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Bolner M, Bovo S, Ballan M, Schiavo G, Taurisano V, Ribani A, Bertolini F, Fontanesi L. A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome. Genet Sel Evol 2024; 56:64. [PMID: 39285356 PMCID: PMC11403998 DOI: 10.1186/s12711-024-00930-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 08/26/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND The integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification. RESULTS We have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5-10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus. CONCLUSIONS This study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species.
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Affiliation(s)
- Matteo Bolner
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Samuele Bovo
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Mohamad Ballan
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Valeria Taurisano
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Francesca Bertolini
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Animal and Food Genomics Group, Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
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Golubenko MV, Puzyrev VP. Liberties of the genome: insertions of mitochondrial DNA fragments into nuclear genome. Vavilovskii Zhurnal Genet Selektsii 2024; 28:467-475. [PMID: 39280847 PMCID: PMC11393654 DOI: 10.18699/vjgb-24-53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 09/18/2024] Open
Abstract
The transition of detached fragments of mitochondrial DNA into the nucleus and their integration into chromosomal DNA is a special kind of genetic variability that highlights the relation between the two genomes and their interaction in a eukaryotic cell. The human genome contains several hundreds of insertions of mtDNA fragments (NUMTS). This paper presents an overview of the current state of research in this area. To date, evidence has been obtained that the occurrence of new mtDNA insertions in the nuclear genome is a seldom but not exceptionally rare event. The integration of new mtDNA fragments into the nuclear genome occurs during double-strand DNA break repair through the non-homologous end joining mechanism. Along with evolutionarily stable "genetic fossils" that were integrated into the nuclear genome millions of years ago and are shared by many species, there are NUMTS that could be species-specific, polymorphic in a species, or "private". Partial copies of mitochondrial DNA in the human nuclear genome can interfere with mtDNA during experimental studies of the mitochondrial genome, such as genotyping, heteroplasmy assessment, mtDNA methylation analysis, and mtDNA copy number estimation. In some cases, the insertion of multiple copies of the complete mitochondrial genome sequence may mimic paternal inheritance of mtDNA. The functional significance of NUMTS is poorly understood. For instance, they may be a source of variability for expression and splicing modulation. The role of NUMTS as a cause of hereditary diseases is negligible, since only a few cases of diseases caused by NUMTS have been described so far. In addition, NUMTS can serve as markers for evolutionary genetic studies. Of particular interest is the meaning of NUMTS in eukaryotic genome evolution. The constant flow of functionally inactive DNA sequences from mitochondria into the nucleus and its significance could be studied in view of the modern concepts of evolutionary theory suggesting non-adaptive complexity and the key role of stochastic processes in the formation of genomic structure.
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Affiliation(s)
- M V Golubenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V P Puzyrev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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3
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Sazonova MA, Kirichenko TV, Ryzhkova AI, Sazonova MD, Doroschuk NA, Omelchenko AV, Nikiforov NG, Ragino YI, Postnov AY. Variability of Mitochondrial DNA Heteroplasmy: Association with Asymptomatic Carotid Atherosclerosis. Biomedicines 2024; 12:1868. [PMID: 39200332 PMCID: PMC11351276 DOI: 10.3390/biomedicines12081868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/05/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Background and Objectives: Atherosclerosis is one of the main reasons for cardiovascular disease development. This study aimed to analyze the association of mtDNA mutations and atherosclerotic plaques in carotid arteries of patients with atherosclerosis and conditionally healthy study participants from the Novosibirsk region. Methods: PCR fragments of DNA containing the regions of 10 investigated mtDNA mutations were pyrosequenced. The heteroplasmy levels of mtDNA mutations were analyzed using a quantitative method based on pyrosequencing technology developed by M. A. Sazonova and colleagues. Results: In the analysis of samples of patients with atherosclerotic plaques of the carotid arteries and conditionally healthy study participants from the Novosibirsk region, four proatherogenic mutations in the mitochondrial genome (m.5178C>A, m.652delG, m.12315G>A and m.3256C>T) and three antiatherogenic mutations in mtDNA (m.13513G>A, m.652insG, and m.14846G>A) were detected. A west-east gradient was found in the distribution of the mtDNA mutations m.5178C>A, m.3256C>T, m.652insG, and m.13513G>A. Conclusions: Therefore, four proatherogenic mutations in the mitochondrial genome (m.5178C>A, m.652delG, m.12315G>A, and m.3256C>T) and three antiatherogenic mutations in mtDNA (m.13513G>A, m.652insG, and m.14846G>A) were detected in patients with atherosclerotic plaques in their carotid arteries from the Novosibirsk region.
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Affiliation(s)
- Margarita A. Sazonova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, Moscow 125315, Russia; (A.I.R.); (M.D.S.); (N.A.D.); (A.V.O.)
- Laboratory of Medical Genetics, Institute of Experimental Cardiology, Chazov National Medical Research Center of Cardiology, 15a, 3rd Cherepkovskaya Str., Moscow 121552, Russia;
| | - Tatiana V. Kirichenko
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Federal State Budgetary Scientific Institution, Petrovsky National Research Centre of Surgery (FSBSI “Petrovsky NRCS”), Moscow 117418, Russia; (T.V.K.); (N.G.N.)
| | - Anastasia I. Ryzhkova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, Moscow 125315, Russia; (A.I.R.); (M.D.S.); (N.A.D.); (A.V.O.)
| | - Marina D. Sazonova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, Moscow 125315, Russia; (A.I.R.); (M.D.S.); (N.A.D.); (A.V.O.)
| | - Natalya A. Doroschuk
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, Moscow 125315, Russia; (A.I.R.); (M.D.S.); (N.A.D.); (A.V.O.)
| | - Andrey V. Omelchenko
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, Moscow 125315, Russia; (A.I.R.); (M.D.S.); (N.A.D.); (A.V.O.)
| | - Nikita G. Nikiforov
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Federal State Budgetary Scientific Institution, Petrovsky National Research Centre of Surgery (FSBSI “Petrovsky NRCS”), Moscow 117418, Russia; (T.V.K.); (N.G.N.)
| | - Yulia I. Ragino
- Research Institute of Internal and Preventive Medicine—Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630089, Russia;
| | - Anton Yu. Postnov
- Laboratory of Medical Genetics, Institute of Experimental Cardiology, Chazov National Medical Research Center of Cardiology, 15a, 3rd Cherepkovskaya Str., Moscow 121552, Russia;
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Federal State Budgetary Scientific Institution, Petrovsky National Research Centre of Surgery (FSBSI “Petrovsky NRCS”), Moscow 117418, Russia; (T.V.K.); (N.G.N.)
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Zhou W, Karan KR, Gu W, Klein HU, Sturm G, De Jager PL, Bennett DA, Hirano M, Picard M, Mills RE. Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. PLoS Biol 2024; 22:e3002723. [PMID: 39172952 PMCID: PMC11340991 DOI: 10.1371/journal.pbio.3002723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/26/2024] [Indexed: 08/24/2024] Open
Abstract
The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in nonhuman species and recently demonstrated to occur in rare instances from one human generation to the next. Here, we investigated numtogenesis dynamics in humans in 2 ways. First, we quantified Numts in 1,187 postmortem brain and blood samples from different individuals. Compared to circulating immune cells (n = 389), postmitotic brain tissue (n = 798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples, we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex (DLPFC) compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, an increase in the number of brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment (NCI) who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures whole-genome sequencing design in a human fibroblast model that recapitulates several molecular hallmarks of aging. These longitudinal experiments revealed a gradual accumulation of 1 Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven by cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human postmitotic tissues produces functionally relevant human Numts over timescales shorter than previously assumed.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kalpita R. Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Wenjin Gu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Michio Hirano
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Neurology, H. Houston Merritt Center, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, New York, United States of America
- New York State Psychiatric Institute, New York, New York, United States of America
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, New York, United States of America
| | - Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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5
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Martinez P, Baghli I, Gourjon G, Seyfried TN. Mitochondrial-Stem Cell Connection: Providing Additional Explanations for Understanding Cancer. Metabolites 2024; 14:229. [PMID: 38668357 PMCID: PMC11051897 DOI: 10.3390/metabo14040229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The cancer paradigm is generally based on the somatic mutation model, asserting that cancer is a disease of genetic origin. The mitochondrial-stem cell connection (MSCC) proposes that tumorigenesis may result from an alteration of the mitochondria, specifically a chronic oxidative phosphorylation (OxPhos) insufficiency in stem cells, which forms cancer stem cells (CSCs) and leads to malignancy. Reviewed evidence suggests that the MSCC could provide a comprehensive understanding of all the different stages of cancer. The metabolism of cancer cells is altered (OxPhos insufficiency) and must be compensated by using the glycolysis and the glutaminolysis pathways, which are essential to their growth. The altered mitochondria regulate the tumor microenvironment, which is also necessary for cancer evolution. Therefore, the MSCC could help improve our understanding of tumorigenesis, metastases, the efficiency of standard treatments, and relapses.
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Affiliation(s)
- Pierrick Martinez
- Scientific and Osteopathic Research Department, Institut de Formation en Ostéopathie du Grand Avignon, 84140 Montfavet, France;
| | - Ilyes Baghli
- International Society for Orthomolecular Medicine, Toronto, ON M4B 3M9, Canada;
| | - Géraud Gourjon
- Scientific and Osteopathic Research Department, Institut de Formation en Ostéopathie du Grand Avignon, 84140 Montfavet, France;
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Biró B, Gál Z, Fekete Z, Klecska E, Hoffmann OI. Mitochondrial genome plasticity of mammalian species. BMC Genomics 2024; 25:278. [PMID: 38486136 PMCID: PMC10941376 DOI: 10.1186/s12864-024-10201-9] [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: 06/27/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
There is an ongoing process in which mitochondrial sequences are being integrated into the nuclear genome. The importance of these sequences has already been revealed in cancer biology, forensic, phylogenetic studies and in the evolution of the eukaryotic genetic information. Human and numerous model organisms' genomes were described from those sequences point of view. Furthermore, recent studies were published on the patterns of these nuclear localised mitochondrial sequences in different taxa.However, the results of the previously released studies are difficult to compare due to the lack of standardised methods and/or using few numbers of genomes. Therefore, in this paper our primary goal is to establish a uniform mining pipeline to explore these nuclear localised mitochondrial sequences.Our results show that the frequency of several repetitive elements is higher in the flanking regions of these sequences than expected. A machine learning model reveals that the flanking regions' repetitive elements and different structural characteristics are highly influential during the integration process.In this paper, we introduce a general mining pipeline for all mammalian genomes. The workflow is publicly available and is believed to serve as a validated baseline for future research in this field. We confirm the widespread opinion, on - as to our current knowledge - the largest dataset, that structural circumstances and events corresponding to repetitive elements are highly significant. An accurate model has also been trained to predict these sequences and their corresponding flanking regions.
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Affiliation(s)
- Bálint Biró
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary.
- Group BM, Data Insights Team, _VOIS, Kerepesi str. 35, 1087, Budapest, Hungary.
| | - Zoltán Gál
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary
| | - Zsófia Fekete
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary
| | - Eszter Klecska
- FamiCord Group, Krio Institute, Kelemen László str, 1026, Budapest, Hungary
| | - Orsolya Ivett Hoffmann
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary.
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7
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Harutyunyan T. The known unknowns of mitochondrial carcinogenesis: de novo NUMTs and intercellular mitochondrial transfer. Mutagenesis 2024; 39:1-12. [PMID: 37804235 DOI: 10.1093/mutage/gead031] [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: 07/20/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023] Open
Abstract
The translocation of mitochondrial DNA (mtDNA) sequences into the nuclear genome, resulted in the occurrence of nuclear sequences of mitochondrial origin (NUMTs) which can be detected in nearly all sequenced eukaryotes. However, de novo mtDNA insertions can contribute to the development of pathological conditions including cancer. Recent data indicate that de novo mtDNA translocation into chromosomes can occur due to genotoxic influence of DNA double-strand break-inducing environmental mutagens. This confirms the hypothesis of the involvement of genome instability in the occurrence of mtDNA fragments in chromosomes. Mounting evidence indicates that mitochondria can be transferred from normal cells to cancer cells and recover cellular respiration. These exchanged mitochondria can facilitate cancer progression and metastasis. This review article provides a comprehensive overview of the potential carcinogenicity of mtDNA insertions, and the relevance of mtDNA escape in cancer progression, metastasis, and treatment resistance in humans. Potential molecular targets involved in mtDNA escape and exchange of mitochondria that can be of possible clinical benefits are presented and discussed. Understanding these processes could lead to improved diagnostic approaches, novel therapeutic strategies, and a deeper understanding of the intricate relationship between mitochondria, nuclear DNA, and cancer biology.
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Affiliation(s)
- Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
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8
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Namasivayam S, Sun C, Bah AB, Oberstaller J, Pierre-Louis E, Etheridge RD, Feschotte C, Pritham EJ, Kissinger JC. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. Proc Natl Acad Sci U S A 2023; 120:e2308569120. [PMID: 37917792 PMCID: PMC10636329 DOI: 10.1073/pnas.2308569120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
Toxoplasma gondii is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
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Affiliation(s)
| | - Cheng Sun
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Assiatu B. Bah
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | | | - Edwin Pierre-Louis
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
| | - Ronald Drew Etheridge
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
| | - Cedric Feschotte
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Ellen J. Pritham
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Jessica C. Kissinger
- Department of Genetics, Institute of Bioinformatics, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
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Stefano GB, Büttiker P, Weissenberger S, Esch T, Anders M, Raboch J, Kream RM, Ptacek R. Independent and sensory human mitochondrial functions reflecting symbiotic evolution. Front Cell Infect Microbiol 2023; 13:1130197. [PMID: 37389212 PMCID: PMC10302212 DOI: 10.3389/fcimb.2023.1130197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
The bacterial origin of mitochondria has been a widely accepted as an event that occurred about 1.45 billion years ago and endowed cells with internal energy producing organelle. Thus, mitochondria have traditionally been viewed as subcellular organelle as any other - fully functionally dependent on the cell it is a part of. However, recent studies have given us evidence that mitochondria are more functionally independent than other organelles, as they can function outside the cells, engage in complex "social" interactions, and communicate with each other as well as other cellular components, bacteria and viruses. Furthermore, mitochondria move, assemble and organize upon sensing different environmental cues, using a process akin to bacterial quorum sensing. Therefore, taking all these lines of evidence into account we hypothesize that mitochondria need to be viewed and studied from a perspective of a more functionally independent entity. This view of mitochondria may lead to new insights into their biological function, and inform new strategies for treatment of disease associated with mitochondrial dysfunction.
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Affiliation(s)
- George B. Stefano
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Pascal Büttiker
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | | | - Tobias Esch
- Institute for Integrative Health Care and Health Promotion, School of Medicine, Witten/Herdecke University, Witten, Germany
| | - Martin Anders
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Jiri Raboch
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Richard M. Kream
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
| | - Radek Ptacek
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
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10
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Namasivayam S, Sun C, Bah AB, Oberstaller J, Pierre-Louis E, Etheridge RD, Feschotte C, Pritham EJ, Kissinger JC. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.539837. [PMID: 37293002 PMCID: PMC10245829 DOI: 10.1101/2023.05.22.539837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Toxoplasma gondii is a zoonotic protist pathogen that infects up to 1/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
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Affiliation(s)
- Sivaranjani Namasivayam
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Present address: Clinical Microbiome Unit, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD 20892, USA
| | - Cheng Sun
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA; Present address: College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Assiatu B Bah
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019
| | - Jenna Oberstaller
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Present address: Department of Global Health, University of South Florida, Tampa, FL 33620, USA
| | - Edwin Pierre-Louis
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Ronald Drew Etheridge
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Cedric Feschotte
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019; Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Ellen J. Pritham
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019
| | - Jessica C. Kissinger
- Department of Genetics, Institute of Bioinformatics, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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11
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Pfotenhauer AC, Occhialini A, Harbison SA, Li L, Piatek AA, Luckett CR, Yang Y, Stewart CN, Lenaghan SC. Genome-Editing of FtsZ1 for Alteration of Starch Granule Size in Potato Tubers. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091878. [PMID: 37176936 PMCID: PMC10180631 DOI: 10.3390/plants12091878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/06/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Genome-editing has enabled rapid improvement for staple food crops, such as potato, a key beneficiary of the technology. In potato, starch contained within tubers represents the primary product for use in food and non-food industries. Starch granules are produced in the plastids of tubers with plastid size correlated with the size of starch grana. The division of plastids is controlled by proteins, including the tubulin-like GTPase FtsZ1. The altered expression of FtsZ1 has been shown to disrupt plastid division, leading to the production of "macro-plastid"-containing plants. These macro-chloroplast plants are characterized by cells containing fewer and enlarged plastids. In this work, we utilize CRISPR/Cas9 to generate FtsZ1 edited potato lines to demonstrate that genome-editing can be used to increase the size of starch granules in tubers. Altered plastid morphology was comparable to the overexpression of FtsZ1 in previous work in potato and other crops. Several lines were generated with up to a 1.98-fold increase in starch granule size that was otherwise phenotypically indistinguishable from wild-type plants. Further, starch paste from one of the most promising lines showed a 2.07-fold increase in final viscosity. The advantages of enlarged starch granules and the potential of CRISPR/Cas9-based technologies for food crop improvement are further discussed.
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Affiliation(s)
- Alexander C Pfotenhauer
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Alessandro Occhialini
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Stacee A Harbison
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Li Li
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - Agnieszka A Piatek
- Department of Food Science, University of Tennessee, Knoxville, TN 37920, USA
| | - Curtis R Luckett
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Yongil Yang
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37920, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, Knoxville, TN 37996, USA
- Department of Food Science, University of Tennessee, Knoxville, TN 37920, USA
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12
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Zhou W, Karan KR, Gu W, Klein HU, Sturm G, De Jager PL, Bennett DA, Hirano M, Picard M, Mills RE. Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527065. [PMID: 36778249 PMCID: PMC9915708 DOI: 10.1101/2023.02.03.527065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species 1-3 and recently demonstrated to occur in rare instances from one human generation to the next 4. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging 5. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kalpita R. Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Wenjin Gu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612 USA
| | - Michio Hirano
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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13
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Baltazar-Soares M, Karell P, Wright D, Nilsson JÅ, Brommer JE. Bringing to light nuclear-mitochondrial insertions in the genomes of nocturnal predatory birds. Mol Phylogenet Evol 2023; 181:107722. [PMID: 36720422 DOI: 10.1016/j.ympev.2023.107722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
Mito-nuclear insertions, or NUMTs, relate to genetic material of mitochondrial origin that have been transferred to the nuclear DNA molecule. The increasing amounts of genomic data currently being produced presents an opportunity to investigate this type of patterns in genome evolution of non-model organisms. Identifying NUMTs across a range of closely related taxa allows one to generalize patterns of insertion and maintenance in autosomes, which is ultimately relevant to the understanding of genome biology and evolution. Here we collected existing pairwise genome-mitogenome data of the order Strigiformes, a group that includes all the nocturnal bird predators. We identified NUMTs by applying percent similarity thresholds after blasting mitochondrial genomes against nuclear genome assemblies. We identified NUMTsin all genomes with numbers ranging from 4 in Bubo bubo to 24 in Ciccaba nigrolineata. Statistical analyses revealed NUMT size to negatively correlate with NUMT's sequence similarity to with original mtDNA region. Lastly, characterizing these nuclear insertions of mitochondrial origin in a comparative genomics framework produced variable phylogenetic patterns, suggesting in some cases that insertions might pre-date speciation events within Strigiformes.
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Affiliation(s)
| | - Patrik Karell
- Bioeconomy Research Team, Novia University of Applied Sciences, Raseborgsvägen 9, FI-10600 Raseborg, Finland; Evolutionary Ecology Unit, Department of Biology, Lund University, Sölvegatan 39 (Ecology Building), SE-223 62 Lund, Sweden
| | - Dominic Wright
- IFM Biology, Linköping University, Linköping 58183, Sweden
| | - Jan-Åke Nilsson
- Department of Biology, Section of Evolutionary Ecology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Jon E Brommer
- Department of Biology, University of Turku, Turku 20500, Finland
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14
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Boguenet M, Desquiret-Dumas V, Reynier P, May-Panloup P. Technical specificities of the study of the mitochondrial genome. Hum Reprod Open 2023; 2023:hoac061. [PMID: 36654692 PMCID: PMC9838312 DOI: 10.1093/hropen/hoac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- M Boguenet
- Correspondence address. Equipe Mitolab, Institut MitoVasc (UMR CNRS 6015, Inserm 1083), CHU Bât IRIS1/IBS, Rue des Capucins 49933, Angers Cedex 9, France. E-mail: https://orcid.org/0000-0002-5368-3402
| | - V Desquiret-Dumas
- Univ Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICAT, Angers, France,Service de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire, Angers, France
| | - P Reynier
- Univ Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICAT, Angers, France,Service de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire, Angers, France
| | - P May-Panloup
- Univ Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICAT, Angers, France,Biologie de la Reproduction, Centre Hospitalier Universitaire, Angers, France
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15
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Triant DA, Pearson WR. Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes. Front Genet 2022; 13:984513. [PMID: 36482890 PMCID: PMC9723244 DOI: 10.3389/fgene.2022.984513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/03/2022] [Indexed: 01/27/2024] Open
Abstract
The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.
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Affiliation(s)
- Deborah A. Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
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16
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Liao WT, Chu PY, Su CC, Wu CC, Li CJ. Mitochondrial AAA protease gene associated with immune infiltration is a prognostic biomarker in human ovarian cancer. Pathol Res Pract 2022; 240:154215. [DOI: 10.1016/j.prp.2022.154215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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17
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Dong R, Cameron D, Bedo J, Papenfuss AT. svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data. GIGABYTE 2022; 2022:gigabyte70. [PMID: 36824522 PMCID: PMC9694029 DOI: 10.46471/gigabyte.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/25/2022] [Indexed: 11/07/2022] Open
Abstract
Nuclear integration of mitochondrial genomes and retrocopied transcript insertion are biologically important but often-overlooked aspects of structural variant (SV) annotation. While tools for their detection exist, these typically rely on reanalysis of primary data using specialised detectors rather than leveraging calls from general purpose structural variant callers. Such reanalysis potentially leads to additional computational expense and does not take advantage of advances in general purpose structural variant calling. Here, we present svaRetro and svaNUMT; R packages that provide functions for annotating novel genomic events, such as nonreference retrocopied transcripts and nuclear integration of mitochondrial DNA. The packages were developed to work within the Bioconductor framework. We evaluate the performance of these packages to detect events using simulations and public benchmarking datasets, and annotate processed transcripts in a public structural variant database. svaRetro and svaNUMT provide modular, SV-caller agnostic tools for downstream annotation of structural variant calls.
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Affiliation(s)
- Ruining Dong
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, VIC 3010, Australia
| | - Daniel Cameron
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, VIC 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Justin Bedo
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- School of Computing and Information Systems, University of Melbourne, VIC 3010, Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, VIC 3010, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia
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18
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González-Sánchez M, García-Martínez V, Bravo S, Kobayashi H, Martínez de Toda I, González-Bermúdez B, Plaza GR, De la Fuente M. Mitochondrial DNA insertions into nuclear DNA affecting chromosome segregation: Insights for a novel mechanism of immunosenescence in mice. Mech Ageing Dev 2022; 207:111722. [PMID: 35961414 DOI: 10.1016/j.mad.2022.111722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
Abstract
Mitochondrial DNA sequences were found inserted in the nuclear genome of mouse peritoneal T lymphocytes that increased progressively with aging. These insertions were preferentially located at the pericentromeric heterochromatin. In the same individuals, binucleated T-cells with micronuclei showed a significantly increased frequency associated with age. Most of them were positive for centromere sequences, reflecting the loss of chromatids or whole chromosomes. The proliferative capacity of T lymphocytes decreased with age as well as the glutathione reductase activity, whereas the oxidized glutathione and malondialdehyde concentrations exhibited a significant increase. These results may point to a common process that provides insights for a new approach to understanding immunosenescence. We propose a novel mechanism in which mitochondrial fragments, originated by the increased oxidative stress status during aging, accumulate inside the nuclear genome of T lymphocytes in a time-dependent way. The primary entrance of mitochondrial fragments at the pericentromeric regions may compromise chromosome segregation, causing genetic loss that leads to micronuclei formation, rendering aneuploid cells with reduced proliferation capacity, one of the hallmark of immunosenescence. Future experiments deciphering the mechanistic basis of this phenomenon are needed.
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Affiliation(s)
- Mónica González-Sánchez
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Víctor García-Martínez
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Sara Bravo
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Hikaru Kobayashi
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Irene Martínez de Toda
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Blanca González-Bermúdez
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain; Department of Materials Science, ETSI de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
| | - Gustavo R Plaza
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain; Department of Materials Science, ETSI de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
| | - Mónica De la Fuente
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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19
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Social Environment as a Modulator of Immunosenescence. Expert Rev Mol Med 2022; 24:e29. [PMID: 35912691 DOI: 10.1017/erm.2022.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Biró B, Gál Z, Schiavo G, Ribari A, Joe Utzeri V, Brookman M, Fontanesi L, Hoffmann OI. Nuclear mitochondrial DNA sequences in the rabbit genome. Mitochondrion 2022; 66:1-6. [PMID: 35842180 DOI: 10.1016/j.mito.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 07/10/2022] [Indexed: 10/17/2022]
Abstract
Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration.
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Affiliation(s)
- Bálint Biró
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary
| | - Zoltán Gál
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary
| | - Giuseppina Schiavo
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribari
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Valerio Joe Utzeri
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Michael Brookman
- Hanze University of Applied Sciences, Department for Biology and Medical Laboratory Research, Zernikeplein 7, 9747 AS Groningen, Netherlands
| | - Luca Fontanesi
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Orsolya Ivett Hoffmann
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary.
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21
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Unraveling mitochondrial piRNAs in mouse embryonic gonadal cells. Sci Rep 2022; 12:10730. [PMID: 35750721 PMCID: PMC9232517 DOI: 10.1038/s41598-022-14414-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Although mitochondria are widely studied organelles, the recent interest in the role of mitochondrial small noncoding RNAs (sncRNAs), miRNAs, and more recently, piRNAs, is providing new functional perspectives in germ cell development and differentiation. piRNAs (PIWI-interacting RNAs) are single-stranded sncRNAs of mostly about 20-35 nucleotides, generated from the processing of pre-piRNAs. We leverage next-generation sequencing data obtained from mouse primordial germ cells and somatic cells purified from early-differentiating embryonic ovaries and testis from 11.5 to 13.5 days postcoitum. Using bioinformatic tools, we elucidate (i) the origins of piRNAs as transcribed from mitochondrial DNA fragments inserted in the nucleus or from the mitochondrial genome; (ii) their levels of expression; and (iii) their potential roles, as well as their association with genomic regions encoding other sncRNAs (such as tRNAs and rRNAs) and the mitochondrial regulatory region (D-loop). Finally, our results suggest how nucleo-mitochondrial communication, both anterograde and retrograde signaling, may be mediated by mitochondria-associated piRNAs.
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22
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Martín Giménez VM, de las Heras N, Lahera V, Tresguerres JAF, Reiter RJ, Manucha W. Melatonin as an Anti-Aging Therapy for Age-Related Cardiovascular and Neurodegenerative Diseases. Front Aging Neurosci 2022; 14:888292. [PMID: 35721030 PMCID: PMC9204094 DOI: 10.3389/fnagi.2022.888292] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/25/2022] [Indexed: 12/15/2022] Open
Abstract
The concept of “aging” is defined as the set of gradual and progressive changes in an organism that leads to an increased risk of weakness, disease, and death. This process may occur at the cellular and organ level, as well as in the entire organism of any living being. During aging, there is a decrease in biological functions and in the ability to adapt to metabolic stress. General effects of aging include mitochondrial, cellular, and organic dysfunction, immune impairment or inflammaging, oxidative stress, cognitive and cardiovascular alterations, among others. Therefore, one of the main harmful consequences of aging is the development and progression of multiple diseases related to these processes, especially at the cardiovascular and central nervous system levels. Both cardiovascular and neurodegenerative pathologies are highly disabling and, in many cases, lethal. In this context, melatonin, an endogenous compound naturally synthesized not only by the pineal gland but also by many cell types, may have a key role in the modulation of multiple mechanisms associated with aging. Additionally, this indoleamine is also a therapeutic agent, which may be administered exogenously with a high degree of safety. For this reason, melatonin could become an attractive and low-cost alternative for slowing the processes of aging and its associated diseases, including cardiovascular and neurodegenerative disorders.
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Affiliation(s)
- Virna Margarita Martín Giménez
- Instituto de Investigaciones en Ciencias Químicas, Facultad de Ciencias Químicas y Tecnológicas, Universidad Católica de Cuyo, San Juan, Argentina
| | - Natalia de las Heras
- Departamento de Fisiología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Vicente Lahera
- Departamento de Fisiología, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | | | - Russel J. Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio Long School of Medicine, San Antonio, TX, United States
| | - Walter Manucha
- Área de Farmacología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Mendoza, Argentina
- Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Mendoza, Argentina
- *Correspondence: Walter Manucha ;
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23
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Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
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Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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Martínez de Toda I, Ceprián N, Díaz-Del Cerro E, De la Fuente M. The Role of Immune Cells in Oxi-Inflamm-Aging. Cells 2021; 10:2974. [PMID: 34831197 PMCID: PMC8616159 DOI: 10.3390/cells10112974] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/30/2021] [Indexed: 02/07/2023] Open
Abstract
Aging is the result of the deterioration of the homeostatic systems (nervous, endocrine, and immune systems), which preserve the organism's health. We propose that the age-related impairment of these systems is due to the establishment of a chronic oxidative stress situation that leads to low-grade chronic inflammation throughout the immune system's activity. It is known that the immune system weakens with age, which increases morbidity and mortality. In this context, we describe how the function of immune cells can be used as an indicator of the rate of aging of an individual. In addition to this passive role as a marker, we describe how the immune system can work as a driver of aging by amplifying the oxidative-inflammatory stress associated with aging (oxi-inflamm-aging) and inducing senescence in far tissue cells. Further supporting our theory, we discuss how certain lifestyle conditions (such as social environment, nutrition, or exercise) can have an impact on longevity by affecting the oxidative and inflammatory state of immune cells, regulating immunosenescence and its contribution to oxi-inflamm-aging.
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Affiliation(s)
- Irene Martínez de Toda
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (N.C.); (E.D.-D.C.); (M.D.l.F.)
- Institute of Investigation 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Noemi Ceprián
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (N.C.); (E.D.-D.C.); (M.D.l.F.)
- Institute of Investigation 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Estefanía Díaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (N.C.); (E.D.-D.C.); (M.D.l.F.)
- Institute of Investigation 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Mónica De la Fuente
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; (N.C.); (E.D.-D.C.); (M.D.l.F.)
- Institute of Investigation 12 de Octubre (i+12), 28041 Madrid, Spain
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25
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Ouyang X, Zhang Y, Zhang L, Luo J, Zhang T, Hu H, Liu L, Zhong L, Zeng S, Xu P, Bai Z, Wong LJ, Wang J, Wang C, Wang B, Zhang VW. Clinical Utility of Rapid Exome Sequencing Combined With Mitochondrial DNA Sequencing in Critically Ill Pediatric Patients With Suspected Genetic Disorders. Front Genet 2021; 12:725259. [PMID: 34490048 PMCID: PMC8416976 DOI: 10.3389/fgene.2021.725259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023] Open
Abstract
Genetic disorders are a frequent cause of hospitalization, morbidity and mortality in pediatric patients, especially in the neonatal or pediatric intensive care unit (NICU/PICU). In recent years, rapid genome-wide sequencing (exome or whole genome sequencing) has been applied in the NICU/PICU. However, mtDNA sequencing is not routinely available in rapid genetic diagnosis programs, which may fail to diagnose mtDNA mutation-associated diseases. Herein, we explored the clinical utility of rapid exome sequencing combined with mtDNA sequencing in critically ill pediatric patients with suspected genetic disorders. Rapid clinical exome sequencing (CES) was performed as a first-tier test in 40 critically ill pediatric patients (aged from 6 days to 15 years) with suspected genetic conditions. Blood samples were also collected from the parents for trio analysis. Twenty-six patients presented with neuromuscular abnormalities or other systemic abnormalities, suggestive of suspected mitochondrial diseases or the necessity for a differential diagnosis of other diseases, underwent rapid mtDNA sequencing concurrently. A diagnosis was made in 18 patients (45.0%, 18/40); three cases with de novo autosomal dominant variants, ten cases with homozygous or compound heterozygous variants, three cases with hemizygous variants inherited from mother, three cases with heterozygous variants inherited from either parent, and one case with a mtDNA mutation. The 18 patients were diagnosed with metabolic (n = 7), immunodeficiency (n = 4), cardiovascular (n = 2), neuromuscular (n = 2) disorders, and others. Genetic testing reports were generated with a median time of 5 days (range, 3–9 days). Thirteen patients that were diagnosed had an available medical treatment and resulted in a positive outcome. We propose that rapid exome sequencing combined with mitochondrial DNA sequencing should be available to patients with suspected mitochondrial diseases or undefined clinical features necessary for making a differential diagnosis of other diseases.
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Affiliation(s)
- Xuejun Ouyang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Zhang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lijuan Zhang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jixuan Luo
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Zhang
- Department of Gastroenterology, Shanghai Children's Hospital, Shanghai, China
| | - Hui Hu
- Department of Gastroenterology, Shanghai Children's Hospital, Shanghai, China
| | - Lin Liu
- Department of Vasculocardiology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Lieqiang Zhong
- Department of Vasculocardiology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Shaoying Zeng
- Department of Vasculocardiology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Pingyi Xu
- Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenjiang Bai
- Department of Critical Care Medicine, Children's Hospital of Soochow University, Suzhou, China
| | - Lee-Jun Wong
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jing Wang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.,AmCare Genomics Lab, Guangzhou, China
| | | | - Bin Wang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Victor Wei Zhang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.,AmCare Genomics Lab, Guangzhou, China
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Brandeis M. Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes. Bioessays 2021; 43:e2000256. [PMID: 33860546 DOI: 10.1002/bies.202000256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/10/2022]
Abstract
I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.
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Affiliation(s)
- Michael Brandeis
- The Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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Kim J, Choi JW, Namkung J. Expression Profile of Mouse Gm20594, Nuclear-Encoded Humanin-Like Gene. J Lifestyle Med 2021; 11:13-22. [PMID: 33763338 PMCID: PMC7957044 DOI: 10.15280/jlm.2021.11.1.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 12/21/2022] Open
Abstract
Background Mitochondrial-derived peptides (MDPs) such as MOTS-c and humanin have been studied for their cytoprotective functions. In mice, humanin-encoding Mtrnr2 is a mitochondrial pseudogene, and the humanin-like peptide is encoded by the nuclear Gm20594 gene. However, endogenous tissue-specific expression profiles of Gm20594 have not yet been identified. Methods Mtrnr1 and Gm20594 expression was profiled via reverse transcription using only oligo(dT) primers from tissues of C57BL6/J mice. To analyze altered expression upon mitochondrial biogenesis, C2C12 myocytes and brown adipocytes were differentiated. Mitochondrial DNA copy numbers were quantified for normalization. Results Both Mtrnr1 and Gm20594 were highly expressed in brown adipose tissue. When normalized against mitochondrial content, Mtrnr1 was identified as being highly expressed in the duodenum, followed by the jejunum. In models of mitochondrial biogenesis, both Mtrnr1 and Gm20594 were upregulated during myocyte and brown adipocyte differentiation. Increased Mtrnr1 expression during brown adipocyte differentiation remained significant after normalization against mitochondrial DNA copy number, whereas myocyte differentiation exhibited biphasic upregulation and downregulation in early and late phases, respectively. Conclusion Nuclear-encoded Gm20594 showed similar expression patterns of mitochondrial-encoded Mtrnr1. Brown adipose tissue presented the highest basal expression levels of Gm20594 and Mtrnr1. When normalized against mitochondrial DNA copy number, gut tissues exhibited the highest expression of Mtrnr1. Upregulation of Mtrnr1 during mitochondrial biogenesis is independent of mitochondrial content.
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Affiliation(s)
- Jihye Kim
- Department of Biochemistry, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jong-Whan Choi
- Department of Biochemistry, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Jun Namkung
- Department of Biochemistry, Yonsei University Wonju College of Medicine, Wonju, Korea
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28
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Hanscom T, McVey M. Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution. Cells 2020; 9:E1657. [PMID: 32660124 PMCID: PMC7407515 DOI: 10.3390/cells9071657] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Double-strand breaks are one of the most deleterious DNA lesions. Their repair via error-prone mechanisms can promote mutagenesis, loss of genetic information, and deregulation of the genome. These detrimental outcomes are significant drivers of human diseases, including many cancers. Mutagenic double-strand break repair also facilitates heritable genetic changes that drive organismal adaptation and evolution. In this review, we discuss the mechanisms of various error-prone DNA double-strand break repair processes and the cellular conditions that regulate them, with a focus on alternative end joining. We provide examples that illustrate how mutagenic double-strand break repair drives genome diversity and evolution. Finally, we discuss how error-prone break repair can be crucial to the induction and progression of diseases such as cancer.
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Affiliation(s)
| | - Mitch McVey
- Department. of Biology, Tufts University, Medford, MA 02155, USA;
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