The Ubiquitin Code

ISBN-13: 9781071628584 / Angielski / Twarda / 2022 / 245 str.

Manuel S. Rodriguez; Rosa Barrio

Opis

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 NEDD8^R74K 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. 

Spis treści

Part I: Chain Diversity                                                         

1            Thioester and oxyester linkages in the ubiquitin system

Alba Ferri-Blazquez, Ernst Jarosch and Thomas Sommer

 

2            Getting to the root of branched ubiquitin chains: A review of current methods and functions

Anita Waltho, Thomas Sommer

 

 

Part II: Ub and UbL Chemical Tools                                                            

3            Chemical synthesis of non-hydrolysable Ubiquitin(-like) hybrid chains

David A. Pérez Berrocal, Gerbrand J. van der Heden van Noort and Monique P. C. Mulder

 

4            Total Linear Chemical Synthesis of LC3A and LC3B

Yara Huppelschoten, Jens Buchardt, Thomas Eiland Nielsen and Gerbrand J. van der Heden van Noort

 

 

Part III: Methods to study Conjugating enzymes (E3s)                                                    

5            A microbead-based flow cytometry assay to assess the activity of Ubiquitin and Ubiquitin-like conjugating enzymes

Clara Recasens-Zorzo, Pierre Gâtel, Frédérique Brockly and Guillaume Bossis

 

6            Monitoring HECT ubiquitination activity in vitro

Vincenzo Taibi, Simona Polo and Elena Maspero1    

 

 

Part IV: Methods to study DUBs                                                                 

7            RNAi-based screening for the identification of specific substrate-deubiquitinase pairs

Nagore Elu, Natalia Presa and Ugo Mayor

 

8            Strategies for monitoring ‘ubiquitin C-terminal hydrolase 1’ (Yuh1) activity

Shahaf Saad, Eden Berda, Yuval Klein, Suha Issa and Elah Pick

 

Part V: Methods to identify new targets and regulators                                                

9            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 and Manuel S. Rodriguez

 

10          A mass spectrometry-based strategy for mapping modification sites for the Ubiquitin-like modifier NEDD8

Caio A.B. Oliveira, Ekaterina Isaakova, Petra Beli and Dimitris P. Xirodimas        

 

11          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 and María Luz Martínez-Chantar

 

12          The Lambda display technology: a useful tool for the identification of ubiquitin and ubiquitin like-binding domains

Elena Santonico

 

13          SUMO-ID: a strategy for the identification of SUMO-dependent proximal interactors

Orhi Barroso-Gomila, Ugo Mayor, Rosa Barrio and James D. Sutherland

 

14          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, Renaud Legouis and Manuel S. Rodriguez

 

15          A computational tool for analysis of mass spectrometry data of ubiquitin enriched samples

Rune Matthiesen, Manuel S. Rodriguez, and Ana Sofia Carvalho

 

Part VI:  to measure proteasome activity                                                              

 

16          In-plate and in-gel assays for the assessment of proteasome activity in Caenorhabditis elegans

Eleni Panagiotidou, Anna Gioran and Niki Chondrogianni

 

17          Isolation of Proteasome-Trapped Peptides (PTPs) for degradome analysis

Indrajit Sahu, Manisha Priyadarsini Sahoo, Oded Kleifeld and Michael H. Glickman