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Salscheider SL, Gerlich S, Cabrera-Orefice A, Peker E, Rothemann RA, Murschall LM, Finger Y, Szczepanowska K, Ahmadi ZA, Guerrero-Castillo S, Erdogan A, Becker M, Ali M, Habich M, Petrungaro C, Burdina N, Schwarz G, Klußmann M, Neundorf I, Stroud DA, Ryan MT, Trifunovic A, Brandt U, Riemer J. AIFM1 is a component of the mitochondrial disulfide relay that drives complex I assembly through efficient import of NDUFS5. EMBO J 2022; 41:e110784. [PMID: 35859387 PMCID: PMC9434101 DOI: 10.15252/embj.2022110784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 12/12/2022] Open
Abstract
The mitochondrial intermembrane space protein AIFM1 has been reported to mediate the import of MIA40/CHCHD4, which forms the import receptor in the mitochondrial disulfide relay. Here, we demonstrate that AIFM1 and MIA40/CHCHD4 cooperate beyond this MIA40/CHCHD4 import. We show that AIFM1 and MIA40/CHCHD4 form a stable long‐lived complex in vitro, in different cell lines, and in tissues. In HEK293 cells lacking AIFM1, levels of MIA40 are unchanged, but the protein is present in the monomeric form. Monomeric MIA40 neither efficiently interacts with nor mediates the import of specific substrates. The import defect is especially severe for NDUFS5, a subunit of complex I of the respiratory chain. As a consequence, NDUFS5 accumulates in the cytosol and undergoes rapid proteasomal degradation. Lack of mitochondrial NDUFS5 in turn results in stalling of complex I assembly. Collectively, we demonstrate that AIFM1 serves two overlapping functions: importing MIA40/CHCHD4 and constituting an integral part of the disulfide relay that ensures efficient interaction of MIA40/CHCHD4 with specific substrates.
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Affiliation(s)
| | - Sarah Gerlich
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Esra Peker
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | | | | | - Yannik Finger
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Karolina Szczepanowska
- Medical Faculty, Institute for Mitochondrial Diseases and Aging, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Zeinab Alsadat Ahmadi
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sergio Guerrero-Castillo
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alican Erdogan
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Mark Becker
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Muna Ali
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Markus Habich
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | | | - Nele Burdina
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Guenter Schwarz
- Institute for Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Merlin Klußmann
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - Ines Neundorf
- Institute for Biochemistry, University of Cologne, Cologne, Germany
| | - David A Stroud
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - Michael T Ryan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Vic., Australia
| | - Aleksandra Trifunovic
- Medical Faculty, Institute for Mitochondrial Diseases and Aging, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Ulrich Brandt
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jan Riemer
- Institute for Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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Finger Y, Habich M, Gerlich S, Urbanczyk S, van de Logt E, Koch J, Schu L, Lapacz KJ, Ali M, Petrungaro C, Salscheider SL, Pichlo C, Baumann U, Mielenz D, Dengjel J, Brachvogel B, Hofmann K, Riemer J. Proteasomal degradation induced by DPP9-mediated processing competes with mitochondrial protein import. EMBO J 2020; 39:e103889. [PMID: 32815200 PMCID: PMC7527813 DOI: 10.15252/embj.2019103889] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Plasticity of the proteome is critical to adapt to varying conditions. Control of mitochondrial protein import contributes to this plasticity. Here, we identified a pathway that regulates mitochondrial protein import by regulated N-terminal processing. We demonstrate that dipeptidyl peptidases 8/9 (DPP8/9) mediate the N-terminal processing of adenylate kinase 2 (AK2) en route to mitochondria. We show that AK2 is a substrate of the mitochondrial disulfide relay, thus lacking an N-terminal mitochondrial targeting sequence and undergoing comparatively slow import. DPP9-mediated processing of AK2 induces its rapid proteasomal degradation and prevents cytosolic accumulation of enzymatically active AK2. Besides AK2, we identify more than 100 mitochondrial proteins with putative DPP8/9 recognition sites and demonstrate that DPP8/9 influence the cellular levels of a number of these proteins. Collectively, we provide in this study a conceptual framework on how regulated cytosolic processing controls levels of mitochondrial proteins as well as their dual localization to mitochondria and other compartments.
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Affiliation(s)
- Yannik Finger
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Markus Habich
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Sarah Gerlich
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Sophia Urbanczyk
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Erik van de Logt
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Julian Koch
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Laura Schu
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Kim Jasmin Lapacz
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Muna Ali
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Carmelina Petrungaro
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | | | - Christian Pichlo
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, Cologne, Germany.,Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- Institute of Genetics, University of Cologne, Cologne, Germany
| | - Jan Riemer
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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3
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Habich M, Salscheider SL, Murschall LM, Hoehne MN, Fischer M, Schorn F, Petrungaro C, Ali M, Erdogan AJ, Abou-Eid S, Kashkar H, Dengjel J, Riemer J. Vectorial Import via a Metastable Disulfide-Linked Complex Allows for a Quality Control Step and Import by the Mitochondrial Disulfide Relay. Cell Rep 2020; 26:759-774.e5. [PMID: 30650365 DOI: 10.1016/j.celrep.2018.12.092] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/15/2018] [Accepted: 12/20/2018] [Indexed: 01/31/2023] Open
Abstract
Disulfide formation in the mitochondrial intermembrane space (IMS) is an essential process. It is catalyzed by the disulfide relay machinery, which couples substrate import and oxidation. The machinery relies on the oxidoreductase and chaperone CHCHD4-Mia40. Here, we report on the driving force for IMS import and on a redox quality control mechanism. We demonstrate that unfolded reduced proteins, upon translocation into the IMS, initiate formation of a metastable disulfide-linked complex with CHCHD4. If this interaction does not result in productive oxidation, then substrates are released to the cytosol and degraded by the proteasome. Based on these data, we propose a redox quality control step at the level of the disulfide-linked intermediate that relies on the vectorial nature of IMS import. Our findings also provide the mechanistic framework to explain failures in import of numerous human disease mutants in CHCHD4 substrates.
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Affiliation(s)
- Markus Habich
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Silja Lucia Salscheider
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Lena Maria Murschall
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Michaela Nicole Hoehne
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Manuel Fischer
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Fabian Schorn
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, CECAD Research Center, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Carmelina Petrungaro
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Muna Ali
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Alican J Erdogan
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany
| | - Shadi Abou-Eid
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Hamid Kashkar
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, CECAD Research Center, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Jan Riemer
- Institute for Biochemistry, Department of Chemistry, University of Cologne, Zuelpicher Str. 47a/R. 3.49, 50674 Cologne, Germany.
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4
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Habich M, Salscheider SL, Riemer J. Cysteine residues in mitochondrial intermembrane space proteins: more than just import. Br J Pharmacol 2018; 176:514-531. [PMID: 30129023 DOI: 10.1111/bph.14480] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/20/2018] [Accepted: 06/26/2018] [Indexed: 12/13/2022] Open
Abstract
The intermembrane space (IMS) is a very small mitochondrial sub-compartment with critical relevance for many cellular processes. IMS proteins fulfil important functions in transport of proteins, lipids, metabolites and metal ions, in signalling, in metabolism and in defining the mitochondrial ultrastructure. Our understanding of the IMS proteome has become increasingly refined although we still lack information on the identity and function of many of its proteins. One characteristic of many IMS proteins are conserved cysteines. Different post-translational modifications of these cysteine residues can have critical roles in protein function, localization and/or stability. The close localization to different ROS-producing enzyme systems, a dedicated machinery for oxidative protein folding, and a unique equipment with antioxidative systems, render the careful balancing of the redox and modification states of the cysteine residues, a major challenge in the IMS. In this review, we discuss different functions of human IMS proteins, the involvement of cysteine residues in these functions, the consequences of cysteine modifications and the consequences of cysteine mutations or defects in the machinery for disulfide bond formation in terms of human health. LINKED ARTICLES: This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.
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Affiliation(s)
- Markus Habich
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Silja Lucia Salscheider
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Jan Riemer
- Department of Chemistry, Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
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Abstract
The bacterial Rcs phosphorelay signals perturbations of the bacterial cell envelope to its response regulator RcsB, which regulates transcription of multiple loci related to motility, biofilm formation and various stress responses. RcsB is unique, as its set of target loci is modulated by interaction with auxiliary regulators including BglJ. The BglJ–RcsB heteromer is known to activate the HNS repressed leuO and bgl loci independent of RcsB phosphorylation. Here, we show that BglJ–RcsB activates the promoters of 10 additional loci (chiA, molR, sfsB, yecT, yqhG, ygiZ, yidL, ykiA, ynbA and ynjI). Furthermore, we mapped the BglJ–RcsB binding site at seven loci and propose a consensus sequence motif. The data suggest that activation by BglJ–RcsB is DNA phasing dependent at some loci, a feature reminiscent of canonical transcriptional activators, while at other loci BglJ–RcsB activation may be indirect by inhibition of HNS-mediated repression. In addition, we show that BglJ–RcsB activates transcription of bgl synergistically with CRP where it shifts the transcription start by 20 bp from a position typical for class I CRP-dependent promoters to a position typical for class II CRP-dependent promoters. Thus, BglJ–RcsB is a pleiotropic transcriptional activator that coordinates regulation with global regulators including CRP, LeuO and HNS.
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Affiliation(s)
- Silja Lucia Salscheider
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
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