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...
Gespeichert in:
Format: | Buch |
---|---|
Sprache: | English |
Veröffentlicht: |
Hoboken, NJ
Wiley
2008
|
Schriftenreihe: | Wiley-Interscience series on mass spectrometry
|
Schlagworte: | |
Online-Zugang: | Publisher description Inhaltsverzeichnis |
Zusammenfassung: | (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. |
Beschreibung: | XLIV, 764 S. Ill. graph. Darst. |
ISBN: | 9780470069769 |
Internformat
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337 | |b n |2 rdamedia | ||
338 | |b nc |2 rdacarrier | ||
490 | 0 | |a Wiley-Interscience series on mass spectrometry | |
520 | 3 | |a (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. | |
650 | 4 | |a Protéines végétales | |
650 | 4 | |a Protéomique végétale | |
650 | 4 | |a Organelles | |
650 | 4 | |a Plant Proteins |x analysis | |
650 | 4 | |a Plant Proteins |x metabolism | |
650 | 4 | |a Plant proteins | |
650 | 4 | |a Plant proteomics | |
650 | 4 | |a Proteome |x analysis | |
650 | 4 | |a Proteomics |x methods | |
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Datensatz im Suchindex
_version_ | 1804137703053197312 |
---|---|
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 |
any_adam_object | 1 |
any_adam_object_boolean | 1 |
building | Verbundindex |
bvnumber | BV023347211 |
callnumber-first | Q - Science |
callnumber-label | QK898 |
callnumber-raw | QK898.P8 |
callnumber-search | QK898.P8 |
callnumber-sort | QK 3898 P8 |
callnumber-subject | QK - Botany |
classification_rvk | WC 4460 WD 5100 |
ctrlnum | (OCoLC)184925240 (DE-599)BVBBV023347211 |
dewey-full | 572.62 572/.62 |
dewey-hundreds | 500 - Natural sciences and mathematics |
dewey-ones | 572 - Biochemistry |
dewey-raw | 572.62 572/.62 |
dewey-search | 572.62 572/.62 |
dewey-sort | 3572.62 |
dewey-tens | 570 - Biology |
discipline | Biologie |
discipline_str_mv | Biologie |
format | Book |
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genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
genre_facet | Aufsatzsammlung |
id | DE-604.BV023347211 |
illustrated | Illustrated |
index_date | 2024-07-02T21:03:51Z |
indexdate | 2024-07-09T21:16:30Z |
institution | BVB |
isbn | 9780470069769 |
language | English |
lccn | 2007051404 |
oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016530875 |
oclc_num | 184925240 |
open_access_boolean | |
owner | DE-355 DE-BY-UBR DE-11 DE-188 |
owner_facet | DE-355 DE-BY-UBR DE-11 DE-188 |
physical | XLIV, 764 S. Ill. graph. Darst. |
publishDate | 2008 |
publishDateSearch | 2008 |
publishDateSort | 2008 |
publisher | Wiley |
record_format | marc |
series2 | Wiley-Interscience series on mass spectrometry |
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 |
work_keys_str_mv | AT agrawalganeshkumar plantproteomicstechnologiesstrategiesandapplications |