OPEN ACCESS ARTICLE

This Article Free via Open Access: OA OA Full Text Full Text (PDF) Supplemental Data OA All Versions of this Article: 148/4/1809    most recent pp.108.129999v1 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 (7) Citing Articles via Google Scholar Google Scholar Articles by Eubel, H. Articles by Millar, A. H. Search for Related Content PubMed PubMed Citation Articles by Eubel, H. Articles by Millar, A. H. Agricola Articles by Eubel, H. Articles by Millar, A. H. Related Collections Membrane Trafficking

BIOCHEMICAL PROCESSES AND MACROMOLECULAR STRUCTURES

Novel Proteins, Putative Membrane Transporters, and an Integrated Metabolic Network Are Revealed by Quantitative Proteomic Analysis of Arabidopsis Cell Culture Peroxisomes^1,[W],[OA]

Australian Research Council Centre of Excellence in Plant Energy Biology, M316 (H.E., E.H.M., N.L.T., J.D.B., J.L.H., I.D.S., S.M.S., A.H.M.), and Centre of Excellence for Computational Systems Biology (N.O., I.C., I.D.S.), University of Western Australia, Crawley, Western Australia 6009, Australia

Peroxisomes play key roles in energy metabolism, cell signaling, and plant development. A better understanding of these important functions will be achieved with a more complete definition of the peroxisome proteome. The isolation of peroxisomes and their separation from mitochondria and other major membrane systems have been significant challenges in the Arabidopsis (Arabidopsis thaliana) model system. In this study, we present new data on the Arabidopsis peroxisome proteome obtained using two new technical advances that have not previously been applied to studies of plant peroxisomes. First, we followed density gradient centrifugation with free-flow electrophoresis to improve the separation of peroxisomes from mitochondria. Second, we used quantitative proteomics to identify proteins enriched in the peroxisome fractions relative to mitochondrial fractions. We provide evidence for peroxisomal localization of 89 proteins, 36 of which have not previously been identified in other analyses of Arabidopsis peroxisomes. Chimeric green fluorescent protein constructs of 35 proteins have been used to confirm their localization in peroxisomes or to identify endoplasmic reticulum contaminants. The distribution of many of these peroxisomal proteins between soluble, membrane-associated, and integral membrane locations has also been determined. This core peroxisomal proteome from nonphotosynthetic cultured cells contains a proportion of proteins that cannot be predicted to be peroxisomal due to the lack of recognizable peroxisomal targeting sequence 1 (PTS1) or PTS2 signals. Proteins identified are likely to be components in peroxisome biogenesis, β-oxidation for fatty acid degradation and hormone biosynthesis, photorespiration, and metabolite transport. A considerable number of the proteins found in peroxisomes have no known function, and potential roles of these proteins in peroxisomal metabolism are discussed. This is aided by a metabolic network analysis that reveals a tight integration of functions and highlights specific metabolite nodes that most probably represent entry and exit metabolites that could require transport across the peroxisomal membrane.

² These authors contributed equally to the article.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: A. Harvey Millar (hmillar{at}cyllene.uwa.edu.au).

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.108.129999

^* Corresponding author; e-mail hmillar{at}cyllene.uwa.edu.au.

Received September 16, 2008; accepted October 10, 2008; published October 17, 2008.

This article has been cited by other articles:

				M. J. Lingard and B. Bartel Arabidopsis LON2 Is Necessary for Peroxisomal Function and Sustained Matrix Protein Import Plant Physiology, November 1, 2009; 151(3): 1354 - 1365. [Abstract] [Full Text] [PDF]

				A. H. Millar, C. Carrie, B. Pogson, and J. Whelan Exploring the Function-Location Nexus: Using Multiple Lines of Evidence in Defining the Subcellular Location of Plant Proteins PLANT CELL, June 1, 2009; 21(6): 1625 - 1631. [Abstract] [Full Text] [PDF]

				S. Reumann, S. Quan, K. Aung, P. Yang, K. Manandhar-Shrestha, D. Holbrook, N. Linka, R. Switzenberg, C. G. Wilkerson, A. P.M. Weber, et al. In-Depth Proteome Analysis of Arabidopsis Leaf Peroxisomes Combined with in Vivo Subcellular Targeting Verification Indicates Novel Metabolic and Regulatory Functions of Peroxisomes Plant Physiology, May 1, 2009; 150(1): 125 - 143. [Abstract] [Full Text] [PDF]