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Molecular and Cellular Biology, February 2006, p. 762-776, Vol. 26, No. 3
0270-7306/06/$08.00+0     doi:10.1128/MCB.26.3.762-776.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Proteomic Analysis of Mitochondrial Protein Turnover: Identification of Novel Substrate Proteins of the Matrix Protease Pim1{dagger}

Tamara Major,1,2 Birgit von Janowsky,1,2 Thomas Ruppert,3 Axel Mogk,3 and Wolfgang Voos1*

Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann Herder Str. 7, 79104 Freiburg,1 Fakultät für Biologie, Universität Freiburg, 79104 Freiburg,2 ZMBH, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany3

Received 30 June 2005/ Returned for modification 8 August 2005/ Accepted 4 November 2005

ATP-dependent oligomeric proteases are major components of cellular protein quality control systems. To investigate the role of proteolytic processes in the maintenance of mitochondrial functions, we analyzed the dynamic behavior of the mitochondrial proteome of Saccharomyces cerevisiae by two-dimensional (2D) polyacrylamide gel electrophoresis. By a characterization of the influence of temperature on protein turnover in isolated mitochondria, we were able to define four groups of proteins showing a differential susceptibility to proteolysis. The protein Pim1/LON has been shown to be the main protease in the mitochondrial matrix responsible for the removal of damaged or nonnative proteins. To assess the substrate range of Pim1 under in vivo conditions, we performed a quantitative comparison of the 2D protein spot patterns between wild-type and pim1{Delta} mitochondria. We were able to identify a novel subset of mitochondrial proteins that are putative endogenous substrates of Pim1. Using an in organello degradation assay, we confirmed the Pim1-specific, ATP-dependent proteolysis of the newly identified substrate proteins. We could demonstrate that the functional integrity of the Pim1 substrate proteins, in particular, the presence of intact prosthetic groups, had a major influence on the susceptibility to proteolysis.

* Corresponding author. Mailing address: Institut für Biochemie und Molekularbiologie, Universität Freiburg, Hermann Herder Str. 7, 79104 Freiburg, Germany. Phone: 49-761-203-5280. Fax: 49-761-203-5261. E-mail: wolfgang.voos{at}biochemie.uni-freiburg.de.

{dagger} Supplemental material for this article may be found at http://mcb.asm.org/.

Molecular and Cellular Biology, February 2006, p. 762-776, Vol. 26, No. 3
0270-7306/06/$08.00+0     doi:10.1128/MCB.26.3.762-776.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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