1
|
Kremer LS, Rehling P. Coordinating mitochondrial translation with assembly of the OXPHOS complexes. Hum Mol Genet 2024; 33:R47-R52. [PMID: 38779773 PMCID: PMC11112383 DOI: 10.1093/hmg/ddae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/31/2024] [Accepted: 02/09/2024] [Indexed: 05/25/2024] Open
Abstract
The mitochondrial oxidative phosphorylation (OXPHOS) system produces the majority of energy required by cells. Given the mitochondrion's endosymbiotic origin, the OXPHOS machinery is still under dual genetic control where most OXPHOS subunits are encoded by the nuclear DNA and imported into mitochondria, while a small subset is encoded on the mitochondrion's own genome, the mitochondrial DNA (mtDNA). The nuclear and mtDNA encoded subunits must be expressed and assembled in a highly orchestrated fashion to form a functional OXPHOS system and meanwhile prevent the generation of any harmful assembly intermediates. While several mechanisms have evolved in eukaryotes to achieve such a coordinated expression, this review will focus on how the translation of mtDNA encoded OXPHOS subunits is tailored to OXPHOS assembly.
Collapse
Affiliation(s)
- Laura S Kremer
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, Göttingen 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Humboldtallee 23, Göttingen 37073, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Robert-Koch-Str. 40, Göttingen 37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology, Translational Neuroinflammation and Automated Microscopy, Robert-Koch-Str. 40, Göttingen 37075, Germany
- Max Planck Institute for Multidisciplinary Science, Am Faßberg 11, Göttingen 37077, Germany
| |
Collapse
|
2
|
Eldeeb MH, Camacho Lopez LJ, Fontanesi F. Mitochondrial respiratory supercomplexes of the yeast Saccharomyces cerevisiae. IUBMB Life 2024. [PMID: 38529880 DOI: 10.1002/iub.2817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
The functional and structural relationship among the individual components of the mitochondrial respiratory chain constitutes a central aspect of our understanding of aerobic catabolism. This interplay has been a subject of intense debate for over 50 years. It is well established that individual respiratory enzymes associate into higher-order structures known as respiratory supercomplexes, which represent the evolutionarily conserved organizing principle of the mitochondrial respiratory chain. In the yeast Saccharomyces cerevisiae, supercomplexes are formed by a complex III homodimer flanked by one or two complex IV monomers, and their high-resolution structures have been recently elucidated. Despite the wealth of structural information, several proposed supercomplex functions remain speculative and our understanding of their physiological relevance is still limited. Recent advances in the field were made possible by the construction of yeast strains where the association of complex III and IV into supercomplexes is impeded, leading to diminished respiratory capacity and compromised cellular competitive fitness. Here, we discuss the experimental evidence and hypotheses relative to the functional roles of yeast respiratory supercomplexes. Moreover, we review the current models of yeast complex III and IV assembly in the context of supercomplex formation and highlight the data scattered throughout the literature suggesting the existence of cross talk between their biogenetic processes.
Collapse
Affiliation(s)
- Mazzen H Eldeeb
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Lizeth J Camacho Lopez
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, Florida, USA
| |
Collapse
|
3
|
Jung SJ, Sridhara S, Ott M. Early steps in the biogenesis of mitochondrially encoded oxidative phosphorylation subunits. IUBMB Life 2024; 76:125-139. [PMID: 37712772 DOI: 10.1002/iub.2784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
The complexes mediating oxidative phosphorylation (OXPHOS) in the inner mitochondrial membrane consist of proteins encoded in the nuclear or the mitochondrial DNA. The mitochondrially encoded membrane proteins (mito-MPs) represent the catalytic core of these complexes and follow complicated pathways for biogenesis. Owing to their overall hydrophobicity, mito-MPs are co-translationally inserted into the inner membrane by the Oxa1 insertase. After insertion, OXPHOS biogenesis factors mediate the assembly of mito-MPs into complexes and participate in the regulation of mitochondrial translation, while protein quality control factors recognize and degrade faulty or excess proteins. This review summarizes the current understanding of these early steps occurring during the assembly of mito-MPs by concentrating on results obtained in the model organism baker's yeast.
Collapse
Affiliation(s)
- Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Martin Ott
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| |
Collapse
|
4
|
Nishimura A. Regulations and functions of proline utilization in yeast Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2024; 88:131-137. [PMID: 37994668 DOI: 10.1093/bbb/zbad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
The quality of alcoholic beverages strongly depends on the metabolic characteristics of the yeast cells being used. To control the aroma and the taste of alcoholic beverages, as well as the production of ethanol in them, it is thus crucial to select yeast cells with the proper characteristics. Grape must contain a high concentration of proline, an amino acid that can potentially be a useful nitrogen source. However, Saccharomyces cerevisiae cannot utilize proline during the wine-making process, resulting in the elevated levels of proline in wine and consequent negative effects on wine quality. In this article, I review and discuss recent discoveries about the inhibitory mechanisms and roles of proline utilization in yeast. The information can help in developing novel yeast strains that can improve fermentation and enhance the quality and production efficiency of wine.
Collapse
Affiliation(s)
- Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| |
Collapse
|
5
|
Nishimura A, Tanahashi R, Nakazawa H, Oi T, Mima M, Takagi H. PKA-Msn2/4-Shy1 cascade controls inhibition of proline utilization under wine fermentation models. J Biosci Bioeng 2023; 136:438-442. [PMID: 37940488 DOI: 10.1016/j.jbiosc.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Proline, which is a predominant amino acid in grape musts, is involved in the taste and flavor of foods and beverages. The yeast Saccharomyces cerevisiae poorly utilizes proline in wine-making processes, leading to a nitrogen deficiency during fermentation and proline accumulation in wine. Previous studies have shown that the protein kinase A (PKA) pathway is involved in inhibitory mechanisms of proline utilization. In this study, we screened the PKA pathway-related genes that regulate proline utilization. Using a yeast culture collection of disrupted strains associated with the downstream of the PKA cascade, we revealed that the stress-responsive transcription factor genes MSN2/4 regulate proline utilization. Moreover, we found that Msn2/4 up-regulate the SHY1 gene during the cell growth of the wine fermentation model, which may cause the inhibition of proline utilization. The SHY1-deleted strain of the commercial wine yeast clearly showed proline consumption and average ethanol production under the wine fermentation model. The present data indicate that the PKA-Msn2/4-Shy1 cascade controls the inhibition of proline utilization under wine-making processes. Our study could hold promise for the development of wine yeast strains that can efficiently reduce proline during wine fermentation.
Collapse
Affiliation(s)
- Akira Nishimura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan; Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.
| | - Ryoya Tanahashi
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan; Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Hayate Nakazawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoki Oi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Misaki Mima
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Takagi
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| |
Collapse
|
6
|
Kohler A, Carlström A, Nolte H, Kohler V, Jung SJ, Sridhara S, Tatsuta T, Berndtsson J, Langer T, Ott M. Early fate decision for mitochondrially encoded proteins by a molecular triage. Mol Cell 2023; 83:3470-3484.e8. [PMID: 37751741 DOI: 10.1016/j.molcel.2023.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 07/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
Folding of newly synthesized proteins poses challenges for a functional proteome. Dedicated protein quality control (PQC) systems either promote the folding of nascent polypeptides at ribosomes or, if this fails, ensure their degradation. Although well studied for cytosolic protein biogenesis, it is not understood how these processes work for mitochondrially encoded proteins, key subunits of the oxidative phosphorylation (OXPHOS) system. Here, we identify dedicated hubs in proximity to mitoribosomal tunnel exits coordinating mitochondrial protein biogenesis and quality control. Conserved prohibitin (PHB)/m-AAA protease supercomplexes and the availability of assembly chaperones determine the fate of newly synthesized proteins by molecular triaging. The localization of these competing activities in the vicinity of the mitoribosomal tunnel exit allows for a prompt decision on whether newly synthesized proteins are fed into OXPHOS assembly or are degraded.
Collapse
Affiliation(s)
- Andreas Kohler
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden; Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Verena Kohler
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Sung-Jun Jung
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Takashi Tatsuta
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Jens Berndtsson
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.
| |
Collapse
|
7
|
Wang PY, Ma J, Kim YC, Son AY, Syed AM, Liu C, Mori MP, Huffstutler RD, Stolinski JL, Talagala SL, Kang JG, Walitt BT, Nath A, Hwang PM. WASF3 disrupts mitochondrial respiration and may mediate exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome. Proc Natl Acad Sci U S A 2023; 120:e2302738120. [PMID: 37579159 PMCID: PMC10450651 DOI: 10.1073/pnas.2302738120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/27/2023] [Indexed: 08/16/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by various disabling symptoms including exercise intolerance and is diagnosed in the absence of a specific cause, making its clinical management challenging. A better understanding of the molecular mechanism underlying this apparent bioenergetic deficiency state may reveal insights for developing targeted treatment strategies. We report that overexpression of Wiskott-Aldrich Syndrome Protein Family Member 3 (WASF3), here identified in a 38-y-old woman suffering from long-standing fatigue and exercise intolerance, can disrupt mitochondrial respiratory supercomplex formation and is associated with endoplasmic reticulum (ER) stress. Increased expression of WASF3 in transgenic mice markedly decreased their treadmill running capacity with concomitantly impaired respiratory supercomplex assembly and reduced complex IV levels in skeletal muscle mitochondria. WASF3 induction by ER stress using endotoxin, well known to be associated with fatigue in humans, also decreased skeletal muscle complex IV levels in mice, while decreasing WASF3 levels by pharmacologic inhibition of ER stress improved mitochondrial function in the cells of the patient with chronic fatigue. Expanding on our findings, skeletal muscle biopsy samples obtained from a cohort of patients with ME/CFS showed increased WASF3 protein levels and aberrant ER stress activation. In addition to revealing a potential mechanism for the bioenergetic deficiency in ME/CFS, our study may also provide insights into other disorders associated with fatigue such as rheumatic diseases and long COVID.
Collapse
Affiliation(s)
- Ping-yuan Wang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Jin Ma
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Young-Chae Kim
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Annie Y. Son
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Abu Mohammad Syed
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Chengyu Liu
- Transgenic Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Mateus P. Mori
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Rebecca D. Huffstutler
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - JoEllyn L. Stolinski
- NIH MRI Research Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
| | - S. Lalith Talagala
- NIH MRI Research Facility, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
| | - Ju-Gyeong Kang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Brian T. Walitt
- Clinical Neurosciences Program, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
| | - Avindra Nath
- Clinical Neurosciences Program, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD20892
| | - Paul M. Hwang
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| |
Collapse
|
8
|
Proteomics as a Tool for the Study of Mitochondrial Proteome, Its Dysfunctionality and Pathological Consequences in Cardiovascular Diseases. Int J Mol Sci 2023; 24:ijms24054692. [PMID: 36902123 PMCID: PMC10003354 DOI: 10.3390/ijms24054692] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
The focus of this review is on the proteomic approaches applied to the study of the qualitative/quantitative changes in mitochondrial proteins that are related to impaired mitochondrial function and consequently different types of pathologies. Proteomic techniques developed in recent years have created a powerful tool for the characterization of both static and dynamic proteomes. They can detect protein-protein interactions and a broad repertoire of post-translation modifications that play pivotal roles in mitochondrial regulation, maintenance and proper function. Based on accumulated proteomic data, conclusions can be derived on how to proceed in disease prevention and treatment. In addition, this article will present an overview of the recently published proteomic papers that deal with the regulatory roles of post-translational modifications of mitochondrial proteins and specifically with cardiovascular diseases connected to mitochondrial dysfunction.
Collapse
|
9
|
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] [MESH Headings] [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.
Collapse
Affiliation(s)
- Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Fabian den Brave
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Alexander Haupt
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Arushi Gupta
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiyao Song
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Catrin S Müller
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jeannine Engelke
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Swadha Mishra
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Christoph Mårtensson
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- MTIP, Basel, Switzerland
| | - Lars Ellenrieder
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Novartis, Basel, Switzerland
| | - Chantal Priesnitz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian P Straub
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Sanofi-Aventis (Suisse), Vernier, Switzerland
| | - Kim Nguyen Doan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bogusz Kulawiak
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wolfgang Bildl
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Rampelt
- 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
| | - Nils Wiedemann
- 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
| | - 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
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, Bonn, Germany
| |
Collapse
|
10
|
Hubble KA, Henry MF. DPC29 promotes post-initiation mitochondrial translation in Saccharomyces cerevisiae. Nucleic Acids Res 2023; 51:1260-1276. [PMID: 36620885 PMCID: PMC9943650 DOI: 10.1093/nar/gkac1229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial ribosomes synthesize essential components of the oxidative phosphorylation (OXPHOS) system in a tightly regulated process. In the yeast Saccharomyces cerevisiae, mitochondrial mRNAs require specific translational activators, which orchestrate protein synthesis by recognition of their target gene's 5'-untranslated region (UTR). Most of these yeast genes lack orthologues in mammals, and only one such gene-specific translational activator has been proposed in humans-TACO1. The mechanism by which TACO1 acts is unclear because mammalian mitochondrial mRNAs do not have significant 5'-UTRs, and therefore must promote translation by alternative mechanisms. In this study, we examined the role of the TACO1 orthologue in yeast. We found this 29 kDa protein to be a general mitochondrial translation factor, Dpc29, rather than a COX1-specific translational activator. Its activity was necessary for the optimal expression of OXPHOS mtDNA reporters, and mutations within the mitoribosomal large subunit protein gene MRP7 produced a global reduction of mitochondrial translation in dpc29Δ cells, indicative of a general mitochondrial translation factor. Northern-based mitoribosome profiling of dpc29Δ cells showed higher footprint frequencies at the 3' ends of mRNAs, suggesting a role in translation post-initiation. Additionally, human TACO1 expressed at native levels rescued defects in dpc29Δ yeast strains, suggesting that the two proteins perform highly conserved functions.
Collapse
Affiliation(s)
- Kyle A Hubble
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA,Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ 08084, USA
| | - Michael F Henry
- To whom correspondence should be addressed. Tel: +1 856 566 6970; Fax: +1 856 566 6291; E-mail:
| |
Collapse
|
11
|
Priesnitz C, Böttinger L, Zufall N, Gebert M, Guiard B, van der Laan M, Becker T. Coupling to Pam16 differentially controls the dual role of Pam18 in protein import and respiratory chain formation. Cell Rep 2022; 39:110619. [PMID: 35385740 DOI: 10.1016/j.celrep.2022.110619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 01/31/2022] [Accepted: 03/15/2022] [Indexed: 11/03/2022] Open
Abstract
The presequence translocase (TIM23 complex) imports precursor proteins into the mitochondrial inner membrane and matrix. The presequence translocase-associated motor (PAM) provides a driving force for transport into the matrix. The J-protein Pam18 stimulates the ATPase activity of the mitochondrial Hsp70 (mtHsp70). Pam16 recruits Pam18 to the TIM23 complex to ensure protein import. The Pam16-Pam18 module also associates with components of the respiratory chain, but the function of the dual localization of Pam16-Pam18 is largely unknown. Here, we show that disruption of the Pam16-Pam18 heterodimer causes redistribution of Pam18 to the respiratory chain supercomplexes, where it forms a homodimer. Redistribution of Pam18 decreases protein import into mitochondria but stimulates mtHsp70-dependent assembly of respiratory chain complexes. We conclude that coupling to Pam16 differentially controls the dual function of Pam18. It recruits Pam18 to the TIM23 complex to promote protein import but attenuates the Pam18 function in the assembly of respiratory chain complexes.
Collapse
Affiliation(s)
- Chantal Priesnitz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lena Böttinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Nicole Zufall
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Michael Gebert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | | | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany.
| |
Collapse
|
12
|
Criscuolo D, Avolio R, Matassa DS, Esposito F. Targeting Mitochondrial Protein Expression as a Future Approach for Cancer Therapy. Front Oncol 2021; 11:797265. [PMID: 34888254 PMCID: PMC8650000 DOI: 10.3389/fonc.2021.797265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
Extensive metabolic remodeling is a fundamental feature of cancer cells. Although early reports attributed such remodeling to a loss of mitochondrial functions, it is now clear that mitochondria play central roles in cancer development and progression, from energy production to synthesis of macromolecules, from redox modulation to regulation of cell death. Biosynthetic pathways are also heavily affected by the metabolic rewiring, with protein synthesis dysregulation at the hearth of cellular transformation. Accumulating evidence in multiple organisms shows that the metabolic functions of mitochondria are tightly connected to protein synthesis, being assembly and activity of respiratory complexes highly dependent on de novo synthesis of their components. In turn, protein synthesis within the organelle is tightly connected with the cytosolic process. This implies an entire network of interactions and fine-tuned regulations that build up a completely under-estimated level of complexity. We are now only preliminarily beginning to reconstitute such regulatory level in human cells, and to perceive its role in diseases. Indeed, disruption or alterations of these connections trigger conditions of proteotoxic and energetic stress that could be potentially exploited for therapeutic purposes. In this review, we summarize the available literature on the coordinated regulation of mitochondrial and cytosolic mRNA translation, and their effects on the integrity of the mitochondrial proteome and functions. Finally, we highlight the potential held by this topic for future research directions and for the development of innovative therapeutic approaches.
Collapse
Affiliation(s)
- Daniela Criscuolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Rosario Avolio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Danilo Swann Matassa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Franca Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| |
Collapse
|
13
|
Rivett ED, Heo L, Feig M, Hegg EL. Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer. Crit Rev Biochem Mol Biol 2021; 56:640-668. [PMID: 34428995 DOI: 10.1080/10409238.2021.1957668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Aerobic respiration is a key energy-producing pathway in many prokaryotes and virtually all eukaryotes. The final step of aerobic respiration is most commonly catalyzed by heme-copper oxidases embedded in the cytoplasmic or mitochondrial membrane. The majority of these terminal oxidases contain a prenylated heme (typically heme a or occasionally heme o) in the active site. In addition, many heme-copper oxidases, including mitochondrial cytochrome c oxidases, possess a second heme a cofactor. Despite the critical role of heme a in the electron transport chain, the details of the mechanism by which heme b, the prototypical cellular heme, is converted to heme o and then to heme a remain poorly understood. Recent structural investigations, however, have helped clarify some elements of heme a biosynthesis. In this review, we discuss the insight gained from these advances. In particular, we present a new structural model of heme o synthase (HOS) based on distance restraints from inferred coevolutionary relationships and refined by molecular dynamics simulations that are in good agreement with the experimentally determined structures of HOS homologs. We also analyze the two structures of heme a synthase (HAS) that have recently been solved by other groups. For both HOS and HAS, we discuss the proposed catalytic mechanisms and highlight how new insights into the heme-binding site locations shed light on previously obtained biochemical data. Finally, we explore the implications of the new structural data in the broader context of heme trafficking in the heme a biosynthetic pathway and heme-copper oxidase assembly.
Collapse
Affiliation(s)
- Elise D Rivett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Eric L Hegg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
14
|
Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
Collapse
|
15
|
Xue Y, Li PD, Tang XM, Yan ZH, Xia SS, Tian HP, Liu ZL, Zhou T, Tang XG, Zhang GJ. Cytochrome C Oxidase Assembly Factor 1 Homolog Predicts Poor Prognosis and Promotes Cell Proliferation in Colorectal Cancer by Regulating PI3K/AKT Signaling. Onco Targets Ther 2020; 13:11505-11516. [PMID: 33204105 PMCID: PMC7667209 DOI: 10.2147/ott.s279024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/22/2020] [Indexed: 01/22/2023] Open
Abstract
Purpose Colorectal cancer (CRC) is one of the most common malignancies in the world. The prognosis of advanced CRC is still poor. The purpose of this study was to identify a gene expression profile associated with CRC that may contribute to the early diagnosis of CRC and improve patient prognosis. Patients and Methods Five pairs of CRC tissues and paracancerous tissues were used to identify causative genes using microarray assays. The prognostic value of Cytochrome C Oxidase Assembly Factor 1 Homolog (COA1) in CRC was assessed in 90 CRC patients. Loss-of-function assays, cell proliferation assays using Celigo and MTT, colony formation assays, a subcutaneous xenograft mouse model, and apoptosis assays were used to define the effects of downregulation of COA1 in CRC cells in vitro and in vivo. The underlying molecular mechanisms of COA1 in CRC were also investigated. Results The causative gene COA1 was identified through microarray analysis. COA1 expression in CRC was notably associated with pathologic differentiation, tumor size, and tumor depth. COA1 expression may act as an independent prognostic factor for overall survival of CRC. Knockdown of COA1 inhibited the proliferation of CRC cells in vitro and the tumorigenicity of CRC cells in vivo. Decreased COA1 expression induced apoptosis of CRC cells. Based on the microarray assay results comparing HCT116 cells transfected with lentivirus encoding anti-COA1 shRNA or negative control shRNA, ingenuity pathway analysis (IPA) revealed that the PI3K/AKT signaling pathway was significantly enriched. Moreover, CCND1, mTOR, AKT1, and MDM2 were identified as the downstream genes of COA1. Conclusion These findings demonstrate that COA1 promotes CRC cell proliferation and inhibits apoptosis by regulating the PI3K/AKT signaling pathway. Our results implicate COA1 as a potential oncogene involved in tumor growth and progression of CRC.
Collapse
Affiliation(s)
- Yuan Xue
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Pei-Dong Li
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Xue-Mei Tang
- Department of Ultrasound, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Zai-Hua Yan
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Shu-Sen Xia
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Hong-Peng Tian
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Zuo-Liang Liu
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Tong Zhou
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Xue-Gui Tang
- Anorectal Department of Integrated Traditional Chinese and Western Medicine, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| | - Guang-Jun Zhang
- The Second Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China.,Institute of Hepatobiliary, Pancreatic and Intestinal Disease, North Sichuan Medical College, Nanchong, Sichuan, People's Republic of China
| |
Collapse
|
16
|
Cobine PA, Moore SA, Leary SC. Getting out what you put in: Copper in mitochondria and its impacts on human disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118867. [PMID: 32979421 DOI: 10.1016/j.bbamcr.2020.118867] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/22/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
Mitochondria accumulate copper in their matrix for the eventual maturation of the cuproenzymes cytochrome c oxidase and superoxide dismutase. Transport into the matrix is achieved by mitochondrial carrier family (MCF) proteins. The major copper transporting MCF described to date in yeast is Pic2, which imports the metal ion into the matrix. Pic2 is one of ~30 MCFs that move numerous metabolites, nucleotides and co-factors across the inner membrane for use in the matrix. Genetic and biochemical experiments showed that Pic2 is required for cytochrome c oxidase activity under copper stress, and that it is capable of transporting ionic and complexed forms of copper. The Pic2 ortholog SLC25A3, one of 53 mammalian MCFs, functions as both a copper and a phosphate transporter. Depletion of SLC25A3 results in decreased accumulation of copper in the matrix, a cytochrome c oxidase defect and a modulation of cytosolic superoxide dismutase abundance. The regulatory roles for copper and cuproproteins resident to the mitochondrion continue to expand beyond the organelle. Mitochondrial copper chaperones have been linked to the modulation of cellular copper uptake and export and the facilitation of inter-organ communication. Recently, a role for matrix copper has also been proposed in a novel cell death pathway termed cuproptosis. This review will detail our understanding of the maturation of mitochondrial copper enzymes, the roles of mitochondrial signals in regulating cellular copper content, the proposed mechanisms of copper transport into the organelle and explore the evolutionary origins of copper homeostasis pathways.
Collapse
Affiliation(s)
- Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| | - Stanley A Moore
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scot C Leary
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
| |
Collapse
|
17
|
Functions of Cytochrome c oxidase Assembly Factors. Int J Mol Sci 2020; 21:ijms21197254. [PMID: 33008142 PMCID: PMC7582755 DOI: 10.3390/ijms21197254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
Cytochrome c oxidase is the terminal complex of eukaryotic oxidative phosphorylation in mitochondria. This process couples the reduction of electron carriers during metabolism to the reduction of molecular oxygen to water and translocation of protons from the internal mitochondrial matrix to the inter-membrane space. The electrochemical gradient formed is used to generate chemical energy in the form of adenosine triphosphate to power vital cellular processes. Cytochrome c oxidase and most oxidative phosphorylation complexes are the product of the nuclear and mitochondrial genomes. This poses a series of topological and temporal steps that must be completed to ensure efficient assembly of the functional enzyme. Many assembly factors have evolved to perform these steps for insertion of protein into the inner mitochondrial membrane, maturation of the polypeptide, incorporation of co-factors and prosthetic groups and to regulate this process. Much of the information about each of these assembly factors has been gleaned from use of the single cell eukaryote Saccharomyces cerevisiae and also mutations responsible for human disease. This review will focus on the assembly factors of cytochrome c oxidase to highlight some of the outstanding questions in the assembly of this vital enzyme complex.
Collapse
|
18
|
Singh AP, Salvatori R, Aftab W, Kohler A, Carlström A, Forne I, Imhof A, Ott M. Molecular Connectivity of Mitochondrial Gene Expression and OXPHOS Biogenesis. Mol Cell 2020; 79:1051-1065.e10. [PMID: 32877643 DOI: 10.1016/j.molcel.2020.07.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 01/05/2023]
Abstract
Mitochondria contain their own gene expression systems, including membrane-bound ribosomes dedicated to synthesizing a few hydrophobic subunits of the oxidative phosphorylation (OXPHOS) complexes. We used a proximity-dependent biotinylation technique, BioID, coupled with mass spectrometry to delineate in baker's yeast a comprehensive network of factors involved in biogenesis of mitochondrial encoded proteins. This mitochondrial gene expression network (MiGENet) encompasses proteins involved in transcription, RNA processing, translation, or protein biogenesis. Our analyses indicate the spatial organization of these processes, thereby revealing basic mechanistic principles and the proteins populating strategically important sites. For example, newly synthesized proteins are directly handed over to ribosomal tunnel exit-bound factors that mediate membrane insertion, co-factor acquisition, or their mounting into OXPHOS complexes in a special early assembly hub. Collectively, the data reveal the connectivity of mitochondrial gene expression, reflecting a unique tailoring of the mitochondrial gene expression system.
Collapse
Affiliation(s)
- Abeer Prakash Singh
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Roger Salvatori
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Wasim Aftab
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Andreas Kohler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Carlström
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ignasi Forne
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig Maximilians University of Munich, 82152 Planegg-Martinsried, Germany
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden.
| |
Collapse
|
19
|
Grevel A, Pfanner N, Becker T. Coupling of import and assembly pathways in mitochondrial protein biogenesis. Biol Chem 2020; 401:117-129. [PMID: 31513529 DOI: 10.1515/hsz-2019-0310] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
Biogenesis and function of mitochondria depend on the import of about 1000 precursor proteins that are produced on cytosolic ribosomes. The translocase of the outer membrane (TOM) forms the entry gate for most proteins. After passage through the TOM channel, dedicated preprotein translocases sort the precursor proteins into the mitochondrial subcompartments. Many proteins have to be assembled into oligomeric membrane-integrated complexes in order to perform their functions. In this review, we discuss a dual role of mitochondrial preprotein translocases in protein translocation and oligomeric assembly, focusing on the biogenesis of the TOM complex and the respiratory chain. The sorting and assembly machinery (SAM) of the outer mitochondrial membrane forms a dynamic platform for coupling transport and assembly of TOM subunits. The biogenesis of the cytochrome c oxidase of the inner membrane involves a molecular circuit to adjust translation of mitochondrial-encoded core subunits to the availability of nuclear-encoded partner proteins. Thus, mitochondrial protein translocases not only import precursor proteins but can also support their assembly into functional complexes.
Collapse
Affiliation(s)
- Alexander Grevel
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| |
Collapse
|
20
|
Zha L, Chen M, Yu C, Guo Q, Zhao X, Li Z, Zhao Y, Li C, Yang H. Differential proteomics study of postharvest Volvariella volvacea during storage at 4 °C. Sci Rep 2020; 10:13134. [PMID: 32753745 PMCID: PMC7403728 DOI: 10.1038/s41598-020-69988-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 07/20/2020] [Indexed: 11/21/2022] Open
Abstract
The postharvest storage of Volvariella volvacea is an important factor limiting the industry development. Low-temperature storage is the traditional storage method used for most edible fungi, but V. volvacea undergoes autolysis at low temperature. To understand the molecular mechanism underlying the low-temperature autolysis of V. volvacea after harvesting, fruiting bodies of V. volvacea strain V23 were stored at 4 °C. Based on our previous study, in which the changes of morphological and physiological indexes during storage for 0, 6, 12, 24, 30, 36, 48 and 60 h were measured; four time points, namely, 0, 12, 24 and 60 h, were selected for this differential proteomics study. The proteomic changes in the postharvest storage samples were studied by isobaric tags for relative and absolute quantification-coupled two-dimensional liquid chromatography-tandem mass spectrometry (2D LC–MS/MS). A total of 2,063 proteins were identified, and 192 differentially expressed proteins (DEPs), including 24 up-regulated proteins and 168 down-regulated proteins, were detected after 12 h of storage. After 24 h of storage, 234 DEPs, including 48 up-regulated and 186 down-regulated proteins, were observed, and after 60 h, 415 DEPs, including 65 up-regulated proteins and 350 down-regulated proteins, were observed. An in-depth data analysis showed that the DEPs participated in various cellular processes, particularly metabolic processes. In this study, we combined Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, and the results focused on oxidative phosphorylation and ubiquitin mediated proteolysis pathways. In addition, sdh2, uba1 and ubc1 was confirmed by quantitative real-time polymerase chain reaction, and the results showed that the expression of these genes were consistent with their protein level. Based on the literature and our results, it is speculated that the identified DEPs, such as ATP1, SDH2, COR1, UBA1, COX4, UBC1 and SKP1 play a key role in the low-temperature autolysis of V. volvacea.
Collapse
Affiliation(s)
- Lei Zha
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Mingjie Chen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Changxia Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Qian Guo
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Xu Zhao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Zhengpeng Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Yan Zhao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
| | - Chuanhua Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Huanling Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| |
Collapse
|
21
|
Hillman GA, Henry MF. The yeast protein Mam33 functions in the assembly of the mitochondrial ribosome. J Biol Chem 2019; 294:9813-9829. [PMID: 31053642 DOI: 10.1074/jbc.ra119.008476] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/24/2019] [Indexed: 02/04/2023] Open
Abstract
Mitochondrial ribosomes are functionally specialized for the synthesis of several essential inner membrane proteins of the respiratory chain. Although remarkable progress has been made toward understanding the structure of mitoribosomes, the pathways and factors that facilitate their biogenesis remain largely unknown. The long unstructured domains of unassembled ribosomal proteins are highly prone to misfolding and often require dedicated chaperones to prevent aggregation. To date, chaperones that ensure safe delivery to the assembling ribosome have not been identified in the mitochondrion. In this study, a respiratory synthetic lethality screen revealed a role for an evolutionarily conserved mitochondrial matrix protein called Mam33 in Saccharomyces cerevisiae mitoribosome biogenesis. We found that the absence of Mam33 results in misassembled, aggregated ribosomes and a respiratory lethal phenotype in combination with other ribosome-assembly mutants. Using sucrose gradient sedimentation, native affinity purifications, in vitro binding assays, and SILAC-based quantitative proteomics, we found that Mam33 does not associate with the mature mitoribosome, but directly binds a subset of unassembled large subunit proteins. Based on these data, we propose that Mam33 binds specific mitoribosomal proteins to ensure proper assembly.
Collapse
Affiliation(s)
- Gabrielle A Hillman
- From the Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084 and.,the Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey 08084
| | - Michael F Henry
- From the Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, New Jersey 08084 and .,the Graduate School of Biomedical Sciences, Rowan University, Stratford, New Jersey 08084
| |
Collapse
|
22
|
Cogliati S, Lorenzi I, Rigoni G, Caicci F, Soriano ME. Regulation of Mitochondrial Electron Transport Chain Assembly. J Mol Biol 2018; 430:4849-4873. [DOI: 10.1016/j.jmb.2018.09.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
|
23
|
Abstract
Together, the nuclear and mitochondrial genomes encode the oxidative phosphorylation (OXPHOS) complexes that reside in the mitochondrial inner membrane and enable aerobic life. Mitochondria maintain their own genome that is expressed and regulated by factors distinct from their nuclear counterparts. For optimal function, the cell must ensure proper stoichiometric production of OXPHOS subunits by coordinating two physically separated and evolutionarily distinct gene expression systems. Here, we review our current understanding of mitonuclear coregulation primarily at the levels of transcription and translation. Additionally, we discuss other levels of coregulation that may exist but remain largely unexplored, including mRNA modification and stability and posttranslational protein degradation.
Collapse
Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; , ,
| | - Erik McShane
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; , ,
| | - L Stirling Churchman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; , ,
| |
Collapse
|
24
|
Herwaldt EJ, Rivett ED, White AJ, Hegg EL. Cox15 interacts with the cytochrome bc 1 dimer within respiratory supercomplexes as well as in the absence of cytochrome c oxidase. J Biol Chem 2018; 293:16426-16439. [PMID: 30181213 DOI: 10.1074/jbc.ra118.002496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022] Open
Abstract
The heme a molecule is an obligatory cofactor in the terminal enzyme complex of the electron transport chain, cytochrome c oxidase. Heme a is synthesized from heme o by a multi-spanning inner membrane protein, heme a synthase (Cox15 in the yeast Saccharomyces cerevisiae). The insertion of heme a is critical for cytochrome c oxidase function and assembly, but this process has not been fully elucidated. To improve our understanding of heme a insertion into cytochrome c oxidase, here we investigated the protein-protein interactions that involve Cox15 in S. cerevisiae In addition to observing Cox15 in homooligomeric complexes, we found that a portion of Cox15 also associates with the mitochondrial respiratory supercomplexes. When supercomplex formation was abolished, as in the case of stalled cytochrome bc 1 or cytochrome c oxidase assembly, Cox15 maintained an interaction with select proteins from both respiratory complexes. In the case of stalled cytochrome bc 1 assembly, Cox15 interacted with the late-assembling cytochrome c oxidase subunit, Cox13. When cytochrome c oxidase assembly was stalled, Cox15 unexpectedly maintained its interaction with the cytochrome bc 1 protein, Cor1. Our results indicate that Cox15 and Cor1 continue to interact in the cytochrome bc 1 dimer even in the absence of supercomplexes or when the supercomplexes are destabilized. These findings reveal that Cox15 not only associates with respiratory supercomplexes, but also interacts with the cytochrome bc 1 dimer even in the absence of cytochrome c oxidase.
Collapse
Affiliation(s)
- Emily J Herwaldt
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Elise D Rivett
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Antoineen J White
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Eric L Hegg
- From the Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
25
|
Böttinger L, Mårtensson CU, Song J, Zufall N, Wiedemann N, Becker T. Respiratory chain supercomplexes associate with the cysteine desulfurase complex of the iron-sulfur cluster assembly machinery. Mol Biol Cell 2018; 29:776-785. [PMID: 29386296 PMCID: PMC5905291 DOI: 10.1091/mbc.e17-09-0555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial cytochrome bc1 complex and cytochrome c oxidase associate in respiratory chain supercomplexes. We identified a specific association of the iron–sulfur cluster biogenesis desulfurase with the respiratory chain supercomplexes. Our finding reveals a novel link between respiration and iron–sulfur cluster formation. Mitochondria are the powerhouses of eukaryotic cells. The activity of the respiratory chain complexes generates a proton gradient across the inner membrane, which is used by the F1FO-ATP synthase to produce ATP for cellular metabolism. In baker’s yeast, Saccharomyces cerevisiae, the cytochrome bc1 complex (complex III) and cytochrome c oxidase (complex IV) associate in respiratory chain supercomplexes. Iron–sulfur clusters (ISC) form reactive centers of respiratory chain complexes. The assembly of ISC occurs in the mitochondrial matrix and is essential for cell viability. The cysteine desulfurase Nfs1 provides sulfur for ISC assembly and forms with partner proteins the ISC-biogenesis desulfurase complex (ISD complex). Here, we report an unexpected interaction of the active ISD complex with the cytochrome bc1 complex and cytochrome c oxidase. The individual deletion of complex III or complex IV blocks the association of the ISD complex with respiratory chain components. We conclude that the ISD complex binds selectively to respiratory chain supercomplexes. We propose that this molecular link contributes to coordination of iron–sulfur cluster formation with respiratory activity.
Collapse
Affiliation(s)
- Lena Böttinger
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Christoph U Mårtensson
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | - Jiyao Song
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Nicole Zufall
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Centre for Biochemistry and Molecular Cell Research (ZBMZ), Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany
| |
Collapse
|
26
|
Derbikova KS, Levitsky SA, Chicherin IV, Vinogradova EN, Kamenski PA. Activation of Yeast Mitochondrial Translation: Who Is in Charge? BIOCHEMISTRY (MOSCOW) 2018; 83:87-97. [DOI: 10.1134/s0006297918020013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
27
|
Plasticity of Mitochondrial Translation. Trends Cell Biol 2017; 27:712-721. [DOI: 10.1016/j.tcb.2017.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 11/21/2022]
|
28
|
Timón-Gómez A, Nývltová E, Abriata LA, Vila AJ, Hosler J, Barrientos A. Mitochondrial cytochrome c oxidase biogenesis: Recent developments. Semin Cell Dev Biol 2017; 76:163-178. [PMID: 28870773 DOI: 10.1016/j.semcdb.2017.08.055] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 12/21/2022]
Abstract
Mitochondrial cytochrome c oxidase (COX) is the primary site of cellular oxygen consumption and is essential for aerobic energy generation in the form of ATP. Human COX is a copper-heme A hetero-multimeric complex formed by 3 catalytic core subunits encoded in the mitochondrial DNA and 11 subunits encoded in the nuclear genome. Investigations over the last 50 years have progressively shed light into the sophistication surrounding COX biogenesis and the regulation of this process, disclosing multiple assembly factors, several redox-regulated processes leading to metal co-factor insertion, regulatory mechanisms to couple synthesis of COX subunits to COX assembly, and the incorporation of COX into respiratory supercomplexes. Here, we will critically summarize recent progress and controversies in several key aspects of COX biogenesis: linear versus modular assembly, the coupling of mitochondrial translation to COX assembly and COX assembly into respiratory supercomplexes.
Collapse
Affiliation(s)
- Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eva Nývltová
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling & Protein Purification and Structure Facility, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Switzerland
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Jonathan Hosler
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, MS, United States
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, United States; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States.
| |
Collapse
|
29
|
García-Villegas R, Camacho-Villasana Y, Shingú-Vázquez MÁ, Cabrera-Orefice A, Uribe-Carvajal S, Fox TD, Pérez-Martínez X. The Cox1 C-terminal domain is a central regulator of cytochrome c oxidase biogenesis in yeast mitochondria. J Biol Chem 2017; 292:10912-10925. [PMID: 28490636 DOI: 10.1074/jbc.m116.773077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/09/2017] [Indexed: 12/21/2022] Open
Abstract
Cytochrome c oxidase (CcO) is the last electron acceptor in the respiratory chain. The CcO core is formed by mitochondrial DNA-encoded Cox1, Cox2, and Cox3 subunits. Cox1 synthesis is highly regulated; for example, if CcO assembly is blocked, Cox1 synthesis decreases. Mss51 activates translation of COX1 mRNA and interacts with Cox1 protein in high-molecular-weight complexes (COA complexes) to form the Cox1 intermediary assembly module. Thus, Mss51 coordinates both Cox1 synthesis and assembly. We previously reported that the last 15 residues of the Cox1 C terminus regulate Cox1 synthesis by modulating an interaction of Mss51 with Cox14, another component of the COA complexes. Here, using site-directed mutagenesis of the mitochondrial COX1 gene from Saccharomyces cerevisiae, we demonstrate that mutations P521A/P522A and V524E disrupt the regulatory role of the Cox1 C terminus. These mutations, as well as C terminus deletion (Cox1ΔC15), reduced binding of Mss51 and Cox14 to COA complexes. Mss51 was enriched in a translationally active form that maintains full Cox1 synthesis even if CcO assembly is blocked in these mutants. Moreover, Cox1ΔC15, but not Cox1-P521A/P522A and Cox1-V524E, promoted formation of aberrant supercomplexes in CcO assembly mutants lacking Cox2 or Cox4 subunits. The aberrant supercomplex formation depended on the presence of cytochrome b and Cox3, supporting the idea that supercomplex assembly factors associate with Cox3 and demonstrating that supercomplexes can be formed even if CcO is inactive and not fully assembled. Our results indicate that the Cox1 C-terminal end is a key regulator of CcO biogenesis and that it is important for supercomplex formation/stability.
Collapse
Affiliation(s)
- Rodolfo García-Villegas
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Yolanda Camacho-Villasana
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Miguel Ángel Shingú-Vázquez
- the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Alfredo Cabrera-Orefice
- the Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands, and
| | - Salvador Uribe-Carvajal
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
| | - Thomas D Fox
- the Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Xochitl Pérez-Martínez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico,
| |
Collapse
|
30
|
Cytochrome c Oxidase Biogenesis and Metallochaperone Interactions: Steps in the Assembly Pathway of a Bacterial Complex. PLoS One 2017; 12:e0170037. [PMID: 28107462 PMCID: PMC5249081 DOI: 10.1371/journal.pone.0170037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/27/2016] [Indexed: 12/31/2022] Open
Abstract
Biogenesis of mitochondrial cytochrome c oxidase (COX) is a complex process involving the coordinate expression and assembly of numerous subunits (SU) of dual genetic origin. Moreover, several auxiliary factors are required to recruit and insert the redox-active metal compounds, which in most cases are buried in their protein scaffold deep inside the membrane. Here we used a combination of gel electrophoresis and pull-down assay techniques in conjunction with immunostaining as well as complexome profiling to identify and analyze the composition of assembly intermediates in solubilized membranes of the bacterium Paracoccus denitrificans. Our results show that the central SUI passes through at least three intermediate complexes with distinct subunit and cofactor composition before formation of the holoenzyme and its subsequent integration into supercomplexes. We propose a model for COX biogenesis in which maturation of newly translated COX SUI is initially assisted by CtaG, a chaperone implicated in CuB site metallation, followed by the interaction with the heme chaperone Surf1c to populate the redox-active metal-heme centers in SUI. Only then the remaining smaller subunits are recruited to form the mature enzyme which ultimately associates with respiratory complexes I and III into supercomplexes.
Collapse
|
31
|
Bareth B, Nikolov M, Lorenzi I, Hildenbeutel M, Mick DU, Helbig C, Urlaub H, Ott M, Rehling P, Dennerlein S. Oms1 associates with cytochrome c oxidase assembly intermediates to stabilize newly synthesized Cox1. Mol Biol Cell 2016; 27:1570-80. [PMID: 27030670 PMCID: PMC4865315 DOI: 10.1091/mbc.e15-12-0811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial cytochrome c oxidase assembles in the inner membrane from subunits of dual genetic origin. The assembly process of the enzyme is initiated by membrane insertion of the mitochondria-encoded Cox1 subunit. During complex maturation, transient assembly intermediates, consisting of structural subunits and specialized chaperone-like assembly factors, are formed. In addition, cofactors such as heme and copper have to be inserted into the nascent complex. To regulate the assembly process, the availability of Cox1 is under control of a regulatory feedback cycle in which translation of COX1 mRNA is stalled when assembly intermediates of Cox1 accumulate through inactivation of the translational activator Mss51. Here we isolate a cytochrome c oxidase assembly intermediate in preparatory scale from coa1Δ mutant cells, using Mss51 as bait. We demonstrate that at this stage of assembly, the complex has not yet incorporated the heme a cofactors. Using quantitative mass spectrometry, we define the protein composition of the assembly intermediate and unexpectedly identify the putative methyltransferase Oms1 as a constituent. Our analyses show that Oms1 participates in cytochrome c oxidase assembly by stabilizing newly synthesized Cox1.
Collapse
Affiliation(s)
- Bettina Bareth
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Miroslav Nikolov
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Isotta Lorenzi
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Markus Hildenbeutel
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - David U Mick
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Christin Helbig
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany Bioanalytik Group, Department of Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Martin Ott
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| |
Collapse
|
32
|
Levchenko M, Wuttke JM, Römpler K, Schmidt B, Neifer K, Juris L, Wissel M, Rehling P, Deckers M. Cox26 is a novel stoichiometric subunit of the yeast cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1624-32. [PMID: 27083394 DOI: 10.1016/j.bbamcr.2016.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/31/2016] [Accepted: 04/06/2016] [Indexed: 11/25/2022]
Abstract
The cytochrome c oxidase (COX) is the terminal enzyme of the respiratory chain. The complex accepts electrons from cytochrome c and passes them onto molecular oxygen. This process contributes to energy capture in the form of a membrane potential across the inner membrane. The enzyme complex assembles in a stepwise process from the three mitochondria-encoded core subunits Cox1, Cox2 and Cox3, which associate with nuclear-encoded subunits and cofactors. In the yeast Saccharomyces cerevisiae, the cytochrome c oxidase associates with the bc1-complex into supercomplexes, allowing efficient energy transduction. Here we report on Cox26 as a protein found in respiratory chain supercomplexes containing cytochrome c oxidase. Our analyses reveal Cox26 as a novel stoichiometric structural subunit of the cytochrome c oxidase. A loss of Cox26 affects cytochrome c oxidase activity and respirasome organization.
Collapse
Affiliation(s)
- Maria Levchenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Jan-Moritz Wuttke
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Katharina Römpler
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Bernhard Schmidt
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Klaus Neifer
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Lisa Juris
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Mirjam Wissel
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| |
Collapse
|
33
|
Mayorga JP, Camacho-Villasana Y, Shingú-Vázquez M, García-Villegas R, Zamudio-Ochoa A, García-Guerrero AE, Hernández G, Pérez-Martínez X. A Novel Function of Pet54 in Regulation of Cox1 Synthesis in Saccharomyces cerevisiae Mitochondria. J Biol Chem 2016; 291:9343-55. [PMID: 26929411 DOI: 10.1074/jbc.m116.721985] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/21/2022] Open
Abstract
Cytochrome c oxidase assembly requires the synthesis of the mitochondria-encoded core subunits, Cox1, Cox2, and Cox3. In yeast, Pet54 protein is required to activate translation of the COX3 mRNA and to process the aI5β intron on the COX1 transcript. Here we report a third, novel function of Pet54 on Cox1 synthesis. We observed that Pet54 is necessary to achieve an efficient Cox1 synthesis. Translation of the COX1 mRNA is coupled to the assembly of cytochrome c oxidase by a mechanism that involves Mss51. This protein activates translation of the COX1 mRNA by acting on the COX1 5'-UTR, and, in addition, it interacts with the newly synthesized Cox1 protein in high molecular weight complexes that include the factors Coa3 and Cox14. Deletion of Pet54 decreased Cox1 synthesis, and, in contrast to what is commonly observed for other assembly mutants, double deletion of cox14 or coa3 did not recover Cox1 synthesis. Our results show that Pet54 is a positive regulator of Cox1 synthesis that renders Mss51 competent as a translational activator of the COX1 mRNA and that this role is independent of the assembly feedback regulatory loop of Cox1 synthesis. Pet54 may play a role in Mss51 hemylation/conformational change necessary for translational activity. Moreover, Pet54 physically interacts with the COX1 mRNA, and this binding was independent of the presence of Mss51.
Collapse
Affiliation(s)
- Juan Pablo Mayorga
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Yolanda Camacho-Villasana
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Miguel Shingú-Vázquez
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences Monash University, Clayton, Victoria 3800, Australia, and
| | - Rodolfo García-Villegas
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Angélica Zamudio-Ochoa
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Aldo E García-Guerrero
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Greco Hernández
- the Division of Basic Research, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Xochitl Pérez-Martínez
- From the Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico,
| |
Collapse
|
34
|
Soto IC, Barrientos A. Mitochondrial Cytochrome c Oxidase Biogenesis Is Regulated by the Redox State of a Heme-Binding Translational Activator. Antioxid Redox Signal 2016; 24:281-98. [PMID: 26415097 PMCID: PMC4761835 DOI: 10.1089/ars.2015.6429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AIM Mitochondrial cytochrome c oxidase (COX), the last enzyme of the respiratory chain, catalyzes the reduction of oxygen to water and therefore is essential for cell function and viability. COX is a multimeric complex, whose biogenesis is extensively regulated. One type of control targets cytochrome c oxidase subunit 1 (Cox1), a key COX enzymatic core subunit translated on mitochondrial ribosomes. In Saccharomyces cerevisiae, Cox1 synthesis and COX assembly are coordinated through a negative feedback regulatory loop. This coordination is mediated by Mss51, a heme-sensing COX1 mRNA-specific processing factor and translational activator that is also a Cox1 chaperone. In this study, we investigated whether Mss51 hemylation and Mss51-mediated Cox1 synthesis are both modulated by the reduction-oxidation (redox) environment. RESULTS We report that Cox1 synthesis is attenuated under oxidative stress conditions and have identified one of the underlying mechanisms. We show that in vitro and in vivo exposure to hydrogen peroxide induces the formation of a disulfide bond in Mss51 involving CPX motif heme-coordinating cysteines. Mss51 oxidation results in a heme ligand switch, thereby lowering heme-binding affinity and promoting its release. We demonstrate that in addition to affecting Mss51-dependent heme sensing, oxidative stress compromises Mss51 roles in COX1 mRNA processing and translation. INNOVATION H2O2-induced downregulation of mitochondrial translation has so far not been reported. We show that high H2O2 concentrations induce a global attenuation effect, but milder concentrations specifically affect COX1 mRNA processing and translation in an Mss51-dependent manner. CONCLUSION The redox environment modulates Mss51 functions, which are essential for regulation of COX biogenesis and aerobic energy production.
Collapse
Affiliation(s)
- Iliana C Soto
- 1 Department of Neurology, University of Miami Miller School of Medicine , Miami, Florida
| | - Antoni Barrientos
- 1 Department of Neurology, University of Miami Miller School of Medicine , Miami, Florida.,2 Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine , Miami, Florida
| |
Collapse
|
35
|
Heininger AU, Hackert P, Andreou AZ, Boon KL, Memet I, Prior M, Clancy A, Schmidt B, Urlaub H, Schleiff E, Sloan KE, Deckers M, Lührmann R, Enderlein J, Klostermeier D, Rehling P, Bohnsack MT. Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways. RNA Biol 2016; 13:320-30. [PMID: 26821976 PMCID: PMC4829300 DOI: 10.1080/15476286.2016.1142038] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A rapidly increasing number of RNA helicases are implicated in several distinct cellular processes, however, the modes of regulation of multifunctional RNA helicases and their recruitment to different target complexes have remained unknown. Here, we show that the distribution of the multifunctional DEAH-box RNA helicase Prp43 between its diverse cellular functions can be regulated by the interplay of its G-patch protein cofactors. We identify the orphan G-patch protein Cmg1 (YLR271W) as a novel cofactor of Prp43 and show that it stimulates the RNA binding and ATPase activity of the helicase. Interestingly, Cmg1 localizes to the cytoplasm and to the intermembrane space of mitochondria and its overexpression promotes apoptosis. Furthermore, our data reveal that different G-patch protein cofactors compete for interaction with Prp43. Changes in the expression levels of Prp43-interacting G-patch proteins modulate the cellular localization of Prp43 and G-patch protein overexpression causes accumulation of the helicase in the cytoplasm or nucleoplasm. Overexpression of several G-patch proteins also leads to defects in ribosome biogenesis that are consistent with withdrawal of the helicase from this pathway. Together, these findings suggest that the availability of cofactors and the sequestering of the helicase are means to regulate the activity of multifunctional RNA helicases and their distribution between different cellular processes.
Collapse
Affiliation(s)
- Annika U Heininger
- a Institute for Molecular Biology, Georg-August University , Goettingen , Germany
| | - Philipp Hackert
- a Institute for Molecular Biology, Georg-August University , Goettingen , Germany
| | - Alexandra Z Andreou
- b Institute for Physical Chemistry, University of Muenster , Muenster , Germany
| | - Kum-Loong Boon
- c Max-Planck-Institute for Biophysical Chemistry , Goettingen , Germany
| | - Indira Memet
- a Institute for Molecular Biology, Georg-August University , Goettingen , Germany
| | - Mira Prior
- d III. Institute of Physics-Biophysics, Georg-August University , Goettingen , Germany
| | - Anne Clancy
- a Institute for Molecular Biology, Georg-August University , Goettingen , Germany
| | - Bernhard Schmidt
- e Institute of Cellular Biochemistry, Georg-August University , Goettingen , Germany
| | - Henning Urlaub
- c Max-Planck-Institute for Biophysical Chemistry , Goettingen , Germany
| | - Enrico Schleiff
- f Institute for Molecular Biosciences, Goethe University , Frankfurt , Germany
| | - Katherine E Sloan
- a Institute for Molecular Biology, Georg-August University , Goettingen , Germany
| | - Markus Deckers
- e Institute of Cellular Biochemistry, Georg-August University , Goettingen , Germany
| | - Reinhard Lührmann
- c Max-Planck-Institute for Biophysical Chemistry , Goettingen , Germany
| | - Jörg Enderlein
- d III. Institute of Physics-Biophysics, Georg-August University , Goettingen , Germany
| | - Dagmar Klostermeier
- b Institute for Physical Chemistry, University of Muenster , Muenster , Germany
| | - Peter Rehling
- c Max-Planck-Institute for Biophysical Chemistry , Goettingen , Germany.,e Institute of Cellular Biochemistry, Georg-August University , Goettingen , Germany.,g Goettingen Center for Molecular Biosciences, Georg-August-University , Goettingen , Germany
| | - Markus T Bohnsack
- a Institute for Molecular Biology, Georg-August University , Goettingen , Germany.,g Goettingen Center for Molecular Biosciences, Georg-August-University , Goettingen , Germany
| |
Collapse
|
36
|
Kovářová N, Pecina P, Nůsková H, Vrbacký M, Zeviani M, Mráček T, Viscomi C, Houštěk J. Tissue- and species-specific differences in cytochrome c oxidase assembly induced by SURF1 defects. Biochim Biophys Acta Mol Basis Dis 2016; 1862:705-715. [PMID: 26804654 PMCID: PMC4793088 DOI: 10.1016/j.bbadis.2016.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/08/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022]
Abstract
Mitochondrial protein SURF1 is a specific assembly factor of cytochrome c oxidase (COX), but its function is poorly understood. SURF1 gene mutations cause a severe COX deficiency manifesting as the Leigh syndrome in humans, whereas in mice SURF1−/− knockout leads only to a mild COX defect. We used SURF1−/− mouse model for detailed analysis of disturbed COX assembly and COX ability to incorporate into respiratory supercomplexes (SCs) in different tissues and fibroblasts. Furthermore, we compared fibroblasts from SURF1−/− mouse and SURF1 patients to reveal interspecies differences in kinetics of COX biogenesis using 2D electrophoresis, immunodetection, arrest of mitochondrial proteosynthesis and pulse-chase metabolic labeling. The crucial differences observed are an accumulation of abundant COX1 assembly intermediates, low content of COX monomer and preferential recruitment of COX into I–III2–IVn SCs in SURF1 patient fibroblasts, whereas SURF1−/− mouse fibroblasts were characterized by low content of COX1 assembly intermediates and milder decrease in COX monomer, which appeared more stable. This pattern was even less pronounced in SURF1−/− mouse liver and brain. Both the control and SURF1−/− mice revealed only negligible formation of the I–III2–IVn SCs and marked tissue differences in the contents of COX dimer and III2–IV SCs, also less noticeable in liver and brain than in heart and muscle. Our studies support the view that COX assembly is much more dependent on SURF1 in humans than in mice. We also demonstrate markedly lower ability of mouse COX to form I–III2–IVn supercomplexes, pointing to tissue-specific and species-specific differences in COX biogenesis. In SURF1 −/− mouse the decrease of COX amount and activity was tissue/cell specific. Assembly kinetics proceeded to the level of stable COX monomer in SURF1 −/− mouse. COX assembly intermediates were faster degraded/depleted in time in SURF1 −/− mouse. COX was preferentially recruited in supercomplex I–III2–IV1 in SURF1 patient cells. Newly synthesized COX monomer was unstable and rapidly degraded in SURF1 patient.
Collapse
Affiliation(s)
- Nikola Kovářová
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Petr Pecina
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Hana Nůsková
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Marek Vrbacký
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Massimo Zeviani
- Molecular Neurogenetics Unit, Instituto Neurologico "C. Besta", via Temolo 4, 20126 Milan, Italy; MRC-Mitochondrial Biology Unit, Wellcome Trust MRC Bldg, Addenbrookes Hospital Hills Rd, Cambridge CB2 0XY, UK
| | - Tomáš Mráček
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Carlo Viscomi
- MRC-Mitochondrial Biology Unit, Wellcome Trust MRC Bldg, Addenbrookes Hospital Hills Rd, Cambridge CB2 0XY, UK
| | - Josef Houštěk
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic.
| |
Collapse
|
37
|
Roloff GA, Henry MF. Mam33 promotes cytochrome c oxidase subunit I translation in Saccharomyces cerevisiae mitochondria. Mol Biol Cell 2015; 26:2885-94. [PMID: 26108620 PMCID: PMC4571327 DOI: 10.1091/mbc.e15-04-0222] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/16/2015] [Indexed: 12/22/2022] Open
Abstract
Expression of genes encoded by the mitochondrial genome is dependent on gene-specific translational activators. Mam33, the yeast homologue of p32/gC1qR/C1QBP/HABP1, promotes the translation of Cox1, a core catalytic subunit of respiratory chain complex IV. Three mitochondrial DNA–encoded proteins, Cox1, Cox2, and Cox3, comprise the core of the cytochrome c oxidase complex. Gene-specific translational activators ensure that these respiratory chain subunits are synthesized at the correct location and in stoichiometric ratios to prevent unassembled protein products from generating free oxygen radicals. In the yeast Saccharomyces cerevisiae, the nuclear-encoded proteins Mss51 and Pet309 specifically activate mitochondrial translation of the largest subunit, Cox1. Here we report that Mam33 is a third COX1 translational activator in yeast mitochondria. Mam33 is required for cells to adapt efficiently from fermentation to respiration. In the absence of Mam33, Cox1 translation is impaired, and cells poorly adapt to respiratory conditions because they lack basal fermentative levels of Cox1.
Collapse
Affiliation(s)
- Gabrielle A Roloff
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, and Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ 08084
| | - Michael F Henry
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, and Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ 08084
| |
Collapse
|
38
|
Gurumoorthy P, Ludwig B. Deciphering protein-protein interactions during the biogenesis of cytochrome c oxidase from Paracoccus denitrificans. FEBS J 2014; 282:537-49. [PMID: 25420759 DOI: 10.1111/febs.13160] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 02/01/2023]
Abstract
Biogenesis of the mitochondrial cytochrome c oxidase (COX) is a complex process due to its numerous subunits encoded by two genomes, as well as the localization of redox centers deep within the membrane. Here, we have assessed the biogenesis of the homologous aa₃-type oxidase of the soil bacterium Paracoccus denitrificans. First, protein partners were analyzed using various membrane solubilization strategies to show interactions between COX and CtaG, a chaperone implicated in CuB site metallation. Using an unbiased MS approach after immunological pull-down from untreated or cross-linked membranes, we then extend our view towards a hypothetical 'biogenesis complex' by identifying two further metal-inserting chaperones, Surf1c and Sco, together with enzymes catalyzing heme a synthesis. Our study also tentatively supports previous speculation regarding the existence of a predominantly co-translational mechanism for cofactor insertion during COX biogenesis.
Collapse
Affiliation(s)
- Priya Gurumoorthy
- Institute of Biochemistry, Molecular Genetics, Goethe University, Frankfurt am Main, Germany
| | | |
Collapse
|
39
|
Da-Rè C, von Stockum S, Biscontin A, Millino C, Cisotto P, Zordan MA, Zeviani M, Bernardi P, De Pittà C, Costa R. Leigh syndrome in Drosophila melanogaster: morphological and biochemical characterization of Surf1 post-transcriptional silencing. J Biol Chem 2014; 289:29235-46. [PMID: 25164807 PMCID: PMC4200275 DOI: 10.1074/jbc.m114.602938] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 08/26/2014] [Indexed: 01/20/2023] Open
Abstract
Leigh Syndrome (LS) is the most common early-onset, progressive mitochondrial encephalopathy usually leading to early death. The single most prevalent cause of LS is occurrence of mutations in the SURF1 gene, and LS(Surf1) patients show a ubiquitous and specific decrease in the activity of mitochondrial respiratory chain complex IV (cytochrome c oxidase, COX). SURF1 encodes an inner membrane mitochondrial protein involved in COX assembly. We established a Drosophila melanogaster model of LS based on the post-transcriptional silencing of CG9943, the Drosophila homolog of SURF1. Knockdown of Surf1 was induced ubiquitously in larvae and adults, which led to lethality; in the mesodermal derivatives, which led to pupal lethality; or in the central nervous system, which allowed survival. A biochemical characterization was carried out in knockdown individuals, which revealed that larvae unexpectedly displayed defects in all complexes of the mitochondrial respiratory chain and in the F-ATP synthase, while adults had a COX-selective impairment. Silencing of Surf1 expression in Drosophila S2R(+) cells led to selective loss of COX activity associated with decreased oxygen consumption and respiratory reserve. We conclude that Surf1 is essential for COX activity and mitochondrial function in D. melanogaster, thus providing a new tool that may help clarify the pathogenic mechanisms of LS.
Collapse
Affiliation(s)
| | | | | | - Caterina Millino
- CRIBI Biotechnology Centre, University of Padova, 35121 Padova, Italy and
| | | | | | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | | | | | | |
Collapse
|
40
|
Abstract
The yeast cytochrome oxidase Cox3p assembly module is shown to consist of Cox3p, Cox4p, Cox7p, Cox13p, and accessory factor Rcf1p. The results support an assembly model in which three modules, each containing one of the three core subunits and a unique subset of nuclear-derived subunits, interact to form the holoenzyme. Yeast cytochrome oxidase (COX) was previously inferred to assemble from three modules, each containing one of the three mitochondrially encoded subunits and a different subset of the eight nuclear gene products that make up this respiratory complex. Pull-down assays of pulse-labeled mitochondria enabled us to characterize Cox3p subassemblies that behave as COX precursors and contain Cox4p, Cox7p, and Cox13p. Surprisingly, Cox4p is a constituent of two other complexes, one of which was previously proposed to be an intermediate of Cox1p biogenesis. This suggests that Cox4p, which contacts Cox1p and Cox3p in the holoenzyme, can be incorporated into COX by two alternative pathways. In addition to subunits of COX, some Cox3p intermediates contain Rcf1p, a protein associated with the supercomplex that stabilizes the interaction of COX with the bc1 (ubiquinol-cytochrome c reductase) complex. Finally, our results indicate that although assembly of the Cox1p module is not contingent on the presence of Cox3p, the converse is not true, as none of the Cox3p subassemblies were detected in a mutant blocked in translation of Cox1p. These studies support our proposal that Cox3p and Cox1p are separate assembly modules with unique compositions of ancillary factors and subunits derived from the nuclear genome.
Collapse
Affiliation(s)
- Chen-Hsien Su
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | | | | |
Collapse
|
41
|
Cui TZ, Conte A, Fox JL, Zara V, Winge DR. Modulation of the respiratory supercomplexes in yeast: enhanced formation of cytochrome oxidase increases the stability and abundance of respiratory supercomplexes. J Biol Chem 2014; 289:6133-41. [PMID: 24421313 DOI: 10.1074/jbc.m113.523688] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast cells deficient in the Rieske iron-sulfur subunit (Rip1) of ubiquinol-cytochrome c reductase (bc1) accumulate a late core assembly intermediate, which weakly associates with cytochrome oxidase (CcO) in a respiratory supercomplex. Expression of the N-terminal half of Rip1, which lacks the C-terminal FeS-containing globular domain (designated N-Rip1), results in a marked stabilization of trimeric and tetrameric bc1-CcO supercomplexes. Another bc1 mutant (qcr9Δ) stalled at the same assembly intermediate is likewise converted to stable supercomplex species by the expression of N-Rip1, but not by expression of intact Rip1. The N-Rip1-induced stabilization of bc1-CcO supercomplexes is independent of the Bcs1 translocase, which mediates Rip1 translocation during bc1 biogenesis. N-Rip1 induces the stabilization of bc1-CcO supercomplexes through an enhanced formation of CcO. The association of N-Rip1 with the late core bc1 assembly intermediate appears to confer stabilization of a CcO assembly intermediate. This induced stabilization of CcO is dependent on the Rcf1 supercomplex stabilization factor and only partially dependent on the presence of cardiolipin. N-Rip1 exerts a related induction of CcO stabilization in WT yeast, resulting in enhanced respiration. Additionally, the impact of CcO stabilization on supercomplexes was observed by means other than expression of N-Rip1 (via overexpression of CcO subunits Cox4 and Cox5a), demonstrating that this is a general phenomenon. This study presents the first evidence showing that supercomplexes can be stabilized by the stimulated formation of CcO.
Collapse
Affiliation(s)
- Tie-Zhong Cui
- From the Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84132 and
| | | | | | | | | |
Collapse
|
42
|
Bourens M, Fontanesi F, Soto IC, Liu J, Barrientos A. Redox and reactive oxygen species regulation of mitochondrial cytochrome C oxidase biogenesis. Antioxid Redox Signal 2013; 19:1940-52. [PMID: 22937827 PMCID: PMC3852343 DOI: 10.1089/ars.2012.4847] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SIGNIFICANCE Cytochrome c oxidase (COX), the last enzyme of the mitochondrial respiratory chain, is the major oxygen consumer enzyme in the cell. COX biogenesis involves several redox-regulated steps. The process is highly regulated to prevent the formation of pro-oxidant intermediates. RECENT ADVANCES Regulation of COX assembly involves several reactive oxygen species and redox-regulated steps. These include: (i) Intricate redox-controlled machineries coordinate the expression of COX isoenzymes depending on the environmental oxygen concentration. (ii) COX is a heme A-copper metalloenzyme. COX copper metallation involves the copper chaperone Cox17 and several other recently described cysteine-rich proteins, which are oxidatively folded in the mitochondrial intermembrane space. Copper transfer to COX subunits 1 and 2 requires concomitant transfer of redox power. (iii) To avoid the accumulation of reactive assembly intermediates, COX is regulated at the translational level to minimize synthesis of the heme A-containing Cox1 subunit when assembly is impaired. CRITICAL ISSUES An increasing number of regulatory pathways converge to facilitate efficient COX assembly, thus preventing oxidative stress. FUTURE DIRECTIONS Here we will review on the redox-regulated COX biogenesis steps and will discuss their physiological relevance. Forthcoming insights into the precise regulation of mitochondrial COX biogenesis in normal and stress conditions will likely open future perspectives for understanding mitochondrial redox regulation and prevention of oxidative stress.
Collapse
Affiliation(s)
- Myriam Bourens
- 1 Department of Neurology, University of Miami Miller School of Medicine , Miami, Florida
| | | | | | | | | |
Collapse
|
43
|
The heme a synthase Cox15 associates with cytochrome c oxidase assembly intermediates during Cox1 maturation. Mol Cell Biol 2013; 33:4128-37. [PMID: 23979592 DOI: 10.1128/mcb.00747-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cox1, the core subunit of the cytochrome c oxidase, receives two heme a cofactors during assembly of the 13-subunit enzyme complex. However, at which step of the assembly process and how heme is inserted into Cox1 have remained an enigma. Shy1, the yeast SURF1 homolog, has been implicated in heme transfer to Cox1, whereas the heme a synthase, Cox15, catalyzes the final step of heme a synthesis. Here we performed a comprehensive analysis of cytochrome c oxidase assembly intermediates containing Shy1. Our analyses suggest that Cox15 displays a role in cytochrome c oxidase assembly, which is independent of its functions as the heme a synthase. Cox15 forms protein complexes with Shy1 and also associates with Cox1-containing complexes independently of Shy1 function. These findings indicate that Shy1 does not serve as a mobile heme carrier between the heme a synthase and maturing Cox1 but rather cooperates with Cox15 for heme transfer and insertion in early assembly intermediates of cytochrome c oxidase.
Collapse
|
44
|
McStay GP, Su CH, Thomas SM, Xu JT, Tzagoloff A. Characterization of assembly intermediates containing subunit 1 of yeast cytochrome oxidase. J Biol Chem 2013; 288:26546-56. [PMID: 23897805 DOI: 10.1074/jbc.m113.498592] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial-encoded Cox1p, one of the three core subunits of yeast cytochrome oxidase (COX), was previously shown to associate with regulatory proteins and nuclear-encoded subunits into five high molecular weight complexes that were proposed to constitute the pathway for biogenesis of the Cox1p assembly module. One of the intermediates (D5) was inferred, but not directly shown to exist. In the present study mitochondria of strains expressing C-terminal-tagged subunits of COX that had not been looked at previously were pulse-labeled and analyzed for the presence of newly translated Cox1p in the immunoprecipitates. These studies revealed that of the eight nuclear-encoded COX subunits, only Cox5ap, Cox6p, and Cox8p are present in the Cox1p module. Both Cox5ap and Cox8p share interfaces with Cox1p in the holoenzyme, whereas Cox6p interacts indirectly through Cox5ap. These results suggest that the subunit contacts in the holoenzyme are probably established during biogenesis of the Cox1p module. To confirm the existence of the largest Cox1p intermediates (D5), which was only inferred previously, radiolabeled Cox1p with a C-terminal tag was expressed in COX-deficient pet111 and pet494 mutants. Pulldown assays confirmed the presence of newly translated Cox1p in D5, which in wild type cannot be demonstrated directly because of its co-migration with COX in the native electrophoresis system used to separate the intermediates. Jointly, the results of these analyses substantiate our previous proposal that COX is assembled from separate assembly modules, each containing one of the mitochondrial-translated core subunits in association with a unique set of nuclear-encoded subunits.
Collapse
Affiliation(s)
- Gavin P McStay
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | | | | | | | | |
Collapse
|
45
|
Böttinger L, Guiard B, Oeljeklaus S, Kulawiak B, Zufall N, Wiedemann N, Warscheid B, van der Laan M, Becker T. A complex of Cox4 and mitochondrial Hsp70 plays an important role in the assembly of the cytochrome c oxidase. Mol Biol Cell 2013; 24:2609-19. [PMID: 23864706 PMCID: PMC3756914 DOI: 10.1091/mbc.e13-02-0106] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The biogenesis of Cox4 is unknown. Cox4, mtHsp70, and Mge1 form a complex that promotes the assembly of cytochrome c oxidase. In the absence of the mature cytochrome c oxidase, Cox4 arrests at the chaperone complex. This complex delivers Cox4 into the assembly line of complex IV when needed. The formation of the mature cytochrome c oxidase (complex IV) involves the association of nuclear- and mitochondria-encoded subunits. The assembly of nuclear-encoded subunits like cytochrome c oxidase subunit 4 (Cox4) into the mature complex is poorly understood. Cox4 is crucial for the stability of complex IV. To find specific biogenesis factors, we analyze interaction partners of Cox4 by affinity purification and mass spectroscopy. Surprisingly, we identify a complex of Cox4, the mitochondrial Hsp70 (mtHsp70), and its nucleotide-exchange factor mitochondrial GrpE (Mge1). We generate a yeast mutant of mtHsp70 specifically impaired in the formation of this novel mtHsp70-Mge1-Cox4 complex. Strikingly, the assembly of Cox4 is strongly decreased in these mutant mitochondria. Because Cox4 is a key factor for the biogenesis of complex IV, we conclude that the mtHsp70-Mge1-Cox4 complex plays an important role in the formation of cytochrome c oxidase. Cox4 arrests at this chaperone complex in the absence of mature complex IV. Thus the mtHsp70-Cox4 complex likely serves as a novel delivery system to channel Cox4 into the assembly line when needed.
Collapse
Affiliation(s)
- Lena Böttinger
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
The mitochondrion is arguably the most complex organelle in the budding yeast cell cytoplasm. It is essential for viability as well as respiratory growth. Its innermost aqueous compartment, the matrix, is bounded by the highly structured inner membrane, which in turn is bounded by the intermembrane space and the outer membrane. Approximately 1000 proteins are present in these organelles, of which eight major constituents are coded and synthesized in the matrix. The import of mitochondrial proteins synthesized in the cytoplasm, and their direction to the correct soluble compartments, correct membranes, and correct membrane surfaces/topologies, involves multiple pathways and macromolecular machines. The targeting of some, but not all, cytoplasmically synthesized mitochondrial proteins begins with translation of messenger RNAs localized to the organelle. Most proteins then pass through the translocase of the outer membrane to the intermembrane space, where divergent pathways sort them to the outer membrane, inner membrane, and matrix or trap them in the intermembrane space. Roughly 25% of mitochondrial proteins participate in maintenance or expression of the organellar genome at the inner surface of the inner membrane, providing 7 membrane proteins whose synthesis nucleates the assembly of three respiratory complexes.
Collapse
|
47
|
Fontanesi F. Mechanisms of mitochondrial translational regulation. IUBMB Life 2013; 65:397-408. [PMID: 23554047 DOI: 10.1002/iub.1156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/31/2013] [Indexed: 11/11/2022]
Abstract
The mitochondrial oxidative phosphorylation system is formed by multimeric enzymes. In the yeast Saccharomyces cerevisiae, the bc1 complex, cytochrome c oxidase and the F1 FO ATP synthase contain subunits of dual genetic origin. It has been recently established that key subunits of these enzymes, translated on mitochondrial ribosomes, are the subjects of assembly-dependent translational regulation. This type of control of gene expression plays a pivotal role in optimizing the biogenesis of mitochondrial respiratory membranes by coordinating protein synthesis and complex assembly and by limiting the accumulation of potentially harmful assembly intermediates. Here, the author will discuss the mechanisms governing translational regulation in yeast mitochondria in the light of the most recent discoveries in the field.
Collapse
Affiliation(s)
- Flavia Fontanesi
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
48
|
Baile MG, Claypool SM. The power of yeast to model diseases of the powerhouse of the cell. FRONT BIOSCI-LANDMRK 2013; 18:241-78. [PMID: 23276920 PMCID: PMC3874933 DOI: 10.2741/4098] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondria participate in a variety of cellular functions. As such, mitochondrial diseases exhibit numerous clinical phenotypes. Because mitochondrial functions are highly conserved between humans and Saccharomyces cerevisiae, yeast are an excellent model to study mitochondrial disease, providing insight into both physiological and pathophysiological processes.
Collapse
Affiliation(s)
- Matthew G Baile
- Dept. of Physiology, Johns Hopkins School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205-2185, USA
| | | |
Collapse
|
49
|
Abstract
Pulse-chase labeling of isolated yeast mitochondria identifies new assembly intermediates of Cox1p, characterizes their compositions, and orders them sequentially. The results indicate that cytochrome oxidase is assembled from separate modules, each consisting of different mitochondrial and nuclear gene products. Previous studies of yeast cytochrome oxidase (COX) biogenesis identified Cox1p, one of the three mitochondrially encoded core subunits, in two high–molecular weight complexes combined with regulatory/assembly factors essential for expression of this subunit. In the present study we use pulse-chase labeling experiments in conjunction with isolated mitochondria to identify new Cox1p intermediates and place them in an ordered pathway. Our results indicate that before its assimilation into COX, Cox1p transitions through five intermediates that are differentiated by their compositions of accessory factors and of two of the eight imported subunits. We propose a model of COX biogenesis in which Cox1p and the two other mitochondrial gene products, Cox2p and Cox3p, constitute independent assembly modules, each with its own complement of subunits. Unlike their bacterial counterparts, which are composed only of the individual core subunits, the final sequence in which the mitochondrial modules associate to form the holoenzyme may have been conserved during evolution.
Collapse
Affiliation(s)
- Gavin P McStay
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | | |
Collapse
|
50
|
Soto IC, Fontanesi F, Myers RS, Hamel P, Barrientos A. A heme-sensing mechanism in the translational regulation of mitochondrial cytochrome c oxidase biogenesis. Cell Metab 2012; 16:801-13. [PMID: 23217259 PMCID: PMC3523284 DOI: 10.1016/j.cmet.2012.10.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/19/2012] [Accepted: 10/25/2012] [Indexed: 12/01/2022]
Abstract
Heme plays fundamental roles as cofactor and signaling molecule in multiple pathways devoted to oxygen sensing and utilization in aerobic organisms. For cellular respiration, heme serves as a prosthetic group in electron transfer proteins and redox enzymes. Here we report that in the yeast Saccharomyces cerevisiae, a heme-sensing mechanism translationally controls the biogenesis of cytochrome c oxidase (COX), the terminal mitochondrial respiratory chain enzyme. We show that Mss51, a COX1 mRNA-specific translational activator and Cox1 chaperone, which coordinates Cox1 synthesis in mitoribosomes with its assembly in COX, is a heme-binding protein. Mss51 contains two heme regulatory motifs or Cys-Pro-X domains located in its N terminus. Using a combination of in vitro and in vivo approaches, we have demonstrated that these motifs are important for heme binding and efficient performance of Mss51 functions. We conclude that heme sensing by Mss51 regulates COX biogenesis and aerobic energy production.
Collapse
Affiliation(s)
- Iliana C Soto
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | | | | | | |
Collapse
|