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Published on March 27, 2009; 10.1104/pp.109.137703

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Received February 25, 2009
Accepted March 23, 2009

In-depth proteome analysis of Arabidopsis leaf peroxisomes combined with in vivo subcellular targeting verification indicates novel metabolic and regulatory functions of peroxisomes

Sigrun Reumann , Sheng Quan , Kyaw Aung , Pingfang Yang , Kalpana Manandhar-Shrestha , Danielle Holbrook , Nicole Linka , Robert Switzenberg , Curtis G. Wilkerson , Andreas P. M. Weber , Laura J. Olsen , and Jianping Hu *

MSU-DOE Plant Research Laboratory; Plant Biology Department; Biochemistry and Molecular Biology Department, Michigan State University, East Lansing, MI 48824; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109

* Corresponding author; email: huji{at}msu.edu.

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 leaf peroxisomes, using one-dimensional gel electrophoresis (1-DE) followed by liquid chromato-graphy and tandem mass spectrometry (LC-MS/MS). 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 (YFP) 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> 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.




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