Plant Proteomics

by Thiellement, Herve; Zivy, Michel; Damerval, Catherine; Mechin, Valerie

• ISBN13: 9781588296351
• ISBN10: 1588296350
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-09-30
• Publisher: Humana Pr Inc

Summary

Plant Proteomics: Methods and Protocols provides up-to-date methods and protocols for plant proteomics, each written by expert researchers from leading laboratories. Experimental methodologies are explained in clear and complete detail for both the wet and dry laboratories. The methods and protocols presented in this volume will inspire the novice as well as the expert researcher to undertake new experimental endeavors in plant proteomics. Chapters 1 and 2 describe standard protocols and chapters 3 through 10 contain optimized protocols for protein extraction of tissues such as cereal seeds, xylem, phloem sap, of woody plants, and of cellular compartments, such as chloroplasts and mitochondria. These methods rely on improvements to solubilization of proteins, which is the emphasis of Chapters 11 and 12. Chapters 13 to 23 outline methods for protein identification, including 2DLC or LC of intact proteins, mass spectrometry (MALDI-TOF and MS/MS) with proteins separated by 2D gels, blue native ID gels, and Edman sequencing. Chapters 24 to 29 focus on the rapidly expanding area of analysis of post-translational modifications and protein-protein relationships. Attention is also given to data that proteomics produces, including management of that data, and to statistical tools used for effective analysis.

Table of Contents

Preface	v
Contributors	xi
1 Total Protein Extraction with TCA-Acetone
Valérie Méchin, Catherine Damerval, and Michel Zivy	1	(8)
2 Phenol Extraction of Proteins for Proteomic Studies of Recalcitrant Plant Tissues
Mireille Faurobert, Esther Pelpoir, and Jamila Chaib	9	(6)
3 Protein Extraction from Cereal Seeds
Gérard Branlard and Emmanuelle Bancel	15	(12)
4 Protein Extraction from Xylem and Phloem Sap
Julia Kehr and Martijn Rep	27	(10)
5 Protein Extraction from Woody Plants
Christophe Plomion and Céline Lalanne	37	(6)
6 Isolation of Chloroplast Proteins from Arabidopsis thaliana for Proteome Analysis
Klaas J. van Wijk, Jean-Benoit Peltier, and Lisa Giacomelli	43	(6)
7 Isolation and Subfractionation of Plant Mitochondria for Proteomic Analysis
Holger Eubel, Joshua L. Heazlewood, and A. Harvey Millar	49	(14)
8 Extraction of Nuclear Proteins from Root Meristematic Cells
Fernando González-Camacho and Francisco Javier Medina	63	(10)
9 Isolation of Nuclear Proteins
Setsuko Komatsu	73	(6)
10 Isolation of Cell Wall Proteins from Medicago sativa Stems
Bonnie S. Watson and Lloyd W. Sumner	79	(14)
11 Plant Plasma Membrane Protein Extraction and Solubilization for Proteomic Analysis
Véronique Santoni	93	(18)
12 Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis
Thierry Rabilloud, Sylvie Luche, Véronique Santoni, and Mireille Chevallet	111	(10)
13 Two-Dimensional Electrophoresis for Plant Proteomics
Walter Weiss and Angelika Görg	121	(24)
14 Visible and Fluorescent Staining of Two-Dimensional Gels
François Chevalier, Valérie Rofidal, and Michel Rossignol	145	(12)
15 Two-Dimensional Differential In-Gel Electrophoresis (DIGE) of Leaf and Roots of Lycopersicon esculentum
Matthew Keeler, Jessica Letarte, Emily Hattrup, Fatimah Hickman and Paul A. Haynes	157	(18)
16 Quantitative Analysis of 2D Gels
Michel Zivy	175	(20)
17 Multivariate Data Analysis of Proteome Data
Kåre Engkilde, Susanne Jacobsen, and lb Søndergaard	195	(16)
18 Edman Sequencing of Plant Proteins from 2D Gels
Setsuko Komatsu	211	(8)
19 Peptide Mass Fingerprinting: Identification of Proteins by MALDI-TOF
Nicolas Sommerer, Delphine Centeno, and Michel Rossignol	219	(16)
20 Protein Identification using Nano Liquid Chromatography–Tandem Mass Spectrometry
Luc Negroni	235	(14)
21 Two-Dimensional Nanoflow Liquid Chromatography–Tandem Mass Spectrometry of Proteins Extracted from Rice Leaves and Roots
Linda Breci and Paul A. Haynes	249	(18)
22 Separation, Identification, and Profiling of Membrane Proteins by GFC/IEC/SDS-PAGE and MALDI TOF MS
Wojciech Szponarski, Frédéric Delom, Nicolas Sommerer, Michel Rossignol, and Rémy Gibrat	267	(12)
23 The PROTICdb Database for 2-DE Proteomics
Olivier Langella, Michel Zivy, and Johann Joets	279	(26)
24 Identification of Phosphorylated Proteins
Maria V. Turkina and Alexander V. Vener	305	(12)
25 Plant Proteomics and Glycosylation
Anne-Catherine Fitchette, Olivia Tran Dinh, Loic Faye, and Muriel Bardor	317	(26)
26 Blue-Native Gel Electrophoresis for the Characterization of Protein Complexes in Plants
Jesco Heinemeyer, Dagmar Lewejohann, and Hans-Peter Braun	343	(10)
27 Electroelution of Intact Proteins from SDS-PAGE Gels and Their Subsequent MALDI-TOF MS Analysis
Zhentian Lei, Ajith Anand, Kirankumar S. Mysore, and Lloyd W. Sumner	353	(12)
28 Generation of Plant Protein Microarrays and Investigation of Antigen–Antibody Interactions
Birgit Kersten and Tanja Feilner	365	(14)
29 Phosphorylation Studies Using Plant Protein Microarrays
Tanja Feilner and Birgit Kersten	379	(12)
Index	391