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Xie G, Shao Z. SPP-5 affects larval arrest via insulin signaling pathway in Caenorhabditis elegans. J Mol Histol 2024:10.1007/s10735-024-10205-5. [PMID: 38869752 DOI: 10.1007/s10735-024-10205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/18/2024] [Indexed: 06/14/2024]
Abstract
Diapause is an endocrine-mediated metabolic and growth arrest state in response to unfavorable external environments. The nematode Caenorhabditis elegans can enter diapause/arrest during embryonic, larval, or adult stages when subjected to detrimental external environments. Larval stage 1 (L1) arrest happens when animals hatch without food. Previous work has shown that the insulin pathway plays a prominent role in regulating L1 arrest. However, the downstream signal molecular mechanisms and biomarkers are still missing. In this study, we showed that SaPosin-like Protein family member SPP-5 is significantly upregulated during L1 arrest, suggesting that it could act as an L1 arrest biomarker. Using RNA interference we demonstrated that spp-5 knockdown accelerated larval development, while the overexpression resulted in L1 arrest. Consistently, SPP-5 level was significantly up-regulated in the L1 arrest daf-2(e1370) mutants, and spp-5(RNAi) suppressed the daf-2(e1370) induced L1 arrest. These results suggest that SPP-5 can serve as an L1 arrest biomarker and promote the arrest probably via the insulin signaling pathway.
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Affiliation(s)
- Guangjie Xie
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Fudan University, Shanghai, China
| | - Zhiyong Shao
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Fudan University, Shanghai, China.
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2
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Onraet T, Zuryn S. C. elegans as a model to study mitochondrial biology and disease. Semin Cell Dev Biol 2024; 154:48-58. [PMID: 37149409 DOI: 10.1016/j.semcdb.2023.04.006] [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: 03/06/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 05/08/2023]
Abstract
Mitochondria perform a myriad of essential functions that ensure organismal homeostasis, including maintaining bioenergetic capacity, sensing and signalling the presence of pathogenic threats, and determining cell fate. Their function is highly dependent on mitochondrial quality control and the appropriate regulation of mitochondrial size, shape, and distribution during an entire lifetime, as well as their inheritance across generations. The roundworm Caenorhabditis elegans has emerged as an ideal model organism through which to study mitochondria. The remarkable conservation of mitochondrial biology has allowed C. elegans researchers to investigate complex processes that are challenging to study in higher organisms. In this review, we explore the key recent contributions of C. elegans to mitochondrial biology through the lens of mitochondrial dynamics, organellar removal, and mitochondrial inheritance, as well as their involvement in immune responses, various types of stress, and transgenerational signalling.
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Affiliation(s)
- Tessa Onraet
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane 4072, Australia.
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3
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Vozdek R, Wang B, Li KH, Pramstaller PP, Hicks AA, Ma DK. Fluorescent reporter of Caenorhabditis elegans Parkin: Regulators of its abundance and role in autophagy-lysosomal dynamics. OPEN RESEARCH EUROPE 2023; 2:23. [PMID: 37811477 PMCID: PMC10556562 DOI: 10.12688/openreseurope.14235.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/10/2023]
Abstract
Background: Parkin, which when mutated leads to early-onset Parkinson's disease, acts as an E3 ubiquitin ligase. How Parkin is regulated for selective protein and organelle targeting is not well understood. Here, we used protein interactor and genetic screens in Caenorhabditis elegans ( C. elegans) to identify new regulators of Parkin abundance and showed their impact on autophagy-lysosomal dynamics and alpha-Synuclein processing. Methods: We generated a transgene encoding mCherry-tagged C. elegans Parkin - Parkinson's Disease Related 1 (PDR-1). We performed protein interactor screen using Co-immunoprecipitation followed by mass spectrometry analysis to identify putative interacting partners of PDR-1. Ribonucleic acid interference (RNAi) screen and an unbiased mutagenesis screen were used to identify genes regulating PDR-1 abundance. Confocal microscopy was used for the identification of the subcellular localization of PDR-1 and alpha-Synuclein processing. Results: We show that the mCherry::pdr-1 transgene rescues the mitochondrial phenotype of pdr-1 mutants and that the expressed PDR-1 reporter is localized in the cytosol with enriched compartmentalization in the autophagy-lysosomal system. We determined that the transgenic overexpression of the PDR-1 reporter, due to inactivated small interfering RNA (siRNA) generation pathway, disrupts autophagy-lysosomal dynamics. From the RNAi screen of putative PDR-1 interactors we found that the inactivated Adenine Nucleotide Translocator ant-1.1/hANT, or hybrid ubiquitin genes ubq-2/h UBA52 and ubl-1/h RPS27A encoding a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively, induced PDR-1 abundance and affected lysosomal dynamics. In addition, we demonstrate that the abundant PDR-1 plays a role in alpha-Synuclein processing. Conclusions: These data show that the abundant reporter of C. elegans Parkin affects the autophagy-lysosomal system together with alpha-Synuclein processing which can help in understanding the pathology in Parkin-related diseases.
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Affiliation(s)
- Roman Vozdek
- Institute for Biomedicine, Eurac Research, Affiliated institute of the University of Lübeck, Bolzano, 39100, Italy
| | - Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kathy H. Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Peter P. Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated institute of the University of Lübeck, Bolzano, 39100, Italy
| | - Andrew A. Hicks
- Institute for Biomedicine, Eurac Research, Affiliated institute of the University of Lübeck, Bolzano, 39100, Italy
| | - Dengke K. Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, CA, 94158, USA
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4
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Karaa A, Klopstock T. Clinical trials in mitochondrial diseases. HANDBOOK OF CLINICAL NEUROLOGY 2023; 194:229-250. [PMID: 36813315 DOI: 10.1016/b978-0-12-821751-1.00002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Primary mitochondrial diseases are some of the most common and complex inherited inborn errors of metabolism. Their molecular and phenotypic diversity has led to difficulties in finding disease-modifying therapies and clinical trial efforts have been slow due to multiple significant challenges. Lack of robust natural history data, difficulties in finding specific biomarkers, absence of well-validated outcome measures, and small patient numbers have made clinical trial design and conduct difficult. Encouragingly, new interest in treating mitochondrial dysfunction in common diseases and regulatory incentives to develop therapies for rare conditions have led to significant interest and efforts to develop drugs for primary mitochondrial diseases. Here, we review past and present clinical trials and future strategies of drug development in primary mitochondrial diseases.
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Affiliation(s)
- Amel Karaa
- Mitochondrial Disease Program, Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Boston, MA, United States; Department of Pediatrics, Harvard Medical School, Boston, MA, United States.
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; German Network for mitochondrial disorders (mitoNET), Munich, Germany
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5
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Verma M, Francis L, Lizama BN, Callio J, Fricklas G, Wang KZQ, Kaufman BA, D'Aiuto L, Stolz DB, Watkins SC, Nimgaonkar VL, Soto-Gutierrez A, Goldstein A, Chu CT. iPSC-Derived Neurons from Patients with POLG Mutations Exhibit Decreased Mitochondrial Content and Dendrite Simplification. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:201-212. [PMID: 36414085 PMCID: PMC9976192 DOI: 10.1016/j.ajpath.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
Abstract
Mutations in POLG, the gene encoding the catalytic subunit of DNA polymerase gamma, result in clinical syndromes characterized by mitochondrial DNA (mtDNA) depletion in affected tissues with variable organ involvement. The brain is one of the most affected organs, and symptoms include intractable seizures, developmental delay, dementia, and ataxia. Patient-derived induced pluripotent stem cells (iPSCs) provide opportunities to explore mechanisms in affected cell types and potential therapeutic strategies. Fibroblasts from two patients were reprogrammed to create new iPSC models of POLG-related mitochondrial diseases. Compared with iPSC-derived control neurons, mtDNA depletion was observed upon differentiation of the POLG-mutated lines to cortical neurons. POLG-mutated neurons exhibited neurite simplification with decreased mitochondrial content, abnormal mitochondrial structure and function, and increased cell death. Expression of the mitochondrial kinase PTEN-induced kinase 1 (PINK1) mRNA was decreased in patient neurons. Overexpression of PINK1 increased mitochondrial content and ATP:ADP ratios in neurites, decreasing cell death and rescuing neuritic complexity. These data indicate an intersection of polymerase gamma and PINK1 pathways that may offer a novel therapeutic option for patients affected by this spectrum of disorders.
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Affiliation(s)
- Manish Verma
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lily Francis
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Britney N Lizama
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jason Callio
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Gabriella Fricklas
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kent Z Q Wang
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Brett A Kaufman
- Department of Medicine, Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Leonardo D'Aiuto
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Donna B Stolz
- Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Simon C Watkins
- Center for Biologic Imaging (CBI), University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Vishwajit L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | | | - Amy Goldstein
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charleen T Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
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6
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Uma Naresh N, Kim S, Shpilka T, Yang Q, Du Y, Haynes CM. Mitochondrial genome recovery by ATFS-1 is essential for development after starvation. Cell Rep 2022; 41:111875. [PMID: 36577367 PMCID: PMC9922093 DOI: 10.1016/j.celrep.2022.111875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/09/2022] [Accepted: 12/01/2022] [Indexed: 12/28/2022] Open
Abstract
Nutrient availability regulates the C. elegans life cycle as well as mitochondrial physiology. Food deprivation significantly reduces mitochondrial genome (mtDNA) numbers and leads to aging-related phenotypes. Here we show that the bZIP (basic leucine zipper) protein ATFS-1, a mediator of the mitochondrial unfolded protein response (UPRmt), is required to promote growth and establish a functional germline after prolonged starvation. We find that recovery of mtDNA copy numbers and development after starvation requires mitochondrion-localized ATFS-1 but not its nuclear transcription activity. We also find that the insulin-like receptor DAF-2 functions upstream of ATFS-1 to modulate mtDNA content. We show that reducing DAF-2 activity represses ATFS-1 nuclear function while causing an increase in mtDNA content, partly mediated by mitochondrion-localized ATFS-1. Our data indicate the importance of the UPRmt in recovering mitochondrial mass and suggest that atfs-1-dependent mtDNA replication precedes mitochondrial network expansion after starvation.
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Affiliation(s)
- Nandhitha Uma Naresh
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Sookyung Kim
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tomer Shpilka
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Qiyuan Yang
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yunguang Du
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Cole M Haynes
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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7
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Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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8
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Tostes K, dos Santos AC, Alves LO, Bechara LRG, Marascalchi R, Macabelli CH, Grejo MP, Festuccia WT, Gottlieb RA, Ferreira JCB, Chiaratti MR. Autophagy deficiency abolishes liver mitochondrial DNA segregation. Autophagy 2022; 18:2397-2408. [PMID: 35220898 PMCID: PMC9542960 DOI: 10.1080/15548627.2022.2038501] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mutations in the mitochondrial genome (mtDNA) are ubiquitous in humans and can lead to a broad spectrum of disorders. However, due to the presence of multiple mtDNA molecules in the cell, co-existence of mutant and wild-type mtDNAs (termed heteroplasmy) can mask disease phenotype unless a threshold of mutant molecules is reached. Importantly, the mutant mtDNA level can change across lifespan as mtDNA segregates in an allele- and cell-specific fashion, potentially leading to disease. Segregation of mtDNA is mainly evident in hepatic cells, resulting in an age-dependent increase of mtDNA variants, including non-synonymous potentially deleterious mutations. Here we modeled mtDNA segregation using a well-established heteroplasmic mouse line with mtDNA of NZB/BINJ and C57BL/6N origin on a C57BL/6N nuclear background. This mouse line showed a pronounced age-dependent NZB mtDNA accumulation in the liver, thus leading to enhanced respiration capacity per mtDNA molecule. Remarkably, liver-specific atg7 (autophagy related 7) knockout abolished NZB mtDNA accumulat ion, resulting in close-to-neutral mtDNA segregation through development into adulthood. prkn (parkin RBR E3 ubiquitin protein ligase) knockout also partially prevented NZB mtDNA accumulation in the liver, but to a lesser extent. Hence, we propose that age-related liver mtDNA segregation is a consequence of macroautophagic clearance of the less-fit mtDNA. Considering that NZB/BINJ and C57BL/6N mtDNAs have a level of divergence comparable to that between human Eurasian and African mtDNAs, these findings have potential implications for humans, including the safe use of mitochondrial replacement therapy.Abbreviations: Apob: apolipoprotein B; Atg1: autophagy-related 1; Atg7: autophagy related 7; Atp5a1: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1; BL6: C57BL/6N mouse strain; BNIP3: BCL2/adenovirus E1B interacting protein 3; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; MAP1LC3A: microtubule-associated protein 1 light chain 3 alpha; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; mt-Atp8: mitochondrially encoded ATP synthase 8; MT-CO1: mitochondrially encoded cytochrome c oxidase I; MT-CO2: mitochondrially encoded cytochrome c oxidase II; mt-Co3: mitochondrially encoded cytochrome c oxidase III; mt-Cytb: mitochondrially encoded cytochrome b; mtDNA: mitochondrial DNA; MUL1: mitochondrial ubiquitin ligase activator of NFKB 1; nDNA: nuclear DNA; Ndufa9: NADH:ubiquinone oxireductase subunit A9; NDUFB8: NADH:ubiquinone oxireductase subunit B8; Nnt: nicotinamide nucleotide transhydrogenase; NZB: NZB/BINJ mouse strain; OXPHOS: oxidative phosphorylation; PINK1: PTEN induced putative kinase 1; Polg2: polymerase (DNA directed), gamma 2, accessory subunit; Ppara: peroxisome proliferator activated receptor alpha; Ppia: peptidylprolyl isomerase A; Prkn: parkin RBR E3 ubiquitin protein ligase; P10: post-natal day 10; P21: post-natal day 21; P100: post-natal day 100; qPCR: quantitative polymerase chain reaction; Rpl19: ribosomal protein L19; Rps18: ribosomal protein S18; SD: standard deviation; SEM: standard error of the mean; SDHB: succinate dehydrogenase complex, subunit B, iron sulfur (Ip); SQSTM1: sequestosome 1; Ssbp1: single-stranded DNA binding protein 1; TFAM: transcription factor A, mitochondrial; Tfb1m: transcription factor B1, mitochondrial; Tfb2m: transcription factor B2, mitochondrial; TOMM20: translocase of outer mitochondrial membrane 20; UQCRC2: ubiquinol cytochrome c reductase core protein 2; WT: wild-type.
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Affiliation(s)
- Katiane Tostes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Angélica C. dos Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Lindomar O. Alves
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Luiz R. G. Bechara
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Rachel Marascalchi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carolina H. Macabelli
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Mateus P. Grejo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - William T. Festuccia
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Roberta A. Gottlieb
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Julio C. B. Ferreira
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil,Department of Chemical and Systems Biology, Stanford University School of Medicine, CA, USA
| | - Marcos R. Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil,CONTACT Marcos R. Chiaratti Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos13565-905, Brazil
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9
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Leuthner T, Benzing L, Kohrn B, Bergemann C, Hipp M, Hershberger K, Mello D, Sokolskyi T, Stevenson K, Merutka I, Seay S, Gregory S, Kennedy S, Meyer J. Resistance of mitochondrial DNA to cadmium and Aflatoxin B1 damage-induced germline mutation accumulation in C. elegans. Nucleic Acids Res 2022; 50:8626-8642. [PMID: 35947695 PMCID: PMC9410910 DOI: 10.1093/nar/gkac666] [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: 12/13/2021] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is prone to mutation in aging and over evolutionary time, yet the processes that regulate the accumulation of de novo mtDNA mutations and modulate mtDNA heteroplasmy are not fully elucidated. Mitochondria lack certain DNA repair processes, which could contribute to polymerase error-induced mutations and increase susceptibility to chemical-induced mtDNA mutagenesis. We conducted error-corrected, ultra-sensitive Duplex Sequencing to investigate the effects of two known nuclear genome mutagens, cadmium and Aflatoxin B1, on germline mtDNA mutagenesis in Caenorhabditis elegans. Detection of thousands of mtDNA mutations revealed pervasive heteroplasmy in C. elegans and that mtDNA mutagenesis is dominated by C:G → A:T mutations generally attributed to oxidative damage. However, there was no effect of either exposure on mtDNA mutation frequency, spectrum, or trinucleotide context signature despite a significant increase in nuclear mutation rate after aflatoxin B1 exposure. Mitophagy-deficient mutants pink-1 and dct-1 accumulated significantly higher levels of mtDNA damage compared to wild-type C. elegans after exposures. However, there were only small differences in mtDNA mutation frequency, spectrum, or trinucleotide context signature compared to wild-type after 3050 generations, across all treatments. These findings suggest mitochondria harbor additional previously uncharacterized mechanisms that regulate mtDNA mutational processes across generations.
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Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Laura Benzing
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Danielle F Mello
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Tymofii Sokolskyi
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Kevin Stevenson
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Ilaria R Merutka
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Sarah A Seay
- Nicholas School of the Environment, Duke University, Durham, NC 27708, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27701, USA,Department of Neurology, Duke University, Durham, NC 27708, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Joel N Meyer
- To whom correspondence should be addressed. Tel: +1 919 613 8109;
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10
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Activation of the Mitochondrial Unfolded Protein Response: A New Therapeutic Target? Biomedicines 2022; 10:biomedicines10071611. [PMID: 35884915 PMCID: PMC9313171 DOI: 10.3390/biomedicines10071611] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is a key hub that is common to many diseases. Mitochondria’s role in energy production, calcium homeostasis, and ROS balance makes them essential for cell survival and fitness. However, there are no effective treatments for most mitochondrial and related diseases to this day. Therefore, new therapeutic approaches, such as activation of the mitochondrial unfolded protein response (UPRmt), are being examined. UPRmt englobes several compensation processes related to proteostasis and antioxidant mechanisms. UPRmt activation, through an hormetic response, promotes cell homeostasis and improves lifespan and disease conditions in biological models of neurodegenerative diseases, cardiopathies, and mitochondrial diseases. Although UPRmt activation is a promising therapeutic option for many conditions, its overactivation could lead to non-desired side effects, such as increased heteroplasmy of mitochondrial DNA mutations or cancer progression in oncologic patients. In this review, we present the most recent UPRmt activation therapeutic strategies, UPRmt’s role in diseases, and its possible negative consequences in particular pathological conditions.
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11
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Meshnik L, Bar-Yaacov D, Kasztan D, Neiger T, Cohen T, Kishner M, Valenci I, Dadon S, Klein CJ, Vance JM, Nevo Y, Züchner S, Ovadia O, Mishmar D, Ben-Zvi A. Mutant C. elegans mitofusin leads to selective removal of mtDNA heteroplasmic deletions across generations to maintain fitness. BMC Biol 2022; 20:40. [PMID: 35139855 PMCID: PMC8829988 DOI: 10.1186/s12915-022-01241-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/28/2022] [Indexed: 11/20/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) is present at high copy numbers in animal cells, and though characterized by a single haplotype in each individual due to maternal germline inheritance, deleterious mutations and intact mtDNA molecules frequently co-exist (heteroplasmy). A number of factors, such as replicative segregation, mitochondrial bottlenecks, and selection, may modulate the exitance of heteroplasmic mutations. Since such mutations may have pathological consequences, they likely survive and are inherited due to functional complementation via the intracellular mitochondrial network. Here, we hypothesized that compromised mitochondrial fusion would hamper such complementation, thereby affecting heteroplasmy inheritance. Results We assessed heteroplasmy levels in three Caenorhabditis elegans strains carrying different heteroplasmic mtDNA deletions (ΔmtDNA) in the background of mutant mitofusin (fzo-1). Animals displayed severe embryonic lethality and developmental delay. Strikingly, observed phenotypes were relieved during subsequent generations in association with complete loss of ΔmtDNA molecules. Moreover, deletion loss rates were negatively correlated with the size of mtDNA deletions, suggesting that mitochondrial fusion is essential and sensitive to the nature of the heteroplasmic mtDNA mutations. Introducing the ΔmtDNA into a fzo-1;pdr-1;+/ΔmtDNA (PARKIN ortholog) double mutant resulted in a skewed Mendelian progeny distribution, in contrast to the normal distribution in the fzo-1;+/ΔmtDNA mutant, and severely reduced brood size. Notably, the ΔmtDNA was lost across generations in association with improved phenotypes. Conclusions Taken together, our findings show that when mitochondrial fusion is compromised, deleterious heteroplasmic mutations cannot evade natural selection while inherited through generations. Moreover, our findings underline the importance of cross-talk between mitochondrial fusion and mitophagy in modulating the inheritance of mtDNA heteroplasmy. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01241-2.
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Affiliation(s)
- Lana Meshnik
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dan Bar-Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dana Kasztan
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tali Neiger
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Mor Kishner
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Itay Valenci
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sara Dadon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Christopher J Klein
- Department of Neurology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jeffery M Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Yoram Nevo
- Institute of Neurology, Schneider Children's Medical Center of Israel, Tel-Aviv University, Petach Tikva, Israel
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ofer Ovadia
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Anat Ben-Zvi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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12
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Yang Q, Liu P, Anderson NS, Shpilka T, Du Y, Naresh NU, Li R, Zhu LJ, Luk K, Lavelle J, Zeinert RD, Chien P, Wolfe SA, Haynes CM. LONP-1 and ATFS-1 sustain deleterious heteroplasmy by promoting mtDNA replication in dysfunctional mitochondria. Nat Cell Biol 2022; 24:181-193. [PMID: 35165413 PMCID: PMC8868506 DOI: 10.1038/s41556-021-00840-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/29/2021] [Indexed: 12/13/2022]
Abstract
The accumulation of deleterious mitochondrial DNA (∆mtDNA) causes inherited mitochondrial diseases and ageing-associated decline in mitochondrial functions such as oxidative phosphorylation. Following mitochondrial perturbations, the bZIP protein ATFS-1 induces a transcriptional programme to restore mitochondrial function. Paradoxically, ATFS-1 is also required to maintain ∆mtDNAs in heteroplasmic worms. The mechanism by which ATFS-1 promotes ∆mtDNA accumulation relative to wild-type mtDNAs is unclear. Here we show that ATFS-1 accumulates in dysfunctional mitochondria. ATFS-1 is absent in healthy mitochondria owing to degradation by the mtDNA-bound protease LONP-1, which results in the nearly exclusive association between ATFS-1 and ∆mtDNAs in heteroplasmic worms. Moreover, we demonstrate that mitochondrial ATFS-1 promotes the binding of the mtDNA replicative polymerase (POLG) to ∆mtDNAs. Interestingly, inhibition of the mtDNA-bound protease LONP-1 increased ATFS-1 and POLG binding to wild-type mtDNAs. LONP-1 inhibition in Caenorhabditis elegans and human cybrid cells improved the heteroplasmy ratio and restored oxidative phosphorylation. Our findings suggest that ATFS-1 promotes mtDNA replication in dysfunctional mitochondria by promoting POLG-mtDNA binding, which is antagonized by LONP-1.
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Affiliation(s)
- Qiyuan Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nadine S Anderson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tomer Shpilka
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - YunGuang Du
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nandhitha Uma Naresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Josh Lavelle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Rilee D Zeinert
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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13
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Leuthner TC, Meyer JN. Mitochondrial DNA Mutagenesis: Feature of and Biomarker for Environmental Exposures and Aging. Curr Environ Health Rep 2021; 8:294-308. [PMID: 34761353 PMCID: PMC8826492 DOI: 10.1007/s40572-021-00329-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE OF REVIEW Mitochondrial dysfunction is a hallmark of aging. Mitochondrial genome (mtDNA) instability contributes to mitochondrial dysfunction, and mtDNA mutagenesis may contribute to aging. However, the origin of mtDNA mutations remains somewhat controversial. The goals of this review are to introduce and review recent literature on mtDNA mutagenesis and aging, address recent animal and epidemiological evidence for the effects of chemicals on mtDNA damage and mutagenesis, propose hypotheses regarding the contribution of environmental toxicant exposure to mtDNA mutagenesis in the context of aging, and suggest future directions and approaches for environmental health researchers. RECENT FINDINGS Stressors such as pollutants, pharmaceuticals, and ultraviolet radiation can damage the mitochondrial genome or disrupt mtDNA replication, repair, and organelle homeostatic processes, potentially influencing the rate of accumulation of mtDNA mutations. Accelerated mtDNA mutagenesis could contribute to aging, diseases of aging, and sensitize individuals with pathogenic mtDNA variants to stressors. We propose three potential mechanisms of toxicant-induced effects on mtDNA mutagenesis over lifespan: (1) increased de novo mtDNA mutations, (2) altered frequencies of mtDNA mutations, or (3) both. There are remarkably few studies that have investigated the impact of environmental chemical exposures on mtDNA instability and mutagenesis, and even fewer in the context of aging. More studies are warranted because people are exposed to tens of thousands of chemicals, and are living longer. Finally, we suggest that toxicant-induced mtDNA damage and mutational signatures may be a sensitive biomarker for some exposures.
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Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA
| | - Joel N Meyer
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA.
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14
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Rewiring cell signalling pathways in pathogenic mtDNA mutations. Trends Cell Biol 2021; 32:391-405. [PMID: 34836781 DOI: 10.1016/j.tcb.2021.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022]
Abstract
Mitochondria generate the energy to sustain cell viability and serve as a hub for cell signalling. Their own genome (mtDNA) encodes genes critical for oxidative phosphorylation. Mutations of mtDNA cause major disease and disability with a wide range of presentations and severity. We review here an emerging body of data suggesting that changes in cell metabolism and signalling pathways in response to the presence of mtDNA mutations play a key role in shaping disease presentation and progression. Understanding the impact of mtDNA mutations on cellular energy homeostasis and signalling pathways seems fundamental to identify novel therapeutic interventions with the potential to improve the prognosis for patients with primary mitochondrial disease.
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15
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Pereira CV, Gitschlag BL, Patel MR. Cellular mechanisms of mtDNA heteroplasmy dynamics. Crit Rev Biochem Mol Biol 2021; 56:510-525. [PMID: 34120542 DOI: 10.1080/10409238.2021.1934812] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.
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Affiliation(s)
- Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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16
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Zakirova EG, Muzyka VV, Mazunin IO, Orishchenko KE. Natural and Artificial Mechanisms of Mitochondrial Genome Elimination. Life (Basel) 2021; 11:life11020076. [PMID: 33498399 PMCID: PMC7909434 DOI: 10.3390/life11020076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/11/2023] Open
Abstract
The generally accepted theory of the genetic drift of mitochondrial alleles during mammalian ontogenesis is based on the presence of a selective bottleneck in the female germline. However, there is a variety of different theories on the pathways of genetic regulation of mitochondrial DNA (mtDNA) dynamics in oogenesis and adult somatic cells. The current review summarizes present knowledge on the natural mechanisms of mitochondrial genome elimination during mammalian development. We also discuss the variety of existing and developing methodologies for artificial manipulation of the mtDNA heteroplasmy level. Understanding of the basics of mtDNA dynamics will shed the light on the pathogenesis and potential therapies of human diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Elvira G. Zakirova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
| | - Vladimir V. Muzyka
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ilya O. Mazunin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia;
| | - Konstantin E. Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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17
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Shpilka T, Du Y, Yang Q, Melber A, Uma Naresh N, Lavelle J, Kim S, Liu P, Weidberg H, Li R, Yu J, Zhu LJ, Strittmatter L, Haynes CM. UPR mt scales mitochondrial network expansion with protein synthesis via mitochondrial import in Caenorhabditis elegans. Nat Commun 2021; 12:479. [PMID: 33473112 PMCID: PMC7817664 DOI: 10.1038/s41467-020-20784-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
As organisms develop, individual cells generate mitochondria to fulfill physiological requirements. However, it remains unknown how mitochondrial network expansion is scaled to cell growth. The mitochondrial unfolded protein response (UPRmt) is a signaling pathway mediated by the transcription factor ATFS-1 which harbors a mitochondrial targeting sequence (MTS). Here, using the model organism Caenorhabditis elegans we demonstrate that ATFS-1 mediates an adaptable mitochondrial network expansion program that is active throughout normal development. Mitochondrial network expansion requires the relatively inefficient MTS in ATFS-1, which allows the transcription factor to be responsive to parameters that impact protein import capacity of the mitochondrial network. Increasing the strength of the ATFS-1 MTS impairs UPRmt activity by increasing accumulation within mitochondria. Manipulations of TORC1 activity increase or decrease ATFS-1 activity in a manner that correlates with protein synthesis. Lastly, expression of mitochondrial-targeted GFP is sufficient to expand the muscle cell mitochondrial network in an ATFS-1-dependent manner. We propose that mitochondrial network expansion during development is an emergent property of the synthesis of highly expressed mitochondrial proteins that exclude ATFS-1 from mitochondrial import, causing UPRmt activation. The mitochondrial network expands to accommodate cell growth, but how scaling occurs is unclear. Here, the authors show in C. elegans that ATFS-1 mitochondrial import is reduced when mitochondrial proteins are highly expressed, activating the unfolded protein response and causing expansion.
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Affiliation(s)
- Tomer Shpilka
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - YunGuang Du
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Qiyuan Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Andrew Melber
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Nandhitha Uma Naresh
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Joshua Lavelle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sookyung Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Hilla Weidberg
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Jun Yu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Lara Strittmatter
- Electron Microscopy Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Cole M Haynes
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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18
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Gitschlag BL, Tate AT, Patel MR. Nutrient status shapes selfish mitochondrial genome dynamics across different levels of selection. eLife 2020; 9:56686. [PMID: 32959778 PMCID: PMC7508553 DOI: 10.7554/elife.56686] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/17/2020] [Indexed: 12/23/2022] Open
Abstract
Cooperation and cheating are widespread evolutionary strategies. While cheating confers an advantage to individual entities within a group, competition between groups favors cooperation. Selfish or cheater mitochondrial DNA (mtDNA) proliferates within hosts while being selected against at the level of host fitness. How does environment shape cheater dynamics across different selection levels? Focusing on food availability, we address this question using heteroplasmic Caenorhabditis elegans. We find that the proliferation of selfish mtDNA within hosts depends on nutrient status stimulating mtDNA biogenesis in the developing germline. Interestingly, mtDNA biogenesis is not sufficient for this proliferation, which also requires the stress-response transcription factor FoxO/DAF-16. At the level of host fitness, FoxO/DAF-16 also prevents food scarcity from accelerating the selection against selfish mtDNA. This suggests that the ability to cope with nutrient stress can promote host tolerance of cheaters. Our study delineates environmental effects on selfish mtDNA dynamics at different levels of selection.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, United States
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19
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Shanmughapriya S, Langford D, Natarajaseenivasan K. Inter and Intracellular mitochondrial trafficking in health and disease. Ageing Res Rev 2020; 62:101128. [PMID: 32712108 DOI: 10.1016/j.arr.2020.101128] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/13/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Neurons and glia maintain central nervous system (CNS) homeostasis through diverse mechanisms of intra- and intercellular signaling. Some of these interactions include the exchange of soluble factors between cells via direct cell-to-cell contact for both short and long-distance transfer of biological materials. Transcellular transfer of mitochondria has emerged as a key example of this communication. This transcellular transfer of mitochondria are dynamically involved in the cellular and tissue response to CNS injury and play beneficial roles in recovery. This review highlights recent research addressing the cause and effect of intra- and intercellular mitochondrial transfer with a specific focus on the future of mitochondrial transplantation therapy. We believe that mitochondrial transfer plays a crucial role during bioenergetic crisis/deficit, but the quality, quantity and mode of mitochondrial transfer determines the protective capacity for the receiving cells. Mitochondrial transplantation is a new treatment paradigm and will overcome the major bottleneck of traditional approach of correcting mitochondria-related disorders.
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20
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Leboutet R, Chen Y, Legouis R, Culetto E. Mitophagy during development and stress in C. elegans. Mech Ageing Dev 2020; 189:111266. [DOI: 10.1016/j.mad.2020.111266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022]
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21
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Mitochondrial Diseases: Hope for the Future. Cell 2020; 181:168-188. [PMID: 32220313 DOI: 10.1016/j.cell.2020.02.051] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 01/15/2023]
Abstract
Mitochondrial diseases are clinically heterogeneous disorders caused by a wide spectrum of mutations in genes encoded by either the nuclear or the mitochondrial genome. Treatments for mitochondrial diseases are currently focused on symptomatic management rather than improving the biochemical defect caused by a particular mutation. This review focuses on the latest advances in the development of treatments for mitochondrial disease, both small molecules and gene therapies, as well as methods to prevent transmission of mitochondrial disease through the germline.
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22
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Lewis CJ, Dixit B, Batiuk E, Hall CJ, O'Connor MS, Boominathan A. Codon optimization is an essential parameter for the efficient allotopic expression of mtDNA genes. Redox Biol 2020; 30:101429. [PMID: 31981894 PMCID: PMC6976934 DOI: 10.1016/j.redox.2020.101429] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 11/29/2022] Open
Abstract
Mutations in mitochondrial DNA can be inherited or occur de novo leading to several debilitating myopathies with no curative option and few or no effective treatments. Allotopic expression of recoded mitochondrial genes from the nucleus has potential as a gene therapy strategy for such conditions, however progress in this field has been hampered by technical challenges. Here we employed codon optimization as a tool to re-engineer the protein-coding genes of the human mitochondrial genome for robust, efficient expression from the nucleus. All 13 codon-optimized constructs exhibited substantially higher protein expression than minimally-recoded genes when expressed transiently, and steady-state mRNA levels for optimized gene constructs were 5-180 fold enriched over recoded versions in stably-selected wildtype cells. Eight of thirteen mitochondria-encoded oxidative phosphorylation (OxPhos) proteins maintained protein expression following stable selection, with mitochondrial localization of expression products. We also assessed the utility of this strategy in rescuing mitochondrial disease cell models and found the rescue capacity of allotopic expression constructs to be gene specific. Allotopic expression of codon optimized ATP8 in disease models could restore protein levels and respiratory function, however, rescue of the pathogenic phenotype for another gene, ND1 was only partially successful. These results imply that though codon-optimization alone is not sufficient for functional allotopic expression of most mitochondrial genes, it is an essential consideration in their design.
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Affiliation(s)
- Caitlin J Lewis
- Department of Mitochondrial Research, SENS Research Foundation, Mountain View, CA, 94041, USA
| | - Bhavna Dixit
- Department of Mitochondrial Research, SENS Research Foundation, Mountain View, CA, 94041, USA
| | - Elizabeth Batiuk
- Department of Mitochondrial Research, SENS Research Foundation, Mountain View, CA, 94041, USA
| | - Carter J Hall
- Department of Mitochondrial Research, SENS Research Foundation, Mountain View, CA, 94041, USA
| | - Matthew S O'Connor
- Department of Mitochondrial Research, SENS Research Foundation, Mountain View, CA, 94041, USA.
| | - Amutha Boominathan
- Department of Mitochondrial Research, SENS Research Foundation, Mountain View, CA, 94041, USA.
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23
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Knorre DA. Intracellular quality control of mitochondrial DNA: evidence and limitations. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190176. [PMID: 31787047 DOI: 10.1098/rstb.2019.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent 'leakage' of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Dmitry A Knorre
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow 119991, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, Moscow 119991, Russia
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24
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Shtolz N, Mishmar D. The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00342] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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25
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Al Khatib I, Shutt TE. Advances Towards Therapeutic Approaches for mtDNA Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:217-246. [PMID: 31452143 DOI: 10.1007/978-981-13-8367-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondria maintain and express their own genome, referred to as mtDNA, which is required for proper mitochondrial function. While mutations in mtDNA can cause a heterogeneous array of disease phenotypes, there is currently no cure for this collection of diseases. Here, we will cover characteristics of the mitochondrial genome important for understanding the pathology associated with mtDNA mutations, and review recent approaches that are being developed to treat and prevent mtDNA disease. First, we will discuss mitochondrial replacement therapy (MRT), where mitochondria from a healthy donor replace maternal mitochondria harbouring mutant mtDNA. In addition to ethical concerns surrounding this procedure, MRT is only applicable in cases where the mother is known or suspected to carry mtDNA mutations. Thus, there remains a need for other strategies to treat patients with mtDNA disease. To this end, we will also discuss several alternative means to reduce the amount of mutant mtDNA present in cells. Such methods, referred to as heteroplasmy shifting, have proven successful in animal models. In particular, we will focus on the approach of targeting engineered endonucleases to specifically cleave mutant mtDNA. Together, these approaches offer hope to prevent the transmission of mtDNA disease and potentially reduce the impact of mtDNA mutations.
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Affiliation(s)
- Iman Al Khatib
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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26
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Abstract
The maintenance of a healthy and functional mitochondrial network is critical during development as well as throughout life in the response to physiological adaptations and stress conditions. Owing to their role in energy production, mitochondria are exposed to high levels of reactive oxygen species, making them particularly vulnerable to mitochondrial DNA mutations and protein misfolding. Given that mitochondria are formed from proteins encoded by both nuclear and mitochondrial genomes, an additional layer of complexity is inherent in the coordination of protein synthesis and the mitochondrial import of nuclear-encoded proteins. For these reasons, mitochondria have evolved multiple systems of quality control to ensure that the requisite number of functional mitochondria are present to meet the demands of the cell. These pathways work to eliminate damaged mitochondrial proteins or parts of the mitochondrial network by mitophagy and renew components by adding protein and lipids through biogenesis, collectively resulting in mitochondrial turnover. Mitochondrial quality control mechanisms are multi-tiered, operating at the protein, organelle and cell levels. Herein, we discuss mitophagy in different physiological contexts and then relate it to other quality control pathways, including the unfolded protein response, shedding of vesicles, proteolysis, and degradation by the ubiquitin-proteasome system. Understanding how these pathways contribute to the maintenance of mitochondrial homeostasis could provide insights into the development of targeted treatments when these systems fail in disease.
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27
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Hahn A, Zuryn S. The Cellular Mitochondrial Genome Landscape in Disease. Trends Cell Biol 2018; 29:227-240. [PMID: 30509558 DOI: 10.1016/j.tcb.2018.11.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022]
Abstract
Mitochondrial genome (mitochondrial DNA, mtDNA) lesions that unbalance bioenergetic and oxidative outputs are an important cause of human disease. A major impediment in our understanding of the pathophysiology of mitochondrial disorders is the complexity with which mtDNA mutations are spatiotemporally distributed and managed within individual cells, tissues, and organs. Unlike the comparatively static nuclear genome, accumulating evidence highlights the variability, dynamism, and modifiability of the mtDNA nucleotide sequence between individual cells over time. In this review, we summarize and discuss the impact of mtDNA defects on disease within the context of a mosaic and shifting mutational landscape.
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Affiliation(s)
- Anne Hahn
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Australia
| | - Steven Zuryn
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Australia.
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Abstract
The mitochondrial network is not only required for the production of energy, essential cofactors and amino acids, but also serves as a signaling hub for innate immune and apoptotic pathways. Multiple mechanisms have evolved to identify and combat mitochondrial dysfunction to maintain the health of the organism. One such pathway is the mitochondrial unfolded protein response (UPRmt), which is regulated by the mitochondrial import efficiency of the transcription factor ATFS-1 in C. elegans and potentially orthologous transcription factors in mammals (ATF4, ATF5, CHOP). Upon mitochondrial dysfunction, import of ATFS-1 into mitochondria is reduced, allowing it to be trafficked to the nucleus where it promotes the expression of genes that promote survival and recovery of the mitochondrial network. Here, we discuss recent findings underlying UPRmt signal transduction and how this adaptive transcriptional response may interact with other mitochondrial stress response pathways.
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Cooper JF, Machiela E, Dues DJ, Spielbauer KK, Senchuk MM, Van Raamsdonk JM. Activation of the mitochondrial unfolded protein response promotes longevity and dopamine neuron survival in Parkinson's disease models. Sci Rep 2017; 7:16441. [PMID: 29180793 PMCID: PMC5703891 DOI: 10.1038/s41598-017-16637-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/15/2017] [Indexed: 12/24/2022] Open
Abstract
While the pathogenesis of Parkinson's disease (PD) is incompletely understood, mitochondrial dysfunction is thought to play a crucial role in disease pathogenesis. Here, we examined the relationship between mitochondrial function and dopamine neuron dysfunction and death using C. elegans mutants for three mitochondria-related genes implicated in monogenic PD (pdr-1/PRKN, pink-1/PINK1 and djr-1.1/DJ-1). We found that pdr-1 and pink-1 mutants exhibit deficits in dopamine-dependent behaviors, but no loss of dopamine neurons, while djr-1.1 mutants showed an increased sensitivity to oxidative stress. In examining mitochondrial morphology and function, we found that djr-1.1 mutants exhibit increased mitochondrial fragmentation leading to decreased rate of oxidative phosphorylation and ATP levels. pdr-1 and pink-1 mutants show an accumulation of dysfunctional mitochondria with age, which leads to activation of the mitochondrial unfolded protein response (mitoUPR). Preventing the upregulation of the mitoUPR with a deletion in atfs-1 results in decreased lifespan and dopamine neuronal loss in pdr-1 and pink-1 mutants but not in wild-type worms. Overall, our results suggest that mutations in pdr-1 and pink-1 cause the accumulation of dysfunctional mitochondria, which activates the mitoUPR to mitigate the detrimental effect of these mutations on dopamine neuron survival.
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Affiliation(s)
- Jason F Cooper
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Emily Machiela
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Dylan J Dues
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Katie K Spielbauer
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Megan M Senchuk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Jeremy M Van Raamsdonk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA.
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada.
- Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
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30
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van der Bliek AM, Sedensky MM, Morgan PG. Cell Biology of the Mitochondrion. Genetics 2017; 207:843-871. [PMID: 29097398 PMCID: PMC5676242 DOI: 10.1534/genetics.117.300262] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/05/2017] [Indexed: 01/19/2023] Open
Abstract
Mitochondria are best known for harboring pathways involved in ATP synthesis through the tricarboxylic acid cycle and oxidative phosphorylation. Major advances in understanding these roles were made with Caenorhabditiselegans mutants affecting key components of the metabolic pathways. These mutants have not only helped elucidate some of the intricacies of metabolism pathways, but they have also served as jumping off points for pharmacology, toxicology, and aging studies. The field of mitochondria research has also undergone a renaissance, with the increased appreciation of the role of mitochondria in cell processes other than energy production. Here, we focus on discoveries that were made using C. elegans, with a few excursions into areas that were studied more thoroughly in other organisms, like mitochondrial protein import in yeast. Advances in mitochondrial biogenesis and membrane dynamics were made through the discoveries of novel functions in mitochondrial fission and fusion proteins. Some of these functions were only apparent through the use of diverse model systems, such as C. elegans Studies of stress responses, exemplified by mitophagy and the mitochondrial unfolded protein response, have also benefitted greatly from the use of model organisms. Recent developments include the discoveries in C. elegans of cell autonomous and nonautonomous pathways controlling the mitochondrial unfolded protein response, as well as mechanisms for degradation of paternal mitochondria after fertilization. The evolutionary conservation of many, if not all, of these pathways ensures that results obtained with C. elegans are equally applicable to studies of human mitochondria in health and disease.
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Affiliation(s)
- Alexander M van der Bliek
- Department of Biological Chemistry, Jonsson Comprehensive Cancer Center and Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, California 90024
| | - Margaret M Sedensky
- Department of Anesthesiology and Pain Medicine, University of Washington and Center for Developmental Therapeutics, Seattle Children's Research Institute, Washington 98101
| | - Phil G Morgan
- Department of Anesthesiology and Pain Medicine, University of Washington and Center for Developmental Therapeutics, Seattle Children's Research Institute, Washington 98101
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Knowlton WM, Hubert T, Wu Z, Chisholm AD, Jin Y. A Select Subset of Electron Transport Chain Genes Associated with Optic Atrophy Link Mitochondria to Axon Regeneration in Caenorhabditis elegans. Front Neurosci 2017; 11:263. [PMID: 28539870 PMCID: PMC5423972 DOI: 10.3389/fnins.2017.00263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022] Open
Abstract
The role of mitochondria within injured neurons is an area of active interest since these organelles are vital for the production of cellular energy in the form of ATP. Using mechanosensory neurons of the nematode Caenorhabditis elegans to test regeneration after neuronal injury in vivo, we surveyed genes related to mitochondrial function for effects on axon regrowth after laser axotomy. Genes involved in mitochondrial transport, calcium uptake, mitophagy, or fission and fusion were largely dispensable for axon regrowth, with the exception of eat-3/Opa1. Surprisingly, many genes encoding components of the electron transport chain were dispensable for regrowth, except for the iron-sulfur proteins gas-1, nduf-2.2, nduf-7, and isp-1, and the putative oxidoreductase rad-8. In these mutants, axonal development was essentially normal and axons responded normally to injury by forming regenerative growth cones, but were impaired in subsequent axon extension. Overexpression of nduf-2.2 or isp-1 was sufficient to enhance regrowth, suggesting that mitochondrial function is rate-limiting in axon regeneration. Moreover, loss of function in isp-1 reduced the enhanced regeneration caused by either a gain-of-function mutation in the calcium channel EGL-19 or overexpression of the MAP kinase DLK-1. While the cellular function of RAD-8 remains unclear, our genetic analyses place rad-8 in the same pathway as other electron transport genes in axon regeneration. Unexpectedly, rad-8 regrowth defects were suppressed by altered function in the ubiquinone biosynthesis gene clk-1. Furthermore, we found that inhibition of the mitochondrial unfolded protein response via deletion of atfs-1 suppressed the defective regrowth in nduf-2.2 mutants. Together, our data indicate that while axon regeneration is not significantly affected by general dysfunction of cellular respiration, it is sensitive to the proper functioning of a select subset of electron transport chain genes, or to the cellular adaptations used by neurons under conditions of injury.
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Affiliation(s)
- Wendy M Knowlton
- Section of Neurobiology, Division of Biological Sciences, University of CaliforniaSan Diego, CA, USA
| | - Thomas Hubert
- Section of Neurobiology, Division of Biological Sciences, University of CaliforniaSan Diego, CA, USA
| | - Zilu Wu
- Howard Hughes Medical Institute, University of CaliforniaSan Diego, CA, USA
| | - Andrew D Chisholm
- Section of Neurobiology, Division of Biological Sciences, University of CaliforniaSan Diego, CA, USA
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of CaliforniaSan Diego, CA, USA.,Howard Hughes Medical Institute, University of CaliforniaSan Diego, CA, USA.,Department of Cellular and Molecular Medicine, School of Medicine, University of CaliforniaSan Diego, CA, USA
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32
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Kandul NP, Zhang T, Hay BA, Guo M. Selective removal of deletion-bearing mitochondrial DNA in heteroplasmic Drosophila. Nat Commun 2016; 7:13100. [PMID: 27841259 PMCID: PMC5114534 DOI: 10.1038/ncomms13100] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/01/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) often exists in a state of heteroplasmy, in which mutant mtDNA co-exists in cells with wild-type mtDNA. High frequencies of pathogenic mtDNA result in maternally inherited diseases; maternally and somatically acquired mutations also accumulate over time and contribute to diseases of ageing. Reducing heteroplasmy is therefore a therapeutic goal and in vivo models in post-mitotic tissues are needed to facilitate these studies. Here we describe a transgene-based model of a heteroplasmic lethal mtDNA deletion (mtDNAΔ) in adult Drosophila muscle. Stimulation of autophagy, activation of the PINK1/parkin pathway or decreased levels of mitofusin result in a selective decrease in mtDNAΔ. Decreased levels of mitofusin and increased levels of ATPIF1, an inhibitor of ATP synthase reversal-dependent mitochondrial repolarization, result in a further decrease in mtDNAΔ levels. These results show that an adult post-mitotic tissue can be cleansed of a deleterious genome, suggesting that therapeutic removal of mutant mtDNA can be achieved.
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Affiliation(s)
- Nikolay P. Kandul
- Division of Biology and Biological Engineering, California Institute of Technology, Mail Code 156-29, 1200 E. California blvd., Pasadena, California 91125, USA
| | - Ting Zhang
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Molecular and Medical Pharmacology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Bruce A. Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Mail Code 156-29, 1200 E. California blvd., Pasadena, California 91125, USA
| | - Ming Guo
- Department of Neurology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
- Department of Molecular and Medical Pharmacology, Brain Research Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
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Torralba D, Baixauli F, Sánchez-Madrid F. Mitochondria Know No Boundaries: Mechanisms and Functions of Intercellular Mitochondrial Transfer. Front Cell Dev Biol 2016; 4:107. [PMID: 27734015 PMCID: PMC5039171 DOI: 10.3389/fcell.2016.00107] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/14/2016] [Indexed: 12/25/2022] Open
Abstract
Mitochondria regulate multiple cell processes, including calcium signaling, apoptosis and cell metabolism. Mitochondria contain their own circular genome encoding selected subunits of the oxidative phosphorylation complexes. Recent findings reveal that, in addition to being maternally inherited, mitochondria can traverse cell boundaries and thus be horizontally transferred between cells. Although, the physiological relevance of this phenomenon is still under debate, mitochondria uptake rescues mitochondrial respiration defects in recipient cells and regulates signaling, proliferation or chemotherapy resistance in vitro and in vivo. In this review, we outline the pathophysiological consequences of horizontal mitochondrial transfer and offer a perspective on the cellular and molecular mechanisms mediating their intercellular transmission, including tunneling nanotubes, extracellular vesicles, cellular fusion, and GAP junctions. The physiological relevance of mitochondrial transfer and the potential therapeutic application of this exchange for treating mitochondrial-related diseases are discussed.
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Affiliation(s)
- Daniel Torralba
- Signaling and Inflammation Program, Centro Nacional Investigaciones CardiovascularesMadrid, Spain; Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autonoma de MadridMadrid, Spain
| | - Francesc Baixauli
- Signaling and Inflammation Program, Centro Nacional Investigaciones CardiovascularesMadrid, Spain; Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autonoma de MadridMadrid, Spain
| | - Francisco Sánchez-Madrid
- Signaling and Inflammation Program, Centro Nacional Investigaciones CardiovascularesMadrid, Spain; Servicio de Inmunología, Instituto Investigación Sanitaria Princesa, Universidad Autonoma de MadridMadrid, Spain
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Malena A, Pantic B, Borgia D, Sgarbi G, Solaini G, Holt IJ, Spinazzola A, Perissinotto E, Sandri M, Baracca A, Vergani L. Mitochondrial quality control: Cell-type-dependent responses to pathological mutant mitochondrial DNA. Autophagy 2016; 12:2098-2112. [PMID: 27627835 DOI: 10.1080/15548627.2016.1226734] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pathological mutations in the mitochondrial DNA (mtDNA) produce a diverse range of tissue-specific diseases and the proportion of mutant mitochondrial DNA can increase or decrease with time via segregation, dependent on the cell or tissue type. Previously we found that adenocarcinoma (A549.B2) cells favored wild-type (WT) mtDNA, whereas rhabdomyosarcoma (RD.Myo) cells favored mutant (m3243G) mtDNA. Mitochondrial quality control (mtQC) can purge the cells of dysfunctional mitochondria via mitochondrial dynamics and mitophagy and appears to offer the perfect solution to the human diseases caused by mutant mtDNA. In A549.B2 and RD.Myo cybrids, with various mutant mtDNA levels, mtQC was explored together with macroautophagy/autophagy and bioenergetic profile. The 2 types of tumor-derived cell lines differed in bioenergetic profile and mitophagy, but not in autophagy. A549.B2 cybrids displayed upregulation of mitophagy, increased mtDNA removal, mitochondrial fragmentation and mitochondrial depolarization on incubation with oligomycin, parameters that correlated with mutant load. Conversely, heteroplasmic RD.Myo lines had lower mitophagic markers that negatively correlated with mutant load, combined with a fully polarized and highly fused mitochondrial network. These findings indicate that pathological mutant mitochondrial DNA can modulate mitochondrial dynamics and mitophagy in a cell-type dependent manner and thereby offer an explanation for the persistence and accumulation of deleterious variants.
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Affiliation(s)
- Adriana Malena
- a Department of Neurosciences , University of Padova , Italy
| | - Boris Pantic
- a Department of Neurosciences , University of Padova , Italy
| | - Doriana Borgia
- a Department of Neurosciences , University of Padova , Italy
| | - Gianluca Sgarbi
- b Department of Biomedical and Neuromotor Sciences , University of Bologna , Italy
| | - Giancarlo Solaini
- b Department of Biomedical and Neuromotor Sciences , University of Bologna , Italy
| | - Ian J Holt
- c Medical Research Council, Mill Hill Laboratory , London , United Kingdom
| | | | - Egle Perissinotto
- d Department of Cardiac, Thoracic and Vascular Sciences, Biostatistics, Epidemiology and Public Health Unit , University of Padova , Padova , Italy
| | - Marco Sandri
- e Department of Biomedical Sciences , University of Padova , Italy.,f Venetian Institute of Molecular Medicine , Padova , Italy
| | - Alessandra Baracca
- b Department of Biomedical and Neuromotor Sciences , University of Bologna , Italy
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Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab 2016; 24:91-103. [PMID: 27411011 PMCID: PMC5287496 DOI: 10.1016/j.cmet.2016.06.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/27/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023]
Abstract
Mutant mitochondrial genomes (mtDNA) can be viewed as selfish genetic elements that persist in a state of heteroplasmy despite having potentially deleterious metabolic consequences. We sought to study regulation of selfish mtDNA dynamics. We establish that the large 3.1-kb deletion-bearing mtDNA variant uaDf5 is a selfish genome in Caenorhabditis elegans. Next, we show that uaDf5 mutant mtDNA replicates in addition to, not at the expense of, wild-type mtDNA. These data suggest the existence of a homeostatic copy-number control that is exploited by uaDf5 to "hitchhike" to high frequency. We also observe activation of the mitochondrial unfolded protein response (UPR(mt)) in uaDf5 animals. Loss of UPR(mt) causes a decrease in uaDf5 frequency, whereas its constitutive activation increases uaDf5 levels. UPR(mt) activation protects uaDf5 from mitophagy. Taken together, we propose that mtDNA copy-number control and UPR(mt) represent two homeostatic response mechanisms that play important roles in regulating selfish mitochondrial genome dynamics.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Interdisciplinary Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Biological Sciences Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rama D Gangula
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon A Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA 6150, Australia
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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Lin YF, Schulz AM, Pellegrino MW, Lu Y, Shaham S, Haynes CM. Maintenance and propagation of a deleterious mitochondrial genome by the mitochondrial unfolded protein response. Nature 2016; 533:416-9. [PMID: 27135930 PMCID: PMC4873342 DOI: 10.1038/nature17989] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/08/2016] [Indexed: 12/19/2022]
Abstract
Mitochondrial genomes (mitochondrial DNA, mtDNA) encode essential oxidative phosphorylation (OXPHOS) components. Because hundreds of mtDNAs exist per cell, a deletion in a single mtDNA has little impact. However, if the deletion genome is enriched, OXPHOS declines, resulting in cellular dysfunction. For example, Kearns-Sayre syndrome is caused by a single heteroplasmic mtDNA deletion. More broadly, mtDNA deletion accumulation has been observed in individual muscle cells and dopaminergic neurons during ageing. It is unclear how mtDNA deletions are tolerated or how they are propagated in somatic cells. One mechanism by which cells respond to OXPHOS dysfunction is by activating the mitochondrial unfolded protein response (UPR(mt)), a transcriptional response mediated by the transcription factor ATFS-1 that promotes the recovery and regeneration of defective mitochondria. Here we investigate the role of ATFS-1 in the maintenance and propagation of a deleterious mtDNA in a heteroplasmic Caenorhabditis elegans strain that stably expresses wild-type mtDNA and mtDNA with a 3.1-kilobase deletion (∆mtDNA) lacking four essential genes. The heteroplasmic strain, which has 60% ∆mtDNA, displays modest mitochondrial dysfunction and constitutive UPR(mt) activation. ATFS-1 impairment reduced the ∆mtDNA nearly tenfold, decreasing the total percentage to 7%. We propose that in the context of mtDNA heteroplasmy, UPR(mt) activation caused by OXPHOS defects propagates or maintains the deleterious mtDNA in an attempt to recover OXPHOS activity by promoting mitochondrial biogenesis and dynamics.
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Affiliation(s)
- Yi-Fan Lin
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna M. Schulz
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark W. Pellegrino
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yun Lu
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Cole M. Haynes
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- BCMB Allied Program, Weill Cornell Medical College, 1300 York Avenue, New York, NY, USA
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Villanueva Paz M, Cotán D, Garrido-Maraver J, Cordero MD, Oropesa-Ávila M, de La Mata M, Delgado Pavón A, de Lavera I, Alcocer-Gómez E, Sánchez-Alcázar JA. Targeting autophagy and mitophagy for mitochondrial diseases treatment. Expert Opin Ther Targets 2015; 20:487-500. [PMID: 26523761 DOI: 10.1517/14728222.2016.1101068] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Mitochondrial diseases are a group of rare genetic diseases with complex and heterogeneous origins which manifest a great variety of phenotypes. Disruption of the oxidative phosphorylation system is the main cause of pathogenicity in mitochondrial diseases since it causes accumulation of reactive oxygen species (ROS) and ATP depletion. AREAS COVERED Current evidences support the main protective role of autophagy and mitophagy in mitochondrial diseases and other diseases associated with mitochondrial dysfunction. EXPERT OPINION The use of autophagy and/or mitophagy inducers may allow a novel strategy for improving mitochondrial function for both mitochondrial diseases and other diseases with altered mitochondrial metabolism. However, a deeper investigation of the molecular mechanisms behind mitophagy and mitochondrial biogenesis is needed in order to safely modulate these processes. In the coming years, we will also see an increase in awareness of mitochondrial dynamics modulation that will allow the therapeutic use of new drugs for improving mitochondrial function in a great variety of mitochondrial disorders.
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Affiliation(s)
- Marina Villanueva Paz
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - David Cotán
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - Juan Garrido-Maraver
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - Mario D Cordero
- b Facultad de Odontología , Universidad de Sevilla , Sevilla 41009 , Spain
| | - Manuel Oropesa-Ávila
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - Mario de La Mata
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - Ana Delgado Pavón
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - Isabel de Lavera
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - Elizabet Alcocer-Gómez
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
| | - José A Sánchez-Alcázar
- a Centro Andaluz de Biología del Desarrollo (CABD), and Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III , Universidad Pablo de Olavide-Consejo Superior de Investigaciones Científicas , Carretera de Utrera Km 1, Sevilla 41013 , Spain
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