Technologies, Strategies, and Applications fileWiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic

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


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


3.2 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


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


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


6.2 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


References 89

7 PEPTIDOMICS 91Peter Schulz-Knappe


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


References 103

PART II COMPUTATIONAL PROTEOMICS8 BIOINFORMATICS IN GEL-BASED PROTEOMICS 107

Åsa M. Wheelock and Craig E. Wheelock



8.3 Experimental Results and Applications 120

8.4 Conclusions 122


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






References 161

11 RICE PROTEOME AT A GLANCE 165Ganesh Kumar Agrawal and Randeep Rakwal






References 178

12 PROTEOMICS OF LEGUME PLANTS 179Satish Nagaraj, Zhentian Lei, Bonnie Watson, and Lloyd W. Sumner


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



References 187

13 PROTEOME OF SEED DEVELOPMENT AND GERMINATION 191Julie Catusse, Loı̈c Rajjou, Claudette Job, and Dominique Job


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


13.8 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


14.2 Fractionation and Analysis of Endosperm Proteins 208

14.3 The Endosperm Proteome 210

14.4 The Amyloplast Proteome 215



References 220

15 ROOT PROTEOME 223Kuo-Chen Yeh, Chyi-Chuann Chen, and Chuan-Ming Yeh


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


References 237

16 LEAF PROTEOME 239Bin Kang, Shuyang Tu, Jiyuan Zhang, and Siqi Liu


16.2 Proteomics Studies in Plant Leaf 240



References 248

17 ANTHER PROTEOME 249Nijat Imin




x CONTENTS


References 259

18 POLLEN PROTEOME 261Sandra Noir


18.2 Bibliographic Review: Pollen Development and Function 262

18.3 Methodology and Experimental Results 264



References 272

19 MICROTUBULE-BINDING PROTEINS 275Lori A. Vickerman and Douglas G. Muench


19.2 Brief Bibliographic Review 276

19.3 Strategies and Methodologies 277




References 287

PART IV ORGANELLE PROTEOMICS20 CELL WALL 293

Elisabeth Jamet, Hervé Canut, Cécile Albenne, Georges Boudart, andRafael Pont-Lezica



20.3 Specific Methodology and Strategies 296




References 306

21 PLASMA MEMBRANE: A PECULIAR STATUS AMONG THE CELLMEMBRANE SYSTEMS 309Geneviève Ephritikhine, Anne Marmagne, Thierry Meinnel, and Myriam Ferro


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



References 325

22 NUCLEUS 327Subhra Chakraborty, Aarti Pandey, Asis Datta, and Niranjan Chakraborty



22.3 Experimental Results and Discussion 330



References 337

23 CHLOROPLAST 339Thomas Kieselbach and Wolfgang P. Schröder







References 349

24 ETIOPLAST 351Anne von Zychlinski, Sonja Reiland, Wilhelm Gruissem,and Sacha Baginsky


24.2 Etioplast Proteome Analysis 352



References 359

25 THE PLANT MITOCHONDRIAL PROTEOME AND THECHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS 361Yew-Foon Tan and A. Harvey Millar





xii CONTENTS



References 374

26 PEROXISOME 377Yuko Arai, Youichiro Fukao, Makoto Hayashi, and Mikio Nishimura



26.3 Specific Methodologies and Strategies 379




References 388

27 UNRAVELING PLANT VACUOLES BY PROTEOMICS 391Songqin Pan and Natasha Raikhel


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



References 404

28 OIL BODIES 407Pascale Jolivet, Luc Negroni, Sabine d’Andréa, and Thierry Chardot





References 416

PART V MODIFICATION PROTEOMICS29 PHOSPHOPROTEINS: WHERE ARE WE TODAY? 421

Florian Wolschin and Wolfram Weckwerth


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


References 438

30 PROTEOME ANALYSIS OF THE UBIQUITIN PATHWAY 443Junmin Peng







References 452

31 ANALYSIS OF THE N-GLYCOSYLATION OF PROTEINSIN PLANTS 455Willy Morelle






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





References 482

33 TIME TO SEARCH FOR PROTEIN KINASE SUBSTRATES 485Birgit Kersten



xiv CONTENTS

33.3 Experimental Results on Plant MAPK Downstream Signaling andApplications 494



References 497

34 TYROSINE PHOSPHORYLATION IN PLANTS: EMERGINGEVIDENCE 499Andrea Carpi, Valeria Rossi, and Francesco Filippini







References 512

35 14–3–3 PROTEINS: REGULATORS OF KEY CELLULARFUNCTIONS 515Peter C. Morris






References 523

PART VI MULTIPROTEIN COMPLEX36 TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX

ISOLATION 527Jai S. Rohila and Michael E. Fromm


36.2 Methodolgy and Strategy 528




References 541

CONTENTS xv

37 TAP STRATEGY IN ARABIDOPSIS PROTEIN COMPLEXISOLATION 543Vicente Rubio and Xing Wang Deng


37.2 Specific Methodology and Strategies 546




References 555

38 BLUE-NATIVE PAGE IN STUDYING PROTEIN COMPLEXES 557Holger Eubel and A. Harvey Millar







References 568

39 PROTEIN–PROTEIN INTERACTION MAPPING IN PLANTS 571Joachim F. Uhrig






References 581

PART VII PLANT DEFENSE AND STRESS40 PROTEOMICS IN PLANT DEFENSE RESPONSE 587

Sun Tae Kim and Kyu Young Kang



40.3 Methodology and Strategies 589



xvi CONTENTS


References 603

41 PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTICSTRESSES IN PLANTS 605Hans-Peter Mock and Andrea Matros


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



References 625

42 PROTEOMICS OF BIOTROPHIC PLANT–MICROBEINTERACTIONS: SYMBIOSES LEAD THE MARCH 629Ghislaine Recorbet and Eliane Dumas-Gaudot


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



References 642

43 PROTEOMICS APPROACHES TO CONSTRUCT CALCIUMSIGNALING NETWORKS IN PLANTS 645Irene S. Day and A.S.N. Reddy


43.2 Methodology and Experimental Results 649



References 657

PART VIII STRUCTURAL PROTEOMICS44 CELL-FREE EXPRESSION SYSTEM FOR EUKARYOTIC PROTEINS 661

Yaeta Endo and Tatsuya Sawasaki


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


References 668

45 PROTEIN STRUCTURE DETERMINATION 671Jian-Hua Zhao and Hsuan-Liang Liu


45.2 Instrumental Methods for Protein Structure Determination 672

45.3 Computational Approaches for Protein Structure Prediction 678



References 689

PART IX OTHER TOPICS IN PLANT PROTEOMICS46 PROTEOMICS IN CONTEXT OF SYSTEMS BIOLOGY 695

Serhiy Souchelnytskyi


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



References 709

47 PROTEOMICS IN DEVELOPING COUNTRIES 713Nat N. V. Kav, Sanjeeva Srivastava, William Yajima, and Shakir Ali


47.2 Proteome Research in the Developing World 719



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.


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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