Conjugation and Deconjugation of Ubiquitin Family Modifiers (eBook)

MARCUS GROETTRUP is a Professor for Immunology in the Department of Biology of Konstanz University in Germany. His main interests are in the role of the immunoproteasome in antigen fragmentation and autoimmunity. Moreover, he has studied the function and conjugation of the ubiquitin‑like protein FAT10. He studied biochemistry in Tübingen and ET H Zürich and did his diploma thesis in the laboratory of H. Hengartner and R. Zinkernagel. During his PhD at the Basel Institute for Immunology with H. von Boehmer he discovered the pre T cell receptor. After habilitation at Humboldt University Berlin in the group of P‑M. Kloetzel on the topic of antigen processing he founded his own group at the Cantonal Hospital St. Gallen, Switzerland. Since 2002 he holds the Chair of Immunology at the University of Konstanz, Germany. Several prizes were awarded to Dr. Groettrup like the Award of the Sandoz Foundation for Therapeutic Research, the Karl Lohmann Prize of the German Society for Biological Chemistry, the Langener Science Prize of the Paul Ehrlich Institute, and the Research Award by the CaP CURE foundation.

Title Page 3
Copyright Page 4
INTERNATIONAL ADVISORY EDITORIAL BOARD 5
DEDICATION 6
ABOUT THE EDITOR... 7
Table of Contents 8
LIST OF CONTRIBUTORS 10
PREFACE 14
References 16
CHAPTER 1 ACTIVATION OF UBIQUITIN AND UBIQUITIN-LIKE PROTEINS 18
INTRODUCTION 18
GENERAL MECHANISM OF CONJUGATION 19
CO-EVOLUTION OF E1 AND UBIQUITIN 20
EVERALL STRUCTURAL TOPOLOGY OF E1 21
TERNARY COMPLEX FORMATION 24
RECOGNITION OF THE UBIQUITIN-LIKE PROTEIN 25
E1 THIOLESTER FORMATION 28
E2 TRANSTHIOLATION 28
CONCLUSION 30
REFERENCES 31
CHAPTER 2 CONTROL OF UBIQUITIN CONJUGATION BY Cdc48 AND ITS COFACTORS 34
INTRODUCTION 34
Cdc48 COFACTORS 36
N Domain Binding Cofactors 36
Carboxy Terminus Binding Cofactors 37
Substrate-Recruiting and Substrate-Processing Cofactors 38
CONTROL OF UBIQUITYLATION STATE BY SUBSTRATE-PROCESSING COFACTORS 39
Cofactors with E3/E4 Ubiquitin Ligase Activity 39
Cofactors with Deubiquitylation Activity 42
COMBINED ACTION OF E3/E4 AND DUB SUBSTRATE-PROCESSING COFACTORS 43
CONCLUSION AND FUTURE PERSPECTIVES 44
REFERENCES 44
CHAPTER 3 REGULATION OF UBIQUITIN RECEPTORS BY COUPLED MONOUBIQUITINATION 48
UBIQUITINATION 48
UB-RECEPTORS ARE EQUIPPED WITH UB-BINDING DOMAINS (UBDs) 49
FUNCTIONAL CONSEQUENCES OF COUPLED MONOUBIQUITINATION 51
E3-DEPENDENT COUPLED MONOUBIQUITINATION 52
E3-INDEPENDENT COUPLED MONOUBIQUITINATION 55
CONCLUSION AND FUTURE PERSPECTIVES 55
REFERENCES 56
CHAPTER 4 CONTROL OF CULLIN-RING UBIQUITIN LIGASE ACTIVITY BY Nedd8 58
THE UBIQUITIN-PROTEASOME SYSTEM 58
CULLIN-RING UBIQUITIN LIGASES 59
General Principles of CRL Organization 59
Recruitment of E2 Enzymes by CRLs 60
Substrate Recruitment to CRLs 62
MECHANISM AND REGULATION OF CRLs 62
CRLs Are Activated by Nedd8 Conjugation 63
Nedd8 Conjugation Causes a Major Conformational Change in Cul5 64
DECONJUGATION OF Nedd8 BY THE COP9-SIGNALOSOME (CSN) 65
COP9-Signalosome Defines a Novel Class of Metalloproteases 66
COP9-Signalosome as a Regulator of Human Disease 66
CONCLUSION AND FUTURE PERSPECTIVES 67
Other Functions for the Nedd8 Regulatory System 67
The Nedd8 Pathway as a Target for Therapeutic Intervention 68
Unresolved Questions 68
REFERENCES 69
CHAPTER 5 CONTROL OF DENEDDYLATION BY THE COP9 SIGNALOSOME 74
INTRODUCTION 74
THE NEDDYLATION-DENEDDYLATION SYSTEM AND ITS PHYSIOLOGICAL SIGNIFICANCE 75
TARGETS OF NEDDYLATION AND THEIR FUNCTIONS 77
Nedd8 as a Positive Regulator of Cullin-Ring Ub Ligases 77
THE DIVERSITY OF DENEDDYLASES 78
Den1, a Dual Functional Peptidase 78
Further Deneddylases 79
THE CSN-MEDIATED DENEDDYLATION AND ITS FUNCTIONS 79
Supercomplexes and Deneddylation 79
The MPN+/JAMM Motif 79
REGULATION OF CSN-MEDIATED DENEDDYLATION 80
INVOLVEMENT OF THE CSN-MEDIATED DENEDDYLATION IN THE PATHOGENESIS OF DISEASES 81
CONCLUSION AND FUTURE PERSPECTIVES 81
REFERENCES 82
CHAPTER 6 MECHANISM, SPECIFICITY AND STRUCTURE OF THE DEUBIQUITINASES 86
INTRODUCTION 86
MECHANISMS OF DEUBIQUITINATION 88
Mechanism of Cys-Dependent DUBs 88
Mechanism of Metalloprotease DUBs 89
CONSIDERATIONS FOR DEUBIQUITINASE SPECIFICITY 89
Ubiquitin versus Ubiquitin-Like Protein Cleave 89
Isopeptide versus Peptide Bond Cleavage 90
Linkage Specificity within a Ubiquitin Chain 90
Exo- vs. Endo Activity within a Ubiquitin Chain 90
Chain Cleavage versus Substrate Deubiquitination 91
Sequence Specific Deubiquitination 91
Substrate Recognition and Specificity 91
THE FIVE HUMAN DUB FAMILIES 91
USP Domain DUBs 92
OTU Domain DUBs 94
UCH Domain DUBs 95
Josephin Domain DUBs 97
JAMM/MPN+ Domain DUBs 97
CONCLUSION AND FUTURE PERSPECTIVES 100
REFERENCES 101
CHAPTER 7 UBIQUITIN CONJUGATION AND DECONJUGATION IN NF-kB SIGNALING 105
INTRODUCTION 105
UBIQUITIN CONJUGATION ACTIVATES NF-kB SIGNALING 106
The Ubiquitin Proteasome System Dictates Nuclear Entry of NF-kB 106
Ubiquitin Chains Mediate IKK Activation 107
Ubiquitin Conjugation Bridges Upstream Receptors to the IKK Complex 107
UBIQUITIN DECONJUGATION TERMINATES NF-kB Signaling 110
CYLD Acts as a Pleiotropic DUB in NF-kB Signaling 110
A20 Balances NF-kB Signaling by an Ubiquitin Editing Mechanism 111
Other DUBs Implicated in the NF-kB Pathway 112
CONCLUSION AND FUTURE PERSPECTIVES 113
REFERENCES 113
CHAPTER 8 FUNCTIONS OF LINEAR UBIQUITIN CHAINS IN THE NF-kB PATHWAY Linear Polyubiquitin in NF-kB Signaling 117
IDENTIFICATION OF A UBIQUITIN LIGASE COMPLEX THAT SPECIFICALLY GENERATES HEAD-TO-TAIL LINEAR POLYUBIQUITIN CHAINS 118
LUBAC SPECIFICALLY ACTIVATES NF-kB 119
DISTINCT ROLES OF LINEAR POLYUBIQUITIN AND K63-LINKED POLYUBIQUITIN CHAINS IN TNF-a SIGNALING 120
THE MECHANISM UNDERLYING LUBAC-MEDIATED NF-kB ACTIVATION 121
ROLES OF K63-LINKED AND LINEAR UBIQUITIN CHAINS IN NF-kB ACTIVATION IN CELLS STIMULATED BY SIGNALS OTHER THAN TNF-a 121
CONCLUSION AND FUTURE PERSPECTIVES 122
REFERENCES 122
CHAPTER 9 ASSEMBLY OF K11-LINKED UBIQUITIN CHAINS BY THE ANAPHASE-PROMOTING COMPLEX 124
INTRODUCTION 124
K11-LINKED UBIQUITIN CHAINS TARGET PROTEINS FOR DEGRADATION BY THE PROTEASOME 126
ASSEMBLY OF K11-LINKED UBIQUITIN CHAINS BY THE APC/C 126
Initiation of K11-Linked Ubiquitin Chain Formation 126
Elongation of K11-Linked Ubiquitin Chains 128
WHAT IS SPECIAL ABOUT K11-LINKED CHAINS? 129
CONCLUSION 130
REFERENCES 130
CHAPTER 10 UBIQUITIN FAMILY MEMBERS IN THE REGULATION OF THE TUMOR SUPPRESSOR p53 133
INTRODUCTION 133
p53 AND UBIQUITIN I: TARGETING p53 FOR DEGRADATION 135
p53 AND MDM2 137
p53 AND OTHER UBIQUITIN LIGASES 140
p53 AND VIRUSES 141
p53 AND UBIQUITIN II: NONPROTEOLYTIC UBIQUITINATION 142
p53 AND UBIQUITIN III: DEUBIQUITINATION 143
p53 AND NEDD8 144
p53 AND SUMO-1 145
CONCLUSION 146
REFERENCES 146
CHAPTER 11 UBIQUITYLATION IN THE ERAD PATHWAY 153
PROTEIN FOLDING, QUALITY CONTROL IN THE ER AND THE ERAD DEGRADATION SIGNAL 154
UBIQUITYLATION AND DEGRADATION OF ER-LUMENAL SUBSTRATES: THE HRD-DER LIGASE COMPLEX 156
UBIQUITYLATION AND DEGRADATION OF ER SUBSTRATES CONTAINING A MISFOLDED CYTOPLASMIC DOMAIN: THE UBIQUITIN LIGASE DOA10 159
MAMMALIAN E3S INVOLVED IN ERAD 159
CONCLUSION 160
REFERENCES 161
CHAPTER 12 PUPYLATION A Signal for Proteasomal Degradation in Mycobacterium tuberculosis 166
INTRODUCTION 166
DISCOVERY OF A BACTERIAL “UBIQUITIN-LIKE” MODIFIER 168
PUP CONJUGATION (“PUPYLATION”) 169
PUP DECONJUGATION (“DEPUPYLATION”) 171
CONCLUSION AND FUTURE PERSPECTIVES 172
REFERENCES 174
CHAPTER 13 SUMO CONTROL 175
INTRODUCTION 175
THE SUMO MODIFICATION CYCLE ALLOWS DIFFERENT LEVELS OF REGULATION 176
REGULATING THE SUBSTRATE 178
REGULATING SUMO 178
REGULATING THE E1 ACTIVATING ENZYME 179
REGULATING THE E2 CONJUGATING ENZYME 179
REGULATING THE E3 LIGASES 179
REGULATING THE SUMO SPECIFIC PROTEASES 181
CONCLUSION AND FUTURE PERSPECTIVES 182
REFERENCES 183
CHAPTER 14 THE IN VIVO FUNCTIONS OF DESUMOYLATING ENZYMES 187
INTRODUCTION TO THE SUMO-SPECIFIC PROTEASE FAMILY 187
C-TERMINAL HYDROLASE ACTIVITY 189
ISOPEPTIDASE ACTIVITY 190
Subcellular Localization 190
Level of Expression 191
GENE TRANSCRIPTION AND mRNA PROCESSING 192
CELL CYCLE AND CELL GROWTH 195
ROLE IN DEVELOPMENT 196
CONTRIBUTION TO PATHOPHYSIOLOGICAL CONDITIONS 196
CONCLUSION AND CURRENT PERSPECTIVE 198
REFERENCES 198
CHAPTER 15 REGULATORY FUNCTIONS OF UBIQUITIN AND SUMO IN DNA REPAIR PATHWAYS 201
MECHANISMS OF UBIQUITIN AND SUMO CONJUGATION 201
UBIQUITIN AND SUMO AS KEY REGULATORS OF DNA REPAIR PATHWAYS 203
A SUMO-UBIQUITIN SWITCH ON PCNA 203
AN INTRAMOLECULAR SUMO/SIM-MEDIATED INTERACTION CONTROLS A CRITICAL STEP OF BASE EXCISION REPAIR 205
A UBIQUITYLATION CASCADE FOR THE ASSEMBLY OF DNA REPAIR COMPLEXES OF CHROMATING 205
SUMO-DEPENDENT SUBNUCLEAR COMPARTMENTALIZATION OF DOUBLE-STRAND BREAKS AND TELOMERES 208
CONCLUSION AND FUTURE PERSPECTIVES 210
REFERENCES 210
CHAPTER 16 SUMOYLATION AS A SIGNAL FOR POLYUBIQUITYLATION AND PROTEASOMAL DEGRADATION 212
INTRODUCTION 212
FUNCTIONAL INTERACTIONS OF SUMOYLATED PROTEINS AND THEIR REGULATION 215
SUMO INTERACTION MOTIFS (SIM) 218
PROTEASOMAL DEGRADATION OF SUMO CONJUGATES 219
UBIQUITIN LIGASES RECOGNIZING SUMOYLATED PROTEINS IN S. CEREVISIAE 220
PROPERTIES AND FUNCTIONS OF Slx5-Slx8 220
PROPERTIES AND FUNCTIONS OF Uls1-Ris1 223
SUMO TARGETED UBIQUITIN LIGASE Rfp1,2-Slx8 IN SCHIZOSACCHAROMYCES POMBE 224
MAMMALIAN SUMO TARGETED UBIQUITIN LIGASE RNF4 224
REGULATION OF PML BY RNF4-MEDIATED SUMO-DEPENDENT PROTEOLYSIS 225
POSSIBLE TARGETS OF ATO LEADING TO DEGRADATION OF PML 226
SUMO-DEPENDENT REGULATION OF HIF1a 227
CONCLUSION 227
REFERENCES 228
CHAPTER 17 IN VIVO FUNCTIONS OF ISGYLATION 232
INTRODUCTION 232
IN VIVO ANALYSIS OF THE ISGYLATION SYSTEM 234
ISGYLATION AND CANCER 238
MOLECULAR MECHANISMS 239
ISGylation of Proteins Causing Altered Function or Stability of the Target Substrate 240
Competition with Ubiquitin Modification 240
Functions Mediated by Unconjugated ISG15 241
CONCLUSION AND FUTURE PERSPECTIVES 241
REFERENCES 242
CHAPTER 18 IDENTIFICATION AND VALIDATION OF ISG15 TARGET PROTEINS 245
INTRODUCTION 245
DETECTION OF ISG15 CONJUGATION 248
IDENTIFICATION OF ISG15 TARGETS 249
VALIDATION OF ISG15 TARGETS 250
THE EFFECTS OF ISGYLATION OF TARGET PROTEIN FUNCTION 251
CONCLUSION 252
REFERENCES 253
CHAPTER 19 FAT10 Activated by UBA6 and Functioning in Protein Degradation 255
INTRODUCTION 255
E1 ENZYMES AND THE ACTIVATION MECHANISM 257
UBA6: AN ACTIVATING ENZYME OF UBIQUITIN AND FAT10 257
FAT10: A MEMBER OF THE UBIQUITIN-LIKE PROTEIN FAMILY 258
THE ROLE OF FAT10 IN PROTEIN DEGRADATION 260
CONCLUSION AND FUTURE PERSPECTIVES 260
REFERENCES 261
INDEX 264