1
|
Ni J, Huang S, Yang W, Chen Q, Lin Z. Electrochemiluminescence Detecting and Imaging of Yeast Metabolism Indicated by Endogenetic Co-reactant. Anal Chem 2024. [PMID: 39700391 DOI: 10.1021/acs.analchem.4c05663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Glycolysis, a pivotal step in yeast metabolism, plays an indispensable role as a carbohydrate utilization process crucial for cellular survival. Developing advanced technologies to elucidate this fundamental physiological process holds significant scientific implications. Electrochemiluminescence (ECL) imaging exhibits the advantage of negligible background interference and facilitates straightforward visualization, thereby conferring significant value in biomolecular observation. In this study, we present an ECL imaging method for investigating yeast metabolism by utilizing the endogenetic NADH as an efficient coreactant for ECL generation. The yeast glycolysis process drives the conversion of NAD+ to NADH, resulting in enhanced ECL response as well as the increased brightness of ECL images that can be used for quantification of yeast activity. There was a linear correlation between the reciprocal of both the gray value of ECL image and yeast concentration within the range of 6.25 × 106 - 6.25 × 108 CFU/mL. Due to the highly efficient coreactant behavior of NADH, our method demonstrated excellent selectivity with minimal interference. Furthermore, we employed this approach to investigate some toxic inhibitors on yeast metabolism, yielding reliable results. This ECL imaging method not only avoids the use of additional coreactants but also provides a sensitive and intuitive approach for monitoring yeast metabolism, demonstrating great potential in revealing various complex biological processes.
Collapse
Affiliation(s)
- Jiancong Ni
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, College of Chemistry, Chemical Engineering and Environment, Minnan Normal University, Zhangzhou 363000, China
| | - Shengxiu Huang
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, College of Chemistry, Chemical Engineering and Environment, Minnan Normal University, Zhangzhou 363000, China
| | - Weiqiang Yang
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, College of Chemistry, Chemical Engineering and Environment, Minnan Normal University, Zhangzhou 363000, China
| | - Qiaoling Chen
- Fujian Provincial Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, College of Chemistry, Chemical Engineering and Environment, Minnan Normal University, Zhangzhou 363000, China
| | - Zhenyu Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China
| |
Collapse
|
2
|
Figuccia S, Izzo R, Legati A, Nasca A, Goffrini P, Ghezzi D, Ceccatelli Berti C. Investigation in yeast of novel variants in mitochondrial aminoacyl-tRNA synthetases WARS2, NARS2, and RARS2 genes associated with mitochondrial diseases. Hum Mol Genet 2024; 33:1630-1641. [PMID: 39230874 DOI: 10.1093/hmg/ddae104] [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: 02/26/2024] [Revised: 06/13/2024] [Indexed: 09/05/2024] Open
Abstract
Aminoacyl-transfer RiboNucleic Acid synthetases (ARSs) are essential enzymes that catalyze the attachment of each amino acid to their cognate tRNAs. Mitochondrial ARSs (mtARSs), which ensure protein synthesis within the mitochondria, are encoded by nuclear genes and imported into the organelle after translation in the cytosol. The extensive use of next generation sequencing (NGS) has resulted in an increasing number of variants in mtARS genes being identified and associated with mitochondrial diseases. The similarities between yeast and human mitochondrial translation machineries make yeast a good model to quickly and efficiently evaluate the effect of variants in mtARS genes. Genetic screening of patients with a clinical suspicion of mitochondrial disorders through a customized gene panel of known disease-genes, including all genes encoding mtARSs, led to the identification of missense variants in WARS2, NARS2 and RARS2. Most of them were classified as Variant of Uncertain Significance. We exploited yeast models to assess the functional consequences of the variants found in these genes encoding mitochondrial tryptophanyl-tRNA, asparaginyl-tRNA, and arginyl-tRNA synthetases, respectively. Mitochondrial phenotypes such as oxidative growth, oxygen consumption rate, Cox2 steady-state level and mitochondrial protein synthesis were analyzed in yeast strains deleted in MSW1, SLM5, and MSR1 (the yeast orthologues of WARS2, NARS2 and RARS2, respectively), and expressing the wild type or the mutant alleles. Pathogenicity was confirmed for most variants, leading to their reclassification as Likely Pathogenic. Moreover, the beneficial effects observed after asparagine and arginine supplementation in the growth medium suggest them as a potential therapeutic approach.
Collapse
Affiliation(s)
- Sonia Figuccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, Parma 43124, Italy
| | - Rossella Izzo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Temolo 4, Milan 20126, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Temolo 4, Milan 20126, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Temolo 4, Milan 20126, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, Parma 43124, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, via Temolo 4, Milan 20126, Italy
- Department of Pathophysiology and Transplantation, University of Milan, via F. Sforza 35, Milan 20122, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, Parma 43124, Italy
| |
Collapse
|
3
|
Di Nottia M, Rizza T, Baruffini E, Nesti C, Torraco A, Diodato D, Martinelli D, Dal Canto F, Gilea AI, Zoccola M, Siri B, Dionisi-Vici C, Bertini E, Santorelli FM, Goffrini P, Carrozzo R. Severe mitochondrial encephalomyopathy caused by de novo variants in OPA1 gene. Front Genet 2024; 15:1437959. [PMID: 39233737 PMCID: PMC11372846 DOI: 10.3389/fgene.2024.1437959] [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: 05/24/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024] Open
Abstract
Background Mitochondria adjust their shape in response to the different energetic and metabolic requirements of the cell, through extremely dynamic fusion and fission events. Several highly conserved dynamin-like GTPases are involved in these processes and, among those, the OPA1 protein is a key player in the fusion of inner mitochondrial membranes. Hundreds of monoallelic or biallelic pathogenic gene variants have been described in OPA1, all associated with a plethora of clinical phenotypes without a straightforward genotype-phenotype correlation. Methods Here we report two patients harboring novel de novo variants in OPA1. DNA of two patients was analyzed using NGS technology and the pathogenicity has been evaluated through biochemical and morphological studies in patient's derived fibroblasts and in yeast model. Results The two patients here reported manifest with neurological signs resembling Leigh syndrome, thus further expanding the clinical spectrum associated with variants in OPA1. In cultured skin fibroblasts we observed a reduced amount of mitochondrial DNA (mtDNA) and altered mitochondrial network characterized by more fragmented mitochondria. Modeling in yeast allowed to define the deleterious mechanism and the pathogenicity of the identified gene mutations. Conclusion We have described two novel-single OPA1 mutations in two patients characterized by early-onset neurological signs, never documented, thus expanding the clinical spectrum of this complex syndrome. Moreover, both yeast model and patients derived fibroblasts showed mitochondrial defects, including decreased mtDNA maintenance, correlating with patients' clinical phenotypes.
Collapse
Affiliation(s)
- Michela Di Nottia
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Neuromuscular Disorders Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Teresa Rizza
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Claudia Nesti
- Molecular Medicine, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Alessandra Torraco
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daria Diodato
- Neuromuscular Disorders Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Diego Martinelli
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | | | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Martina Zoccola
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Neuromuscular Disorders Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Barbara Siri
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Carlo Dionisi-Vici
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Enrico Bertini
- Neuromuscular Disorders Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosalba Carrozzo
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| |
Collapse
|
4
|
Jiang T, Hou L, Rahman SM, Gong Z, Bai X, Vulpe C, Fasullo M, Gu AZ. Amplified and distinctive genotoxicity of titanium dioxide nanoparticles in transformed yeast reporters with human cytochrome P450 (CYP) genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134850. [PMID: 38850947 DOI: 10.1016/j.jhazmat.2024.134850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024]
Abstract
Titanium dioxide nanoparticles (nTiO2) have been considered a possible carcinogen to humans, but most existing studies have overlooked the role of human enzymes in assessing the genotoxicity of nTiO2. Here, a toxicogenomics-based in vitro genotoxicity assay using a GFP-fused yeast reporter library was employed to elucidate the genotoxic potential and mechanisms of nTiO2. Moreover, two new GFP-fused yeast reporter libraries containing either human CYP1A1 or CYP1A2 genes were constructed by transformation to investigate the potential modulation of nTiO2 genotoxicity in the presence of human CYP enzymes. This study found a lack of appreciable nTiO2 genotoxicity as indicated by the yeast reporter library in the absence of CYP expression but a significantly elevated indication of genotoxicity in either CYP1A1- or CYP1A2-expressing yeast. The intracellular reactive oxygen species (ROS) measurement indicated significantly higher ROS in yeast expressing either enzyme. The detected mitochondrial DNA damage suggested mitochondria as one of the target sites for oxidative damage by nTiO2 in the presence of either one of the CYP enzymes. The results thus indicated that the genotoxicity of nTiO2 was enhanced by human CYP1A1 or CYP1A2 enzyme and was associated with elevated oxidative stress, which suggested that the similar mechanisms could occur in human cells.
Collapse
Affiliation(s)
- Tao Jiang
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA; Department of Environmental and Sustainable Engineering, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Liyuan Hou
- Department of Civil and Environmental Engineering, Utah State University, Logan, UT 84322, USA; Utah Water Research Laboratory, Utah State University, Logan, UT 84322, USA
| | - Sheikh Mokhlesur Rahman
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, USA; Department of Civil Engineering, Bangladesh University of Engineering and Technology, BUET Central Road, Dhaka 1000, Bangladesh
| | - Zixuan Gong
- Department of Materials, Imperial College London, London LND SW7 2AZ, UK
| | - Xueke Bai
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, UK
| | - Christopher Vulpe
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA
| | - Michael Fasullo
- Department of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY 12222, USA
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
5
|
Rzepnikowska W, Kaminska J, Kochański A. The molecular mechanisms that underlie IGHMBP2-related diseases. Neuropathol Appl Neurobiol 2024; 50:e13005. [PMID: 39119929 DOI: 10.1111/nan.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 08/10/2024]
Abstract
Immunoglobulin Mu-binding protein 2 (IGHMBP2) pathogenic variants result in the fatal, neurodegenerative disease spinal muscular atrophy with respiratory distress type 1 (SMARD1) and the milder, Charcot-Marie-Tooth (CMT) type 2S (CMT2S) neuropathy. More than 20 years after the link between IGHMBP2 and SMARD1 was revealed, and 10 years after the discovery of the association between IGHMBP2 and CMT2S, the pathogenic mechanism of these diseases is still not well defined. The discovery that IGHMBP2 functions as an RNA/DNA helicase was an important step, but it did not reveal the pathogenic mechanism. Helicases are enzymes that use ATP hydrolysis to catalyse the separation of nucleic acid strands. They are involved in numerous cellular processes, including DNA repair and transcription; RNA splicing, transport, editing and degradation; ribosome biogenesis; translation; telomere maintenance; and homologous recombination. IGHMBP2 appears to be a multifunctional factor involved in several cellular processes that regulate gene expression. It is difficult to determine which processes, when dysregulated, lead to pathology. Here, we summarise our current knowledge of the clinical presentation of IGHMBP2-related diseases. We also overview the available models, including yeast, mice and cells, which are used to study the function of IGHMBP2 and the pathogenesis of the related diseases. Further, we discuss the structure of the IGHMBP2 protein and its postulated roles in cellular functioning. Finally, we present potential anomalies that may result in the neurodegeneration observed in IGHMBP2-related disease and highlight the most prominent ones.
Collapse
Affiliation(s)
- Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, 02-106, Poland
| |
Collapse
|
6
|
Gouiza I, Hechmi M, Zioudi A, Dallali H, Kheriji N, Charif M, Le Mao M, Galai S, Kraoua L, Ben Youssef-Turki I, Kraoua I, Lenaers G, Kefi R. Expanding the genetic spectrum of mitochondrial diseases in Tunisia: novel variants revealed by whole-exome sequencing. Front Genet 2024; 14:1259826. [PMID: 38283147 PMCID: PMC10811255 DOI: 10.3389/fgene.2023.1259826] [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: 07/16/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024] Open
Abstract
Introduction: Inherited mitochondrial diseases are the most common group of metabolic disorders caused by a defect in oxidative phosphorylation. They are characterized by a wide clinical and genetic spectrum and can manifest at any age. In this study, we established novel phenotype-genotype correlations between the clinical and molecular features of a cohort of Tunisian patients with mitochondrial diseases. Materials and methods: Whole-exome sequencing was performed on five Tunisian patients with suspected mitochondrial diseases. Then, a combination of filtering and bioinformatics prediction tools was utilized to assess the pathogenicity of genetic variations. Sanger sequencing was subsequently performed to confirm the presence of potential deleterious variants in the patients and verify their segregation within families. Structural modeling was conducted to study the effect of novel variants on the protein structure. Results: We identified two novel homozygous variants in NDUFAF5 (c.827G>C; p.Arg276Pro) and FASTKD2 (c.496_497del; p.Leu166GlufsTer2) associated with a severe clinical form of Leigh and Leigh-like syndromes, respectively. Our results further disclosed two variants unreported in North Africa, in GFM2 (c.569G>A; p.Arg190Gln) and FOXRED1 (c.1261G>A; p.Val421Met) genes, and we described the first case of fumaric aciduria in a Tunisian patient harboring the c.1358T>C; p.Leu453Pro FH variant. Conclusion: Our study expands the mutational and phenotypic spectrum of mitochondrial diseases in Tunisia and highlights the importance of next-generation sequencing to decipher the pathomolecular mechanisms responsible for these disorders in an admixed population.
Collapse
Affiliation(s)
- Ismail Gouiza
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS (Unité mixte de recherche Centre national de la recherche scientifique) 6015 INSERM (Institut national de la santé et de la recherche médicale) U1083, SFR ICAT, University of Angers, Angers, France
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Abir Zioudi
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Research Laboratory LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| | - Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Majida Charif
- Genetics and Immuno-Cell Therapy Team, Mohammed First University, Oujda, Morocco
| | - Morgane Le Mao
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS (Unité mixte de recherche Centre national de la recherche scientifique) 6015 INSERM (Institut national de la santé et de la recherche médicale) U1083, SFR ICAT, University of Angers, Angers, France
| | - Said Galai
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Department of Clinical Biology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Lilia Kraoua
- Tunis El Manar University, Tunis, Tunisia
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ilhem Ben Youssef-Turki
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Research Laboratory LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Ichraf Kraoua
- Tunis El Manar University, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Research Laboratory LR18SP04, Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, Tunis, Tunisia
| | - Guy Lenaers
- University of Angers, MitoLab Team, Unité MitoVasc, UMR CNRS (Unité mixte de recherche Centre national de la recherche scientifique) 6015 INSERM (Institut national de la santé et de la recherche médicale) U1083, SFR ICAT, University of Angers, Angers, France
- Department of Neurology, CHU d’Angers, Angers, France
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- Tunis El Manar University, Tunis, Tunisia
| |
Collapse
|
7
|
Gilea AI, Magistrati M, Notaroberto I, Tiso N, Dallabona C, Baruffini E. The Saccharomyces cerevisiae mitochondrial DNA polymerase and its contribution to the knowledge about human POLG-related disorders. IUBMB Life 2023; 75:983-1002. [PMID: 37470284 DOI: 10.1002/iub.2770] [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: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
Most eukaryotes possess a mitochondrial genome, called mtDNA. In animals and fungi, the replication of mtDNA is entrusted by the DNA polymerase γ, or Pol γ. The yeast Pol γ is composed only of a catalytic subunit encoded by MIP1. In humans, Pol γ is a heterotrimer composed of a catalytic subunit homolog to Mip1, encoded by POLG, and two accessory subunits. In the last 25 years, more than 300 pathological mutations in POLG have been identified as the cause of several mitochondrial diseases, called POLG-related disorders, which are characterized by multiple mtDNA deletions and/or depletion in affected tissues. In this review, at first, we summarize the biochemical properties of yeast Mip1, and how mutations, especially those introduced recently in the N-terminal and C-terminal regions of the enzyme, affect the in vitro activity of the enzyme and the in vivo phenotype connected to the mtDNA stability and to the mtDNA extended and point mutability. Then, we focus on the use of yeast harboring Mip1 mutations equivalent to the human ones to confirm their pathogenicity, identify the phenotypic defects caused by these mutations, and find both mechanisms and molecular compounds able to rescue the detrimental phenotype. A closing chapter will be dedicated to other polymerases found in yeast mitochondria, namely Pol ζ, Rev1 and Pol η, and to their genetic interactions with Mip1 necessary to maintain mtDNA stability and to avoid the accumulation of spontaneous or induced point mutations.
Collapse
Affiliation(s)
- Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Ilenia Notaroberto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padova, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| |
Collapse
|
8
|
Lewis GR, Marshall WF. Mitochondrial networks through the lens of mathematics. Phys Biol 2023; 20:051001. [PMID: 37290456 PMCID: PMC10347554 DOI: 10.1088/1478-3975/acdcdb] [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: 12/09/2022] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/10/2023]
Abstract
Mitochondria serve a wide range of functions within cells, most notably via their production of ATP. Although their morphology is commonly described as bean-like, mitochondria often form interconnected networks within cells that exhibit dynamic restructuring through a variety of physical changes. Further, though relationships between form and function in biology are well established, the extant toolkit for understanding mitochondrial morphology is limited. Here, we emphasize new and established methods for quantitatively describing mitochondrial networks, ranging from unweighted graph-theoretic representations to multi-scale approaches from applied topology, in particular persistent homology. We also show fundamental relationships between mitochondrial networks, mathematics, and physics, using ideas of graph planarity and statistical mechanics to better understand the full possible morphological space of mitochondrial network structures. Lastly, we provide suggestions for how examination of mitochondrial network form through the language of mathematics can inform biological understanding, and vice versa.
Collapse
Affiliation(s)
- Greyson R Lewis
- Biophysics Graduate Program, University of California—San Francisco, San Francisco, CA, United States of America
- NSF Center for Cellular Construction, Department of Biochemistry and Biophysics, UCSF, 600 16th St., San Francisco, CA, United States of America
- Department of Biochemistry and Biophysics, Center for Cellular Construction, University of California San Francisco, San Francisco, CA, United States of America
| | - Wallace F Marshall
- NSF Center for Cellular Construction, Department of Biochemistry and Biophysics, UCSF, 600 16th St., San Francisco, CA, United States of America
- Department of Biochemistry and Biophysics, Center for Cellular Construction, University of California San Francisco, San Francisco, CA, United States of America
| |
Collapse
|
9
|
Magistrati M, Gilea AI, Gerra MC, Baruffini E, Dallabona C. Drug Drop Test: How to Quickly Identify Potential Therapeutic Compounds for Mitochondrial Diseases Using Yeast Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:10696. [PMID: 37445873 DOI: 10.3390/ijms241310696] [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: 05/30/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Mitochondrial diseases (MDs) refer to a group of clinically and genetically heterogeneous pathologies characterized by defective mitochondrial function and energy production. Unfortunately, there is no effective treatment for most MDs, and current therapeutic management is limited to relieving symptoms. The yeast Saccharomyces cerevisiae has been efficiently used as a model organism to study mitochondria-related disorders thanks to its easy manipulation and well-known mitochondrial biogenesis and metabolism. It has been successfully exploited both to validate alleged pathogenic variants identified in patients and to discover potential beneficial molecules for their treatment. The so-called "drug drop test", a phenotype-based high-throughput screening, especially if coupled with a drug repurposing approach, allows the identification of molecules with high translational potential in a cost-effective and time-saving manner. In addition to drug identification, S. cerevisiae can be used to point out the drug's target or pathway. To date, drug drop tests have been successfully carried out for a variety of disease models, leading to very promising results. The most relevant aspect is that studies on more complex model organisms confirmed the effectiveness of the drugs, strengthening the results obtained in yeast and demonstrating the usefulness of this screening as a novel approach to revealing new therapeutic molecules for MDs.
Collapse
Affiliation(s)
- Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Maria Carla Gerra
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| |
Collapse
|
10
|
Cavestro C, Diodato D, Tiranti V, Di Meo I. Inherited Disorders of Coenzyme A Biosynthesis: Models, Mechanisms, and Treatments. Int J Mol Sci 2023; 24:ijms24065951. [PMID: 36983025 PMCID: PMC10054636 DOI: 10.3390/ijms24065951] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Coenzyme A (CoA) is a vital and ubiquitous cofactor required in a vast number of enzymatic reactions and cellular processes. To date, four rare human inborn errors of CoA biosynthesis have been described. These disorders have distinct symptoms, although all stem from variants in genes that encode enzymes involved in the same metabolic process. The first and last enzymes catalyzing the CoA biosynthetic pathway are associated with two neurological conditions, namely pantothenate kinase-associated neurodegeneration (PKAN) and COASY protein-associated neurodegeneration (CoPAN), which belong to the heterogeneous group of neurodegenerations with brain iron accumulation (NBIA), while the second and third enzymes are linked to a rapidly fatal dilated cardiomyopathy. There is still limited information about the pathogenesis of these diseases, and the knowledge gaps need to be resolved in order to develop potential therapeutic approaches. This review aims to provide a summary of CoA metabolism and functions, and a comprehensive overview of what is currently known about disorders associated with its biosynthesis, including available preclinical models, proposed pathomechanisms, and potential therapeutic approaches.
Collapse
Affiliation(s)
- Chiara Cavestro
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Daria Diodato
- Unit of Muscular and Neurodegenerative Disorders, Ospedale Pediatrico Bambino Gesù, 00165 Rome, Italy
| | - Valeria Tiranti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Ivano Di Meo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Rzepnikowska W, Kaminska J, Kochański A. Validation of the Pathogenic Effect of IGHMBP2 Gene Mutations Based on Yeast S. cerevisiae Model. Int J Mol Sci 2022; 23:ijms23179913. [PMID: 36077311 PMCID: PMC9456350 DOI: 10.3390/ijms23179913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/28/2022] [Accepted: 08/29/2022] [Indexed: 11/29/2022] Open
Abstract
Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a heritable neurodegenerative disease characterized by rapid respiratory failure within the first months of life and progressive muscle weakness and wasting. Although the causative gene, IGHMBP2, is well defined, information on IGHMBP2 mutations is not always sufficient to diagnose particular patients, as the gene is highly polymorphic and the pathogenicity of many gene variants is unknown. In this study, we generated a simple yeast model to establish the significance of IGHMBP2 variants for disease development, especially those that are missense mutations. We have shown that cDNA of the human gene encodes protein which is functional in yeast cells and different pathogenic mutations affect this functionality. Furthermore, there is a correlation between the phenotype estimated in in vitro studies and our results, indicating that our model may be used to quickly and simply distinguish between pathogenic and non-pathogenic mutations identified in IGHMBP2 in patients.
Collapse
Affiliation(s)
- Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
- Correspondence:
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| |
Collapse
|
13
|
Wongkittichote P, Magistrati M, Shimony JS, Smyser CD, Fatemi SA, Fine AS, Bellacchio E, Dallabona C, Shinawi M. Functional analysis of missense DARS2 variants in siblings with leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation. Mol Genet Metab 2022; 136:260-267. [PMID: 35820270 DOI: 10.1016/j.ymgme.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022]
Abstract
Biallelic pathogenic variants in the nuclear gene DARS2 (MIM# 610956), encoding the mitochondrial enzyme aspartyl-tRNA synthetase (MT-ASPRS) cause leukoencephalopathy with Brain Stem and Spinal Cord Involvement and Lactate Elevation (LBSL) (MIM# 611105), a neurometabolic disorder characterized by progressive ataxia, spasticity, developmental arrest or regression and characteristic brain MRI findings. Most patients exhibit a slowly progressive disease course with motor deterirartion that begins in childhood or adolescence, but can also occasionaly occur in adulthood. More severe LBSL presentations with atypical brain MRI findings have been recently described. Baker's yeast orthologue of DARS2, MSD1, is required for growth on oxidative carbon sources. A yeast with MSD1 knockout (msd1Δ) demonstrated a complete lack of oxidative growth which could be rescued by wild-type MSD1 but not MSD1 with pathogenic variants. Here we reported two siblings who exhibited developmental regression and ataxia with different age of onset and phenotypic severity. Exome sequencing revealed 2 compound heterozygous missense variants in DARS2: c.473A>T (p.Glu158Val) and c.829G>A (p.Glu277Lys); this variant combination has not been previously reported. The msd1Δ yeast transformed with plasmids expressing p.Glu259Lys, equivalent to human p.Glu277Lys, showed complete loss of oxidative growth and oxygen consumption, while the strain carrying p.Gln137Val, equivalent to human p.Glu158Val, showed a significant reduction of oxidative growth, but a residual ability to grow was retained. Structural analysis indicated that p.Glu158Val may interfere with protein binding of tRNAAsp, while p.Glu277Lys may impact both homodimerization and catalysis of MT-ASPRS. Our data illustrate the utility of yeast model and in silico analysis to determine pathogenicity of DARS2 variants, expand the genotypic spectrum and suggest intrafamilial variability in LBSL.
Collapse
Affiliation(s)
- Parith Wongkittichote
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Joshua S Shimony
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Christopher D Smyser
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA; Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Seyed Ali Fatemi
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Amena S Fine
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
14
|
Kaminska J, Soczewka P, Rzepnikowska W, Zoladek T. Yeast as a Model to Find New Drugs and Drug Targets for VPS13-Dependent Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23095106. [PMID: 35563497 PMCID: PMC9104724 DOI: 10.3390/ijms23095106] [Citation(s) in RCA: 6] [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: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 12/10/2022] Open
Abstract
Mutations in human VPS13A-D genes result in rare neurological diseases, including chorea-acanthocytosis. The pathogenesis of these diseases is poorly understood, and no effective treatment is available. As VPS13 genes are evolutionarily conserved, the effects of the pathogenic mutations could be studied in model organisms, including yeast, where one VPS13 gene is present. In this review, we summarize advancements obtained using yeast. In recent studies, vps13Δ and vps13-I2749 yeast mutants, which are models of chorea-acanthocytosis, were used to screen for multicopy and chemical suppressors. Two of the suppressors, a fragment of the MYO3 and RCN2 genes, act by downregulating calcineurin activity. In addition, vps13Δ suppression was achieved by using calcineurin inhibitors. The other group of multicopy suppressors were genes: FET4, encoding iron transporter, and CTR1, CTR3 and CCC2, encoding copper transporters. Mechanisms of their suppression rely on causing an increase in the intracellular iron content. Moreover, among the identified chemical suppressors were copper ionophores, which require a functional iron uptake system for activity, and flavonoids, which bind iron. These findings point at areas for further investigation in a higher eukaryotic model of VPS13-related diseases and to new therapeutic targets: calcium signalling and copper and iron homeostasis. Furthermore, the identified drugs are interesting candidates for drug repurposing for these diseases.
Collapse
Affiliation(s)
- Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Piotr Soczewka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
| | - Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland; (J.K.); (P.S.)
- Correspondence:
| |
Collapse
|
15
|
Saccharomyces cerevisiae as a Tool for Studying Mutations in Nuclear Genes Involved in Diseases Caused by Mitochondrial DNA Instability. Genes (Basel) 2021; 12:genes12121866. [PMID: 34946817 PMCID: PMC8701800 DOI: 10.3390/genes12121866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial DNA (mtDNA) maintenance is critical for oxidative phosphorylation (OXPHOS) since some subunits of the respiratory chain complexes are mitochondrially encoded. Pathological mutations in nuclear genes involved in the mtDNA metabolism may result in a quantitative decrease in mtDNA levels, referred to as mtDNA depletion, or in qualitative defects in mtDNA, especially in multiple deletions. Since, in the last decade, most of the novel mutations have been identified through whole-exome sequencing, it is crucial to confirm the pathogenicity by functional analysis in the appropriate model systems. Among these, the yeast Saccharomyces cerevisiae has proved to be a good model for studying mutations associated with mtDNA instability. This review focuses on the use of yeast for evaluating the pathogenicity of mutations in six genes, MPV17/SYM1, MRM2/MRM2, OPA1/MGM1, POLG/MIP1, RRM2B/RNR2, and SLC25A4/AAC2, all associated with mtDNA depletion or multiple deletions. We highlight the techniques used to construct a specific model and to measure the mtDNA instability as well as the main results obtained. We then report the contribution that yeast has given in understanding the pathogenic mechanisms of the mutant variants, in finding the genetic suppressors of the mitochondrial defects and in the discovery of molecules able to improve the mtDNA stability.
Collapse
|
16
|
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: 0.8] [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.
Collapse
|
17
|
Bakare AB, Lesnefsky EJ, Iyer S. Leigh Syndrome: A Tale of Two Genomes. Front Physiol 2021; 12:693734. [PMID: 34456746 PMCID: PMC8385445 DOI: 10.3389/fphys.2021.693734] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022] Open
Abstract
Leigh syndrome is a rare, complex, and incurable early onset (typically infant or early childhood) mitochondrial disorder with both phenotypic and genetic heterogeneity. The heterogeneous nature of this disorder, based in part on the complexity of mitochondrial genetics, and the significant interactions between the nuclear and mitochondrial genomes has made it particularly challenging to research and develop therapies. This review article discusses some of the advances that have been made in the field to date. While the prognosis is poor with no current substantial treatment options, multiple studies are underway to understand the etiology, pathogenesis, and pathophysiology of Leigh syndrome. With advances in available research tools leading to a better understanding of the mitochondria in health and disease, there is hope for novel treatment options in the future.
Collapse
Affiliation(s)
- Ajibola B. Bakare
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Edward J. Lesnefsky
- Division of Cardiology, Pauley Heart Center, Department of Internal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Physiology/Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Department of Biochemistry and Molecular Biology, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR, United States
| |
Collapse
|
18
|
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: 1.8] [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.
Collapse
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.)
| |
Collapse
|
19
|
A Yeast-Based Screening Unravels Potential Therapeutic Molecules for Mitochondrial Diseases Associated with Dominant ANT1 Mutations. Int J Mol Sci 2021; 22:ijms22094461. [PMID: 33923309 PMCID: PMC8123201 DOI: 10.3390/ijms22094461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial diseases result from inherited or spontaneous mutations in mitochondrial or nuclear DNA, leading to an impairment of the oxidative phosphorylation responsible for the synthesis of ATP. To date, there are no effective pharmacological therapies for these pathologies. We performed a yeast-based screening to search for therapeutic drugs to be used for treating mitochondrial diseases associated with dominant mutations in the nuclear ANT1 gene, which encodes for the mitochondrial ADP/ATP carrier. Dominant ANT1 mutations are involved in several degenerative mitochondrial pathologies characterized by the presence of multiple deletions or depletion of mitochondrial DNA in tissues of affected patients. Thanks to the presence in yeast of the AAC2 gene, orthologue of human ANT1, a yeast mutant strain carrying the M114P substitution equivalent to adPEO-associated L98P mutation was created. Five molecules were identified for their ability to suppress the defective respiratory growth phenotype of the haploid aac2M114P. Furthermore, these molecules rescued the mtDNA mutability in the heteroallelic AAC2/aac2M114P strain, which mimics the human heterozygous condition of adPEO patients. The drugs were effective in reducing mtDNA instability also in the heteroallelic strain carrying the R96H mutation equivalent to the more severe de novo dominant missense mutation R80H, suggesting a general therapeutic effect on diseases associated with dominant ANT1 mutations.
Collapse
|