Proteomics: A biotechnology tool for crop improvement

Frontiers in Plant Science

Volumn 4, Issue FEB, 2013, Pages

  Eldakak, Moustafa ^a,b   Milad, Sanaa I M ^b   Nawar, Ali I ^b   Rohila, Jai S ^a  

^a SOUTH DAKOTA STATE UNIVERSITY   (United States)

^b ALEXANDRIA UNIVERSITY   (Egypt)

Author keywords

Biotechnology; Crop improvement; Proteomics; Sustainable agriculture

Indexed keywords

EID: 84900866831     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2013.00035     Document Type: Review

References (170)

1. Abdi, N., Holford, P., and Mcglasson, B. (2002). Application of two-dimensional gel electrophoresis to detect proteins associated with harvest maturity in stonefruit. Postharvest Biol. Technol. 26, 1-13.
2. Acero, F. J., Carbu, M., El-Akhal, M. R., Garrido, C., Gonzalez-Rodriguez, V. E., and Cantoral, J. M. (2011). Development of proteomics-based fungicides: new strategies for environmentally friendly control of fungal plant diseases. Int. J. Mol. Sci. 12, 795-816.
3. Afroz, A., Khan, M. R., Ahsan, N., and Komatsu, S. (2009). Comparative proteomic analysis of bacterial wilt susceptible and resistant tomato cultivars. Peptides 30, 1600-1607.
4. Agrawal, G. K., Pedreschi, R., Barkla, B. J., Bindschedler, L. V., Cramer, R., Sarkar, A., et al. (2012). Translational plant proteomics: a perspective. J. Proteomics 75, 4588-4601.
5. Agrawal, G. K., and Rakwal, R. (2006). Rice proteomics: a cornerstone for cereal food crop proteomes. Mass Spectrom. Rev. 25, 1-53.
6. Akagawa, M., Handoyo, T., Ishii, T., Kumazawa, S., Morita, N., and Suyama, K. (2007). Proteomic analysis of wheat flour allergens. J. Agric. Food Chem. 55, 6863-6870.
7. Alvarez, S., Marsh, E. L., Schroeder, S. G., and Schachtman, D. P. (2008). Metabolomic and proteomic changes in the xylem sap of maize under drought. Plant Cell Environ. 31, 325-340.
8. Amara, I., Odena, A., Oliveira, E., Moreno, A., Masmoudi, K., Pages, M., et al. (2012). Insights into Maize LEA proteins: from proteomics to functional approaches. Plant Cell Physiol. 53, 312-329.
9. Amiour, N., Merlino, M., Leroy, P., and Branlard, G. (2002). Proteomic analysis of amphiphilic proteins of hexaploid wheat kernels. Proteomics 2, 632-641.
10. Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
11. Arakawa, T., Chong, D. K. X., and Langridge, W. H. R. (1998). Efficacy of a food plant-based oral cholera toxin B subunit vaccine. Nat. Biotechnol. 16, 292-297.
12. Baggerman, G., Vierstraete, E., Loof, A. D., and Schoofs, L. (2005). Gel-based versus gel-free proteomics: a review. Comb. Chem. High Throughput Screen. 8, 669-677.
13. Balmer, Y., Vensel, W. H., Dupont, F. M., Buchanan, B. B., and Hurkman, W. J. (2006). Proteome of amyloplasts isolated from developing wheat endosperm presents evidence of broad metabolic capability. J. Exp. Bot. 57, 1591-1602.
14. Barros, E., Lezar, S., Anttonen, M. J., Van Dijk, J. P., Rohlig, R. M., Kok, E. J., et al. (2010). Comparison of two GM maize varieties with a near-isogenic non-GM variety using transcriptomics, proteomics and metabolomics. Plant Biotechnol. J. 8, 436-451.
15. Bazargani, M. M., Sarhadi, E., Bushehri, A. A., Matros, A., Mock, H. P., Naghavi, M. R., et al. (2011). A proteomics view on the role of drought-induced senescence and oxidative stress defense in enhanced stem reserves remobilization in wheat. J. Proteomics 74, 1959-1973.
16. Beddington, J., Asaduzzaman, M., Clark, M., Bremauntz, A., Guillou, M., Jahn, M., et al. (2012). The role for scientists in tackling food insecurity and climate change. Agric. Food Sec. 1, 10.
17. Beroza, P., Villar, H. O., Wick, M. M., and Martin, G. R. (2002). Chemoproteomics as a basis for post-genomic drug discovery. Drug Discov. Today 7, 807-814.
18. Beyer, K., Bardina, L., Grishina, G., and Sampson, H. A. (2002). Identification of sesame seed allergens by 2-dimensional proteomics and Edman sequencing: seed storage proteins as common food allergens. J. Allergy Clin. Immunol. 110, 154-159.
19. Boyer, J. S. (1982). Plant productivity and environment. Science 218, 443-448.
20. Brambilla, F., Resta, D., Isak, I., Zanotti, M., and Arnoldi, A. (2009). A label-free internal standard method for the differential analysis of bioactive lupin proteins using nano HPLC-Chip coupled with Ion Trap mass spectrometry. Proteomics 9, 272-286.
21. Calviño, M., and Messing, J. (2012). Sweet sorghum as a model system for bioenergy crops. Curr. Opin. Biotechnol23, 323-329.
22. Campo, S., Carrascal, M., Coca, M., Abián, J., and San Segundo, B. (2004). The defense response of germinating maize embryos against fungal infection: a proteomics approach. Proteomics 4, 383-396.
23. Chargelegue, D., Obregon, P., and Drake, P. M. (2001). Transgenic plants for vaccine production: expectations and limitations. Trends Plant Sci. 6, 495-496.
24. Chassaigne, H., Nørgaard, J. V., and Van Hengel, A. J. (2007). Proteomics-based approach to detect and identify major allergens in processed peanuts by capillary LC-Q-TOF (MS/MS). J. Agric. Food Chem. 55, 4461-4473.
25. Chen, F., Yuan, Y., Li, Q., and He, Z. (2007). Proteomic analysis of rice plasma membrane reveals proteins involved in early defense response to bacterial blight. Proteomics 7, 1529-1539.
26. Chivasa, S., Simon, W. J., Yu, X.-L., Yalpani, N., and Slabas, A. R. (2005). Pathogen elicitor-induced changes in the maize extracellular matrix proteome. Proteomics 5, 4894-4904.
27. Coaker, G. L., Willard, B., Kinter, M., Stockinger, E. J., and Francis, D. M. (2004). Proteomic analysis of resistance mediated by Rcm 2.0 and Rcm 5.1, two loci controlling resistance to bacterial canker of tomato. Mol. Plant Microbe Interact. 17, 1019-1028.
28. Collado, I. G., Sanchez, A. J. M., and Hanson, J. R. (2007). Fungal terpene metabolites: biosynthetic relationships and the control of the phytopathogenic fungus Botrytis cinerea. Nat. Prod. Rep. 24, 674-686.
29. Collard, B. C. Y., and Mackill, D. J. (2008). Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363, 557-572.
30. Cox, J., and Mann, M. (2007). Is proteomics the new genomics? Cell 130, 395-398.
31. D'Amato, A., Fasoli, E., Kravchuk, A. V., and Righetti, P. G. (2011). Going nuts for nuts? The trace proteome of a Cola drink, as detected via combinatorial peptide ligand libraries. J. Proteome Res. 10, 2684-2686.
32. Damerval, C., Maurice, A., Josse, J. M., and De Vienne, D. (1994). Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137, 289-301.
33. De Angelis, M., Minervini, F., Caputo, L., Cassone, A., Coda, R., Calasso, M. P., et al. (2008). Proteomic analysis by two-dimensional gel electrophoresis and starch characterization of Triticum turgidum L. var. durum cultivars for pasta making. J. Agric. Food Chem. 56, 8619-8628.
34. de Lumen, B. O. (2005). Lunasin: a cancer-preventive soy peptide. Nutr. Rev. 63, 16-21.
35. Di Carli, M., Zamboni, A., Pé, M. E., Pezzotti, M., Lilley, K. S., Benvenuto, E., et al. (2011). Two-dimensional differential in gel electrophoresis (2D-DIGE) analysis of grape berry proteome during postharvest withering. J. Proteome Res. 10, 429-446.
36. Dixon, R. A. (2005). Plant biotechnology kicks off into the 21st century. Trends Plant Sci. 10, 560-561.
37. Donnelly, B. E., Madden, R. D., Ayoubi, P., Porter, D. R., and Dillwith, J. W. (2005). The wheat (Triticum aestivumL.) leaf proteome. Proteomics 5, 1624-1633.
38. Dubey, H., and Grover, A. (2001). Current initiatives in proteomics research: the plant perspective. Curr. Sci. 80, 262-269.
39. Dupont, F. M. (2008). Metabolic pathways of the wheat (Triticum aestivum) endosperm amyloplast revealed by proteomics. BMC Plant Biol. 8:39. doi: 10.1186/1471-2229-8-39
40. Fasoli, E., D'Amato, A., Kravchuk, A. V., Citterio, A., and Righetti, P. G. (2011). In-depth proteomic analysis of non-alcoholic beverages with peptide ligand libraries. I: almond milk and orgeat syrup. J. Proteomics 74, 1080-1090.
41. Ford, K. L., Cassin, A., and Bacic, A. (2011). Quantitative proteomic analysis of wheat cultivars with differing drought stress tolerance. Front. Plant Sci. 2:44. doi: 10.3389/fpls.2011.00044
42. Foroud, N., Laroche, A., Jordan, M., Ellis, B., and Eudes, F. (2008). Fusarium graminearum-and trichothecene-induced differential transcriptomics and proteomics in resistant and susceptible wheat genotypes. Cereal Res. Commun. 36, 239-243.
43. Galant, A., Koester, R. P., Ainsworth, E. A., Hicks, L. M., and Jez, J. M. (2012). From climate change to molecular response: redox proteomics of ozone-induced responses in soybean. New Phytol. 194, 220-229.
44. Gao, L., Yan, X., Li, X., Guo, G., Hu, Y., Ma, W., et al. (2011). Proteome analysis of wheat leaf under salt stress by two-dimensional difference gel electrophoresis (2D-DIGE). Phytochemistry 72, 1180-1191.
45. Garrido, C., Cantoral, J. M., Carbu, M., Gonzalez-Rodriguez, V. E., and Fernandez-Acero, F. J. (2010). New proteomic approaches to plant pathogenic fungi. Curr. Proteomics 7, 306-315.
46. Gil-Agusti, M. T., Campostrini, N., Zolla, L., Ciambella, C., Invernizzi, C., and Righetti, P. G. (2005). Two-dimensional mapping as a tool for classification of green coffee bean species. Proteomics 5, 710-718.
47. Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., et al. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92-100.
48. Gong, C. Y., Li, Q., Yu, H. T., Wang, Z., and Wang, T. (2012). Proteomics insight into the biological safety of transgenic modification of rice as compared with conventional genetic breeding and spontaneous genotypic variation. J. Proteome Res. 11, 3019-3029.
49. Gu, C., Kolodziejek, I., Misas-Villamil, J., Shindo, T., Colby, T., Verdoes, M., et al. (2010). Proteasome activity profiling: a simple, robust and versatile method revealing subunit-selective inhibitors and cytoplasmic, defense-induced proteasome activities. Plant J. 62, 160-170.
50. Gygi, S. P., Rist, B., and Aebersold, R. (2000). Measuring gene expression by quantitative proteome analysis. Curr. Opin. Biotechnol. 11, 396-401.
51. Hajheidari, M., Abdollahian-Noghabi, M., Askari, H., Heidari, M., Sadeghian, S. Y., Ober, E. S., et al. (2005). Proteome analysis of sugar beet leaves under drought stress. Proteomics 5, 950-960.
52. Hare, P. D., Cress, W. A., and Van Staden, J. (1998). Dissecting the roles of osmolyte accumulation during stress. Plant Cell Environ. 21, 535-553.
53. Hashiguchi, A., Ahsan, N., and Komatsu, S. (2010). Proteomics application of crops in the context of climatic changes. Food Res. Int. 43, 1803-1813.
54. Heick, J., Fischer, M., Kerbach, S., Tamm, U., and Popping, B. (2011a). Application of a liquid chromatography tandem mass spectrometry method for the simultaneous detection of seven allergenic foods in flour and bread and comparison of the method with commercially available ELISA test kits. J. AOAC Int. 94, 1060-1068.
55. Heick, J., Fischer, M., and Pöpping, B. (2011b). First screening method for the simultaneous detection of seven allergens by liquid chromatography mass spectrometry. J. Chromatogr. A 1218, 938-943.
56. Herndl, A., Marzban, G., Kolarich, D., Hahn, R., Boscia, D., Hemmer, W., et al. (2007). Mapping of Malus domesticaallergens by 2-D electrophoresis and IgE-reactivity. Electrophoresis 28, 437-448.
57. Hu, H., Boisson-Dernier, A., Israelsson-Nordström, M., Böhmer, M., Xue, S., Ries, A., et al. (2009). Carbonic anhydrases are upstream regulators of CO2-controlled stomatal movements in guard cells. Nat. Cell Biol. 12, 87-93.
58. Huang, B. (1986). Chlamydomonas reinhardtii: a model system for the genetic analysis of flagellar structure and motility. Int. Rev. Cytol. 99, 181-215.
59. Huang, B., and Xu, C. (2008). Identification and characterization of proteins associated with plant tolerance to heat stress. J. Integr. Plant Biol. 50, 1230-1237.
60. Huang, H., Moller, I. M., and Song, S. Q. (2012). Proteomics of desiccation tolerance during development and germination of maize embryos. J. Proteomics 75, 1247-1262.
61. Iimure, T., Nankaku, N., Hirota, N., Tiansu, Z., Hoki, T., Kihara, M., et al. (2010). Construction of a novel beer proteome map and its use in beer quality control. Food Chem. 118, 566-574.
62. Irar, S., Brini, F., Goday, A., Masmoudi, K., and Pagès, M. (2010). Proteomic analysis of wheat embryos with 2-DE and liquid-phase chromatography (ProteomeLab PF-2D)-a wider perspective of the proteome. J. Proteomics 73, 1707-1721.
63. Iwahashi, Y., and Hosoda, H. (2000). Effect of heat stress on tomato fruit protein expression. Electrophoresis 21, 1766-1771.
64. Jagadish, S. V. K., Muthurajan, R., Oane, R., Wheeler, T. R., Heuer, S., Bennett, J., et al. (2010). Physiological and proteomic approaches to address heat tolerance during anthesis in rice (Oryza sativa L.). J. Exp. Bot. 61, 143-156.
65. Jayaraman, D., Forshey, K. L., Grimsrud, P. A., and Ane, J. M. (2012). Leveraging proteomics to understand plant-microbe interactions. Front. Plant. Sci. 3:44. doi: 10.3389/fpls.2012.00044
66. Johnson, T. S., Eswaran, N., and Sujatha, M. (2011). Molecular approaches to improvement of Jatropha curcasLinn. as a sustainable energy crop. Plant Cell Rep. 30, 1573-1591.
67. Judge, N. A., Mason, H. S., and O'Brien, A. D. (2004). Plant cell-based intimin vaccine given orally to mice primed with intimin reduces time of Escherichia coli O157:H7 shedding in feces. Infect. Immun. 72, 168-175.
68. Kalluri, U. C., Hurst, G. B., Lankford, P. K., Ranjan, P., and Pelletier, D. A. (2009). Shotgun proteome profile of Populus developing xylem. Proteomics 9, 4871-4880.
69. Kapusta, J., Modelska, A., Figlerowicz, M., Pniewski, T., Letellier, M., Lisowa, O., et al. (1999). A plant-derived edible vaccine against hepatitis B virus. FASEB J. 13, 1796-1799.
70. Karimizadeh, R., Mohammadi, M., Ghaffaripour, S., Karimpour, F., and Shefazadeh, M. K. (2011). Evaluation of physiological screening techniques for drought-resistant breeding of durum wheat genotypes in Iran. Afr. J. Biotechnol. 10, 12107-12117.
71. Khatoon, A., Rehman, S., Hiraga, S., Makino, T., and Komatsu, S. (2012). Organ-specific proteomics analysis for identification of response mechanism in soybean seedlings under flooding stress. J. Proteomics 75, 5706-5723.
72. Khush, G. (2012). Genetically modified crops: the fastest adopted crop technology in the history of modern agriculture. Agric. Food Sec. 1, 14.
73. Kitano, H. (2002). Computational systems biology. Nature 420, 206-210.
74. Koller, A., Washburn, M. P., Lange, B. M., Andon, N. L., Deciu, C., Haynes, P. A., et al. (2002). Proteomic survey of metabolic pathways in rice. Proc. Natl. Acad. Sci. U.S.A. 99, 11969-11974.
75. Komatsu, S. (2008). Crop proteomics and its application to biotechnology. J. Proteome Res. 7, 2183.
76. Komatsu, S., Yamamoto, A., Nakamura, T., Nouri, M. Z., Nanjo, Y., Nishizawa, K., et al. (2011). Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. J. Proteome Res. 10, 3993-4004.
77. Kong, F. J., Oyanagi, A., and Komatsu, S. (2010). Cell wall proteome of wheat roots under flooding stress using gel-based and LC MS/MS-based proteomics approaches. Biochim. Biophys. Acta. 1804, 124-136.
78. Konishi, H., Ishiguro, K., and Komatsu, S. (2001). A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization. Proteomics 1, 1162-1171.
79. Koprowski, H., and Yusibov, V. (2001). The green revolution: plants as heterologous expression vectors. Vaccine19, 2735-2741.
80. Kullander, S. (2010). Food security: crops for people not for cars. Ambio 39, 249-256.
81. Kussmann, M., Panchaud, A., and Affolter, M. (2010). Proteomics in nutrition: status quo and outlook for biomarkers and bioactives. J. Proteome Res. 9, 4876-4887.
82. Laino, P., Shelton, D., Finnie, C., De Leonardis, A. M., Mastrangelo, A. M., Svensson, B., et al. (2010). Comparative proteome analysis of metabolic proteins from seeds of durum wheat (cv. Svevo) subjected to heat stress. Proteomics 10, 2359-2368.
83. Lambert, J.-P., Ethier, M., Smith, J. C., and Figeys, D. (2005). Proteomics: from gel based to gel free. Anal. Chem.77, 3771-3788.
84. Langridge, P., and Fleury, D. (2011). Making the most of 'omics' for crop breeding. Trends Biotechnol. 29, 33-40.
85. Lee, J., and Koh, H. J. (2011). A label-free quantitative shotgun proteomics analysis of rice grain development. Proteome Sci. 9, 61.
86. Liu, H., Liu, Y.-J., Yang, M.-F., and Shen, S.-H. (2009). A comparative analysis of embryo and endosperm proteome from seeds of Jatropha curcas. J. Integr. Plant Biol. 51, 850-857.
87. Liu, X. Y., Wu, Y. D., Shen, Z. Y., Shen, Z., Li, H. H., Yu, X. M., et al. (2011). Shotgun proteomics analysis on maize chloroplast thylakoid membrane. Front. Biosci. (Elite Ed.) 3, 250-255.
88. Lliso, I., Tadeo, F. R., Phinney, B. S., Wilkerson, C. G., and Talón, M. (2007). Protein changes in the albedo of citrus fruits on postharvesting storage. J. Agric. Food Chem. 55, 9047-9053.
89. Lutter, P., Parisod, V., and Weymuth, H. (2011). Development and validation of a method for the quantification of milk proteins in food products based on liquid chromatography with mass spectrometric detection. J. AOAC Int.94, 1043-1059.
90. Mahmood, T., Jan, A., and Komatsu, S. (2009). Proteomic analysis of bacterial blight defence signalling pathway using transgenic rice overexpressing thaumatin-like protein. Biologia Plantarum 53, 285-293.
91. Majeran, W., Friso, G., Ponnala, L., Connolly, B., Huang, M., Reidel, E., et al. (2010). Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize. Plant Cell 22, 3509-3542.
92. Majoul, T., Bancel, E., Triboï, E., Ben Hamida, J., and Branlard, G. (2004). Proteomic analysis of the effect of heat stress on hexaploid wheat grain: characterization of heat-responsive proteins from non-prolamins fraction. Proteomics 4, 505-513.
93. Mason, H. S., Haq, T. A., Clements, J. D., and Arntzen, C. J. (1998). Edible vaccine protects mice against Escherichia coli heat-labile enterotoxin (LT): potatoes expressing a synthetic LT-B gene. Vaccine 16, 1336-1343.
94. Mathesius, U., Mulders, S., Gao, M., Teplitski, M., Caetano-Anollés, G., Rolfe, B. G., et al. (2003). Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals. Proc. Natl. Acad. Sci. U.S.A. 100, 1444-1449.
95. May, G. D., Afza, R., Mason, H. S., Wiecko, A., Novak, F. J., and Arntzen, C. J. (1995). Generation of transgenic banana (Musa acuminata) plants via Agrobacterium-mediated transformation. Nat. Biotechnol. 13, 486-492.
96. Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., et al. (2007). TheChlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245-250.
97. Mittler, R. (2002). Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 7, 405-410.
98. Mittler, R. (2006). Abiotic stress, the field environment and stress combination. Trends Plant Sci. 11, 15-19.
99. Modelska, A., Dietzschold, B., Sleysh, N., Fu, Z. F., Steplewski, K., Hooper, D. C., et al. (1998). Immunization against rabies with plant-derived antigen. Proc. Natl. Acad. Sci. U.S.A. 95, 2481-2485.
100. Mohammadi, M., Anoop, V., Gleddie, S., and Harris, L. J. (2011). Proteomic profiling of two maize inbreds during early gibberella ear rot infection. Proteomics 11, 3675-3684.
101. Möller, N., Scholz-Ahrens, K., Roos, N., and Schrezenmeir, J. (2008). Bioactive peptides and proteins from foods: indication for health effects. Eur. J. Nutr. 47, 171-182.
102. Moroney, J. V., Ma, Y., Frey, W. D., Fusilier, K. A., Pham, T. T., Simms, T. A., et al. (2011). The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: Intracellular location, expression, and physiological roles. Photosyn. Res. 109, 133-149.
103. Muthurajan, R., Shobbar, Z.-S., Jagadish, S., Bruskiewich, R., Ismail, A., Leung, H., et al. (2011). Physiological and proteomic responses of rice peduncles to drought stress. Mol. Biotechnol. 48, 173-182.
104. Narciso, J., and Hossain, M. (2002). IRRI. Los Banos, The Philippines.
105. Nat, N. V. K., Sanjeeva, S., William, Y., and Nidhi, S. (2007). Application of proteomics to investigate plant-microbe interactions. Curr. Proteomics 4, 28-43.
106. Neilson, K. A., Mariani, M., and Haynes, P. A. (2011). Quantitative proteomic analysis of cold-responsive proteins in rice. Proteomics 11, 1696-1706.
107. Ngara, R., Jasper, D., Rees, G., and Ndimba, B. K. (2008). Establishment of sorghum cell suspension culture system for proteomics studies. Afr. J. Biotechnol. 7, 744-749.
108. Ngara, R., and Ndimba, B. K. (2011). Mapping and characterisation of the sorghum cell suspension culture secretome. Afr. J. Biotechnol. 10, 253-266.
109. Nguyen, T. H. N., Brechenmacher, L., Aldrich, J., Clauss, T., Gritsenko, M., Hixson, K., et al. (2012). Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum. Mol. Cell. Proteomics 11, 1140-1155.
110. Nishikawa, M., Hosokawa, K., Ishiguro, M., Minamioka, H., Tamura, K., Hara-Nishimura, I., et al. (2008). Degradation of sphingoid long-chain base 1-phosphates (LCB-1Ps): functional characterization and expression of AtDPL1 encoding LCB-1P lyase involved in the dehydration stress response in Arabidopsis. Plant Cell Physiol. 49, 1758-1763.
111. Park, O. K. (2004). Proteomic studies in plants. J. Biochem. Mol. Biol. 133-138.
112. Pedreschi, R., Hertog, M., Robben, J., Lilley, K. S., Karp, N. A., Baggerman, G., et al. (2009). Gel-based proteomics approach to the study of metabolic changes in pear tissue during storage. J. Agric. Food Chem. 57, 6997-7004.
113. Pedreschi, R., Hertog, M., Robben, J., Noben, J. P., and Nicolai, B. (2008). Physiological implications of controlled atmosphere storage of 'Conference' pears (Pyrus communis L.): a proteomic approach. Postharvest Biol. Technol.50, 110-116.
114. Pedreschi, R., Vanstreels, E., Carpentier, S., Hertog, M., Lammertyn, J., Robben, J., et al. (2007). Proteomic analysis of core breakdown disorder in Conference pears (Pyrus communis L.). Proteomics 7, 2083-2099.
115. Peng, S., Huang, J., Sheehy, J. E., Laza, R. C., Visperas, R. M., Zhong, X., et al. (2004). Rice yields decline with higher night temperature from global warming. Proc. Natl. Acad. Sci. U.S.A. 101, 9971-9975.
116. Petersen, A., Dresselhaus, T., Grobe, K., and Becker, W.-M. (2006). Proteome analysis of maize pollen for allergy-relevant components. Proteomics 6, 6317-6325.
117. Pinedo, C., Wang, C.-M., Pradier, J.-M., Dalmais, B. R. R., Choquer, M., Le PêCheur, P., et al. (2008). Sesquiterpene synthase from the Botrydial biosynthetic gene cluster of the phytopathogen Botrytis cinerea. ACS Chem. Biol. 3, 791-801.
118. Pischetsrieder, M., and Baeuerlein, R. (2009). Proteome research in food science. Chem. Soc. Rev. 38, 2600-2608.
119. Popping, B., and Godefroy, S. B. (2011). Allergen detection by mass spectrometry-the new way forward. J. AOAC Int. 94, 1005.
120. Reddy, A. R., Chaitanya, K. V., and Vivekanandan, M. (2004). Drought-induced responses of photosynthesis and antioxidant metabolism in higher plants. J. Plant Physiol. 161, 1189-1202.
121. Ribas-Carbo, M., Taylor, N. L., Giles, L., Busquets, S., Finnegan, P. M., Day, D. A., et al. (2005). Effects of water stress on respiration in Soybean leaves. Plant Physiol. 139, 466-473.
122. Richau, K. H., and van der Hoorn, R. A. L. (2010). Studies on plant-pathogen interactions using activity-based proteomics. Curr. Proteomics 7, 328-336.
123. Rohila, J. S., Chen, M., Chen, S., Chen, J., Cerny, R. L., Dardick, C., et al. (2009). Protein-protein interactions of tandem affinity purified protein kinases from rice. PLoS ONE 4:e6685. doi: 10.1371/journal.pone.0006685
124. Roy, A., Rushton, P. J., and Rohila, J. S. (2011). The potential of proteomics technologies for crop improvement under drought conditions. Crit. Rev. Plant Sci. 30, 471-490.
125. Salekdeh, G. H., and Komatsu, S. (2007). Crop proteomics: aim at sustainable agriculture of tomorrow. Proteomics7, 2976-2996.
126. Salt, L. J., Robertson, J. A., Jenkins, J. A., Mulholland, F., and Mills, E. N. C. (2005). The identification of foam-forming soluble proteins from wheat (Triticum aestivum) dough. Proteomics 5, 1612-1623.
127. Sandhu, J. S., Krasnyanski, S. F., Domier, L. L., Korban, S. S., Osadjan, M. D., and Buetow, D. E. (2000). Oral immunization of mice with transgenic tomato fruit expressing respiratory syncytial virus-F protein induces a systemic immune response. Transgenic Res. 9, 127-135.
128. Sanford, J., Smith, F., and Russell, J. (1993). Optimizing the biolistic process for different biological applications. Methods Enzymol. 217, 483-509.
129. Scarselli, M., Giuliani, M. M., Adu-Bobie, J., Pizza, M., and Rappuoli, R. (2005). The impact of genomics on vaccine design. Trends Biotechnol. 23, 84-91.
130. Scherp, P., Ku, G., Coleman, L., and Kheterpal, I. (2011). Gel-based and gel-free proteomic technologies. Methods Mol. Biol. 702, 163-190.
131. Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183.
132. Schnoor, J. L. (2010). Highlighting biofuels research. Environ. Sci. Technol. 44, 8796.
133. Shen, Z., Li, P., Ni, R.-J., Ritchie, M., Yang, C.-P., Liu, G.-F., et al. (2009). Label-free quantitative proteomics analysis of etiolated maize seedling leaves during greening. Mol. Cell. Proteomics 8, 2443-2460.
134. Singh, A., Nigam, P. S., and Murphy, J. D. (2011). Renewable fuels from algae: an answer to debatable land based fuels. Bioresour. Technol. 102, 10-16.
135. Sixma, T. K., Pronk, S. E., Kalk, K. H., Wartna, E. S., Van Zanten, B. A. M., Witholt, B., et al. (1991). Crystal structure of a cholera toxin-related heat-labile enterotoxin from E. coli. Nature 351, 371-377.
136. Somerville, C., Youngs, H., Taylor, C., Davis, S. C., and Long, S. P. (2010). Feedstocks for lignocellulosic biofuels. Science 329, 790-792.
137. Song, X., Ni, Z., Yao, Y., Xie, C., Li, Z., Wu, H., et al. (2007). Wheat (Triticum aestivum L.) root proteome and differentially expressed root proteins between hybrid and parents. Proteomics 7, 3538-3557.
138. Streatfield, S. J. (2005). Plant-based vaccines for animal health. Rev. Sci. Tech. 24, 189-199.
139. Süle, A., Vanrobaeys, F., Hajós, G., Van Beeumen, J., and Devreese, B. (2004). Proteomic analysis of small heat shock protein isoforms in barley shoots. Phytochemistry 65, 1853-1863.
140. Tacket, C., Mason, H., Losonsky, G., Clements, J., Levine, M., and Arntzen, C. (1998a). Immunogenicity in humans of a recombinant bacterial antigen delivered in a transgenic potato. Nat. Med. 4, 607-609.
141. Tacket, C. O., Mason, H. S., Losonsky, G., Clements, J. D., Levine, M. M., and Arntzen, C. J. (1998b). Immunogenicity in humans of a recombinant bacterial antigen delivered in a transgenic potato. Nat. Med. 4, 607-609.
142. Tacket, C. O., Mason, H. S., Losonsky, G., Estes, M. K., Levine, M. M., and Arntzen, C. J. (2000). Human immune responses to a novel Norwalk virus vaccine delivered in transgenic potatoes. J. Infect. Dis. 182, 302-305.
143. Taiz, L., and Zeiger, E. (2010). Plant Physiology. Sunderland, MA: Sinauer Associates, Inc.
144. Tester, M., and Bacic, A. (2005). Abiotic stress tolerance in grasses. From model plants to crop plants. Plant Physiol. 137, 791-793.
145. Thelen, J. J. (2009). Proteomics tools and resources for investigating protein allergens in oilseeds. Regul. Toxicol. Pharmacol. 54, S41-S45.
146. Thurston, G., Regan, S., Rampitsch, C., and Xing, T. (2005). Proteomic and phosphoproteomic approaches to understand plant-pathogen interactions. Physiol. Mol. Plant Pathol. 66, 3-11.
147. Toorchi, M., Yukawa, K., Nouri, M. Z., and Komatsu, S. (2009). Proteomics approach for identifying osmotic-stress-related proteins in soybean roots. Peptides 30, 2108-2117.
148. UN. (2012). Food Security and Sustainable Agriculture [Online]. Available at:http://www.un.org/en/sustainablefuture/food.shtml (Accessed september 20, 2012).
149. Varshney, R. K., Bansal, K. C., Aggarwal, P. K., Datta, S. K., and Craufurd, P. Q. (2011). Agricultural biotechnology for crop improvement in a variable climate: hope or hype? Trends Plant Sci. 16, 363-371.
150. Vensel, W. H., Tanaka, C. K., Cai, N., Wong, J. H., Buchanan, B. B., and Hurkman, W. J. (2005). Developmental changes in the metabolic protein profiles of wheat endosperm. Proteomics 5, 1594-1611.
151. Virdi, A. S., Thakur, A., Dutt, S., Kumar, S., and Singh, P. (2009). A sorghum 85 kDa heat stress-modulated protein shows calmodulin-binding properties and cross-reactivity to anti-Neurospora crassa Hsp 80 antibodies. FEBS Lett.583, 767-770.
152. Wang, L., Ma, H., Song, L., Shu, Y., and Gu, W. (2012). Comparative proteomics analysis reveals the mechanism of pre-harvest seed deterioration of soybean under high temperature and humidity stress. J. Proteomics 75, 2109-2127.
153. Wang, W., Vinocur, B., and Altman, A. (2003). Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218, 1-14.
154. Wang, Y., Yang, L., Xu, H., Li, Q., Ma, Z., and Chu, C. (2005). Differential proteomic analysis of proteins in wheat spikes induced by Fusarium graminearum. Proteomics 5, 4496-4503.
155. Wienkoop, S., May, P., Kempa, S., Irgang, S., Recuenco-Munoz, L., Pietzke, M., et al. (2010). Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses. Mol. Biosystems 6, 1018-1031.
156. Wilkins, M. R., Sanchez, J. C., Gooley, A. A., Appel, R. D., Humphery-Smith, I., Hochstrasser, D. F., et al. (1995). Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev. 13, 19-50.
157. Wirz, H., Sauer-Budge, A. F., Briggs, J., Sharpe, A., Shu, S., and Sharon, A. (2012). Automated production of plant-based vaccines and pharmaceuticals. J. Lab. Autom. 17, 449-457.
158. Xue, S., Hu, H., Ries, A., Merilo, E., Kollist, H., and Schroeder, J. I. (2011). Central functions of bicarbonate in S-type anion channel activation and OST1 protein kinase in CO2 signal transduction in guard cell. EMBO J. 30, 1645-1658.
159. Yahata, E., Maruyama-Funatsuki, W., Nishio, Z., Tabiki, T., Takata, K., Yamamoto, Y., et al. (2005). Wheat cultivar-specific proteins in grain revealed by 2-DE and their application to cultivar identification of flour. Proteomics 5, 3942-3953.
160. Yang, J.-Y., Sun, Y., Sun, A.-Q., Yi, S.-Y., Qin, J., Li, M.-H., et al. (2006). The involvement of chloroplast HSP100/ClpB in the acquired thermotolerance in tomato. Plant Mol. Biol. 62, 385-395.
161. Yang, M.-F., Liu, Y.-J., Liu, Y., Chen, H., Chen, F., and Shen, S.-H. (2009). Proteomic analysis of oil mobilization in seed germination and postgermination development of Jatropha curcas. J. Proteome Res. 8, 1441-1451.
162. Yu, J., Hu, S., Wang, J., Wong, G. K., Li, S., Liu, B., et al. (2002). A draft sequence of the rice genome (Oryza sativaL. ssp. indica). Science 296, 79-92.
163. Yuan, J. S., Tiller, K. H., Al-Ahmad, H., Stewart, N. R., and Stewart, C. N. Jr. (2008). Plants to power: bioenergy to fuel the future. Trends Plant Sci. 13, 421-429.
164. Zhang, L., Yu, Z., Jiang, L., Jiang, J., Luo, H., and Fu, L. (2011a). Effect of post-harvest heat treatment on proteome change of peach fruit during ripening. J. Proteomics 74, 1135-1149.
165. Zhang, Y., Zhao, J., Xiang, Y., Bian, X., Zuo, Q., Shen, Q., et al. (2011b). Proteomics study of changes in soybean lines resistant and sensitive to Phytophthora sojae. Proteome Sci. 9, 52.
166. Zhang, W., Zhou, R. G., Gao, Y. J., Zheng, S. Z., Xu, P., Zhang, S. Q., et al. (2009). Molecular and genetic evidence for the key role of AtCaM3 in heat-shock signal transduction in Arabidopsis. Plant Physiol. 149, 1773-1784.
167. Zhao, Z., Zhang, W., Stanley, B. A., and Assmann, S. M. (2008). Functional Proteomics of Arabidopsis thalianaguard cells uncovers new stomatal signaling pathways. Plant Cell 20, 3210-3226.
168. Zhou, W., Eudes, F., and Laroche, A. (2006). Identification of differentially regulated proteins in response to a compatible interaction between the pathogen Fusarium graminearum and its host, Triticum aestivum. Proteomics6, 4599-4609.
169. Zhu, B., Ye, C., Lü, H., Chen, X., Chai, G., Chen, J., et al. (2006). Identification and characterization of a novel heat shock transcription factor gene, GmHsfA1, in soybeans (Glycine max). J. Plant Res. 119, 247-256.
170. Zi, J., Zhang, J., Wang, Q., Lin, L., Tong, W., Bai, X., et al. (2012). Proteomics study of rice embryogenesis: discovery of the embryogenesis-dependent globulins. Electrophoresis 33, 1129-1138.