This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (33) Citing Articles via Google Scholar Google Scholar Articles by Lonosky, P. M. Articles by Rodermel, S. R. Search for Related Content PubMed PubMed Citation Articles by Lonosky, P. M. Articles by Rodermel, S. R. Agricola Articles by Lonosky, P. M. Articles by Rodermel, S. R.

BIOINFORMATICS

A Proteomic Analysis of Maize Chloroplast Biogenesis¹

Departments of Genetics, Development, and Cell Biology (P.M.L., D.L.D., A.F., S.R.R.) and Computer Science (X.Z., V.G.H.) and Bioinformatics and Computational Biology Major (P.M.L., X.Z., V.G.H., D.L.D., S.R.R.), Iowa State University, Ames, Iowa 50011

Proteomics studies to explore global patterns of protein expression in plant and green algal systems have proliferated within the past few years. Although most of these studies have involved mapping of the proteomes of various organs, tissues, cells, or organelles, comparative proteomics experiments have also led to the identification of proteins that change in abundance in various developmental or physiological contexts. Despite the growing use of proteomics in plant studies, questions of reproducibility have not generally been addressed, nor have quantitative methods been widely used, for example, to identify protein expression classes. In this report, we use the de-etiolation ("greening") of maize (Zea mays) chloroplasts as a model system to explore these questions, and we outline a reproducible protocol to identify changes in the plastid proteome that occur during the greening process using techniques of two-dimensional gel electrophoresis and mass spectrometry. We also evaluate hierarchical and nonhierarchical statistical methods to analyze the patterns of expression of 526 "high-quality," unique spots on the two-dimensional gels. We conclude that Adaptive Resonance Theory 2—a nonhierarchical, neural clustering technique that has not been previously applied to gene expression data—is a powerful technique for discriminating protein expression classes during greening. Our experiments provide a foundation for the use of proteomics in the design of experiments to address fundamental questions in plant physiology and molecular biology.

¹ This work was supported by the National Science Foundation (Integrative Graduate Education and Research Traineeship [IGERT] training grant in Bioinformatics and Computational Biology to P.L.) and by the U.S. Department of Energy (Energy Biosciences; grant no. DE–FG02–94ER20147 to S.R.).

^* Corresponding author; e-mail rodermel{at}iastate.edu; fax 515–294–1337.

Received August 20, 2003; returned for revision October 7, 2003; accepted October 23, 2003.

This article has been cited by other articles:

				A. Brautigam and A. P.M. Weber Proteomic Analysis of the Proplastid Envelope Membrane Provides Novel Insights into Small Molecule and Protein Transport across Proplastid Membranes Mol Plant, November 1, 2009; 2(6): 1247 - 1261. [Abstract] [Full Text] [PDF]

				G. Lochmanova, Z. Zdrahal, H. Konecna, S. Koukalova, J. Malbeck, P. Soucek, M. Valkova, N. S. Kiran, and B. Brzobohaty Cytokinin-induced photomorphogenesis in dark-grown Arabidopsis: a proteomic analysis J. Exp. Bot., October 1, 2008; 59(13): 3705 - 3719. [Abstract] [Full Text] [PDF]

				C.-S. Lin, N.-T. Liu, D.-C. Liao, J.-S. Yu, C.-H. Tsao, C.-H. Lin, C.-W. Sun, W.-N. Jane, H. S. Tsay, J. Jian-Wei Chen, et al. Differential Protein Expression of Two Photosystem II Subunits, PsbO and PsbP, in an Albino Mutant of Bambusa edulis with Chloroplast DNA Aberration J. Amer. Soc. Hort. Sci., March 1, 2008; 133(2): 270 - 277. [Abstract] [Full Text] [PDF]

				E. Kanervo, M. Singh, M. Suorsa, V. Paakkarinen, E. Aro, N. Battchikova, and E.-M. Aro Expression of Protein Complexes and Individual Proteins Upon Transition of Etioplasts to Chloroplasts in Pea (Pisum sativum) Plant Cell Physiol., March 1, 2008; 49(3): 396 - 410. [Abstract] [Full Text] [PDF]

				T. Kleffmann, A. von Zychlinski, D. Russenberger, M. Hirsch-Hoffmann, P. Gehrig, W. Gruissem, and S. Baginsky Proteome Dynamics during Plastid Differentiation in Rice Plant Physiology, February 1, 2007; 143(2): 912 - 923. [Abstract] [Full Text] [PDF]

				C. C. Subbaiah, A. Palaniappan, K. Duncan, D. M. Rhoads, S. C. Huber, and M. M. Sachs Mitochondrial Localization and Putative Signaling Function of Sucrose Synthase in Maize J. Biol. Chem., June 9, 2006; 281(23): 15625 - 15635. [Abstract] [Full Text] [PDF]

				M. Fujiwara, K. Umemura, T. Kawasaki, and K. Shimamoto Proteomics of Rac GTPase Signaling Reveals Its Predominant Role in Elicitor-Induced Defense Response of Cultured Rice Cells Plant Physiology, February 1, 2006; 140(2): 734 - 745. [Abstract] [Full Text] [PDF]

				W. Majeran, Y. Cai, Q. Sun, and K. J. van Wijk Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative Proteomics PLANT CELL, November 1, 2005; 17(11): 3111 - 3140. [Abstract] [Full Text] [PDF]

				A. von Zychlinski, T. Kleffmann, N. Krishnamurthy, K. Sjolander, S. Baginsky, and W. Gruissem Proteome Analysis of the Rice Etioplast: Metabolic and Regulatory Networks and Novel Protein Functions Mol. Cell. Proteomics, August 1, 2005; 4(8): 1072 - 1084. [Abstract] [Full Text] [PDF]

				N. Tanaka, S. Mitsui, H. Nobori, K. Yanagi, and S. Komatsu Expression and Function of Proteins during Development of the Basal Region in Rice Seedlings Mol. Cell. Proteomics, June 1, 2005; 4(6): 796 - 808. [Abstract] [Full Text] [PDF]