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J. Biol. Chem., Vol. 282, Issue 32, 23055-23069, August 10, 2007

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Rat Liver Peroxisomes after Fibrate Treatment

A SURVEY USING QUANTITATIVE MASS SPECTROMETRY^*

Markus Islinger¹², Georg H. Lüers¹, Ka Wan Li^¶, Maarten Loos^¶, and Alfred Völkl

From the Department of Anatomy and Cell Biology, Ruprecht-Karl University, 69120 Heidelberg, Germany, the Department of Anatomy and Cell Biology, Phillips-University, 35033 Marburg, Germany, and the ^¶Research Institute of Neurosciences, Vrije Universiteit, 1081 HV Amsterdam, Netherlands

Fibrates are known to induce peroxisome proliferation and the expression of peroxisomal -oxidation enzymes. To analyze fibrate-induced changes of complex metabolic networks, we have compared the proteome of rat liver peroxisomes from control and bezafibrate-treated rats. Highly purified peroxisomes were subfractionated, and the proteins of the matrix, peripheral, and integral membrane subfractions thus obtained were analyzed by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry after labeling of tryptic peptides with the iTRAQ reagent. By means of this quantitative technique, we were able to identify 134 individual proteins, covering most of the known peroxisomal proteome. Ten predicted new open reading frames were verified by cDNA cloning, and seven of them could be localized to peroxisomes by immunocytochemistry. Moreover, quantitative mass spectrometry substantiated the induction of most of the known peroxisome proliferator-activated receptor -regulated peroxisomal proteins upon treatment with bezafibrate, documenting the suitability of the iTRAQ procedure in larger scale experiments. However, not all proteins reacted to a similar extent but exerted a fibrate-specific induction scheme showing the variability of peroxisome proliferator-activated receptor-transmitted responses to specific ligands. In view of our data, rat hepatic peroxisomes are apparently not specialized to sequester very long chain fatty acids (C22–C26) but rather metabolize preferentially long chain fatty acids (C16–18).

Received for publication, November 27, 2006 , and in revised form, May 16, 2007.

^* This work was supported by the German Federal Ministry for Education and Research FKZ 031U108F (subproject B5). 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.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1 and S2.

¹ Both authors contributed equally to this work.

² To whom correspondence should be addressed: Dept. of Anatomy and Cell Biology, Medical Cell Biology, University of Heidelberg, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany. E-mail: Markus.Islinger{at}urz.uni-heidelberg.de.

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