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Mizrahi R, Ostersetzer-Biran O. Mitochondrial RNA Helicases: Key Players in the Regulation of Plant Organellar RNA Splicing and Gene Expression. Int J Mol Sci 2024; 25:5502. [PMID: 38791540 PMCID: PMC11122041 DOI: 10.3390/ijms25105502] [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: 03/12/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial genomes of land plants are large and exhibit a complex mode of gene organization and expression, particularly at the post-transcriptional level. The primary organellar transcripts in plants undergo extensive maturation steps, including endo- and/or exo-nucleolytic cleavage, RNA-base modifications (mostly C-to-U deaminations) and both 'cis'- and 'trans'-splicing events. These essential processing steps rely on the activities of a large set of nuclear-encoded factors. RNA helicases serve as key players in RNA metabolism, participating in the regulation of transcription, mRNA processing and translation. They unwind RNA secondary structures and facilitate the formation of ribonucleoprotein complexes crucial for various stages of gene expression. Furthermore, RNA helicases are involved in RNA metabolism by modulating pre-mRNA maturation, transport and degradation processes. These enzymes are, therefore, pivotal in RNA quality-control mechanisms, ensuring the fidelity and efficiency of RNA processing and turnover in plant mitochondria. This review summarizes the significant roles played by helicases in regulating the highly dynamic processes of mitochondrial transcription, RNA processing and translation in plants. We further discuss recent advancements in understanding how dysregulation of mitochondrial RNA helicases affects the splicing of organellar genes, leading to respiratory dysfunctions, and consequently, altered growth, development and physiology of land plants.
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Affiliation(s)
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus—Givat Ram, Jerusalem 9190401, Israel
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2
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Amberg KL, Hao L, Cranz-Mileva S, Zaratiegui M. Proteasome regulation of petite-negativity in fission yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593392. [PMID: 38798546 PMCID: PMC11118472 DOI: 10.1101/2024.05.09.593392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Mitochondria carry out essential functions in eukaryotic cells. The mitochondrial genome encodes factors critical to support oxidative phosphorylation and mitochondrial protein import necessary for these functions. However, organisms like budding yeast can readily lose their mitochondrial genome, yielding respiration-deficient petite mutants. The fission yeast Schizosaccharomyces pombe is petite-negative, but some nuclear mutations enable the loss of its mitochondrial genome. Here, we characterize the classical petite-positive mutation ptp1-1 as a loss of function allele of the proteasome 19S regulatory subunit component mts4/rpn1, involved in the Ubiquitin-dependent degradation pathway. The mutation results in an altered oxidative stress response, with increased levels of oxidized glutathione, and increased levels of mitochondrial and cytoplasmic chaperones. We propose that Ubiquitin-proteasome regulation of chaperones involved in the Unfolded Protein Response and mitochondrial protein import underlies petite-negativity in fission yeast.
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Affiliation(s)
- Katie Lin Amberg
- Department of Molecular Biology and Biochemistry, Division of Life Sciences Rutgers, the State University of new Jersey
| | - Lyrica Hao
- Department of Molecular Biology and Biochemistry, Division of Life Sciences Rutgers, the State University of new Jersey
| | - Susanne Cranz-Mileva
- Department of Molecular Biology and Biochemistry, Division of Life Sciences Rutgers, the State University of new Jersey
| | - Mikel Zaratiegui
- Department of Molecular Biology and Biochemistry, Division of Life Sciences Rutgers, the State University of new Jersey
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3
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Putnam CD. Loss of mitochondrial DNA is associated with reduced DNA content variability in Saccharomyces cerevisiae. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001117. [PMID: 38533353 PMCID: PMC10964099 DOI: 10.17912/micropub.biology.001117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/20/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024]
Abstract
DNA content measurement by fluorescence-assisted cell sorting (FACS) provides information on cell cycle progression and DNA content variability. Saccharomyces cerevisiae mutants with DNA content variability that was reduced relative to wild-type strains had defects in mitochondrial DNA (mtDNA) maintenance and mitochondrial gene expression and were correlated with strains found to lack mtDNA ([ rho 0 ] cells) by genome sequencing and fluorescence microscopy. In contrast, mutants with increased variability had defects in cell cycle progression, which may indicate a loss of coordination between mtDNA and nuclear DNA replication. Thus, FACS measurement of DNA content variability can provide insight into cell-to-cell heterogeneity in mtDNA copy number.
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Affiliation(s)
- Christopher D. Putnam
- Department of Medicine, University of California, San Diego, San Diego, California, United States
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4
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Chu Y, Li M, Sun M, Wang J, Xin W, Xu L. Gene crosstalk between COVID-19 and preeclampsia revealed by blood transcriptome analysis. Front Immunol 2024; 14:1243450. [PMID: 38259479 PMCID: PMC10800816 DOI: 10.3389/fimmu.2023.1243450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Background The extensive spread of coronavirus disease 2019 (COVID-19) has led to a rapid increase in global mortality. Preeclampsia is a commonly observed pregnancy ailment characterized by high maternal morbidity and mortality rates, in addition to the restriction of fetal growth within the uterine environment. Pregnant individuals afflicted with vascular disorders, including preeclampsia, exhibit an increased susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection via mechanisms that have not been fully delineated. Additionally, the intricate molecular mechanisms underlying preeclampsia and COVID-19 have not been fully elucidated. This study aimed to discern commonalities in gene expression, regulators, and pathways shared between COVID-19 and preeclampsia. The objective was to uncover potential insights that could contribute to novel treatment strategies for both COVID-19 and preeclampsia. Method Transcriptomic datasets for COVID-19 peripheral blood (GSE152418) and preeclampsia blood (GSE48424) were initially sourced from the Gene Expression Omnibus (GEO) database. Subsequent to that, we conducted a subanalysis by selecting females from the GSE152418 dataset and employed the "Deseq2" package to identify genes that exhibited differential expression. Simultaneously, the "limma" package was applied to identify differentially expressed genes (DEGs) in the preeclampsia dataset (GSE48424). Following that, an intersection analysis was conducted to identify the common DEGs obtained from both the COVID-19 and preeclampsia datasets. The identified shared DEGs were subsequently utilized for functional enrichment analysis, transcription factor (TF) and microRNAs (miRNA) prediction, pathway analysis, and identification of potential candidate drugs. Finally, to validate the bioinformatics findings, we collected peripheral blood mononuclear cell (PBMC) samples from healthy individuals, COVID-19 patients, and Preeclampsia patients. The abundance of the top 10 Hub genes in both diseases was assessed using real-time quantitative polymerase chain reaction (RT-qPCR). Result A total of 355 overlapping DEGs were identified in both preeclampsia and COVID-19 datasets. Subsequent ontological analysis, encompassing Gene Ontology (GO) functional assessment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, revealed a significant association between the two conditions. Protein-protein interactions (PPIs) were constructed using the STRING database. Additionally, the top 10 hub genes (MRPL11, MRPS12, UQCRH, ATP5I, UQCRQ, ATP5D, COX6B1, ATP5O, ATP5H, NDUFA6) were selected based on their ranking scores using the degree algorithm, which considered the shared DEGs. Moreover, transcription factor-gene interactions, protein-drug interactions, co-regulatory networks of DEGs and miRNAs, and protein-drug interactions involving the shared DEGs were also identified in the datasets. Finally, RT-PCR results confirmed that 10 hub genes do exhibit distinct expression profiles in the two diseases. Conclusion This study successfully identified overlapping DEGs, functional pathways, and regulatory elements between COVID-19 and preeclampsia. The findings provide valuable insights into the shared molecular mechanisms and potential therapeutic targets for both diseases. The validation through RT-qPCR further supports the distinct expression profiles of the identified hub genes in COVID-19 and preeclampsia, emphasizing their potential roles as biomarkers or therapeutic targets in these conditions.
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Affiliation(s)
| | | | | | | | | | - Lin Xu
- Department of Obstetrics, the Affiliated Hospital of Qingdao University, Qingdao, China
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5
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Baranowska E, Niedzwiecka K, Panja C, Charles C, Dautant A, Poznanski J, di Rago JP, Tribouillard-Tanvier D, Kucharczyk R. Probing the pathogenicity of patient-derived variants of MT-ATP6 in yeast. Dis Model Mech 2023; 16:307138. [PMID: 37083953 PMCID: PMC10151828 DOI: 10.1242/dmm.049783] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/28/2023] [Indexed: 04/22/2023] Open
Abstract
The list of mitochondrial DNA (mtDNA) variants detected in individuals with neurodegenerative diseases is constantly growing. Evaluating their functional consequences and pathogenicity is not easy, especially when they are found in only a limited number of patients together with wild-type mtDNA (heteroplasmy). Owing to its amenability to mitochondrial genetic transformation and incapacity to stably maintain heteroplasmy, and the strong evolutionary conservation of the proteins encoded in mitochondria, Saccharomyces cerevisiae provides a convenient model to investigate the functional consequences of human mtDNA variants. We herein report the construction and energy-transducing properties of yeast models of eight MT-ATP6 gene variants identified in patients with various disorders: m.8843T>C, m.8950G>A, m.9016A>G, m.9025G>A, m.9029A>G, m.9058A>G, m.9139G>A and m.9160T>C. Significant defect in growth dependent on respiration and deficits in ATP production were observed in yeast models of m.8950G>A, m.9025G>A and m.9029A>G, providing evidence of pathogenicity for these variants. Yeast models of the five other variants showed very mild, if any, effect on mitochondrial function, suggesting that the variants do not have, at least alone, the potential to compromise human health.
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Affiliation(s)
- Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Camille Charles
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Jarosław Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
| | - Jean-Paul di Rago
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Déborah Tribouillard-Tanvier
- University of Bordeaux, Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02106 Warsaw, Poland
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6
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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.
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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:
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7
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Flores-Mireles D, Camacho-Villasana Y, Pérez-Martínez X. The ARG8 m Reporter for the Study of Yeast Mitochondrial Translation. Methods Mol Biol 2023; 2661:281-301. [PMID: 37166643 DOI: 10.1007/978-1-0716-3171-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitochondrial translation is an intricate process involving both general and mRNA-specific factors. In addition, in the yeast Saccharomyces cerevisiae, translation of mitochondrial mRNAs is coupled to assembly of nascent polypeptides into the membrane. ARG8m is a reporter gene widely used to study the mechanisms of yeast mitochondrial translation. This reporter is a recodified gene that uses the mitochondrial genetic code and is inserted at the desired locus in the mitochondrial genome. After deletion of the endogenous nuclear gene, this reporter produces Arg8, an enzyme necessary for arginine biosynthesis. Since Arg8 is a soluble protein with no relation to oxidative phosphorylation, it is a reliable reporter to study mitochondrial mRNAs translation and dissect translation form assembly processes. In this chapter, we explain how to insert the ARG8m reporter in the desired spot in the mitochondrial DNA, how to analyze Arg8 synthesis inside mitochondria, and how to follow steady-state levels of the protein. We also explain how to use it to find spontaneous suppressors of translation defects.
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Affiliation(s)
- Daniel Flores-Mireles
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yolanda Camacho-Villasana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Xochitl Pérez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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8
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Baranowska E, Niedzwiecka K, Panja C, Charles C, Dautant A, di Rago JP, Tribouillard-Tanvier D, Kucharczyk R. Molecular basis of diseases induced by the mitochondrial DNA mutation m.9032 T > C. Hum Mol Genet 2022; 32:1313-1323. [PMID: 36434790 PMCID: PMC10077503 DOI: 10.1093/hmg/ddac292] [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: 09/05/2022] [Revised: 11/08/2022] [Accepted: 11/22/2022] [Indexed: 11/28/2022] Open
Abstract
The mitochondrial DNA mutation m.9032 T > C was previously identified in patients presenting with NARP (Neuropathy Ataxia Retinitis Pigmentosa). Their clinical features had a maternal transmission and patient's cells showed a reduced oxidative phosphorylation capacity, elevated reactive oxygen species (ROS) production and hyperpolarization of the mitochondrial inner membrane, providing evidence that m.9032 T > C is truly pathogenic. This mutation leads to replacement of a highly conserved leucine residue with proline at position 169 of ATP synthase subunit a (L169P). This protein and a ring of identical c-subunits (c-ring) move protons through the mitochondrial inner membrane coupled to ATP synthesis. We herein investigated the consequences of m.9032 T > C on ATP synthase in a strain of Saccharomyces cerevisiae with an equivalent mutation (L186P). The mutant enzyme assembled correctly but was mostly inactive as evidenced by a > 95% drop in the rate of mitochondrial ATP synthesis and absence of significant ATP-driven proton pumping across the mitochondrial membrane. Intragenic suppressors selected from L186P yeast restoring ATP synthase function to varying degrees (30-70%) were identified at the original mutation site (L186S) or in another position of the subunit a (H114Q, I118T). In light of atomic structures of yeast ATP synthase recently described, we conclude from these results that m.9032 T > C disrupts proton conduction between the external side of the membrane and the c-ring, and that H114Q and I118T enable protons to access the c-ring through a modified pathway.
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Affiliation(s)
- Emilia Baranowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Chiranjit Panja
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Camille Charles
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Alain Dautant
- Univ. Bordeaux, CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | | | | | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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9
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Dewar CE, Oeljeklaus S, Wenger C, Warscheid B, Schneider A. Characterization of a highly diverged mitochondrial ATP synthase F o subunit in Trypanosoma brucei. J Biol Chem 2022; 298:101829. [PMID: 35293314 PMCID: PMC9034290 DOI: 10.1016/j.jbc.2022.101829] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 11/24/2022] Open
Abstract
The mitochondrial F1Fo ATP synthase of the parasite Trypanosoma brucei has been previously studied in detail. This unusual enzyme switches direction in functionality during the life cycle of the parasite, acting as an ATP synthase in the insect stages, and as an ATPase to generate mitochondrial membrane potential in the mammalian bloodstream stages. Whereas the trypanosome F1 moiety is relatively highly conserved in structure and composition, the Fo subcomplex and the peripheral stalk have been shown to be more variable. Interestingly, a core subunit of the latter, the normally conserved subunit b, has been resistant to identification by sequence alignment or biochemical methods. Here, we identified a 17 kDa mitochondrial protein of the inner membrane, Tb927.8.3070, that is essential for normal growth, efficient oxidative phosphorylation, and membrane potential maintenance. Pull-down experiments and native PAGE analysis indicated that the protein is both associated with the F1Fo ATP synthase and integral to its assembly. In addition, its knockdown reduced the levels of Fo subunits, but not those of F1, and disturbed the cell cycle. Finally, analysis of structural homology using the HHpred algorithm showed that this protein has structural similarities to Fo subunit b of other species, indicating that this subunit may be a highly diverged form of the elusive subunit b.
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Affiliation(s)
- Caroline E Dewar
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Silke Oeljeklaus
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Christoph Wenger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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The δ subunit of F 1F o-ATP synthase is required for pathogenicity of Candida albicans. Nat Commun 2021; 12:6041. [PMID: 34654833 PMCID: PMC8519961 DOI: 10.1038/s41467-021-26313-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/24/2021] [Indexed: 11/08/2022] Open
Abstract
Fungal infections, especially candidiasis and aspergillosis, claim a high fatality rate. Fungal cell growth and function requires ATP, which is synthesized mainly through oxidative phosphorylation, with the key enzyme being F1Fo-ATP synthase. Here, we show that deletion of the Candida albicans gene encoding the δ subunit of the F1Fo-ATP synthase (ATP16) abrogates lethal infection in a mouse model of systemic candidiasis. The deletion does not substantially affect in vitro fungal growth or intracellular ATP concentrations, because the decrease in oxidative phosphorylation-derived ATP synthesis is compensated by enhanced glycolysis. However, the ATP16-deleted mutant displays decreased phosphofructokinase activity, leading to low fructose 1,6-bisphosphate levels, reduced activity of Ras1-dependent and -independent cAMP-PKA pathways, downregulation of virulence factors, and reduced pathogenicity. A structure-based virtual screening of small molecules leads to identification of a compound potentially targeting the δ subunit of fungal F1Fo-ATP synthases. The compound induces in vitro phenotypes similar to those observed in the ATP16-deleted mutant, and protects mice from succumbing to invasive candidiasis. Our findings indicate that F1Fo-ATP synthase δ subunit is required for C. albicans lethal infection and represents a potential therapeutic target.
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11
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Bahri H, Buratto J, Rojo M, Dompierre JP, Salin B, Blancard C, Cuvellier S, Rose M, Ben Ammar Elgaaied A, Tetaud E, di Rago JP, Devin A, Duvezin-Caubet S. TMEM70 forms oligomeric scaffolds within mitochondrial cristae promoting in situ assembly of mammalian ATP synthase proton channel. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118942. [PMID: 33359711 DOI: 10.1016/j.bbamcr.2020.118942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/28/2020] [Accepted: 12/18/2020] [Indexed: 01/14/2023]
Abstract
Mitochondrial ATP-synthesis is catalyzed by a F1Fo-ATP synthase, an enzyme of dual genetic origin enriched at the edge of cristae where it plays a key role in their structure/stability. The enzyme's biogenesis remains poorly understood, both from a mechanistic and a compartmentalization point of view. The present study provides novel molecular insights into this process through investigations on a human protein called TMEM70 with an unclear role in the assembly of ATP synthase. A recent study has revealed the existence of physical interactions between TMEM70 and the subunit c (Su.c), a protein present in 8 identical copies forming a transmembrane oligomeric ring (c-ring) within the ATP synthase proton translocating domain (Fo). Herein we analyzed the ATP-synthase assembly in cells lacking TMEM70, mitochondrial DNA or F1 subunits and observe a direct correlation between TMEM70 and Su.c levels, regardless of the status of other ATP synthase subunits or of mitochondrial bioenergetics. Immunoprecipitation, two-dimensional blue-native/SDS-PAGE, and pulse-chase experiments reveal that TMEM70 forms large oligomers that interact with Su.c not yet incorporated into ATP synthase complexes. Moreover, discrete TMEM70-Su.c complexes with increasing Su.c contents can be detected, suggesting a role for TMEM70 oligomers in the gradual assembly of the c-ring. Furthermore, we demonstrate using expansion super-resolution microscopy the specific localization of TMEM70 at the inner cristae membrane, distinct from the MICOS component MIC60. Taken together, our results show that TMEM70 oligomers provide a scaffold for c-ring assembly and that mammalian ATP synthase is assembled within inner cristae membranes.
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Affiliation(s)
- Hela Bahri
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France; Laboratoire de génétique, Immunologie et Pathologie Humaine, Faculté des sciences de Tunis, Université Tunis-El Manar FST, Tunis, Tunisie
| | - Jeremie Buratto
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France; Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Manuel Rojo
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Jim Paul Dompierre
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Bénédicte Salin
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Corinne Blancard
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Sylvain Cuvellier
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Marie Rose
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Amel Ben Ammar Elgaaied
- Laboratoire de génétique, Immunologie et Pathologie Humaine, Faculté des sciences de Tunis, Université Tunis-El Manar FST, Tunis, Tunisie
| | - Emmanuel Tetaud
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France; Laboratoire de Microbiologie Fondamentale et Pathogénicité UMR-CNRS 5234, 146 rue Léo Saignat, CEDEX F-33076 Bordeaux, France
| | - Jean-Paul di Rago
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Anne Devin
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France
| | - Stéphane Duvezin-Caubet
- Université Bordeaux, IBGC, UMR 5095, F-33000 Bordeaux, France; CNRS, IBGC, UMR 5095, F-33000 Bordeaux, France.
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12
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Bertgen L, Mühlhaus T, Herrmann JM. Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148275. [PMID: 32712152 DOI: 10.1016/j.bbabio.2020.148275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 11/18/2022]
Abstract
Why mitochondria still retain their own genome is a puzzle given the enormous effort to maintain a mitochondrial translation machinery. Most mitochondrially encoded proteins are membrane-embedded subunits of the respiratory chain. Their hydrophobicity presumably impedes their import into mitochondria. However, many mitochondrial genomes also encode protein subunits of the mitochondrial ribosome. These proteins lack transmembrane domains and hydrophobicity cannot explain why their genes remained in mitochondria. In this review, we provide an overview about mitochondrially encoded subunits of mitochondrial ribosomes of fungi, plants and protists. Moreover, we discuss and evaluate different hypotheses which were put forward to explain why (ribosomal) proteins remained mitochondrially encoded. It seems likely that the synthesis of ribosomal proteins in the mitochondrial matrix is used to regulate the assembly of the mitochondrial ribosome within mitochondria and to avoid problems that mitochondrial proteins might pose for cytosolic proteostasis and for the assembly of cytosolic ribosomes.
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Affiliation(s)
- Lea Bertgen
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 23, 67663 Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Straße 13, 67663 Kaiserslautern, Germany.
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13
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Stenger M, Le DT, Klecker T, Westermann B. Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae. MICROBIAL CELL 2020; 7:234-249. [PMID: 32904421 PMCID: PMC7453639 DOI: 10.15698/mic2020.09.729] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The production of metabolic energy in form of ATP by oxidative phosphorylation depends on the coordinated action of hundreds of nuclear-encoded mitochondrial proteins and a handful of proteins encoded by the mitochondrial genome (mtDNA). We used the yeast Saccharomyces cerevisiae as a model system to systematically identify the genes contributing to this process. Integration of genome-wide high-throughput growth assays with previously published large data sets allowed us to define with high confidence a set of 254 nuclear genes that are indispensable for respiratory growth. Next, we induced loss of mtDNA in the yeast deletion collection by growth on ethidium bromide-containing medium and identified twelve genes that are essential for viability in the absence of mtDNA (i.e. petite-negative). Replenishment of mtDNA by cytoduction showed that respiratory-deficient phenotypes are highly variable in many yeast mutants. Using a mitochondrial genome carrying a selectable marker, ARG8m, we screened for mutants that are specifically defective in maintenance of mtDNA and mitochondrial protein synthesis. We found that up to 176 nuclear genes are required for expression of mitochondria-encoded proteins during fermentative growth. Taken together, our data provide a comprehensive picture of the molecular processes that are required for respiratory metabolism in a simple eukaryotic cell.
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Affiliation(s)
- Maria Stenger
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Duc Tung Le
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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14
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Ndi M, Marin-Buera L, Salvatori R, Singh AP, Ott M. Biogenesis of the bc 1 Complex of the Mitochondrial Respiratory Chain. J Mol Biol 2018; 430:3892-3905. [PMID: 29733856 DOI: 10.1016/j.jmb.2018.04.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 11/26/2022]
Abstract
The oxidative phosphorylation system contains four respiratory chain complexes that connect the transport of electrons to oxygen with the establishment of an electrochemical gradient over the inner membrane for ATP synthesis. Due to the dual genetic source of the respiratory chain subunits, its assembly requires a tight coordination between nuclear and mitochondrial gene expression machineries. In addition, dedicated assembly factors support the step-by-step addition of catalytic and accessory subunits as well as the acquisition of redox cofactors. Studies in yeast have revealed the basic principles underlying the assembly pathways. In this review, we summarize work on the biogenesis of the bc1 complex or complex III, a central component of the mitochondrial energy conversion system.
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Affiliation(s)
- Mama Ndi
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lorena Marin-Buera
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Roger Salvatori
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Abeer Prakash Singh
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Ott
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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15
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Pecina P, Nůsková H, Karbanová V, Kaplanová V, Mráček T, Houštěk J. Role of the mitochondrial ATP synthase central stalk subunits γ and δ in the activity and assembly of the mammalian enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:374-381. [DOI: 10.1016/j.bbabio.2018.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/05/2018] [Accepted: 02/24/2018] [Indexed: 10/17/2022]
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16
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du Mee DJM, Ivanov M, Parker JP, Buratowski S, Marquardt S. Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance. eLife 2018; 7:31989. [PMID: 29504936 PMCID: PMC5837560 DOI: 10.7554/elife.31989] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/08/2018] [Indexed: 12/27/2022] Open
Abstract
Most DNA in the genomes of higher organisms does not code for proteins. RNA Polymerase II (Pol II) transcribes non-coding DNA into long non-coding RNAs (lncRNAs), but biological roles of lncRNA are unclear. We find that mutations in the yeast lncRNA CUT60 result in poor growth. Defective termination of CUT60 transcription causes read-through transcription across the ATP16 gene promoter. Read-through transcription localizes chromatin signatures associated with Pol II elongation to the ATP16 promoter. The act of Pol II elongation across this promoter represses functional ATP16 expression by a Transcriptional Interference (TI) mechanism. Atp16p function in the mitochondrial ATP-synthase complex promotes mitochondrial DNA stability. ATP16 repression by TI through inefficient termination of CUT60 therefore triggers mitochondrial genome loss. Our results expand the functional and mechanistic implications of non-coding DNA in eukaryotes by highlighting termination of nuclear lncRNA transcription as mechanism to stabilize an organellar genome.
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Affiliation(s)
- Dorine Jeanne Mariëtte du Mee
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Joseph Paul Parker
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
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17
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Richman TR, Spåhr H, Ermer JA, Davies SMK, Viola HM, Bates KA, Papadimitriou J, Hool LC, Rodger J, Larsson NG, Rackham O, Filipovska A. Loss of the RNA-binding protein TACO1 causes late-onset mitochondrial dysfunction in mice. Nat Commun 2016; 7:11884. [PMID: 27319982 PMCID: PMC4915168 DOI: 10.1038/ncomms11884] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/09/2016] [Indexed: 11/30/2022] Open
Abstract
The recognition and translation of mammalian mitochondrial mRNAs are poorly understood. To gain further insights into these processes in vivo, we characterized mice with a missense mutation that causes loss of the translational activator of cytochrome oxidase subunit I (TACO1). We report that TACO1 is not required for embryonic survival, although the mutant mice have substantially reduced COXI protein, causing an isolated complex IV deficiency. We show that TACO1 specifically binds the mt-Co1 mRNA and is required for translation of COXI through its association with the mitochondrial ribosome. We determined the atomic structure of TACO1, revealing three domains in the shape of a hook with a tunnel between domains 1 and 3. Mutations in the positively charged domain 1 reduce RNA binding by TACO1. The Taco1 mutant mice develop a late-onset visual impairment, motor dysfunction and cardiac hypertrophy and thus provide a useful model for future treatment trials for mitochondrial disease. Mutations in the translational activator of cytochrome c oxidase subunit I (TACO1) causes cytochrome c oxidase deficiency and Leigh Syndrome in patients. Here, the authors characterize mice with a mutation that causes lack of TACO1 expression, identifying a mouse model that could be useful for preclinical trials.
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Affiliation(s)
- Tara R Richman
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Stefan M K Davies
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Helena M Viola
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Kristyn A Bates
- Experimental and Regenerative Neuroscience, School of Animal Biology, University of Western Australia Crawley, Western Australia 6009, Australia
| | - John Papadimitriou
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Livia C Hool
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Crawley, Western Australia 6009, Australia.,Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Jennifer Rodger
- Experimental and Regenerative Neuroscience, School of Animal Biology, University of Western Australia Crawley, Western Australia 6009, Australia
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia.,School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia.,School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
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18
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He K, Yan L, Pan CS, Liu YY, Cui YC, Hu BH, Chang X, Li Q, Sun K, Mao XW, Fan JY, Han JY. ROCK-dependent ATP5D modulation contributes to the protection of notoginsenoside NR1 against ischemia-reperfusion-induced myocardial injury. Am J Physiol Heart Circ Physiol 2014; 307:H1764-76. [PMID: 25305180 DOI: 10.1152/ajpheart.00259.2014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cardiac ischemia-reperfusion (I/R) injury remains a challenge for clinicians, which initiates with energy metabolism disorder. The present study was designed to investigate the protective effect of notoginsenoside R1 (NR1) on I/R-induced cardiac injury and underlying mechanism. Male Sprague-Dawley rats were subjected to 30-min occlusion of the left coronary anterior descending artery followed by reperfusion with or without NR1 pretreatment (5 mg·kg(-1)·h(-1)). In vitro, H9c2 cells were cultured under oxygen and glucose deprivation/reoxygenation conditions after NR1 (0.1 mM), Rho kinase (ROCK) inhibitor Y-27632 (10 μM), or RhoA/ROCK activator U-46619 (10 nM) administration. Myocardial infarct size, myocardial histology, and cardiac function were evaluated. Myofibril and mitochondria morphology were observed by transmission electron microscopy. F-actin and apoptosis were determined by immunofluorescence and TUNEL staining. ATP and AMP content were assessed by ELISA. Phosphorylated-AMP-activated protein kinase, ATP synthase subunits, apoptosis-related molecules, and the level and activity of ROCK were determined by Western blot analysis. We found that NR1 pretreatment ameliorated myocardial infarction, histological injury, and cardiac function induced by I/R. Furthermore, similar to the effect of Y-27632, NR1 improved H9c2 cell viability, maintained actin skeleton and mitochondria morphology, and attenuated apoptosis induced by oxygen and glucose deprivation/reoxygenation. Importantly, NR1 prevented energy abnormity, inhibited the expression and activation of ROCK, and restored the expression of the mitochondrial ATP synthase δ-subunit both in vivo and in vitro, whereas U-46619 suppressed the effect of NR1. These results prove NR1 as an agent able to prevent I/R-induced energy metabolism disorder via inhibiting ROCK and enhancing mitochondrial ATP synthase δ-subunits, which at least partially contributes to its protection against cardiac I/R injury.
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Affiliation(s)
- Ke He
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Li Yan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Chun-Shui Pan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Yu-Ying Liu
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Yuan-Chen Cui
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Bai-He Hu
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Xin Chang
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Quan Li
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Kai Sun
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Xiao-Wei Mao
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
| | - Jing-Yu Fan
- Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China
| | - Jing-Yan Han
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, Beijing, China; Tasly Microcirculation Research Center, Peking University Health Science Center, Beijing, China; Key Laboratory of Microcirculation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China; and Key Laboratory of Stasis and Phlegm, State Administration of Traditional Chinese Medicine of the People's Republic of China, Beijing, China
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19
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Fukuoh A, Cannino G, Gerards M, Buckley S, Kazancioglu S, Scialo F, Lihavainen E, Ribeiro A, Dufour E, Jacobs HT. Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase. Mol Syst Biol 2014; 10:734. [PMID: 24952591 PMCID: PMC4265055 DOI: 10.15252/msb.20145117] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The machinery of mitochondrial DNA (mtDNA) maintenance is only partially characterized and is of wide interest due to its involvement in disease. To identify novel components of this machinery, plus other cellular pathways required for mtDNA viability, we implemented a genome-wide RNAi screen in Drosophila S2 cells, assaying for loss of fluorescence of mtDNA nucleoids stained with the DNA-intercalating agent PicoGreen. In addition to previously characterized components of the mtDNA replication and transcription machineries, positives included many proteins of the cytosolic proteasome and ribosome (but not the mitoribosome), three proteins involved in vesicle transport, some other factors involved in mitochondrial biogenesis or nuclear gene expression, > 30 mainly uncharacterized proteins and most subunits of ATP synthase (but no other OXPHOS complex). ATP synthase knockdown precipitated a burst of mitochondrial ROS production, followed by copy number depletion involving increased mitochondrial turnover, not dependent on the canonical autophagy machinery. Our findings will inform future studies of the apparatus and regulation of mtDNA maintenance, and the role of mitochondrial bioenergetics and signaling in modulating mtDNA copy number.
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Affiliation(s)
- Atsushi Fukuoh
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate school of Medical Sciences, Fukuoka, Japan Department of Medical Laboratory Science, Junshin Gakuen University, Fukuoka, Japan
| | - Giuseppe Cannino
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Mike Gerards
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Suzanne Buckley
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Selena Kazancioglu
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Filippo Scialo
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Eero Lihavainen
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Andre Ribeiro
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Eric Dufour
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Howard T Jacobs
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland Research Program of Molecular Neurology, University of Helsinki, Helsinki, Finland
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20
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Tetaud E, Godard F, Giraud MF, Ackerman SH, di Rago JP. The depletion of F₁ subunit ε in yeast leads to an uncoupled respiratory phenotype that is rescued by mutations in the proton-translocating subunits of F₀. Mol Biol Cell 2014; 25:791-9. [PMID: 24451261 PMCID: PMC3952849 DOI: 10.1091/mbc.e13-02-0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 01/08/2014] [Accepted: 01/14/2014] [Indexed: 01/15/2023] Open
Abstract
The central stalk of the ATP synthase is an elongated hetero-oligomeric structure providing a physical connection between the catalytic sites in F₁ and the proton translocation channel in F₀ for energy transduction between the two subdomains. The shape of the central stalk and relevance to energy coupling are essentially the same in ATP synthases from all forms of life, yet the protein composition of this domain changed during evolution of the mitochondrial enzyme from a two- to a three-subunit structure (γ, δ, ε). Whereas the mitochondrial γ- and δ-subunits are homologues of the bacterial central stalk proteins, the deliberate addition of subunit ε is poorly understood. Here we report that down-regulation of the gene (ATP15) encoding the ε-subunit rapidly leads to lethal F₀-mediated proton leaks through the membrane because of the loss of stability of the ATP synthase. The ε-subunit is thus essential for oxidative phosphorylation. Moreover, mutations in F₀ subunits a and c, which slow the proton translocation rate, are identified that prevent ε-deficient ATP synthases from dissipating the electrochemical potential. Cumulatively our data lead us to propose that the ε-subunit evolved to permit operation of the central stalk under the torque imposed at the normal speed of proton movement through mitochondrial F₀.
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Affiliation(s)
- Emmanuel Tetaud
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
- Université Victor Segalen Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
| | - François Godard
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
- Université Victor Segalen Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
| | - Marie-France Giraud
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
- Université Victor Segalen Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
| | - Sharon H. Ackerman
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201
| | - Jean-Paul di Rago
- Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
- Université Victor Segalen Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33077 Bordeaux, France
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21
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Szczesny RJ, Wojcik MA, Borowski LS, Szewczyk MJ, Skrok MM, Golik P, Stepien PP. Yeast and human mitochondrial helicases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:842-53. [PMID: 23454114 DOI: 10.1016/j.bbagrm.2013.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 11/19/2022]
Abstract
Mitochondria are semiautonomous organelles which contain their own genome. Both maintenance and expression of mitochondrial DNA require activity of RNA and DNA helicases. In Saccharomyces cerevisiae the nuclear genome encodes four DExH/D superfamily members (MSS116, SUV3, MRH4, IRC3) that act as helicases and/or RNA chaperones. Their activity is necessary for mitochondrial RNA splicing, degradation, translation and genome maintenance. In humans the ortholog of SUV3 (hSUV3, SUPV3L1) so far is the best described mitochondrial RNA helicase. The enzyme, together with the matrix-localized pool of PNPase (PNPT1), forms an RNA-degrading complex called the mitochondrial degradosome, which localizes to distinct structures (D-foci). Global regulation of mitochondrially encoded genes can be achieved by changing mitochondrial DNA copy number. This way the proteins involved in its replication, like the Twinkle helicase (c10orf2), can indirectly regulate gene expression. Here, we describe yeast and human mitochondrial helicases that are directly involved in mitochondrial RNA metabolism, and present other helicases that participate in mitochondrial DNA replication and maintenance. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.
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Affiliation(s)
- Roman J Szczesny
- Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
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22
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Bietenhader M, Martos A, Tetaud E, Aiyar RS, Sellem CH, Kucharczyk R, Clauder-Münster S, Giraud MF, Godard F, Salin B, Sagot I, Gagneur J, Déquard-Chablat M, Contamine V, Denmat SHL, Sainsard-Chanet A, Steinmetz LM, di Rago JP. Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS Genet 2012; 8:e1002876. [PMID: 22916027 PMCID: PMC3420929 DOI: 10.1371/journal.pgen.1002876] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/19/2012] [Indexed: 01/21/2023] Open
Abstract
Only a few genes remain in the mitochondrial genome retained by every eukaryotic organism that carry out essential functions and are implicated in severe diseases. Experimentally relocating these few genes to the nucleus therefore has both therapeutic and evolutionary implications. Numerous unproductive attempts have been made to do so, with a total of only 5 successes across all organisms. We have taken a novel approach to relocating mitochondrial genes that utilizes naturally nuclear versions from other organisms. We demonstrate this approach on subunit 9/c of ATP synthase, successfully relocating this gene for the first time in any organism by expressing the ATP9 genes from Podospora anserina in Saccharomyces cerevisiae. This study substantiates the role of protein structure in mitochondrial gene transfer: expression of chimeric constructs reveals that the P. anserina proteins can be correctly imported into mitochondria due to reduced hydrophobicity of the first transmembrane segment. Nuclear expression of ATP9, while permitting almost fully functional oxidative phosphorylation, perturbs many cellular properties, including cellular morphology, and activates the heat shock response. Altogether, our study establishes a novel strategy for allotopic expression of mitochondrial genes, demonstrates the complex adaptations required to relocate ATP9, and indicates a reason that this gene was only transferred to the nucleus during the evolution of multicellular organisms.
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Affiliation(s)
- Maïlis Bietenhader
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - Alexandre Martos
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - Emmanuel Tetaud
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - Raeka S. Aiyar
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Carole H. Sellem
- Université Paris-Sud, Centre de Génétique Moléculaire, UPR3404, CNRS, Gif-sur-Yvette, France
| | - Roza Kucharczyk
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | | | - Marie-France Giraud
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - François Godard
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - Bénédicte Salin
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - Isabelle Sagot
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
| | - Julien Gagneur
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michelle Déquard-Chablat
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Véronique Contamine
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Sylvie Hermann-Le Denmat
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Ecole Normale Supérieure, Paris, France
| | - Annie Sainsard-Chanet
- Université Paris-Sud, Centre de Génétique Moléculaire, UPR3404, CNRS, Gif-sur-Yvette, France
| | - Lars M. Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- * E-mail: (J-PdR); (LMS)
| | - Jean-Paul di Rago
- Université Bordeaux, IBGC, UMR5095 CNRS, Bordeaux, France
- CNRS, IBGC, UMR5095 CNRS, Bordeaux, France
- * E-mail: (J-PdR); (LMS)
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Herrmann JM, Woellhaf MW, Bonnefoy N. Control of protein synthesis in yeast mitochondria: the concept of translational activators. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:286-94. [PMID: 22450032 DOI: 10.1016/j.bbamcr.2012.03.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/01/2012] [Accepted: 03/08/2012] [Indexed: 12/18/2022]
Abstract
Mitochondria contain their own genome which codes for a small number of proteins. Most mitochondrial translation products are part of the membrane-embedded reaction centers of the respiratory chain complexes. In the yeast Saccharomyces cerevisiae, the expression of these proteins is regulated by translational activators that bind mitochondrial mRNAs, in most cases to their 5'-untranslated regions, and each mitochondrial mRNA appears to have its own translational activator(s). Recent studies showed that these translational activators can be part of feedback control loops which only permit translation if the downstream assembly of nascent translation products can occur. In several cases, the accumulation of a non-assembled protein prevents further synthesis of this protein but not translation in general. These control loops prevent the synthesis of potentially harmful assembly intermediates of the reaction centers of mitochondrial enzymes. Since such regulatory feedback loops only work if translation occurs in the compartment in which the complexes of the respiratory chain are assembled, these control mechanisms require the presence of a translation machinery in mitochondria. This might explain why eukaryotic cells maintained DNA in mitochondria during the last two billion years of evolution. This review gives an overview of the mitochondrial translation system and summarizes the current knowledge on translational activators and their role in the regulation of mitochondrial protein synthesis. This article is part of a Special Issue entitled: Protein import and quality control in mitochondria and plastids.
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Affiliation(s)
- Johannes M Herrmann
- Cell Biology, Erwin-Schrödinger-Strasse 13, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
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24
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Godard F, Tetaud E, Duvezin-Caubet S, di Rago JP. A genetic screen targeted on the FO component of mitochondrial ATP synthase in Saccharomyces cerevisiae. J Biol Chem 2011; 286:18181-9. [PMID: 21454598 DOI: 10.1074/jbc.m110.214825] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In yeast, the two main F(O) proton-translocating subunits of the ATP synthase (subunits 6/a and 9/c) are encoded by mitochondrial DNA (mtDNA). Unfortunately, mutations that inactivate the F(O) typically result in loss of mtDNA under the form of ρ(-)/ρ(0) cells. Thus, we have designed a novel genetic strategy to circumvent this problem. It exploits previous findings that a null mutation in the nuclear ATP16 gene encoding ATP synthase subunit δ results in massive and lethal F(O)-mediated protons leaks across the inner mitochondrial membrane. Mutations that inactivate the F(O) can thus, in these conditions, be selected positively as cell viability rescuing events. A first set of seven mutants was analyzed and all showed, as expected, very severe F(O) deficiencies. Two mutants carried nuclear mutations in known genes (AEP1, AEP2) required for subunit c expression. The five other mutations were located in mtDNA. Of these, three affect synthesis or stability of subunit a transcripts and the two last consisted in a single amino acid replacement in subunit c. One of the subunit c mutations is particularly interesting. It consists in an alanine to valine change at position 60 of subunit c adjacent to the essential glutamate of subunit c (at position 59) that interacts with the essential arginine 186 of subunit a. The properties of this mutant suggest that the contact zone between subunit a and the ten subunits c-ring structure only involves critical transient interactions confined to the region where protons are exchanged between the subunit a and the c-ring.
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Affiliation(s)
- François Godard
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS, Université Victor Segalen Bordeaux 2, 33077 Bordeaux, France
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25
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Pang Y, Wang H, Song WQ, Zhu YX. The cotton ATP synthase δ1 subunit is required to maintain a higher ATP/ADP ratio that facilitates rapid fibre cell elongation. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:903-9. [PMID: 21040305 DOI: 10.1111/j.1438-8677.2009.00313.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The δ subunit of mitochondrial ATP synthase serves as a linker between the F(0) and F(1) sectors. Here, through microarray and quantitative RT-PCR, we found that the δ1 subunit was significantly up-regulated during cotton fibre cell elongation. Both the relative level and duration of GhATPδ1 transcripts correlated positively with the final length of different cotton germplasms. Elongating fibre cells had a significantly elevated ATP/ADP ratio, suggesting that a higher energy input is probably required for primary fibre cell wall formation and elongation. We obtained a putative full-length GhATPδ1 cDNA that shows 37% sequence identity to the Saccharomyces cerevisiae ATP16 at the deduced amino acid level. An almost wild-type growth rate was restored in atp16Δ cells that expressed GhATPδ1, with a resultant ATP/ADP ratio similar to that found in wild-type cells, indicating that the cotton gene was functional in yeast. Mitochondria prepared from 10 dpa wild-type fibre cells showed significantly higher ATP synthase activity in comparison to ovule samples from wild type and leaf samples. Exogenous application of piceatannol (PA) or oligomycin (OM), inhibitors of ATP synthase F(1) or F(0) subunits, respectively, in ovule culture media resulted in much shorter fibre cells and a significantly lower ATP/ADP ratio. Our data suggest that GhATPδ1 is important for activity of mitochondrial ATP synthase and is probably related to cotton fibre elongation.
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Affiliation(s)
- Y Pang
- The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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26
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DMR1 (CCM1/YGR150C) of Saccharomyces cerevisiae encodes an RNA-binding protein from the pentatricopeptide repeat family required for the maintenance of the mitochondrial 15S ribosomal RNA. Genetics 2010; 184:959-73. [PMID: 20124025 DOI: 10.1534/genetics.110.113969] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins form the largest known RNA-binding protein family and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly in mitochondria and chloroplasts, where they modulate organellar genome expression on the post-transcriptional level. The Saccharomyces cerevisiae DMR1 (CCM1, YGR150C) encodes a PPR protein that localizes to mitochondria. Deletion of DMR1 results in a complete and irreversible loss of respiratory capacity and loss of wild-type mtDNA by conversion to rho(-)/rho(0) petites, regardless of the presence of introns in mtDNA. The phenotype of the dmr1Delta mitochondria is characterized by fragmentation of the small subunit mitochondrial rRNA (15S rRNA), that can be reversed by wild-type Dmr1p. Other mitochondrial transcripts, including the large subunit mitochondrial rRNA (21S rRNA), are not affected by the lack of Dmr1p. The purified Dmr1 protein specifically binds to different regions of 15S rRNA in vitro, consistent with the deletion phenotype. Dmr1p is therefore the first yeast PPR protein, which has an rRNA target and is probably involved in the biogenesis of mitochondrial ribosomes and translation.
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27
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Lipinski KA, Kaniak-Golik A, Golik P. Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1086-98. [PMID: 20056105 DOI: 10.1016/j.bbabio.2009.12.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Revised: 12/18/2009] [Accepted: 12/24/2009] [Indexed: 10/20/2022]
Abstract
As a legacy of their endosymbiotic eubacterial origin, mitochondria possess a residual genome, encoding only a few proteins and dependent on a variety of factors encoded by the nuclear genome for its maintenance and expression. As a facultative anaerobe with well understood genetics and molecular biology, Saccharomyces cerevisiae is the model system of choice for studying nucleo-mitochondrial genetic interactions. Maintenance of the mitochondrial genome is controlled by a set of nuclear-coded factors forming intricately interconnected circuits responsible for replication, recombination, repair and transmission to buds. Expression of the yeast mitochondrial genome is regulated mostly at the post-transcriptional level, and involves many general and gene-specific factors regulating splicing, RNA processing and stability and translation. A very interesting aspect of the yeast mitochondrial system is the relationship between genome maintenance and gene expression. Deletions of genes involved in many different aspects of mitochondrial gene expression, notably translation, result in an irreversible loss of functional mtDNA. The mitochondrial genetic system viewed from the systems biology perspective is therefore very fragile and lacks robustness compared to the remaining systems of the cell. This lack of robustness could be a legacy of the reductive evolution of the mitochondrial genome, but explanations involving selective advantages of increased evolvability have also been postulated.
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Affiliation(s)
- Kamil A Lipinski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106, Warsaw, Poland
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28
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Merz S, Westermann B. Genome-wide deletion mutant analysis reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis in Saccharomyces cerevisiae. Genome Biol 2009; 10:R95. [PMID: 19751518 PMCID: PMC2768984 DOI: 10.1186/gb-2009-10-9-r95] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 09/14/2009] [Indexed: 12/13/2022] Open
Abstract
A genome-wide deletion mutant analysis in budding yeast reveals genes required for respiratory growth, mitochondrial genome maintenance and mitochondrial protein synthesis. Background The mitochondrial respiratory chain produces metabolic energy by oxidative phosphorylation. Biogenesis of the respiratory chain requires the coordinated expression of two genomes: the nuclear genome encoding the vast majority of mitochondrial proteins, and the mitochondrial genome encoding a handful of mitochondrial proteins. The understanding of the molecular processes contributing to respiratory chain assembly and maintenance requires the systematic identification and functional analysis of the genes involved. Results We pursued a systematic, genome-wide approach to define the sets of genes required for respiratory activity and maintenance and expression of the mitochondrial genome in yeast. By comparative gene deletion analysis we found an unexpected phenotypic plasticity among respiratory-deficient mutants, and we identified ten previously uncharacterized genes essential for respiratory growth (RRG1 through RRG10). Systematic functional analysis of 319 respiratory-deficient mutants revealed 16 genes essential for maintenance of the mitochondrial genome, 88 genes required for mitochondrial protein translation, and 10 genes required for expression of specific mitochondrial gene products. A group of mutants acquiring irreversible damage compromising respiratory capacity includes strains defective in assembly of the cytochrome c oxidase that were found to be particularly sensitive to aging. Conclusions These data advance the understanding of the molecular processes contributing to maintenance of the mitochondrial genome, mitochondrial protein translation, and assembly of the respiratory chain. They revealed a number of previously uncharacterized components, and provide a comprehensive picture of the molecular processes required for respiratory activity in a simple eukaryotic cell.
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Affiliation(s)
- Sandra Merz
- Institut für Zellbiologie, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany.
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29
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Soto IC, Fontanesi F, Valledor M, Horn D, Singh R, Barrientos A. Synthesis of cytochrome c oxidase subunit 1 is translationally downregulated in the absence of functional F1F0-ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:1776-86. [PMID: 19735676 DOI: 10.1016/j.bbamcr.2009.09.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 10/20/2022]
Abstract
The mitochondrial F(1)F(0)-ATP synthase or ATPase is a key enzyme for aerobic energy production in eukaryotic cells. Mutations in ATPase structural and assembly genes are the primary cause of severe human encephalomyopathies, frequently associated with a pleiotropic decrease in cytochrome c oxidase (COX) activity. We have studied the structural and functional constraints underlying the COX defect using Saccharomyces cerevisiae genetic and pharmacological models of ATPase deficiency. In both yeast Deltaatp10 and oligomycin-treated wild type cells, COX assembly is selectively impaired in the absence of functional ATPase. The COX biogenesis defect does not involve a primary alteration in the expression of the COX subunits as previously suggested but in their maturation and/or assembly. Expression of COX subunit 1, however, is translationally regulated as in most bona fide COX assembly mutants. Additionally, the COX defect in oligomycin-inhibited ATPase-deficient yeast cells, but not in atp10 cells could be partially prevented by partially dissipating the mitochondrial membrane potential using the uncoupler CCCP. Similar results were obtained with oligomycin-treated and ATP12-deficient human fibroblasts respectively. Our findings imply that fully assembled ATPase and its proton pumping function are both required for COX biogenesis in yeast and mammalian cells through a mechanism independent of Cox1p synthesis.
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Affiliation(s)
- Ileana C Soto
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine. Miami, FL 33136, USA
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30
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Zick M, Duvezin-Caubet S, Schäfer A, Vogel F, Neupert W, Reichert AS. Distinct roles of the two isoforms of the dynamin-like GTPase Mgm1 in mitochondrial fusion. FEBS Lett 2009; 583:2237-43. [PMID: 19505460 DOI: 10.1016/j.febslet.2009.05.053] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 05/08/2009] [Accepted: 05/29/2009] [Indexed: 01/05/2023]
Abstract
The mitochondrial dynamin-like GTPase Mgm1 exists as a long (l-Mgm1) and a short isoform (s-Mgm1). They both are essential for mitochondrial fusion. Here we show that the isoforms interact in a homotypic and heterotypic manner. Their submitochondrial distribution between inner boundary membrane and cristae was markedly different. Overexpression of l-Mgm1 exerts a dominant negative effect on mitochondrial fusion. A functional GTPase domain is required only in s-Mgm1 but not in l-Mgm1. We propose that l-Mgm1 acts primarily as an anchor in the inner membrane that in concert with the GTPase activity of s-Mgm1 mediates the fusion of inner membranes.
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Affiliation(s)
- Michael Zick
- Adolf-Butenandt-Institut für Physiologische Chemie, Ludwig-Maximilians-Universität München, München, Germany
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31
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Rak M, Zeng X, Brière JJ, Tzagoloff A. Assembly of F0 in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2008; 1793:108-16. [PMID: 18672007 DOI: 10.1016/j.bbamcr.2008.07.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 06/26/2008] [Accepted: 07/01/2008] [Indexed: 11/30/2022]
Abstract
Respiratory deficient mutants of Saccharomyces cerevisiae have been instrumental in identifying an increasing number of nuclear gene products that promote pre- and post-translational steps of the pathway responsible for biogenesis of the mitochondrial ATP synthase. In this article we have attempted to marshal current information about the functions of such accessory factors and the roles they play in expression and assembly of the mitochondrially encoded subunits of the ATP synthase. We also discuss evidence that the ATP synthase may be built up from three separate modules corresponding to the F1 ATPase, the stator and F0.
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Affiliation(s)
- Malgorzata Rak
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
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32
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Rizzo JM, Tarsio M, Martínez-Muñoz GA, Kane PM. Diploids heterozygous for a vma13Delta mutation in Saccharomyces cerevisiae highlight the importance of V-ATPase subunit balance in supporting vacuolar acidification and silencing cytosolic V1-ATPase activity. J Biol Chem 2007; 282:8521-32. [PMID: 17234635 DOI: 10.1074/jbc.m607092200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The V-ATPase H subunit (encoded by the VMA13 gene) activates ATP-driven proton pumping in intact V-ATPase complexes and inhibits MgATPase activity in cytosolic V1 sectors (Parra, K. J., Keenan, K. L., and Kane, P. M. (2000) J. Biol. Chem. 275, 21761-21767). Yeast diploids heterozygous for a vma13Delta mutation show the pH- and calcium-dependent conditional lethality characteristic of mutants lacking V-ATPase activity, although they still contain one wild-type copy of VMA13. Vacuolar vesicles from this strain have approximately 50% of the ATPase activity of those from a wild-type diploid but do not support formation of a proton gradient. Compound heterozygotes with a second heterozygous deletion in another V1 subunit gene exhibit improved growth, vacuolar acidification, and ATP-driven proton transport in vacuolar vesicles. In contrast, compound heterozygotes with a second deletion in a Vo subunit grow even more poorly than the vma13Delta heterozygote, have very little vacuolar acidification, and have very low levels of V-ATPase subunits in isolated vacuoles. In addition, cytosolic V1 sectors from this strain and from the strain containing only the heterozygous vma13Delta mutation have elevated MgATPase activity. The results suggest that balancing levels of subunit H with those of other V-ATPase subunits is critical, both for allowing organelle acidification and for preventing unproductive hydrolysis of cytosolic ATP.
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Affiliation(s)
- Jason M Rizzo
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA
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33
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Bonnefoy N, Remacle C, Fox TD. Genetic transformation of Saccharomyces cerevisiae and Chlamydomonas reinhardtii mitochondria. Methods Cell Biol 2007; 80:525-48. [PMID: 17445712 DOI: 10.1016/s0091-679x(06)80026-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nathalie Bonnefoy
- Centre de Génétique Moléculaire, CNRS UPR2167, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France
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34
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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