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J. Biol. Chem., Vol. 279, Issue 1, 421-428, January 2, 2004
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Proteomic Analysis of Rat Liver Peroxisome
PRESENCE OF PEROXISOME-SPECIFIC ISOZYME OF LON PROTEASE*
**
From the
Harima Institute at SPring-8, RIKEN, Mikazuki, Sayo, Hyogo 679-5148, Yamanashi Medical University, Tamaho, Yamanashi, 409-3898, the ¶School of Medicine, Gifu University, Gifu 500-8705, the ||Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Toyama 930-0194, and the **Institute for Enzyme Research, The University of Tokushima, Tokushima 770-8503, Japan
Subcellular proteomics, which includes isolation of subcellular components prior to a proteomic analysis, is advantageous not only in characterizing large macro-molecular complexes such as organelles but also in elucidating mechanisms of protein transport and organelle biosynthesis. Because of the high sensitivity achieved by the present proteomics technology, the purity of samples to be analyzed is important for the interpretation of the results obtained. In the present study, peroxisomes isolated from rat liver by usual cell fractionation were further purified by immunoisolation using a specific antibody raised against a peroxisomal membrane protein, PMP70. The isolated peroxisomes were analyzed by SDS-PAGE combined with liquid chromatography/mass spectrometry. Altogether 34 known peroxisomal proteins were identified in addition to several mitochondrial and microsomal proteins. Some of the latter may reside in the peroxisomes as well. Analysis of membrane fractions identified all known peroxins except for Pex7. Two new peroxisomal proteins of unknown function were of high abundance. One is a bi-functional protein consisting of an aminoglycoside phosphotransferase-domain and an acyl-CoA dehydrogenase domain. The other is a newly identified peroxisome-specific isoform of Lon protease, an ATP-dependent protease with chaperone-like activity. The peroxisomal localization of the protein was confirmed by immunological techniques. The peroxisome-type Lon protease, which is distinct from the mitochondrial isoform, may play an important role in the peroxisomal biogenesis.
Received for publication, May 29, 2003 , and in revised form, October 13, 2003.
* This work was supported in part by grants-in-aid for scientific research and Special Coordination Funds for promoting Science and Technology (Genome Frontier) from the Ministry of Education, Culture, Sports, Science and Technology, and a grant from the Uehara Memorial Foundation. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
To whom correspondence should be addressed: Harima Institute at Spring-8, RIKEN, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148, Japan. Tel.: 81-791-58-1825; Fax: 81-791-58-1826; E-mail: hisatan{at}spring8.or.jp.
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