Plant Proteomics

Name: Plant Proteomics | Technologies, Strategies, and Applications
Brand: Wiley
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Technologies, Strategies, and Applications

Ganesh K. Agrawal Randeep Rakwal(Herausgeber*in)

Wiley (Verlag)

Erschienen am 8. Oktober 2008

600 Seiten

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978-0-470-36983-8 (ISBN)

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Inhalt

Intro
PLANT PROTEOMICS
CONTENTS
PREFACE
CONTRIBUTORS
ACRONYMS AND ABBREVIATIONS
1 AN INTRODUCTION TO PROTEOMICS: APPLICATIONS TO PLANT BIOLOGY
1.1 Proteomics Defined
1.2 Proteomics Applied
References
PART I TECHNOLOGIES
2 GEL-BASED PROTEOMICS
2.1 Introduction and Brief Bibliographic Review
2.2 SDS-PAGE
2.3 IEF
2.4 2D Maps
2.5 Conclusions
2.6 Five-Year Viewpoint
References
3 MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYING PLANT PROTEINS
3.1 Introduction and Brief Bibliographic Review
3.2 Instrumentation
3.3 MALDI
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
4 CHEMICAL PROTEOMICS
4.1 Introduction
4.2 Strategies For Activity-Based Protein Profiling (ABPP)
4.3 Case Study: Development of Molecular Tools Targeting Plant Kinases
4.4 Conclusions
4.5 Five-Year Viewpoint
References
5 THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEIN LOCALIZATION AND INTERACTIONS IN ARABIDOPSIS
5.1 Protein Compartmentalization in Plant Cells
5.2 Experimental Determination of Protein Localization
5.3 In Vivo Imaging Approaches to Protein Localization and Interaction
5.4 Plant Cell Cultures for Studying Protein Localization
5.5 Protein-Protein Interaction In Vivo: FRET
5.6 Perspectives: Integrating Predictive and Experimental Protein Localization Data
References
6 SECRETOME: TOWARD DECIPHERING THE SECRETORY PATHWAYS AND BEYOND
6.1 Introduction and Brief Bibliographic Review
6.2 Methodology and Strategy
6.3 A Case Study: In Planta and In Vitro Protein Profiles of Soluble and Secreted Proteins in Rice
6.4 Conclusions
6.5 Five-Year Viewpoint
References
7 PEPTIDOMICS
7.1 Introduction and Brief Bibliographic Review
7.2 Separation Technology
7.3 MS Technology
7.4 Bioinformatics and Data Mining
7.5 Differential Peptide Display
7.6 ID LC-MALDI
7.7 2D CA-RP-LC-ESI-MS
7.8 Applications
7.9 Peptides and Proteases
7.10 Conclusions
7.11 Five-Year Viewpoint
References
PART II COMPUTATIONAL PROTEOMICS
8 BIOINFORMATICS IN GEL-BASED PROTEOMICS
8.1 Introduction and Brief Bibliographic Review
8.2 Methodology and Strategy
8.3 Experimental Results and Applications
8.4 Conclusions
8.5 Five-Year Viewpoint
References
9 BIOINFORMATICS IN MS-BASED PROTEOMICS
9.1 Introduction
9.2 Database Searching
9.3 Peptide De Novo Sequencing
9.4 Conclusions and Five-Year Viewpoint
References
PART III EXPRESSION PROTEOMICS
10 AN OVERVIEW OF THE ARABIDOPSIS PROTEOME
10.1 Introduction and Brief Bibliographic Review
10.2 Methodology and Strategy
10.3 Experimental Results and Applications
10.4 Conclusions
10.5 Five-Year Viewpoint
References
11 RICE PROTEOME AT A GLANCE
11.1 Introduction and Brief Bibliographic Review
11.2 Methodology and Strategy
11.3 Experimental Results and Applications
11.4 Conclusions
11.5 Five-Year Viewpoint
References
12 PROTEOMICS OF LEGUME PLANTS
12.1 Introduction and Brief Bibliographic Review
12.2 Proteomics of Model Legume Medicago truncatula
12.3 Proteomics of Model System Lotus japonicus
12.4 Proteomics of Soybean, Glycine max
12.5 Proteomics of Alfalfa, Medicago sativa
12.6 Conclusions
12.7 Five-Year Viewpoint
References
13 PROTEOME OF SEED DEVELOPMENT AND GERMINATION
13.1 Introduction
13.2 Proteomics of Developing Seeds
13.3 Proteomics of Mature Seeds
13.4 Proteomics of Germinating Seeds
13.5 Proteomics of Somatic Embryogenesis
13.6 Metabolic Control of Seed Development and Germination
13.7 Conclusions
13.8 Five-year Viewpoint
References
14 ENDOSPERM AND AMYLOPLAST PROTEOMES OF WHEAT GRAIN
14.1 Introduction
14.2 Fractionation and Analysis of Endosperm Proteins
14.3 The Endosperm Proteome
14.4 The Amyloplast Proteome
14.5 Conclusions
14.6 Five-Year Viewpoint
References
15 ROOT PROTEOME
15.1 Introduction
15.2 Application of Proteomics in the Study of Root Development
15.3 Proteome Analysis of Response to Plant Hormones
15.4 Proteome Analysis of Gravity Response
15.5 Action to Microbe-Plant Symbiosis
15.6 Proteome to Cope With Environmental Stresses
15.7 Conclusions and Five-Year Viewpoint
References
16 LEAF PROTEOME
16.1 Introduction
16.2 Proteomics Studies in Plant Leaf
16.3 Conclusions
16.4 Five-Year Viewpoint
References
17 ANTHER PROTEOME
17.1 Introduction and Brief Bibliographic Review
17.2 Methodology and Strategy
17.3 Conclusions
17.4 Five-Year Viewpoint
References
18 POLLEN PROTEOME
18.1 Introduction
18.2 Bibliographic Review: Pollen Development and Function
18.3 Methodology and Experimental Results
18.4 Conclusions
18.5 Five-Year Viewpoint
References
19 MICROTUBULE-BINDING PROTEINS
19.1 Introduction
19.2 Brief Bibliographic Review
19.3 Strategies and Methodologies
19.4 Experimental Results and Applications
19.5 Conclusions
19.6 Five-Year Viewpoint
References
PART IV ORGANELLE PROTEOMICS
20 CELL WALL
20.1 Introduction
20.2 Brief Bibliographic Review
20.3 Specific Methodology and Strategies
20.4 Experimental Results and Applications
20.5 Conclusions
20.6 Five-Year Viewpoint
References
21 PLASMA MEMBRANE: A PECULIAR STATUS AMONG THE CELL MEMBRANE SYSTEMS
21.1 Introduction and Brief Bibliographic Review
21.2 Specific Methodologies and Strategies (Box 21.1)
21.3 Experimental Results and Applications: Toward an Informative Database of the Plant PM Proteome
21.4 Conclusions
21.5 Five-Year Viewpoint
References
22 NUCLEUS
22.1 Introduction and Brief Bibliographic Review
22.2 Methodology and Strategy
22.3 Experimental Results and Discussion
22.4 Conclusions
22.5 Five-Year Viewpoint
References
23 CHLOROPLAST
23.1 Introduction
23.2 Brief Bibliographic Review
23.3 Methodology and Strategy
23.4 Experimental Results and Applications
23.5 Conclusions
23.6 Five-Year Viewpoint
References
24 ETIOPLAST
24.1 Introduction
24.2 Etioplast Proteome Analysis
24.3 Conclusions
24.4 Five-Year Viewpoint
References
25 THE PLANT MITOCHONDRIAL PROTEOME AND THE CHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS
25.1 Introduction
25.2 Brief Bibliographic Review
25.3 Methodology and Strategy
25.4 Experimental Results and Applications
25.5 Conclusions
25.6 Five-Year Viewpoint
References
26 PEROXISOME
26.1 Introduction
26.2 Brief Bibliographic Review
26.3 Specific Methodologies and Strategies
26.4 Experimental Results and Applications
26.5 Conclusions
26.6 Five-Year Viewpoint
References
27 UNRAVELING PLANT VACUOLES BY PROTEOMICS
27.1 Introduction
27.2 Bibliographic Review: Role of Proteomics in Understanding Biology of Plant Vacuoles
27.3 Methodology and Strategies
27.4 A Case-Study of Label-Free Quantitative Proteomics
27.5 Conclusions
27.6 Five-Year Viewpoint
References
28 OIL BODIES
28.1 Introduction and Brief Bibliographic Review
28.2 Methodology and Strategy
28.3 Conclusions
28.4 Five-Year Viewpoint
References
PART V MODIFICATION PROTEOMICS
29 PHOSPHOPROTEINS: WHERE ARE WE TODAY?
29.1 Introduction
29.2 Phosphoprotein and Phosphopeptide Enrichment
29.3 Detection of Protein Phosphorylation and Determination of Phosphorylation Sites
29.4 MS-Based Approaches
29.5 Biological Implications of Protein Multisite Phosphorylation in Plants
29.6 Large-Scale Proteomics Studies
29.7 Conclusions and Five-Year Viewpoint
References
30 PROTEOME ANALYSIS OF THE UBIQUITIN PATHWAY
30.1 Introduction
30.2 Brief Bibliographic Review
30.3 Specific Methodologies and Strategies
30.4 Experimental Results and Applications
30.5 Conclusions
30.6 Five-Year Viewpoint
References
31 ANALYSIS OF THE N-GLYCOSYLATION OF PROTEINS IN PLANTS
31.1 Introduction
31.2 Brief Bibliographic Review
31.3 Methodology and Strategy
31.4 Conclusions
31.5 Five-Year Viewpoint
References
32 FUNCTIONAL ANALYSIS AND PHOSPHORYLATION SITE MAPPING OF LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASES
32.1 Introduction and Brief Bibliographic Review
32.2 Specific Methodologies and Strategies
32.3 Experimental Results and Applications
32.4 Conclusions and Five-Year Viewpoint
References
33 TIME TO SEARCH FOR PROTEIN KINASE SUBSTRATES
33.1 Introduction and Brief Bibliographic Review
33.2 Methodology and Strategy
33.3 Experimental Results on Plant MAPK Downstream Signaling and Applications
33.4 Conclusions
33.5 Five-Year Viewpoint
References
34 TYROSINE PHOSPHORYLATION IN PLANTS: EMERGING EVIDENCE
34.1 Introduction
34.2 Brief Bibliographic Review
34.3 Methodology and Strategy
34.4 Experimental Results and Applications
34.5 Conclusions
34.6 Five-Year Viewpoint
References
35 14-3-3 PROTEINS: REGULATORS OF KEY CELLULAR FUNCTIONS
35.1 Introduction and Brief Bibliographic Review
35.2 Methodology and Strategy
35.3 Experimental Results and Applications
35.4 Conclusions
35.5 Five-Year Viewpoint
References
PART VI MULTIPROTEIN COMPLEX
36 TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX ISOLATION
36.1 Introduction
36.2 Methodolgy and Strategy
36.3 Experimental Results and Applications
36.4 Conclusions
36.5 Five-Year Viewpoint
References
37 TAP STRATEGY IN ARABIDOPSIS PROTEIN COMPLEX ISOLATION
37.1 Introduction and Brief Bibliographic Review
37.2 Specific Methodology and Strategies
37.3 Experimental Results and Applications
37.4 Conclusions
37.5 Five-Year Viewpoint
References
38 BLUE-NATIVE PAGE IN STUDYING PROTEIN COMPLEXES
38.1 Introduction
38.2 Brief Bibliographic Review
38.3 Methodology and Strategy
38.4 Experimental Results and Applications
38.5 Conclusions
38.6 Five-Year Viewpoint
References
39 PROTEIN-PROTEIN INTERACTION MAPPING IN PLANTS
39.1 Introduction and Brief Bibliographic Review
39.2 Methodology and Strategy
39.3 Experimental Results and Applications
39.4 Conclusions
39.5 Five-Year Viewpoint
References
PART VII PLANT DEFENSE AND STRESS
40 PROTEOMICS IN PLANT DEFENSE RESPONSE
40.1 Introduction
40.2 Brief Bibliographic Review
40.3 Methodology and Strategies
40.4 Experimental Results and Applications
40.5 Conclusions
40.6 Five-Year Viewpoint
References
41 PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTIC STRESSES IN PLANTS
41.1 Introduction and Brief Bibliographic Review
41.2 Summary of Previous Research on Abiotic Stresses in Plants
41.3 Comparision of Transcriptomics and Proteomics Data in Analysis of Plant Defense Responses Against Abiotic Stress Factors
41.4 Conclusions
41.5 Five-Year Viewpoint
References
42 PROTEOMICS OF BIOTROPHIC PLANT-MICROBE INTERACTIONS: SYMBIOSES LEAD THE MARCH
42.1 Introduction
42.2 AM and RNF Symbioses: No Equal Footing for Proteomics
42.3 A 2005-2006 Update of the Contribution of Proteomics to AM Symbiosis
42.4 A 2005-2006 Update of the Contribution of Proteomics to RNF Symbiosis
42.5 Conclusions
42.6 Five-Year Viewpoint
References
43 PROTEOMICS APPROACHES TO CONSTRUCT CALCIUM SIGNALING NETWORKS IN PLANTS
43.1 Introduction and Brief Bibliographic Review
43.2 Methodology and Experimental Results
43.3 Conclusions
43.4 Five-Year Viewpoint
References
PART VIII STRUCTURAL PROTEOMICS
44 CELL-FREE EXPRESSION SYSTEM FOR EUKARYOTIC PROTEINS
44.1 Introduction
44.2 Development of Wheat Germ Cell-Free Protein Synthesis System
44.3 Application to Functional Proteomics
44.4 Application to Structural Proteomics
44.5 Conclusions and Five-Year Viewpoint
References
45 PROTEIN STRUCTURE DETERMINATION
45.1 Introduction
45.2 Instrumental Methods for Protein Structure Determination
45.3 Computational Approaches for Protein Structure Prediction
45.4 Conclusions
45.5 Five-Year Viewpoint
References
PART IX OTHER TOPICS IN PLANT PROTEOMICS
46 PROTEOMICS IN CONTEXT OF SYSTEMS BIOLOGY
46.1 Introduction
46.2 What Systems Biology Requires
46.3 What Proteomics Provides
46.4 Representation of Information About Proteins and Their Integration into Systems Biology Tools
46.5 Conclusions
46.6 Five-Year Viewpoint
References
47 PROTEOMICS IN DEVELOPING COUNTRIES
47.1 Introduction
47.2 Proteome Research in the Developing World
47.3 Conclusions
47.4 Five-Year Viewpoint
References
INDEX

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