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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.
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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
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2
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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: 1] [Impact Index Per Article: 0.3] [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.
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3
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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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4
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Rzepnikowska W, Kaminska J, Kabzińska D, Binięda K, Kochański A. A Yeast-Based Model for Hereditary Motor and Sensory Neuropathies: A Simple System for Complex, Heterogeneous Diseases. Int J Mol Sci 2020; 21:ijms21124277. [PMID: 32560077 PMCID: PMC7352270 DOI: 10.3390/ijms21124277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Charcot–Marie–Tooth (CMT) disease encompasses a group of rare disorders that are characterized by similar clinical manifestations and a high genetic heterogeneity. Such excessive diversity presents many problems. Firstly, it makes a proper genetic diagnosis much more difficult and, even when using the most advanced tools, does not guarantee that the cause of the disease will be revealed. Secondly, the molecular mechanisms underlying the observed symptoms are extremely diverse and are probably different for most of the disease subtypes. Finally, there is no possibility of finding one efficient cure for all, or even the majority of CMT diseases. Every subtype of CMT needs an individual approach backed up by its own research field. Thus, it is little surprise that our knowledge of CMT disease as a whole is selective and therapeutic approaches are limited. There is an urgent need to develop new CMT models to fill the gaps. In this review, we discuss the advantages and disadvantages of yeast as a model system in which to study CMT diseases. We show how this single-cell organism may be used to discriminate between pathogenic variants, to uncover the mechanism of pathogenesis, and to discover new therapies for CMT disease.
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Affiliation(s)
- Weronika Rzepnikowska
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Dagmara Kabzińska
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
| | - Katarzyna Binięda
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
| | - Andrzej Kochański
- Neuromuscular Unit, Mossakowski Medical Research Centre Polish Academy of Sciences, 02-106 Warsaw, Poland; (W.R.); (D.K.); (K.B.)
- Correspondence:
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5
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Ding C, Han F, Xiang H, Wang Y, Dou M, Xia X, Li Y, Zheng J, Ding X, Xue W, Tian P. Role of prostaglandin E2 receptor 4 in the modulation of apoptosis and mitophagy during ischemia/reperfusion injury in the kidney. Mol Med Rep 2019; 20:3337-3346. [PMID: 31432142 DOI: 10.3892/mmr.2019.10576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 04/04/2019] [Indexed: 11/09/2022] Open
Abstract
The mechanisms by which prostaglandin E2 receptor 4 (EP4) protects against renal ischemia‑reperfusion (I/R) injury (IRI) remain to be fully elucidated. In the present study, the protective effects of EP4 signaling on renal mitochondria and against renal IRI, as well as the underlying mechanisms, were investigated. A rat model of renal IRI was established. The right kidney was separated without damaging the artery clip, and the renal blood perfusion was then restored after 60 min. One group of animals was treated with EP4 agonists prior to I/R. The mitochondrial mass, the copy number of mitochondrial (mt)DNA, adenosine triphosphate (ATP) production and mitochondrial autophagy were analyzed. It was identified that renal IRI reduced the mitochondrial mass, decreased the mtDNA copy number and inhibited ATP production. The loss of renal mitochondria was attributed to the excessive mitochondrial autophagy induced by renal IRI. Pre‑treatment with EP4 agonist inhibited excessive mitochondrial autophagy, the loss of mitochondria and maintained and the energy imbalance within the cells. It was indicated that renal IRI causes excessive mitochondrial autophagy, which is one of the important causes of renal dysfunction.
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Affiliation(s)
- Chenguang Ding
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Feng Han
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Heli Xiang
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yuxiang Wang
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Meng Dou
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Xinxin Xia
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yang Li
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Jin Zheng
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Xiaoming Ding
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Wujun Xue
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Puxun Tian
- Department of Kidney Transplantation, Nephropathy Hospital, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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6
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Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM. Saccharomyces genome database informs human biology. Nucleic Acids Res 2019; 46:D736-D742. [PMID: 29140510 PMCID: PMC5753351 DOI: 10.1093/nar/gkx1112] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.
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Affiliation(s)
- Marek S Skrzypek
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Robert S Nash
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Edith D Wong
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Kevin A MacPherson
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Sage T Hellerstedt
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Travis K Sheppard
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Gail Binkley
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Matt Simison
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - Stuart R Miyasato
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA
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7
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Sowers ML, Anderson APP, Wrabl JO, Yin YW. Networked Communication between Polymerase and Exonuclease Active Sites in Human Mitochondrial DNA Polymerase. J Am Chem Soc 2019; 141:10821-10829. [PMID: 31251605 PMCID: PMC7119269 DOI: 10.1021/jacs.9b04655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High fidelity human mitochondrial DNA polymerase (Pol γ) contains two active sites, a DNA polymerization site (pol) and a 3'-5' exonuclease site (exo) for proofreading. Although separated by 35 Å, coordination between the pol and exo sites is crucial to high fidelity replication. The biophysical mechanisms for this coordination are not completely understood. To understand the communication between the two active sites, we used a statistical-mechanical model of the protein ensemble to calculate the energetic landscape and local stability. We compared a series of structures of Pol γ, complexed with primer/template DNA, and either a nucleotide substrate or a series of nucleotide analogues, which are differentially incorporated and excised by pol and exo activity. Despite the nucleotide or its analogues being bound in the pol, Pol γ residue stability varied across the protein, particularly in the exo domain. This suggests that substrate presence in the pol can be "sensed" in the exo domain. Consistent with this hypothesis, in silico mutations made in one active site mutually perturbed the energetics of the other. To identify specific regions of the polymerase that contributed to this communication, we constructed an allosteric network connectivity map that further demonstrates specific pol-exo cooperativity. Thus, a cooperative network underlies energetic connectivity. We propose that Pol γ and other dual-function polymerases exploit an energetic coupling network that facilitates domain-domain communication to enhance discrimination between correct and incorrect nucleotides.
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Affiliation(s)
- Mark L. Sowers
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Andrew P. P. Anderson
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 71115, United States
| | - James O. Wrabl
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Y. Whitney Yin
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, Texas 71115, United States
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8
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Hynynen J, Pokka T, Komulainen-Ebrahim J, Myllynen P, Kärppä M, Pylvänen L, Kälviäinen R, Sokka A, Jyrkilä A, Lähdetie J, Haataja L, Mäkitalo A, Ylikotila P, Eriksson K, Haapala P, Ansakorpi H, Hinttala R, Vieira P, Majamaa K, Rantala H, Uusimaa J. Variants p.Q1236H and p.E1143G in mitochondrial DNA polymerase gamma POLG1 are not associated with increased risk for valproate-induced hepatotoxicity or pancreatic toxicity: A retrospective cohort study of patients with epilepsy. Epilepsia 2018; 59:2125-2136. [PMID: 30255931 DOI: 10.1111/epi.14568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Previous studies have suggested that heterozygous variants p.Q1236H and p.E1143G in mitochondrial DNA polymerase gamma (POLG1) increase the risk for liver injury for patients on valproate (VPA) therapy. We assessed the prevalence of these common variants and seven other pathogenic mutations in POLG1 and determined the occurrence of VPA-induced hepatotoxicity (VHT) or pancreatic toxicity in a cohort of patients with epilepsy. METHODS Patients with epilepsy (N = 367) were retrospectively identified from medical record files and screened for mutations in POLG1. Patients who had received VPA monotherapy and carried either of the two variants, p.Q1236H or p.E1143G, without other pathogenic mutations in POLG1 (n = 33, variant group) and patients without these variants (n = 28, nonvariant group) were included in the study. Clinical data on epilepsy, characteristics of VPA treatment, risk factors for VHT, laboratory data on liver and pancreas functions, and adverse effects were collected. RESULTS A total of 122 patients had either the POLG1 p.Q1236H (n = 99) or p.E1143G (n = 24) variant in the heterozygous or homozygous state. Transient liver dysfunction was identified in three (n = 33, 9.1%) variant group patients and in one (n = 28, 3.6%) nonvariant group patient (P = 0.62). Mild to moderate elevations in liver enzymes were encountered in both groups. Furthermore, two patients on VPA polytherapy developed acute pancreatitis, and two pediatric patients with heterozygous p.Q1236H variants and mutations in IQSEC2 and GLDC, respectively, had elevated levels of VPA metabolites in urine, elevated plasma glycine, and/or increased acylglycine excretion. SIGNIFICANCE POLG1 p.Q1236H and p.E1143G variants could not be identified as statistically significant risk factors for VHT or pancreatic toxicity. We suggest that VPA treatment could be suitable for patients who harbor these common variants in the absence of other pathogenic mutations in POLG1.
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Affiliation(s)
- Johanna Hynynen
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Tytti Pokka
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Jonna Komulainen-Ebrahim
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | | | - Mikko Kärppä
- Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland
| | - Laura Pylvänen
- Department of Neurology, Oulu University Hospital, Oulu, Finland
| | - Reetta Kälviäinen
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Arja Sokka
- Institute of Clinical Medicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Pediatric Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Aino Jyrkilä
- Institute of Clinical Medicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Pediatric Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana Lähdetie
- Department of Child Neurology, University of Turku and Turku University Central Hospital, Turku, Finland
| | - Leena Haataja
- Department of Pediatric Neurology, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna Mäkitalo
- Department of Child Neurology, University of Turku and Turku University Central Hospital, Turku, Finland.,Department of Geriatric Medicine, University of Turku, Turku, Finland
| | - Pauli Ylikotila
- Department of Neurology, Institute of Clinical Medicine, University of Turku, Turku, Finland.,Division of Clinical Neurosciences, Turku University Hospital, Turku, Finland
| | - Kai Eriksson
- Tampere Center for Child Health Research and Pediatric Neurology, Tampere University Hospital, Tampere, Finland
| | - Piia Haapala
- Outpatient Intellectual Disabilities Clinic, Tampere University Hospital, Tampere, Finland
| | - Hanna Ansakorpi
- Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland
| | - Reetta Hinttala
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Päivi Vieira
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Kari Majamaa
- Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Neurology, Oulu University Hospital, Oulu, Finland.,Research Unit of Clinical Neuroscience, Neurology, University of Oulu, Oulu, Finland
| | - Heikki Rantala
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
| | - Johanna Uusimaa
- Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Division of Pediatric Neurology, Oulu University Hospital, Oulu, Finland
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9
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Tervasmäki A, Mantere T, Hartikainen JM, Kauppila S, Lee HM, Koivuluoma S, Grip M, Karihtala P, Jukkola-Vuorinen A, Mannermaa A, Winqvist R, Pylkäs K. Rare missense mutations in RECQL and POLG associate with inherited predisposition to breast cancer. Int J Cancer 2018; 142:2286-2292. [PMID: 29341116 DOI: 10.1002/ijc.31259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 12/13/2022]
Abstract
Several known breast cancer susceptibility genes with moderate-to-high risk alleles encode proteins involved in DNA damage response (DDR). As these explain less than half of the hereditary breast cancer cases, additional predisposing alleles are likely to be discovered. Many of the previous studies utilizing massive parallel sequencing have focused on the protein-truncating variants, and the role of rare missense mutations has remained poorly addressed. To identify novel susceptibility factors, we have systematically analyzed the data from our parallel sequencing of 796 DDR genes in 189 Northern Finnish hereditary breast cancer patients for rare missense variants, predicted as deleterious. Thirty-five variants were studied here for the disease association using Finnish breast cancer case (n = 492-2,035) and control (n = 277-1,539) cohorts. As a result, two missense variants in genes involved in DNA replication, RECQL p.I156M and POLG p.L392V, the former involving genomic and the latter mitochondrial DNA replication, showed significant association with risk of breast cancer. Rare RECQL p.I156M allele was observed in breast cancer cases only (6/1,946, 0.3%, p = 0.043), whereas POLG p.L392V was two times more frequent in breast cancer cases (53/2,238, 2.4%) compared to controls (18/1,539, 1.2%, OR = 2.1, 95% CI 1.2-3.5, p = 0.010). Based on the current genetic data, both RECQL p.I156M and POLG p.L392V represent novel breast cancer predisposing alleles.
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Affiliation(s)
- Anna Tervasmäki
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, Northern Finland Laboratory Centre Nordlab Oulu, University of Oulu, Oulu, Finland
| | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, Northern Finland Laboratory Centre Nordlab Oulu, University of Oulu, Oulu, Finland
| | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland.,Department of Clinical Pathology, Imaging Center, Kuopio University Hospital, Kuopio, Finland
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Hang-Mao Lee
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Susanna Koivuluoma
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, Northern Finland Laboratory Centre Nordlab Oulu, University of Oulu, Oulu, Finland
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Peeter Karihtala
- Department of Oncology and Radiotherapy, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arja Jukkola-Vuorinen
- Department of Oncology and Radiotherapy, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland.,Department of Clinical Pathology, Imaging Center, Kuopio University Hospital, Kuopio, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, Northern Finland Laboratory Centre Nordlab Oulu, University of Oulu, Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, Northern Finland Laboratory Centre Nordlab Oulu, University of Oulu, Oulu, Finland
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10
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Chan SSL. Inherited mitochondrial genomic instability and chemical exposures. Toxicology 2017; 391:75-83. [PMID: 28756246 DOI: 10.1016/j.tox.2017.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/12/2017] [Accepted: 07/24/2017] [Indexed: 12/21/2022]
Abstract
There are approximately 1500 proteins that are needed for mitochondrial structure and function, most of which are encoded in the nuclear genome (Calvo et al., 2006). Each mitochondrion has its own genome (mtDNA), which in humans encodes 13 polypeptides, 22 tRNAs and 2 rRNAs required for oxidative phosphorylation. The mitochondrial genome of humans and most vertebrates is approximately 16.5kbp, double-stranded, circular, with few non-coding bases. Thus, maintaining mtDNA stability, that is, the ability of the cell to maintain adequate levels of mtDNA template for oxidative phosphorylation is essential and can be impacted by the level of mtDNA mutation currently within the cell or mitochondrion, but also from errors made during normal mtDNA replication, defects in mitochondrial quality control mechanisms, and exacerbated by exposures to exogenous and/or endogenous genotoxic agents. In this review, we expand on the origins and consequences of mtDNA instability, the current state of research regarding the mechanisms by which mtDNA instability can be overcome by cellular and chemical interventions, and the future of research and treatments for mtDNA instability.
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Affiliation(s)
- Sherine S L Chan
- Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, SC 29425, United States; Neuroene Therapeutics, Mt. Pleasant, SC 29464, United States.
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11
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Pitayu L, Baruffini E, Rodier C, Rötig A, Lodi T, Delahodde A. Combined use of Saccharomyces cerevisiae, Caenorhabditis elegans and patient fibroblasts leads to the identification of clofilium tosylate as a potential therapeutic chemical against POLG-related diseases. Hum Mol Genet 2015; 25:715-27. [PMID: 26692522 DOI: 10.1093/hmg/ddv509] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/08/2015] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are organelles that have their own DNA (mitochondrial DNA, mtDNA) whose maintenance is necessary for the majority of ATP production in eukaryotic cells. Defects in mtDNA maintenance or integrity are responsible for numerous diseases. The DNA polymerase γ (POLG) ensures proper mtDNA replication and repair. Mutations in POLG are a major cause of mitochondrial disorders including hepatic insufficiency, Alpers syndrome, progressive external ophthalmoplegia, sensory neuropathy and ataxia. Mutations in POLG are also associated with parkinsonism. To date, no effective therapy is available. Based on the conservation of mitochondrial function from yeast to human, we used Saccharomyces cerevisiae and Caenorhabditis elegans as first pass filters to identify a chemical that suppresses mtDNA instability in cultured fibroblasts of a POLG-deficient patient. We showed that this unsuspected compound, clofilium tosylate (CLO), belonging to a class of anti-arrhythmic agents, prevents mtDNA loss of all yeast mitochondrial polymerase mutants tested, improves behavior and mtDNA content of polg-1-deficient worms and increases mtDNA content of quiescent POLG-deficient fibroblasts. Furthermore, the mode of action of the drug seems conserved as CLO increases POLG steady-state level in yeast and human cells. Two other anti-arrhythmic agents (FDA-approved) sharing common pharmacological properties and chemical structure also show potential benefit for POLG deficiency in C. elegans. Our findings provide evidence of the first mtDNA-stabilizing compound that may be an effective pharmacological alternative for the treatment of POLG-related diseases.
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Affiliation(s)
- Laras Pitayu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Enrico Baruffini
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/a, I-43124 Parma, Italy and
| | - Celine Rodier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Agnès Rötig
- INSERM UMR 1163, Laboratory of Genetics of Mitochondrial Disorders, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, 24 Boulevard du Montparnasse, Paris 75015, France
| | - Tiziana Lodi
- Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/a, I-43124 Parma, Italy and
| | - Agnès Delahodde
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France,
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12
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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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13
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Yeast model analysis of novel polymerase gamma variants found in patients with autosomal recessive mitochondrial disease. Hum Genet 2015; 134:951-66. [PMID: 26077851 PMCID: PMC4529462 DOI: 10.1007/s00439-015-1578-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022]
Abstract
Replication of the mitochondrial genome depends on the single DNA polymerase (pol gamma). Mutations in the POLG gene, encoding the catalytic subunit of the human polymerase gamma, have been linked to a wide variety of mitochondrial disorders that show remarkable heterogeneity, with more than 200 sequence variants, often very rare, found in patients. The pathogenicity and dominance status of many such mutations remain, however, unclear. Remarkable structural and functional conservation of human POLG and its S. cerevisiae ortholog (Mip1p) led to the development of many successful yeast models, enabling to study the phenotype of putative pathogenic mutations. In a group of patients with suspicion of mitochondrial pathology, we identified five novel POLG sequence variants, four of which (p.Arg869Ter, p.Gln968Glu, p.Thr1053Argfs*6, and p.Val1106Ala), together with one previously known but uncharacterised variant (p.Arg309Cys), were amenable to modelling in yeast. Familial analysis indicated causal relationship of these variants with disease, consistent with autosomal recessive inheritance. To investigate the effect of these sequence changes on mtDNA replication, we obtained the corresponding yeast mip1 alleles (Arg265Cys, Arg672Ter, Arg770Glu, Thr809Ter, and Val863Ala, respectively) and tested their effect on mitochondrial genome stability and replication fidelity. For three of them (Arg265Cys, Arg672Ter, and Thr809Ter), we observed a strong, partially dominant phenotype of a complete loss of functional mtDNA, whereas the remaining two led to partial mtDNA depletion and significant increase in point mutation frequencies. These results show good correlation with the severity of symptoms observed in patients and allow to establish these variants as pathogenic mutations.
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14
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Lodi T, Dallabona C, Nolli C, Goffrini P, Donnini C, Baruffini E. DNA polymerase γ and disease: what we have learned from yeast. Front Genet 2015; 6:106. [PMID: 25852747 PMCID: PMC4362329 DOI: 10.3389/fgene.2015.00106] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 03/02/2015] [Indexed: 11/16/2022] Open
Abstract
Mip1 is the Saccharomyces cerevisiae DNA polymerase γ (Pol γ), which is responsible for the replication of mitochondrial DNA (mtDNA). It belongs to the family A of the DNA polymerases and it is orthologs to human POLGA. In humans, mutations in POLG(1) cause many mitochondrial pathologies, such as progressive external ophthalmoplegia (PEO), Alpers' syndrome, and ataxia-neuropathy syndrome, all of which present instability of mtDNA, which results in impaired mitochondrial function in several tissues with variable degrees of severity. In this review, we summarize the genetic and biochemical knowledge published on yeast mitochondrial DNA polymerase from 1989, when the MIP1 gene was first cloned, up until now. The role of yeast is particularly emphasized in (i) validating the pathological mutations found in human POLG and modeled in MIP1, (ii) determining the molecular defects caused by these mutations and (iii) finding the correlation between mutations/polymorphisms in POLGA and mtDNA toxicity induced by specific drugs. We also describe recent findings regarding the discovery of molecules able to rescue the phenotypic defects caused by pathological mutations in Mip1, and the construction of a model system in which the human Pol γ holoenzyme is expressed in yeast and complements the loss of Mip1.
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Affiliation(s)
- Tiziana Lodi
- Department of Life Sciences, University of Parma Parma, Italy
| | | | - Cecilia Nolli
- Department of Life Sciences, University of Parma Parma, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma Parma, Italy
| | - Claudia Donnini
- Department of Life Sciences, University of Parma Parma, Italy
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