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The Ubiquitin Code

  • Book
  • © 2023

Overview

Editors:
  1. Manuel S Rodriguez

    1. LCC-UPR 8241-CNRS Equipe M, Laboratoire de Chimie de Coordination, Toulouse, France

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    You can also search for this editor in PubMed   Google Scholar

  2. Rosa Barrio

    1. CIC bioGUNE, Derio, Spain

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2602)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Chain Diversity

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Thioester and Oxyester Linkages in the Ubiquitin System

      • Alba Ferri-Blazquez, Ernst Jarosch, Thomas Sommer
      Pages 3-18

    3. Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions

      • Anita Waltho, Thomas Sommer
      Pages 19-38

  3. Ub and UbL Chemical Tools

    1. Front Matter

      Pages 39-39
      Download chapter PDF

    2. Chemical Synthesis of Non-hydrolyzable Ubiquitin(-Like) Hybrid Chains

      • David A. Pérez Berrocal, Gerbrand J. van der Heden van Noort, Monique P. C. Mulder
      Pages 41-49

    3. Total Linear Chemical Synthesis of LC3A and LC3B

      • Yara Huppelschoten, Jens Buchardt, Thomas Eiland Nielsen, Gerbrand J. van der Heden van Noort
      Pages 51-61

  4. Methods to Study Ubiquitin Conjugating Enzymes (E3s)

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. A Microbead-Based Flow Cytometry Assay to Assess the Activity of Ubiquitin and Ubiquitin-Like Conjugating Enzymes

      • Clara Recasens-Zorzo, Pierre Gâtel, Frédérique Brockly, Guillaume Bossis
      Pages 65-79

    3. Monitoring HECT Ubiquitination Activity In Vitro

      • Vincenzo Taibi, Simona Polo, Elena Maspero
      Pages 81-92

  5. Methods to Study DUBs

    1. Front Matter

      Pages 93-93
      Download chapter PDF

    2. RNAi-Based Screening for the Identification of Specific Substrate-Deubiquitinase Pairs

      • Nagore Elu, Natalia Presa, Ugo Mayor
      Pages 95-105

    3. Strategies for Monitoring “Ubiquitin C-Terminal Hydrolase 1” (Yuh1) Activity

      • Shahaf Saad, Eden Berda, Yuval Klein, Suha Issa, Elah Pick
      Pages 107-122

  6. Methods to Identify New Targets and Regulators

    1. Front Matter

      Pages 123-123
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    2. Isolation and Mass Spectrometry Identification of K48 and K63 Ubiquitin Proteome Using Chain-Specific Nanobodies

      • Maria Gonzalez-Santamarta, Laurie Ceccato, Ana Sofia Carvalho, Jean-Christophe Rain, Rune Matthiesen, Manuel S. Rodriguez
      Pages 125-136

    3. A Mass Spectrometry-Based Strategy for Mapping Modification Sites for the Ubiquitin-Like Modifier NEDD8

      • Caio A. B. Oliveira, Ekaterina Isaakova, Petra Beli, Dimitris P. Xirodimas
      Pages 137-149

    4. Isolation of the Hepatic Ubiquitome/NEDDylome by Streptavidin Pull-Down Assay in the Biotinylated Ubiquitin (bioUb)/Biotinylated NEDD8 (bioNEDD8) Transgenic Mice

      • Marina Serrano-Maciá, Teresa Cardoso Delgado, María Luz Martínez-Chantar
      Pages 151-162

    5. The Lambda Display Technology: A Useful Tool for the Identification of Ubiquitin-and Ubiquitin-Like-Binding Domains

      • Elena Santonico
      Pages 163-175

    6. SUMO-ID: A Strategy for the Identification of SUMO-Dependent Proximal Interactors

      • Orhi Barroso-Gomila, Ugo Mayor, Rosa Barrio, James D. Sutherland
      Pages 177-189

    7. Analysis of ATG8 Family Members Using LC3-Interacting Regions (LIR)-Based Molecular Traps

      • Grégoire Quinet, Pierre Génin, Naima Belgareh-Touzé, Oznur Ozturk, Robert Weil, Mickael M. Cohen et al.
      Pages 191-204
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Keywords

About this book

This volume details novel and popular approaches to decipher the Ubiquitin Code. Chapters guide readers through ubiquitin chain complexity, methods to generate non-hydrolysable ubiquitin-NEDD8, a fully synthetic method for the linear synthesis of fluorescently labelled rhodamine LC3A and LC3B, a HECT ligase-mediated ubiquitylation in vitro, a RNAi-based screening to identify DUBs, a Yuh1 activity assay, a pull-down to isolate K48 and K63 chains using specific nanobodies, identification of NeDDylated protein based in a NEDD8R74K mutant, in vivo identification of NEDDylated proteins from liver diseases, UbL-ID method to identify ubiquitin-like modified proteins, a LC3/GABARAP capturing system, and methods to isolate peptides that are closely associated with proteasomes or trapped inside the core particle of proteasomes in eukaryotic cells, among others. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, The Ubiquitin Code aims to to be a useful practical guide to researches to help further their study in this field. 

Editors and Affiliations

  • LCC-UPR 8241-CNRS Equipe M, Laboratoire de Chimie de Coordination, Toulouse, France

    Manuel S Rodriguez

  • CIC bioGUNE, Derio, Spain

    Rosa Barrio

Bibliographic Information

  • Book Title: The Ubiquitin Code

  • Editors: Manuel S Rodriguez, Rosa Barrio

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2859-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2858-4Published: 30 November 2022

  • Softcover ISBN: 978-1-0716-2861-4Published: 30 November 2023

  • eBook ISBN: 978-1-0716-2859-1Published: 29 November 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 245

  • Number of Illustrations: 9 b/w illustrations, 36 illustrations in colour

  • Topics: Chemistry/Food Science, general, Cell Biology

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