Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA
Jana Key,
Sylvia Torres-Odio,
Nina C. Bach,
Suzana Gispert,
Gabriele Koepf,
Marina Reichlmeir,
A. Phillip West,
Holger Prokisch,
Peter Freisinger,
William G. Newman,
Stavit Shalev,
Stephan A. Sieber,
Ilka Wittig,
Georg Auburger
Affiliations
Jana Key
Experimental Neurology, Faculty of Medicine, Goethe University, 60590 Frankfurt, Germany
Sylvia Torres-Odio
Experimental Neurology, Faculty of Medicine, Goethe University, 60590 Frankfurt, Germany
Nina C. Bach
Center for Protein Assemblies, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
Suzana Gispert
Experimental Neurology, Faculty of Medicine, Goethe University, 60590 Frankfurt, Germany
Gabriele Koepf
Experimental Neurology, Faculty of Medicine, Goethe University, 60590 Frankfurt, Germany
Marina Reichlmeir
Experimental Neurology, Faculty of Medicine, Goethe University, 60590 Frankfurt, Germany
A. Phillip West
Department of Microbial Pathogenesis and Immunology, College of Medicine, Health Science Center, Texas A&M University, Bryan, TX 77807, USA
Holger Prokisch
Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
Peter Freisinger
Department of Paediatrics, Kreisklinikum Reutlingen, 72764 Reutlingen, Germany
William G. Newman
Division of Evolution Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
Stavit Shalev
Genetic Institute, Emek Medical Center, Afula, Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa 3200003, Israel
Stephan A. Sieber
Center for Protein Assemblies, Chair of Organic Chemistry II, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
Ilka Wittig
Functional Proteomics, Institute for Cardiovascular Physiology, Medical Faculty, Goethe University, 60596 Frankfurt am Main, Germany
Georg Auburger
Experimental Neurology, Faculty of Medicine, Goethe University, 60590 Frankfurt, Germany
Biallelic pathogenic variants in CLPP, encoding mitochondrial matrix peptidase ClpP, cause a rare autosomal recessive condition, Perrault syndrome type 3 (PRLTS3). It is characterized by primary ovarian insufficiency and early sensorineural hearing loss, often associated with progressive neurological deficits. Mouse models showed that accumulations of (i) its main protein interactor, the substrate-selecting AAA+ ATPase ClpX, (ii) mitoribosomes, and (iii) mtDNA nucleoids are the main cellular consequences of ClpP absence. However, the sequence of these events and their validity in human remain unclear. Here, we studied global proteome profiles to define ClpP substrates among mitochondrial ClpX interactors, which accumulated consistently in ClpP-null mouse embryonal fibroblasts and brains. Validation work included novel ClpP-mutant patient fibroblast proteomics. ClpX co-accumulated in mitochondria with the nucleoid component POLDIP2, the mitochondrial poly(A) mRNA granule element LRPPRC, and tRNA processing factor GFM1 (in mouse, also GRSF1). Only in mouse did accumulated ClpX, GFM1, and GRSF1 appear in nuclear fractions. Mitoribosomal accumulation was minor. Consistent accumulations in murine and human fibroblasts also affected multimerizing factors not known as ClpX interactors, namely, OAT, ASS1, ACADVL, STOM, PRDX3, PC, MUT, ALDH2, PMPCB, UQCRC2, and ACADSB, but the impact on downstream metabolites was marginal. Our data demonstrate the primary impact of ClpXP on the assembly of proteins with nucleic acids and show nucleoid enlargement in human as a key consequence.
