Mitochondrial complexome reveals quality-control pathways of protein import

Uwe Schulte, Fabian den Brave, Alexander Haupt, Arushi Gupta, Jiyao Song, Catrin S. Müller, Jeannine Engelke, Swadha Mishra, Christoph Mårtensson, Lars Ellenrieder, Chantal Priesnitz, Sebastian P. Straub, Kim Nguyen Doan, Bogusz Kulawiak, Wolfgang Bildl, Heike Rampelt, Nils Wiedemann, Nikolaus Pfanner (), Bernd Fakler () and Thomas Becker
Additional contact information
Uwe Schulte: University of Freiburg
Fabian den Brave: University of Bonn
Alexander Haupt: University of Freiburg
Arushi Gupta: University of Bonn
Jiyao Song: University of Bonn
Catrin S. Müller: University of Freiburg
Jeannine Engelke: University of Bonn
Swadha Mishra: University of Bonn
Christoph Mårtensson: University of Freiburg
Lars Ellenrieder: University of Freiburg
Chantal Priesnitz: University of Freiburg
Sebastian P. Straub: University of Freiburg
Kim Nguyen Doan: University of Freiburg
Bogusz Kulawiak: University of Freiburg
Wolfgang Bildl: University of Freiburg
Heike Rampelt: University of Freiburg
Nils Wiedemann: University of Freiburg
Nikolaus Pfanner: University of Freiburg
Bernd Fakler: University of Freiburg
Thomas Becker: University of Bonn

Nature, 2023, vol. 614, issue 7946, 153-159

Abstract: Abstract Mitochondria have crucial roles in cellular energetics, metabolism, signalling and quality control1–4. They contain around 1,000 different proteins that often assemble into complexes and supercomplexes such as respiratory complexes and preprotein translocases1,3–7. The composition of the mitochondrial proteome has been characterized1,3,5,6; however, the organization of mitochondrial proteins into stable and dynamic assemblies is poorly understood for major parts of the proteome1,4,7. Here we report quantitative mapping of mitochondrial protein assemblies using high-resolution complexome profiling of more than 90% of the yeast mitochondrial proteome, termed MitCOM. An analysis of the MitCOM dataset resolves >5,200 protein peaks with an average of six peaks per protein and demonstrates a notable complexity of mitochondrial protein assemblies with distinct appearance for respiration, metabolism, biogenesis, dynamics, regulation and redox processes. We detect interactors of the mitochondrial receptor for cytosolic ribosomes, of prohibitin scaffolds and of respiratory complexes. The identification of quality-control factors operating at the mitochondrial protein entry gate reveals pathways for preprotein ubiquitylation, deubiquitylation and degradation. Interactions between the peptidyl-tRNA hydrolase Pth2 and the entry gate led to the elucidation of a constitutive pathway for the removal of preproteins. The MitCOM dataset—which is accessible through an interactive profile viewer—is a comprehensive resource for the identification, organization and interaction of mitochondrial machineries and pathways.

Date: 2023
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DOI: 10.1038/s41586-022-05641-w

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