1
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Bischof L, Schweitzer F, Schmitz HP, Heinisch JJ. The small yeast GTPase Rho5 requires specific mitochondrial outer membrane proteins for translocation under oxidative stress and interacts with the VDAC Por1. Eur J Cell Biol 2024; 103:151405. [PMID: 38503132 DOI: 10.1016/j.ejcb.2024.151405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
Yeast Rho5 is a small GTPase which mediates the response to nutrient and oxidative stress, and triggers mitophagy and apoptosis. We here studied the rapid translocation of a GFP-tagged Rho5 to mitochondria under such stress conditions by live-cell fluorescence microscopy in the background of strains lacking different mitochondrial outer membrane proteins (MOMP). Fun14, Msp1 and Alo1 were found to be required for efficient recruitment of the GTPase, whereas translocation of Dck1 and Lmo1, the subunits of its dimeric GDP/GTP exchange factor (GEF), remained unaffected. An influence of the voltage-dependent anion channel (VDAC) Por1 on the association of GFP-Rho5 with mitochondria under oxidative stress conditions appeared to be strain-dependent. However, epistasis analyses and bimolecular fluorescence complementation (BiFC) studies indicate a genetic and physical interaction. All four strains lacking a single MOMP were investigated for their effect on mitophagy.
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Affiliation(s)
- Linnet Bischof
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany
| | - Franziska Schweitzer
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany
| | - Hans-Peter Schmitz
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany
| | - Jürgen J Heinisch
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany.
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2
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Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
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Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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3
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den Brave F, Pfanner N, Becker T. Mitochondrial entry gate as regulatory hub. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119529. [PMID: 37951505 DOI: 10.1016/j.bbamcr.2023.119529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 11/14/2023]
Abstract
Mitochondria import 1000-1300 different precursor proteins from the cytosol. The main mitochondrial entry gate is formed by the translocase of the outer membrane (TOM complex). Molecular coupling and modification of TOM subunits control and modulate protein import in response to cellular signaling. The TOM complex functions as regulatory hub to integrate mitochondrial protein biogenesis and quality control into the cellular proteostasis network.
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Affiliation(s)
- Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
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4
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Liu Q, Fong B, Yoo S, Unruh JR, Guo F, Yu Z, Chen J, Si K, Li R, Zhou C. Nascent mitochondrial proteins initiate the localized condensation of cytosolic protein aggregates on the mitochondrial surface. Proc Natl Acad Sci U S A 2023; 120:e2300475120. [PMID: 37494397 PMCID: PMC10401023 DOI: 10.1073/pnas.2300475120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Eukaryotes organize cellular contents into membrane-bound organelles and membrane-less condensates, for example, protein aggregates. An unsolved question is why the ubiquitously distributed proteins throughout the cytosol give rise to spatially localized protein aggregates on the organellar surface, like mitochondria. We report that the mitochondrial import receptor Tom70 is involved in the localized condensation of protein aggregates in budding yeast and human cells. This is because misfolded cytosolic proteins do not autonomously aggregate in vivo; instead, they are recruited to the condensation sites initiated by Tom70's substrates (nascent mitochondrial proteins) on the organellar membrane using multivalent hydrophobic interactions. Knocking out Tom70 partially impairs, while overexpressing Tom70 increases the formation and association between cytosolic protein aggregates and mitochondria. In addition, ectopic targeting Tom70 and its substrates to the vacuole surface is able to redirect the localized aggregation from mitochondria to the vacuolar surface. Although other redundant mechanisms may exist, this nascent mitochondrial proteins-based initiation of protein aggregation likely explains the localized condensation of otherwise ubiquitously distributed molecules on the mitochondria. Disrupting the mitochondrial association of aggregates impairs their asymmetric retention during mitosis and reduces the mitochondrial import of misfolded proteins, suggesting a proteostasis role of the organelle-condensate interactions.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on Aging, Novato, CA94945
| | - Benjamin Fong
- Buck Institute for Research on Aging, Novato, CA94945
| | - Seungmin Yoo
- Buck Institute for Research on Aging, Novato, CA94945
| | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Jingjing Chen
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, MO64110
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS66160
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD21218
- Mechanobiology Institute and Department of Biological Science, National University of Singapore, Singapore117411, Singapore
| | - Chuankai Zhou
- Buck Institute for Research on Aging, Novato, CA94945
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5
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Schulte U, den Brave F, Haupt A, Gupta A, Song J, Müller CS, Engelke J, Mishra S, Mårtensson C, Ellenrieder L, Priesnitz C, Straub SP, Doan KN, Kulawiak B, Bildl W, Rampelt H, Wiedemann N, Pfanner N, Fakler B, Becker T. Mitochondrial complexome reveals quality-control pathways of protein import. Nature 2023; 614:153-159. [PMID: 36697829 PMCID: PMC9892010 DOI: 10.1038/s41586-022-05641-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/09/2022] [Indexed: 01/26/2023]
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.
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Affiliation(s)
- Uwe Schulte
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fabian den Brave
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Alexander Haupt
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Arushi Gupta
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiyao Song
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Catrin S. Müller
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jeannine Engelke
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Swadha Mishra
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Christoph Mårtensson
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,Present Address: MTIP, Basel, Switzerland
| | - Lars Ellenrieder
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.419481.10000 0001 1515 9979Present Address: Novartis, Basel, Switzerland
| | - Chantal Priesnitz
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian P. Straub
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9Faculty of Biology, University of Freiburg, Freiburg, Germany ,grid.482402.8Present Address: Sanofi-Aventis (Suisse), Vernier, Switzerland
| | - Kim Nguyen Doan
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bogusz Kulawiak
- grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.413454.30000 0001 1958 0162Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wolfgang Bildl
- grid.5963.9Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Rampelt
- grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- grid.5963.9CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany ,grid.5963.9Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany ,grid.5963.9BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Nikolaus Pfanner
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. .,Center for Basics in NeuroModulation, Freiburg, Germany.
| | - Thomas Becker
- grid.10388.320000 0001 2240 3300Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
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6
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Akhuli D, Dhar A, Viji AS, Bhojappa B, Palani S. ALIBY: ALFA Nanobody-Based Toolkit for Imaging and Biochemistry in Yeast. mSphere 2022; 7:e0033322. [PMID: 36190134 PMCID: PMC9599267 DOI: 10.1128/msphere.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Specialized epitope tags continue to be integral components of various biochemical and cell biological applications such as fluorescence microscopy, immunoblotting, immunoprecipitation, and protein purification. However, until recently, no single tag could offer this complete set of functionalities on its own. Here, we present a plasmid-based toolkit named ALIBY (ALFA toolkit for imaging and biochemistry in yeast) that provides a universal workflow to adopt the versatile ALFA tag/NbALFA system within the well-established model organism Saccharomyces cerevisiae. The kit comprises tagging plasmids for labeling a protein of interest with the ALFA tag and detection plasmids encoding fluorescent-protein-tagged NbALFA for live-cell imaging purposes. We demonstrate the suitability of ALIBY for visualizing the spatiotemporal localization of yeast proteins (i.e., the cytoskeleton, nucleus, centrosome, mitochondria, vacuole, endoplasmic reticulum, exocyst, and divisome) in live cells. Our approach has yielded an excellent signal-to-noise ratio without off-target effects or any effect on cell growth. In summary, our yeast-specific toolkit aims to simplify and further advance the live-cell imaging of differentially abundant yeast proteins while also being suitable for biochemical applications. IMPORTANCE In yeast research, conventional fluorescent protein tags and small epitope tags are widely used to study the spatiotemporal dynamics and activity of proteins. Although proven to be efficient, these tags lack the versatility for use across different cell biological and biochemical studies of a given protein of interest. Therefore, there is an urgent need for a unified platform for visualization and biochemical and functional analyses of proteins of interest in yeast. Here, we have engineered ALIBY, a plasmid-based toolkit that expands the benefits of the recently developed ALFA tag/NbALFA system to studies in the well-established model organism Saccharomyces cerevisiae. We demonstrate that ALIBY provides a simple and versatile strain construction workflow for long-duration live-cell imaging and biochemical applications in yeast.
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Affiliation(s)
- Dipayan Akhuli
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Anubhav Dhar
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Aileen Sara Viji
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Bindu Bhojappa
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Saravanan Palani
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
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7
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Zhou J, Jung M, Dimmer KS, Rapaport D. The multi-factor modulated biogenesis of the mitochondrial multi-span protein Om14. J Biophys Biochem Cytol 2022; 221:213056. [PMID: 35262629 PMCID: PMC8916117 DOI: 10.1083/jcb.202112030] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
The mitochondrial outer membrane (MOM) harbors proteins that traverse the membrane via several helical segments and are called multi-span proteins. To obtain new insights into the biogenesis of these proteins, we utilized yeast mitochondria and the multi-span protein Om14. Testing different truncation variants, we show that while only the full-length protein contains all the information that assures perfect targeting specificity, shorter variants are targeted to mitochondria with compromised fidelity. Employing a specific insertion assay and various deletion strains, we show that proteins exposed to the cytosol do not contribute significantly to the biogenesis process. We further demonstrate that Mim1 and Porin support optimal membrane integration of Om14 but none of them are absolutely required. Unfolding of newly synthesized Om14, its optimal hydrophobicity, and higher fluidity of the membrane enhanced the import capacity of Om14. Collectively, these findings suggest that MOM multi-span proteins follow different biogenesis pathways in which proteinaceous elements and membrane behavior contribute to a variable extent to the combined efficiency.
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Affiliation(s)
- Jialin Zhou
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Kai S Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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8
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Shvetsova A, Masud AJ, Schneider L, Bergmann U, Monteuuis G, Miinalainen IJ, Hiltunen JK, Kastaniotis AJ. A hunt for OM45 synthetic petite interactions in Saccharomyces cerevisiae reveals a role for Miro GTPase Gem1p in cristae structure maintenance. Microbiologyopen 2021; 10:e1238. [PMID: 34713605 PMCID: PMC8501180 DOI: 10.1002/mbo3.1238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022] Open
Abstract
Om45 is a major protein of the yeast's outer mitochondrial membrane under respiratory conditions. However, the cellular role of the protein has remained obscure. Previously, deletion mutant phenotypes have not been found, and clear amino acid sequence similarities that would allow inferring its functional role are not available. In this work, we describe synthetic petite mutants of GEM1 and UGO1 that depend on the presence of OM45 for respiratory growth, as well as the identification of several multicopy suppressors of the synthetic petite phenotypes. In the analysis of our mutants, we demonstrate that Om45p and Gem1p have a collaborative role in the maintenance of mitochondrial morphology, cristae structure, and mitochondrial DNA maintenance. A group of multicopy suppressors rescuing the synthetic lethal phenotypes of the mutants on non-fermentable carbon sources additionally supports this result. Our results imply that the synthetic petite phenotypes we observed are due to the disturbance of the inner mitochondrial membrane and point to this mitochondrial sub-compartment as the main target of action of Om45p, Ugo1p, and the yeast Miro GTPase Gem1p.
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Affiliation(s)
- Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Ali J. Masud
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Laura Schneider
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Ulrich Bergmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
- Present address:
Department of Biochemistry and Developmental BiologyUniversity of HelsinkiHelsinkiFinland
| | - Ilkka J. Miinalainen
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
| | - J. Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter OuluUniversity of OuluOuluFinland
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9
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Grevel A, Becker T. Porins as helpers in mitochondrial protein translocation. Biol Chem 2021; 401:699-708. [PMID: 31967957 DOI: 10.1515/hsz-2019-0438] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 12/22/2022]
Abstract
Mitochondria import the vast majority of their proteins via dedicated protein machineries. The translocase of the outer membrane (TOM complex) forms the main entry site for precursor proteins that are produced on cytosolic ribosomes. Subsequently, different protein sorting machineries transfer the incoming preproteins to the mitochondrial outer and inner membranes, the intermembrane space, and the matrix. In this review, we highlight the recently discovered role of porin, also termed voltage-dependent anion channel (VDAC), in mitochondrial protein biogenesis. Porin forms the major channel for metabolites and ions in the outer membrane of mitochondria. Two different functions of porin in protein translocation have been reported. First, it controls the formation of the TOM complex by modulating the integration of the central receptor Tom22 into the mature translocase. Second, porin promotes the transport of carrier proteins toward the carrier translocase (TIM22 complex), which inserts these preproteins into the inner membrane. Therefore, porin acts as a coupling factor to spatially coordinate outer and inner membrane transport steps. Thus, porin links metabolite transport to protein import, which are both essential for mitochondrial function and biogenesis.
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Affiliation(s)
- Alexander Grevel
- Institute of Biochemistry und Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry und Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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10
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Drwesh L, Rapaport D. Biogenesis pathways of α-helical mitochondrial outer membrane proteins. Biol Chem 2021; 401:677-686. [PMID: 32017702 DOI: 10.1515/hsz-2019-0440] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/21/2020] [Indexed: 01/23/2023]
Abstract
Mitochondria harbor in their outer membrane (OM) proteins of different topologies. These proteins are encoded by the nuclear DNA, translated on cytosolic ribosomes and inserted into their target organelle by sophisticated protein import machineries. Recently, considerable insights have been accumulated on the insertion pathways of proteins into the mitochondrial OM. In contrast, little is known regarding the early cytosolic stages of their biogenesis. It is generally presumed that chaperones associate with these proteins following their synthesis in the cytosol, thereby keeping them in an import-competent conformation and preventing their aggregation and/or mis-folding and degradation. In this review, we outline the current knowledge about the biogenesis of different mitochondrial OM proteins with various topologies, and highlight the recent findings regarding their import pathways starting from early cytosolic events until their recognition on the mitochondrial surface that lead to their final insertion into the mitochondrial OM.
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Affiliation(s)
- Layla Drwesh
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
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11
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Gupta A, Becker T. Mechanisms and pathways of mitochondrial outer membrane protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148323. [PMID: 33035511 DOI: 10.1016/j.bbabio.2020.148323] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 11/29/2022]
Abstract
Outer membrane proteins integrate mitochondria into the cellular environment. They warrant exchange of small molecules like metabolites and ions, transport proteins into mitochondria, form contact sites to other cellular organelles for lipid exchange, constitute a signaling platform for apoptosis and inflammation and mediate organelle fusion and fission. The outer membrane contains two types of integral membrane proteins. Proteins with a transmembrane β-barrel structure and proteins with a single or multiple α-helical membrane spans. All outer membrane proteins are produced on cytosolic ribosomes and imported into the target organelle. Precursors of β-barrel and α-helical proteins are transported into the outer membrane via distinct import routes. The translocase of the outer membrane (TOM complex) transports β-barrel precursors across the outer membrane and the sorting and assembly machinery (SAM complex) inserts them into the target membrane. The mitochondrial import (MIM) complex constitutes the major integration site for α-helical embedded proteins. The import of some MIM-substrates involves TOM receptors, while others are imported in a TOM-independent manner. Remarkably, TOM, SAM and MIM complexes dynamically interact to import a large set of different proteins and to coordinate their assembly into protein complexes. Thus, protein import into the mitochondrial outer membrane involves a dynamic platform of protein translocases.
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Affiliation(s)
- Arushi Gupta
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Universität Bonn, Nussallee 11, 53115 Bonn, Germany.
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12
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Linden A, Deckers M, Parfentev I, Pflanz R, Homberg B, Neumann P, Ficner R, Rehling P, Urlaub H. A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. Mol Cell Proteomics 2020; 19:1161-1178. [PMID: 32332106 PMCID: PMC7338081 DOI: 10.1074/mcp.ra120.002028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/24/2020] [Indexed: 12/13/2022] Open
Abstract
Protein cross-linking and the analysis of cross-linked peptides by mass spectrometry is currently receiving much attention. Not only is this approach applied to isolated complexes to provide information about spatial arrangements of proteins, but it is also increasingly applied to entire cells and their organelles. As in quantitative proteomics, the application of isotopic labeling further makes it possible to monitor quantitative changes in the protein-protein interactions between different states of a system. Here, we cross-linked mitochondria from Saccharomyces cerevisiae grown on either glycerol- or glucose-containing medium to monitor protein-protein interactions under non-fermentative and fermentative conditions. We investigated qualitatively the protein-protein interactions of the 400 most abundant proteins applying stringent data-filtering criteria, i.e. a minimum of two cross-linked peptide spectrum matches and a cut-off in the spectrum scoring of the used search engine. The cross-linker BS3 proved to be equally suited for connecting proteins in all compartments of mitochondria when compared with its water-insoluble but membrane-permeable derivative DSS. We also applied quantitative cross-linking to mitochondria of both the growth conditions using stable-isotope labeled BS3. Significant differences of cross-linked proteins under glycerol and glucose conditions were detected, however, mainly because of the different copy numbers of these proteins in mitochondria under both the conditions. Results obtained from the glycerol condition indicate that the internal NADH:ubiquinone oxidoreductase Ndi1 is part of an electron transport chain supercomplex. We have also detected several hitherto uncharacterized proteins and identified their interaction partners. Among those, Min8 was found to be associated with cytochrome c oxidase. BN-PAGE analyses of min8Δ mitochondria suggest that Min8 promotes the incorporation of Cox12 into cytochrome c oxidase.
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Affiliation(s)
- Andreas Linden
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Iwan Parfentev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ralf Pflanz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bettina Homberg
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
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Avendaño-Monsalve MC, Ponce-Rojas JC, Funes S. From cytosol to mitochondria: the beginning of a protein journey. Biol Chem 2020; 401:645-661. [DOI: 10.1515/hsz-2020-0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 01/18/2023]
Abstract
AbstractMitochondrial protein import is one of the key processes during mitochondrial biogenesis that involves a series of events necessary for recognition and delivery of nucleus-encoded/cytosol-synthesized mitochondrial proteins into the organelle. The past research efforts have mainly unraveled how membrane translocases ensure the correct protein sorting within the different mitochondrial subcompartments. However, early steps of recognition and delivery remain relatively uncharacterized. In this review, we discuss our current understanding about the signals on mitochondrial proteins, as well as in the mRNAs encoding them, which with the help of cytosolic chaperones and membrane receptors support protein targeting to the organelle in order to avoid improper localization. In addition, we discuss recent findings that illustrate how mistargeting of mitochondrial proteins triggers stress responses, aiming to restore cellular homeostasis.
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Affiliation(s)
- Maria Clara Avendaño-Monsalve
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
| | - José Carlos Ponce-Rojas
- Department of Molecular, Cellular, and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Soledad Funes
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n Ciudad Universitaria Coyoacán, México, Cd.Mx. 04510, Mexico
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14
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Multifaceted roles of porin in mitochondrial protein and lipid transport. Biochem Soc Trans 2020; 47:1269-1277. [PMID: 31670371 DOI: 10.1042/bst20190153] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022]
Abstract
Mitochondria are essential eukaryotic organelles responsible for primary cellular energy production. Biogenesis, maintenance, and functions of mitochondria require correct assembly of resident proteins and lipids, which require their transport into and within mitochondria. Mitochondrial normal functions also require an exchange of small metabolites between the cytosol and mitochondria, which is primarily mediated by a metabolite channel of the outer membrane (OM) called porin or voltage-dependent anion channel. Here, we describe recently revealed novel roles of porin in the mitochondrial protein and lipid transport. First, porin regulates the formation of the mitochondrial protein import gate in the OM, the translocase of the outer membrane (TOM) complex, and its dynamic exchange between the major form of a trimer and the minor form of a dimer. The TOM complex dimer lacks a core subunit Tom22 and mediates the import of a subset of mitochondrial proteins while the TOM complex trimer facilitates the import of most other mitochondrial proteins. Second, porin interacts with both a translocating inner membrane (IM) protein like a carrier protein accumulated at the small TIM chaperones in the intermembrane space and the TIM22 complex, a downstream translocator in the IM for the carrier protein import. Porin thereby facilitates the efficient transfer of carrier proteins to the IM during their import. Third, porin facilitates the transfer of lipids between the OM and IM and promotes a back-up pathway for the cardiolipin synthesis in mitochondria. Thus, porin has roles more than the metabolite transport in the protein and lipid transport into and within mitochondria, which is likely conserved from yeast to human.
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15
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Molecular pathways of mitochondrial outer membrane protein degradation. Biochem Soc Trans 2019; 47:1437-1447. [DOI: 10.1042/bst20190275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 01/23/2023]
Abstract
Abstract
Mitochondrial outer membrane (MOM) encloses inner compartments of mitochondria and integrates cytoplasmic signals to regulate essential mitochondrial processes, such as protein import, dynamics, metabolism, cell death, etc. A substantial understanding of MOM associated proteostatic stresses and quality control pathways has been obtained in recent years. Six MOM associated protein degradation (MAD) pathways center on three AAA ATPases: Cdc48 in the cytoplasm, Msp1 integral to MOM, and Yme1 integral to the inner membrane. These pathways survey MOM proteome from the cytoplasmic and the inter-membrane space (IMS) sides. They detect and degrade MOM proteins with misfolded cytoplasmic and IMS domains, remove mistargeted tail-anchored proteins, and clear mitochondrial precursor proteins clogged in the TOM import complex. These MOM associated protein quality control pathways collaboratively maintain mitochondrial proteostasis and cell viability.
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Ellenrieder L, Dieterle MP, Doan KN, Mårtensson CU, Floerchinger A, Campo ML, Pfanner N, Becker T. Dual Role of Mitochondrial Porin in Metabolite Transport across the Outer Membrane and Protein Transfer to the Inner Membrane. Mol Cell 2019; 73:1056-1065.e7. [DOI: 10.1016/j.molcel.2018.12.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 11/09/2018] [Accepted: 12/14/2018] [Indexed: 01/26/2023]
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17
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Sakaue H, Shiota T, Ishizaka N, Kawano S, Tamura Y, Tan KS, Imai K, Motono C, Hirokawa T, Taki K, Miyata N, Kuge O, Lithgow T, Endo T. Porin Associates with Tom22 to Regulate the Mitochondrial Protein Gate Assembly. Mol Cell 2019; 73:1044-1055.e8. [DOI: 10.1016/j.molcel.2019.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/06/2018] [Accepted: 01/02/2019] [Indexed: 10/27/2022]
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18
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Sinzel M, Zeitler A, Dimmer KS. Interaction network of the mitochondrial outer membrane protein Mcp3. FEBS Lett 2018; 592:3210-3220. [PMID: 30192984 DOI: 10.1002/1873-3468.13243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 02/04/2023]
Abstract
Mitochondria are organelles containing two membranes that are distinct in composition and function. A role of the mitochondrial outer membrane (MOM) is to mediate contact of the organelle with the rest of the cell. In yeast, the MOM contains about 40 different integral proteins. Recently, we described the MOM protein Mcp3, which can serve as a multicopy suppressor of loss of ERMES complex that mediates mitochondria-endoplasmic reticulum contacts. To shed further light on the role of Mcp3 in the MOM, we analyzed its physical interaction with other proteins. We show that Mcp3 interacts with the MOM protein Om45 and the inner membrane protein Aim19. Our observations hint toward a potential involvement of Mcp3 in a structural and/or functional link between both mitochondrial membranes.
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Affiliation(s)
- Monika Sinzel
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Andreas Zeitler
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Kai S Dimmer
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
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19
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Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale. Cell Rep 2018; 19:2836-2852. [PMID: 28658629 PMCID: PMC5494306 DOI: 10.1016/j.celrep.2017.06.014] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 12/13/2022] Open
Abstract
Mitochondria perform central functions in cellular bioenergetics, metabolism, and signaling, and their dysfunction has been linked to numerous diseases. The available studies cover only part of the mitochondrial proteome, and a separation of core mitochondrial proteins from associated fractions has not been achieved. We developed an integrative experimental approach to define the proteome of east mitochondria. We classified > 3,300 proteins of mitochondria and mitochondria-associated fractions and defined 901 high-confidence mitochondrial proteins, expanding the set of mitochondrial proteins by 82. Our analysis includes protein abundance under fermentable and nonfermentable growth, submitochondrial localization, single-protein experiments, and subcellular classification of mitochondria-associated fractions. We identified mitochondrial interactors of respiratory chain supercomplexes, ATP synthase, AAA proteases, the mitochondrial contact site and cristae organizing system (MICOS), and the coenzyme Q biosynthesis cluster, as well as mitochondrial proteins with dual cellular localization. The integrative proteome provides a high-confidence source for the characterization of physiological and pathophysiological functions of mitochondria and their integration into the cellular environment. Classification of > 3,300 proteins of mitochondria and associated fractions High-confidence mitochondrial proteome with absolute quantification and topology Interactors of oxidative phosphorylation complexes and cristae organizing system Identification of system linking respiratory chain and AAA quality control
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20
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Niedzwiecka K, Tisi R, Penna S, Lichocka M, Plochocka D, Kucharczyk R. Two mutations in mitochondrial ATP6 gene of ATP synthase, related to human cancer, affect ROS, calcium homeostasis and mitochondrial permeability transition in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1865:117-131. [PMID: 28986220 DOI: 10.1016/j.bbamcr.2017.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 09/15/2017] [Accepted: 10/02/2017] [Indexed: 02/06/2023]
Abstract
The relevance of mitochondrial DNA (mtDNA) mutations in cancer process is still unknown. Since the mutagenesis of mitochondrial genome in mammals is not possible yet, we have exploited budding yeast S. cerevisiae as a model to study the effects of tumor-associated mutations in the mitochondrial MTATP6 gene, encoding subunit 6 of ATP synthase, on the energy metabolism. We previously reported that four mutations in this gene have a limited impact on the production of cellular energy. Here we show that two mutations, Atp6-P163S and Atp6-K90E (human MTATP6-P136S and MTATP6-K64E, found in prostate and thyroid cancer samples, respectively), increase sensitivity of yeast cells both to compounds inducing oxidative stress and to high concentrations of calcium ions in the medium, when Om45p, the component of porin complex in outer mitochondrial membrane (OM), was fused to GFP. In OM45-GFP background, these mutations affect the activation of yeast permeability transition pore (yPTP, also called YMUC, yeast mitochondrial unspecific channel) upon calcium induction. Moreover, we show that calcium addition to isolated mitochondria heavily induced the formation of ATP synthase dimers and oligomers, recently proposed to form the core of PTP, which was slower in the mutants. We show the genetic evidence for involvement of mitochondrial ATP synthase in calcium homeostasis and permeability transition in yeast. This paper is a first to show, although in yeast model organism, that mitochondrial ATP synthase mutations, which accumulate during carcinogenesis process, may be significant for cancer cell escape from apoptosis.
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Affiliation(s)
- Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Renata Tisi
- Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy; Milan Center for Neuroscience, Milan, Italy
| | - Sara Penna
- Dept. Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Malgorzata Lichocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Danuta Plochocka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
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Abstract
Mitochondria have to import the vast majority of their proteins, which are synthesized as precursors on cytosolic ribosomes. The translocase of the outer membrane (TOM complex) forms the general entry gate for the precursor proteins, which are subsequently sorted by protein machineries into the mitochondrial subcompartments: the outer and inner membrane, the intermembrane space and the mitochondrial matrix. The transport across and into the inner membrane is driven by the membrane potential, which is generated by the respiratory chain. Recent studies revealed that the lipid composition of mitochondrial membranes is important for the biogenesis of mitochondrial proteins. Cardiolipin and phosphatidylethanolamine exhibit unexpectedly specific functions for the activity of distinct protein translocases. Both phospholipids are required for full activity of respiratory chain complexes and thus to maintain the membrane potential for protein import. In addition, cardiolipin is required to maintain structural integrity of mitochondrial protein translocases. Finally, the low sterol content in the mitochondrial outer membrane may contribute to the targeting of some outer membrane proteins with a single α-helical membrane anchor. Altogether, mitochondrial lipids modulate protein import on various levels involving precursor targeting, membrane potential generation, stability and activity of protein translocases.
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22
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Konstantinov YM, Dietrich A, Weber-Lotfi F, Ibrahim N, Klimenko ES, Tarasenko VI, Bolotova TA, Koulintchenko MV. DNA import into mitochondria. BIOCHEMISTRY (MOSCOW) 2016; 81:1044-1056. [DOI: 10.1134/s0006297916100035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Lindahl PA, Moore MJ. Labile Low-Molecular-Mass Metal Complexes in Mitochondria: Trials and Tribulations of a Burgeoning Field. Biochemistry 2016; 55:4140-53. [PMID: 27433847 DOI: 10.1021/acs.biochem.6b00216] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Iron, copper, zinc, manganese, cobalt, and molybdenum play important roles in mitochondrial biochemistry, serving to help catalyze reactions in numerous metalloenzymes. These metals are also found in labile "pools" within mitochondria. Although the composition and cellular function of these pools are largely unknown, they are thought to be comprised of nonproteinaceous low-molecular-mass (LMM) metal complexes. Many problems must be solved before these pools can be fully defined, especially problems stemming from the lability of such complexes. This lability arises from inherently weak coordinate bonds between ligands and metals. This is an advantage for catalysis and trafficking, but it makes characterization difficult. The most popular strategy for investigating such pools is to detect them using chelator probes with fluorescent properties that change upon metal coordination. Characterization is limited because of the inevitable destruction of the complexes during their detection. Moreover, probes likely react with more than one type of metal complex, confusing analyses. An alternative approach is to use liquid chromatography (LC) coupled with inductively coupled plasma mass spectrometry (ICP-MS). With help from a previous lab member, the authors recently developed an LC-ICP-MS approach to analyze LMM extracts from yeast and mammalian mitochondria. They detected several metal complexes, including Fe580, Fe1100, Fe1500, Cu5000, Zn1200, Zn1500, Mn1100, Mn2000, Co1200, Co1500, and Mo780 (numbers refer to approximate masses in daltons). Many of these may be used to metalate apo-metalloproteins as they fold inside the organelle. The LC-based approach also has challenges, e.g., in distinguishing artifactual metal complexes from endogenous ones, due to the fact that cells must be disrupted to form extracts before they are passed through chromatography columns prior to analysis. Ultimately, both approaches will be needed to characterize these intriguing complexes and to elucidate their roles in mitochondrial biochemistry.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University , College Station, Texas 77843-3255, United States.,Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843-2128, United States
| | - Michael J Moore
- Department of Chemistry, Texas A&M University , College Station, Texas 77843-3255, United States
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24
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Nucleic acid import into mitochondria: New insights into the translocation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:3165-81. [DOI: 10.1016/j.bbamcr.2015.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/16/2015] [Accepted: 09/10/2015] [Indexed: 11/18/2022]
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25
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Müller CS, Bildl W, Haupt A, Ellenrieder L, Becker T, Hunte C, Fakler B, Schulte U. Cryo-slicing Blue Native-Mass Spectrometry (csBN-MS), a Novel Technology for High Resolution Complexome Profiling. Mol Cell Proteomics 2015; 15:669-81. [PMID: 26598645 DOI: 10.1074/mcp.m115.054080] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 11/06/2022] Open
Abstract
Blue native (BN) gel electrophoresis is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), it enables large scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness, and quantification. Here, we present a new methodology combining defined sub-millimeter slicing of BN gels by a cryo-microtome with high performance LC-MS/MS and label-free quantification of protein amounts. Application of this cryo-slicing BN-MS approach to mitochondria from rat brain demonstrated a high degree of comprehensiveness, accuracy, and size resolution. The technique provided abundance-mass profiles for 774 mitochondrial proteins, including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super-)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct super-complexes and identified novel assemblies of voltage-dependent anion channels/porins and TOM proteins. Together, cryo-slicing BN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.
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Affiliation(s)
- Catrin S Müller
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Wolfgang Bildl
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Alexander Haupt
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Lars Ellenrieder
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg
| | - Thomas Becker
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Carola Hunte
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Bernd Fakler
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Uwe Schulte
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg; ‖Logopharm GmbH, Schlossstrasse 14, 79232 March-Buchheim, Germany
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26
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Cooperation of protein machineries in mitochondrial protein sorting. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1119-29. [DOI: 10.1016/j.bbamcr.2015.01.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 02/07/2023]
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27
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Horvath SE, Rampelt H, Oeljeklaus S, Warscheid B, van der Laan M, Pfanner N. Role of membrane contact sites in protein import into mitochondria. Protein Sci 2015; 24:277-97. [PMID: 25514890 DOI: 10.1002/pro.2625] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 12/08/2014] [Indexed: 12/13/2022]
Abstract
Mitochondria import more than 1,000 different proteins from the cytosol. The proteins are synthesized as precursors on cytosolic ribosomes and are translocated by protein transport machineries of the mitochondrial membranes. Five main pathways for protein import into mitochondria have been identified. Most pathways use the translocase of the outer mitochondrial membrane (TOM) as the entry gate into mitochondria. Depending on specific signals contained in the precursors, the proteins are subsequently transferred to different intramitochondrial translocases. In this article, we discuss the connection between protein import and mitochondrial membrane architecture. Mitochondria possess two membranes. It is a long-standing question how contact sites between outer and inner membranes are formed and which role the contact sites play in the translocation of precursor proteins. A major translocation contact site is formed between the TOM complex and the presequence translocase of the inner membrane (TIM23 complex), promoting transfer of presequence-carrying preproteins to the mitochondrial inner membrane and matrix. Recent findings led to the identification of contact sites that involve the mitochondrial contact site and cristae organizing system (MICOS) of the inner membrane. MICOS plays a dual role. It is crucial for maintaining the inner membrane cristae architecture and forms contacts sites to the outer membrane that promote translocation of precursor proteins into the intermembrane space and outer membrane of mitochondria. The view is emerging that the mitochondrial protein translocases do not function as independent units, but are embedded in a network of interactions with machineries that control mitochondrial activity and architecture.
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Affiliation(s)
- Susanne E Horvath
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104, Freiburg, Germany
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28
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Song J, Tamura Y, Yoshihisa T, Endo T. A novel import route for an N-anchor mitochondrial outer membrane protein aided by the TIM23 complex. EMBO Rep 2014; 15:670-7. [PMID: 24781694 DOI: 10.1002/embr.201338142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The membrane topology of Om45 in the yeast mitochondrial outer membrane (OM) is under debate. Here, we confirm that Om45 is anchored to the OM from the intermembrane space (IMS) by its N-terminal hydrophobic segment. We show that import of Om45 requires the presequence receptors, Tom20 and Tom22, and the import channel of Tom40. Unlike any of the known OM proteins, Om45 import requires the TIM23 complex in the inner membrane, a translocator for presequence-containing proteins, and the membrane potential (ΔΨ). Therefore, Om45 is anchored to the OM via the IMS by a novel import pathway involving the TIM23 complex.
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Affiliation(s)
- Jiyao Song
- Department of Chemistry, Graduate School of Science Nagoya University, Chikusa-ku Nagoya, Japan
| | - Yasushi Tamura
- Research Center for Materials Science Nagoya University, Chikusa-ku Nagoya, Japan
| | - Tohru Yoshihisa
- Graduate School of Life Science University of Hyogo, Hyogo, Japan
| | - Toshiya Endo
- Department of Chemistry, Graduate School of Science Nagoya University, Chikusa-ku Nagoya, Japan Structural Biology Research Center Nagoya University, Chikusa-ku Nagoya, Japan JST CREST Nagoya University, Chikusa-ku Nagoya, Japan
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29
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Wenz LS, Opaliński L, Schuler MH, Ellenrieder L, Ieva R, Böttinger L, Qiu J, van der Laan M, Wiedemann N, Guiard B, Pfanner N, Becker T. The presequence pathway is involved in protein sorting to the mitochondrial outer membrane. EMBO Rep 2014; 15:678-85. [PMID: 24781695 DOI: 10.1002/embr.201338144] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The mitochondrial outer membrane contains integral α-helical and β-barrel proteins that are imported from the cytosol. The machineries importing β-barrel proteins have been identified, however, different views exist on the import of α-helical proteins. It has been reported that the biogenesis of Om45, the most abundant signal-anchored protein, does not depend on proteinaceous components, but involves direct insertion into the outer membrane. We show that import of Om45 occurs via the translocase of the outer membrane and the presequence translocase of the inner membrane. Assembly of Om45 in the outer membrane involves the MIM machinery. Om45 thus follows a new mitochondrial biogenesis pathway that uses elements of the presequence import pathway to direct a protein to the outer membrane.
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Affiliation(s)
- Lena-Sophie Wenz
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Faculty of Biology, Universität Freiburg, Freiburg, Germany
| | - Lukasz Opaliński
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany
| | - Max-Hinderk Schuler
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany
| | - Lars Ellenrieder
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Faculty of Biology, Universität Freiburg, Freiburg, Germany
| | - Raffaele Ieva
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany
| | - Lena Böttinger
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Faculty of Biology, Universität Freiburg, Freiburg, Germany
| | - Jian Qiu
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany Spemann Graduate School of Biology and Medicine, Universität Freiburg, Freiburg, Germany
| | - Martin van der Laan
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, Gif-sur-Yvette, France
| | - Nikolaus Pfanner
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ Universität Freiburg, Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Universität Freiburg, Freiburg, Germany
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Rapaport D. The mitochondrial protein OM45 is exposed to the cytosol. J Biol Chem 2012; 287:27415; author reply 27416. [PMID: 22888114 DOI: 10.1074/jbc.l112.392969] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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