Plant Proteostasis: Methods and Protocols

ISBN-13: 9781071627839 / Angielski / Twarda / 2022 / 415 str.

L. Maria Lois; Marco Trujillo

Opis

 This second edition compiles state-of-art protocols to study the molecular mechanisms that determine proteome composition and contribute to maintaining protein homeostasis. Chapters describe methods that range from the in vitro analysis of enzyme cascades to real-time in vivo studies. 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, Plant Proteostasis: Methods and Protocols, Second Edition aims to be a useful practical guide to researches to help further their study in this field. 

Spis treści

Part I: Ubiquitin Conjugation and Deconjugation Analysis

1. Observing real-time ubiquitination in high throughput with fluorescence polarization

Tyler G. Franklin and Jonathan N. Pruneda

 

2. Identification and Characterization of Physiological Pairing of E2 Ubiquitin-Conjugating-Enzymes and E3 Ubiquitin Ligases

Carla Brillada and Marco Trujillo

 

3. Immunoprecipitation of Cullin Ring Ligases (CRLs) in Arabidopsis thaliana seedlings 

Federica Casagrande and Giovanna Serino

 

4. An in vitro assay to recapitulate hormone-triggered & SCF-mediated protein ubiquitylation

Michael Niemeyer, Jhonny Oscar Figueroa Parra, and Luz Irina A. Calderón Villalobos

 

5. Analysis of proteasome-associated ubiquitin ligase activity

Zhishuo Wang, Beatriz Orosa-Puente, and Steven H. Spoel

 

6.Measuring the DUB Activity of Arabidopsis Deubiquitylating enzymes

Karin Vogel^, Marie-Kristin Nagel^, and Erika Isono

 

Part II: Sumo Conjugation and  Deconjugation

7. SUMO conjugation and SUMO chain formation by plant enzymes

Konstantin Tomanov, Jose Julian, Ionida Ziba, and Andreas Bachmair

 

8. Kinetic analysis of plant SUMO conjugation machinery

Laura Castaño-Miquel and L. Maria Lois

 

9. Expression, purification, and enzymatic analysis of plant SUMO proteases

Prakash Kumar Bhagat, Dipan Roy, and Ari Sadanandom

 

Part III: Analysis Of Autophagy

10. Monitoring autophagic flux in the model single-celled microalga Chlamydomonas reinhardtii

José L. Crespo and María Esther Pérez-Pérez

 

11. Detection of autophagy in plants by fluorescence microscopy

Yunting Pu and Diane C. Bassham

 

12. Characterization of ATG8-family interactors by Isothermal Titration Calorimetry

Lorenzo Picchianti, Arthur Sedivy, and Yasin Dagdas

 

Part IV: Protein Turnover and Stability

13. Protocols for studying protein stability in a Arabidopsis protoplast transient expression system

Séverine PLANCHAIS, Laurent CAMBORDE, and  Isabelle JUPIN

 

14. Relative Protein Lifetime Measurement in Plants using Tandem Fluorescent Protein Timers

Hongtao Zhang, Eric Linster, Markus Wirtz, and Frederica L. Theodoulou

15. Detection and Quantification of Protein Aggregates In Plants

Ujjal Jyoti Phukan, Simon Stael,Amanda Gonçalves, Frank Van Breusegem, and Núria S. Coll

 

16. Using intrinsic fluorescence to measure protein stability upon thermal and chemical denaturation

Nathalia Varejão and David Reverter

 

Part V:  Protein Isolation and Mass Spectrometric Analysis

17. Purification and detection of ubiquitinated plant proteins using Tandem Ubiquitin Binding Entities

DongHyuk Lee and Gitta Coaker

 

18. Titanium oxide-based phosphopeptide enrichment from Arabidopsis seedlings 

Sharon C. Mithoe and Frank L.H. Menke

 

19. Chloroplast Envelope Membrane Subfractionation from Arabidopsis and Pea

Annabel Dischinger and Serena Schwenkert

 

20. Chromatin Enrichment for Proteomics in Plants (ChEP-P)

Isabel Cristina Vélez-Bermúdez and Wolfgang Schmidt

 

21. Proximity-dependent in vivo Biotin Labeling for Interactome Mapping in Marchantia polymorpha

Katharina Melkonian, Sara Christina Stolze, Anne Harzen, and Hirofumi Nakagami

 

22. Tandem mass tag-based phospho-proteomics in plants

Isabel Cristina Vélez-Bermúdez, Dharmesh Jain, Arya Ravindran, Chin, Wen Chen, Chuan-Chih Hsu, and  Schmidt

 

Part VI : Study Of Proteasome and Proteases

23. Analysis of peptide hormone maturation and processing specificity using isotope-labeled peptides

Stefanie Brück, Jens Pfannstiel, Gwyneth Ingram, Annick Stintzi and Andreas Schaller

24. Improved identification of protease cleavage sites by in-gel reductive dimethylation

 

Stefanie Royek, Stefanie Brück, Jens Pfannstiel, Annick Stintzi and Andreas Schaller

25. A Pipeline to Monitor Proteasome Homeostasis in Plants

Gautier Langin and Suayib Üstün

 

Part VII: Bioinformatic Analysis

26. Bioinformatics tools for exploring the SUMO Gene Network, an update

Pedro Humberto Castro, Miguel Ângelo Santos, Alexandre Papadopoulos Magalhães, Rui Manuel Tavares, and Herlander Azevedo

 

27. Coexpression network constriction and visualization from transcriptomes underlying ER stress responses

Dae Kwan Ko and Federica Brandizzi

 

28. Approaches for the identification of intrinsically disordered protein domains

Huqiang Wang, Zhixiang Yang, and Dong Yang