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CELL BIOLOGY AND SIGNAL TRANSDUCTION

In-Depth Proteome Analysis of Arabidopsis Leaf Peroxisomes Combined with in Vivo Subcellular Targeting Verification Indicates Novel Metabolic and Regulatory Functions of Peroxisomes^1,[W],[OA]

Michigan State University-Department of Energy Plant Research Laboratory (S.R., S.Q., K.A., P.Y., K.M.-S., R.S., J.H.), Plant Biology Department (K.A., N.L., C.G.W., A.P.M.W., J.H.), and Biochemistry and Molecular Biology Department (C.G.W.), Michigan State University, East Lansing, Michigan 48824; and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 (S.R., D.H., L.J.O.)

Peroxisomes are metabolically diverse organelles with essential roles in plant development. The major protein constituents of plant peroxisomes are well characterized, whereas only a few low-abundance and regulatory proteins have been reported to date. We performed an in-depth proteome analysis of Arabidopsis (Arabidopsis thaliana) leaf peroxisomes using one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry. We detected 65 established plant peroxisomal proteins, 30 proteins whose association with Arabidopsis peroxisomes had been previously demonstrated only by proteomic data, and 55 putative novel proteins of peroxisomes. We subsequently tested the subcellular targeting of yellow fluorescent protein fusions for selected proteins and confirmed the peroxisomal localization for 12 proteins containing predicted peroxisome targeting signals type 1 or 2 (PTS1/2), three proteins carrying PTS-related peptides, and four proteins that lack conventional targeting signals. We thereby established the tripeptides SLM> and SKV> (where > indicates the stop codon) as new PTS1s and the nonapeptide RVx₅HF as a putative new PTS2. The 19 peroxisomal proteins conclusively identified from this study potentially carry out novel metabolic and regulatory functions of peroxisomes. Thus, this study represents an important step toward defining the complete plant peroxisomal proteome.

² Present address: Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, N–4036 Stavanger, Norway.

³ Present address: Department of Plant Biochemistry, Heinrich-Heine-University, D–40225 Duesseldorf, Germany.

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: Jianping Hu (huji{at}msu.edu).

^[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.109.137703

^* Corresponding author; e-mail huji{at}msu.edu.

Received February 25, 2009; accepted March 23, 2009; published March 27, 2009.

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