E ditor - in - chief
William S. Hancock
Barnett Institute and Department of Chemistry Northeastern University Boston, MA 02115 617-373-4881; fax 617-373-2855
[email protected] Associate E ditors Setsuko Komatsu National Institute of Crop Science and University of Tsukuba Joshua LaBaer Harvard Medical School György Marko-Varga AstraZeneca and Lund University Martin McIntosh Fred Hutchinson Cancer Research Center Cons u lting E ditor Jeremy K. Nicholson Imperial College London E ditorial adv isory board Ruedi H. Aebersold ETH Hönggerberg Rolf Apweiler European Bioinformatics Institute Ronald Beavis Manitoba Centre for Proteomics Rainer Bischoff University of Groningen Dolores Cahill University College Dublin Thomas P. Conrads University of Pittsburgh Cancer Center Thomas E. Fehniger AstraZeneca Catherine Fenselau University of Maryland Daniel Figeys University of Ottawa Craig Gelfand BD Diagnostics Brian Haab Van Andel Institute Sam Hanash Fred Hutchinson Cancer Research Center Albert Heck Utrecht University Stanley Hefta Bristol-Myers Squibb Denis Hochstrasser University of Geneva Elaine Holmes Imperial College London Michael J. Hubbard University of Melbourne Donald F. Hunt University of Virginia Barry L. Karger Northeastern University Joachim Klose Charité-University Medicine Berlin David M. Lubman University of Michigan Matthias Mann Max Planck Institute of Biochemistry David Muddiman North Carolina State University Robert F. Murphy Carnegie Mellon University Gilbert S. Omenn University of Michigan Nicolle Packer Proteome Systems Limited Akhilesh Pandey Johns Hopkins University Peipei Ping University of California, Los Angeles Henry Rodriguez National Cancer Institute Michael Snyder Yale University Clifford H. Spiegelman Texas A&M University Hanno Steen Children’s Hospital Boston Timothy D. Veenstra SAIC-Frederick, National Cancer Institute Scot R. Weinberger Molecular Sensing, Inc. Susan T. Weintraub University of Texas Health Science Center John R. Yates, III The Scripps Research Institute
© 2008 American Chemical Society
editorial
Crop Proteomics and Its Application to Biotechnology
W
orldwide, food shortage is the most serious problem of the current century. To meet the expanding food demands of the rapidly increasing world population, crop production will need to increase by 50% by 2025 (Proc. Nutr. Soc. 2003, 60, 15–26). However, almost all of the land that is not already being farmed is suboptimal for plant growth. Unfavorable physiochemical environments account for ~70% of lost yield potential, even in places with highly developed agriculture (Science 1982, 218, 443–448). To meet these challenges, genes and proteins that control the architecture of crop plants as well as stress resistance and tolerance in a wide range of environments must be identified to improve crop productivity. DNA markers are being used in breeding programs to follow the inheritance of major genes. Proteomic analysis, however, offers a new approach to discovering useful genes and their pathways. The advent of proteomics has allowed researchers to identify a broad spectrum of proteins in living systems. This capability is especially useful for crops because it may give clues not only about nutritional value but also about yield and how these factors are affected by adverse conditions. Rice is an important agricultural resource that is also a model plant for biological research. Now that the rice genome has been completely sequenced, the challenge ahead for the monocot research community is to identify and characterize the functions of these genes. (Monocots are the flowering plants that include maize, wheat, rice, and many other agricultural crops.) Research on rice provides insight into many fundamental aspects of plant biology, but the genome sequencing of major crops is still in its infancy. In this case, a proteomics approach is a powerful tool for the analysis of physiological functions because proteomics can directly analyze the factors from plants that do the work. Genes that have been identified by proteomics can be used for markerassisted breeding or gene-transformation programs to improve the architecture of crop plants and resistance or tolerance to biotic or abiotic stresses. Protein arrays offer a solution and have the potential for high throughput. Many agronomic traits are fraught with complication, and arrays could help researchers identify novel protein markers and molecular pathways. Although protein arrays are still under development, they have already proven their value for the study of protein functions and expression patterns. However, optimization of these techniques is needed before they can be widely used in analyses of crop proteomes. At the moment, it is difficult to draw a consistent conclusion from the results of various studies of crop proteomes, because different plant genotypes and sample preparations as well as proteomic techniques have been applied. A higher conformity of proteomic studies among research groups and investigators, and the application of standard operating procedures, would facilitate the comparability of proteomics results. I hope we will continue this interesting discussion in the pages of JPR in the coming months. SETSUKO KOMATSU National Institute of Crop Science and University of Tsukuba (both in Japan) Associate Editor, JPR
Journal of Proteome Research • Vol. 7, No. 6, 2008 2183
