Annual Plant Reviews, Plant Proteomics (Volume 28)

275 Pages·2006·2.43 MB·English

by  Christine Finnie

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Plant Proteomics
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Plant Proteomics
Edited by
CHRISTINE FINNIE
Biochemistry and Nutrition Group
Biocentrum-DTU
Technical University of Denmark
Kgs Lyngby
Denmark
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©2006 Blackwell Publishing
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First published 2006 by Blackwell Publishing Ltd
ISBN-13: 978-1-4051-4429-2
ISBN-10: 1-4051-4429-7
Library of Congress Cataloging-in-Publication Data
Plant proteomics/edited by Christine Finnie.
p. cm. — (Annual plant reviews)
Includes bibliographical references and index.
ISBN-13: 978-1-4051-4429-2 (hardback: alk. paper)
ISBN-10: 1-4051-4429-7 (hardback: alk. paper)
1. Plant proteins. 2. Plant proteomics.
I. Finnie, Christine. II. Series
QK898.P8P52 2006
572(cid:3).62—dc22
2006009416
A catalogue record for this title is available from the British Library
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Annual Plant Reviews
A series for researchers and postgraduates in the plant sciences. Each volume in this series
focuses on a theme of topical importance and emphasis is placed on rapid publication.
Editorial Board:
Professor Jeremy A. Roberts(Editor-in-Chief), Plant Science Division, School of Biosciences,
University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12
5RD, UK: Dr David Evans, School of Biological and Molecular Sciences, Oxford Brookes
University, Headington, Oxford, OX3 0BP; Professor Hidemasa Imaseki, Obata-Minami
2419,Moriyama-ku, Nagoya 463, Japan; Dr Michael T. McManus, Institute of Molecular
BioSciences, Massey University, Palmerston North, New Zealand; Dr Jocelyn K.C. Rose,
Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA.
Titles in the series:
1. Arabidopsis
Edited by M. Anderson and J.A. Roberts
2. Biochemistry of Plant Secondary Metabolism
Edited by M. Wink
3. Functions of Plant Secondary Metabolites and Their Exploitation in
Biotechnology
Edited by M. Wink
4. Molecular Plant Pathology
Edited by M. Dickinson and J. Beynon
5. Vacuolar Compartments
Edited by D.G. Robinson and J.C. Rogers
6. Plant Reproduction
Edited by S.D. O’Neill and J.A. Roberts
7. Protein–Protein Interactions in Plant Biology
Edited by M.T. McManus, W.A. Laing and A.C. Allan
8. The Plant Cell Wall
Edited by J.K.C. Rose
9. The Golgi Apparatus and the Plant Secretory Pathway
Edited by D.G. Robinson
10. The Plant Cytoskeleton in Cell Differentiation and Development
Edited by P.J. Hussey
11. Plant–Pathogen Interactions
Edited by N.J. Talbot
12. Polarity in Plants
Edited by K. Lindsey
13. Plastids
Edited by S.G. Moller
14. Plant Pigments and Their Manipulation
Edited by K.M. Davies
15. Membrane Transport in Plants
Edited by M.R. Blatt
16. Intercellular Communication in Plants
Edited by A.J. Fleming
17. Plant Architecture and its Manipulation
Edited by C. Turnbull
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18. Plasmodesmata
Edited by K.J. Oparka
19. Plant Epigenetics
Edited by P. Meyer
20. Flowering and Its Manipulation
Edited by C. Ainsworth
21. Endogenous Plant Rhythms
Edited by A. Hall and H. McWatters
22. Control of Primary Metabolism in Plants
Edited by W.C. Plaxton and M.T. McManus
23. Biology of the Plant Cuticle
Edited by M. Riederer
24. Plant Hormone Signaling
Edited by P. Hedden and S.G. Thomas
25. Plant Cell Separation and Adhesion
Edited by J.R. Roberts and Z. Gonzalez-Carranza
26. Senescence Processes in Plants
Edited by S. Gan
27. Seed Development, Dormancy and Germination
Edited by K.J. Bradford and H. Nonogaki
28. Plant Proteomics
Edited by C. Finnie
29. Regulation of Transcription in Plants
Edited by K. Grasser
30. Light and Plant Development
Edited by G. Whitelam and K. Halliday
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Contents
Preface xiii
Contributors xvi
1 Plant proteomics: challenges and resources 1
JOSHUA L. HEAZLEWOOD and A. HARVEY MILLAR
1.1 Introduction 1
1.2 Challenges 2
1.2.1 Sample extraction 2
1.2.1.1 Two-dimensional gel electrophoresis 3
1.2.1.2 Direct MS analysis of samples 4
1.2.2 Sample preparation and arraying 4
1.2.2.1 Two-dimensional gel electrophoresis 5
1.2.2.2 One-dimensional gel electrophoresis 7
1.2.2.3 Blue-native gel electrophoresis 7
1.2.2.4 Direct analysis of samples by MS 7
1.2.3 Mass spectrometry (MALDI and ESI) 9
1.2.3.1 MALDI 9
1.2.3.2 ESI 12
1.2.4 Analysis depth 13
1.2.5 Data analysis 14
1.2.5.1 Peptide mass fingerprints 15
1.2.5.2 Peptide fragmentation data (MS/MS) 16
1.2.5.3 Analysis options 16
1.2.6 Quantitation 17
1.2.6.1 Gel stains 18
1.2.6.2 Chemical labelling of sample 19
1.2.7 Modifications 20
1.2.8 Data 21
1.3 Resources 22
1.3.1 Proteomic databases 22
1.3.2 Online proteomic tools and resources 24
1.4 Future 24
2 Proteomic analysis of post-translational modifications by
mass spectrometry 33
ALBRECHT GRUHLER and OLE N. JENSEN
2.1 Summary 33
2.2 Introduction 33
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viii CONTENTS
2.3 Considerations for the experimental design of PTM analysis
by proteomics 35
2.4 Analysis of PTMs by proteomic approaches 38
2.4.1 Phosphorylation 38
2.4.2 Protein glycosylation 43
2.4.3 GPI-AP 46
2.4.4 Farnesylation 47
2.4.5 N-terminally modified proteins 48
2.5 Conclusions and perspectives 49
3 Strategies for the investigation of protein–protein
interactions in plants 55
HANS-PETER BRAUN and UDO K. SCHMITZ
3.1 Summary 55
3.2 Introduction 55
3.3 Biochemical procedures to characterize protein–protein interactions 56
3.3.1 Chromatographic purifications 56
3.3.2 Sucrose gradient ultrafiltration 56
3.3.3 Native gel electrophoresis 56
3.3.4 Immunoprecipitations 58
3.4 Genetic procedures to characterize protein–protein interactions 58
3.4.1 Yeast two-hybrid system 59
3.4.2 Yeast three-hybrid system 60
3.4.3 Yeast one-hybrid system 61
3.4.4 Limitations of yeast two-hybrid systems 61
3.4.5 Split-ubiquitin system 62
3.4.6 Bimolecular fluorescence complementation (BiFC) 62
3.4.7 Förster resonance energy transfer (FRET) 63
3.4.8 Tagging technologies for the purification of protein complexes 64
3.5 Cytological procedures to characterize protein–protein interactions 64
3.6 Outlook 65
4 Proteomics of disulphide and cysteine oxidoreduction 71
KENJI MAEDA, PER HÄGGLUND, CHRISTINE FINNIE and
BIRTE SVENSSON
4.1 Introduction 71
4.2 Control of cellular redox status 72
4.2.1 Sequence and structural features of proteins catalysing
cysteine redox modifications 73
4.2.2 Catalytic mechanisms of Trxs and Grxs 74
4.3 Proteomics techniques for analysis of cysteine modifications 75
4.3.1 Reagents for cysteine labelling 75
4.3.2 Disulphide mapping 79
4.3.3 S-glutathionylation 81
4.3.4 Cysteine SOH, SO H and SO H 82
2 3
4.3.5 Trxs and disulphide reduction 83
4.3.6 S-nitrosylation 88
4.4 Conclusions and perspectives 89
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CONTENTS ix
5 Structural proteomics 99
RUSSELL L. WROBEL, CRAIG A. BINGMAN, WON BAE JEON,
JIKUI SONG, DMITRIY A. VINAROV, RONNIE O. FREDERICK,
DAVID J. ACETI, HASSAN K. SREENATH, ZSOLT ZOLNAI, FRANK C.
VOJTIK, EDUARD BITTO, BRIAN G. FOX, GEORGE N. PHILLIPS Jr
and JOHN L. MARKLEY
5.1 Introduction 99
5.2 Project data handling: Sesame 101
5.3 ORF cloning 102
5.4 E. colicell-based protein production pipeline 104
5.4.1 Large-scale protein production and labeling 106
5.4.2 Protein purification 107
5.5 Wheat germ cell-free protein production 109
5.6 Mass spectrometry of purified proteins for quality assurance
and analysis 110
5.7 Crystallomics and X-ray structure determination 112
5.7.1 Initial screening 112
5.7.2 Optimizations and salvage 113
5.7.3 Future directions 115
5.8 NMR screening and structure determination 115
5.8.1 Sample screening 115
5.8.2 NMR data collection 116
5.8.3 Chemical shift assignment and structural calculation 117
5.8.4 Structure-based functional annotation 117
5.9 Illustrative structures and functional implications 118
6 Cereal proteomics 129
SETSUKO KOMATSU
6.1 Introduction 129
6.2 Comprehensive analysis and cataloguing of cereal proteins 130
6.2.1 Cataloguing of rice proteins using 2D-PAGE 130
6.2.2 The rice proteomics project 130
6.2.2.1 Proteomics analysis of rice tissues 131
6.2.2.2 Proteomics analysis of subcellular compartments 133
6.3 Functional analysis of cereal using differential proteomics 135
6.3.1 Stresses 135
6.3.1.1 Cold 135
6.3.1.2 Drought 136
6.3.1.3 Salinity 136
6.3.1.4 Ozone 138
6.3.1.5 Fungus 138
6.3.1.6 Virus 139
6.3.2 Hormones 140
6.3.2.1 Gibberellin 140
6.3.2.2 Brassinosteroid 142
6.3.2.3 JA 142
6.3.2.4 Auxin 142
6.4 Future prospects of cereal proteomics 143