Holdings: Plant proteomics :: THWS Bibkatalog

Plant proteomics: technologies, strategies, and applications

(Publisher-supplied data) This book aims to answer the questions: What have we learned from proteomic studies in plants? What is the current status of plant proteomics with respect to technologies and achievements? How do we design and conduct proteomic experiments? And, finally, where will plant pr...

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Bibliographic Details
Format:	Book
Language:	English
Published:	Hoboken, NJ Wiley 2008
Series:	Wiley-Interscience series on mass spectrometry
Subjects:	Protéines végétales Protéomique végétale Organelles Plant Proteins > analysis Plant Proteins > metabolism Plant proteins Plant proteomics Proteome > analysis Proteomics > methods Proteomanalyse Pflanzliche Proteine Proteom Pflanzen Aufsatzsammlung
Online Access:	Publisher description Inhaltsverzeichnis
Summary:	(Publisher-supplied data) This book aims to answer the questions: What have we learned from proteomic studies in plants? What is the current status of plant proteomics with respect to technologies and achievements? How do we design and conduct proteomic experiments? And, finally, where will plant proteomics take us in the near future? Because there are so few books focusing specifically on plant proteomics, this volume will have a tremendous impact on plant proteomics research.
Physical Description:	XLIV, 764 S. Ill. graph. Darst.
ISBN:	9780470069769

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Record in the Search Index

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adam_text	CONTENTS PREFACE xix CONTRIBUTORS xxiii ACRONYMS AND ABBREVIATIONS xxix 1 AN INTRODUCTION TO PROTEOMICS: APPLICATIONS TO PLANT BIOLOGY 1 Ralph A. Bradshaw 1.1 Proteomics Defined 2 1.2 Proteomics Applied 5 References 6 PART I TECHNOLOGIES GEL-BASED PROTEOMICS 11 Pier Giorgio Righetti, Paolo Antonioli, Carolina Simó, and Attilio Citterio 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 MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYING PLANT PROTEINS 33 Eveline Bergmüller, Sacha Baginsky, and Wilhelm Gruissem 3.1 Introduction and Brief Bibliographic Review 33 3.2 Instrumentation 34 3.3 MALDI 35 3.4 ESI 3.5 Mass Analyzers 3.6 Ion Detectors 3.7 Sample Preparation 3.8 Protein Identification 3.9 Conclusions 3.10 Five-Year Viewpoint References Vi CONTENTS 36 36 38 39 40 44 44 44 4 CHEMICAL PROTEOMICS 47 Miriam С 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 Plant Kinases 53 4.4 Conclusions 57 4.5 Fi ve- Year Viewpoint 58 References 58 5 THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEIN LOCALIZATION AND INTERACTIONS IN ARABIDOPSIS 61 Georgios 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 Protein Localization Data 77 References 77 6 SECRETOME: TOWARD DECIPHERING THE SECRETORY PATHWAYS AND BEYOND 83 Young -Но 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 Soluble and Secreted Proteins in Rice 87 CONTENTS VÜ 6.4 Conclusions 87 6.5 Five-Year Viewpoint 89 References 89 7 PEPTIDOMICS 91 Peter 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 PROTEOMICS 8 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 127 Jacques 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 VÜi CONTENTS PART III EXPRESSION PROTEOMICS 10 AN OVERVIEW OF THE ARABfDOPSIS 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 165 Ganesh 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 179 Satish 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 191 Julie Catusse, Loïc 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 ІХ 13.7 Conclusions 204 13.8 Five-year Viewpoint 205 References 205 14 ENDOSPERM AND AMYLOPLAST PROTEOMES OF WHEAT GRAIN 207 William J. Hurktnan, 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 Fi ve- Year Viewpoint 219 References 220 15 ROOT PROTEOME 223 Kuo-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 239 Bin 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 Fi ve- Year Viewpoint 247 References 248 17 ANTHER PROTEOME 249 Nijat 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 261 Sandra 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 275 Lori 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 Fi ve- Year Viewpoint 287 References 287 PART IV ORGANELLE PROTEOMICS 20 CELL WALL 293 Elisabeth Jamet, Hervé Canut, Cécile Alberine, Georges Boudart, and Rafael 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 CELL MEMBRANE SYSTEMS 309 Geneviève 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 ХІ 21.3 Experimental Results and Applications: Toward an Informative Database of the Plant PM Proteome 319 21.4 Conclusions 323 21.5 Five-Year Viewpoint 324 References 325 22 NUCLEUS 327 Subhra 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 339 Thomas 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 351 Anne von Zychlinski, Sonja Reiland, Wilhelm Gruíssem, and Sacha Baginsky 24.1 Introduction 351 24.2 Etíoplast Proteome Analysis 352 24.3 Conclusions 358 24.4 Five-Year Viewpoint 359 References 359 25 THE PLANT MITOCHONDRIAL PROTEOME AND THE CHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS 361 Yew-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 χϋ CONTENTS 25.5 Conclusions 373 25.6 Five-Year Viewpoint 373 References 374 26 PEROXISOME 377 Yuko 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 391 Songqin Pan and Natasha Raikhel 27.1 Introduction 391 27.2 Bibliographic Review: Role of Proteomics in Understanding Biology 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 407 Pascale Jolìvet, Luc Negroni, Sabine d Andréa, and Thierry Chardoî 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 PROTEOMICS 29 PHOSPHOPROTEINS: WHERE ARE WE TODAY? 421 Florian Wolschin and Wolfram Weckwerth 29 Λ Introduction 421 29.2 Phosphoprotein and Phosphopeptide Enrichment 422 CONTENTS ХІІІ 29.3 Detection of Protein Phosphorylation and Determination of Phosphorylation Sites 427 29.4 MS-Based Approaches 432 29.5 Biological Implications of Protein Multisite Phosphorylation in Plants 434 29.6 Large-Scale Proteomics Studies 437 29.7 Conclusions and Five-Year Viewpoint 438 References 438 30 PROTEOME ANALYSIS OF THE UBIQU1TIN PATHWAY 443 Junmin 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 «-GLYCOSYLATION OF PROTEINS IN PLANTS 455 Willy 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 SITE MAPPING OF LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASES 469 Steven 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 RÍÑASE SUBSTRATES 485 Birgit Kersten 33.1 Introduction and Brief Bibliographic Review 485 33.2 Methodology and Strategy 486 xiv CONTENTS 33.3 Experimental Results on Plant МАРК Downstream Signaling and Applications 494 33.4 Conclusions 496 33.5 Five-Year Viewpoint 496 References 497 34 TYROSINE PHOSPHORYLATION IN PLANTS: EMERGING EVIDENCE 499 Andrea 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 CELLULAR FUNCTIONS 515 Peter 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 COMPLEX 36 TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX ISOLATION 527 Jai 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 COMPLEX ISOLATION 543 Vicente 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 557 Holger 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 Fi ve- Year Viewpoint 567 References 568 39 PROTEIN-PROTEIN INTERACTION MAPPING IN PLANTS 571 Joachim 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 STRESS 40 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 CONTENTS 40.6 Five-Year Viewpoint 602 References 603 41 PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTIC STRESSES IN PLANTS 605 Hans-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 of Plant Defense Responses Against Abiotic Stress Factors 621 41.4 Conclusions 624 41.5 Fi ve- Year Viewpoint 624 References 625 42 PROTEOMICS OF BIOTROPHIC PLANT-MICROBE INTERACTIONS: SYMBIOSES LEAD THE MARCH 629 Ghislaine Recorbet and Elione 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 AM Symbiosis 634 42.4 A 2005-2006 Update of the Contribution of Proteomics to RNF Symbiosis 637 42.5 Conclusions 640 42.6 Five-Year Viewpoint 640 References 642 43 PROTEOMICS APPROACHES TO CONSTRUCT CALCIUM SIGNALING NETWORKS IN PLANTS 645 Irene 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 PROTEOMICS 44 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 671 Jian-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 PROTEOMICS 46 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 Integration into Systems Biology Tools 706 46.5 Conclusions 708 46.6 Five-Year Viewpoint 708 References 709 47 PROTEOMICS IN DEVELOPING COUNTRIES 713 Nat N. V. Καν, Sanjeeva Srivastava, William Yajima, and Shakir AH 47.1 Introduction 713 47.2 Proteome Research in the Developing World 719 47.3 Conclusions 725 47.4 Fi ve- Year Viewpoint 726 References 726 INDEX 731
adam_txt	CONTENTS PREFACE xix CONTRIBUTORS xxiii ACRONYMS AND ABBREVIATIONS xxix 1 AN INTRODUCTION TO PROTEOMICS: APPLICATIONS TO PLANT BIOLOGY 1 Ralph A. Bradshaw 1.1 Proteomics Defined 2 1.2 Proteomics Applied 5 References 6 PART I TECHNOLOGIES GEL-BASED PROTEOMICS 11 Pier Giorgio Righetti, Paolo Antonioli, Carolina Simó, and Attilio Citterio 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 MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYING PLANT PROTEINS 33 Eveline Bergmüller, Sacha Baginsky, and Wilhelm Gruissem 3.1 Introduction and Brief Bibliographic Review 33 3.2 Instrumentation 34 3.3 MALDI 35 3.4 ESI 3.5 Mass Analyzers 3.6 Ion Detectors 3.7 Sample Preparation 3.8 Protein Identification 3.9 Conclusions 3.10 Five-Year Viewpoint References Vi CONTENTS 36 36 38 39 40 44 44 44 4 CHEMICAL PROTEOMICS 47 Miriam С 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 Plant Kinases 53 4.4 Conclusions 57 4.5 Fi ve- Year Viewpoint 58 References 58 5 THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEIN LOCALIZATION AND INTERACTIONS IN ARABIDOPSIS 61 Georgios 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 Protein Localization Data 77 References 77 6 SECRETOME: TOWARD DECIPHERING THE SECRETORY PATHWAYS AND BEYOND 83 Young -Но 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 Soluble and Secreted Proteins in Rice 87 CONTENTS VÜ 6.4 Conclusions 87 6.5 Five-Year Viewpoint 89 References 89 7 PEPTIDOMICS 91 Peter 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 PROTEOMICS 8 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 127 Jacques 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 VÜi CONTENTS PART III EXPRESSION PROTEOMICS 10 AN OVERVIEW OF THE ARABfDOPSIS 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 165 Ganesh 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 179 Satish 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 191 Julie Catusse, Loïc 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 ІХ 13.7 Conclusions 204 13.8 Five-year Viewpoint 205 References 205 14 ENDOSPERM AND AMYLOPLAST PROTEOMES OF WHEAT GRAIN 207 William J. Hurktnan, 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 Fi ve- Year Viewpoint 219 References 220 15 ROOT PROTEOME 223 Kuo-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 239 Bin 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 Fi ve- Year Viewpoint 247 References 248 17 ANTHER PROTEOME 249 Nijat 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 261 Sandra 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 275 Lori 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 Fi ve- Year Viewpoint 287 References 287 PART IV ORGANELLE PROTEOMICS 20 CELL WALL 293 Elisabeth Jamet, Hervé Canut, Cécile Alberine, Georges Boudart, and Rafael 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 CELL MEMBRANE SYSTEMS 309 Geneviève 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 ХІ 21.3 Experimental Results and Applications: Toward an Informative Database of the Plant PM Proteome 319 21.4 Conclusions 323 21.5 Five-Year Viewpoint 324 References 325 22 NUCLEUS 327 Subhra 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 339 Thomas 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 351 Anne von Zychlinski, Sonja Reiland, Wilhelm Gruíssem, and Sacha Baginsky 24.1 Introduction 351 24.2 Etíoplast Proteome Analysis 352 24.3 Conclusions 358 24.4 Five-Year Viewpoint 359 References 359 25 THE PLANT MITOCHONDRIAL PROTEOME AND THE CHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS 361 Yew-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 χϋ CONTENTS 25.5 Conclusions 373 25.6 Five-Year Viewpoint 373 References 374 26 PEROXISOME 377 Yuko 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 391 Songqin Pan and Natasha Raikhel 27.1 Introduction 391 27.2 Bibliographic Review: Role of Proteomics in Understanding Biology 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 407 Pascale Jolìvet, Luc Negroni, Sabine d'Andréa, and Thierry Chardoî 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 PROTEOMICS 29 PHOSPHOPROTEINS: WHERE ARE WE TODAY? 421 Florian Wolschin and Wolfram Weckwerth 29 Λ Introduction 421 29.2 Phosphoprotein and Phosphopeptide Enrichment 422 CONTENTS ХІІІ 29.3 Detection of Protein Phosphorylation and Determination of Phosphorylation Sites 427 29.4 MS-Based Approaches 432 29.5 Biological Implications of Protein Multisite Phosphorylation in Plants 434 29.6 Large-Scale Proteomics Studies 437 29.7 Conclusions and Five-Year Viewpoint 438 References 438 30 PROTEOME ANALYSIS OF THE UBIQU1TIN PATHWAY 443 Junmin 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 «-GLYCOSYLATION OF PROTEINS IN PLANTS 455 Willy 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 SITE MAPPING OF LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASES 469 Steven 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 RÍÑASE SUBSTRATES 485 Birgit Kersten 33.1 Introduction and Brief Bibliographic Review 485 33.2 Methodology and Strategy 486 xiv CONTENTS 33.3 Experimental Results on Plant МАРК Downstream Signaling and Applications 494 33.4 Conclusions 496 33.5 Five-Year Viewpoint 496 References 497 34 TYROSINE PHOSPHORYLATION IN PLANTS: EMERGING EVIDENCE 499 Andrea 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 CELLULAR FUNCTIONS 515 Peter 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 COMPLEX 36 TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX ISOLATION 527 Jai 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 COMPLEX ISOLATION 543 Vicente 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 557 Holger 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 Fi ve- Year Viewpoint 567 References 568 39 PROTEIN-PROTEIN INTERACTION MAPPING IN PLANTS 571 Joachim 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 STRESS 40 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 CONTENTS 40.6 Five-Year Viewpoint 602 References 603 41 PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTIC STRESSES IN PLANTS 605 Hans-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 of Plant Defense Responses Against Abiotic Stress Factors 621 41.4 Conclusions 624 41.5 Fi ve- Year Viewpoint 624 References 625 42 PROTEOMICS OF BIOTROPHIC PLANT-MICROBE INTERACTIONS: SYMBIOSES LEAD THE MARCH 629 Ghislaine Recorbet and Elione 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 AM Symbiosis 634 42.4 A 2005-2006 Update of the Contribution of Proteomics to RNF Symbiosis 637 42.5 Conclusions 640 42.6 Five-Year Viewpoint 640 References 642 43 PROTEOMICS APPROACHES TO CONSTRUCT CALCIUM SIGNALING NETWORKS IN PLANTS 645 Irene 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 PROTEOMICS 44 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 671 Jian-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 PROTEOMICS 46 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 Integration into Systems Biology Tools 706 46.5 Conclusions 708 46.6 Five-Year Viewpoint 708 References 709 47 PROTEOMICS IN DEVELOPING COUNTRIES 713 Nat N. V. Καν, Sanjeeva Srivastava, William Yajima, and Shakir AH 47.1 Introduction 713 47.2 Proteome Research in the Developing World 719 47.3 Conclusions 725 47.4 Fi ve- Year Viewpoint 726 References 726 INDEX 731
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spelling	Plant proteomics technologies, strategies, and applications ed. by Ganesh Kumar Agrawal ... Hoboken, NJ Wiley 2008 XLIV, 764 S. Ill. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wiley-Interscience series on mass spectrometry (Publisher-supplied data) This book aims to answer the questions: What have we learned from proteomic studies in plants? What is the current status of plant proteomics with respect to technologies and achievements? How do we design and conduct proteomic experiments? And, finally, where will plant proteomics take us in the near future? Because there are so few books focusing specifically on plant proteomics, this volume will have a tremendous impact on plant proteomics research. Protéines végétales Protéomique végétale Organelles Plant Proteins analysis Plant Proteins metabolism Plant proteins Plant proteomics Proteome analysis Proteomics methods Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Pflanzliche Proteine (DE-588)4251527-0 gnd rswk-swf Proteom (DE-588)4576155-3 gnd rswk-swf Pflanzen (DE-588)4045539-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Pflanzen (DE-588)4045539-7 s Proteom (DE-588)4576155-3 s DE-188 Proteomanalyse (DE-588)4596545-6 s Pflanzliche Proteine (DE-588)4251527-0 s Agrawal, Ganesh Kumar Sonstige oth http://www.loc.gov/catdir/enhancements/fy0808/2007051404-d.html Publisher description Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016530875&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Plant proteomics technologies, strategies, and applications Protéines végétales Protéomique végétale Organelles Plant Proteins analysis Plant Proteins metabolism Plant proteins Plant proteomics Proteome analysis Proteomics methods Proteomanalyse (DE-588)4596545-6 gnd Pflanzliche Proteine (DE-588)4251527-0 gnd Proteom (DE-588)4576155-3 gnd Pflanzen (DE-588)4045539-7 gnd
subject_GND	(DE-588)4596545-6 (DE-588)4251527-0 (DE-588)4576155-3 (DE-588)4045539-7 (DE-588)4143413-4
title	Plant proteomics technologies, strategies, and applications
title_auth	Plant proteomics technologies, strategies, and applications
title_exact_search	Plant proteomics technologies, strategies, and applications
title_exact_search_txtP	Plant proteomics technologies, strategies, and applications
title_full	Plant proteomics technologies, strategies, and applications ed. by Ganesh Kumar Agrawal ...
title_fullStr	Plant proteomics technologies, strategies, and applications ed. by Ganesh Kumar Agrawal ...
title_full_unstemmed	Plant proteomics technologies, strategies, and applications ed. by Ganesh Kumar Agrawal ...
title_short	Plant proteomics
title_sort	plant proteomics technologies strategies and applications
title_sub	technologies, strategies, and applications
topic	Protéines végétales Protéomique végétale Organelles Plant Proteins analysis Plant Proteins metabolism Plant proteins Plant proteomics Proteome analysis Proteomics methods Proteomanalyse (DE-588)4596545-6 gnd Pflanzliche Proteine (DE-588)4251527-0 gnd Proteom (DE-588)4576155-3 gnd Pflanzen (DE-588)4045539-7 gnd
topic_facet	Protéines végétales Protéomique végétale Organelles Plant Proteins analysis Plant Proteins metabolism Plant proteins Plant proteomics Proteome analysis Proteomics methods Proteomanalyse Pflanzliche Proteine Proteom Pflanzen Aufsatzsammlung
url	http://www.loc.gov/catdir/enhancements/fy0808/2007051404-d.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016530875&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
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