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PLANT PROTEOMICSTechnologies, Strategies,
and Applications
Edited by
Ganesh Kumar AgrawalRandeep Rakwal
A JOHN WILEY & SONS, INC., PUBLICATION
InnodataFile Attachment9780470369838.jpg
PLANT PROTEOMICS
PLANT PROTEOMICSTechnologies, Strategies,
and Applications
Edited by
Ganesh Kumar AgrawalRandeep Rakwal
A JOHN WILEY & SONS, INC., PUBLICATION
Copyright © 2008 by John Wiley & Sons, Inc. All rights reserved.
Published by John Wiley & Sons, Inc., Hoboken, New JerseyPublished simultaneously in Canada
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Library of Congress Cataloging-in-Publication Data:
Agrawal, Ganesh Kumar.Plant proteomics : technologies, strategies, and applications / Ganesh Kumar
Agrawal, Randeep Rakwal.p. cm.
Includes index.ISBN 978-0-470-06976-9 (cloth)
1. Plant proteins. 2. Plant proteomics. I. Rakwal, Randeep. II. Title.QK898.P8A37 2008572′ .62–dc22
2007051404
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
http://www.copyright.comhttp://www.wiley.com/go/permissionhttp://www.wiley.com
CONTENTS
PREFACE xix
CONTRIBUTORS xxiii
ACRONYMS AND ABBREVIATIONS xxix
1 AN INTRODUCTION TO PROTEOMICS: APPLICATIONSTO PLANT BIOLOGY 1Ralph A. Bradshaw
1.1 Proteomics Defined 2
1.2 Proteomics Applied 5
References 6
PART I TECHNOLOGIES2 GEL-BASED PROTEOMICS 11
Pier Giorgio Righetti, Paolo Antonioli, Carolina Simò, and AttilioCitterio
2.1 Introduction and Brief Bibliographic Review 11
2.2 SDS-PAGE 12
2.3 IEF 17
2.4 2D Maps 22
2.5 Conclusions 28
2.6 Five-Year Viewpoint 29
References 30
3 MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYINGPLANT PROTEINS 33Eveline Bergmüller, Sacha Baginsky, and Wilhelm Gruissem
3.1 Introduction and Brief Bibliographic Review 33
3.2 Instrumentation 34
3.3 MALDI 35
vi CONTENTS
3.4 ESI 36
3.5 Mass Analyzers 36
3.6 Ion Detectors 38
3.7 Sample Preparation 39
3.8 Protein Identification 40
3.9 Conclusions 44
3.10 Five-Year Viewpoint 44
References 44
4 CHEMICAL PROTEOMICS 47Miriam C. Hagenstein, Olaf Kruse, and Norbert Sewald
4.1 Introduction 47
4.2 Strategies For Activity-Based Protein Profiling (ABPP) 47
4.3 Case Study: Development of Molecular Tools Targeting PlantKinases 53
4.4 Conclusions 57
4.5 Five-Year Viewpoint 58
References 58
5 THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEINLOCALIZATION AND INTERACTIONS IN ARABIDOPSIS 61Georgios Kitsios, Nicolas Tsesmetzis, Max Bush, and John H. Doonan
5.1 Protein Compartmentalization in Plant Cells 61
5.2 Experimental Determination of Protein Localization 66
5.3 In Vivo Imaging Approaches to Protein Localization and Interaction 69
5.4 Plant Cell Cultures for Studying Protein Localization 73
5.5 Protein–Protein Interaction In Vivo: FRET 74
5.6 Perspectives: Integrating Predictive and Experimental ProteinLocalization Data 77
References 77
6 SECRETOME: TOWARD DECIPHERING THE SECRETORYPATHWAYS AND BEYOND 83Young-Ho Jung, Ganesh Kumar Agrawal, Randeep Rakwal,and Nam-Soo Jwa
6.1 Introduction and Brief Bibliographic Review 83
6.2 Methodology and Strategy 86
6.3 A Case Study: In Planta and In Vitro Protein Profiles of Solubleand Secreted Proteins in Rice 87
CONTENTS vii
6.4 Conclusions 87
6.5 Five-Year Viewpoint 89
References 89
7 PEPTIDOMICS 91Peter Schulz-Knappe
7.1 Introduction and Brief Bibliographic Review 91
7.2 Separation Technology 93
7.3 MS Technology 95
7.4 Bioinformatics and Data Mining 97
7.5 Differential Peptide Display 98
7.6 ID LC–MALDI 99
7.7 2D CA–RP–LC–ESI–MS 100
7.8 Applications 100
7.9 Peptides and Proteases 101
7.10 Conclusions 102
7.11 Five-Year Viewpoint 103
References 103
PART II COMPUTATIONAL PROTEOMICS8 BIOINFORMATICS IN GEL-BASED PROTEOMICS 107
Åsa M. Wheelock and Craig E. Wheelock
8.1 Introduction and Brief Bibliographic Review 107
8.2 Methodology and Strategy 112
8.3 Experimental Results and Applications 120
8.4 Conclusions 122
8.5 Five-Year Viewpoint 123
References 124
9 BIOINFORMATICS IN MS-BASED PROTEOMICS 127Jacques Colinge
9.1 Introduction 127
9.2 Database Searching 128
9.3 Peptide De Novo Sequencing 135
9.4 Conclusions and Five-Year Viewpoint 138
References 139
viii CONTENTS
PART III EXPRESSION PROTEOMICS10 AN OVERVIEW OF THE ARABIDOPSIS PROTEOME 143
Jacques Bourguignon and Michel Jaquinod
10.1 Introduction and Brief Bibliographic Review 143
10.2 Methodology and Strategy 146
10.3 Experimental Results and Applications 147
10.4 Conclusions 160
10.5 Five-Year Viewpoint 160
References 161
11 RICE PROTEOME AT A GLANCE 165Ganesh Kumar Agrawal and Randeep Rakwal
11.1 Introduction and Brief Bibliographic Review 165
11.2 Methodology and Strategy 167
11.3 Experimental Results and Applications 172
11.4 Conclusions 177
11.5 Five-Year Viewpoint 177
References 178
12 PROTEOMICS OF LEGUME PLANTS 179Satish Nagaraj, Zhentian Lei, Bonnie Watson, and Lloyd W. Sumner
12.1 Introduction and Brief Bibliographic Review 179
12.2 Proteomics of Model Legume Medicago truncatula 180
12.3 Proteomics of Model System Lotus japonicus 183
12.4 Proteomics of Soybean, Glycine max 183
12.5 Proteomics of Alfalfa, Medicago sativa 184
12.6 Conclusions 186
12.7 Five-Year Viewpoint 187
References 187
13 PROTEOME OF SEED DEVELOPMENT AND GERMINATION 191Julie Catusse, Loı̈c Rajjou, Claudette Job, and Dominique Job
13.1 Introduction 191
13.2 Proteomics of Developing Seeds 192
13.3 Proteomics of Mature Seeds 196
13.4 Proteomics of Germinating Seeds 198
13.5 Proteomics of Somatic Embryogenesis 201
13.6 Metabolic Control of Seed Development and Germination 203
CONTENTS ix
13.7 Conclusions 204
13.8 Five-year Viewpoint 205
References 205
14 ENDOSPERM AND AMYLOPLAST PROTEOMES OF WHEATGRAIN 207William J. Hurkman, William H. Vensel, Frances M. DuPont, Susan B.Altenbach, and Bob B. Buchanan
14.1 Introduction 207
14.2 Fractionation and Analysis of Endosperm Proteins 208
14.3 The Endosperm Proteome 210
14.4 The Amyloplast Proteome 215
14.5 Conclusions 219
14.6 Five-Year Viewpoint 219
References 220
15 ROOT PROTEOME 223Kuo-Chen Yeh, Chyi-Chuann Chen, and Chuan-Ming Yeh
15.1 Introduction 223
15.2 Application of Proteomics in the Study of Root Development 225
15.3 Proteome Analysis of Response to Plant Hormones 232
15.4 Proteome Analysis of Gravity Response 233
15.5 Action to Microbe–Plant Symbiosis 233
15.6 Proteome to Cope With Environmental Stresses 234
15.7 Conclusions and Five-Year Viewpoint 236
References 237
16 LEAF PROTEOME 239Bin Kang, Shuyang Tu, Jiyuan Zhang, and Siqi Liu
16.1 Introduction 239
16.2 Proteomics Studies in Plant Leaf 240
16.3 Conclusions 247
16.4 Five-Year Viewpoint 247
References 248
17 ANTHER PROTEOME 249Nijat Imin
17.1 Introduction and Brief Bibliographic Review 249
17.2 Methodology and Strategy 251
17.3 Conclusions 258
x CONTENTS
17.4 Five-Year Viewpoint 258
References 259
18 POLLEN PROTEOME 261Sandra Noir
18.1 Introduction 261
18.2 Bibliographic Review: Pollen Development and Function 262
18.3 Methodology and Experimental Results 264
18.4 Conclusions 271
18.5 Five-Year Viewpoint 272
References 272
19 MICROTUBULE-BINDING PROTEINS 275Lori A. Vickerman and Douglas G. Muench
19.1 Introduction 275
19.2 Brief Bibliographic Review 276
19.3 Strategies and Methodologies 277
19.4 Experimental Results and Applications 280
19.5 Conclusions 286
19.6 Five-Year Viewpoint 287
References 287
PART IV ORGANELLE PROTEOMICS20 CELL WALL 293
Elisabeth Jamet, Hervé Canut, Cécile Albenne, Georges Boudart, andRafael Pont-Lezica
20.1 Introduction 293
20.2 Brief Bibliographic Review 296
20.3 Specific Methodology and Strategies 296
20.4 Experimental Results and Applications 300
20.5 Conclusions 304
20.6 Five-Year Viewpoint 304
References 306
21 PLASMA MEMBRANE: A PECULIAR STATUS AMONG THE CELLMEMBRANE SYSTEMS 309Geneviève Ephritikhine, Anne Marmagne, Thierry Meinnel, and Myriam Ferro
21.1 Introduction and Brief Bibliographic Review 309
21.2 Specific Methodologies and Strategies (Box 21.1) 310
CONTENTS xi
21.3 Experimental Results and Applications: Toward an InformativeDatabase of the Plant PM Proteome 319
21.4 Conclusions 323
21.5 Five-Year Viewpoint 324
References 325
22 NUCLEUS 327Subhra Chakraborty, Aarti Pandey, Asis Datta, and Niranjan Chakraborty
22.1 Introduction and Brief Bibliographic Review 327
22.2 Methodology and Strategy 328
22.3 Experimental Results and Discussion 330
22.4 Conclusions 335
22.5 Five-Year Viewpoint 336
References 337
23 CHLOROPLAST 339Thomas Kieselbach and Wolfgang P. Schröder
23.1 Introduction 339
23.2 Brief Bibliographic Review 341
23.3 Methodology and Strategy 341
23.4 Experimental Results and Applications 344
23.5 Conclusions 348
23.6 Five-Year Viewpoint 348
References 349
24 ETIOPLAST 351Anne von Zychlinski, Sonja Reiland, Wilhelm Gruissem,and Sacha Baginsky
24.1 Introduction 351
24.2 Etioplast Proteome Analysis 352
24.3 Conclusions 358
24.4 Five-Year Viewpoint 359
References 359
25 THE PLANT MITOCHONDRIAL PROTEOME AND THECHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS 361Yew-Foon Tan and A. Harvey Millar
25.1 Introduction 361
25.2 Brief Bibliographic Review 363
25.3 Methodology and Strategy 364
25.4 Experimental Results and Applications 369
xii CONTENTS
25.5 Conclusions 373
25.6 Five-Year Viewpoint 373
References 374
26 PEROXISOME 377Yuko Arai, Youichiro Fukao, Makoto Hayashi, and Mikio Nishimura
26.1 Introduction 377
26.2 Brief Bibliographic Review 379
26.3 Specific Methodologies and Strategies 379
26.4 Experimental Results and Applications 383
26.5 Conclusions 386
26.6 Five-Year Viewpoint 387
References 388
27 UNRAVELING PLANT VACUOLES BY PROTEOMICS 391Songqin Pan and Natasha Raikhel
27.1 Introduction 391
27.2 Bibliographic Review: Role of Proteomics in UnderstandingBiology of Plant Vacuoles 393
27.3 Methodology and Strategies 395
27.4 A Case-Study of Label-Free Quantitative Proteomics 401
27.5 Conclusions 402
27.6 Five-Year Viewpoint 403
References 404
28 OIL BODIES 407Pascale Jolivet, Luc Negroni, Sabine d’Andréa, and Thierry Chardot
28.1 Introduction and Brief Bibliographic Review 407
28.2 Methodology and Strategy 408
28.3 Conclusions 413
28.4 Five-Year Viewpoint 414
References 416
PART V MODIFICATION PROTEOMICS29 PHOSPHOPROTEINS: WHERE ARE WE TODAY? 421
Florian Wolschin and Wolfram Weckwerth
29.1 Introduction 421
29.2 Phosphoprotein and Phosphopeptide Enrichment 422
CONTENTS xiii
29.3 Detection of Protein Phosphorylation and Determination ofPhosphorylation Sites 427
29.4 MS-Based Approaches 432
29.5 Biological Implications of Protein Multisite Phosphorylationin Plants 434
29.6 Large-Scale Proteomics Studies 437
29.7 Conclusions and Five-Year Viewpoint 438
References 438
30 PROTEOME ANALYSIS OF THE UBIQUITIN PATHWAY 443Junmin Peng
30.1 Introduction 443
30.2 Brief Bibliographic Review 444
30.3 Specific Methodologies and Strategies 445
30.4 Experimental Results and Applications 448
30.5 Conclusions 451
30.6 Five-Year Viewpoint 452
References 452
31 ANALYSIS OF THE N-GLYCOSYLATION OF PROTEINSIN PLANTS 455Willy Morelle
31.1 Introduction 455
31.2 Brief Bibliographic Review 456
31.3 Methodology and Strategy 458
31.4 Conclusions 465
31.5 Five-Year Viewpoint 466
References 467
32 FUNCTIONAL ANALYSIS AND PHOSPHORYLATION SITEMAPPING OF LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASES 469Steven D. Clouse, Michael B. Goshe, Steven C. Huber, and Jia Li
32.1 Introduction and Brief Bibliographic Review 469
32.2 Specific Methodologies and Strategies 473
32.3 Experimental Results and Applications 477
32.4 Conclusions and Five-Year Viewpoint 481
References 482
33 TIME TO SEARCH FOR PROTEIN KINASE SUBSTRATES 485Birgit Kersten
33.1 Introduction and Brief Bibliographic Review 485
33.2 Methodology and Strategy 486
xiv CONTENTS
33.3 Experimental Results on Plant MAPK Downstream Signaling andApplications 494
33.4 Conclusions 496
33.5 Five-Year Viewpoint 496
References 497
34 TYROSINE PHOSPHORYLATION IN PLANTS: EMERGINGEVIDENCE 499Andrea Carpi, Valeria Rossi, and Francesco Filippini
34.1 Introduction 499
34.2 Brief Bibliographic Review 502
34.3 Methodology and Strategy 505
34.4 Experimental Results and Applications 508
34.5 Conclusions 510
34.6 Five-Year Viewpoint 511
References 512
35 14–3–3 PROTEINS: REGULATORS OF KEY CELLULARFUNCTIONS 515Peter C. Morris
35.1 Introduction and Brief Bibliographic Review 515
35.2 Methodology and Strategy 518
35.3 Experimental Results and Applications 519
35.4 Conclusions 522
35.5 Five-Year Viewpoint 522
References 523
PART VI MULTIPROTEIN COMPLEX36 TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX
ISOLATION 527Jai S. Rohila and Michael E. Fromm
36.1 Introduction 527
36.2 Methodolgy and Strategy 528
36.3 Experimental Results and Applications 535
36.4 Conclusions 540
36.5 Five-Year Viewpoint 541
References 541
CONTENTS xv
37 TAP STRATEGY IN ARABIDOPSIS PROTEIN COMPLEXISOLATION 543Vicente Rubio and Xing Wang Deng
37.1 Introduction and Brief Bibliographic Review 543
37.2 Specific Methodology and Strategies 546
37.3 Experimental Results and Applications 552
37.4 Conclusions 554
37.5 Five-Year Viewpoint 555
References 555
38 BLUE-NATIVE PAGE IN STUDYING PROTEIN COMPLEXES 557Holger Eubel and A. Harvey Millar
38.1 Introduction 557
38.2 Brief Bibliographic Review 560
38.3 Methodology and Strategy 561
38.4 Experimental Results and Applications 566
38.5 Conclusions 567
38.6 Five-Year Viewpoint 567
References 568
39 PROTEIN–PROTEIN INTERACTION MAPPING IN PLANTS 571Joachim F. Uhrig
39.1 Introduction and Brief Bibliographic Review 571
39.2 Methodology and Strategy 574
39.3 Experimental Results and Applications 578
39.4 Conclusions 580
39.5 Five-Year Viewpoint 581
References 581
PART VII PLANT DEFENSE AND STRESS40 PROTEOMICS IN PLANT DEFENSE RESPONSE 587
Sun Tae Kim and Kyu Young Kang
40.1 Introduction 587
40.2 Brief Bibliographic Review 588
40.3 Methodology and Strategies 589
40.4 Experimental Results and Applications 595
40.5 Conclusions 601
xvi CONTENTS
40.6 Five-Year Viewpoint 602
References 603
41 PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTICSTRESSES IN PLANTS 605Hans-Peter Mock and Andrea Matros
41.1 Introduction and Brief Bibliographic Review 605
41.2 Summary of Previous Research on Abiotic Stresses in Plants 606
41.3 Comparision of Transcriptomics and Proteomics Data in Analysis ofPlant Defense Responses Against Abiotic Stress Factors 621
41.4 Conclusions 624
41.5 Five-Year Viewpoint 624
References 625
42 PROTEOMICS OF BIOTROPHIC PLANT–MICROBEINTERACTIONS: SYMBIOSES LEAD THE MARCH 629Ghislaine Recorbet and Eliane Dumas-Gaudot
42.1 Introduction 629
42.2 AM and RNF Symbioses: No Equal Footing for Proteomics 631
42.3 A 2005–2006 Update of the Contribution of Proteomics to AMSymbiosis 634
42.4 A 2005–2006 Update of the Contribution of Proteomics to RNFSymbiosis 637
42.5 Conclusions 640
42.6 Five-Year Viewpoint 640
References 642
43 PROTEOMICS APPROACHES TO CONSTRUCT CALCIUMSIGNALING NETWORKS IN PLANTS 645Irene S. Day and A.S.N. Reddy
43.1 Introduction and Brief Bibliographic Review 645
43.2 Methodology and Experimental Results 649
43.3 Conclusions 656
43.4 Five-Year Viewpoint 656
References 657
PART VIII STRUCTURAL PROTEOMICS44 CELL-FREE EXPRESSION SYSTEM FOR EUKARYOTIC PROTEINS 661
Yaeta Endo and Tatsuya Sawasaki
44.1 Introduction 661
CONTENTS xvii
44.2 Development of Wheat Germ Cell-Free Protein Synthesis System 662
44.3 Application to Functional Proteomics 663
44.4 Application to Structural Proteomics 665
44.5 Conclusions and Five-Year Viewpoint 667
References 668
45 PROTEIN STRUCTURE DETERMINATION 671Jian-Hua Zhao and Hsuan-Liang Liu
45.1 Introduction 671
45.2 Instrumental Methods for Protein Structure Determination 672
45.3 Computational Approaches for Protein Structure Prediction 678
45.4 Conclusions 687
45.5 Five-Year Viewpoint 687
References 689
PART IX OTHER TOPICS IN PLANT PROTEOMICS46 PROTEOMICS IN CONTEXT OF SYSTEMS BIOLOGY 695
Serhiy Souchelnytskyi
46.1 Introduction 695
46.2 What Systems Biology Requires 696
46.3 What Proteomics Provides 699
46.4 Representation of Information About Proteins and Their Integrationinto Systems Biology Tools 706
46.5 Conclusions 708
46.6 Five-Year Viewpoint 708
References 709
47 PROTEOMICS IN DEVELOPING COUNTRIES 713Nat N. V. Kav, Sanjeeva Srivastava, William Yajima, and Shakir Ali
47.1 Introduction 713
47.2 Proteome Research in the Developing World 719
47.3 Conclusions 725
47.4 Five-Year Viewpoint 726
References 726
INDEX 731
PREFACE
The beginning of the twenty-first century is certainly a great time to be involvedin plant proteomics. This new millennium has placed an ever growing amount ofsophisticated technology (i.e., the ever growing list of annotated genes and genomesequence databases from Arabidopsis, rice and other plant species) at the disposal ofthe modern scientist to the benefit of all. The research performed with this technologyhas the potential to bring the answers to important and complex biological questionsand problems (especially those relating to crop plants and the human food supply)within reach.
Proteomics in plants began in 1990s, but has accelerated with an unexpectedpace and momentum since 1999 when many economical techniques (which are stan-dard today) were developed to characterize proteins on a proteome-wide scale. Theproteomics burst seen in the literature in recent years has made a significant impact onplant biology mainly by answering many of the questions associated with the genomeannotation and the number of functional proteins expressed in a given organism.Indeed, when one looks at the progress achieved to-date in the field of plant prote-omics and its overall impact on biological research, it is clear just how essential pro-teomics is to our understanding of the physiology of any organism. For example,proteomics is perhaps the only means that enables one to fully understand post-translational modifications of proteins. Thus, it would not be far from the truth tosay that the “power of proteomics” (and indeed the omic sciences as a whole) is oneof the driving forces of twenty-first century biological science.
A current (early 2008) literature survey in PubMed indicates that the numberof publications containing the term “plant proteomics” is 100-fold higher today,compared to same period in 1999. Not surprisingly, this survey also indicates thatproteomic studies have primarily been conducted in the two widely accepted flow-ering model plants, the weed Arabidopsis thaliana and the cereal crop rice (Oryzasativa L.). The publication of the genome sequences of these two plants representsa significant landmark in the history of plant biology. However, one must ask: Arewe fully aware of the true potential of plant proteomics and if so, are we using thisknowledge to its full effect? The principles of good science are as true in this age ofomics still hold true today and the disciplined scientist must keep these principles inmind to avoid rushing blindly into the field (intentionally or unintentionally) withoutfirst obtaining a thorough understanding of its fundamental principles.
When one looks at the impressive progress of proteomics in plant science, as wellas its immense importance in biological sciences as a whole, it is clear that a need for
xx PREFACE
a textbook, exists to translate/disseminate the knowledge acquired by leading expertsin the field to the wider scientific community. This was the impetus for the bookyou are currently reading. Though we knew that such a project would be a dauntingchallenge, we also knew that it would bring the opportunity to work closely with theleading experts of the field. What we did not fully appreciate when we started washow much of a truly unparalleled experience it would be to work with each and everyone of the contributors of this book, whom we genuinely thank for being part of thisambitious endeavor.
This book is composed of 9 sections in the following order: overview of pro-teomics in plant biology, technologies, computational/expression/organelle/modifica-tion proteomics, multiprotein complex, plant defense and stress, structural proteomics,systems biology, and proteomics in developing countries. The 47 chapters a provideexcellent coverage of almost all the studies conducted to-date on plant growth anddevelopment at the proteomics level. Each chapter also contains a five-year viewpointwhich discusses the scope for investigating proteomes and innovative improvementsin proteomic technologies over the next decade. We hope this book will be beneficialin scope and practical knowledge to readers, whose response will be the final judgeof the validity of the work.
As a final point, it is fitting that we acknowledge the people who gave theirunconditional and inspiring support, without which this book would not have reachedcompletion. First and foremost we would like to thank Professor Dominic M. Deside-rio (Department of Neurology, University of Tennessee, Memphis, Tennessee, USA)for being our mentor in this endeavor and enabling completion of this tremendousmilestone in our lives.
Secondly, we wish to thank our colleagues and collaborators around the worldwith whom we have struggled to do “good science,” forming new partnerships andfriendships in the process. There is not room to mention all those who have had aneffect on us here but Masami Yonekura (Ibaraki University, Japan), Shigeru Tamogami(Akita Prefectural University, Japan), Akihiro Kubo (National Institute of Environmen-tal Sciences, Japan), Nam-Soo Jwa (Sejong University, Korea), Oksoo Han (ChonnamNational University, Korea), Birgit Kersten (Max Planck Institute for Molecular PlantPhysiology, Germany), Yu Sam Kim and Hyung Wook Nam (Yonsei University,Korea), Hirohiko Hirochika (National Institute of Agrobiological Sciences, Japan),Shoshi Kikuchi (National Institute of Agrobiological Sciences, Japan), Oliver A.H.Jones (University of Cambridge, United Kingdom), and Yoshinori Masuo and HitoshiIwahashi (National Institute of Advanced Industrial Science and Technology, Japan)all deserve both mention and appreciation. We would especially like to thank Profes-sor Vishwanath Prasad Agrawal (RLABB, Kathmandu, Nepal) for his directions andguidance in our research. (This is especially true for Ganesh who started his researchunder Professor Vishwanath’s watchful eyes).
Thirdly, we thank the Editorial Team (Scientific, Technical, Medical, and Schol-arly Division) at John Wiley & Sons, Inc., especially Executive Editor Bob Esposito,Senior Editorial Assistant Brendan Sullivan, Senior Designer Daniel Timek, and, lastbut not the least, Senior Production Editor Lisa Morano Van Horn for their professionalsupport and patience with our queries and correspondence.
PREFACE xxi
Finally, to this long list of supporters, we must add our thanks for the personalsacrifices by our families, especially our wives and children. Randeep’s wife JunkoShibato also contributed greatly to the technical aspects of the book working alongsidewith him in the laboratory. Our parents who brought us into this world and who taughtand inspired us to contribute to society and do our duty also deserve special mention.To you the reader we also extend our thanks and appreciation. We hope this workwill be useful to you.
Ganesh Kumar AgrawalRandeep Rakwal
Kathmandu, NepalTsukuba, JapanMay 2008
CONTRIBUTORS
Ganesh Kumar Agrawal, Research Laboratory for Biotechnology and Biochemistry(RLABB), Kathmandu, Nepal
Cécile Albenne, Surface Cellular and Signalization for Plants, Projects in PlantBiotechnology, UMR, CNRS, Paul Sabatier-Toulouse III University, Castanet-Tolosan, France
Shakir Ali, Department of Biochemistry, Hamdard University, Hamdard Nagar, NewDelhi, India
Susan B. Altenbach, U.S. Department of Agriculture, Agricultural Research Service,Western Regional Research Center, Albany, California
Paolo Antonioli, Department of Chemistry, Materials and Chemical Engineering“Giulio Natta,” Polytechnic of Milan, Milan, Italy
Yuko Arai, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
Sacha Baginsky, Institute of Plant Sciences, ETH Zurich, Zurich, Switzerland
Eveline Bergmüller, Institute of Plant Sciences, ETH Zurich, Switzerland
Georges Boudart, Surface Cellular and Signalization for Plants, Projects in PlantBiotechnology, UMR, CNRS, Paul Sabatier-Toulouse III University, Castanet-Tolosan, France
Jacques Bourguignon, Laboratory of Cellular Plant Physiology, Institute of Researchand Technologies for Life Sciences, CNRS, UJF, INRA, CEA, Grenoble, France
Ralph A. Bradshaw, Mass Spectrometry Facility, University of California, San Fran-cisco, California
Bob B. Buchanan, Department of Plant and Microbial Biology, University of Cali-fornia, Berkeley, California
Max Bush, John Innes Centre, Norwich, England
Hervé Canut, Surface Cellular and Signalization for Plants, Projects in Plant Biotech-nology, UMR, CNRS, Paul Sabatier-Toulouse III University, Castanet-Tolosan,France
Andrea Carpi, Department of Biological Chemistry, University of Padua, Padua,Italy
Julie Catusse, CNRS/UCBL/INSA/Bayer CropScience Joint Laboratory, Bayer Crop-Science, Lyon, France
xxiv CONTRIBUTORS
Niranjan Chakraborty, National Centre for Plant Genome Research, JNU Campus,New Delhi, India
Subhra Chakraborty, National Centre for Plant Genome Research, JNU Campus,New Delhi, India
Thierry Chardot, UMR 206 Chemical Biology, INRA, INA-PG, Thiverval Grignon,France
Chyi-Chuann Chen, Agricultural Biotechnology Research Center, Academia Sinica,Taipei, Taiwan
Attilio Citterio, Department of Chemistry, Materials and Chemical Engineering“Giulio Natta,” Polytechnic of Milan, Milan, Italy
Steven D. Clouse, Department of Horticultural Science, North Carolina State Uni-versity, Raleigh, North Carolina
Jacques Colinge, Ce-M-M Research Center for Molecular Medicine, AustrianAcademy of Science, Director’s Group, Vienna, Austria
Sabine d’Andréa, UMR 206 Chemical Biology, INRA, INA-PG, Thiverval Grignon,France
Asis Datta, National Center for Plant Genome Research, JNU Campus, New Delhi,India
Irene S. Day, Department of Biology, Programs in Molecular Plant Biology, and Celland Molecular Biology, Colorado State University, Fort Collins, Colorado
Xing Wang Deng, Department of Molecular, cell, and Development Biology, YaleUniversity, New Haven, Connecticut
John H. Doonan, John Innes Centre, Norwich, England
Eliane Dumas-Gaudot, UMR 1088 INRA/CNRS 5184/UB Plant Microbe Environ-nement, INRA/CMSE, Dijon, France
Frances M. DuPont, U.S. Department of Agriculture, Agricultural Research Service,Western Regional Research Center, Albany, California
Yaeta Endo, Cell-Free Science and Technology Research Center, Ehime University,Matsuyama, Japan
Geneviève Ephritikhine, National Center of Scientific Research, Institute of PlantSciences, CNRS, UPR, Gif sur Yvette, France and UFR Natural Biology Sciences,University of Paris, Paris, France
Holger Eubel, Centre of Excellence in Plant Energy Biology, School of Biomedicaland Chemical Sciences/ARC, University of Western Australia, Crawley, Australia
Myriam Ferro, Laboratory for the Study of Dynamic Proteomics, INSERM, IRTSV,CEA-DSV, IUJF, Grenoble, France
Francesco Filippini, Department of Biology, University of Padua, Padua, Italy
Michael E. Fromm, Plant Science Initiative, University of Nebraska, Lincoln,Nebraska
Youichiro Fukao, Nara Institute of Science and Technology, Takayama, Ikoma, Japan
CONTRIBUTORS xxv
Michael B. Goshe, Department of Molecular and Structural Biochemistry, NorthCarolina State University, Raleigh, North Carolina
Wilhelm Gruissem, Institute of Plant Sciences, ETH Zurich, Zurich, Switzerland
Miriam C. Hagenstein, Department of Chemistry, Bielefeld University, Bielefeld,Germany
Makoto Hayashi, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
Steven C. Huber, USDA/ARS, University of Illinois, Urbana, Illinois
William J. Hurkman, U.S. Department of Agriculture, Agricultural Research Ser-vice, Western Regional Research Center, Albany, California
Nijat Imin, ARC Center of Excellence for Integrative Legume Research, GenomicInteractions Group, Research School of Biological Sciences, The AustralianNational University, Canberra, Australia
Elisabeth Jamet, Surface Cellular and Signalization for Plants, Projects in PlantBiotechnology, UMR, CNRS, Paul Sabatier-Toulouse III University, Castanet-Tolosan, France
Michel Jaquinod, Laboratory of Cellular Plant Physiology, Institute of Research andTechnologies for Life Sciences, CNRS, UJF, INRA, CEA, Grenoble, France
Claudette Job, CNRS/UCBL/INSA/Bayer CropScience Joint Laboratory, BayerCropScience, Lyon, France
Dominique Job, CNRS/UCBL/INSA/Bayer CropScience Joint Laboratory, BayerCropScience, Lyon, France
Pascale Jolivet, UMR 206 Chemical Biology, INRA, INA-PG, Thiverval Grignon,France
Young-Ho Jung, Department of Molecular Biology, Sejong University, Gunja-dong,Seoul, South Korea
Nam-Soo Jwa, Department of Molecular Biology, Sejong University, Gunja-dong,Seoul, South Korea
Bin Kang, Center of Proteomic Analysis, Beijing Genomics Institute, Chinese Academyof Sciences, Beijing, China
Kyu Young Kang, Environmental Biotechnology National Core Research Center,Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
Nat N. V. Kav, Department of Agricultural, Food and Nutritional Science, Universityof Alberta, Edmonton, Canada
Birgit Kersten, Max Planck Institute for Molecular Plant Physiology, Potsdam,Germany
Thomas Kieselbach, Department of Chemistry, Umeå University, Umeå, Sweden
Sun Tae Kim, Environmental Biotechnology National Core Research Center, Divi-sion of Applied Life Science, Gyeongsang National University, Jinju, Korea
Georgios Kitsios, John Innes Centre, Norwich, England
Olaf Kruse, Department of Biology, Bielefeld University, Bielefeld, Germany
xxvi CONTRIBUTORS
Zhentian Lei, Biological Mass Spectrometry, Plant Biology Division, The SamuelRoberts Noble Foundation, Ardmore, Oklahoma
Jia Li, Department of Botany and Microbiology, University of Oklahoma, Norman,Oklahoma
Hsuan-Liang Liu, Department of Chemical Engineering and Biotechnology, NationalTaipei University of Technology, Taipei, Taiwan
Siqi Liu, Center of Proteomic Analysis, Beijing Genomics Institute, Chinese Academyof Sciences, Beijing, China
Anne Marmagne, National Center of Scientific Research, Institute of Plant Sciences,CNRS, UPR, Gif sur Yvette, France
Andrea Matros, Leibniz-Institute of Plant Genetics and Crop Plant Research, Gater-sleben, Germany
Thierry Meinnel, National Center of Scientific Research, Institute of Plant Sciences,CNRS, UPR, Gif sur Yvette, France
A. Harvey Millar, ARC Centre of Excellence in Plant Energy Biology, The Univer-sity of Western Australia, Crawley, Australia
Hans-Peter Mock, Leibniz Institute of Plant Genetics and Crop Plant Research,Gatersleben, Germany
Willy Morelle, Structural Glygobiology Unit, Structure and Function Unit for MixedResearche, CNRS/USTL 8576, University of Science and Technology of Lille,Villeneuve d’Ascq, France
Peter C. Morris, School of Life Sciences, Heriot-Watt University, Riccarton, Edin-burgh, United Kingdom
Douglas G. Muench, Department of Biological Sciences, University of Calgary, Cal-gary, Alberta, Canada
Satish Nagaraj, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma
Luc Negroni, Faculty of Medicine, Proteomic Analysis Facility, Nice, France
Mikio Nishimura, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
Sandra Noir, Department of Plant–Microbe Interactions, Max Planck Institute forPlant Breeding Research, Köln, Germany
Songqin Pan, Institute for Integrative Genome Biology, Center for Plant Cell Biologyand Department of Botany and Plant Sciences, University of California, Riverside,California
Aarti Pandey, National Centre for Plant Genome Research, JNU Campus, New Delhi,India
Junmin Peng, Department of Human Genetics, Center for Neurodegenerative Dis-ease, School of Medicine, Emory University, Atlanta, Georgia
Rafael Pont-Lezica, Surface Cellular and Signalization for Plants, Projects in PlantBiotechnology, UMR, CNRS, Paul Sabatier-Toulouse III University, Castanet-Tolosan, France
CONTRIBUTORS xxvii
Natasha Raikhel, Institute for Integrative Genome Biology, Center for Plant CellBiology and Department of Botany and Plant Sciences, University of California,Riverside, California
Loı̈c Rajjou, UMR 204 INRA/AgroParisTech, Seed Biology Laboratory, Paris France
Randeep Rakwal, Research Laboratory for Agricultural Biotechnology and Bio-chemistry (RLABB), Kathmandu, Nepal and Health Technology, Research Cen-ter (HTRC), National Institute of Advanced Industrial Science and Technology(AIST) Tsukuba West, Ibaraki, Japan
Ghislaine Recorbet, UMR 1088 INRA/CNRS 5184/UB Plant Microbe Environnement,INRA/CMSE, Dijon, France
A. S. N. Reddy, Department of Biology, Programs in Molecular Plant Biology andCell and Molecular Biology, Colorado State University, Fort Collins, Colorado
Sonja Reiland, Institute of Plant Sciences, ETH Zurich, Zurich, Switzerland
Pier Giorgio Righetti, Department of Chemistry, Materials and Chemical Engineer-ing “Giulio Natta,” Polytechnic of Milan, Milan, Italy
Jai S. Rohila, Department of Plant Pathology, Pennsylvania State University, Uni-versity Park, Pennsylvania
Valeria Rossi, Department of Biology, University of Padua, Padua, Italy
Vicente Rubio, National Center for Biotechnology—CSIC, Cantoblanco, Madrid,Spain
Tatsuya Sawasaki, Cell-Free Science and Technology Research Center, Ehime Uni-versity, Matsuyama, Japan
Wolfgang P. Schröder, Department of Chemistry, Umeå University, Umeå, Sweden
Peter Schulz-Knappe, Proteome Sciences R&D GmbH & Co., Frankfurt Germany
Norbert Sewald, Department of Chemistry, Bielefeld University, Bielefeld, Germany
Carolina Simò, Department of Chemistry, Materials and Chemical EngineeringGiulio Natta, Polytechnic of Milan, Milan, Italy
Serhiy Souchelnytskyi, Medical Proteomics Group, Karolinska Biomics Center,Karolinska University Hospital, Stockholm, Sweden
Sanjeeva Srivastava, Department of Agricultural, Food and Nutritional Science, Uni-versity of Alberta, Edmonton, Canada
Lloyd W. Sumner, Biological Mass Spectrometry, Plant Biology Division, TheSamuel Roberts Noble Foundation, Ardmore, Oklahoma
Yew-Foon Tan, ARC Centre of Excellence in Plant Energy Biology, The Universityof Western Australia, Crawley, Australia
Nicolas Tsesmetzis, John Innes Centre, Norwich, England
Shuyang Tu, Center of Proteomic Analysis, Beijing Genomics Institute, ChineseAcademy of Sciences, Beijing, China
Joachim F. Uhrig, Botanical Institute III, University of Köln, Köln, Germany
xxviii CONTRIBUTORS
William H. Vensel, U.S. Department of Agriculture, Agricultural Research Service,Western Regional Research Center, Albany, California
Lori A. Vickerman, Department of Biological Sciences, University of Calgary, Cal-gary, Alberta, Canada
Anne von Zychlinski, Institute of Plant Sciences, ETH Zurich, Zurich, Switzerland
Bonnie Watson, Biological Mass Spectrometry, Plant Biology Division, The SamuelRoberts Noble Foundation, Ardmore, Oklahoma
Wolfram Weckwerth, Max Planck Institute of Molecular Plant Physiology, Potsdam,Germany
Åsa M. Wheelock, Karolinska Biomics Center and Department of Medicine, Divisionof Respiratory Medicine, Karolinska Institute, Stockholm, Sweden
Craig E. Wheelock, Karolinska Biomics Center, and Department of Medical Bio-chemistry and Biophysics, Division of Physiological Chemistry II, KarolinskaInstitute, Stockholm, Sweden
Florian Wolschin, Arizona State University, School of Life Sciences, Tempe, Arizona
William Yajima, Department of Agricultural, Food and Nutritional Science, Univer-sity of Alberta, Edmonton, Canada
Chuan-Ming Yeh, Agricultural Biotechnology Research Center, Academia Sinica,Taipei, Taiwan
Kuo-Chen Yeh, Agricultural Biotechnology Research Center, Academia Sinica,Taipei, Taiwan
Jiyuan Zhang, Center of Proteomic Analysis, Beijing Genomics Institute, ChineseAcademy of Sciences, Beijing, China
Jian-Hua Zhao, Department of Chemical Engineering and Biotechnology, NationalTaipei University of Technology, Taipei, Taiwan
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