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Annual Plant Reviews, Plant Proteomics 1405144297_1_pretoc.qxd 16-06-2006 9:40 Page i Plant Proteomics This page intentionally left blank 1405144297_1_pretoc.qxd 16-06-2006 9:40 Page iii Plant Proteomics Edited by CHRISTINE FINNIE Biochemistry and Nutrition Group Biocentrum-DTU Technical University of Denmark Kgs Lyngby Denmark 1405144297_1_pretoc.qxd 16-06-2006 9:40 Page iv © 2006 Blackwell Publishing Editorial Offices: Blackwell Publishing Ltd, 9600 Garsington Road, Oxford OX4 2DQ, UK Tel: ϩ44 (0)1865 776868 Blackwell Publishing Professional, 2121 State Avenue, Ames, Iowa 50014-8300, USA Tel: ϩ1 515 292 0140 Blackwell Publishing Asia Pty Ltd, 550 Swanston Street, Carlton, Victoria 3053, Australia Tel: ϩ61 (0)3 8359 1011 The right of the author to be identified as the author of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher. 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 572Ј.62—dc22 2006009416 A catalogue record for this title is available from the British Library Set in 10/12 pt, Times by Charon Tec Ltd, Chennai, India www.charontec.com Printed and bound in India by Replika Press Pvt. Ltd, Kundli The publisher’s policy is to use permanent paper from mills that operate a sustainable forestry policy, and which has been manufactured from pulp processed using acid-free and elementary chlorine-free practices. Furthermore, the publisher ensures that the text paper and cover board used have met acceptable environmental accreditation standards. For further information on Blackwell Publishing, visit our web site: www.blackwellpublishing.com 1405144297_1_pretoc.qxd 16-06-2006 9:40 Page v 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 1405144297_1_pretoc.qxd 16-06-2006 9:40 Page vi 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 1405144297_2_toc.qxd 16-06-2006 16:18 Page vii 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 1405144297_2_toc.qxd 16-06-2006 16:18 Page viii 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, SO2H and SO3H82 4.3.5 Trxs and disulphide reduction 83 4.3.6 S-nitrosylation 88 4.4 Conclusions and perspectives 89 1405144297_2_toc.qxd 16-06-2006 16:18 Page ix 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. coli cell-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
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