Drawing on the combined knowledge of the world's leading protein degradation experts, this handy reference compiles information on the proteasome-mediated degradation steps of the ubiquitin pathway. In addition to proteasomal function and regulation, it also presents the latest results on novel members of the ubiquitin superfamily and their role in cellular regulation.
Further volumes in the series cover the function of ubiquitin-protein ligases, and the roles of the ubiquitin pathway in regulating key cellular processes, as well as its pathophysiological disease states.
Required reading for molecular biologists, cell biologists and physiologists with an interest in protein degradation.
Aaron Ciechanover obtained his MD from the Hebrew University in Jerusalem (Israel), and his PhD from the Technion-Israel Institute of Technology in Haifa, where he is presently serving as Professor of Biochemistry. Professor Ciechanover is known for his discovery of the first ubiquitin system mutant cell, demonstrating the role of the ubiquitin-proteasome proteolytic system in protein degradation in vivo. In 2004, he has received the Nobel Prize in Chemistry for his ground-breaking work on the ubiquitin-proteasome system.
Martin Rechsteiner is Professor of Biochemistry at the University of Utah in Salt Lake City (USA). He is interested in the proteasome component of the ubiquitin-proteasome pathway. He has identified several key regulators of proteasome function and is currently working on their structural and functional elucidation.
List of Contributors.
1 Molecular Chaperones and the Ubiquitin–Proteasome System (Cam Patterson and J&ounl;rg Höhfeld).
1.1 Introduction.
1.2 A Biomedical Perspective.
1.3 Molecular Chaperones: Mode of Action and Cellular Functions.
1.4 Chaperones: Central Players During Protein Quality Control.
1.5 Chaperones and Protein Degradation.
1.6 The CHIP Ubiquitin Ligase: A Link Between Folding and Degradation Systems.
1.7 Other Proteins That May Influence the Balance Between Chaperoneassisted Folding and Degradation.
1.8 Further Considerations.
1.9 Conclusions.
References.
2 Molecular Dissection of Autophagy in the Yeast Saccharomyces cerevisiae (Yoshinori Ohsumi).
2.1 Introduction.
2.2 Vacuoles as a Lytic Compartment in Yeast.
2.3 Discovery of Autophagy in Yeast.
2.4 Genetic Dissection of Autophagy.
2.5 Characterization of Autophagy-defective Mutants.
2.6 Cloning of ATG Genes.
2.7 Further Genes Required for Autophagy.
2.8 Selectivity of Proteins Degraded.
2.9 Induction of Autophagy.
2.10 Membrane Dynamics During Autophagy.
2.11 Monitoring Methods of Autophagy in the Yeast S. cerevisiae.
2.12 Function of Atg Proteins.
2.13 Site of Atg Protein Functioning: The Pre-autophagosomal Structure.
2.14 Atg Proteins in Higher Eukaryotes.
2.15 Atg Proteins as Markers for Autophagy in Mammalian Cells.
2.16 Physiological Role of Autophagy in Multicellular Organisms.
2.17 Perspectives.
References.
3 Dissecting Intracellular Proteolysis Using Small Molecule Inhibitors and Molecular Probes (Huib Ovaa, Herman S. Overkleeft, Benedikt M. Kessler, and Hidde L. Ploegh).
3.1 Introduction.
3.2 The Proteasome as an Essential Component of Intracellular Proteolysis.
3.3 Proteasome Structure, Function, and Localization.
3.4 Proteasome Inhibitors as Tools to Study Proteasome Function.
3.5 Assessing the Biological Role of the Proteasome With Inhibitors and Probes.
3.6 Proteasome-associated Components: The Role of N-glycanase.
3.7 A Link Between Proteasomal Proteolysis and Deubiquitination.
3.8 Future Developments and Final Remarks.
Acknowledgments.
Abbreviations.
References.
4 MEKK1: Dual Function as a Protein Kinase and a Ubiquitin Protein Ligase (Zhimin Lu and Tony Hunter).
4.1 Introduction.
4.2 Types of Protein Kinases.
4.3 Functions of Protein Kinases.
4.4 Conclusions.
References.
5 Proteasome Activators (Andreas Förster and Christopher P. Hill).
5.1 Introduction.
5.2 11S Activators: Sequence and Structure.
5.3 PA26–Proteasome Complex Structures.
5.4 Biological Roles of 11S Activators.
5.5 PA200/Blm10p.
5.6 Concluding Remarks and Future Challenges.
References.
6 The Proteasome Portal and Regulation of Proteolysis (Monika Bajorek and Michael H. Glickman).
6.1 Background.
6.2 The Importance of Channel Gating.
6.3 A Porthole into the Proteasome.
6.4 Facilitating Traffic Through the Gated Channel.
6.5 Summary: Consequences for Regulated Proteolysis.
References.
7 Ubiquity and Diversity of the Proteasome System (Keiji Tanaka, Hideki Yashiroda, and Shigeo Murata).
7.1 Introduction.
7.2 Catalytic Machine.
7.3 Regulatory Factors.
7.4 Proteasome Assembly.
7.5 Perspectives.
References.
8 Proteasome-Interacting Proteins (Jean E. O’Donoghue and Colin Gordon).
8.1 Introduction.
8.2 Regulators of the Holoenzyme and Chaperones Involved in Assembly of the Proteasome.
8.3 Enzymes Controlling Ubiquitination and Deubiquitination.
8.4 Shuttling Proteins: Rpn10/Pus1 and UBA-UBL Proteins.
8.5 Other UBL-Containing Proteins.
8.6 VCP/p97/cdc48.
8.7 Proteasome Interactions with Transcription, Translation and DNA Repair.
8.8 Concluding Remarks.
References.
9 Structural Studies of Large, Self-compartmentalizing Proteases (Beate Rockel, Jürgen Bosch, and Wolfgang Baumeister).
9.1 Self-compartmentalization: An Effective Way to Control Proteolysis.
9.2 ATP-dependent Proteases: The Initial Steps in the Proteolytic Pathway.
9.3 Beyond the Proteasome: ATP-independent Processing of Oligopeptides Released by the Proteasome.
9.4 Conclusions.
Acknowledgments.
References.
10 What the Archaeal PAN–Proteasome Complex and Bacterial ATP-dependent Proteases Can Teach Us About the 26S Proteasome (Nadia Benaroudj, David Smith, and Alfred L. Goldberg).
10.1 Introduction.
10.2 Archaeal 20S Proteasomes.
10.3 PAN the Archaeal Homologue of the 19S Complex.
10.4 VAT, a Potential Regulator of Proteasome Function.
10.5 The Use of PAN to Understand the Energy Requirement for Proteolysis.
10.6 Direction of Substrate Translocation.
10.7 Degradation of Polyglutamine-containing Proteins.
10.8 Eubacterial ATP-dependent Proteases.
10.9 How AAA ATPases Use ATP to Catalyze Proteolysis.
10.10 Conclusions.
Acknowledgments.
References.
11 Biochemical Functions of Ubiquitin and Ubiquitin-like Protein Conjugation (Mark Hochstrasser).
Abstract.
11.1 Introduction.
11.2 Ubls: A Typical Modification Cycle by an Atypical Set of Modifiers.
11.3 Origins of the Ubiquitin System.
11.4 Ubiquitin-binding Domains and Ubiquitin Receptors in the Proteasome Pathway.
11.5 Ubiquitin-binding Domains and Membrane Protein Trafficking.
11.6 Sumoylation and SUMO-binding Motifs.
11.7 General Biochemical Functions of Protein–Protein Conjugation.
11.8 Conclusions.
Acknowledgments.
References.
Index.
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