplasmic reticulum-associated degradation system to degrade unassembled membrane subunits, but how unassembled soluble proteins are eliminated is undefined. Here we show that degradation of unassembled soluble proteins (referred to as unassembled soluble protein degradation, USPD) requires the ubiquitin selective chaperone p97, its co-factor nuclear protein localization protein 4 (Npl4), and the proteasome. At the ubiquitin ligase level, the previously identified protein quality control ligase UBR1 (ubiquitin protein ligase E3 component n-recognin 1) and the related enzymes only process a subset of unassembled soluble proteins. We identify the homologous to the E6-AP carboxyl terminus (homologous to the E6-AP carboxyl terminus) domain-containing protein HUWE1 as a ubiquitin ligase for substrates bearing unshielded, hydrophobic segments. We used a stable isotope labeling with amino acids-based proteomic approach to identify endogenous HUWE1 substrates. Interestingly, many HUWE1 substrates form multi-protein com- plexes that function in the nucleus although HUWE1 itself is cytoplasmically localized. Inhibition of nuclear entry enhances HUWE1-mediated ubiquitination and degradation, suggesting that USPD occurs primarily in the cytoplasm.
    [Show full text]
  • Ubiquitination Is Not Omnipresent in Myeloid Leukemia Ramesh C
    Editorials Ubiquitination is not omnipresent in myeloid leukemia Ramesh C. Nayak1 and Jose A. Cancelas1,2 1Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center and 2Hoxworth Blood Center, University of Cincinnati Academic Health Center, Cincinnati, OH, USA E-mail: JOSE A. CANCELAS - [email protected] / [email protected] doi:10.3324/haematol.2019.224162 hronic myelogenous leukemia (CML) is a clonal tination of target proteins through their cognate E3 ubiq- biphasic hematopoietic disorder most frequently uitin ligases belonging to three different families (RING, Ccaused by the expression of the BCR-ABL fusion HERCT, RING-between-RING or RBR type E3).7 protein. The expression of BCR-ABL fusion protein with The ubiquitin conjugating enzymes including UBE2N constitutive and elevated tyrosine kinase activity is suffi- (UBC13) and UBE2C are over-expressed in a myriad of cient to induce transformation of hematopoietic stem tumors such as breast, pancreas, colon, prostate, lym- cells (HSC) and the development of CML.1 Despite the phoma, and ovarian carcinomas.8 Higher expression of introduction of tyrosine kinase inhibitors (TKI), the dis- UBE2A is associated with poor prognosis of hepatocellu- ease may progress from a manageable chronic phase to a lar cancer.9 In leukemia, bone marrow (BM) cells from clinically challenging blast crisis phase with a poor prog- pediatric acute lymphoblastic patients show higher levels nosis,2 in which myeloid or lymphoid blasts fail to differ- of UBE2Q2
    [Show full text]
  • Figure S1. DMD Module Network. the Network Is Formed by 260 Genes from Disgenet and 1101 Interactions from STRING. Red Nodes Are the Five Seed Candidate Genes
    Figure S1. DMD module network. The network is formed by 260 genes from DisGeNET and 1101 interactions from STRING. Red nodes are the five seed candidate genes. Figure S2. DMD module network is more connected than a random module of the same size. It is shown the distribution of the largest connected component of 10.000 random modules of the same size of the DMD module network. The green line (x=260) represents the DMD largest connected component, obtaining a z-score=8.9. Figure S3. Shared genes between BMD and DMD signature. A) A meta-analysis of three microarray datasets (GSE3307, GSE13608 and GSE109178) was performed for the identification of differentially expressed genes (DEGs) in BMD muscle biopsies as compared to normal muscle biopsies. Briefly, the GSE13608 dataset included 6 samples of skeletal muscle biopsy from healthy people and 5 samples from BMD patients. Biopsies were taken from either biceps brachii, triceps brachii or deltoid. The GSE3307 dataset included 17 samples of skeletal muscle biopsy from healthy people and 10 samples from BMD patients. The GSE109178 dataset included 14 samples of controls and 11 samples from BMD patients. For both GSE3307 and GSE10917 datasets, biopsies were taken at the time of diagnosis and from the vastus lateralis. For the meta-analysis of GSE13608, GSE3307 and GSE109178, a random effects model of effect size measure was used to integrate gene expression patterns from the two datasets. Genes with an adjusted p value (FDR) < 0.05 and an │effect size│>2 were identified as DEGs and selected for further analysis. A significant number of DEGs (p<0.001) were in common with the DMD signature genes (blue nodes), as determined by a hypergeometric test assessing the significance of the overlap between the BMD DEGs and the number of DMD signature genes B) MCODE analysis of the overlapping genes between BMD DEGs and DMD signature genes.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • UBE2B (HR6B) [Untagged] E2 – Ubiquitin Conjugating Enzyme
    UBE2B (HR6B) [untagged] E2 – Ubiquitin Conjugating Enzyme Alternate Names: HHR6B, HR6B, RAD6B, Ubiquitin carrier protein B, Ubiquitin protein ligase B Cat. No. 62-0004-100 Quantity: 100 µg Lot. No. 1456 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- GPLGSSTPARRRLMRDFKRLQEDPPVGVS ber of cellular processes including Source: E. coli expression GAPSENNIMQWNAVIFGPEGTPFEDGT regulated and targeted proteasomal FKLVIEFSEEYPNKPPTVRFLSKMFHPNVY degradation of substrate proteins. Quantity: 100 μg ADGSICLDILQNRWSPTYDVSSILTSIQSLL DEPNPNSPANSQAAQLYQENKREYEKRV Three classes of enzymes are in- Concentration: 1 mg/ml SAIVEQSWNDS volved in the process of ubiquitylation; 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 of the purification tag. (E3s). UBE2B is a member of the E2 dithiothreitol, 10% glycerol UBE2B (regular text): Start bold italics (amino acid residues ubiquitin-conjugating enzyme family 2-152) and cloning of the human gene was Molecular Weight: ~17 kDa Accession number: NP_003328 first described by Koken et al. (1991). UBE2B shares 70% identity with its Purity: >98% by InstantBlue™ SDS-PAGE yeast homologue but lacks the acidic Stability/Storage: 12 months at -70˚C; C-terminal domain. The ring finger aliquot as required proteins RAD5 and RAD18 interact with UBE2B and other members of the RAD6 pathway (Notenboom et al., Quality Assurance 2007; Ulrich and Jentsch, 2000). In complex UBE2B and RAD18 trigger Purity: Protein Identification: replication fork stalling at DNA dam- 4-12% gradient SDS-PAGE Confirmed by mass spectrometry InstantBlue™ staining age sites during the post replicative Lane 1: MW markers E2-Ubiquitin Thioester Loading Assay: repair process (Tsuji et al., 2008).
    [Show full text]
  • RING-Type E3 Ligases: Master Manipulators of E2 Ubiquitin-Conjugating Enzymes and Ubiquitination☆
    Biochimica et Biophysica Acta 1843 (2014) 47–60 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbamcr Review RING-type E3 ligases: Master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination☆ Meredith B. Metzger a,1, Jonathan N. Pruneda b,1, Rachel E. Klevit b,⁎, Allan M. Weissman a,⁎⁎ a Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, 1050 Boyles Street, Frederick, MD 21702, USA b Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195, USA article info abstract Article history: RING finger domain and RING finger-like ubiquitin ligases (E3s), such as U-box proteins, constitute the vast Received 5 March 2013 majority of known E3s. RING-type E3s function together with ubiquitin-conjugating enzymes (E2s) to medi- Received in revised form 23 May 2013 ate ubiquitination and are implicated in numerous cellular processes. In part because of their importance in Accepted 29 May 2013 human physiology and disease, these proteins and their cellular functions represent an intense area of study. Available online 6 June 2013 Here we review recent advances in RING-type E3 recognition of substrates, their cellular regulation, and their varied architecture. Additionally, recent structural insights into RING-type E3 function, with a focus on im- Keywords: RING finger portant interactions with E2s and ubiquitin, are reviewed. This article is part of a Special Issue entitled: U-box Ubiquitin–Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf. Ubiquitin ligase (E3) Published by Elsevier B.V. Ubiquitin-conjugating enzyme (E2) Protein degradation Catalysis 1.
    [Show full text]
  • Supplementary Material DNA Methylation in Inflammatory Pathways Modifies the Association Between BMI and Adult-Onset Non- Atopic
    Supplementary Material DNA Methylation in Inflammatory Pathways Modifies the Association between BMI and Adult-Onset Non- Atopic Asthma Ayoung Jeong 1,2, Medea Imboden 1,2, Akram Ghantous 3, Alexei Novoloaca 3, Anne-Elie Carsin 4,5,6, Manolis Kogevinas 4,5,6, Christian Schindler 1,2, Gianfranco Lovison 7, Zdenko Herceg 3, Cyrille Cuenin 3, Roel Vermeulen 8, Deborah Jarvis 9, André F. S. Amaral 9, Florian Kronenberg 10, Paolo Vineis 11,12 and Nicole Probst-Hensch 1,2,* 1 Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; [email protected] (A.J.); [email protected] (M.I.); [email protected] (C.S.) 2 Department of Public Health, University of Basel, 4001 Basel, Switzerland 3 International Agency for Research on Cancer, 69372 Lyon, France; [email protected] (A.G.); [email protected] (A.N.); [email protected] (Z.H.); [email protected] (C.C.) 4 ISGlobal, Barcelona Institute for Global Health, 08003 Barcelona, Spain; [email protected] (A.-E.C.); [email protected] (M.K.) 5 Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain 6 CIBER Epidemiología y Salud Pública (CIBERESP), 08005 Barcelona, Spain 7 Department of Economics, Business and Statistics, University of Palermo, 90128 Palermo, Italy; [email protected] 8 Environmental Epidemiology Division, Utrecht University, Institute for Risk Assessment Sciences, 3584CM Utrecht, Netherlands; [email protected] 9 Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College, SW3 6LR London, UK; [email protected] (D.J.); [email protected] (A.F.S.A.) 10 Division of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; [email protected] 11 MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, W2 1PG London, UK; [email protected] 12 Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy * Correspondence: [email protected]; Tel.: +41-61-284-8378 Int.
    [Show full text]
  • Thermal Manipulation of the Chicken Embryo Triggers Differential Gene
    Loyau et al. BMC Genomics (2016) 17:329 DOI 10.1186/s12864-016-2661-y RESEARCH ARTICLE Open Access Thermal manipulation of the chicken embryo triggers differential gene expression in response to a later heat challenge Thomas Loyau1, Christelle Hennequet-Antier1, Vincent Coustham1, Cécile Berri1, Marie Leduc1, Sabine Crochet1, Mélanie Sannier1, Michel Jacques Duclos1, Sandrine Mignon-Grasteau1, Sophie Tesseraud1, Aurélien Brionne1, Sonia Métayer-Coustard1, Marco Moroldo2, Jérôme Lecardonnel2, Patrice Martin3, Sandrine Lagarrigue4, Shlomo Yahav5 and Anne Collin1* Abstract Background: Meat type chickens have limited capacities to cope with high environmental temperatures, this sometimes leading to mortality on farms and subsequent economic losses. A strategy to alleviate this problem is to enhance adaptive capacities to face heat exposure using thermal manipulation (TM) during embryogenesis. This strategy was shown to improve thermotolerance during their life span. The aim of this study was to determine the effects of TM (39.5 °C, 12 h/24 vs 37.8 °C from d7 to d16 of embryogenesis) and of a subsequent heat challenge (32 °C for 5 h) applied on d34 on gene expression in the Pectoralis major muscle (PM). A chicken gene expression microarray (8 × 60 K) was used to compare muscle gene expression profiles of Control (C characterized by relatively high body temperatures, Tb) and TM chickens (characterized by a relatively low Tb) reared at 21 °C and at 32 °C (CHC and TMHC, respectively) in a dye-swap design with four comparisons and 8 broilers per treatment. Real-time quantitative PCR (RT-qPCR) was subsequently performed to validate differential expression in each comparison.
    [Show full text]
  • 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.
    [Show full text]
  • Analysis of Interleukin- 1B-Modulated Mrna Gene Transcription in Human
    J Periodont Res 2006; 41; 426–446 Copyright Ó Blackwell Munksgaard Ltd All rights reserved JOURNAL OF PERIODONTAL RESEARCH doi:10.1111/j.1600-0765.2006.00884.x T. Steinberg1, B. Dannewitz2, Analysis of interleukin- P. Tomakidi1, J. D. Hoheisel3, E. Mssig1, A. Kohl1, M. Nees4 1Department of Orthodontics and Dentofacial 1b-modulated mRNA gene Orthopedics, Dental School, 2Section of Periodontology, Department of Operative Dentistry and Periodontology, Dental School, University of Heidelberg, Im Neuenheimer Feld transcription in human 3 400, 69129 Heidelberg, Germany, Deutsches Krebsforschungszentrum, Division of Functional Genome Analysis, Im Neuenheimer Feld 506, gingival keratinocytes by 69120 Heidelberg, Germany and 4VTT Biotechnology, Itinen Pitkkatu 4, PO Box 106, FIN-20521 Turku, Finland epithelia-specific cDNA The first two authors have contributed microarrays equally to the manuscript. Steinberg T, Dannewitz B, Tomakidi P, Hoheisel JD, Mu¨ssig E, Kohl A, Nees M. Analysis of interleukin-1b-modulated mRNA gene transcription in human gingival keratinocytes by epithelia-specific cDNA microarrays. J Periodont Res 2006; 41: 426–446. Ó Blackwell Munksgaard 2006. Background/objectives: Proinflammatory cytokines such as interleukin-1b are known to be synthesized in oral gingivitis and periodontitis and lead to the acti- vation of the transcription factor nuclear factor-jB (NF-jB). Although numerous effects of interleukin-1b on mesenchymal cells are known, e.g. up-regulation of intercellular adhesion moelcule-1 in endothelial cells, little is known of the effects of interleukin-1b on oral keratinocytes. The purpose of the present study was to seek interleukin-1b-mediated alterations in mRNA gene transcription and a putative activation of NF-jB in oral gingival keratinocytes.
    [Show full text]
  • Cascade Profiling of the Ubiquitin-Proteasome System in Cancer Anastasiia Rulina
    Cascade profiling of the ubiquitin-proteasome system in cancer Anastasiia Rulina To cite this version: Anastasiia Rulina. Cascade profiling of the ubiquitin-proteasome system in cancer. Agricultural sciences. Université Grenoble Alpes, 2015. English. NNT : 2015GREAV028. tel-01321321 HAL Id: tel-01321321 https://tel.archives-ouvertes.fr/tel-01321321 Submitted on 25 May 2016 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. THÈSE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITÉ GRENOBLE ALPES Spécialité : Biodiversite du Developpement Oncogenese Arrêté ministériel : 7 août 2006 Présentée par Anastasiia Rulina Thèse dirigée par Maxim Balakirev préparée au sein du Laboratoire BIOMICS dans l'École Doctorale Chimie et Sciences du Vivant Profilage en cascade du système ubiquitine- protéasome dans le cancer Thèse soutenue publiquement le «17/12/2015», devant le jury composé de : M. Damien ARNOULT Docteur CR1, CNRS, Rapporteur M. Matthias NEES Professor Adjunct, University of Turku, Rapporteur M. Philippe SOUBEYRAN Docteur, INSERM, Membre Mme. Jadwiga CHROBOCZEK Directeur de recherche DR1, CNRS, Membre M. Xavier GIDROL Directeur de laboratoire, CEA, Président du jury M. Maxim BALAKIREV Docteur, CEA, Membre, Directeur de Thèse 2 Я посвящаю эту научную работу моей маме, Рулиной Людмиле Михайловне, с любовью и благодарностью.
    [Show full text]
  • Integrative Approach Using Liver and Duodenum RNA-Seq Data Identifies
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE www.nature.com/scientificreportsprovided by IRTA Pubpro OPEN Integrative approach using liver and duodenum RNA-Seq data identifes candidate genes and pathways Received: 30 August 2017 Accepted: 21 December 2017 associated with feed efciency in Published: xx xx xxxx pigs Yuliaxis Ramayo-Caldas 1, Maria Ballester1, Juan Pablo Sánchez1, Olga González- Rodríguez1, Manuel Revilla 2,3, Henry Reyer4, Klaus Wimmers 4,5, David Torrallardona 6 & Raquel Quintanilla1 This study aims identifying candidate genes and pathways associated with feed efciency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through diferential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 diferentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern. Four modules, one in liver (with 444 co-expressed genes) and three in duodenum (gathering 37, 126 and 41 co- expressed genes), were signifcantly associated with FE indicators. Intra-module analyses revealed tissue-specifc candidate genes; 12 of these genes were also identifed as DE between individuals with high and low RFI. Pathways enriched by the list of genes showing DE and/or belonging to FE co-expressed modules included response to oxidative stress, infammation, immune response, lipid metabolism and thermoregulation. Low overlapping between genes identifed in duodenum and liver tissues was observed but heat shock proteins were associated to FE in both tissues.
    [Show full text]