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Yardımcı BK, Tarhan L. Oxidative effects of the human antifungal drug clotrimazole on the eucaryotic model organism Saccharomyces cerevisiae. Arch Microbiol 2024; 206:290. [PMID: 38847903 DOI: 10.1007/s00203-024-04031-2] [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: 05/03/2024] [Revised: 05/27/2024] [Accepted: 06/04/2024] [Indexed: 08/07/2024]
Abstract
Clotrimazole is a type of antifungal medication developed from azole compounds. It exhibits several biological actions linked to oxidative stress. This study focuses on the oxidative effects of clotrimazole on the eukaryotic model yeast, Saccharomyces cerevisiae. Our results showed that although initial nitric oxide levels were above control in clotrimazole exposed cells, they showed decreasing tendencies from the beginning of incubation and dropped below control at 125 µM from the 60th min. The highest superoxide anion and hydrogen peroxide levels were 1.95- and 2.85-folds of controls at 125 µM after 15 and 60 min, respectively. Hydroxyl radical levels slightly increased throughout the incubation period in all concentrations and reached 1.3-fold of control, similarly at 110 and 125 µM in the 90th min. The highest level of reactive oxygen species was observed at 110 µM, 2.31-fold of control. Although NADH/NADPH oxidase activities showed similar tendencies for all conditions, the highest activities were found as 3.07- and 2.27-folds of control at 125 and 110 µM in the 15th and 30th min, respectively. The highest superoxide dismutase and catalase activities were 1.59- and 1.21-folds of controls at 110 µM clotrimazole in 30 and 90 min, respectively. While the drug generally induced glutathione-related enzyme activities, the ratios of glutathione to oxidized glutathione were above the control only at low concentrations of the drug. The levels of lipid peroxidation in all treated cells were significantly higher than the controls. The findings crucially demonstrate that this medicine can generate serious oxidative stress in organisms.
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Affiliation(s)
| | - Leman Tarhan
- Chemistry Department, Faculty of Sciences, Dokuz Eylul University, Buca, Izmir, 35160, Turkey
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2
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Phua CZJ, Zhao X, Turcios-Hernandez L, McKernan M, Abyadeh M, Ma S, Promislow D, Kaeberlein M, Kaya A. Genetic perturbation of mitochondrial function reveals functional role for specific mitonuclear genes, metabolites, and pathways that regulate lifespan. GeroScience 2023; 45:2161-2178. [PMID: 37086368 PMCID: PMC10651825 DOI: 10.1007/s11357-023-00796-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023] Open
Abstract
Altered mitochondrial function is tightly linked to lifespan regulation, but underlying mechanisms remain unclear. Here, we report the chronological and replicative lifespan variation across 167 yeast knock-out strains, each lacking a single nuclear-coded mitochondrial gene, including 144 genes with human homologs, many associated with diseases. We dissected the signatures of observed lifespan differences by analyzing profiles of each strain's proteome, lipidome, and metabolome under fermentative and respiratory culture conditions, which correspond to the metabolic states of replicative and chronologically aging cells, respectively. Examination of the relationships among extended longevity phenotypes, protein, and metabolite levels revealed that although many of these nuclear-encoded mitochondrial genes carry out different functions, their inhibition attenuates a common mechanism that controls cytosolic ribosomal protein abundance, actin dynamics, and proteasome function to regulate lifespan. The principles of lifespan control learned through this work may be applicable to the regulation of lifespan in more complex organisms, since many aspects of mitochondrial function are highly conserved among eukaryotes.
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Affiliation(s)
- Cheryl Zi Jin Phua
- Genome Institute of Singapore, Agency for Science, Technology, and Research (A* STAR), Singapore, Singapore
| | - Xiaqing Zhao
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Lesly Turcios-Hernandez
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA
| | - Morrigan McKernan
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA
| | - Morteza Abyadeh
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology, and Research (A* STAR), Singapore, Singapore
| | - Daniel Promislow
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Room 126, 1000 West Cary St. , Richmond, VA, 23284, USA.
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3
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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4
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di Punzio G, Gilberti M, Baruffini E, Lodi T, Donnini C, Dallabona C. A Yeast-Based Repurposing Approach for the Treatment of Mitochondrial DNA Depletion Syndromes Led to the Identification of Molecules Able to Modulate the dNTP Pool. Int J Mol Sci 2021; 22:ijms222212223. [PMID: 34830106 PMCID: PMC8621932 DOI: 10.3390/ijms222212223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/30/2022] Open
Abstract
Mitochondrial DNA depletion syndromes (MDS) are clinically heterogenous and often severe diseases, characterized by a reduction of the number of copies of mitochondrial DNA (mtDNA) in affected tissues. In the context of MDS, yeast has proved to be both an excellent model for the study of the mechanisms underlying mitochondrial pathologies and for the discovery of new therapies via high-throughput assays. Among the several genes involved in MDS, it has been shown that recessive mutations in MPV17 cause a hepatocerebral form of MDS and Navajo neurohepatopathy. MPV17 encodes a non selective channel in the inner mitochondrial membrane, but its physiological role and the nature of its cargo remains elusive. In this study we identify ten drugs active against MPV17 disorder, modelled in yeast using the homologous gene SYM1. All ten of the identified molecules cause a concomitant increase of both the mitochondrial deoxyribonucleoside triphosphate (mtdNTP) pool and mtDNA stability, which suggests that the reduced availability of DNA synthesis precursors is the cause for the mtDNA deletion and depletion associated with Sym1 deficiency. We finally evaluated the effect of these molecules on mtDNA stability in two other MDS yeast models, extending the potential use of these drugs to a wider range of MDS patients.
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5
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Annesley SJ, Fisher PR. Lymphoblastoid Cell Lines as Models to Study Mitochondrial Function in Neurological Disorders. Int J Mol Sci 2021; 22:4536. [PMID: 33926115 PMCID: PMC8123577 DOI: 10.3390/ijms22094536] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022] Open
Abstract
Neurological disorders, including neurodegenerative diseases, are collectively a major cause of death and disability worldwide. Whilst the underlying disease mechanisms remain elusive, altered mitochondrial function has been clearly implicated and is a key area of study in these disorders. Studying mitochondrial function in these disorders is difficult due to the inaccessibility of brain tissue, which is the key tissue affected in these diseases. To overcome this issue, numerous cell models have been used, each providing unique benefits and limitations. Here, we focussed on the use of lymphoblastoid cell lines (LCLs) to study mitochondrial function in neurological disorders. LCLs have long been used as tools for genomic analyses, but here we described their use in functional studies specifically in regard to mitochondrial function. These models have enabled characterisation of the underlying mitochondrial defect, identification of altered signalling pathways and proteins, differences in mitochondrial function between subsets of particular disorders and identification of biomarkers of the disease. The examples provided here suggest that these cells will be useful for development of diagnostic tests (which in most cases do not exist), identification of drug targets and testing of pharmacological agents, and are a worthwhile model for studying mitochondrial function in neurological disorders.
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Affiliation(s)
- Sarah Jane Annesley
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia;
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6
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Figuccia S, Degiorgi A, Ceccatelli Berti C, Baruffini E, Dallabona C, Goffrini P. Mitochondrial Aminoacyl-tRNA Synthetase and Disease: The Yeast Contribution for Functional Analysis of Novel Variants. Int J Mol Sci 2021; 22:ijms22094524. [PMID: 33926074 PMCID: PMC8123711 DOI: 10.3390/ijms22094524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
In most eukaryotes, mitochondrial protein synthesis is essential for oxidative phosphorylation (OXPHOS) as some subunits of the respiratory chain complexes are encoded by the mitochondrial DNA (mtDNA). Mutations affecting the mitochondrial translation apparatus have been identified as a major cause of mitochondrial diseases. These mutations include either heteroplasmic mtDNA mutations in genes encoding for the mitochondrial rRNA (mtrRNA) and tRNAs (mttRNAs) or mutations in nuclear genes encoding ribosomal proteins, initiation, elongation and termination factors, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (mtARSs). Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to their cognate tRNAs. Differently from most mttRNAs, which are encoded by mitochondrial genome, mtARSs are encoded by nuclear genes and then imported into the mitochondria after translation in the cytosol. Due to the extensive use of next-generation sequencing (NGS), an increasing number of mtARSs variants associated with large clinical heterogeneity have been identified in recent years. Being most of these variants private or sporadic, it is crucial to assess their causative role in the disease by functional analysis in model systems. This review will focus on the contributions of the yeast Saccharomyces cerevisiae in the functional validation of mutations found in mtARSs genes associated with human disorders.
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Affiliation(s)
| | | | | | | | - Cristina Dallabona
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
| | - Paola Goffrini
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
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7
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Ceccatelli Berti C, di Punzio G, Dallabona C, Baruffini E, Goffrini P, Lodi T, Donnini C. The Power of Yeast in Modelling Human Nuclear Mutations Associated with Mitochondrial Diseases. Genes (Basel) 2021; 12:300. [PMID: 33672627 PMCID: PMC7924180 DOI: 10.3390/genes12020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022] Open
Abstract
The increasing application of next generation sequencing approaches to the analysis of human exome and whole genome data has enabled the identification of novel variants and new genes involved in mitochondrial diseases. The ability of surviving in the absence of oxidative phosphorylation (OXPHOS) and mitochondrial genome makes the yeast Saccharomyces cerevisiae an excellent model system for investigating the role of these new variants in mitochondrial-related conditions and dissecting the molecular mechanisms associated with these diseases. The aim of this review was to highlight the main advantages offered by this model for the study of mitochondrial diseases, from the validation and characterisation of novel mutations to the dissection of the role played by genes in mitochondrial functionality and the discovery of potential therapeutic molecules. The review also provides a summary of the main contributions to the understanding of mitochondrial diseases emerged from the study of this simple eukaryotic organism.
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Affiliation(s)
| | | | | | | | | | | | - Claudia Donnini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (C.C.B.); (G.d.P.); (C.D.); (E.B.); (P.G.); (T.L.)
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8
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Kwon YY, Kim SS, Lee HJ, Sheen SH, Kim KH, Lee CK. Long-Living Budding Yeast Cell Subpopulation Induced by Ethanol/Acetate and Respiration. J Gerontol A Biol Sci Med Sci 2021; 75:1448-1456. [PMID: 31541249 DOI: 10.1093/gerona/glz202] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 01/14/2023] Open
Abstract
Budding yeast generate heterogeneous cells that can be separated into two distinctive cell types: short-living low-density and long-living high-density (HD) cells by density gradient centrifugation. We found that ethanol and acetate induce formation of HD cells, and mitochondrial respiration is required. From their transcriptomes and metabolomes, we found upregulated differentially expressed genes in HD cells involved in the RGT2/RGT1 glucose sensing pathway and its downstream genes encoding hexose transporters. For HD cells, we determined an abundance of various carbon sources including glucose, lactate, pyruvate, trehalose, mannitol, mannose, and galactose. Other upregulated differentially expressed genes in HD cells were involved in the TORC1-SCH9 signaling pathway and its downstream genes involved in cytoplasmic translation. We also measured an abundance of free amino acids in HD cells including valine, proline, isoleucine, and glutamine. These characteristics of the HD cell transcriptome and metabolome may be important conditions for maintaining a long-living phenotype.
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Affiliation(s)
- Young-Yon Kwon
- Institute of Animal Molecular Biotechnology and Korea University, Seoul, Republic of Korea
| | - Seung-Soo Kim
- Institute of Animal Molecular Biotechnology and Korea University, Seoul, Republic of Korea
| | - Han-Jun Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Seo-Hyeong Sheen
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Cheol-Koo Lee
- Institute of Animal Molecular Biotechnology and Korea University, Seoul, Republic of Korea.,Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
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9
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Povea-Cabello S, Villanueva-Paz M, Suárez-Rivero JM, Álvarez-Córdoba M, Villalón-García I, Talaverón-Rey M, Suárez-Carrillo A, Munuera-Cabeza M, Sánchez-Alcázar JA. Advances in mt-tRNA Mutation-Caused Mitochondrial Disease Modeling: Patients' Brain in a Dish. Front Genet 2021; 11:610764. [PMID: 33510772 PMCID: PMC7835939 DOI: 10.3389/fgene.2020.610764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/26/2020] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial diseases are a heterogeneous group of rare genetic disorders that can be caused by mutations in nuclear (nDNA) or mitochondrial DNA (mtDNA). Mutations in mtDNA are associated with several maternally inherited genetic diseases, with mitochondrial dysfunction as a main pathological feature. These diseases, although frequently multisystemic, mainly affect organs that require large amounts of energy such as the brain and the skeletal muscle. In contrast to the difficulty of obtaining neuronal and muscle cell models, the development of induced pluripotent stem cells (iPSCs) has shed light on the study of mitochondrial diseases. However, it is still a challenge to obtain an appropriate cellular model in order to find new therapeutic options for people suffering from these diseases. In this review, we deepen the knowledge in the current models for the most studied mt-tRNA mutation-caused mitochondrial diseases, MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) and MERRF (myoclonic epilepsy with ragged red fibers) syndromes, and their therapeutic management. In particular, we will discuss the development of a novel model for mitochondrial disease research that consists of induced neurons (iNs) generated by direct reprogramming of fibroblasts derived from patients suffering from MERRF syndrome. We hypothesize that iNs will be helpful for mitochondrial disease modeling, since they could mimic patient’s neuron pathophysiology and give us the opportunity to correct the alterations in one of the most affected cellular types in these disorders.
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Affiliation(s)
- Suleva Povea-Cabello
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - Marina Villanueva-Paz
- Instituto de Investigación Biomédica de Málaga, Departamento de Farmacología y Pediatría, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Juan M Suárez-Rivero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - Mónica Álvarez-Córdoba
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - Irene Villalón-García
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - Marta Talaverón-Rey
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - Alejandra Suárez-Carrillo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - Manuel Munuera-Cabeza
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
| | - José A Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, Seville, Spain
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10
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Cirigliano A, Amelina A, Biferali B, Macone A, Mozzetta C, Bianchi MM, Mori M, Botta B, Pick E, Negri R, Rinaldi T. Statins interfere with the attachment of S. cerevisiae mtDNA to the inner mitochondrial membrane. J Enzyme Inhib Med Chem 2020; 35:129-137. [PMID: 31694426 PMCID: PMC6844431 DOI: 10.1080/14756366.2019.1687461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/16/2022] Open
Abstract
The 3-hydroxy-3-methylglutaryl-CoA reductase, a key enzyme of the mevalonate pathway for the synthesis of cholesterol in mammals (ergosterol in fungi), is inhibited by statins, a class of cholesterol lowering drugs. Indeed, statins are in a wide medical use, yet statins treatment could induce side effects as hepatotoxicity and myopathy in patients. We used Saccharomyces cerevisiae as a model to investigate the effects of statins on mitochondria. We demonstrate that statins are active in S.cerevisiae by lowering the ergosterol content in cells and interfering with the attachment of mitochondrial DNA to the inner mitochondrial membrane. Experiments on murine myoblasts confirmed these results in mammals. We propose that the instability of mitochondrial DNA is an early indirect target of statins.
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Affiliation(s)
- Angela Cirigliano
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Antonia Amelina
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Beatrice Biferali
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Alberto Macone
- Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | - Chiara Mozzetta
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Michele Maria Bianchi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, Rome, Italy
| | - Elah Pick
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon, Israel
| | - Rodolfo Negri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- Institute of Molecular Biology and Pathology, CNR, Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Teresa Rinaldi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
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11
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Moosavi B, Zhu XL, Yang WC, Yang GF. Molecular pathogenesis of tumorigenesis caused by succinate dehydrogenase defect. Eur J Cell Biol 2020; 99:151057. [DOI: 10.1016/j.ejcb.2019.151057] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022] Open
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12
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Klucnika A, Ma H. Mapping and editing animal mitochondrial genomes: can we overcome the challenges? Philos Trans R Soc Lond B Biol Sci 2019; 375:20190187. [PMID: 31787046 DOI: 10.1098/rstb.2019.0187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The animal mitochondrial genome, although small, can have a big impact on health and disease. Non-pathogenic sequence variation among mitochondrial DNA (mtDNA) haplotypes influences traits including fertility, healthspan and lifespan, whereas pathogenic mutations are linked to incurable mitochondrial diseases and other complex conditions like ageing, diabetes, cancer and neurodegeneration. However, we know very little about how mtDNA genetic variation contributes to phenotypic differences. Infrequent recombination, the multicopy nature and nucleic acid-impenetrable membranes present significant challenges that hamper our ability to precisely map mtDNA variants responsible for traits, and to genetically modify mtDNA so that we can isolate specific mutants and characterize their biochemical and physiological consequences. Here, we summarize the past struggles and efforts in developing systems to map and edit mtDNA. We also assess the future of performing forward and reverse genetic studies on animal mitochondrial genomes. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Anna Klucnika
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Hansong Ma
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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13
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Malina C, Larsson C, Nielsen J. Yeast mitochondria: an overview of mitochondrial biology and the potential of mitochondrial systems biology. FEMS Yeast Res 2019; 18:4969682. [PMID: 29788060 DOI: 10.1093/femsyr/foy040] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 12/29/2022] Open
Abstract
Mitochondria are dynamic organelles of endosymbiotic origin that are essential components of eukaryal cells. They contain their own genetic machinery, have multicopy genomes and like their bacterial ancestors they consist of two membranes. However, the majority of the ancestral genome has been lost or transferred to the nuclear genome of the host, preserving only a core set of genes involved in oxidative phosphorylation. Mitochondria perform numerous biological tasks ranging from bioenergetics to production of protein co-factors, including heme and iron-sulfur clusters. Due to the importance of mitochondria in many cellular processes, mitochondrial dysfunction is implicated in a wide variety of human disorders. Much of our current knowledge on mitochondrial function and dysfunction comes from studies using Saccharomyces cerevisiae. This yeast has good fermenting capacity, rendering tolerance to mutations that inactivate oxidative phosphorylation and complete loss of mitochondrial DNA. Here, we review yeast mitochondrial metabolism and function with focus on S. cerevisiae and its contribution in understanding mitochondrial biology. We further review how systems biology studies, including mathematical modeling, has allowed gaining new insight into mitochondrial function, and argue that this approach may enable us to gain a holistic view on how mitochondrial function interacts with different cellular processes.
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Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Christer Larsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
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14
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Abstract
The budding yeast Saccharomyces cerevisiae (S. cerevisiae) has been a remarkable experimental model for the discovery of fundamental biological processes. The high degree of conservation of cellular and molecular processes between the budding yeast and higher eukaryotes has made it a valuable system for the investigation of the molecular mechanisms behind various types of devastating human pathologies. Genetic screens in yeast provided important insight into the toxic mechanisms associated with the accumulation of misfolded proteins. Thus, using yeast genetics and high-throughput screens, novel molecular targets with therapeutic potential have been identified. Here, we describe a yeast screen protocol for the identification of genetic modifiers of alpha-synuclein (aSyn) toxicity, thereby accelerating the identification of novel potential targets for intervention in Parkinson's disease (PD) and other synucleinopathies.
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Affiliation(s)
- Inês Caldeira Brás
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany
| | - Blagovesta Popova
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany.
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany.
- Max Planck Institute for Experimental Medicine, Goettingen, Germany.
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15
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Nolli C, Goffrini P, Lazzaretti M, Zanna C, Vitale R, Lodi T, Baruffini E. Validation of a MGM1/OPA1 chimeric gene for functional analysis in yeast of mutations associated with dominant optic atrophy. Mitochondrion 2015; 25:38-48. [PMID: 26455272 DOI: 10.1016/j.mito.2015.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/24/2015] [Accepted: 10/01/2015] [Indexed: 01/08/2023]
Abstract
Mutations in OPA1 are associated with DOA or DOA plus. Novel mutations in OPA1 are periodically identified, but often the causative effect of the mutation is not demonstrated. A chimeric protein containing the N-terminal region of Mgm1, the yeast orthologue of OPA1, and the C-terminal region of OPA1 was constructed. This chimeric construct can be exploited to evaluate the pathogenicity of most of the missense mutations in OPA1 as well as to determine whether the dominance of the mutation is due to haploinsufficiency or to gain of function.
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Affiliation(s)
- Cecilia Nolli
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Mirca Lazzaretti
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy; IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Via Altura 3, 40139 Bologna, Italy
| | - Rita Vitale
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Tiziana Lodi
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Enrico Baruffini
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy.
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16
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Tigano M, Ruotolo R, Dallabona C, Fontanesi F, Barrientos A, Donnini C, Ottonello S. Elongator-dependent modification of cytoplasmic tRNALysUUU is required for mitochondrial function under stress conditions. Nucleic Acids Res 2015; 43:8368-80. [PMID: 26240381 PMCID: PMC4787798 DOI: 10.1093/nar/gkv765] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 07/15/2015] [Indexed: 11/12/2022] Open
Abstract
To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae. We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3) and urmylation (e.g., NCS6) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNA(Lys) UUU as well by overexpression of genes (BCK1 and HFM1) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease.
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Affiliation(s)
- Marco Tigano
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Roberta Ruotolo
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | | | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Antoni Barrientos
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Claudia Donnini
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Simone Ottonello
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
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17
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Menezes R, Tenreiro S, Macedo D, Santos CN, Outeiro TF. From the baker to the bedside: yeast models of Parkinson's disease. MICROBIAL CELL 2015; 2:262-279. [PMID: 28357302 PMCID: PMC5349099 DOI: 10.15698/mic2015.08.219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The baker’s yeast Saccharomyces cerevisiae has been extensively explored for our understanding of fundamental cell biology processes highly conserved in the eukaryotic kingdom. In this context, they have proven invaluable in the study of complex mechanisms such as those involved in a variety of human disorders. Here, we first provide a brief historical perspective on the emergence of yeast as an experimental model and on how the field evolved to exploit the potential of the model for tackling the intricacies of various human diseases. In particular, we focus on existing yeast models of the molecular underpinnings of Parkinson’s disease (PD), focusing primarily on the central role of protein quality control systems. Finally, we compile and discuss the major discoveries derived from these studies, highlighting their far-reaching impact on the elucidation of PD-associated mechanisms as well as in the identification of candidate therapeutic targets and compounds with therapeutic potential.
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Affiliation(s)
- Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2781-901, Portugal. ; Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157 Oeiras, Universidade Nova de Lisboa, Portugal
| | - Sandra Tenreiro
- Instituto de Medicina Molecular, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal. ; CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 130, Lisboa 1169-056, Portugal
| | - Diana Macedo
- Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157 Oeiras, Universidade Nova de Lisboa, Portugal
| | - Cláudia N Santos
- Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras 2781-901, Portugal. ; Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157 Oeiras, Universidade Nova de Lisboa, Portugal
| | - Tiago F Outeiro
- Instituto de Fisiologia, Faculdade de Medicina da Universidade de Lisboa, Lisboa 1649-028, Portugal. ; CEDOC - Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Campo dos Mártires da Pátria, 130, Lisboa 1169-056, Portugal. ; Department of NeuroDegeneration and Restorative Research, University Medical Center Göttingen, Waldweg 33, Göttingen 37073, Germany
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18
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Ceccatelli Berti C, Dallabona C, Lazzaretti M, Dusi S, Tosi E, Tiranti V, Goffrini P. Modeling human Coenzyme A synthase mutation in yeast reveals altered mitochondrial function, lipid content and iron metabolism. MICROBIAL CELL 2015; 2:126-135. [PMID: 28357284 PMCID: PMC5348974 DOI: 10.15698/mic2015.04.196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in nuclear genes associated with defective coenzyme A biosynthesis have been identified as responsible for some forms of neurodegeneration with brain iron accumulation (NBIA), namely PKAN and CoPAN. PKAN are defined by mutations in PANK2, encoding the pantothenate kinase 2 enzyme, that account for about 50% of cases of NBIA, whereas mutations in CoA synthase COASY have been recently reported as the second inborn error of CoA synthesis leading to CoPAN. As reported previously, yeast cells expressing the pathogenic mutation exhibited a temperature-sensitive growth defect in the absence of pantothenate and a reduced CoA content. Additional characterization revealed decreased oxygen consumption, reduced activities of mitochondrial respiratory complexes, higher iron content, increased sensitivity to oxidative stress and reduced amount of lipid droplets, thus partially recapitulating the phenotypes found in patients and establishing yeast as a potential model to clarify the pathogenesis underlying PKAN and CoPAN diseases.
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Affiliation(s)
| | | | | | - Sabrina Dusi
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta", Milan, Italy
| | - Elena Tosi
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta", Milan, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma, Parma, Italy
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19
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Hartman JL, Stisher C, Outlaw DA, Guo J, Shah NA, Tian D, Santos SM, Rodgers JW, White RA. Yeast Phenomics: An Experimental Approach for Modeling Gene Interaction Networks that Buffer Disease. Genes (Basel) 2015; 6:24-45. [PMID: 25668739 PMCID: PMC4377832 DOI: 10.3390/genes6010024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/12/2015] [Indexed: 01/10/2023] Open
Abstract
The genome project increased appreciation of genetic complexity underlying disease phenotypes: many genes contribute each phenotype and each gene contributes multiple phenotypes. The aspiration of predicting common disease in individuals has evolved from seeking primary loci to marginal risk assignments based on many genes. Genetic interaction, defined as contributions to a phenotype that are dependent upon particular digenic allele combinations, could improve prediction of phenotype from complex genotype, but it is difficult to study in human populations. High throughput, systematic analysis of S. cerevisiae gene knockouts or knockdowns in the context of disease-relevant phenotypic perturbations provides a tractable experimental approach to derive gene interaction networks, in order to deduce by cross-species gene homology how phenotype is buffered against disease-risk genotypes. Yeast gene interaction network analysis to date has revealed biology more complex than previously imagined. This has motivated the development of more powerful yeast cell array phenotyping methods to globally model the role of gene interaction networks in modulating phenotypes (which we call yeast phenomic analysis). The article illustrates yeast phenomic technology, which is applied here to quantify gene X media interaction at higher resolution and supports use of a human-like media for future applications of yeast phenomics for modeling human disease.
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Affiliation(s)
- John L Hartman
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Chandler Stisher
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Darryl A Outlaw
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Jingyu Guo
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Najaf A Shah
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Dehua Tian
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Sean M Santos
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - John W Rodgers
- Department of Genetics, University of Alabama at Birmingham, 730 Hugh Kaul Human Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA.
| | - Richard A White
- Department of Statistics and Michael Smith Laboratories, University of British Columbia, 3182 Earth Sciences Building, 2207 Main Mall, Vancouver, BC V6T-1Z4, Canada.
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20
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Biolistic Transformation for Delivering DNA into the Mitochondria. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Ruan ZR, Fang ZP, Ye Q, Lei HY, Eriani G, Zhou XL, Wang ED. Identification of lethal mutations in yeast threonyl-tRNA synthetase revealing critical residues in its human homolog. J Biol Chem 2014; 290:1664-78. [PMID: 25416776 DOI: 10.1074/jbc.m114.599886] [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] [Indexed: 01/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knock-out strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS has a unique modular structure containing four structural domains and a eukaryote-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs.
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Affiliation(s)
- Zhi-Rong Ruan
- From the Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Zhi-Peng Fang
- From the Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Qing Ye
- From the Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Hui-Yan Lei
- From the Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, 67084 Strasbourg, France
| | - Xiao-Long Zhou
- From the Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China,
| | - En-Duo Wang
- From the Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China, the School of Life Science and Technology, ShanghaiTech University, 320 Yue Yang Road, Shanghai 200031, China, and
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22
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Fernandes JTS, Tenreiro S, Gameiro A, Chu V, Outeiro TF, Conde JP. Modulation of alpha-synuclein toxicity in yeast using a novel microfluidic-based gradient generator. LAB ON A CHIP 2014; 14:3949-3957. [PMID: 25167219 DOI: 10.1039/c4lc00756e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Parkinson's disease (PD) is a common age-associated neurodegenerative disorder. The protein α-synuclein (aSyn) is a key factor in PD both due to its association with familial and sporadic cases and because it is the main component of the pathological protein aggregates known as Lewy bodies. However, the precise cellular effects of aSyn aggregation are still elusive. Here, we developed an elastomeric microfluidic device equipped with a chemical gradient generator and 9 chambers containing cell traps to study aSyn production and aggregation in Saccharomyces cerevisiae. This study involved capturing single cells, exposing them to specific chemical environments and imaging the expression of aSyn by means of a GFP fusion (aSyn-GFP). Using a galactose (GAL) gradient we modulated aSyn expression and, surprisingly, by tracking the behavior of single cells, we found that the response of individual cells in a population to a given stimulus can differ widely. To study the combined effect of environmental factors and aSyn expression levels, we exposed cells to a gradient of FeCl3. We found a dramatic increase in the percentage of cells displaying aSyn inclusions from 27% to 96%. Finally, we studied the effects of ascorbic acid, an antioxidant, on aSyn aggregation and found a significant reduction in the percentage of cells bearing aSyn inclusions from 87% to 37%. In summary, the device developed here offers a powerful way of studying aSyn biology with single-cell resolution and high throughput using genetically modified yeast cells.
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Affiliation(s)
- João Tiago S Fernandes
- INESC Microsistemas e Nanotecnologias and IN - Institute of Nanoscience and Nanotechnology, R. Alves Redol, 9, 1000-029, Lisbon, Portugal
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23
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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.
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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
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24
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Pathological Mutations of the Mitochondrial Human Genome: the Instrumental Role of the Yeast S. cerevisiae. Diseases 2014. [DOI: 10.3390/diseases2010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Qian Y, Kachroo AH, Yellman CM, Marcotte EM, Johnson KA. Yeast cells expressing the human mitochondrial DNA polymerase reveal correlations between polymerase fidelity and human disease progression. J Biol Chem 2014; 289:5970-85. [PMID: 24398692 DOI: 10.1074/jbc.m113.526418] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in the human mitochondrial polymerase (polymerase-γ (Pol-γ)) are associated with various mitochondrial disorders, including mitochondrial DNA (mtDNA) depletion syndrome, Alpers syndrome, and progressive external opthamalplegia. To correlate biochemically quantifiable defects resulting from point mutations in Pol-γ with their physiological consequences, we created "humanized" yeast, replacing the yeast mtDNA polymerase (MIP1) with human Pol-γ. Despite differences in the replication and repair mechanism, we show that the human polymerase efficiently complements the yeast mip1 knockouts, suggesting common fundamental mechanisms of replication and conserved interactions between the human polymerase and other components of the replisome. We also examined the effects of four disease-related point mutations (S305R, H932Y, Y951N, and Y955C) and an exonuclease-deficient mutant (D198A/E200A). In haploid cells, each mutant results in rapid mtDNA depletion, increased mutation frequency, and mitochondrial dysfunction. Mutation frequencies measured in vivo equal those measured with purified enzyme in vitro. In heterozygous diploid cells, wild-type Pol-γ suppresses mutation-associated growth defects, but continuous growth eventually leads to aerobic respiration defects, reduced mtDNA content, and depolarized mitochondrial membranes. The severity of the Pol-γ mutant phenotype in heterozygous diploid humanized yeast correlates with the approximate age of disease onset and the severity of symptoms observed in humans.
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Affiliation(s)
- Yufeng Qian
- From the Institute for Cellular and Molecular Biology
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26
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Rackham O, Filipovska A. Supernumerary proteins of mitochondrial ribosomes. Biochim Biophys Acta Gen Subj 2013; 1840:1227-32. [PMID: 23958563 DOI: 10.1016/j.bbagen.2013.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 01/13/2023]
Abstract
BACKGROUND Messenger RNAs encoded by mitochondrial genomes are translated on mitochondrial ribosomes that have unique structure and protein composition compared to prokaryotic and cytoplasmic ribosomes. Mitochondrial ribosomes are a patchwork of core proteins that share homology with prokaryotic ribosomal proteins and new, supernumerary proteins that can be unique to different organisms. In mammals, there are specific supernumerary ribosomal proteins that are not present in other eukaryotes. SCOPE OF REVIEW Here we discuss the roles of supernumerary proteins in the regulation of mitochondrial gene expression and compare them among different eukaryotic systems. Furthermore, we consider if differences in the structure and organization of mitochondrial genomes may have contributed to the acquisition of mitochondrial ribosomal proteins with new functions. MAJOR CONCLUSIONS The distinct and diverse compositions of mitochondrial ribosomes illustrate the high evolutionary divergence found between mitochondrial genetic systems. GENERAL SIGNIFICANCE Elucidating the role of the organism-specific supernumerary proteins may provide a window into the regulation of mitochondrial gene expression through evolution in response to distinct evolutionary paths taken by mitochondria in different organisms. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.
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Affiliation(s)
- Oliver Rackham
- Western Australian Institute for Medical Research, Western Australia 6000, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Western Australian Institute for Medical Research, Western Australia 6000, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Western Australia 6009, Australia.
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27
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Tenreiro S, Munder MC, Alberti S, Outeiro TF. Harnessing the power of yeast to unravel the molecular basis of neurodegeneration. J Neurochem 2013; 127:438-52. [DOI: 10.1111/jnc.12271] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Sandra Tenreiro
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Lisboa Portugal
| | - Matthias C. Munder
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics; Dresden Germany
| | - Tiago F. Outeiro
- Instituto de Medicina Molecular; Faculdade de Medicina da Universidade de Lisboa; Lisboa Portugal
- Instituto de Fisiologia; Faculdade de Medicina da Universidade de Lisboa; Lisboa Portugal
- Department of NeuroDegeneration and Restorative Research; University Medizin Göttingen; Göttingen Germany
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28
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Garrido-Maraver J, Cordero MD, Moñino ID, Pereira-Arenas S, Lechuga-Vieco AV, Cotán D, De la Mata M, Oropesa-Ávila M, De Miguel M, Bautista Lorite J, Rivas Infante E, Alvarez-Dolado M, Navas P, Jackson S, Francisci S, Sánchez-Alcázar JA. Screening of effective pharmacological treatments for MELAS syndrome using yeasts, fibroblasts and cybrid models of the disease. Br J Pharmacol 2013; 167:1311-28. [PMID: 22747838 DOI: 10.1111/j.1476-5381.2012.02086.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND PURPOSE MELAS (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes) is a mitochondrial disease most usually caused by point mutations in tRNA genes encoded by mitochondrial DNA (mtDNA). Approximately 80% of cases of MELAS syndrome are associated with a m.3243A > G mutation in the MT-TL1 gene, which encodes the mitochondrial tRNALeu (UUR). Currently, no effective treatments are available for this chronic progressive disorder. Treatment strategies in MELAS and other mitochondrial diseases consist of several drugs that diminish the deleterious effects of the abnormal respiratory chain function, reduce the presence of toxic agents or correct deficiencies in essential cofactors. EXPERIMENTAL APPROACH We evaluated the effectiveness of some common pharmacological agents that have been utilized in the treatment of MELAS, in yeast, fibroblast and cybrid models of the disease. The yeast model harbouring the A14G mutation in the mitochondrial tRNALeu(UUR) gene, which is equivalent to the A3243G mutation in humans, was used in the initial screening. Next, the most effective drugs that were able to rescue the respiratory deficiency in MELAS yeast mutants were tested in fibroblasts and cybrid models of MELAS disease. KEY RESULTS According to our results, supplementation with riboflavin or coenzyme Q(10) effectively reversed the respiratory defect in MELAS yeast and improved the pathologic alterations in MELAS fibroblast and cybrid cell models. CONCLUSIONS AND IMPLICATIONS Our results indicate that cell models have great potential for screening and validating the effects of novel drug candidates for MELAS treatment and presumably also for other diseases with mitochondrial impairment.
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Affiliation(s)
- Juan Garrido-Maraver
- Centro Andaluz de Biología del Desarrollo (CABD) and Centro de Investigación Biomédica en Red: Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
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Panizza E, Ercolino T, Mori L, Rapizzi E, Castellano M, Opocher G, Ferrero I, Neumann HPH, Mannelli M, Goffrini P. Yeast model for evaluating the pathogenic significance of SDHB, SDHC and SDHD mutations in PHEO-PGL syndrome. Hum Mol Genet 2012; 22:804-15. [PMID: 23175444 DOI: 10.1093/hmg/dds487] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SDH genes, encoding succinate dehydrogenase, act as tumour suppressor genes, linking mitochondrial dysfunction with tumourigenesis. Heterozygous germline mutations in SDHA, SDHB, SDHC, SDHD and in the assembly factor encoding gene SDHAF2 have all been shown to predispose to heritable endocrine neoplasias such as pheochromocytomas (PHEO) and paragangliomas (PGLs) called 'PHEO-PGL syndrome'. SDH genes mutations, in addition to deletions or truncations which are most likely pathogenic, often include missense substitutions which can be of uncertain significance. Unclassified missense substitutions may be difficult to interpret unless the cause-effect link between mutation and the disease is established by functional and in silico studies or by the familial segregation with the phenotype. Using the yeast model, here, we report functional investigations on several missense SDH mutations found in patients affected by pheochromocytomas or paragangliomas. The aim of this study was to evaluate whether and to which extent the yeast model may be useful for establishing the pathological significance of missense SDH mutations in humans. The results of our study demonstrate that the yeast is a good functional model to validate the pathogenic significance of SDHB missense mutations while, for missense mutations in SDHC and SDHD genes, the model can be informative only when the variation involves a conserved residue in a conserved domain.
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Affiliation(s)
- Elena Panizza
- Department of Life Sciences, University of Parma, Parma 43124, Italy
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Eletsky A, Jeong MY, Kim H, Lee HW, Xiao R, Pagliarini DJ, Prestegard JH, Winge DR, Montelione GT, Szyperski T. Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1 binding site. Biochemistry 2012; 51:8475-7. [PMID: 23062074 PMCID: PMC3667956 DOI: 10.1021/bi301171u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The yeast mitochondrial protein Sdh5 is required for the covalent attachment of flavin adenine dinucleotide (FAD) to protein Sdh1, a subunit of the heterotetrameric enzyme succinate dehydrogenase. The NMR structure of Sdh5 represents the first eukaryotic structure of Pfam family PF03937 and reveals a conserved surface region, which likely represents a putative Sdh1-Sdh5 interaction interface. Point mutations in this region result in the loss of covalent flavinylation of Sdh1. Moreover, chemical shift perturbation measurements showed that Sdh5 does not bind FAD in vitro, indicating that it is not a simple cofactor transporter in vivo.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Mi-Young Jeong
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Hyung Kim
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey 08854, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - David J. Pagliarini
- Department of Biochemistry and the Mitochondrial Protein Partnership, The University of Wisconsin – Madison, Madison, Wisconsin 53562, United States
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Dennis R. Winge
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey 08854, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
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Callegari S, Gregory PA, Sykes MJ, Bellon J, Andrews S, McKinnon RA, de Barros Lopes MA. Polymorphisms in the mitochondrial ribosome recycling factor EF-G2mt/MEF2 compromise cell respiratory function and increase atorvastatin toxicity. PLoS Genet 2012; 8:e1002755. [PMID: 22719265 PMCID: PMC3375252 DOI: 10.1371/journal.pgen.1002755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 04/25/2012] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial translation, essential for synthesis of the electron transport chain complexes in the mitochondria, is governed by nuclear encoded genes. Polymorphisms within these genes are increasingly being implicated in disease and may also trigger adverse drug reactions. Statins, a class of HMG-CoA reductase inhibitors used to treat hypercholesterolemia, are among the most widely prescribed drugs in the world. However, a significant proportion of users suffer side effects of varying severity that commonly affect skeletal muscle. The mitochondria are one of the molecular targets of statins, and these drugs have been known to uncover otherwise silent mitochondrial mutations. Based on yeast genetic studies, we identify the mitochondrial translation factor MEF2 as a mediator of atorvastatin toxicity. The human ortholog of MEF2 is the Elongation Factor Gene (EF-G) 2, which has previously been shown to play a specific role in mitochondrial ribosome recycling. Using small interfering RNA (siRNA) silencing of expression in human cell lines, we demonstrate that the EF-G2mt gene is required for cell growth on galactose medium, signifying an essential role for this gene in aerobic respiration. Furthermore, EF-G2mt silenced cell lines have increased susceptibility to cell death in the presence of atorvastatin. Using yeast as a model, conserved amino acid variants, which arise from non-synonymous single nucleotide polymorphisms (SNPs) in the EF-G2mt gene, were generated in the yeast MEF2 gene. Although these mutations do not produce an obvious growth phenotype, three mutations reveal an atorvastatin-sensitive phenotype and further analysis uncovers a decreased respiratory capacity. These findings constitute the first reported phenotype associated with SNPs in the EF-G2mt gene and implicate the human EF-G2mt gene as a pharmacogenetic candidate gene for statin toxicity in humans. The mitochondria are responsible for producing the cell's energy. Energy production is the result of carefully orchestrated interactions between proteins encoded by the mitochondrial DNA and by nuclear DNA. Sequence variations in genes encoding these proteins have been shown to cause disease and adverse drug reactions in patients. The cholesterol-lowering drugs statins are one class of drugs that interfere with mitochondrial function. Statins are one of the most prescribed drugs in the western world, but many users suffer side effects, commonly muscle pain. In severe cases this can lead to muscle breakdown and liver failure. In this study, we discover that disruption of a mitochondrial translation gene, EF-G2mt, impedes respiration and increases cell death when exposed to statin. Using the simple unicellular organism yeast as a model, the activity of naturally occurring human EF-G2mt variants is tested. Three of these variants render yeast cells more sensitive to statin. Patients who possess these EF-G2mt variations may be more susceptible to statin side effects. Importantly, the test for statin sensitivity also led to the discovery of mutants that have a reduced energy production capacity. The decreased ability to produce energy is linked to a number of diseases, including myopathies and liver failure.
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Affiliation(s)
- Sylvie Callegari
- School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Philip A. Gregory
- Division of Human Immunology, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
- Discipline of Medicine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew J. Sykes
- School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Sansom Institute, Division of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Jennifer Bellon
- Australian Wine Research Institute, Glen Osmond, South Australia, Australia
| | - Stuart Andrews
- School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Ross A. McKinnon
- Flinders Centre for Innovation in Cancer, School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Miguel A. de Barros Lopes
- School of Pharmacy and Medical Sciences, Division of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- * E-mail:
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Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 2011; 40:D700-5. [PMID: 22110037 PMCID: PMC3245034 DOI: 10.1093/nar/gkr1029] [Citation(s) in RCA: 1271] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use.
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Affiliation(s)
- J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
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Faure E, Delaye L, Tribolo S, Levasseur A, Seligmann H, Barthélémy RM. Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene. Biol Direct 2011; 6:56. [PMID: 22024028 PMCID: PMC3214167 DOI: 10.1186/1745-6150-6-56] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 10/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as mitochondrial DNA (mtDNA). Despite a disparity in gene content, all mtDNAs encode at least two components of the mitochondrial electron transport chain, including cytochrome c oxidase I (Cox1). PRESENTATION OF THE HYPOTHESIS A positionally conserved ORF has been found on the complementary strand of the cox1 genes of both eukaryotic mitochondria (protist, plant, fungal and animal) and alpha-proteobacteria. This putative gene has been named gau for gene antisense ubiquitous in mtDNAs. The length of the deduced protein is approximately 100 amino acids. In vertebrates, several stop codons have been found in the mt gau region, and potentially functional gau regions have been found in nuclear genomes. However, a recent bioinformatics study showed that several hypothetical overlapping mt genes could be predicted, including gau; this involves the possible import of the cytosolic AGR tRNA into the mitochondria and/or the expression of mt antisense tRNAs with anticodons recognizing AGR codons according to an alternative genetic code that is induced by the presence of suppressor tRNAs. Despite an evolutionary distance of at least 1.5 to 2.0 billion years, the deduced Gau proteins share some conserved amino acid signatures and structure, which suggests a possible conserved function. Moreover, BLAST analysis identified rare, sense-oriented ESTs with poly(A) tails that include the entire gau region. Immunohistochemical analyses using an anti-Gau monoclonal antibody revealed strict co-localization of Gau proteins and a mitochondrial marker. TESTING THE HYPOTHESIS This hypothesis could be tested by purifying the gau gene product and determining its sequence. Cell biological experiments are needed to determine the physiological role of this protein. IMPLICATIONS OF THE HYPOTHESIS Studies of the gau ORF will shed light on the origin of novel genes and their functions in organelles and could also have medical implications for human diseases that are caused by mitochondrial dysfunction. Moreover, this strengthens evidence for mitochondrial genes coded according to an overlapping genetic code.
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Affiliation(s)
- Eric Faure
- Université de Provence, Marseille cedex 3, France.
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