1
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Xu L, Tan C, Barr J, Talaba N, Verheyden J, Chin JS, Gaboyan S, Kasaraneni N, Elgamal RM, Gaulton KJ, Lin G, Afshar K, Golts E, Meier A, Alexander LEC, Borok Z, Shen Y, Chung WK, McCulley DJ, Sun X. Context-dependent roles of mitochondrial LONP1 in orchestrating the balance between airway progenitor versus progeny cells. Cell Stem Cell 2024:S1934-5909(24)00287-X. [PMID: 39181129 DOI: 10.1016/j.stem.2024.08.001] [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: 09/16/2023] [Revised: 06/12/2024] [Accepted: 08/01/2024] [Indexed: 08/27/2024]
Abstract
While all eukaryotic cells are dependent on mitochondria for function, in a complex tissue, which cell type and which cell behavior are more sensitive to mitochondrial deficiency remain unpredictable. Here, we show that in the mouse airway, compromising mitochondrial function by inactivating mitochondrial protease gene Lonp1 led to reduced progenitor proliferation and differentiation during development, apoptosis of terminally differentiated ciliated cells and their replacement by basal progenitors and goblet cells during homeostasis, and failed airway progenitor migration into damaged alveoli following influenza infection. ATF4 and the integrated stress response (ISR) pathway are elevated and responsible for the airway phenotypes. Such context-dependent sensitivities are predicted by the selective expression of Bok, which is required for ISR activation. Reduced LONP1 expression is found in chronic obstructive pulmonary disease (COPD) airways with squamous metaplasia. These findings illustrate a cellular energy landscape whereby compromised mitochondrial function could favor the emergence of pathological cell types.
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Affiliation(s)
- Le Xu
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chunting Tan
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justinn Barr
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole Talaba
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jamie Verheyden
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ji Sun Chin
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samvel Gaboyan
- Pulmonary and Critical Care Section, Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nikita Kasaraneni
- Pulmonary and Critical Care Section, Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ruth M Elgamal
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kyle J Gaulton
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace Lin
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Kamyar Afshar
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Eugene Golts
- Department of Surgery, Division of Cardiovascular and Thoracic Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Angela Meier
- Department of Anesthesiology, Division of Critical Care, University of California, San Diego, La Jolla, CA, USA
| | - Laura E Crotty Alexander
- Pulmonary and Critical Care Section, Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA; Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David J McCulley
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Sun
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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2
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Riccio A, Brannon A, Krahn J, Bouvette J, Williams J, Borgnia M, Copeland W. Coordinated DNA polymerization by Polγ and the region of LonP1 regulated proteolysis. Nucleic Acids Res 2024; 52:7863-7875. [PMID: 38932681 PMCID: PMC11260448 DOI: 10.1093/nar/gkae539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
The replicative mitochondrial DNA polymerase, Polγ, and its protein regulation are essential for the integrity of the mitochondrial genome. The intricacies of Polγ regulation and its interactions with regulatory proteins, which are essential for fine-tuning polymerase function, remain poorly understood. Misregulation of the Polγ heterotrimer, consisting of (i) PolG, the polymerase catalytic subunit and (ii) PolG2, the accessory subunit, ultimately results in mitochondrial diseases. Here, we used single particle cryo-electron microscopy to resolve the structure of PolG in its apoprotein state and we captured Polγ at three intermediates within the catalytic cycle: DNA bound, engaged, and an active polymerization state. Chemical crosslinking mass spectrometry, and site-directed mutagenesis uncovered the region of LonP1 engagement of PolG, which promoted proteolysis and regulation of PolG protein levels. PolG2 clinical variants, which disrupted a stable Polγ complex, led to enhanced LonP1-mediated PolG degradation. Overall, this insight into Polγ aids in an understanding of mitochondrial DNA replication and characterizes how machinery of the replication fork may be targeted for proteolytic degradation when improperly functioning.
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Affiliation(s)
- Amanda A Riccio
- Mitochondrial DNA Replication group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Asia J Brannon
- Mitochondrial DNA Replication group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Jonathan Bouvette
- Molecular Microscopy Consortium, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Mass Spectrometry Research and Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Molecular Microscopy Consortium, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, 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, NIH, Research Triangle Park, NC 27709, USA
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3
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Yadav A, Tiwari P, Dada R. Yoga and Lifestyle Changes: A Path to Improved Fertility - A Narrative Review. Int J Yoga 2024; 17:10-19. [PMID: 38899142 PMCID: PMC11185437 DOI: 10.4103/ijoy.ijoy_211_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 06/21/2024] Open
Abstract
Infertility, a widespread medical condition affecting numerous couples globally, persists as a challenge despite advances in assisted reproductive technologies (ARTs), often burdened by financial, physical, and emotional strains. Complementary and alternative approaches, notably yoga, have garnered attention for potentially enhancing fertility outcomes. Studies reveal yoga's influence on factors contributing to infertility, including reduced oxidative stress (OS) and oxidative DNA damage (ODD). OS, linked to mutagenic base formation, higher malondialdehyde levels, abnormal methylation, and altered gene expression, can impair sperm genome integrity. Yoga's efficacy is evident in lowering OS, positively affecting signal transmission, gene expression, and physiological systems. Furthermore, yoga has a positive impact on addressing the dysregulation of apoptosis, resulting in improved processes such as spermatogenesis, sperm maturation, and motility, while also reducing DNA fragmentation. OS correlates with genome-wide hypomethylation, telomere shortening, and mitochondrial dysfunction, contributing to genome instability. Yoga and meditation significantly reduce OS and ODD, ensuring proper reactive oxygen levels and preserving physiological systems. The review explores potential mechanisms underlying yoga's positive impact on infertility, including enhanced blood flow, reduced inflammation, relaxation response, and modulation of the hypothalamic-pituitary-adrenal axis. Furthermore, a comprehensive review of the literature reveals substantial evidence supporting the positive effects of yoga on infertility factors. These include oxidative stress (OS), oxidative DNA damage (ODD), epigenetic changes, hormonal balance, ovarian function, menstrual irregularities, and stress reduction. In summary, yoga emerges as a promising adjunctive therapy for infertility, demonstrating the potential to mitigate key factors influencing reproductive success. Although preliminary evidence indicates the positive effects of yoga on infertility, further clinical research is imperative to define specific benefits, molecular mechanisms associated, optimal protocols, and long-term effects in infertility treatment plans.
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Affiliation(s)
- Anjali Yadav
- Department of Anatomy, Lab for Molecular Reproduction and Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Prabhakar Tiwari
- Department of Anatomy, Lab for Molecular Reproduction and Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Rima Dada
- Department of Anatomy, Lab for Molecular Reproduction and Genetics, All India Institute of Medical Sciences, New Delhi, India
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4
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Rey T, Tábara LC, Prudent J, Minczuk M. mtFociCounter for automated single-cell mitochondrial nucleoid quantification and reproducible foci analysis. Nucleic Acids Res 2023; 51:e107. [PMID: 37850644 PMCID: PMC10681798 DOI: 10.1093/nar/gkad864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 10/01/2023] [Indexed: 10/19/2023] Open
Abstract
Mitochondrial DNA (mtDNA) encodes the core subunits for OXPHOS, essential in near-all eukaryotes. Packed into distinct foci (nucleoids) inside mitochondria, the number of mtDNA copies differs between cell-types and is affected in several human diseases. Currently, common protocols estimate per-cell mtDNA-molecule numbers by sequencing or qPCR from bulk samples. However, this does not allow insight into cell-to-cell heterogeneity and can mask phenotypical sub-populations. Here, we present mtFociCounter, a single-cell image analysis tool for reproducible quantification of nucleoids and other foci. mtFociCounter is a light-weight, open-source freeware and overcomes current limitations to reproducible single-cell analysis of mitochondrial foci. We demonstrate its use by analysing 2165 single fibroblasts, and observe a large cell-to-cell heterogeneity in nucleoid numbers. In addition, mtFociCounter quantifies mitochondrial content and our results show good correlation (R = 0.90) between nucleoid number and mitochondrial area, and we find nucleoid density is less variable than nucleoid numbers in wild-type cells. Finally, we demonstrate mtFociCounter readily detects differences in foci-numbers upon sample treatment, and applies to Mitochondrial RNA Granules and superresolution microscopy. mtFociCounter provides a versatile solution to reproducibly quantify cellular foci in single cells and our results highlight the importance of accounting for cell-to-cell variance and mitochondrial context in mitochondrial foci analysis.
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Affiliation(s)
- Timo Rey
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Luis Carlos Tábara
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
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5
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Potter A, Cabrera-Orefice A, Spelbrink JN. Let's make it clear: systematic exploration of mitochondrial DNA- and RNA-protein complexes by complexome profiling. Nucleic Acids Res 2023; 51:10619-10641. [PMID: 37615582 PMCID: PMC10602928 DOI: 10.1093/nar/gkad697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
Complexome profiling (CP) is a powerful tool for systematic investigation of protein interactors that has been primarily applied to study the composition and dynamics of mitochondrial protein complexes. Here, we further optimized this method to extend its application to survey mitochondrial DNA- and RNA-interacting protein complexes. We established that high-resolution clear native gel electrophoresis (hrCNE) is a better alternative to preserve DNA- and RNA-protein interactions that are otherwise disrupted when samples are separated by the widely used blue native gel electrophoresis (BNE). In combination with enzymatic digestion of DNA, our CP approach improved the identification of a wide range of protein interactors of the mitochondrial gene expression system without compromising the detection of other multiprotein complexes. The utility of this approach was particularly demonstrated by analysing the complexome changes in human mitochondria with impaired gene expression after transient, chemically induced mitochondrial DNA depletion. Effects of RNase on mitochondrial protein complexes were also evaluated and discussed. Overall, our adaptations significantly improved the identification of mitochondrial DNA- and RNA-protein interactions by CP, thereby unlocking the comprehensive analysis of a near-complete mitochondrial complexome in a single experiment.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Functional Proteomics, Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Johannes N Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands
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6
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Wojtaszek JL, Hoff KE, Longley MJ, Kaur P, Andres S, Wang H, Williams R, Copeland W. Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA. Nucleic Acids Res 2023; 51:9716-9732. [PMID: 37592734 PMCID: PMC10570022 DOI: 10.1093/nar/gkad679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 08/09/2023] [Indexed: 08/19/2023] Open
Abstract
The homodimeric PolG2 accessory subunit of the mitochondrial DNA polymerase gamma (Pol γ) enhances DNA binding and processive DNA synthesis by the PolG catalytic subunit. PolG2 also directly binds DNA, although the underlying molecular basis and functional significance are unknown. Here, data from Atomic Force Microscopy (AFM) and X-ray structures of PolG2-DNA complexes define dimeric and hexameric PolG2 DNA binding modes. Targeted disruption of PolG2 DNA-binding interfaces impairs processive DNA synthesis without diminishing Pol γ subunit affinities. In addition, a structure-specific DNA-binding role for PolG2 oligomers is supported by X-ray structures and AFM showing that oligomeric PolG2 localizes to DNA crossings and targets forked DNA structures resembling the mitochondrial D-loop. Overall, data indicate that PolG2 DNA binding has both PolG-dependent and -independent functions in mitochondrial DNA replication and maintenance, which provide new insight into molecular defects associated with PolG2 disruption in mitochondrial disease.
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Affiliation(s)
- Jessica L Wojtaszek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Kirsten E Hoff
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Sara N Andres
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC 27695, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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7
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Kristiansen CK, Furriol J, Chen A, Sullivan GJ, Bindoff LA, Liang KX. Deoxyribonucleoside treatment rescues EtBr-induced mtDNA depletion in iPSC-derived neural stem cells with POLG mutations. FASEB J 2023; 37:e23139. [PMID: 37584631 DOI: 10.1096/fj.202300650rr] [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: 04/04/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
Mutations in POLG, the gene encoding the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase gamma (Pol-γ), lead to diseases driven by defective mtDNA maintenance. Despite being the most prevalent cause of mitochondrial disease, treatments for POLG-related disorders remain elusive. In this study, we used POLG patient-induced pluripotent stem cell (iPSC)-derived neural stem cells (iNSCs), one homozygous for the POLG mutation c.2243G>C and one compound heterozygous with c.2243G>C and c.1399G>A, and treated these iNSCs with ethidium bromide (EtBr) to study the rate of depletion and repopulation of mtDNA. In addition, we investigated the effect of deoxyribonucleoside (dNs) supplementation on mtDNA maintenance during EtBr treatment and post-treatment repopulation in the same cells. EtBr-induced mtDNA depletion occurred at a similar rate in both patient and control iNSCs, however, restoration of mtDNA levels was significantly delayed in iNSCs carrying the compound heterozygous POLG mutations. In contrast, iNSC with the homozygous POLG mutation recovered their mtDNA at a rate similar to controls. When we treated cells with dNs, we found that this reduced EtBr-induced mtDNA depletion and significantly increased repopulation rates in both patient iNSCs. These observations are consistent with the hypothesis that mutations in POLG impair mtDNA repopulation also within intact neural lineage cells and suggest that those with compound heterozygous mutation have a more severe defect of mtDNA synthesis. Our findings further highlight the potential for dNs to improve mtDNA replication in the presence of POLG mutations, suggesting that this may offer a new therapeutic modality for mitochondrial diseases caused by disturbed mtDNA homeostasis.
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Affiliation(s)
- Cecilie Katrin Kristiansen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Haukeland University Hospital, Bergen, Norway
| | - Jessica Furriol
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anbin Chen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurosurgery, Xinhua Hospital Affiliated with Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gareth John Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Institute of Immunology, Oslo University Hospital, Oslo, Norway
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Laurence A Bindoff
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
- National Advisory Unit for Congenital Metabolic Diseases, Oslo University Hospital, Oslo, Norway
| | - Kristina Xiao Liang
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Haukeland University Hospital, Bergen, Norway
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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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Ozaki M, Le TD, Inoue YH. Downregulating Mitochondrial DNA Polymerase γ in the Muscle Stimulated Autophagy, Apoptosis, and Muscle Aging-Related Phenotypes in Drosophila Adults. Biomolecules 2022; 12:biom12081105. [PMID: 36008999 PMCID: PMC9405705 DOI: 10.3390/biom12081105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Reactive oxygen species, generated as by-products of mitochondrial electron transport, can induce damage to mitochondrial DNA (mtDNA) and proteins. Here, we investigated whether the moderate accumulation of mtDNA damage in adult muscles resulted in accelerated aging-related phenotypes in Drosophila. DNA polymerase γ (Polγ) is the sole mitochondrial DNA polymerase. The muscle-specific silencing of the genes encoding the polymerase subunits resulted in the partial accumulation of mtDNA with oxidative damage and a reduction in the mtDNA copy number. This subsequently resulted in the production of abnormal mitochondria with reduced membrane potential and, consequently, a partially reduced ATP quantity in the adult muscle. Immunostaining indicated a moderate increase in autophagy and mitophagy in adults with RNA interference of Polγ (PolγRNAi) muscle cells with abnormal mitochondria. In adult muscles showing continuous silencing of Polγ, malformation of both myofibrils and mitochondria was frequently observed. This was associated with the partially enhanced activation of pro-apoptotic caspases in the muscle. Adults with muscle-specific PolγRNAi exhibited a shortened lifespan, accelerated age-dependent impairment of locomotor activity, and disturbed circadian rhythms. Our findings in this Drosophila model contribute to understanding how the accumulation of mtDNA damage results in impaired mitochondrial activity and how this contributes to muscle aging.
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10
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Schreier HK, Wiehe RS, Ricchetti M, Wiesmüller L. Polymerase ζ is Involved in Mitochondrial DNA Maintenance Processes in Concert with APE1 Activity. Genes (Basel) 2022; 13:genes13050879. [PMID: 35627264 PMCID: PMC9141751 DOI: 10.3390/genes13050879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial DNA (mtDNA) damaged by reactive oxygen species (ROS) triggers so far poorly understood processes of mtDNA maintenance that are coordinated by a complex interplay among DNA repair, DNA degradation, and DNA replication. This study was designed to identify the proteins involved in mtDNA maintenance by applying a special long-range PCR, reflecting mtDNA integrity in the minor arc. A siRNA screening of literature-based candidates was performed under conditions of enforced oxidative phosphorylation revealing the functional group of polymerases and therein polymerase ζ (POLZ) as top hits. Thus, POLZ knockdown caused mtDNA accumulation, which required the activity of the base excision repair (BER) nuclease APE1, and was followed by compensatory mtDNA replication determined by the single-cell mitochondrial in situ hybridization protocol (mTRIP). Quenching reactive oxygen species (ROS) in mitochondria unveiled an additional, ROS-independent involvement of POLZ in the formation of a typical deletion in the minor arc region. Together with data demonstrating the localization of POLZ in mitochondria, we suggest that POLZ plays a significant role in mtDNA turnover, particularly under conditions of oxidative stress.
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Affiliation(s)
- Heike Katrin Schreier
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Rahel Stefanie Wiehe
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, CEDEX 15, 75724 Paris, France;
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
- Correspondence:
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11
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Mitochondrial Neurodegeneration. Cells 2022; 11:cells11040637. [PMID: 35203288 PMCID: PMC8870525 DOI: 10.3390/cells11040637] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/28/2022] [Accepted: 02/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mitochondria are cytoplasmic organelles, which generate energy as heat and ATP, the universal energy currency of the cell. This process is carried out by coupling electron stripping through oxidation of nutrient substrates with the formation of a proton-based electrochemical gradient across the inner mitochondrial membrane. Controlled dissipation of the gradient can lead to production of heat as well as ATP, via ADP phosphorylation. This process is known as oxidative phosphorylation, and is carried out by four multiheteromeric complexes (from I to IV) of the mitochondrial respiratory chain, carrying out the electron flow whose energy is stored as a proton-based electrochemical gradient. This gradient sustains a second reaction, operated by the mitochondrial ATP synthase, or complex V, which condensates ADP and Pi into ATP. Four complexes (CI, CIII, CIV, and CV) are composed of proteins encoded by genes present in two separate compartments: the nuclear genome and a small circular DNA found in mitochondria themselves, and are termed mitochondrial DNA (mtDNA). Mutations striking either genome can lead to mitochondrial impairment, determining infantile, childhood or adult neurodegeneration. Mitochondrial disorders are complex neurological syndromes, and are often part of a multisystem disorder. In this paper, we divide the diseases into those caused by mtDNA defects and those that are due to mutations involving nuclear genes; from a clinical point of view, we discuss pediatric disorders in comparison to juvenile or adult-onset conditions. The complementary genetic contributions controlling organellar function and the complexity of the biochemical pathways present in the mitochondria justify the extreme genetic and phenotypic heterogeneity of this new area of inborn errors of metabolism known as ‘mitochondrial medicine’.
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Silva-Pinheiro P, Pardo-Hernández C, Reyes A, Tilokani L, Mishra A, Cerutti R, Li S, Rozsivalova DH, Valenzuela S, Dogan SA, Peter B, Fernández-Silva P, Trifunovic A, Prudent J, Minczuk M, Bindoff L, Macao B, Zeviani M, Falkenberg M, Viscomi C. Correction to 'DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion'. Nucleic Acids Res 2021; 49:10803. [PMID: 34520541 PMCID: PMC8501975 DOI: 10.1093/nar/gkab837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Pedro Silva-Pinheiro
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Carlos Pardo-Hernández
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Aurelio Reyes
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Lisa Tilokani
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Anup Mishra
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Raffaele Cerutti
- Department of Neurosciences, University of Padova, via Giustiniani, 2-35128 Padova, Italy
| | - Shuaifeng Li
- Center for Cancer Biology, Life Science of Institution, Zhejiang University, Hangzhou 310058, China
| | - Dieu-Hien Rozsivalova
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Sukru A Dogan
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, 34342 Istanbul, Turkey
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Patricio Fernández-Silva
- Biochemistry and Molecular and Cell Biology Department, University of Zaragoza, C/ Pedro Cerbuna s/n 50.009-Zaragoza, and Biocomputation and Complex Systems Physics Institute (BIFI), C/ Mariano Esquillor, 50.018-Zaragoza, Spain
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Julien Prudent
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Michal Minczuk
- MRC/University of Cambridge Mitochondrial Biology Unit, Hills Road, CB2 0XY Cambridge, UK
| | - Laurence Bindoff
- Department of Clinical Medicine, University of Bergen, 5007 Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Massimo Zeviani
- Department of Neurosciences, University of Padova, via Giustiniani, 2-35128 Padova, Italy
- Venetian Institute of Molecular Medicine, via Orus 2-35128 Padova, Italy
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Medicinaregatan 9A P.O. Box 440, SE405 30 Gothenburg, Sweden
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B-35131 Padova, Italy
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Ramón J, Vila-Julià F, Molina-Granada D, Molina-Berenguer M, Melià MJ, García-Arumí E, Torres-Torronteras J, Cámara Y, Martí R. Therapy Prospects for Mitochondrial DNA Maintenance Disorders. Int J Mol Sci 2021; 22:6447. [PMID: 34208592 PMCID: PMC8234938 DOI: 10.3390/ijms22126447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial DNA depletion and multiple deletions syndromes (MDDS) constitute a group of mitochondrial diseases defined by dysfunctional mitochondrial DNA (mtDNA) replication and maintenance. As is the case for many other mitochondrial diseases, the options for the treatment of these disorders are rather limited today. Some aggressive treatments such as liver transplantation or allogeneic stem cell transplantation are among the few available options for patients with some forms of MDDS. However, in recent years, significant advances in our knowledge of the biochemical pathomechanisms accounting for dysfunctional mtDNA replication have been achieved, which has opened new prospects for the treatment of these often fatal diseases. Current strategies under investigation to treat MDDS range from small molecule substrate enhancement approaches to more complex treatments, such as lentiviral or adenoassociated vector-mediated gene therapy. Some of these experimental therapies have already reached the clinical phase with very promising results, however, they are hampered by the fact that these are all rare disorders and so the patient recruitment potential for clinical trials is very limited.
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Affiliation(s)
- Javier Ramón
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ferran Vila-Julià
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - David Molina-Granada
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel Molina-Berenguer
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria Jesús Melià
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Elena García-Arumí
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier Torres-Torronteras
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Yolanda Cámara
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ramon Martí
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d’Hebron Research Institute, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain; (J.R.); (F.V.-J.); (D.M.-G.); (M.M.-B.); (M.J.M.); (E.G.-A.); (J.T.-T.); (Y.C.)
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
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