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Holt IJ. The mitochondrial R-loop. Nucleic Acids Res 2019; 47:5480-5489. [PMID: 31045202 PMCID: PMC6582354 DOI: 10.1093/nar/gkz277] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/11/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
The DNA in mitochondria contributes essential components of the organelle’s energy producing machinery that is essential for life. In 1971, many mitochondrial DNA molecules were found to have a third strand of DNA that maps to a region containing critical regulatory elements for transcription and replication. Forty-five years later, a third strand of RNA in the same region has been reported. This mitochondrial R-loop is present on thousands of copies of mitochondrial DNA per cell making it potentially the most abundant R-loop in nature. Here, I assess the discovery of the mitochondrial R-loop, discuss why it remained unrecognized for almost half a century and propose for it central roles in the replication, organization and expression of mitochondrial DNA, which if compromised can lead to disease states.
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Affiliation(s)
- Ian J Holt
- Biodonostia Health Research Institute, 20014 San Sebastián, Spain & IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London, NW3 2PF, UK.,CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), Madrid, Spain
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152
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Mammalian mitochondrial translation - revealing consequences of divergent evolution. Biochem Soc Trans 2019; 47:1429-1436. [PMID: 31551356 DOI: 10.1042/bst20190265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022]
Abstract
Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.
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153
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Saoura M, Powell CA, Kopajtich R, Alahmad A, AL‐Balool HH, Albash B, Alfadhel M, Alston CL, Bertini E, Bonnen PE, Bratkovic D, Carrozzo R, Donati MA, Di Nottia M, Ghezzi D, Goldstein A, Haan E, Horvath R, Hughes J, Invernizzi F, Lamantea E, Lucas B, Pinnock K, Pujantell M, Rahman S, Rebelo‐Guiomar P, Santra S, Verrigni D, McFarland R, Prokisch H, Taylor RW, Levinger L, Minczuk M. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing. Hum Mutat 2019; 40:1731-1748. [PMID: 31045291 PMCID: PMC6764886 DOI: 10.1002/humu.23777] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]
Abstract
Mutations in either the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA metabolism, including ELAC2. The ELAC2 gene codes for the mitochondrial RNase Z, responsible for endonucleolytic cleavage of the 3' ends of mitochondrial pre-tRNAs. Here, we report the identification of 16 novel ELAC2 variants in individuals presenting with mitochondrial respiratory chain deficiency, hypertrophic cardiomyopathy (HCM), and lactic acidosis. We provide evidence for the pathogenicity of the novel missense variants by studying the RNase Z activity in an in vitro system. We also modeled the residues affected by a missense mutation in solved RNase Z structures, providing insight into enzyme structure and function. Finally, we show that primary fibroblasts from the affected individuals have elevated levels of unprocessed mitochondrial RNA precursors. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction. One rare missense variant associated with the occurrence of prostate cancer (p.Arg781His) impairs the mitochondrial RNase Z activity of ELAC2, suggesting a functional link between tumorigenesis and mitochondrial RNA metabolism.
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Affiliation(s)
| | | | - Robert Kopajtich
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Kuwait Medical Genetics CenterKuwait CityKuwait
| | | | | | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research CentreKing Saud bin Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Penelope E. Bonnen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Drago Bratkovic
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | | | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Daniele Ghezzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
- Department of Pathophysiology and TransplantationUniversity of MilanMilanItaly
| | - Amy Goldstein
- Mitochondrial Medicine Frontier ProgramChildren's Hospital of PhiladelphiaPhiladelphiaUSA
| | - Eric Haan
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Joanne Hughes
- National Centre for Inherited Metabolic DisordersTemple Street Children's University HospitalDublinIreland
| | - Federica Invernizzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Eleonora Lamantea
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Benjamin Lucas
- York CollegeThe City University of New YorkJamaicaNew York
| | | | | | - Shamima Rahman
- Mitochondrial Research GroupUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Pedro Rebelo‐Guiomar
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Graduate Program in Areas of Basic and Applied BiologyUniversity of PortoPortoPortugal
| | - Saikat Santra
- Department of Clinical Inherited Metabolic DisordersBirmingham Children's HospitalBirminghamUK
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Robert McFarland
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Louis Levinger
- York CollegeThe City University of New YorkJamaicaNew York
| | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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154
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Baechler SA, Dalla Rosa I, Spinazzola A, Pommier Y. Beyond the unwinding: role of TOP1MT in mitochondrial translation. Cell Cycle 2019; 18:2377-2384. [PMID: 31345095 DOI: 10.1080/15384101.2019.1646563] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mitochondria contain their own genome (mtDNA), encoding 13 proteins of the enzyme complexes of the oxidative phosphorylation. Synthesis of these 13 mitochondrial proteins requires a specific translation machinery, the mitoribosomes whose RNA components are encoded by the mtDNA, whereas more than 80 proteins are encoded by nuclear genes. It has been well established that mitochondrial topoisomerase I (TOP1MT) is important for mtDNA integrity and mitochondrial transcription as it prevents excessive mtDNA negative supercoiling and releases topological stress during mtDNA replication and transcription. We recently showed that TOP1MT also supports mitochondrial protein synthesis, and thus is critical for promoting tumor growth. Impaired mitochondrial protein synthesis leads to activation of the mitonuclear stress response through the transcription factor ATF4, and induces cytoprotective genes in order to prevent mitochondrial and cellular dysfunction. In this perspective, we highlight the novel role of TOP1MT in mitochondrial protein synthesis and as potential target for chemotherapy.
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Affiliation(s)
- Simone A Baechler
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH , Bethesda , MD , USA
| | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology , London , UK
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology , London , UK
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH , Bethesda , MD , USA
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155
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Tan MH, Gan HM, Lee YP, Bracken-Grissom H, Chan TY, Miller AD, Austin CM. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci Rep 2019; 9:10756. [PMID: 31341205 PMCID: PMC6656734 DOI: 10.1038/s41598-019-47145-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/05/2019] [Indexed: 01/21/2023] Open
Abstract
The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.
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Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia.
- Deakin Genomics Centre, Deakin University, Geelong, Australia.
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Heather Bracken-Grissom
- Department of Biological Sciences, Florida International University, North Miami, Florida, 33181, USA
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Road, Keelung, 20224, Taiwan
| | - Adam D Miller
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Australia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Petaling Jaya, Selangor, Malaysia
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156
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Dong Z, Abbas MN, Kausar S, Yang J, Li L, Tan L, Cui H. Biological Functions and Molecular Mechanisms of Antibiotic Tigecycline in the Treatment of Cancers. Int J Mol Sci 2019; 20:ijms20143577. [PMID: 31336613 PMCID: PMC6678986 DOI: 10.3390/ijms20143577] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
As an FDA-approved drug, glycylcycline tigecycline has been used to treat complicated microbial infections. However, recent studies in multiple hematologic and malignant solid tumors reveal that tigecycline treatment induces cell cycle arrest, apoptosis, autophagy and oxidative stress. In addition, tigecycline also inhibits mitochondrial oxidative phosphorylation, cell proliferation, migration, invasion and angiogenesis. Importantly, combinations of tigecycline with chemotherapeutic or targeted drugs such as venetoclax, doxorubicin, vincristine, paclitaxel, cisplatin, and imatinib, have shown to be promising strategies for cancer treatment. Mechanism of action studies reveal that tigecycline leads to the inhibition of mitochondrial translation possibly through interacting with mitochondrial ribosome. Meanwhile, this drug also interferes with several other cell pathways/targets including MYC, HIFs, PI3K/AKT or AMPK-mediated mTOR, cytoplasmic p21 CIP1/Waf1, and Wnt/β-catenin signaling. These evidences indicate that antibiotic tigecycline is a promising drug for cancer treatment alone or in combination with other anticancer drugs. This review summarizes the biological function of tigecycline in the treatment of tumors and comprehensively discusses its mode of action.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Jie Yang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Lin Li
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Li Tan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400716, China.
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China.
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China.
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China.
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157
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Abstract
Perturbed mitochondrial bioenergetics constitute a core pillar of cancer-associated metabolic dysfunction. While mitochondrial dysfunction in cancer may result from myriad biochemical causes, a historically neglected source is that of the mitochondrial genome. Recent large-scale sequencing efforts and clinical studies have highlighted the prevalence of mutations in mitochondrial DNA (mtDNA) in human tumours and their potential roles in cancer progression. In this review we discuss the biology of the mitochondrial genome, sources of mtDNA mutations, and experimental evidence of a role for mtDNA mutations in cancer. We also propose a ‘metabolic licensing’ model for mtDNA mutation-derived dysfunction in cancer initiation and progression.
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Affiliation(s)
- Payam A Gammage
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK. .,CRUK Beatson Institute for Cancer Research, Glasgow, UK.
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158
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Zhou Y, Chen B, Li L, Pan H, Liu B, Li T, Wang R, Ma X, Wang B, Cao Y. Novel alanyl-tRNA synthetase 2 (AARS2) homozygous mutation in a consanguineous Chinese family with premature ovarian insufficiency. Fertil Steril 2019; 112:569-576.e2. [PMID: 31280959 DOI: 10.1016/j.fertnstert.2019.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To explore the candidate pathogenic gene in a premature ovarian insufficiency (POI) proband from a consanguineous marriage and detect the potential effects of mutation on cellular energy metabolism. DESIGN Genetic and functional studies. SETTING Reproductive medicine center. PATIENT(S) A patient with POI, from a consanguineous family, and her family members were recruited from the Reproductive Center of the First Affiliated Hospital of Anhui Medical University. INTERVENTION(S) Whole exome sequencing (WES) was performed for the proband. Variation revealed by WES sequencing was validated by Sanger sequencing in her family. Sequencing data were combined with those of other sporadic cases listed in public databases to identify the causative gene. MAIN OUTCOME MEASURE(S) Rare homozygous nonsynonymous variants were identified and included in subsequent analysis. Metabolic analyzes were performed using Seahorse XFe96 analyzers to measure oxygen consumption and then obtain further results of ATP production and extracellular acidification rate. The differences in energy metabolism measurements between wild type and mutation were analyzed and compared. RESULT(S) A novel alanyl-tRNA synthetase 2 (AARS2) homozygous mutation (NM_020745: exon2: c.337G>C: p. G113R) was identified in the aminoacylation region using WES. The mutation was highly conserved among species and predicted to be disease causing. AARS2 encodes mitochondrial alanyl-tRNA synthetase, which attaches alanine onto tRNA-ala. AARS2 mutations were previously reported in female leukodystrophy patients with POI. In mitochondrial stress tests, the ATP productions of the mutation group (3.58 ± 0.46 fmol/min/cell) was significantly lower than that of the wild type group (6.96 ± 1.56 fmol/min/cell). CONCLUSION(S) This is the first report of a homozygous pathogenic AARS2 mutation in POI. This mutation may lead to incorrect aminoacylation of tRNA, affect mitochondrial translation, and cause oxidative phosphorylation defects, which may be responsible for POI.
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Affiliation(s)
- Yiran Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China; Anhui Province Key Laboratory of Reproductive Health and Genetics, Biopreservation and Artificial Organs, Hefei, People's Republic of China; Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, People's Republic of China
| | - Beili Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China; Anhui Province Key Laboratory of Reproductive Health and Genetics, Biopreservation and Artificial Organs, Hefei, People's Republic of China; Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, People's Republic of China
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Chaoyang, People's Republic of China
| | - Hong Pan
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China; Center for Genetics, National Research Institute of Family Planning, Beijing, People's Republic of China
| | - Beihong Liu
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China; Center for Genetics, National Research Institute of Family Planning, Beijing, People's Republic of China
| | - Tengyan Li
- Center for Genetics, National Research Institute of Family Planning, Beijing, People's Republic of China
| | - Ruyi Wang
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China; Center for Genetics, National Research Institute of Family Planning, Beijing, People's Republic of China
| | - Xu Ma
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China; Center for Genetics, National Research Institute of Family Planning, Beijing, People's Republic of China
| | - Binbin Wang
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China; Center for Genetics, National Research Institute of Family Planning, Beijing, People's Republic of China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, People's Republic of China; Anhui Province Key Laboratory of Reproductive Health and Genetics, Biopreservation and Artificial Organs, Hefei, People's Republic of China; Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, People's Republic of China.
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159
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Bugiardini E, Mitchell AL, Rosa ID, Horning-Do HT, Pitmann AM, Poole OV, Holton JL, Shah S, Woodward C, Hargreaves I, Quinlivan R, Amunts A, Wiesner RJ, Houlden H, Holt IJ, Hanna MG, Pitceathly RDS, Spinazzola A. MRPS25 mutations impair mitochondrial translation and cause encephalomyopathy. Hum Mol Genet 2019; 28:2711-2719. [PMID: 31039582 PMCID: PMC6687946 DOI: 10.1093/hmg/ddz093] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial disorders are clinically and genetically heterogeneous and are associated with a variety of disease mechanisms. Defects of mitochondrial protein synthesis account for the largest subgroup of disorders manifesting with impaired respiratory chain capacity; yet, only a few have been linked to dysfunction in the protein components of the mitochondrial ribosomes. Here, we report a subject presenting with dyskinetic cerebral palsy and partial agenesis of the corpus callosum, while histochemical and biochemical analyses of skeletal muscle revealed signs of mitochondrial myopathy. Using exome sequencing, we identified a homozygous variant c.215C>T in MRPS25, which encodes for a structural component of the 28S small subunit of the mitochondrial ribosome (mS25). The variant segregated with the disease and substitutes a highly conserved proline residue with leucine (p.P72L) that, based on the high-resolution structure of the 28S ribosome, is predicted to compromise inter-protein contacts and destabilize the small subunit. Concordant with the in silico analysis, patient’s fibroblasts showed decreased levels of MRPS25 and other components of the 28S subunit. Moreover, assembled 28S subunits were scarce in the fibroblasts with mutant mS25 leading to impaired mitochondrial translation and decreased levels of multiple respiratory chain subunits. Crucially, these abnormalities were rescued by transgenic expression of wild-type MRPS25 in the mutant fibroblasts. Collectively, our data demonstrate the pathogenicity of the p.P72L variant and identify MRPS25 mutations as a new cause of mitochondrial translation defect.
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Affiliation(s)
- Enrico Bugiardini
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Alice L Mitchell
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Hue-Tran Horning-Do
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Köln, 50931 Köln, Germany
| | - Alan M Pitmann
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Olivia V Poole
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Janice L Holton
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Sachit Shah
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Cathy Woodward
- Neurogenetic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Iain Hargreaves
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Rosaline Quinlivan
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Rudolf J Wiesner
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Köln, 50931 Köln, Germany
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
- Biodonostia Health Research Institute, 20014 San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
- CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), Madrid, Spain
| | - Michael G Hanna
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Robert D S Pitceathly
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Antonella Spinazzola
- MRC Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
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160
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Strieskova L, Gazdaricova I, Kajsik M, Soltys K, Budis J, Pos O, Lickova M, Klempa B, Szemes T. Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome. J Biotechnol 2019; 299:8-12. [PMID: 31022426 DOI: 10.1016/j.jbiotec.2019.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 12/23/2022]
Abstract
The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases.
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Affiliation(s)
| | - Iveta Gazdaricova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Michal Kajsik
- Comenius University Science Park, Bratislava, Slovakia
| | - Katarina Soltys
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
| | - Jaroslav Budis
- Geneton Ltd., Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Ondrej Pos
- Geneton Ltd., Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Martina Lickova
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava, Slovakia; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia
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161
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Abstract
An emergent theme in cancer biology is that dysregulated energy metabolism may directly influence oncogenic gene expression. This is due to the fact that many enzymes involved in gene regulation use cofactors derived from primary metabolism, including acetyl-CoA, S-adenosylmethionine, and 2-ketoglutarate. While this phenomenon was first studied through the prism of histone and DNA modifications (the epigenome), recent work indicates metabolism can also impact gene regulation by disrupting the balance of RNA post-transcriptional modifications (the epitranscriptome). Here we review recent studies that explore how metabolic regulation of writers and erasers of the epitranscriptome (FTO, TET2, NAT10, MTO1, and METTL16) helps shape gene expression through three distinct mechanisms: cofactor inhibition, cofactor depletion, and writer localization. Our brief survey underscores similarities and differences between the metabolic regulation of the epigenome and epitranscriptome, and highlights fertile ground for future investigation.
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Affiliation(s)
- Justin M. Thomas
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Pedro J. Batista
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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162
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Rohr M, Ries F, Herkt C, Gotsmann VL, Westrich LD, Gries K, Trösch R, Christmann J, Chaux-Jukic F, Jung M, Zimmer D, Mühlhaus T, Sommer F, Schroda M, Keller S, Möhlmann T, Willmund F. The Role of Plastidic Trigger Factor Serving Protein Biogenesis in Green Algae and Land Plants. PLANT PHYSIOLOGY 2019; 179:1093-1110. [PMID: 30651302 PMCID: PMC6393800 DOI: 10.1104/pp.18.01252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/07/2019] [Indexed: 05/07/2023]
Abstract
Biochemical processes in chloroplasts are important for virtually all life forms. Tight regulation of protein homeostasis and the coordinated assembly of protein complexes, composed of both imported and locally synthesized subunits, are vital to plastid functionality. Protein biogenesis requires the action of cotranslationally acting molecular chaperones. One such chaperone is trigger factor (TF), which is known to cotranslationally bind most newly synthesized proteins in bacteria, thereby assisting their correct folding and maturation. However, how these processes are regulated in chloroplasts remains poorly understood. We report here functional investigation of chloroplast-localized TF (TIG1) in the green alga (Chlamydomonas reinhardtii) and the vascular land plant Arabidopsis (Arabidopsis thaliana). We show that chloroplastic TIG1 evolved as a specialized chaperone. Unlike other plastidic chaperones that are functionally interchangeable with their prokaryotic counterpart, TIG1 was not able to complement the broadly acting ortholog in Escherichia coli. Whereas general chaperone properties such as the prevention of aggregates or substrate recognition seems to be conserved between bacterial and plastidic TFs, plant TIG1s differed by associating with only a relatively small population of translating ribosomes. Furthermore, a reduction of plastidic TIG1 levels leads to deregulated protein biogenesis at the expense of increased translation, thereby disrupting the chloroplast energy household. This suggests a central role of TIG1 in protein biogenesis in the chloroplast.
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Affiliation(s)
- Marina Rohr
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Vincent Leon Gotsmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Lisa Désirée Westrich
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Karin Gries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Raphael Trösch
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Jens Christmann
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | | | - Martin Jung
- Medical Biochemistry and Molecular Biology, Building 44, Saarland University, 66421 Homburg, Germany
| | - David Zimmer
- Computational Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
| | - Torsten Möhlmann
- Plant Physiology, University of Kaiserslautern, Paul-Ehrlich Strasse 22, 67663 Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Strasse 23, 67663 Kaiserslautern, Germany
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163
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Abstract
The maternally inherited mitochondrial DNA (mtDNA) is located inside every mitochondrion, in variable number of copies, and it contains 37 crucial genes for cellular bioenergetics. This chapter will discuss the unique features of this circular genome including heteroplasmy, haplogroups, among others, along with the corresponding clinical relevance for each. The discussion also covers the nuclear-encoded mitochondrial genes (N > 1000) and the epistatic interactions between mtDNA and the nuclear genome. Examples of mitochondrial diseases related to specific mtDNA mutation sites of relevance for humans are provided. This chapter aims to provide an overview of mitochondrial genetics as an emerging hot topic for the future of medicine.
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Affiliation(s)
- Vanessa F Gonçalves
- Molecular Brain Sciences Department, Centre for Addiction and Mental Health, Toronto, Canada.
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164
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Rebelo-Guiomar P, Powell CA, Van Haute L, Minczuk M. The mammalian mitochondrial epitranscriptome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:429-446. [PMID: 30529456 PMCID: PMC6414753 DOI: 10.1016/j.bbagrm.2018.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/16/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023]
Abstract
Correct expression of the mitochondrially-encoded genes is critical for the production of the components of the oxidative phosphorylation machinery. Post-transcriptional modifications of mitochondrial transcripts have been emerging as an important regulatory feature of mitochondrial gene expression. Here we review the current knowledge on how the mammalian mitochondrial epitranscriptome participates in regulating mitochondrial homeostasis. In particular, we focus on the latest breakthroughs made towards understanding the roles of the modified nucleotides in mitochondrially-encoded ribosomal and transfer RNAs, the enzymes responsible for introducing these modifications and on recent transcriptome-wide studies reporting modifications to mitochondrial messenger RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Matthias Soller and Dr. Rupert Fray. Human mtDNA encodes 13 proteins and all the RNAs necessary for their expression Post-transcriptional modifications of RNA, the epitranscriptome, play a regulatory role in mitochondrial gene expression Several enzymes involved in the shaping of the mitochondrial epitranscriptome have recently been characterised. Our understanding of the extent and nature of mtRNA modifications is rapidly expanding. Recent transcriptome-wide studies suggest modifications in mitochondrial mRNAs
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Affiliation(s)
- Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK; Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, Portugal
| | | | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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165
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Mitochondrial DNA transcription and translation: clinical syndromes. Essays Biochem 2018; 62:321-340. [PMID: 29980628 PMCID: PMC6056718 DOI: 10.1042/ebc20170103] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/17/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
Abstract
Diagnosing primary mitochondrial diseases is challenging in clinical practice. Although, defective oxidative phosphorylation (OXPHOS) is the common final pathway, it is unknown why different mtDNA or nuclear mutations result in largely heterogeneous and often tissue -specific clinical presentations. Mitochondrial tRNA (mt-tRNA) mutations are frequent causes of mitochondrial diseases both in children and adults. However numerous nuclear mutations involved in mitochondrial protein synthesis affecting ubiquitously expressed genes have been reported in association with very tissue specific clinical manifestations suggesting that there are so far unknown factors determining the tissue specificity in mitochondrial translation. Most of these gene defects result in histological abnormalities and multiple respiratory chain defects in the affected organs. The clinical phenotypes are usually early-onset, severe, and often fatal, implying the importance of mitochondrial translation from birth. However, some rare, reversible infantile mitochondrial diseases are caused by very specific defects of mitochondrial translation. An unbiased genetic approach (whole exome sequencing, RNA sequencing) combined with proteomics and functional studies revealed novel factors involved in mitochondrial translation which contribute to the clinical manifestation and recovery in these rare reversible mitochondrial conditions.
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