Plant proteostasis : methods and protocols / edited by L. Maria Lois, Marco Trujillo. -- Second edition -- New York, NY : Humana Press, 2023. – (58.17/M592/v.2581)

Contents

Preface "Plant Proteostasis"
Contributors
PART I  UBIQUITIN CONJUGATION AND DECONJUGATION ANALYSIS
1  Observing Real-Time Ubiquitination in High Throughput with Fluorescence Polarization
2  Identification and Characterization of Physiological Pairing of E2 Ubiquitin-Conjugating Enzymes and E3 Ubiquitin Ligases
3  Immunoprecipitation of Cullin-Ring Ligases (CRLs) in Arabidopsis thaliana Seedlings
4  An In vitro Assay to Recapitulate Hormone-Triggered and SCF-Mediated Protein Ubiquitylation
5  Analysis of Proteasome-Associated Ubiquitin Ligase Activity
6  Measuring the DUB Activity of Arabidopsis Deubiquitylating Enzymes
PART II  SUMO CONJUGATION AND DECONJUGATION
7  SUMO Conjugation and SUMO Chain Formation by Plant Enzymes
8  Kinetic Analysis of Plant SUMO Conjugation Machinery
9  Expression, Purification, and Enzymatic Analysis of Plant SUMO Proteases
PART III  ANALYSIS OF AUTOPHAGY
10  Monitoring Autophagic Flux in the Model Single-Celled Microalga Chlamydomonas reinhardtii
11  Detection of Autophagy in Plants by Fluorescence Microscopy
12  Characterization of ATG8-Family Interactors by Isothermal Titration Calorimetry
PART IV  PROTEIN TURNOVER AND STABILITY
13  Protocols for Studying Protein Stability in an Arabidopsis Protoplast Transient Expression System
14  Relative Protein Lifetime Measurement in Plants Using Tandem Fluorescent Protein Timers
15  Detection and Quantification of Protein Aggregates in Plants
16  Using Intrinsic Fluorescence to Measure Protein Stability Upon Thermal and Chemical Denaturation
PART V  PROTEIN ISOLATION AND MASS SPECTROMETRIC ANALYSIS
17  Purification and Detection of Ubiquitinated Plant Proteins Using Tandem Ubiquitin Binding Entities
18  Titanium Oxide-Based Phosphopeptide Enrichment from Arabidopsis Seedlings
19  Chloroplast Envelope Membrane Subfractionation from Arabidopsis and Pea
20  Chromatin Enrichment for Proteomics in Plants (ChEP-P)
21  Proximity-Dependent In Vivo Biotin Labeling for Interactome Mapping in Marchantia polymorpha
22  Tandem Mass Tag-Based Phosphoproteomics in Plants
PART VI  STUDY OF PROTEASOME AND PROTEASES
23  Analysis of Peptide Hormone Maturation and Processing Specificity Using Isotope-Labeled Peptides
24  Improved Identification of Protease Cleavage Sites by In-gel Reductive Dimethylation
25  A Pipeline to Monitor Proteasome Homeostasis in Plants
PART VII  BIOINFORMATIC ANALYSIS
26  Bioinformatic Tools for Exploring the SUMO Gene Network: An Update
27  Coexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress Responses
28  Approaches for the Identification of Intrinsically Disordered Protein Domains
Index