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Brañas Casas R, Zuppardo A, Risato G, Dinarello A, Celeghin R, Fontana C, Grelloni E, Gilea AI, Viscomi C, Rasola A, Dalla Valle L, Lodi T, Baruffini E, Facchinello N, Argenton F, Tiso N. Zebrafish polg2 knock-out recapitulates human POLG-disorders; implications for drug treatment. Cell Death Dis 2024; 15:281. [PMID: 38643274 PMCID: PMC11032366 DOI: 10.1038/s41419-024-06622-9] [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: 11/30/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
The human mitochondrial DNA polymerase gamma is a holoenzyme, involved in mitochondrial DNA (mtDNA) replication and maintenance, composed of a catalytic subunit (POLG) and a dimeric accessory subunit (POLG2) conferring processivity. Mutations in POLG or POLG2 cause POLG-related diseases in humans, leading to a subset of Mendelian-inherited mitochondrial disorders characterized by mtDNA depletion (MDD) or accumulation of multiple deletions, presenting multi-organ defects and often leading to premature death at a young age. Considering the paucity of POLG2 models, we have generated a stable zebrafish polg2 mutant line (polg2ia304) by CRISPR/Cas9 technology, carrying a 10-nucleotide deletion with frameshift mutation and premature stop codon. Zebrafish polg2 homozygous mutants present slower development and decreased viability compared to wild type siblings, dying before the juvenile stage. Mutants display a set of POLG-related phenotypes comparable to the symptoms of human patients affected by POLG-related diseases, including remarkable MDD, altered mitochondrial network and dynamics, and reduced mitochondrial respiration. Histological analyses detected morphological alterations in high-energy demanding tissues, along with a significant disorganization of skeletal muscle fibres. Consistent with the last finding, locomotor assays highlighted a decreased larval motility. Of note, treatment with the Clofilium tosylate drug, previously shown to be effective in POLG models, could partially rescue MDD in Polg2 mutant animals. Altogether, our results point at zebrafish as an effective model to study the etiopathology of human POLG-related disorders linked to POLG2, and a suitable platform to screen the efficacy of POLG-directed drugs in POLG2-associated forms.
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Affiliation(s)
| | - Alessandro Zuppardo
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | - Giovanni Risato
- Department of Biology, University of Padova, Padova, 35131, Italy
- Department of Cardio-Thoraco-Vascular Sciences and Public Health, University of Padova, Padova, 35128, Italy
| | - Alberto Dinarello
- Department of Biology, University of Padova, Padova, 35131, Italy
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, 2200, Denmark
| | - Rudy Celeghin
- Department of Cardio-Thoraco-Vascular Sciences and Public Health, University of Padova, Padova, 35128, Italy
| | - Camilla Fontana
- Department of Biology, University of Padova, Padova, 35131, Italy
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | | | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, Padova, 35131, Italy
| | | | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Nicola Facchinello
- Neuroscience Institute, Italian Research Council (CNR), 35131, Padova, Italy.
| | | | - Natascia Tiso
- Department of Biology, University of Padova, Padova, 35131, Italy.
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2
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Cheng Q, Liu QQ, Lu CA. A state-of-the-science review of using mitochondrial DNA copy number as a biomarker for environmental exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123642. [PMID: 38402934 DOI: 10.1016/j.envpol.2024.123642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Mitochondria are bioenergetic, biosynthetic, and signaling organelles in eukaryotes, and contain their own genomes, mitochondrial DNA (mtDNA), to supply energy to cells by generating ATP via oxidative phosphorylation. Therefore, the threat to mitochondria' integrity and health resulting from environmental exposure could induce adverse health effects in organisms. In this review, we summarized the association between mtDNA copy number (mtDNAcn), and environmental exposures as reported in the literature. We conducted a literature search in the Web of Science using [Mitochondrial DNA copy number] and [Exposure] as two keywords and employed three selection criteria for the final inclusion of 97 papers for review. The consensus of data was that mtDNAcn could be used as a plausible biomarker for cumulative exposures to environmental chemical and physical agents. In order to furtherly expand the application of mtDNAcn in ecological and environmental health research, we suggested a series of algorithms aiming to standardize the calculation of mtDNAcn based on the PCR results in this review. We also discussed the pitfalls of using whole blood/plasma samples for mtDNAcn measurements and regard buccal cells a plausible and practical alternative. Finally, we recognized the importance of better understanding the mechanistic analysis and regulatory mechanism of mtDNAcn, in particular the signals release and regulation pathways. We believe that the development of using mtDNAcn as an exposure biomarker will revolutionize the evaluation of chronic sub-lethal toxicity of chemicals to organisms in ecological and environmental health research that has not yet been implemented.
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Affiliation(s)
- Qing Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qing Qing Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chensheng Alex Lu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China; School of Public Health, University of Washington, Seattle, WA, 98195, USA.
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Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [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: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
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Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
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4
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Kanazashi Y, Maejima K, Johnson TA, Sasagawa S, Jikuya R, Hasumi H, Matsumoto N, Maekawa S, Obara W, Nakagawa H. Mitochondrial DNA Variants at Low-Level Heteroplasmy and Decreased Copy Numbers in Chronic Kidney Disease (CKD) Tissues with Kidney Cancer. Int J Mol Sci 2023; 24:17212. [PMID: 38139039 PMCID: PMC10743237 DOI: 10.3390/ijms242417212] [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: 09/13/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The human mitochondrial genome (mtDNA) is a circular DNA molecule with a length of 16.6 kb, which contains a total of 37 genes. Somatic mtDNA mutations accumulate with age and environmental exposure, and some types of mtDNA variants may play a role in carcinogenesis. Recent studies observed mtDNA variants not only in kidney tumors but also in adjacent kidney tissues, and mtDNA dysfunction results in kidney injury, including chronic kidney disease (CKD). To investigate whether a relationship exists between heteroplasmic mtDNA variants and kidney function, we performed ultra-deep sequencing (30,000×) based on long-range PCR of DNA from 77 non-tumor kidney tissues of kidney cancer patients with CKD (stages G1 to G5). In total, this analysis detected 697 single-nucleotide variants (SNVs) and 504 indels as heteroplasmic (0.5% ≤ variant allele frequency (VAF) < 95%), and the total number of detected SNVs/indels did not differ between CKD stages. However, the number of deleterious low-level heteroplasmic variants (pathogenic missense, nonsense, frameshift and tRNA) significantly increased with CKD progression (p < 0.01). In addition, mtDNA copy numbers (mtDNA-CNs) decreased with CKD progression (p < 0.001). This study demonstrates that mtDNA damage, which affects mitochondrial genes, may be involved in reductions in mitochondrial mass and associated with CKD progression and kidney dysfunction.
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Affiliation(s)
- Yuki Kanazashi
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
- Department of Human Genetics, Yokohama City University, Yokohama 236-0004, Japan;
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Todd A. Johnson
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Shota Sasagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
| | - Ryosuke Jikuya
- Department of Urology, Yokohama City University, Yokohama 236-0004, Japan; (R.J.); (H.H.)
| | - Hisashi Hasumi
- Department of Urology, Yokohama City University, Yokohama 236-0004, Japan; (R.J.); (H.H.)
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Yokohama 236-0004, Japan;
| | - Shigekatsu Maekawa
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (S.M.); (W.O.)
| | - Wataru Obara
- Department of Urology, Iwate Medical University, Iwate 028-3694, Japan; (S.M.); (W.O.)
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; (Y.K.); (K.M.); (T.A.J.); (S.S.)
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Sack T, Dhavarasa P, Szames D, O'Brien S, Angers S, Kelley SO. CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560559. [PMID: 37873237 PMCID: PMC10592966 DOI: 10.1101/2023.10.03.560559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A major impediment to the characterization of mtDNA repair mechanisms, in comparison to nuclear DNA repair mechanisms, is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of a mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox) we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted Dox screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentially of our top hit - WRNIP1 - observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.
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Bastos-Moreira Y, Ouédraogo L, De Boevre M, Argaw A, de Kok B, Hanley-Cook GT, Deng L, Ouédraogo M, Compaoré A, Tesfamariam K, Ganaba R, Huybregts L, Toe LC, Lachat C, Kolsteren P, De Saeger S, Dailey-Chwalibóg T. A Multi-Omics and Human Biomonitoring Approach to Assessing the Effectiveness of Fortified Balanced Energy-Protein Supplementation on Maternal and Newborn Health in Burkina Faso: A Study Protocol. Nutrients 2023; 15:4056. [PMID: 37764838 PMCID: PMC10535470 DOI: 10.3390/nu15184056] [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: 08/07/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Fortified balanced energy-protein (BEP) supplementation is a promising intervention for improving maternal health, birth outcomes and infant growth in low- and middle-income countries. This nested biospecimen sub-study aimed to evaluate the physiological effect of multi-micronutrient-fortified BEP supplementation on pregnant and lactating women and their infants. Pregnant women (15-40 years) received either fortified BEP and iron-folic acid (IFA) (intervention) or IFA only (control) throughout pregnancy. The same women were concurrently randomized to receive either a fortified BEP supplement during the first 6 months postpartum in combination with IFA for the first 6 weeks (i.e., intervention) or the postnatal standard of care, which comprised IFA alone for 6 weeks postpartum (i.e., control). Biological specimens were collected at different timepoints. Multi-omics profiles will be characterized to assess the mediating effect of BEP supplementation on the different trial arms and its effect on maternal health, as well as birth and infant growth outcomes. The mediating effect of the exposome in the relationship between BEP supplementation and maternal health, birth outcomes and infant growth were characterized via biomonitoring markers of air pollution, mycotoxins and environmental contaminants. The results will provide holistic insight into the granular physiological effects of prenatal and postnatal BEP supplementation.
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Affiliation(s)
- Yuri Bastos-Moreira
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Lionel Ouédraogo
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Centre Muraz, Bobo-Dioulasso 01 BP 390, Burkina Faso
| | - Marthe De Boevre
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
| | - Alemayehu Argaw
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Brenda de Kok
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Giles T. Hanley-Cook
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Lishi Deng
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Moctar Ouédraogo
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Anderson Compaoré
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Kokeb Tesfamariam
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Rasmané Ganaba
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Lieven Huybregts
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Nutrition, Diets, and Health Unit, Department of Food and Nutrition Policy, International Food Policy Research Institute (IFPRI), Washington, DC 20005, USA
| | - Laeticia Celine Toe
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Unité Nutrition et Maladies Métaboliques, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
| | - Carl Lachat
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Patrick Kolsteren
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Sarah De Saeger
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng 2028, South Africa
| | - Trenton Dailey-Chwalibóg
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
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Nakazato I, Okuno M, Itoh T, Tsutsumi N, Arimura SI. Characterization and development of a plastid genome base editor, ptpTALECD. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1151-1162. [PMID: 37265080 DOI: 10.1111/tpj.16311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
The modification of photosynthesis-related genes in plastid genomes may improve crop yields. Recently, we reported that a plastid-targeting base editor named ptpTALECD, in which a cytidine deaminase DddA functions as the catalytic domain, can homoplasmically substitute a targeted C to T in plastid genomes of Arabidopsis thaliana. However, some target Cs were not substituted. In addition, although ptpTALECD could substitute Cs on the 3' side of T and A, it was unclear whether it could also substitute Cs on the 3' side of G and C. In this study, we identified the preferential positions of the substituted Cs in ptpTALECD-targeting sequences in the Arabidopsis plastid genome. We also found that ptpTALECD could substitute Cs on the 3' side of all four bases in plastid genomes of Arabidopsis. More recently, a base editor containing an improved version of DddA (DddA11) was reported to substitute Cs more efficiently, and to substitute Cs on the 3' side of more varieties of bases in human mitochondrial genomes than a base editor containing DddA. Here, we also show that ptpTALECD_v2, in which a modified version of DddA11 functions as the catalytic domain, more frequently substituted Cs than ptpTALECD in the Arabidopsis plastid genome. We also found that ptpTALECD_v2 tended to substitute Cs at more positions than ptpTALECD. Our results reveal that ptpTALECD can cause a greater variety of codon changes and amino acid substitutions than previously thought, and that ptpTALECD and ptpTALECD_v2 are useful tools for the targeted base editing of plastid genomes.
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Affiliation(s)
- Issei Nakazato
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Japan, 67, Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
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8
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Erdinc D, Macao B, Valenzuela S, Lesko N, Naess K, Peter B, Bruhn H, Wedell A, Wredenberg A, Falkenberg M. The disease-causing mutation p.F907I reveals a novel pathogenic mechanism for POLγ-related diseases. Biochim Biophys Acta Mol Basis Dis 2023:166786. [PMID: 37302426 DOI: 10.1016/j.bbadis.2023.166786] [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: 03/23/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/13/2023]
Abstract
Mutations in the catalytic domain of mitochondrial DNA polymerase γ (POLγ) cause a broad spectrum of clinical conditions. POLγ mutations impair mitochondrial DNA replication, thereby causing deletions and/or depletion of mitochondrial DNA, which in turn impair biogenesis of the oxidative phosphorylation system. We here identify a patient with a homozygous p.F907I mutation in POLγ, manifesting a severe clinical phenotype with developmental arrest and rapid loss of skills from 18 months of age. Magnetic resonance imaging of the brain revealed extensive white matter abnormalities, Southern blot of muscle mtDNA demonstrated depletion of mtDNA and the patient deceased at 23 months of age. Interestingly, the p.F907I mutation does not affect POLγ activity on single-stranded DNA or its proofreading activity. Instead, the mutation affects unwinding of parental double-stranded DNA at the replication fork, impairing the ability of the POLγ to support leading-strand DNA synthesis with the TWINKLE helicase. Our results thus reveal a novel pathogenic mechanism for POLγ-related diseases.
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Affiliation(s)
- Direnis Erdinc
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Nicole Lesko
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17177, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Naess
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17177, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Helene Bruhn
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17177, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm SE-17177, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg SE-40530, Sweden.
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9
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Makinde E, Ma L, Mellick GD, Feng Y. Mitochondrial Modulators: The Defender. Biomolecules 2023; 13:biom13020226. [PMID: 36830595 PMCID: PMC9953029 DOI: 10.3390/biom13020226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023] Open
Abstract
Mitochondria are widely considered the "power hub" of the cell because of their pivotal roles in energy metabolism and oxidative phosphorylation. However, beyond the production of ATP, which is the major source of chemical energy supply in eukaryotes, mitochondria are also central to calcium homeostasis, reactive oxygen species (ROS) balance, and cell apoptosis. The mitochondria also perform crucial multifaceted roles in biosynthetic pathways, serving as an important source of building blocks for the biosynthesis of fatty acid, cholesterol, amino acid, glucose, and heme. Since mitochondria play multiple vital roles in the cell, it is not surprising that disruption of mitochondrial function has been linked to a myriad of diseases, including neurodegenerative diseases, cancer, and metabolic disorders. In this review, we discuss the key physiological and pathological functions of mitochondria and present bioactive compounds with protective effects on the mitochondria and their mechanisms of action. We highlight promising compounds and existing difficulties limiting the therapeutic use of these compounds and potential solutions. We also provide insights and perspectives into future research windows on mitochondrial modulators.
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10
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White K, Someya S. The roles of NADPH and isocitrate dehydrogenase in cochlear mitochondrial antioxidant defense and aging. Hear Res 2023; 427:108659. [PMID: 36493529 DOI: 10.1016/j.heares.2022.108659] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 11/04/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022]
Abstract
Hearing loss is the third most prevalent chronic health condition affecting older adults. Age-related hearing loss affects one in three adults over 65 years of age and is caused by both extrinsic and intrinsic factors, including genetics, aging, and exposure to noise and toxins. All cells possess antioxidant defense systems that play an important role in protecting cells against these factors. Reduced nicotinamide adenine dinucleotide phosphate (NADPH) serves as a co-factor for antioxidant enzymes such as glutathione reductase and thioredoxin reductase and is produced by glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, isocitrate dehydrogenase 1 (IDH1) or malic enzyme 1 in the cytosol, while in the mitochondria, NADPH is generated from mitochondrial transhydrogenase, glutamate dehydrogenase, malic enzyme 3 or IDH2. There are three isoforms of IDH: cytosolic IDH1, and mitochondrial IDH2 and IDH3. Of these, IDH2 is thought to be the major supplier of NADPH to the mitochondrial antioxidant defense system. The NADP+/NADPH and NAD+/NADH couples are essential for maintaining a large array of biological processes, including cellular redox state, and energy metabolism, mitochondrial function. A growing body of evidence indicates that mitochondrial dysfunction contributes to age-related structural or functional changes of cochlear sensory hair cells and neurons, leading to hearing impairments. In this review, we describe the current understanding of the roles of NADPH and IDHs in cochlear mitochondrial antioxidant defense and aging.
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Affiliation(s)
- Karessa White
- Charlie Brigade Support Medical Company, 2/1 ABCT, United States Army, Fort Riley, KS, USA
| | - Shinichi Someya
- Department of Physiology and Aging, University of Florida, Gainesville, Florida, USA.
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11
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Yan S, Zhao J, Kemp M, Sobol RW. Editorial: Mechanistic studies of genome integrity, environmental health, and cancer etiology. Front Cell Dev Biol 2022; 10:1026326. [PMID: 36247007 PMCID: PMC9554606 DOI: 10.3389/fcell.2022.1026326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/07/2022] [Indexed: 01/31/2023] Open
Affiliation(s)
- Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
| | - Jianjun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
| | - Michael Kemp
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL, United States,Correspondence: Shan Yan, ; Jianjun Zhao, ; Michael Kemp, ; Robert W. Sobol,
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12
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DNA2 mutation causing multisystemic disorder with impaired mitochondrial DNA maintenance. J Hum Genet 2022; 67:691-699. [PMID: 36064591 DOI: 10.1038/s10038-022-01075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE To describe a novel DNA2 variant contributing to defects in mtDNA maintenance and mtDNA depletion syndrome (MDS), and the clinical and histological findings associated with this variation. METHODS Herein, we describe the case of a patient who presented with hearing loss and myopathy, given the family history of similar findings in the father, was evaluated by sequencing of the deafness gene panel, mitochondrial genome, and the exome. Furthermore, tissue staining, mtDNA copy number detection, mtDNA sequencing, and long-range polymerase chain reaction tests were also conducted on the muscle biopsy specimen. In vitro experiments, including analyses of the mtDNA copy number; levels of ATP, ATPase, and reactive oxygen species (ROS); and the membrane potential, were performed. RESULTS The DNA2 heterozygous truncating variant c. 2368C > T (p.Q790X) was identified and verified as the cause of an mtDNA copy number decrement in both functional experiments and muscle tissue analyses. These changes were accompanied by reductions in ATP, ATPase, and ROS levels. CONCLUSION The DNA2 variant was a likely cause of MDS in this patient. These findings expand the mutational spectrum of MDS and improve our understanding of the functions of DNA2 by revealing its novel role in mtDNA maintenance.
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13
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Sharma N, Thompson MK, Arrington JF, Terry DM, Chakravarthy S, Prevelige PE, Prakash A. Novel interaction interfaces mediate the interaction between the NEIL1 DNA glycosylase and mitochondrial transcription factor A. Front Cell Dev Biol 2022; 10:893806. [PMID: 35938152 PMCID: PMC9354671 DOI: 10.3389/fcell.2022.893806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
The maintenance of human mitochondrial DNA (mtDNA) is critical for proper cellular function as damage to mtDNA, if left unrepaired, can lead to a diverse array of pathologies. Of the pathways identified to participate in DNA repair within the mitochondria, base excision repair (BER) is the most extensively studied. Protein-protein interactions drive the step-by-step coordination required for the successful completion of this pathway and are important for crosstalk with other mitochondrial factors involved in genome maintenance. Human NEIL1 is one of seven DNA glycosylases that initiates BER in both the nuclear and mitochondrial compartments. In the current work, we scrutinized the interaction between NEIL1 and mitochondrial transcription factor A (TFAM), a protein that is essential for various aspects of mtDNA metabolism. We note, for the first time, that both the N- and C- terminal domains of NEIL1 interact with TFAM revealing a unique NEIL1 protein-binding interface. The interaction between the two proteins, as observed biochemically, appears to be transient and is most apparent at concentrations of low salt. The presence of DNA (or RNA) also positively influences the interaction between the two proteins, and molar mass estimates indicate that duplex DNA is required for complex formation at higher salt concentrations. Hydrogen deuterium exchange mass spectrometry data reveal that both proteins exchange less deuterium upon DNA binding, indicative of an interaction, and the addition of NEIL1 to the TFAM-DNA complex alters the interaction landscape. The transcriptional activity of TFAM appears to be independent of NEIL1 expression under normal cellular conditions, however, in the presence of DNA damage, we observe a significant reduction in the mRNA expression of TFAM-transcribed mitochondrial genes in the absence of NEIL1. Overall, our data indicate that the interaction between NEIL1 and TFAM can be modulated by local environment such as salt concentrations, protein availability, the presence of nucleic acids, as well as the presence of DNA damage.
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Affiliation(s)
- Nidhi Sharma
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Marlo K. Thompson
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Jennifer F. Arrington
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Dava M. Terry
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
| | - Srinivas Chakravarthy
- Advanced Photon Source, Illinois Institute of Technology, Chicago, IL, United States
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Aishwarya Prakash
- Department of Biochemistry and Molecular Biology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, United States
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14
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Karlowicz A, Dubiel AB, Czerwinska J, Bledea A, Purzycki P, Grzelewska M, McAuley RJ, Szczesny RJ, Brzuska G, Krol E, Szczesny B, Szymanski MR. In vitro reconstitution reveals a key role of human mitochondrial EXOG in RNA primer processing. Nucleic Acids Res 2022; 50:7991-8007. [PMID: 35819194 PMCID: PMC9371904 DOI: 10.1093/nar/gkac581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/01/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022] Open
Abstract
The removal of RNA primers is essential for mitochondrial DNA (mtDNA) replication. Several nucleases have been implicated in RNA primer removal in human mitochondria, however, no conclusive mechanism has been elucidated. Here, we reconstituted minimal in vitro system capable of processing RNA primers into ligatable DNA ends. We show that human 5'-3' exonuclease, EXOG, plays a fundamental role in removal of the RNA primer. EXOG cleaves short and long RNA-containing flaps but also in cooperation with RNase H1, processes non-flap RNA-containing intermediates. Our data indicate that the enzymatic activity of both enzymes is necessary to process non-flap RNA-containing intermediates and that regardless of the pathway, EXOG-mediated RNA cleavage is necessary prior to ligation by DNA Ligase III. We also show that upregulation of EXOG levels in mitochondria increases ligation efficiency of RNA-containing substrates and discover physical interactions, both in vitro and in cellulo, between RNase H1 and EXOG, Pol γA, Pol γB and Lig III but not FEN1, which we demonstrate to be absent from mitochondria of human lung epithelial cells. Together, using human mtDNA replication enzymes, we reconstitute for the first time RNA primer removal reaction and propose a novel model for RNA primer processing in human mitochondria.
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Affiliation(s)
- Anna Karlowicz
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Andrzej B Dubiel
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106 Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Adela Bledea
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Piotr Purzycki
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Marta Grzelewska
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Ryan J McAuley
- Department of Ophthalmology and Visual Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Gabriela Brzuska
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Ewelina Krol
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Bartosz Szczesny
- Department of Ophthalmology and Visual Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Michal R Szymanski
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
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15
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Roy A, Kandettu A, Ray S, Chakrabarty S. Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148554. [PMID: 35341749 DOI: 10.1016/j.bbabio.2022.148554] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria is a unique cellular organelle involved in multiple cellular processes and is critical for maintaining cellular homeostasis. This semi-autonomous organelle contains its circular genome - mtDNA (mitochondrial DNA), that undergoes continuous cycles of replication and repair to maintain the mitochondrial genome integrity. The majority of the mitochondrial genes, including mitochondrial replisome and repair genes, are nuclear-encoded. Although the repair machinery of mitochondria is quite efficient, the mitochondrial genome is highly susceptible to oxidative damage and other types of exogenous and endogenous agent-induced DNA damage, due to the absence of protective histones and their proximity to the main ROS production sites. Mutations in replication and repair genes of mitochondria can result in mtDNA depletion and deletions subsequently leading to mitochondrial genome instability. The combined action of mutations and deletions can result in compromised mitochondrial genome maintenance and lead to various mitochondrial disorders. Here, we review the mechanism of mitochondrial DNA replication and repair process, key proteins involved, and their altered function in mitochondrial disorders. The focus of this review will be on the key genes of mitochondrial DNA replication and repair machinery and the clinical phenotypes associated with mutations in these genes.
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Affiliation(s)
- Abhipsa Roy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Swagat Ray
- Department of Life Sciences, School of Life and Environmental Sciences, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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16
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Salidroside attenuates myocardial ischemia/reperfusion injury via AMPK-induced suppression of endoplasmic reticulum stress and mitochondrial fission. Toxicol Appl Pharmacol 2022; 448:116093. [PMID: 35659894 DOI: 10.1016/j.taap.2022.116093] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 12/19/2022]
Abstract
Ischemic heart disease (IHD) is the primary cause of death worldwide. Salidroside (Sal), the major active compound derived from Rhodiola rosea, is believed to have cardioprotective effects. AMP-activated protein kinase (AMPK), is a pivotal AMP-activated protein kinase in energy metabolism. Whether Sal plays an anti-endoplasmic reticulum stress/mitochondrial fission role through AMPK remains elusive. In this study, we established a myocardial ischemia/reperfusion (I/R) rat model. Rat hearts exposed to Sal with or without compound C were then subjected to I/R. Further, H9c2 cardiomyocytes were subjected to simulated ischemia/reperfusion (SIR) by hypoxia-reoxygenation. The rats and cardiomyocytes were pretreated with Sal, followed by Compound C and AMPK-siRNA to block AMPK activity. We found that Sal significantly ameliorated cardiac function, mitigated infarct size and serum content of lactate dehydrogenase and creatine kinase, improved mitochondrial function, and reduced mitochondrial fission and apoptosis. Furthermore, in cultured H9c2 cardiomyocytes, Sal increased the cell viability and inhibited SIR-induced myocardial apoptosis and mitochondrial fission. Furthermore, the translocation of Drp1 from the cytoplasm to mitochondria induced by salidroside was confirmed both in vivo and in vitro. However, the use of Compound C or AMPK siRNA to block AMPK activity leads to blockade of the protective effects of Sal. In summary, protects against myocardial I/R by activating the AMPK signaling pathway, inhibiting ER stress, and reducing mitochondrial fission and apoptosis.
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17
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Mitochondrial DNA Is a Vital Driving Force in Ischemia-Reperfusion Injury in Cardiovascular Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6235747. [PMID: 35620580 PMCID: PMC9129988 DOI: 10.1155/2022/6235747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/06/2022] [Indexed: 11/28/2022]
Abstract
According to the latest Global Burden of Disease Study, cardiovascular disease (CVD) is the leading cause of death, and ischemic heart disease and stroke are the cause of death in approximately half of CVD patients. In CVD, mitochondrial dysfunction following ischemia-reperfusion (I/R) injury results in heart failure. The proper functioning of oxidative phosphorylation (OXPHOS) and the mitochondrial life cycle in cardiac mitochondria are closely related to mitochondrial DNA (mtDNA). Following myocardial I/R injury, mitochondria activate multiple repair and clearance mechanisms to repair damaged mtDNA. When these repair mechanisms are insufficient to restore the structure and function of mtDNA, irreversible mtDNA damage occurs, leading to mtDNA mutations. Since mtDNA mutations aggravate OXPHOS dysfunction and affect mitophagy, mtDNA mutation accumulation leads to leakage of mtDNA and proteins outside the mitochondria, inducing an innate immune response, aggravating cardiovascular injury, and leading to the need for external interventions to stop or slow the disease course. On the other hand, mtDNA released into the circulation after cardiac injury can serve as a biomarker for CVD diagnosis and prognosis. This article reviews the pathogenic basis and related research findings of mtDNA oxidative damage and mtDNA leak-triggered innate immune response associated with I/R injury in CVD and summarizes therapeutic options that target mtDNA.
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18
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Relationship between oxidative stress and lifespan in Daphnia pulex. Sci Rep 2022; 12:2354. [PMID: 35149730 PMCID: PMC8837783 DOI: 10.1038/s41598-022-06279-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022] Open
Abstract
Macromolecular damage leading to cell, tissue and ultimately organ dysfunction is a major contributor to aging. Intracellular reactive oxygen species (ROS) resulting from normal metabolism cause most damage to macromolecules and the mitochondria play a central role in this process as they are the principle source of ROS. The relationship between naturally occurring variations in the mitochondrial (MT) genomes leading to correspondingly less or more ROS and macromolecular damage that changes the rate of aging associated organismal decline remains relatively unexplored. MT complex I, a component of the electron transport chain (ETC), is a key source of ROS and the NADH dehydrogenase subunit 5 (ND5) is a highly conserved core protein of the subunits that constitute the backbone of complex I. Using Daphnia as a model organism, we explored if the naturally occurring sequence variations in ND5 correlate with a short or long lifespan. Our results indicate that the short-lived clones have ND5 variants that correlate with reduced complex I activity, increased oxidative damage, and heightened expression of ROS scavenger enzymes. Daphnia offers a unique opportunity to investigate the association between inherited variations in components of complex I and ROS generation which affects the rate of aging and lifespan.
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19
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Nadalutti CA, Ayala-Peña S, Santos JH. Mitochondrial DNA damage as driver of cellular outcomes. Am J Physiol Cell Physiol 2022; 322:C136-C150. [PMID: 34936503 PMCID: PMC8799395 DOI: 10.1152/ajpcell.00389.2021] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mitochondria are primarily involved in energy production through the process of oxidative phosphorylation (OXPHOS). Increasing evidence has shown that mitochondrial function impacts a plethora of different cellular activities, including metabolism, epigenetics, and innate immunity. Like the nucleus, mitochondria own their genetic material, but this organellar genome is circular, present in multiple copies, and maternally inherited. The mitochondrial DNA (mtDNA) encodes 37 genes that are solely involved in OXPHOS. Maintenance of mtDNA, through replication and repair, requires the import of nuclear DNA-encoded proteins. Thus, mitochondria completely rely on the nucleus to prevent mitochondrial genetic alterations. As most cells contain hundreds to thousands of mitochondria, it follows that the shear number of organelles allows for the buffering of dysfunction-at least to some extent-before tissue homeostasis becomes impaired. Only red blood cells lack mitochondria entirely. Impaired mitochondrial function is a hallmark of aging and is involved in a number of different disorders, including neurodegenerative diseases, diabetes, cancer, and autoimmunity. Although alterations in mitochondrial processes unrelated to OXPHOS, such as fusion and fission, contribute to aging and disease, maintenance of mtDNA integrity is critical for proper organellar function. Here, we focus on how mtDNA damage contributes to cellular dysfunction and health outcomes.
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Affiliation(s)
- Cristina A. Nadalutti
- 1Mechanistic Toxicology Branch, Division of the National Toxicology
Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, North Carolina
| | - Sylvette Ayala-Peña
- 2Department of Pharmacology and Toxicology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Janine H. Santos
- 1Mechanistic Toxicology Branch, Division of the National Toxicology
Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, North Carolina
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20
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Chan W, Ham YH. Probing the Hidden Role of Mitochondrial DNA Damage and Dysfunction in the Etiology of Aristolochic Acid Nephropathy. Chem Res Toxicol 2021; 34:1903-1909. [PMID: 34255491 DOI: 10.1021/acs.chemrestox.1c00175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aristolochic acid nephropathy (AAN) is a unique type of progressive renal interstitial fibrotic disease caused by prolonged exposure to aristolochic acids (AAs) through AA-containing herbal medicines or AA-tainted food. Despite decades of research and affecting millions of people around the world, the pathophysiology of AAN remains incompletely understood. In this study, we tested the potential causative role of mitochondrial dysfunction in AAN development. Our findings revealed AA exposure induces an exposure concentration and duration dependent lowering of adenosine triphosphate in both cultured human kidney and liver cells, highlighting an AA exposure effect on mitochondrial energy production in the kidney and liver, which both are highly metabolically active and energy-demanding organs. Analysis with liquid chromatography-tandem mass spectrometry coupled with stable isotope dilution method detected high levels of mutagenic 8-oxo-2'-deoxyguanosine and 7-(deoxyadenosine-N6-yl)-aristolactam adduct on mitochondrial DNA isolated from AA-treated cells, unmasking a potentially important causative, but previously unknown role of mitochondrial DNA mutation in the pathophysiology of AAN development.
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Affiliation(s)
- Wan Chan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Yat-Hing Ham
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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21
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Barchiesi A, Bazzani V, Jabczynska A, Borowski LS, Oeljeklaus S, Warscheid B, Chacinska A, Szczesny RJ, Vascotto C. DNA Repair Protein APE1 Degrades Dysfunctional Abasic mRNA in Mitochondria Affecting Oxidative Phosphorylation. J Mol Biol 2021; 433:167125. [PMID: 34224750 DOI: 10.1016/j.jmb.2021.167125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/19/2022]
Abstract
APE1 is a multifunctional protein which plays a central role in the maintenance of nuclear and mitochondrial genomes repairing DNA lesions caused by oxidative and alkylating agents. In addition, it works as a redox signaling protein regulating gene expression by interacting with many transcriptional factors. Apart from these canonical activities, recent studies have shown that APE1 is also enzymatically active on RNA molecules. The present study unveils for the first time a new role of the mitochondrial form of APE1 protein in the metabolism of RNA in mitochondria. Our data demonstrate that APE1 is associated with mitochondrial messenger RNA and exerts endoribonuclease activity on abasic sites. Loss of APE1 results in the accumulation of damaged mitochondrial mRNA species, determining impairment in protein translation and reduced expression of mitochondrial-encoded proteins, finally leading to less efficient mitochondrial respiration. Altogether, our data demonstrate that APE1 plays an active role in the degradation of the mitochondrial mRNA and has a profound impact on mitochondrial well-being.
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Affiliation(s)
| | | | - Agata Jabczynska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Germany
| | - Agnieszka Chacinska
- Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; ReMedy International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Carlo Vascotto
- Department of Medicine, University of Udine, 33100 Udine, Italy; Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland.
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22
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Mitochondrial dysfunction: A potential target for Alzheimer's disease intervention and treatment. Drug Discov Today 2021; 26:1991-2002. [PMID: 33962036 DOI: 10.1016/j.drudis.2021.04.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/05/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is an irreversible neurodegenerative brain disorder which manifests as a progressive decline in cognitive function. Mitochondrial dysfunction plays a critical role in the early stages of AD, and advances the progression of this age-related neurodegenerative disorder. Therefore, it can be a potential target for interventions to treat AD. Several therapeutic strategies to target mitochondrial dysfunction have gained significant attention in the preclinical stage, but the clinical trials performed to date have shown little progress. Thus, we discuss the mechanisms and strategies of different therapeutic agents for targeting mitochondrial dysfunction in AD. We hope that this review will inspire and guide the development of efficient AD drugs in the future.
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Sullivan ED, Longley MJ, Copeland WC. Polymerase γ efficiently replicates through many natural template barriers but stalls at the HSP1 quadruplex. J Biol Chem 2021; 295:17802-17815. [PMID: 33454015 DOI: 10.1074/jbc.ra120.015390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/05/2020] [Indexed: 12/27/2022] Open
Abstract
Faithful replication of the mitochondrial genome is carried out by a set of key nuclear-encoded proteins. DNA polymerase γ is a core component of the mtDNA replisome and the only replicative DNA polymerase localized to mitochondria. The asynchronous mechanism of mtDNA replication predicts that the replication machinery encounters dsDNA and unique physical barriers such as structured genes, G-quadruplexes, and other obstacles. In vitro experiments here provide evidence that the polymerase γ heterotrimer is well-adapted to efficiently synthesize DNA, despite the presence of many naturally occurring roadblocks. However, we identified a specific G-quadruplex-forming sequence at the heavy-strand promoter (HSP1) that has the potential to cause significant stalling of mtDNA replication. Furthermore, this structured region of DNA corresponds to the break site for a large (3,895 bp) deletion observed in mitochondrial disease patients. The presence of this deletion in humans correlates with UV exposure, and we have found that efficiency of polymerase γ DNA synthesis is reduced after this quadruplex is exposed to UV in vitro.
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Affiliation(s)
- Eric D Sullivan
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Matthew J Longley
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - William C Copeland
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, USA.
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Gustafson MA, Sullivan ED, Copeland WC. Consequences of compromised mitochondrial genome integrity. DNA Repair (Amst) 2021; 93:102916. [PMID: 33087282 DOI: 10.1016/j.dnarep.2020.102916] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Maintenance and replication of the mitochondrial genome (mtDNA) is essential to mitochondrial function and eukaryotic energy production through the electron transport chain. mtDNA is replicated by a core set of proteins: Pol γ, Twinkle, and the single-stranded DNA binding protein. Fewer pathways exist for repair of mtDNA than nuclear DNA, and unrepaired damage to mtDNA may accumulate and lead to dysfunctional mitochondria. The mitochondrial genome is susceptible to damage by both endogenous and exogenous sources. Missense mutations to the nuclear genes encoding the core mtDNA replisome (POLG, POLG2, TWNK, and SSBP1) cause changes to the biochemical functions of their protein products. These protein variants can damage mtDNA and perturb oxidative phosphorylation. Ultimately, these mutations cause a diverse set of diseases that can affect virtually every system in the body. Here, we briefly review the mechanisms of mtDNA damage and the clinical consequences of disease variants of the core mtDNA replisome.
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Affiliation(s)
- Margaret A Gustafson
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, NC, 27709, USA
| | - Eric D Sullivan
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, NC, 27709, USA
| | - William C Copeland
- Mitochondrial DNA Replication Group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), NIH, Research Triangle Park, NC, 27709, USA.
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Mitroshina IY, Sirota NP, Prokofiev VN, Kuznetsova EA. Levels of Circulating DNA in Blood Serum and DNA Damage in Leukocytes of Healthy Donors of Different Genders and Ages. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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26
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Effects of mitoTALENs-Directed Double-Strand Breaks on Plant Mitochondrial Genomes. Genes (Basel) 2021; 12:genes12020153. [PMID: 33503806 PMCID: PMC7911708 DOI: 10.3390/genes12020153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes in flowering plants differ from those in animals and yeasts in several ways, including having large and variable sizes, circular, linear and branched structures, long repeat sequences that participate in homologous recombinations, and variable genes orders, even within a species. Understanding these differences has been hampered by a lack of genetic methods for transforming plant mitochondrial genomes. We recently succeeded in disrupting targeted genes in mitochondrial genomes by mitochondria-targeted transcription activator-like effector nucleases (mitoTALENs) in rice, rapeseed, and Arabidopsis. Double-strand breaks created by mitoTALENs were repaired not by non-homologous end-joining (NHEJ) but by homologous recombination (HR) between repeats near and far from the target sites, resulting in new genomic structures with large deletions and different configurations. On the other hand, in mammals, TALENs-induced DSBs cause small insertions or deletions in nuclear genomes and degradation of mitochondrial genomes. These results suggest that the mitochondrial and nuclear genomes of plants and mammals have distinct mechanisms for responding to naturally occurring DSBs. The different responses appear to be well suited to differences in size and copy numbers of each genome.
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p53 is required for nuclear but not mitochondrial DNA damage-induced degeneration. Cell Death Dis 2021; 12:104. [PMID: 33473103 PMCID: PMC7817838 DOI: 10.1038/s41419-020-03373-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
While the consequences of nuclear DNA damage have been well studied, the exact consequences of acute and selective mitochondrial DNA (mtDNA) damage are less understood. DNA damaging chemotherapeutic drugs are known to activate p53-dependent apoptosis in response to sustained nuclear DNA damage. While it is recognized that whole-cell exposure to these drugs also damages mtDNA, the specific contribution of mtDNA damage to cellular degeneration is less clear. To examine this, we induced selective mtDNA damage in neuronal axons using microfluidic chambers that allow for the spatial and fluidic isolation of neuronal cell bodies (containing nucleus and mitochondria) from the axons (containing mitochondria). Exposure of the DNA damaging drug cisplatin selectively to only the axons induced mtDNA damage in axonal mitochondria, without nuclear damage. We found that this resulted in the selective degeneration of only the targeted axons that were exposed to DNA damage, where ROS was induced but mitochondria were not permeabilized. mtDNA damage-induced axon degeneration was not mediated by any of the three known axon degeneration pathways: apoptosis, axon pruning, and Wallerian degeneration, as Bax-deficiency, or Casp3-deficiency, or Sarm1-deficiency failed to protect the degenerating axons. Strikingly, p53, which is essential for degeneration after nuclear DNA damage, was also not required for degeneration induced with mtDNA damage. This was most evident when the p53-deficient neurons were globally exposed to cisplatin. While the cell bodies of p53-deficient neurons were protected from degeneration in this context, the axons farthest from the cell bodies still underwent degeneration. These results highlight how whole cell exposure to DNA damage activates two pathways of degeneration; a faster, p53-dependent apoptotic degeneration that is triggered in the cell bodies with nuclear DNA damage, and a slower, p53-independent degeneration that is induced with mtDNA damage.
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Dashti M, Alsaleh H, Rodriguez-Flores JL, Eaaswarkhanth M, Al-Mulla F, Thanaraj TA. Mitochondrial haplogroup J associated with higher risk of obesity in the Qatari population. Sci Rep 2021; 11:1091. [PMID: 33441698 PMCID: PMC7806807 DOI: 10.1038/s41598-020-80040-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
Obesity, a major risk factor for metabolic disorders, is highly prevalent in Qatari population. Maternal transmission of obesity traits can be significant; for example, X haplogroup is known to be associated with lower BMI and body fat mass in Northern Europeans and T haplogroup which is a sister haplogroup of J is known to be associated with obesity in Caucasian subjects from Austria and Southern Italy. We aimed to delineate the mitochondrial haplogroups and variants associated with obesity in Qatari population. Mitochondrial genomes of 864 Qatari individuals were extracted from whole exome sequencing data with an average coverage of 77X. We distributed the participants into 2 sub-cohorts: obese (BMI ≥ 30) and non-obese (BMI < 30); the mean value of BMI from these two groups were 36.5 ± 5.7 and 26.5 ± 2.6, respectively. Mitochondrial haplogroup profiling followed by uni- and multivariant association tests adjusted for covariates were performed. Qatari individuals with mitochondrial haplogroup J had an increased (twofold) risk of obesity (odds ratio [OR] 1.925; 95% CI 1.234–3.002; P = 0.0038; the Bonferroni adjusted P value threshold is 0.0041), whereas the individuals with haplogroup X were at low risk of obesity (OR 0.387; 95% CI 0.175–0.857; P = 0.019). Further, a set of 38 mitochondrial variants were found to be associated (at P ≤ 0.05) with obesity in models adjusted for age, sex and haplogroup.
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Affiliation(s)
- Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Hussain Alsaleh
- Kuwait Identification DNA Laboratory, General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | | | | | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait.
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MutaCheck: A novel pipeline to check for single nucleotide polymorphism (SNP) and associated diseases in mitochondrial DNA. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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De Miranda BR, Rocha EM, Castro SL, Greenamyre JT. Protection from α-Synuclein induced dopaminergic neurodegeneration by overexpression of the mitochondrial import receptor TOM20. NPJ Parkinsons Dis 2020; 6:38. [PMID: 33293540 PMCID: PMC7722884 DOI: 10.1038/s41531-020-00139-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
Dopaminergic neurons of the substantia nigra are selectively vulnerable to mitochondrial dysfunction, which is hypothesized to be an early and fundamental pathogenic mechanism in Parkinson's disease (PD). Mitochondrial function depends on the successful import of nuclear-encoded proteins, many of which are transported through the TOM20-TOM22 outer mitochondrial membrane import receptor machinery. Recent data suggests that post-translational modifications of α-synuclein promote its interaction with TOM20 at the outer mitochondrial membrane and thereby inhibit normal protein import, leading to dysfunction, and death of dopaminergic neurons. As such, preservation of mitochondrial import in the face of α-synuclein accumulation might be a strategy to prevent dopaminergic neurodegeneration, however, this is difficult to assess using current in vivo models of PD. To this end, we established an exogenous co-expression system, utilizing AAV2 vectors to overexpress human α-synuclein and TOM20, individually or together, in the adult Lewis rat substantia nigra to assess whether TOM20 overexpression attenuates α-synuclein-induced dopaminergic neurodegeneration. Twelve weeks after viral injection, we observed that AAV2-TOM20 expression was sufficient to prevent loss of nigral dopaminergic neurons caused by AAV2-αSyn overexpression. The observed TOM20-mediated dopaminergic neuron preservation appeared to be due, in part, to the rescued expression (and presumed import) of nuclear-encoded mitochondrial electron transport chain proteins that were inhibited by α-synuclein overexpression. In addition, TOM20 overexpression rescued the expression of the chaperone protein GRP75/mtHSP70/mortalin, a stress-response protein involved in α-synuclein-induced injury. Collectively, these data indicate that TOM20 expression prevents α-synuclein-induced mitochondrial dysfunction, which is sufficient to rescue dopaminergic neurons in the adult rat brain.
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Affiliation(s)
- Briana R De Miranda
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily M Rocha
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra L Castro
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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Abstract
Autophagy is an adaptive catabolic process functioning to promote cell survival in the event of inappropriate living conditions such as nutrient shortage and to cope with diverse cytotoxic insults. It is regarded as one of the key survival mechanisms of living organisms. Cells undergo autophagy to accomplish the lysosomal digestion of intracellular materials including damaged proteins, organelles, and foreign bodies, in a bulk, non-selective or a cargo-specific manner. Studies in the past decades have shed light on the association of autophagy pathways with various diseases and also highlighted the therapeutic value of autophagy modulation. Hence, it is crucial to develop effective approaches for monitoring intracellular autophagy dynamics, as a comprehensive account of methodology establishment is far from complete. In this review, we aim to provide an overview of the major current fluorescence-based techniques utilized for visualizing, sensing or measuring autophagic activities in cells or tissues, which are categorized firstly by targets detected and further by the types of fluorescence tools. We will mainly focus on the working mechanisms of these techniques, put emphasis on the insight into their roles in biomedical science and provide perspectives on the challenges and future opportunities in this field.
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Affiliation(s)
- Siyang Ding
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne Victoria 3086, Australia.
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Age-Related Deterioration of Mitochondrial Function in the Intestine. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:4898217. [PMID: 32922652 PMCID: PMC7453234 DOI: 10.1155/2020/4898217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/22/2020] [Indexed: 12/29/2022]
Abstract
Aging is an important and inevitable biological process in human life, associated with the onset of chronic disease and death. The mechanisms behind aging remain unclear. However, changes in mitochondrial function and structure, including reduced activity of the mitochondrial respiratory chain and increased production of reactive oxygen species—thus oxidative damage—are believed to play a major role. Mitochondria are the main source of cellular energy, producing adenosine triphosphate (ATP) via oxidative phosphorylation. Accumulation of damaged cellular components reduces a body's capacity to preserve tissue homeostasis and affects biological aging and all age-related chronic conditions. This includes the onset and progression of classic degenerative diseases such as cardiovascular disease, kidney failure, neurodegenerative diseases, and cancer. Clinical manifestations of intestinal disorders, such as mucosal barrier dysfunction, intestinal dysmotility, and chronic obstipation, are highly prevalent in the elderly population and have been shown to be associated with an age-dependent decline of mitochondrial function. This review summarizes our current understanding of the role of mitochondrial dysfunction in intestinal aging.
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Bordoni L, Gabbianelli R. Mitochondrial DNA and Neurodegeneration: Any Role for Dietary Antioxidants? Antioxidants (Basel) 2020; 9:E764. [PMID: 32824558 PMCID: PMC7466149 DOI: 10.3390/antiox9080764] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
The maintenance of the mitochondrial function is essential in preventing and counteracting neurodegeneration. In particular, mitochondria of neuronal cells play a pivotal role in sustaining the high energetic metabolism of these cells and are especially prone to oxidative damage. Since overproduction of reactive oxygen species (ROS) is involved in the pathogenesis of neurodegeneration, dietary antioxidants have been suggested to counteract the detrimental effects of ROS and to preserve the mitochondrial function, thus slowing the progression and limiting the extent of neuronal cell loss in neurodegenerative disorders. In addition to their role in the redox-system homeostasis, mitochondria are unique organelles in that they contain their own genome (mtDNA), which acts at the interface between environmental exposures and the molecular triggers of neurodegeneration. Indeed, it has been demonstrated that mtDNA (including both genetics and, from recent evidence, epigenetics) might play relevant roles in modulating the risk for neurodegenerative disorders. This mini-review describes the link between the mitochondrial genome and cellular oxidative status, with a particular focus on neurodegeneration; moreover, it provides an overview on potential beneficial effects of antioxidants in preserving mitochondrial functions through the protection of mtDNA.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, 62032 Camerino, Italy;
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de Oliveira VC, Gomes Mariano Junior C, Belizário JE, Krieger JE, Fernandes Bressan F, Roballo KCS, Fantinato-Neto P, Meirelles FV, Chiaratti MR, Concordet JP, Ambrósio CE. Characterization of post-edited cells modified in the TFAM gene by CRISPR/Cas9 technology in the bovine model. PLoS One 2020; 15:e0235856. [PMID: 32649732 PMCID: PMC7351154 DOI: 10.1371/journal.pone.0235856] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Gene editing in large animal models for future applications in translational medicine and food production must be deeply investigated for an increase of knowledge. The mitochondrial transcription factor A (TFAM) is a member of the HMGB subfamily that binds to mtDNA promoters. This gene maintains mtDNA, and it is essential for the initiation of mtDNA transcription. Lately, we generated a new cell line through the disruption of the TFAM gene in bovine fibroblast cells by CRISPR/Cas 9 technology. We showed that the CRISPR/Cas9 design was efficient through the generation of heterozygous mutant clones. In this context, once this gene regulates the mtDNA replication specificity, the study aimed to determine if the post-edited cells are capable of in vitro maintenance and assess if they present changes in mtDNA copies and mitochondrial membrane potential after successive passages in culture. The post-edited cells were expanded in culture, and we performed a growth curve, doubling time, cell viability, mitochondrial DNA copy number, and mitochondrial membrane potential assays. The editing process did not make cell culture unfeasible, even though cell growth rate and viability were decreased compared to control since we observed the cells grow well when cultured in a medium supplemented with uridine and pyruvate. They also exhibited a classical fibroblastoid appearance. The RT-qPCR to determine the mtDNA copy number showed a decrease in the edited clones compared to the non-edited ones (control) in different cell passages. Cell staining with Mitotracker Green and red suggests a reduction in red fluorescence in the edited cells compared to the non-edited cells. Thus, through characterization, we demonstrated that the TFAM gene is critical to mitochondrial maintenance due to its interference in the stability of the mitochondrial DNA copy number in different cell passages and membrane potential confirming the decrease in mitochondrial activity in cells edited in heterozygosis.
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Affiliation(s)
- Vanessa Cristina de Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
- * E-mail: ,
| | - Clésio Gomes Mariano Junior
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - José Ernesto Belizário
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - José Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo Medical School, São Paulo, Brazil
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Kelly Cristine Santos Roballo
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
- School of Pharmacy at College of Health Sciences, University of Wyoming, Laramie, WY, United States of America
| | - Paulo Fantinato-Neto
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Flávio Vieira Meirelles
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM U1154, CNRS UMR7196, Paris, France
| | - Carlos Eduardo Ambrósio
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
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Zhao L, Sumberaz P. Mitochondrial DNA Damage: Prevalence, Biological Consequence, and Emerging Pathways. Chem Res Toxicol 2020; 33:2491-2502. [PMID: 32486637 DOI: 10.1021/acs.chemrestox.0c00083] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria have a plethora of functions within a eukaryotic cell, ranging from energy production, cell signaling, and protein cofactor synthesis to various aspects of metabolism. Mitochondrial dysfunction is known to cause over 200 named disorders and has been implicated in many human diseases and aging. Mitochondria have their own genetic material, mitochondrial DNA (mtDNA), which encodes 13 protein subunits in the oxidative phosphorylation system and a full set of transfer and rRNAs. Although more than 99% of the proteins in mitochondria are nuclear DNA (nDNA)-encoded, the integrity of mtDNA is critical for mitochondrial functions, as evidenced by mitochondrial diseases sourced from mtDNA mutations and depletions and the vital role of fragmented mtDNA molecules in cell signaling pathways. Previous research has shown that mtDNA is an important target of genotoxic assaults by a variety of chemical and physical factors. This Perspective discusses the prevalence of mtDNA damage by comparing the abundance of lesions in mDNA and nDNA and summarizes current knowledge on the biological pathways to cope with mtDNA damage, including mtDNA repair, mtDNA degradation, and mitochondrial fission and fusion. Also, emerging roles of mtDNA damage in mutagenesis and immune responses are reviewed.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
| | - Philip Sumberaz
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521, United States
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Zhao X, Yang A, Fu Y, Zhang B, Li X, Pan B, Li Q, Dong J, Nie J, Yang J. Reduction of mitochondrial DNA copy number in peripheral blood is related to polycyclic aromatic hydrocarbons exposure in coke oven workers: Bayesian kernel machine regression. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:114026. [PMID: 32006885 DOI: 10.1016/j.envpol.2020.114026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/04/2020] [Accepted: 01/19/2020] [Indexed: 06/10/2023]
Abstract
Although association between polycyclic aromatic hydrocarbons (PAHs) exposure and mitochondrial DNA copy number (mtDNAcn) was researched by traditional linear model extensively, most of these studies analyzed independent effect of each PAHs metabolite and adjust for the confounding other metabolites concomitantly, without considering others interactions. As a complex organic pollutant, a reasonable statistical method is needed to study toxic effects of PAHs. Therefore, we aimed to conduct a novel statistical approach, Bayesian Kernel Machine Regression (BKMR), to explore the effect of PAHs exposure on mtDNAcn among coke oven workers. In this cross-sectional study, the concentrations urinary of PAHs metabolites were measured using high performance liquid chromatography mass spectrometry (HPLC-MS). The mtDNAcn was measured using real-time quantitative polymerase chain reaction (RT-PCR) in peripheral blood of 696 Chinese coke oven workers. The relationship of urinary of PAHs metabolites and mtDNAcn were evaluated by BKMR model. And the results showed a significant negative effect of PAHs metabolites on mtDNAcn when PAHs metabolites concentrations were all above 35th percentile compared to the median and the statistically significant negative single-exposure effect of 2-OHNAP and 2-OHPHE on mtDNAcn when all of the other PAHs are fixed at a particular threshold (25th, 50th, 75th percentile). The changes in log 2-OHNAP and 2-OHPHE from the 25th to the 75th percentile when other PAHs metabolites were at the 50th percentile were associated with change in mtDNAcn of -0.082 (-0.021, -0.124) and -0.048 (-0.021, -0.090) respectively. And evidence of a linear effect of urinary 2-OHNAP and 2-OHPHE were found. Finally, our findings suggested that PAHs cumulative exposures and particularly single-exposure of 2-OHNAP and 2-OHPHE might compromise mitochondrial function by decreasing mtDNAcn in Chinese coke oven workers.
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Affiliation(s)
- Xinyu Zhao
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Aimin Yang
- Hong Kong Institutes of Diabetes and Obesity, The Chinese University of Hong Kong, Taiyuan, 030001, Shanxi, China
| | - Ye Fu
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Bin Zhang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Xuejing Li
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Baolong Pan
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; General Hospital of Taiyuan Iron & Steel (Group) Co., Ltd, Taiyuan, 030001, Shanxi, China
| | - Qiang Li
- Center of Occupational Disease Prevention, Xishan Coal Electricity (Group) Co., Ltd, Taiyuan, 030001, Shanxi, China
| | - Jun Dong
- Center of Occupational Disease Prevention, Xishan Coal Electricity (Group) Co., Ltd, Taiyuan, 030001, Shanxi, China
| | - Jisheng Nie
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jin Yang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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Kaur P, Longley MJ, Pan H, Wang W, Countryman P, Wang H, Copeland WC. Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase. J Biol Chem 2020; 295:5564-5576. [PMID: 32213598 PMCID: PMC7186178 DOI: 10.1074/jbc.ra120.012795] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/24/2020] [Indexed: 11/06/2022] Open
Abstract
Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA-binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695.
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695
| | - Wendy Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695; Toxicology Program, North Carolina State University, Raleigh, North Carolina 27695
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.
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Nadalutti CA, Stefanick DF, Zhao ML, Horton JK, Prasad R, Brooks AM, Griffith JD, Wilson SH. Mitochondrial dysfunction and DNA damage accompany enhanced levels of formaldehyde in cultured primary human fibroblasts. Sci Rep 2020; 10:5575. [PMID: 32221313 PMCID: PMC7101401 DOI: 10.1038/s41598-020-61477-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Formaldehyde (FA) is a simple biological aldehyde that is produced inside cells by several processes such as demethylation of DNA and proteins, amino acid metabolism, lipid peroxidation and one carbon metabolism (1-C). Although accumulation of excess FA in cells is known to be cytotoxic, it is unknown if an increase in FA level might be associated with mitochondrial dysfunction. We choose to use primary human fibroblasts cells in culture (foreskin, FSK) as a physiological model to gain insight into whether an increase in the level of FA might affect cellular physiology, especially with regard to the mitochondrial compartment. FSK cells were exposed to increasing concentrations of FA, and different cellular parameters were studied. Elevation in intracellular FA level was achieved and was found to be cytotoxic by virtue of both apoptosis and necrosis and was accompanied by both G2/M arrest and reduction in the time spent in S phase. A gene expression assessment by microarray analysis revealed FA affected FSK cells by altering expression of many genes including genes involved in mitochondrial function and electron transport. We were surprised to observe increased DNA double-strand breaks (DSBs) in mitochondria after exposure to FA, as revealed by accumulation of γH2A.X and 53BP1 at mitochondrial DNA foci. This was associated with mitochondrial structural rearrangements, loss of mitochondrial membrane potential and activation of mitophagy. Collectively, these results indicate that an increase in the cellular level of FA can trigger mitochondrial DNA double-strand breaks and dysfunction.
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Affiliation(s)
- Cristina A Nadalutti
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Donna F Stefanick
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Ashley M Brooks
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA.
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Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M. Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon. BMC Genet 2020; 21:25. [PMID: 32138667 PMCID: PMC7059407 DOI: 10.1186/s12863-020-0828-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/19/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF. RESULTS Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z. CONCLUSIONS We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding.
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Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - James C Wright
- Functional Proteomics, Division of Cancer Biology, Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Andrew E Firth
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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40
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The alterations of mitochondrial DNA in coronary heart disease. Exp Mol Pathol 2020; 114:104412. [PMID: 32113905 DOI: 10.1016/j.yexmp.2020.104412] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022]
Abstract
Coronary heart disease (CHD) is the major cause of death in modern society. CHD is characterized by atherosclerosis, which could lead to vascular cavity stenosis or obstruction, resulting in ischemic cardiac conditions such as angina and myocardial infarction. In terms of the mitochondrion, the main function is to produce adenosine triphosphate (ATP) for cells. And the alterations (including mutations, altered copy number and haplogroups) of mitochondrial DNA (mtDNA) are associated with the abnormal expression of oxidative phosphorylation (OXPHOS) system, resulting in mitochondrial dysfunction, then leading to perturbation on the electron transport chain and increased ROS generation and reduction in ATP level, contributing to ATP-producing disorders and oxidative stress, which may further accelerate development or vulnerability of atherosclerosis and myocardial ischemic injury. Therefore, the mtDNA defects may play an important role in making an early diagnosis, identifying disease-specific biomarkers and therapeutic targets, and predicting outcomes for patients with atherosclerosis and CHD. In this review, we aim to summarize the contribution of mtDNA mutations, altered mtDNA copy number and mtDNA haplogroups on the occurrence and development of CHD.
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Abstract
The POLG gene encodes the mitochondrial DNA polymerase that is responsible for replication of the mitochondrial genome. Mutations in POLG can cause early childhood mitochondrial DNA (mtDNA) depletion syndromes or later-onset syndromes arising from mtDNA deletions. POLG mutations are the most common cause of inherited mitochondrial disorders, with as many as 2% of the population carrying these mutations. POLG-related disorders comprise a continuum of overlapping phenotypes with onset from infancy to late adulthood. The six leading disorders caused by POLG mutations are Alpers-Huttenlocher syndrome, which is one of the most severe phenotypes; childhood myocerebrohepatopathy spectrum, which presents within the first 3 years of life; myoclonic epilepsy myopathy sensory ataxia; ataxia neuropathy spectrum; autosomal recessive progressive external ophthalmoplegia; and autosomal dominant progressive external ophthalmoplegia. This Review describes the clinical features, pathophysiology, natural history and treatment of POLG-related disorders, focusing particularly on the neurological manifestations of these conditions.
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Kotrys AV, Szczesny RJ. Mitochondrial Gene Expression and Beyond-Novel Aspects of Cellular Physiology. Cells 2019; 9:cells9010017. [PMID: 31861673 PMCID: PMC7017415 DOI: 10.3390/cells9010017] [Citation(s) in RCA: 40] [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: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are peculiar organelles whose proper function depends on the crosstalk between two genomes, mitochondrial and nuclear. The human mitochondrial genome (mtDNA) encodes only 13 proteins; nevertheless, its proper expression is essential for cellular homeostasis, as mtDNA-encoded proteins are constituents of mitochondrial respiratory complexes. In addition, mtDNA expression results in the production of RNA molecules, which influence cell physiology once released from the mitochondria into the cytoplasm. As a result, dysfunctions of mtDNA expression may lead to pathologies in humans. Here, we review the mechanisms of mitochondrial gene expression with a focus on recent findings in the field. We summarize the complex turnover of mitochondrial transcripts and present an increasing body of evidence indicating new functions of mitochondrial transcripts. We discuss mitochondrial gene regulation in different cellular contexts, focusing on stress conditions. Finally, we highlight the importance of emerging aspects of mitochondrial gene regulation in human health and disease.
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Mitochondrial transcription factor A promotes DNA strand cleavage at abasic sites. Proc Natl Acad Sci U S A 2019; 116:17792-17799. [PMID: 31413200 DOI: 10.1073/pnas.1911252116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In higher eukaryotic cells, mitochondria are essential subcellular organelles for energy production, cell signaling, and the biosynthesis of biomolecules. The mitochondrial DNA (mtDNA) genome is indispensable for mitochondrial function because it encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. MtDNA degradation has emerged as an essential quality control measure to maintain mtDNA and to cope with mtDNA damage resulting from endogenous and environmental factors. Among all types of DNA damage known, abasic (AP) sites, sourced from base excision repair and spontaneous base loss, are the most abundant endogenous DNA lesions in cells. In mitochondria, AP sites trigger rapid DNA loss; however, the mechanism and molecular factors involved in the process remain elusive. Herein, we demonstrate that the stability of AP sites is reduced dramatically upon binding to a major mtDNA packaging protein, mitochondrial transcription factor A (TFAM). The half-life of AP lesions within TFAM-DNA complexes is 2 to 3 orders of magnitude shorter than that in free DNA, depending on their position. The TFAM-catalyzed AP-DNA destabilization occurs with nonspecific DNA or mitochondrial light-strand promoter sequence, yielding DNA single-strand breaks and DNA-TFAM cross-links. TFAM-DNA cross-link intermediates prior to the strand scission were also observed upon treating AP-DNA with mitochondrial extracts of human cells. In situ trapping of the reaction intermediates (DNA-TFAM cross-links) revealed that the reaction proceeds via Schiff base chemistry facilitated by lysine residues. Collectively, our data suggest a novel role of TFAM in facilitating the turnover of abasic DNA.
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Kim Y, Vadodaria KC, Lenkei Z, Kato T, Gage FH, Marchetto MC, Santos R. Mitochondria, Metabolism, and Redox Mechanisms in Psychiatric Disorders. Antioxid Redox Signal 2019; 31:275-317. [PMID: 30585734 PMCID: PMC6602118 DOI: 10.1089/ars.2018.7606] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/17/2022]
Abstract
Significance: Our current knowledge of the pathophysiology and molecular mechanisms causing psychiatric disorders is modest, but genetic susceptibility and environmental factors are central to the etiology of these conditions. Autism, schizophrenia, bipolar disorder and major depressive disorder show genetic gene risk overlap and share symptoms and metabolic comorbidities. The identification of such common features may provide insights into the development of these disorders. Recent Advances: Multiple pieces of evidence suggest that brain energy metabolism, mitochondrial functions and redox balance are impaired to various degrees in psychiatric disorders. Since mitochondrial metabolism and redox signaling can integrate genetic and environmental environmental factors affecting the brain, it is possible that they are implicated in the etiology and progression of psychiatric disorders. Critical Issue: Evidence for direct links between cellular mitochondrial dysfunction and disease features are missing. Future Directions: A better understanding of the mitochondrial biology and its intracellular connections to the nuclear genome, the endoplasmic reticulum and signaling pathways, as well as its role in intercellular communication in the organism, is still needed. This review focuses on the findings that implicate mitochondrial dysfunction, the resultant metabolic changes and oxidative stress as important etiological factors in the context of psychiatric disorders. We also propose a model where specific pathophysiologies of psychiatric disorders depend on circuit-specific impairments of mitochondrial dysfunction and redox signaling at specific developmental stages.
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Affiliation(s)
- Yeni Kim
- Department of Child and Adolescent Psychiatry, National Center for Mental Health, Seoul, South Korea
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Krishna C. Vadodaria
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Zsolt Lenkei
- Laboratory of Dynamic of Neuronal Structure in Health and Disease, Institute of Psychiatry and Neuroscience of Paris (UMR_S1266 INSERM, University Paris Descartes), Paris, France
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Japan
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Maria C. Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Renata Santos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
- Laboratory of Dynamic of Neuronal Structure in Health and Disease, Institute of Psychiatry and Neuroscience of Paris (UMR_S1266 INSERM, University Paris Descartes), Paris, France
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Increased burden of mitochondrial DNA deletions and point mutations in early-onset age-related hearing loss in mitochondrial mutator mice. Exp Gerontol 2019; 125:110675. [PMID: 31344454 DOI: 10.1016/j.exger.2019.110675] [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] [Received: 01/14/2019] [Revised: 07/14/2019] [Accepted: 07/20/2019] [Indexed: 11/20/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations are thought to have a causal role in a variety of age-related neurodegenerative diseases, including age-related hearing loss (AHL). In the current study, we investigated the roles of mtDNA deletions and point mutations in AHL in mitochondrial mutator mice (Polgmut/mut) that were backcrossed onto CBA/CaJ mice, a well-established model of late-onset AHL. mtDNA deletions accumulated significantly with age in the inner ears of Polgmut/mut mice, while there were no differences in mtDNA deletion frequencies in the inner ears between 5 and 17 months old Polg+/+ mice or 5 months old Polg+/+ and Polgmut/mut mice. mtDNA deletions also accumulated significantly in the inner ears of CBA/CaJ mice during normal aging. In contrast, 5 months old Polgmut/mut mice displayed a 238-fold increase in mtDNA point mutation frequencies in the inner ears compared to age-matched Polg+/+ mice, but there were no differences in mtDNA point mutation frequencies in the inner ears between 5 and 17 months old Polgmut/mut mice. Seventeen-month-old Polgmut/mut mice also displayed early-onset severe hearing loss associated with a significant reduction in neural output of the cochlea, while age-matched Polg+/+ mice displayed little or no hearing impairment. Consistent with the physiological and mtDNA deletion test result, 17-month-old Polgmut/mut mice displayed a profound loss of spiral ganglion neurons in the cochlea. Thus, our data suggest that a higher burden of mtDNA point mutations from a young age and age-related accumulation of mtDNA deletions likely contribute to early-onset AHL in mitochondrial mutator mice.
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Wanrooij PH, Chabes A. Ribonucleotides in mitochondrial DNA. FEBS Lett 2019; 593:1554-1565. [PMID: 31093968 DOI: 10.1002/1873-3468.13440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
The incorporation of ribonucleotides (rNMPs) into DNA during genome replication has gained substantial attention in recent years and has been shown to be a significant source of genomic instability. Studies in yeast and mammals have shown that the two genomes, the nuclear DNA (nDNA) and the mitochondrial DNA (mtDNA), differ with regard to their rNMP content. This is largely due to differences in rNMP repair - whereas rNMPs are efficiently removed from the nuclear genome, mitochondria lack robust mechanisms for removal of single rNMPs incorporated during DNA replication. In this minireview, we describe the processes that determine the frequency of rNMPs in the mitochondrial genome and summarise recent findings regarding the effect of incorporated rNMPs on mtDNA stability and function.
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Affiliation(s)
- Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Sweden
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Vriens A, Nawrot TS, Janssen BG, Baeyens W, Bruckers L, Covaci A, De Craemer S, De Henauw S, Den Hond E, Loots I, Nelen V, Schettgen T, Schoeters G, Martens DS, Plusquin M. Exposure to Environmental Pollutants and Their Association with Biomarkers of Aging: A Multipollutant Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:5966-5976. [PMID: 31041867 DOI: 10.1021/acs.est.8b07141] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Mitochondrial DNA (mtDNA) content and telomere length are putative aging biomarkers and are sensitive to environmental stressors, including pollutants. Our objective was to identify, from a set of environmental exposures, which exposure is associated with leukocyte mtDNA content and telomere length in adults. This study includes 175 adults from 50 to 65 years old from the cross-sectional Flemish Environment and Health study, of whom leukocyte telomere length and mtDNA content were determined using qPCR. The levels of exposure of seven metals, 11 organohalogens, and four perfluorinated compounds (PFHxS, PFNA, PFOA, PFOS) were measured. We performed sparse partial least-squares regression analyses followed by ordinary least-squares regression to assess the multipollutant associations. While accounting for possible confounders and coexposures, we identified that urinary cadmium (6.52%, 95% confidence interval, 1.06, 12.28), serum hexachlorobenzene (2.89%, 018, 5.68), and perfluorooctanesulfonic acid (11.38%, 5.97, 17.08) exposure were positively associated ( p < 0.05) with mtDNA content, while urinary copper (-9.88%, -14.82, -4.66) and serum perfluorohexanesulfonic acid (-4.75%, -8.79, -0.54) exposure were inversely associated with mtDNA content. Urinary antimony (2.69%, 0.45, 4.99) and mercury (1.91%, 0.42, 3.43) exposure were positively associated with leukocyte telomere length, while urinary copper (-3.52%, -6.60, -0.34) and serum perfluorooctanesulfonic acid (-3.64%, -6.60, -0.60) showed an inverse association. Our findings support the hypothesis that environmental pollutants interact with molecular hallmarks of aging.
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Affiliation(s)
- Annette Vriens
- Centre for Environmental Sciences , Hasselt University , Hasselt 3500 , Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences , Hasselt University , Hasselt 3500 , Belgium
- Department of Public Health & Primary Care , Leuven University , Leuven 3000 , Belgium
| | - Bram G Janssen
- Centre for Environmental Sciences , Hasselt University , Hasselt 3500 , Belgium
| | - Willy Baeyens
- Department of Analytical and Environmental Chemistry , Vrije Universiteit Brussel , Brussels 1050 , Belgium
| | - Liesbeth Bruckers
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics , Hasselt University , Diepenbeek 3590 , Belgium
| | | | - Sam De Craemer
- Department of Analytical and Environmental Chemistry , Vrije Universiteit Brussel , Brussels 1050 , Belgium
| | - Stefaan De Henauw
- Department of Public Health , Ghent University , Ghent 9000 , Belgium
| | - Elly Den Hond
- Provincial Institute for Hygiene , Antwerp 2000 , Belgium
| | | | - Vera Nelen
- Provincial Institute for Hygiene , Antwerp 2000 , Belgium
| | - Thomas Schettgen
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty , RWTH Aachen University , Aachen 52062 , Germany
| | - Greet Schoeters
- Environmental Risk and Health , Flemish Institute for Technological Research (VITO) , Mol 2400 , Belgium
| | - Dries S Martens
- Centre for Environmental Sciences , Hasselt University , Hasselt 3500 , Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences , Hasselt University , Hasselt 3500 , Belgium
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Activated mTOR signaling pathway in myofibers with inherited metabolic defect might be an evidence for mTOR inhibition therapies. Chin Med J (Engl) 2019; 132:805-810. [PMID: 30897595 PMCID: PMC6595864 DOI: 10.1097/cm9.0000000000000144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background: Abnormally activated mechanistic target of rapamycin (mTOR) pathway has been reported in several model animals with inherited metabolic myopathies (IMMs). However, the profiles of mTOR pathway in skeletal muscles from patients are still unknown. This study aimed to analyze the activity of mTOR pathway in IMMs muscles. Methods: We collected muscle samples from 25 patients with mitochondrial myopathy (MM), lipid storage disease (LSD) or Pompe disease (PD). To evaluate the activity of mTOR pathway in muscle specimens, phosphorylation of S6 ribosomal protein (p-S6) and p70S6 kinase (p-p70S6K) were analyzed by Western blotting and immunohistochemistry. Results: Western blotting results showed that p-p70S6K/p70S6K in muscles from LSD and MM was up-regulated when compared with normal controls (NC) (NC vs. LSD, U = 2.000, P = 0.024; NC vs. MM: U = 6.000, P = 0.043). Likewise, p-S6/S6 was also up-regulated in muscles from all three subgroups of IMMs (NC vs. LSD, U = 0.000, P = 0.006; NC vs. PD, U = 0.000, P = 0.006; NC vs. MM, U = 1.000, P = 0.007). Immunohistochemical study revealed that p-S6 was mainly expressed in fibers with metabolic defect. In MM muscles, most p-S6 positive fibers showed cytochrome C oxidase (COX) deficiency (U = 5.000, P = 0.001). In LSD and PD muscles, p-S6 was mainly overexpressed in fibers with intramuscular vacuoles containing lipid droplets (U = 0.000, P = 0.002) or basophilic materials (U = 0.000, P = 0.002). Conclusion: The mTOR pathway might be activated in myofibers with various metabolic defects, which might provide evidence for mTOR inhibition therapy in human IMMs.
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Veronese N, Stubbs B, Koyanagi A, Vaona A, Demurtas J, Schofield P, Maggi S. Mitochondrial genetic haplogroups and cardiovascular diseases: Data from the Osteoarthritis Initiative. PLoS One 2019; 14:e0213656. [PMID: 30921349 PMCID: PMC6438497 DOI: 10.1371/journal.pone.0213656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/26/2019] [Indexed: 12/13/2022] Open
Abstract
Background Some case-control studies reported that mitochondrial haplogroups could be associated with the onset of cardiovascular diseases (CVD), but the literature regarding this topic is limited. We aimed to investigate whether any mitochondrial haplogroup carried a higher or lower risk of CVD in a large cohort of North American people affected by knee osteoarthritis or at high risk for this condition. Materials and methods A longitudinal cohort study including individuals from the Osteoarthritis Initiative was done. Haplogroups were assigned through a combination of sequencing and PCR-RFLP techniques. All the mitochondrial haplogroups have been named following this nomenclature: HV, JT, UK, IWX, and superHV/others. The strength of the association between mitochondrial haplogroups and incident CVD was evaluated through a Cox’s regression analysis, adjusted for potential confounders, and reported as hazard ratios (HRs) with their 95% confidence intervals (CIs). Results Overall, 3,288 Caucasian participants (56.8% women) with a mean age of 61.3±9.2 years without CVD at baseline were included. During a median follow-up of 8 years, 322 individuals (= 9.8% of baseline population) developed a CVD. After adjusting for 11 potential confounders at baseline and taking those with the HV haplotype as reference (the most frequent), those with JT carried a significant lower risk of CVD (HR = 0.75; 95%CI: 0.54–0.96; p = 0.03). Participants with the J haplogroup had the lowest risk of CVD (HR = 0.71; 95%CI: 0.46–0.95; p = 0.02). Conclusions The presence of JT haplogroups (particularly J) may be associated with a reduced risk of CVD. However, this result was not based on a high level of statistical significance. Thus, future research with larger sample size is needed to assess whether our results can be corroborated.
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Affiliation(s)
- Nicola Veronese
- National Research Council, Neuroscience Institute, Aging Branch, Padova, National Institute of Gastroenterology “S. De Bellis” Research Hospital, Castellana Grotte (Ba), Italy
- * E-mail:
| | - Brendon Stubbs
- South London and Maudsley NHS Foundation Trust, Denmark Hill, London, United Kingdom
| | - Ai Koyanagi
- Research and Development Unit, Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Déu, CIBERSAM, Sant Boi de Llobregat, Barcelona, Spain
| | - Alberto Vaona
- Primary Care Department, Azienda ULSS20 Verona, Verona, Italy
| | - Jacopo Demurtas
- Primary Care Department, Azienda USL Toscana Sud Est, Grosseto, Italy
| | - Patricia Schofield
- Faculty of Health, Social Care and Education, Anglia Ruskin University, Chelmsford, United Kingdom
| | - Stefania Maggi
- National Research Council, Neuroscience Institute, Aging Branch, Padova, National Institute of Gastroenterology “S. De Bellis” Research Hospital, Castellana Grotte (Ba), Italy
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Zhao L. Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response. Enzymes 2019; 45:311-341. [PMID: 31627882 DOI: 10.1016/bs.enz.2019.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
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