Plant Proteomics

Ganesh Kumar Agrawal, PhD, is the Associate Director of the Research Laboratory for Biotechnology and Biochemistry (RLABB) in Kathmandu, Nepal. He earned his doctorate in applied biological chemistry at the Tokyo University of Agriculture and Technology in 1998. His research objective is to unravel the "regulatory networks" of the signaling and metabolic pathways in proteomes to improve seed quality and yield in plants using integrated OMICS approaches. Randeep Rakwal, PhD, is presently a researcher on the Tsukuba Mental Stress Team at the Health Technology Research Center (HTRC), National Institute of Advanced Industrial Science and Technology (AIST) in Japan. He earned his doctorate in applied biological chemistry at the Tokyo University of Agriculture and Technology in 1997. His current research focuses on the genomics, proteomics, and metabolomics of environmental stress responses in plant and animal systems.

PREFACE. CONTRIBUTORS.

ACRONYMS AND ABBREVIATIONS.

1. AN INTRODUCTION TO PROTEOMICS: APPLICATIONS TO PLANT BIOLOGY (Ralph A. Bradshaw).

PART I: TECHNOLOGIES.

2. GEL-BASED PROTEOMICS (Pier Giorgio Righetti, Paolo Antonioli, Carolina Simo, and Attilio Citterio).

3. MASS SPECTROMETRY-BASED PROTEOMICS: IDENTIFYING PLANT PROTEINS (Eveline Bergmuller, Sacha Baginsky, and Wilhelm Gruissem).

4. CHEMICAL PROTEOMICS (Miriam C. Hagenstein, Olaf Kruse, and Norbert Sewald).

5. THE ARABIDOPSIS LOCALIZOME: SUBCELLULAR PROTEIN LOCALIZATION AND INTERACTIONS IN ARABIDOPSIS (Georgios Kitsios, Nicolas Tsesmetzis, Max Bush, and John H. Doonan).

6. SECRETOME: TOWARD DECIPHERING THE SECRETORY PATHWAYS AND BEYOND (Young-Ho Jung, Ganesh Kumar Agrawal, Randeep Rakwal, and Nam-Soo Jwa).

7. PEPTIDOMICS (Peter Schulz-Knappe).

PART II: COMPUTATIONAL PROTEOMICS.

8. BIOINFORMATICS IN GEL-BASED PROTEOMICS (Asa M. Wheelock and Craig E. Wheelock).

9. BIOINFORMATICS IN MS-BASED PROTEOMICS (Jacques Colinge).

PART III: EXPRESSION PROTEOMICS.

10. AN OVERVIEW OF THE ARABIDOPSIS PROTEOME (Jacques Bourguignon and Michel Jaquinod).

11. RICE PROTEOME AT A GLANCE (Ganesh Kumar Agrawal and Randeep Rakwal).

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

13. PROTEOME OF SEED DEVELOPMENT AND GERMINATION (Julie Catusse, Loıc Rajjou, Claudette Job, and Dominique Job).

14. ENDOSPERM AND AMYLOPLAST PROTEOMES OF WHEAT GRAIN (William J. Hurkman, William H. Vensel, Frances M. DuPont, Susan B. Altenbach, and Bob B. Buchanan).

15. ROOT PROTEOME (Kuo-Chen Yeh, Chyi-Chuann Chen, and Chuan-Ming Yeh).

16. LEAF PROTEOME (Bin Kang, Shuyang Tu, Jiyuan Zhang, and Siqi Liu).

17. ANTHER PROTEOME (Nijat Imin).

18. POLLEN PROTEOME (Sandra Noir).

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

PART IV: ORGANELLE PROTEOMICS.

20. CELL WALL (Elisabeth Jamet, Herv´e Canut, Cecile Albenne, Georges Boudart, and Rafael Pont-Lezica).

21. PLASMA MEMBRANE: A PECULIAR STATUS AMONG THE CELL MEMBRANE SYSTEMS (Geneviève Ephritikhine, Anne Marmagne, Thierry Meinnel, and Myriam Ferro).

22. NUCLEUS (Subhra Chakraborty, Aarti Pandey, Asis Datta, and Niranjan Chakraborty).

23. CHLOROPLAST (Thomas Kieselbach and Wolfgang P. Schröder).

24. ETIOPLAST (Anne von Zychlinski, Sonja Reiland, Wilhelm Gruissem, and Sacha Baginsky).

25. THE PLANT MITOCHONDRIAL PROTEOME AND THE CHALLENGE OF HYDROPHOBIC PROTEIN ANALYSIS (Yew-Foon Tan and A. Harvey Millar).

26. PEROXISOME (Yuko Arai, Youichiro Fukao, Makoto Hayashi, and Mikio Nishimura).

27. UNRAVELING PLANT VACUOLES BY PROTEOMICS (Songqin Pan and Natasha Raikhel).

28. OIL BODIES (Pascale Jolivet, Luc Negroni, Sabine d’Andrea, and Thierry Chardot).

PART V: MODIFICATION PROTEOMICS.

29. PHOSPHOPROTEINS: WHERE ARE WE TODAY? (Florian Wolschin and Wolfram Weckwerth).

30. PROTEOME ANALYSIS OF THE UBIQUITIN PATHWAY (Junmin Peng).

31. ANALYSIS OF THE N-GLYCOSYLATION OF PROTEINS IN PLANTS (Willy Morelle).

32. FUNCTIONAL ANALYSIS AND PHOSPHORYLATION SITE MAPPING OF LEUCINE-RICH REPEAT RECEPTOR-LIKE KINASES (Steven D. Clouse, Michael B. Goshe, Steven C. Huber, and Jia Li).

33. TIME TO SEARCH FOR PROTEIN KINASE SUBSTRATES (Birgit Kersten).

34. TYROSINE PHOSPHORYLATION IN PLANTS: EMERGING EVIDENCE (Andrea Carpi, Valeria Rossi, and Francesco Filippini).

35. 14–3–3 PROTEINS: REGULATORS OF KEY CELLULAR FUNCTIONS (Peter C. Morris).

PART VI: MULTIPROTEIN COMPLEX.

36. TAP-TAGGING SYSTEM IN RICE FOR PROTEIN COMPLEX ISOLATION (Jai S. Rohila and Michael E. Fromm).

37. TAP STRATEGY IN ARABIDOPSIS PROTEIN COMPLEX ISOLATION (Vicente Rubio and Xing Wang Deng).

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

39. PROTEIN–PROTEIN INTERACTION MAPPING IN PLANTS (Joachim F. Uhrig).

PART VII: PLANT DEFENSE AND STRESS.

40. PROTEOMICS IN PLANT DEFENSE RESPONSE (Sun Tae Kim and Kyu Young Kang).

41. PROTEOME ANALYSIS OF CELLULAR RESPONSES TO ABIOTIC STRESSES IN PLANTS (Hans-Peter Mock and Andrea Matros).

42. PROTEOMICS OF BIOTROPHIC PLANT–MICROBE INTERACTIONS: SYMBIOSES LEAD THE MARCH (Ghislaine Recorbet and Eliane Dumas-Gaudot).

43. PROTEOMICS APPROACHES TO CONSTRUCT CALCIUM SIGNALING NETWORKS IN PLANTS (Irene S. Day and A.S.N. Reddy).

PART VIII: STRUCTURAL PROTEOMICS.

44. CELL-FREE EXPRESSION SYSTEM FOR EUKARYOTIC PROTEINS (Yaeta Endo and Tatsuya Sawasaki).

45. PROTEIN STRUCTURE DETERMINATION (Jian-Hua Zhao and Hsuan-Liang Liu).

PART IX: OTHER TOPICS IN PLANT PROTEOMICS.

46. PROTEOMICS IN CONTEXT OF SYSTEMS BIOLOGY (Serhiy Souchelnytskyi).

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

INDEX.