1
|
Moraes CT. Tools for editing the mammalian mitochondrial genome. Hum Mol Genet 2024; 33:R92-R99. [PMID: 38779768 DOI: 10.1093/hmg/ddae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 05/25/2024] Open
Abstract
The manipulation of animal mitochondrial genomes has long been a challenge due to the lack of an effective transformation method. With the discovery of specific gene editing enzymes, designed to target pathogenic mitochondrial DNA mutations (often heteroplasmic), the selective removal or modification of mutant variants has become a reality. Because mitochondria cannot efficiently import RNAs, CRISPR has not been the first choice for editing mitochondrial genes. However, the last few years witnessed an explosion in novel and optimized non-CRISPR approaches to promote double-strand breaks or base-edit of mtDNA in vivo. Engineered forms of specific nucleases and cytidine/adenine deaminases form the basis for these techniques. I will review the newest developments that constitute the current toolbox for animal mtDNA gene editing in vivo, bringing these approaches not only to the exploration of mitochondrial function, but also closer to clinical use.
Collapse
Affiliation(s)
- Carlos T Moraes
- Miller School of Medicine, University of Miami, 1600 NW 10th Ave, room 7044, Miami, FL 33136, United States
| |
Collapse
|
2
|
Edmands S. Mother's Curse effects on lifespan and aging. FRONTIERS IN AGING 2024; 5:1361396. [PMID: 38523670 PMCID: PMC10957651 DOI: 10.3389/fragi.2024.1361396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
The Mother's Curse hypothesis posits that mothers curse their sons with harmful mitochondria, because maternal mitochondrial inheritance makes selection blind to mitochondrial mutations that harm only males. As a result, mitochondrial function may be evolutionarily optimized for females. This is an attractive explanation for ubiquitous sex differences in lifespan and aging, given the prevalence of maternal mitochondrial inheritance and the established relationship between mitochondria and aging. This review outlines patterns expected under the hypothesis, and traits most likely to be affected, chiefly those that are sexually dimorphic and energy intensive. A survey of the literature shows that evidence for Mother's Curse is limited to a few taxonomic groups, with the strongest support coming from experimental crosses in Drosophila. Much of the evidence comes from studies of fertility, which is expected to be particularly vulnerable to male-harming mitochondrial mutations, but studies of lifespan and aging also show evidence of Mother's Curse effects. Despite some very compelling studies supporting the hypothesis, the evidence is quite patchy overall, with contradictory results even found for the same traits in the same taxa. Reasons for this scarcity of evidence are discussed, including nuclear compensation, factors opposing male-specific mutation load, effects of interspecific hybridization, context dependency and demographic effects. Mother's Curse effects may indeed contribute to sex differences, but the complexity of other contributing factors make Mother's Curse a poor general predictor of sex-specific lifespan and aging.
Collapse
Affiliation(s)
- Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
3
|
Zhang F, Lee A, Freitas A, Herb J, Wang Z, Gupta S, Chen Z, Xu H. Genetic and bioinformatic analyses reveal transcriptional networks underlying dual genomic coordination of mitochondrial biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577217. [PMID: 38410491 PMCID: PMC10896348 DOI: 10.1101/2024.01.25.577217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Mitochondrial genome encodes handful genes of respiratory chain complexes, whereas all the remaining mitochondrial proteins are encoded on the nuclear genome. However, the mechanisms coordinating these two genomes to control mitochondrial biogenesis remain largely unknown. To identify transcription circuits involved in these processes, we performed a candidate RNAi screen in developing eyes that had reduced mitochondrial DNA contents. We reasoned that impaired mitochondrial biogenesis would synergistically interact with mtDNA deficiency in disrupting tissue development. Over 638 transcription factors annotated in the fly genome, we identified 77 transcription factors that may be involved in mitochondrial genome maintenance and gene expression. Additional genetic and genomic analyses revealed that a novel transcription factor, CG1603, and its upstream factor YL-1 are essential for mitochondrial biogenesis. We constructed a regulator network among positive hits using the published CHIP-seq data. The network analysis revealed extensive connections, and complex hierarchical organization underlying the transcription regulation of mitochondrial biogenesis.
Collapse
Affiliation(s)
- Fan Zhang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Annie Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Freitas
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jake Herb
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zongheng Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Snigdha Gupta
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
4
|
Chiang ACY, Ježek J, Mu P, Di Y, Klucnika A, Jabůrek M, Ježek P, Ma H. Two mitochondrial DNA polymorphisms modulate cardiolipin binding and lead to synthetic lethality. Nat Commun 2024; 15:611. [PMID: 38242869 PMCID: PMC10799063 DOI: 10.1038/s41467-024-44964-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024] Open
Abstract
Genetic screens have been used extensively to probe interactions between nuclear genes and their impact on phenotypes. Probing interactions between mitochondrial genes and their phenotypic outcome, however, has not been possible due to a lack of tools to map the responsible polymorphisms. Here, using a toolkit we previously established in Drosophila, we isolate over 300 recombinant mitochondrial genomes and map a naturally occurring polymorphism at the cytochrome c oxidase III residue 109 (CoIII109) that fully rescues the lethality and other defects associated with a point mutation in cytochrome c oxidase I (CoIT300I). Through lipidomics profiling, biochemical assays and phenotypic analyses, we show that the CoIII109 polymorphism modulates cardiolipin binding to prevent complex IV instability caused by the CoIT300I mutation. This study demonstrates the feasibility of genetic interaction screens in animal mitochondrial DNA. It unwraps the complex intra-genomic interplays underlying disorders linked to mitochondrial DNA and how they influence disease expression.
Collapse
Affiliation(s)
- Ason C Y Chiang
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jan Ježek
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- University College London Queen Square Institute of Neurology, Royal Free Hospital, Rowland Hill Street, London, NW3 2PF, UK
| | - Peiqiang Mu
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Tianhe District, 510642, Guangzhou, Guangdong, P. R. China
| | - Ying Di
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Anna Klucnika
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Laverock Therapeutics, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - Martin Jabůrek
- Laboratory of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Petr Ježek
- Laboratory of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Hansong Ma
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| |
Collapse
|
5
|
Nieto-Panqueva F, Rubalcava-Gracia D, Hamel PP, González-Halphen D. The constraints of allotopic expression. Mitochondrion 2023; 73:30-50. [PMID: 37739243 DOI: 10.1016/j.mito.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Allotopic expression is the functional transfer of an organellar gene to the nucleus, followed by synthesis of the gene product in the cytosol and import into the appropriate organellar sub compartment. Here, we focus on mitochondrial genes encoding OXPHOS subunits that were naturally transferred to the nucleus, and critically review experimental evidence that claim their allotopic expression. We emphasize aspects that may have been overlooked before, i.e., when modifying a mitochondrial gene for allotopic expression━besides adapting the codon usage and including sequences encoding mitochondrial targeting signals━three additional constraints should be considered: (i) the average apparent free energy of membrane insertion (μΔGapp) of the transmembrane stretches (TMS) in proteins earmarked for the inner mitochondrial membrane, (ii) the final, functional topology attained by each membrane-bound OXPHOS subunit; and (iii) the defined mechanism by which the protein translocator TIM23 sorts cytosol-synthesized precursors. The mechanistic constraints imposed by TIM23 dictate the operation of two pathways through which alpha-helices in TMS are sorted, that eventually determine the final topology of membrane proteins. We used the biological hydrophobicity scale to assign an average apparent free energy of membrane insertion (μΔGapp) and a "traffic light" color code to all TMS of OXPHOS membrane proteins, thereby predicting which are more likely to be internalized into mitochondria if allotopically produced. We propose that the design of proteins for allotopic expression must make allowance for μΔGapp maximization of highly hydrophobic TMS in polypeptides whose corresponding genes have not been transferred to the nucleus in some organisms.
Collapse
Affiliation(s)
- Felipe Nieto-Panqueva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico; Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA; Vellore Institute of Technology (VIT), School of BioScience and Technology, Vellore, Tamil Nadu, India
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| |
Collapse
|
6
|
Dowling DK, Wolff JN. Evolutionary genetics of the mitochondrial genome: insights from Drosophila. Genetics 2023; 224:iyad036. [PMID: 37171259 PMCID: PMC10324950 DOI: 10.1093/genetics/iyad036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/05/2023] [Indexed: 05/13/2023] Open
Abstract
Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.
Collapse
Affiliation(s)
- Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Jonci N Wolff
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| |
Collapse
|
7
|
Varte V, Munkelwitz JW, Rincon-Limas DE. Insights from Drosophila on Aβ- and tau-induced mitochondrial dysfunction: mechanisms and tools. Front Neurosci 2023; 17:1184080. [PMID: 37139514 PMCID: PMC10150963 DOI: 10.3389/fnins.2023.1184080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative dementia in older adults worldwide. Sadly, there are no disease-modifying therapies available for treatment due to the multifactorial complexity of the disease. AD is pathologically characterized by extracellular deposition of amyloid beta (Aβ) and intracellular neurofibrillary tangles composed of hyperphosphorylated tau. Increasing evidence suggest that Aβ also accumulates intracellularly, which may contribute to the pathological mitochondrial dysfunction observed in AD. According with the mitochondrial cascade hypothesis, mitochondrial dysfunction precedes clinical decline and thus targeting mitochondria may result in new therapeutic strategies. Unfortunately, the precise mechanisms connecting mitochondrial dysfunction with AD are largely unknown. In this review, we will discuss how the fruit fly Drosophila melanogaster is contributing to answer mechanistic questions in the field, from mitochondrial oxidative stress and calcium dysregulation to mitophagy and mitochondrial fusion and fission. In particular, we will highlight specific mitochondrial insults caused by Aβ and tau in transgenic flies and will also discuss a variety of genetic tools and sensors available to study mitochondrial biology in this flexible organism. Areas of opportunity and future directions will be also considered.
Collapse
Affiliation(s)
- Vanlalrinchhani Varte
- Department of Neurology, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Jeremy W. Munkelwitz
- Department of Neurology, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
| | - Diego E. Rincon-Limas
- Department of Neurology, McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, United States
- Department of Neuroscience, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| |
Collapse
|
8
|
Mitochondrial Neurodegeneration: Lessons from Drosophila melanogaster Models. Biomolecules 2023; 13:biom13020378. [PMID: 36830747 PMCID: PMC9953451 DOI: 10.3390/biom13020378] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
The fruit fly-i.e., Drosophila melanogaster-has proven to be a very useful model for the understanding of basic physiological processes, such as development or ageing. The availability of straightforward genetic tools that can be used to produce engineered individuals makes this model extremely interesting for the understanding of the mechanisms underlying genetic diseases in physiological models. Mitochondrial diseases are a group of yet-incurable genetic disorders characterized by the malfunction of the oxidative phosphorylation system (OXPHOS), which is the highly conserved energy transformation system present in mitochondria. The generation of D. melanogaster models of mitochondrial disease started relatively recently but has already provided relevant information about the molecular mechanisms and pathological consequences of mitochondrial dysfunction. Here, we provide an overview of such models and highlight the relevance of D. melanogaster as a model to study mitochondrial disorders.
Collapse
|
9
|
Creation of Mitochondrial Disease Models Using Mitochondrial DNA Editing. Biomedicines 2023; 11:biomedicines11020532. [PMID: 36831068 PMCID: PMC9953118 DOI: 10.3390/biomedicines11020532] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Mitochondrial diseases are a large class of human hereditary diseases, accompanied by the dysfunction of mitochondria and the disruption of cellular energy synthesis, that affect various tissues and organ systems. Mitochondrial DNA mutation-caused disorders are difficult to study because of the insufficient number of clinical cases and the challenges of creating appropriate models. There are many cellular models of mitochondrial diseases, but their application has a number of limitations. The most proper and promising models of mitochondrial diseases are animal models, which, unfortunately, are quite rare and more difficult to develop. The challenges mainly arise from the structural features of mitochondria, which complicate the genetic editing of mitochondrial DNA. This review is devoted to discussing animal models of human mitochondrial diseases and recently developed approaches used to create them. Furthermore, this review discusses mitochondrial diseases and studies of metabolic disorders caused by the mitochondrial DNA mutations underlying these diseases.
Collapse
|
10
|
Chen MY, Duan X, Wang Q, Ran MJ, Ai H, Zheng Y, Wang YF. Cytochrome c1-like is required for mitochondrial morphogenesis and individualization during spermatogenesis in Drosophila melanogaster. J Exp Biol 2023; 226:286665. [PMID: 36645102 DOI: 10.1242/jeb.245277] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023]
Abstract
The Drosophila testis is an excellent system for studying the process from germ stem cells to motile sperm, including the proliferation of male germ cells, meiosis of primary spermatocytes, mitochondrial morphogenesis, and spermatid individualization. We previously demonstrated that ocnus (ocn) plays an essential role in male germ cell development. Among those genes and proteins whose expression levels were changed as a result of ocn knockdown, cytochrome c1-like (cyt-c1L) was downregulated significantly. Here, we show that cyt-c1L is highly expressed in the testis of D. melanogaster. Knockdown or mutation of cyt-c1L in early germ cells of flies resulted in male sterility. Immunofluorescence staining showed that cyt-c1L knockdown testes had no defects in early spermatogenesis; however, in late stages, in contrast to many individualization complexes (ICs) composed of F-actin cones that appeared at different positions in control testes, no actin cones or ICs were observed in cyt-c1L knockdown testes. Furthermore, no mature sperm were found in the seminal vesicle of cyt-c1L knockdown testes whereas the control seminal vesicle was full of mature sperm with needle-like nuclei. cyt-c1L knockdown also caused abnormal mitochondrial morphogenesis during spermatid elongation. Excessive apoptotic signals accumulated in the base of cyt-c1L knockdown fly testes. These results suggest that cyt-c1L may play an important role in spermatogenesis by affecting the mitochondrial morphogenesis and individualization of sperm in D. melanogaster.
Collapse
Affiliation(s)
- Meng-Yan Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Xin Duan
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Qian Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Mao-Jiu Ran
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Hui Ai
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Ya Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| | - Yu-Feng Wang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, PR China
| |
Collapse
|
11
|
Mutations in Complex I of the Mitochondrial Electron-Transport Chain Sensitize the Fruit Fly ( Drosophila melanogaster) to Ether and Non-Ether Volatile Anesthetics. Int J Mol Sci 2023; 24:ijms24031843. [PMID: 36768163 PMCID: PMC9915120 DOI: 10.3390/ijms24031843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The mitochondrial electron transport chain (mETC) contains molecular targets of volatile general anesthetics (VGAs), which places carriers of mutations at risk for anesthetic complications. The ND-2360114 and mt:ND2del1 lines of fruit flies (Drosophila melanogaster) that carry mutations in core subunits of Complex I of the mETC replicate numerous characteristics of Leigh syndrome (LS) caused by orthologous mutations in mammals and serve as models of LS. ND-2360114 flies are behaviorally hypersensitive to volatile anesthetic ethers and develop an age- and oxygen-dependent anesthetic-induced neurotoxicity (AiN) phenotype after exposure to isoflurane but not to the related anesthetic sevoflurane. The goal of this paper was to investigate whether the alkane volatile anesthetic halothane and other mutations in Complex I and in Complexes II-V of the mETC cause AiN. We found that (i) ND-2360114 and mt:ND2del1 were susceptible to toxicity from halothane; (ii) in wild-type flies, halothane was toxic under anoxic conditions; (iii) alleles of accessory subunits of Complex I predisposed to AiN; and (iv) mutations in Complexes II-V did not result in an AiN phenotype. We conclude that AiN is neither limited to ether anesthetics nor exclusive to mutations in core subunits of Complex I.
Collapse
|
12
|
Klucnika A, Mu P, Jezek J, McCormack M, Di Y, Bradshaw CR, Ma H. REC drives recombination to repair double-strand breaks in animal mtDNA. J Cell Biol 2023; 222:e202201137. [PMID: 36355348 PMCID: PMC9652705 DOI: 10.1083/jcb.202201137] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Mechanisms that safeguard mitochondrial DNA (mtDNA) limit the accumulation of mutations linked to mitochondrial and age-related diseases. Yet, pathways that repair double-strand breaks (DSBs) in animal mitochondria are poorly understood. By performing a candidate screen for mtDNA repair proteins, we identify that REC-an MCM helicase that drives meiotic recombination in the nucleus-also localizes to mitochondria in Drosophila. We show that REC repairs mtDNA DSBs by homologous recombination in somatic and germline tissues. Moreover, REC prevents age-associated mtDNA mutations. We further show that MCM8, the human ortholog of REC, also localizes to mitochondria and limits the accumulation of mtDNA mutations. This study provides mechanistic insight into animal mtDNA recombination and demonstrates its importance in safeguarding mtDNA during ageing and evolution.
Collapse
Affiliation(s)
- Anna Klucnika
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Peiqiang Mu
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jan Jezek
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthew McCormack
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ying Di
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Hansong Ma
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| |
Collapse
|
13
|
Palozzi JM, Jeedigunta SP, Minenkova AV, Monteiro VL, Thompson ZS, Lieber T, Hurd TR. Mitochondrial DNA quality control in the female germline requires a unique programmed mitophagy. Cell Metab 2022; 34:1809-1823.e6. [PMID: 36323236 DOI: 10.1016/j.cmet.2022.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2022]
Abstract
Mitochondria have their own DNA (mtDNA), which is susceptible to the accumulation of disease-causing mutations. To prevent deleterious mutations from being inherited, the female germline has evolved a conserved quality control mechanism that remains poorly understood. Here, through a large-scale screen, we uncover a unique programmed germline mitophagy (PGM) that is essential for mtDNA quality control. We find that PGM is developmentally triggered as germ cells enter meiosis by inhibition of the target of rapamycin complex 1 (TORC1). We identify a role for the RNA-binding protein Ataxin-2 (Atx2) in coordinating the timing of PGM with meiosis. We show that PGM requires the mitophagy receptor BNIP3, mitochondrial fission and translation factors, and members of the Atg1 complex, but not the mitophagy factors PINK1 and Parkin. Additionally, we report several factors that are critical for germline mtDNA quality control and show that pharmacological manipulation of one of these factors promotes mtDNA quality control.
Collapse
Affiliation(s)
- Jonathan M Palozzi
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Swathi P Jeedigunta
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Anastasia V Minenkova
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Vernon L Monteiro
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Zoe S Thompson
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Toby Lieber
- HHMI and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Thomas R Hurd
- Department of Molecular Genetics, University of Toronto, 661 University Avenue, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|
14
|
Wada KI, Hosokawa K, Ito Y, Mizuo M, Harada Y, Yonemitsu Y. Generation of transmitochondrial cybrids using a microfluidic device. Exp Cell Res 2022; 418:113233. [PMID: 35659971 DOI: 10.1016/j.yexcr.2022.113233] [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: 03/19/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 11/04/2022]
Abstract
Mitochondrial cloning is a promising approach to achieve homoplasmic mitochondrial DNA (mtDNA) mutations. We previously developed a microfluidic device that performs single mitochondrion transfer from a mtDNA-intact cell to a mtDNA-less (ρ0) cell by promoting cytoplasmic connection through a microtunnel between them. In the present study, we described a method for generating transmitochondrial cybrids using the microfluidic device. After achieving mitochondrial transfer between HeLa cells and thymidine kinase-deficient ρ0143B cells using the microfluidic device, selective culture was carried out using a pyruvate and uridine (PU)-absent and 5-bromo-2'-deoxyuridine-supplemented culture medium. The resulting cells contained HeLa mtDNA and 143B nuclei, but both 143B mtDNA and HeLa nuclei were absent in these cells. Additionally, these cells showed lower lactate production than parent ρ0143B cells and disappearance of PU auxotrophy for cell growth. These results suggest successful generation of transmitochondrial cybrids using the microfluidic device. Furthermore, we succeeded in selective harvest of generated transmitochondrial cybrids under a PU-supplemented condition by removing unfused ρ0 cells with puromycin-based selection in the microfluidic device.
Collapse
Affiliation(s)
- Ken-Ichi Wada
- R&D Laboratory for Innovative Biotherapeutics, Graduate School of Pharmaceutical Sciences, Kyushu Univ., 3-1-1 Maidasi, Higashi, Fukuoka, 8112-8582, Japan; Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Nano Medical Engineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Kazuo Hosokawa
- Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maeda Mizuo
- Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yui Harada
- R&D Laboratory for Innovative Biotherapeutics, Graduate School of Pharmaceutical Sciences, Kyushu Univ., 3-1-1 Maidasi, Higashi, Fukuoka, 8112-8582, Japan
| | - Yoshikazu Yonemitsu
- R&D Laboratory for Innovative Biotherapeutics, Graduate School of Pharmaceutical Sciences, Kyushu Univ., 3-1-1 Maidasi, Higashi, Fukuoka, 8112-8582, Japan
| |
Collapse
|
15
|
Lang M, Grünewald A, Pramstaller PP, Hicks AA, Pichler I. A genome on shaky ground: exploring the impact of mitochondrial DNA integrity on Parkinson's disease by highlighting the use of cybrid models. Cell Mol Life Sci 2022; 79:283. [PMID: 35513611 PMCID: PMC9072496 DOI: 10.1007/s00018-022-04304-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
Abstract
Mitochondria play important roles in the regulation of key cellular processes, including energy metabolism, oxidative stress response, and signaling towards cell death or survival, and are distinguished by carrying their own genome (mtDNA). Mitochondrial dysfunction has emerged as a prominent cellular mechanism involved in neurodegeneration, including Parkinson’s disease (PD), a neurodegenerative movement disorder, characterized by progressive loss of dopaminergic neurons and the occurrence of proteinaceous Lewy body inclusions. The contribution of mtDNA variants to PD pathogenesis has long been debated and is still not clearly answered. Cytoplasmic hybrid (cybrid) cell models provided evidence for a contribution of mtDNA variants to the PD phenotype. However, conclusive evidence of mtDNA mutations as genetic cause of PD is still lacking. Several models have shown a role of somatic, rather than inherited mtDNA variants in the impairment of mitochondrial function and neurodegeneration. Accordingly, several nuclear genes driving inherited forms of PD are linked to mtDNA quality control mechanisms, and idiopathic as well as familial PD tissues present increased mtDNA damage. In this review, we highlight the use of cybrids in this PD research field and summarize various aspects of how and to what extent mtDNA variants may contribute to the etiology of PD.
Collapse
Affiliation(s)
- Martin Lang
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| |
Collapse
|
16
|
Barrera-Paez JD, Moraes CT. Mitochondrial genome engineering coming-of-age. Trends Genet 2022; 38:869-880. [PMID: 35599021 PMCID: PMC9283244 DOI: 10.1016/j.tig.2022.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/11/2022] [Accepted: 04/27/2022] [Indexed: 12/16/2022]
Abstract
The mitochondrial genome has been difficult to manipulate because it is shielded by the organelle double membranes, preventing efficient nucleic acid entry. Moreover, mitochondrial DNA (mtDNA) recombination is not a robust system in most species. This limitation has forced investigators to rely on naturally occurring alterations to study both mitochondrial function and pathobiology. Because most pathogenic mtDNA mutations are heteroplasmic, the development of specific nucleases has allowed us to selectively eliminate mutant species. Several 'protein only' gene-editing platforms have been successfully used for this purpose. More recently, a DNA double-strand cytidine deaminase has been identified and adapted to edit mtDNA. This enzyme was also used as a component to adapt a DNA single-strand deoxyadenosine deaminase to mtDNA editing. These are major advances in our ability to precisely alter the mtDNA in animal cells.
Collapse
|
17
|
Silva-Pinheiro P, Minczuk M. The potential of mitochondrial genome engineering. Nat Rev Genet 2022; 23:199-214. [PMID: 34857922 DOI: 10.1038/s41576-021-00432-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
Collapse
Affiliation(s)
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| |
Collapse
|
18
|
Anoar S, Woodling NS, Niccoli T. Mitochondria Dysfunction in Frontotemporal Dementia/Amyotrophic Lateral Sclerosis: Lessons From Drosophila Models. Front Neurosci 2021; 15:786076. [PMID: 34899176 PMCID: PMC8652125 DOI: 10.3389/fnins.2021.786076] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by declining motor and cognitive functions. Even though these diseases present with distinct sets of symptoms, FTD and ALS are two extremes of the same disease spectrum, as they show considerable overlap in genetic, clinical and neuropathological features. Among these overlapping features, mitochondrial dysfunction is associated with both FTD and ALS. Recent studies have shown that cells derived from patients' induced pluripotent stem cells (iPSC)s display mitochondrial abnormalities, and similar abnormalities have been observed in a number of animal disease models. Drosophila models have been widely used to study FTD and ALS because of their rapid generation time and extensive set of genetic tools. A wide array of fly models have been developed to elucidate the molecular mechanisms of toxicity for mutations associated with FTD/ALS. Fly models have been often instrumental in understanding the role of disease associated mutations in mitochondria biology. In this review, we discuss how mutations associated with FTD/ALS disrupt mitochondrial function, and we review how the use of Drosophila models has been pivotal to our current knowledge in this field.
Collapse
Affiliation(s)
- Sharifah Anoar
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
| | - Nathaniel S Woodling
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
| | - Teresa Niccoli
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
| |
Collapse
|
19
|
The relationship of C and N stable isotopes to high-latitude moss-associated N 2 fixation. Oecologia 2021; 197:283-295. [PMID: 34319437 DOI: 10.1007/s00442-021-05005-7] [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: 02/11/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
Moss-associated N2 fixation by epiphytic microbes is a key biogeochemical process in nutrient-limited high-latitude ecosystems. Abiotic drivers, such as temperature and moisture, and the identity of host mosses are critical sources of variation in N2 fixation rates. An understanding of the potential interaction between these factors is essential for predicting N inputs as moss communities change with the climate. To further understand the drivers and results of N2 fixation rate variation, we obtained natural abundance values of C and N isotopes and an associated rate of N2 fixation with 15N2 gas incubations in 34 moss species collected in three regions across Alaska, USA. We hypothesized that δ15N values would increase toward 0‰ with higher N2 fixation to reflect the increasing contribution of fixed N2 in moss biomass. Second, we hypothesized that δ13C and N2 fixation would be positively related, as enriched δ13C signatures reflect abiotic conditions favorable to N2 fixation. We expected that the magnitude of these relationships would vary among types of host mosses, reflecting differences in anatomy and habitat. We found little support for our first hypothesis, with only a modest positive relationship between N2 fixation rates and δ15N in a structural equation model. We found a significant positive relationship between δ13C and N2 fixation only in Hypnales, where the probability of N2 fixation activity reached 95% when δ13C values exceeded - 30.4‰. We conclude that moisture and temperature interact strongly with host moss identity in determining the extent to which abiotic conditions impact associated N2 fixation rates.
Collapse
|
20
|
Rossmann MP, Dubois SM, Agarwal S, Zon LI. Mitochondrial function in development and disease. Dis Model Mech 2021; 14:269120. [PMID: 34114603 PMCID: PMC8214736 DOI: 10.1242/dmm.048912] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are organelles with vital functions in almost all eukaryotic cells. Often described as the cellular ‘powerhouses’ due to their essential role in aerobic oxidative phosphorylation, mitochondria perform many other essential functions beyond energy production. As signaling organelles, mitochondria communicate with the nucleus and other organelles to help maintain cellular homeostasis, allow cellular adaptation to diverse stresses, and help steer cell fate decisions during development. Mitochondria have taken center stage in the research of normal and pathological processes, including normal tissue homeostasis and metabolism, neurodegeneration, immunity and infectious diseases. The central role that mitochondria assume within cells is evidenced by the broad impact of mitochondrial diseases, caused by defects in either mitochondrial or nuclear genes encoding for mitochondrial proteins, on different organ systems. In this Review, we will provide the reader with a foundation of the mitochondrial ‘hardware’, the mitochondrion itself, with its specific dynamics, quality control mechanisms and cross-organelle communication, including its roles as a driver of an innate immune response, all with a focus on development, disease and aging. We will further discuss how mitochondrial DNA is inherited, how its mutation affects cell and organismal fitness, and current therapeutic approaches for mitochondrial diseases in both model organisms and humans. Summary: Mitochondria have a plethora of functions beyond metabolism. This Review discusses the emerging and multifaceted roles of mitochondria in different model organisms and human disease biology.
Collapse
Affiliation(s)
- Marlies P Rossmann
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Sonia M Dubois
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| |
Collapse
|
21
|
Jeedigunta SP, Minenkova AV, Palozzi JM, Hurd TR. Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline. Annu Rev Genomics Hum Genet 2021; 22:55-80. [PMID: 34038145 DOI: 10.1146/annurev-genom-121420-081805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are unusual organelles in that they contain their own genomes, which are kept apart from the rest of the DNA in the cell. While mitochondrial DNA (mtDNA) is essential for respiration and most multicellular life, maintaining a genome outside the nucleus brings with it a number of challenges. Chief among these is preserving mtDNA genomic integrity from one generation to the next. In this review, we discuss what is known about negative (purifying) selection mechanisms that prevent deleterious mutations from accumulating in mtDNA in the germline. Throughout, we focus on the female germline, as it is the tissue through which mtDNA is inherited in most organisms and, therefore, the tissue that most profoundly shapes the genome. We discuss recent progress in uncovering the mechanisms of germline mtDNA selection, from humans to invertebrates.
Collapse
Affiliation(s)
- Swathi P Jeedigunta
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Anastasia V Minenkova
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Jonathan M Palozzi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Thomas R Hurd
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| |
Collapse
|
22
|
Stewart JB. Current progress with mammalian models of mitochondrial DNA disease. J Inherit Metab Dis 2021; 44:325-342. [PMID: 33099782 DOI: 10.1002/jimd.12324] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial disorders make up a large class of heritable diseases that cause a broad array of different human pathologies. They can affect many different organ systems, or display very specific tissue presentation, and can lead to illness either in childhood or later in life. While the over 1200 genes encoded in the nuclear DNA play an important role in human mitochondrial disease, it has been known for over 30 years that mutations of the mitochondria's own small, multicopy DNA chromosome (mtDNA) can lead to heritable human diseases. Unfortunately, animal mtDNA has resisted transgenic and directed genome editing technologies until quite recently. As such, animal models to aid in our understanding of these diseases, and to explore preclinical therapeutic research have been quite rare. This review will discuss the unusual properties of animal mitochondria that have hindered the generation of animal models. It will also discuss the existing mammalian models of human mtDNA disease, describe the methods employed in their generation, and will discuss recent advances in the targeting of DNA-manipulating enzymes to the mitochondria and how these may be employed to generate new models.
Collapse
Affiliation(s)
- James Bruce Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
23
|
Spierer AN, Yoon D, Zhu CT, Rand DM. FreeClimber: automated quantification of climbing performance in Drosophila. J Exp Biol 2021; 224:jeb229377. [PMID: 33188065 PMCID: PMC7823161 DOI: 10.1242/jeb.229377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/05/2020] [Indexed: 12/26/2022]
Abstract
Negative geotaxis (climbing) performance is a useful metric for quantifying Drosophila health. Manual methods to quantify climbing performance are tedious and often biased, while many available computational methods have challenging hardware or software requirements. We present an alternative: FreeClimber. This open source, Python-based platform subtracts a video's static background to improve detection for flies moving across heterogeneous backgrounds. FreeClimber calculates a cohort's velocity as the slope of the most linear portion of a mean vertical position versus time curve. It can run from a graphical user interface for optimization or a command line interface for high-throughput and automated batch processing, improving accessibility for users with different expertise. FreeClimber outputs calculated slopes, spot locations for follow-up analyses (e.g. tracking), and several visualizations and plots. We demonstrate FreeClimber's utility in a longitudinal study for endurance exercise performance in Drosophila mitonuclear genotypes using six distinct mitochondrial haplotypes paired with a common D. melanogaster nuclear background.
Collapse
Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Denise Yoon
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chen-Tseh Zhu
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
- Global Plant Breeding, Bayer Crop Science, Chesterfield, MO 63017, USA
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| |
Collapse
|
24
|
Towarnicki SG, Ballard JWO. Towards understanding the evolutionary dynamics of mtDNA. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:355-364. [PMID: 33026269 DOI: 10.1080/24701394.2020.1830076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Historically, mtDNA was considered a selectively neutral marker that was useful for estimating the population genetic history of the maternal lineage. Over time there has been an increasing appreciation of mtDNA and mitochondria in maintaining cellular and organismal health. Beyond energy production, mtDNA and mitochondria have critical cellular roles in signalling. Here we briefly review the structure of mtDNA and the role of the mitochondrion in energy production. We then discuss the predictions that can be obtained from quaternary structure modelling and focus on mitochondrial complex I. Complex I is the primary entry point for electrons into the electron transport system is the largest respiratory complex of the chain and produces about 40% of the proton flux used to synthesize ATP. A focus of the review is Drosophila's utility as a model organism to study the selective advantage of specific mutations. However, we note that the incorporation of insights from a multitude of systems is necessary to fully understand the range of roles that mtDNA has in organismal fitness. We speculate that dietary changes can illicit stress responses that influence the selective advantage of specific mtDNA mutations and cause spatial and temporal fluctuations in the frequencies of mutations. We conclude that developing our understanding of the roles mtDNA has in determining organismal fitness will enable increased evolutionary insight and propose we can no longer assume it is evolving as a strictly neutral marker without testing this hypothesis.
Collapse
Affiliation(s)
- Samuel G Towarnicki
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| |
Collapse
|
25
|
Fu Y, Tigano M, Sfeir A. Safeguarding mitochondrial genomes in higher eukaryotes. Nat Struct Mol Biol 2020; 27:687-695. [PMID: 32764737 DOI: 10.1038/s41594-020-0474-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Mitochondria respond to DNA damage and preserve their own genetic material in a manner distinct from that of the nucleus but that requires organized mito-nuclear communication. Failure to resolve mtDNA breaks leads to mitochondrial dysfunction and affects host cells and tissues. Here, we review the pathways that safeguard mitochondrial genomes and examine the insights gained from studies of cellular and tissue-wide responses to mtDNA damage and mito-nuclear genome incompatibility.
Collapse
Affiliation(s)
- Yi Fu
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Marco Tigano
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA.
| |
Collapse
|
26
|
Keaney TA, Wong HWS, Dowling DK, Jones TM, Holman L. Sibling rivalry versus mother's curse: can kin competition facilitate a response to selection on male mitochondria? Proc Biol Sci 2020; 287:20200575. [PMID: 32605521 DOI: 10.1098/rspb.2020.0575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Assuming that fathers never transmit mitochondrial DNA (mtDNA) to their offspring, mitochondrial mutations that affect male fitness are invisible to direct selection on males, leading to an accumulation of male-harming alleles in the mitochondrial genome (mother's curse). However, male phenotypes encoded by mtDNA can still undergo adaptation via kin selection provided that males interact with females carrying related mtDNA, such as their sisters. Here, using experiments with Drosophila melanogaster carrying standardized nuclear DNA but distinct mitochondrial DNA, we test whether the mitochondrial haplotype carried by interacting pairs of larvae affects survival to adulthood, as well as the fitness of the adults. Although mtDNA had no detectable direct or indirect genetic effect on larva-to-adult survival, the fitness of male and female adults was significantly affected by their own mtDNA and the mtDNA carried by their social partner in the larval stage. Thus, mtDNA mutations that alter the effect of male larvae on nearby female larvae (which often carry the same mutation, due to kinship) could theoretically respond to kin selection. We discuss the implications of our findings for the evolution of mitochondria and other maternally inherited endosymbionts.
Collapse
Affiliation(s)
- Thomas A Keaney
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| | - Heidi W S Wong
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Vic. 3800, Australia
| | - Therésa M Jones
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| | - Luke Holman
- School of Biosciences, The University of Melbourne, Vic. 3010, Australia
| |
Collapse
|
27
|
Teem JL, Alphey L, Descamps S, Edgington MP, Edwards O, Gemmell N, Harvey-Samuel T, Melnick RL, Oh KP, Piaggio AJ, Saah JR, Schill D, Thomas P, Smith T, Roberts A. Genetic Biocontrol for Invasive Species. Front Bioeng Biotechnol 2020; 8:452. [PMID: 32523938 PMCID: PMC7261935 DOI: 10.3389/fbioe.2020.00452] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Invasive species are increasingly affecting agriculture, food, fisheries, and forestry resources throughout the world. As a result of global trade, invasive species are often introduced into new environments where they become established and cause harm to human health, agriculture, and the environment. Prevention of new introductions is a high priority for addressing the harm caused by invasive species, but unfortunately efforts to prevent new introductions do not address the economic harm that is presently manifested where invasive species have already become established. Genetic biocontrol can be defined as the release of organisms with genetic methods designed to disrupt the reproduction of invasive populations. While these methods offer the potential to control or even eradicate invasive species, there is a need to ensure that genetic biocontrol methods can be deployed in a way that minimizes potential harm to the environment. This review provides an overview of the state of genetic biocontrol, focusing on several approaches that were the subject of presentations at the Genetic Biocontrol for Invasive Species Workshop in Tarragona, Spain, March 31st, 2019, a workshop sponsored by the OECD’s Co-operative Research Program on Biological Resource Management for Sustainable Agricultural Systems. The review considers four different approaches to genetic biocontrol for invasive species; sterile-release, YY Males, Trojan Female Technique, and gene drive. The different approaches will be compared with respect to the efficiency each affords as a genetic biocontrol tool, the practical utility and cost/benefits associated with implementation of the approach, and the regulatory considerations that will need to be addressed for each. The opinions expressed and arguments employed in this publication are the sole responsibility of the authors and do not necessarily reflect those of the OECD or of the governments of its Member countries.
Collapse
Affiliation(s)
- John L Teem
- ILSI Research Foundation, Washington, DC, United States
| | - Luke Alphey
- The Pirbright Institute, Woking, United Kingdom
| | - Sarah Descamps
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Owain Edwards
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Wembley, WA, Australia
| | - Neil Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | | | - Kevin P Oh
- National Wildlife Research Center, USDA/APHIS-Wildlife Services, Fort Collins, CO, United States
| | - Antoinette J Piaggio
- National Wildlife Research Center, USDA/APHIS-Wildlife Services, Fort Collins, CO, United States
| | | | - Dan Schill
- Fisheries Management Solutions, Inc., Boise, ID, United States
| | - Paul Thomas
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Trevor Smith
- Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States
| | | |
Collapse
|
28
|
Zhang F, Pirooznia M, Xu H. Mitochondria regulate intestinal stem cell proliferation and epithelial homeostasis through FOXO. Mol Biol Cell 2020; 31:1538-1549. [PMID: 32374658 PMCID: PMC7359575 DOI: 10.1091/mbc.e19-10-0560] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A metabolic transition from glycolysis to oxidative phosphorylation is often associated with differentiation of many types of stem cells. However, the link between mitochondrial respiration and stem cells' behavior is not fully understood. We genetically disrupted electron transport chain (ETC) complexes in the intestinal stem cells (ISCs) of Drosophila. We found that ISCs carrying impaired ETC proliferated much more slowly than normal and produced very few enteroblasts, which failed to further differentiate into enterocytes. One of the main impediments to ISC proliferation and lineage specification appeared to be abnormally elevated forkhead box O (FOXO) signaling in the ETC-deficient ISCs, as genetically suppressing the signaling pathway partially restored the number of enterocytes. Contrary to common belief, reactive oxygen species (ROS) accumulation did not appear to mediate the ETC mutant phenotype. Our results demonstrate that mitochondrial respiration is essential for Drosophila ISC proliferation and lineage specification in vivo and acts at least partially by repressing endogenous FOXO signaling.
Collapse
Affiliation(s)
- Fan Zhang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
29
|
Jackson CB, Turnbull DM, Minczuk M, Gammage PA. Therapeutic Manipulation of mtDNA Heteroplasmy: A Shifting Perspective. Trends Mol Med 2020; 26:698-709. [PMID: 32589937 DOI: 10.1016/j.molmed.2020.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Mutations of mitochondrial DNA (mtDNA) often underlie mitochondrial disease, one of the most common inherited metabolic disorders. Since the sequencing of the human mitochondrial genome and the discovery of pathogenic mutations in mtDNA more than 30 years ago, a movement towards generating methods for robust manipulation of mtDNA has ensued, although with relatively few advances and some controversy. While developments in the transformation of mammalian mtDNA have stood still for some time, recent demonstrations of programmable nuclease-based technology suggest that clinical manipulation of mtDNA heteroplasmy may be on the horizon for these largely untreatable disorders. Here we review historical and recent developments in mitochondrially targeted nuclease technology and the clinical outlook for treatment of hereditary mitochondrial disease.
Collapse
Affiliation(s)
- Christopher B Jackson
- Stem Cells and Metabolism, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Payam A Gammage
- CRUK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
30
|
Salminen TS, Vale PF. Drosophila as a Model System to Investigate the Effects of Mitochondrial Variation on Innate Immunity. Front Immunol 2020; 11:521. [PMID: 32269576 PMCID: PMC7109263 DOI: 10.3389/fimmu.2020.00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/06/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding why the response to infection varies between individuals remains one of the major challenges in immunology and infection biology. A substantial proportion of this heterogeneity can be explained by individual genetic differences which result in variable immune responses, and there are many examples of polymorphisms in nuclear-encoded genes that alter immunocompetence. However, how immunity is affected by genetic polymorphism in an additional genome, inherited maternally inside mitochondria (mtDNA), has been relatively understudied. Mitochondria are increasingly recognized as important mediators of innate immune responses, not only because they are the main source of energy required for costly immune responses, but also because by-products of mitochondrial metabolism, such as reactive oxygen species (ROS), may have direct microbicidal action. Yet, it is currently unclear how naturally occurring variation in mtDNA contributes to heterogeneity in infection outcomes. In this review article, we describe potential sources of variation in mitochondrial function that may arise due to mutations in vital nuclear and mitochondrial components of energy production or due to a disruption in mito-nuclear crosstalk. We then highlight how these changes in mitochondrial function can impact immune responses, focusing on their effects on ATP- and ROS-generating pathways, as well as immune signaling. Finally, we outline how being a powerful and genetically tractable model of infection, immunity and mitochondrial genetics makes the fruit fly Drosophila melanogaster ideally suited to dissect mitochondrial effects on innate immune responses to infection.
Collapse
Affiliation(s)
- Tiina S. Salminen
- School of Biological Sciences, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pedro F. Vale
- School of Biological Sciences, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
31
|
Klucnika A, Ma H. A battle for transmission: the cooperative and selfish animal mitochondrial genomes. Open Biol 2020; 9:180267. [PMID: 30890027 PMCID: PMC6451365 DOI: 10.1098/rsob.180267] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.
Collapse
Affiliation(s)
- Anna Klucnika
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
| | - Hansong Ma
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
| |
Collapse
|
32
|
Vaught RC, Voigt S, Dobler R, Clancy DJ, Reinhardt K, Dowling DK. Interactions between cytoplasmic and nuclear genomes confer sex-specific effects on lifespan in Drosophila melanogaster. J Evol Biol 2020; 33:694-713. [PMID: 32053259 DOI: 10.1111/jeb.13605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
Genetic variation outside of the cell nucleus can affect the phenotype. The cytoplasm is home to the mitochondria, and in arthropods often hosts intracellular bacteria such as Wolbachia. Although numerous studies have implicated epistatic interactions between cytoplasmic and nuclear genetic variation as mediators of phenotypic expression, two questions remain. Firstly, it remains unclear whether outcomes of cyto-nuclear interactions will manifest differently across the sexes, as might be predicted given that cytoplasmic genomes are screened by natural selection only through females as a consequence of their maternal inheritance. Secondly, the relative contribution of mitochondrial genetic variation to other cytoplasmic sources of variation, such as Wolbachia infection, in shaping phenotypic outcomes of cyto-nuclear interactions remains unknown. Here, we address these questions, creating a fully crossed set of replicated cyto-nuclear populations derived from three geographically distinct populations of Drosophila melanogaster, measuring the lifespan of males and females from each population. We observed that cyto-nuclear interactions shape lifespan and that the outcomes of these interactions differ across the sexes. Yet, we found no evidence that placing the cytoplasms from one population alongside the nuclear background of others (generating putative cyto-nuclear mismatches) leads to decreased lifespan in either sex. Although it was difficult to partition mitochondrial from Wolbachia effects, our results suggest at least some of the cytoplasmic genotypic contribution to lifespan was directly mediated by an effect of sequence variation in the mtDNA. Future work should explore the degree to which cyto-nuclear interactions result in sex differences in the expression of other components of organismal life history.
Collapse
Affiliation(s)
- Rebecca C Vaught
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Susanne Voigt
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - Ralph Dobler
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - David J Clancy
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Klaus Reinhardt
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| |
Collapse
|
33
|
Montooth KL, Dhawanjewar AS, Meiklejohn CD. Temperature-Sensitive Reproduction and the Physiological and Evolutionary Potential for Mother's Curse. Integr Comp Biol 2020; 59:890-899. [PMID: 31173136 PMCID: PMC6797906 DOI: 10.1093/icb/icz091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Strict maternal transmission of mitochondrial DNA (mtDNA) is hypothesized to permit the accumulation of mitochondrial variants that are deleterious to males but not females, a phenomenon called mother’s curse. However, direct evidence that mtDNA mutations exhibit such sexually antagonistic fitness effects is sparse. Male-specific mutational effects can occur when the physiological requirements of the mitochondria differ between the sexes. Such male-specific effects could potentially occur if sex-specific cell types or tissues have energy requirements that are differentially impacted by mutations affecting energy metabolism. Here we summarize findings from a model mitochondrial–nuclear incompatibility in the fruit fly Drosophila that demonstrates sex-biased effects, but with deleterious effects that are generally larger in females. We present new results showing that the mitochondrial–nuclear incompatibility does negatively affect male fertility, but only when males are developed at high temperatures. The temperature-dependent male sterility can be partially rescued by diet, suggesting an energetic basis. Finally, we discuss fruitful paths forward in understanding the physiological scope for sex-specific effects of mitochondrial mutations in the context of the recent discovery that many aspects of metabolism are sexually dimorphic and downstream of sex-determination pathways in Drosophila. A key parameter of these models that remains to be quantified is the fraction of mitochondrial mutations with truly male-limited fitness effects across extrinsic and intrinsic environments. Given the energy demands of reproduction in females, only a small fraction of the mitochondrial mutational spectrum may have the potential to contribute to mother’s curse in natural populations.
Collapse
Affiliation(s)
- Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, 1104 T Street, Lincoln, NE 68502, USA
| | - Abhilesh S Dhawanjewar
- School of Biological Sciences, University of Nebraska-Lincoln, 1104 T Street, Lincoln, NE 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, 1104 T Street, Lincoln, NE 68502, USA
| |
Collapse
|
34
|
Havird JC, McConie HJ. Sexually Antagonistic Mitonuclear Coevolution in Duplicate Oxidative Phosphorylation Genes. Integr Comp Biol 2020; 59:864-874. [PMID: 30942855 DOI: 10.1093/icb/icz021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Mitochondrial function is critical in eukaryotes. To maintain an adequate supply of energy, precise interactions must be maintained between nuclear- and mitochondrial-encoded gene products. Such interactions are paramount in chimeric enzymes such as the oxidative phosphorylation (OXPHOS) complexes. Mutualistic coevolution between the two genomes has therefore been suggested to be a critical, ubiquitous feature of eukaryotes that acts to maintain cellular function. However, mitochondrial genomes can also act selfishly and increase their own transmission at the expense of organismal function. For example, male-harming mutations are predisposed to accumulate in mitochondrial genomes due to their maternal inheritance ("mother's curse"). Here, we investigate sexually antagonistic mitonuclear coevolution in nuclear-encoded OXPHOS paralogs from mammals and Drosophila. These duplicate genes are highly divergent but must interact with the same set of mitochondrial-encoded genes. Many such paralogs show testis-specific expression, prompting previous hypotheses suggesting they may have evolved under selection to counteract male-harming mitochondrial mutations. We found increased rates of evolution in OXPHOS paralogs with testis-specific expression in mammals and Drosophila, supporting this hypothesis. However, further analyses suggested such patterns may be due to relaxed, not positive selection, especially in Drosophila. Structural data also suggest that mitonuclear interactions do not play a major role in the evolution of many OXPHOS paralogs in a consistent way. In conclusion, no single OXPHOS paralog met all our criteria for being under selection to counteract male-harming mitochondrial mutations. We discuss alternative explanations for the drastic patterns of evolution in these genes, including mutualistic mitonuclear coevolution, adaptive subfunctionalization after gene duplication, and relaxed selection on OXPHOS in male tissues.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hunter J McConie
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
35
|
Dowling DK, Adrian RE. Challenges and Prospects for Testing the Mother's Curse Hypothesis. Integr Comp Biol 2020; 59:875-889. [PMID: 31225591 DOI: 10.1093/icb/icz110] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Maternal inheritance of mitochondrial DNA (mtDNA) renders selection blind to mutations whose effects are limited to males. Evolutionary theory predicts this will lead to the accumulation of a male-specific genetic load within the mitochondrial genomes of populations; that is, a pool of mutations that negatively affects male, but not female, fitness components. This principle has been termed the Mother's Curse hypothesis. While the hypothesis has received some empirical support, its relevance to natural populations of metazoans remains unclear, and these ambiguities are compounded by the lack of a clear predictive framework for studies attempting to test Mother's Curse. Here, we seek to redress this by outlining the core predictions of the hypothesis, as well as the key features of the experimental designs that are required to enable direct testing of the predictions. Our goal is to provide a roadmap for future research seeking to elucidate the evolutionary significance of the Mother's Curse hypothesis.
Collapse
Affiliation(s)
- Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Rebecca E Adrian
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
36
|
Wallis CP, Scott LH, Filipovska A, Rackham O. Manipulating and elucidating mitochondrial gene expression with engineered proteins. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190185. [PMID: 31787043 DOI: 10.1098/rstb.2019.0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many conventional, modern genome engineering tools cannot be used to study mitochondrial genetics due to the unusual structure and physiology of the mitochondrial genome. Here, we review a number of newly developed, synthetic biology-based approaches for altering levels of mutant mammalian mitochondrial DNA and mitochondrial RNAs, including transcription activator-like effector nucleases, zinc finger nucleases and engineered RNA-binding proteins. These approaches allow researchers to manipulate and visualize mitochondrial processes and may provide future therapeutics. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
Collapse
Affiliation(s)
- Christopher P Wallis
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Louis H Scott
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| |
Collapse
|
37
|
Nagarajan-Radha V, Aitkenhead I, Clancy DJ, Chown SL, Dowling DK. Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190178. [PMID: 31787038 DOI: 10.1098/rstb.2019.0178] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Evolutionary theory proposes that maternal inheritance of mitochondria will facilitate the accumulation of mitochondrial DNA (mtDNA) mutations that are harmful to males but benign or beneficial to females. Furthermore, mtDNA haplotypes sampled from across a given species distribution are expected to differ in the number and identity of these 'male-harming' mutations they accumulate. Consequently, it is predicted that the genetic variation which delineates distinct mtDNA haplotypes of a given species should confer larger phenotypic effects on males than females (reflecting mtDNA mutations that are male-harming, but female-benign), or sexually antagonistic effects (reflecting mutations that are male-harming, but female-benefitting). These predictions have received support from recent work examining mitochondrial haplotypic effects on adult life-history traits in Drosophila melanogaster. Here, we explore whether similar signatures of male-bias or sexual antagonism extend to a key physiological trait-metabolic rate. We measured the effects of mitochondrial haplotypes on the amount of carbon dioxide produced by individual flies, controlling for mass and activity, across 13 strains of D. melanogaster that differed only in their mtDNA haplotype. The effects of mtDNA haplotype on metabolic rate were larger in males than females. Furthermore, we observed a negative intersexual correlation across the haplotypes for metabolic rate. Finally, we uncovered a male-specific negative correlation, across haplotypes, between metabolic rate and longevity. These results are consistent with the hypothesis that maternal mitochondrial inheritance has led to the accumulation of a sex-specific genetic load within the mitochondrial genome, which affects metabolic rate and that may have consequences for the evolution of sex differences in life history. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
Collapse
Affiliation(s)
| | - Ian Aitkenhead
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - David J Clancy
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
38
|
Klucnika A, Ma H. Mapping and editing animal mitochondrial genomes: can we overcome the challenges? Philos Trans R Soc Lond B Biol Sci 2019; 375:20190187. [PMID: 31787046 DOI: 10.1098/rstb.2019.0187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The animal mitochondrial genome, although small, can have a big impact on health and disease. Non-pathogenic sequence variation among mitochondrial DNA (mtDNA) haplotypes influences traits including fertility, healthspan and lifespan, whereas pathogenic mutations are linked to incurable mitochondrial diseases and other complex conditions like ageing, diabetes, cancer and neurodegeneration. However, we know very little about how mtDNA genetic variation contributes to phenotypic differences. Infrequent recombination, the multicopy nature and nucleic acid-impenetrable membranes present significant challenges that hamper our ability to precisely map mtDNA variants responsible for traits, and to genetically modify mtDNA so that we can isolate specific mutants and characterize their biochemical and physiological consequences. Here, we summarize the past struggles and efforts in developing systems to map and edit mtDNA. We also assess the future of performing forward and reverse genetic studies on animal mitochondrial genomes. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
Collapse
Affiliation(s)
- Anna Klucnika
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Hansong Ma
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| |
Collapse
|
39
|
Keaney TA, Wong HWS, Dowling DK, Jones TM, Holman L. Mother’s curse and indirect genetic effects: Do males matter to mitochondrial genome evolution? J Evol Biol 2019; 33:189-201. [DOI: 10.1111/jeb.13561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Thomas A. Keaney
- School of Biosciences The University of Melbourne Melbourne Victoria Australia
| | - Heidi W. S. Wong
- School of Biosciences The University of Melbourne Melbourne Victoria Australia
| | - Damian K. Dowling
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Therésa M. Jones
- School of Biosciences The University of Melbourne Melbourne Victoria Australia
| | - Luke Holman
- School of Biosciences The University of Melbourne Melbourne Victoria Australia
| |
Collapse
|
40
|
Bahhir D, Yalgin C, Ots L, Järvinen S, George J, Naudí A, Krama T, Krams I, Tamm M, Andjelković A, Dufour E, González de Cózar JM, Gerards M, Parhiala M, Pamplona R, Jacobs HT, Jõers P. Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms. PLoS Genet 2019; 15:e1008410. [PMID: 31584940 PMCID: PMC6795474 DOI: 10.1371/journal.pgen.1008410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 10/16/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Mitochondria have been increasingly recognized as a central regulatory nexus for multiple metabolic pathways, in addition to ATP production via oxidative phosphorylation (OXPHOS). Here we show that inducing mitochondrial DNA (mtDNA) stress in Drosophila using a mitochondrially-targeted Type I restriction endonuclease (mtEcoBI) results in unexpected metabolic reprogramming in adult flies, distinct from effects on OXPHOS. Carbohydrate utilization was repressed, with catabolism shifted towards lipid oxidation, accompanied by elevated serine synthesis. Cleavage and translocation, the two modes of mtEcoBI action, repressed carbohydrate rmetabolism via two different mechanisms. DNA cleavage activity induced a type II diabetes-like phenotype involving deactivation of Akt kinase and inhibition of pyruvate dehydrogenase, whilst translocation decreased post-translational protein acetylation by cytonuclear depletion of acetyl-CoA (AcCoA). The associated decrease in the concentrations of ketogenic amino acids also produced downstream effects on physiology and behavior, attributable to decreased neurotransmitter levels. We thus provide evidence for novel signaling pathways connecting mtDNA to metabolism, distinct from its role in supporting OXPHOS. Mitochondria, subcellular compartments (organelles) found in virtually all eukaryotes, contain DNA which is believed to be a remnant of an ancestral bacterial genome. They are best known for the synthesis of the universal energy carrier ATP, but also serve as the hub of various metabolic and signalling pathways. We report here that mtDNA integrity is linked to a signaling system that influences metabolic fuel selection between fats and sugars. By disrupting mtDNA in the fruit fly we induced a strong shift towards lipid catabolism. This was caused both by a widespread decrease in post-translational acetylation of proteins, as well as specific inhibition of the machinery that transports glucose into cells across the plasma membrane. This phenomenon is very similar to the pathophysiology of diabetes, where the inability to transport glucose to cells is considered the main hallmark of the disease. Moreover, decreased protein acetylation was associated with lower levels of certain neurotransmitters, causing various effects on feeding and fertility. Our discovery reveals an unexpected role for mtDNA stability in regulating global metabolic balance and suggests that it could be instrumental in pandemic metabolic disorders such as diabetes and obesity.
Collapse
Affiliation(s)
- Diana Bahhir
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Cagri Yalgin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Liina Ots
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Sampsa Järvinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jack George
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alba Naudí
- Experimental Medicine Department, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLLEIDA), Lleida, Spain
| | - Tatjana Krama
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Science, Tartu, Estonia
| | - Indrikis Krams
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Zoology and Animal Ecology, Faculty of Biology, University of Latvia, Rīga, Latvia
- Department of Biotechnology, Daugavpils University, Daugavpils, Latvia
| | - Mairi Tamm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Ana Andjelković
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Eric Dufour
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Mike Gerards
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Mikael Parhiala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Reinald Pamplona
- Experimental Medicine Department, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLLEIDA), Lleida, Spain
| | - Howard T. Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Priit Jõers
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- * E-mail:
| |
Collapse
|
41
|
Haroon S, Li A, Weinert JL, Fritsch C, Ericson NG, Alexander-Floyd J, Braeckman BP, Haynes CM, Bielas JH, Gidalevitz T, Vermulst M. Multiple Molecular Mechanisms Rescue mtDNA Disease in C. elegans. Cell Rep 2019; 22:3115-3125. [PMID: 29562168 PMCID: PMC6106782 DOI: 10.1016/j.celrep.2018.02.099] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/07/2017] [Accepted: 02/25/2018] [Indexed: 01/03/2023] Open
Abstract
Genetic instability of the mitochondrial genome (mtDNA) plays an important role in human aging and disease. Thus far, it has proven difficult to develop successful treatment strategies for diseases that are caused by mtDNA instability. To address this issue, we developed a model of mtDNA disease in the nematode C. elegans, an animal model that can rapidly be screened for genes and biological pathways that reduce mitochondrial pathology. These worms recapitulate all the major hallmarks of mtDNA disease in humans, including increased mtDNA instability, loss of respiration, reduced neuromuscular function, and a shortened lifespan. We found that these phenotypes could be rescued by intervening in numerous biological pathways, including IGF-1/insulin signaling, mitophagy, and the mitochondrial unfolded protein response, suggesting that it may be possible to ameliorate mtDNA disease through multiple molecular mechanisms.
Collapse
Affiliation(s)
- Suraiya Haroon
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, PA 19104, USA
| | - Annie Li
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, PA 19104, USA
| | - Jaye L Weinert
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, PA 19104, USA
| | - Clark Fritsch
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, PA 19104, USA
| | - Nolan G Ericson
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Bart P Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, 9000 Ghent, Belgium
| | - Cole M Haynes
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jason H Bielas
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Tali Gidalevitz
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Marc Vermulst
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, PA 19104, USA.
| |
Collapse
|
42
|
Andreazza S, Samstag CL, Sanchez-Martinez A, Fernandez-Vizarra E, Gomez-Duran A, Lee JJ, Tufi R, Hipp MJ, Schmidt EK, Nicholls TJ, Gammage PA, Chinnery PF, Minczuk M, Pallanck LJ, Kennedy SR, Whitworth AJ. Mitochondrially-targeted APOBEC1 is a potent mtDNA mutator affecting mitochondrial function and organismal fitness in Drosophila. Nat Commun 2019; 10:3280. [PMID: 31337756 PMCID: PMC6650417 DOI: 10.1038/s41467-019-10857-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/06/2019] [Indexed: 12/22/2022] Open
Abstract
Somatic mutations in the mitochondrial genome (mtDNA) have been linked to multiple disease conditions and to ageing itself. In Drosophila, knock-in of a proofreading deficient mtDNA polymerase (POLG) generates high levels of somatic point mutations and also small indels, but surprisingly limited impact on organismal longevity or fitness. Here we describe a new mtDNA mutator model based on a mitochondrially-targeted cytidine deaminase, APOBEC1. mito-APOBEC1 acts as a potent mutagen which exclusively induces C:G>T:A transitions with no indels or mtDNA depletion. In these flies, the presence of multiple non-synonymous substitutions, even at modest heteroplasmy, disrupts mitochondrial function and dramatically impacts organismal fitness. A detailed analysis of the mutation profile in the POLG and mito-APOBEC1 models reveals that mutation type (quality) rather than quantity is a critical factor in impacting organismal fitness. The specificity for transition mutations and the severe phenotypes make mito-APOBEC1 an excellent mtDNA mutator model for ageing research.
Collapse
Affiliation(s)
- Simonetta Andreazza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Colby L Samstag
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Alvaro Sanchez-Martinez
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Erika Fernandez-Vizarra
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Aurora Gomez-Duran
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Juliette J Lee
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Roberta Tufi
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Michael J Hipp
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | | | - Thomas J Nicholls
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Payam A Gammage
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Leo J Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander J Whitworth
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
| |
Collapse
|
43
|
Abstract
Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA.
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
44
|
Affiliation(s)
- Jun-Yuan Ji
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University Health Science Center, College Station, TX, 77843, USA.
| | - Chun Han
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| |
Collapse
|
45
|
Camus MF, Dowling DK. Mitochondrial genetic effects on reproductive success: signatures of positive intrasexual, but negative intersexual pleiotropy. Proc Biol Sci 2019; 285:rspb.2018.0187. [PMID: 29794041 DOI: 10.1098/rspb.2018.0187] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/30/2018] [Indexed: 01/03/2023] Open
Abstract
Theory predicts that maternal inheritance of mitochondria will facilitate the accumulation of mtDNA mutations that are male biased, or even sexually antagonistic, in effect. While there are many reported cases of mtDNA mutations conferring cytoplasmic male sterility in plants, historically it was assumed such mutations would not persist in the streamlined mitochondrial genomes of bilaterian metazoans. Intriguingly, recent cases of mitochondrial variants exerting male biases in effect have come to light in bilaterians. These cases aside, it remains unknown whether the mitochondrial genetic variation affecting phenotypic expression, and in particular reproductive performance, in bilaterians is routinely composed of sex-biased or sex-specific variation. If selection consistently favours mtDNA variants that augment female fitness, but at cost to males, this could shape patterns of pleiotropy and lead to negative intersexual correlations across mtDNA haplotypes. Here, we show that genetic variation across naturally occurring mitochondrial haplotypes affects components of reproductive success in both sexes, in the fruit fly Drosophila melanogaster We find that intrasexual correlations across mitochondrial haplotypes, for components of reproductive success, are generally positive, while intersexual correlations are negative. These results accord with theoretical predictions, suggesting that maternal inheritance has led to the fixation of numerous mutations of sexually antagonistic effect.
Collapse
Affiliation(s)
- M Florencia Camus
- School of Biological Sciences, Monash University, Victoria 3800, Australia .,Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| |
Collapse
|
46
|
Chen Z, Zhang F, Xu H. Human mitochondrial DNA diseases and Drosophila models. J Genet Genomics 2019; 46:201-212. [DOI: 10.1016/j.jgg.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/25/2019] [Indexed: 01/06/2023]
|
47
|
Chen W, Xue Y, Scarfe L, Wang D, Zhang Y. Loss of Prune in Circadian Cells Decreases the Amplitude of the Circadian Locomotor Rhythm in Drosophila. Front Cell Neurosci 2019; 13:76. [PMID: 30881291 PMCID: PMC6405476 DOI: 10.3389/fncel.2019.00076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/14/2019] [Indexed: 01/10/2023] Open
Abstract
The circadian system, which has a period of about 24 h, is import for organismal health and fitness. The molecular circadian clock consists of feedback loops involving both transcription and translation, and proper function of the circadian system also requires communication among intracellular organelles. As important hubs for signaling in the cell, mitochondria integrate a variety of signals. Mitochondrial dysfunction and disruption of circadian rhythms are observed in neurodegenerative diseases and during aging. However, how mitochondrial dysfunction influences circadian rhythm is largely unknown. Here, we report that Drosophila prune (pn), which localizes to the mitochondrial matrix, most likely affects the function of certain clock neurons.Deletion of pn in flies caused decreased expression of mitochondrial transcription factor TFAM and reductions in levels of mitochondrial DNA, which resulted in mitochondrial dysfunction. Loss of pn decreased the amplitude of circadian rhythms.In addition, we showed that depletion of mtDNA by overexpression of a mitochondrially targeted restriction enzyme mitoXhoI also decreased the robustness of circadian rhythms. Our work demonstrates that pn is important for mitochondrial function thus involved in the regulation of circadian rhythms.
Collapse
Affiliation(s)
- Wenfeng Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, China.,Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Yongbo Xue
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Lisa Scarfe
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| | - Danfeng Wang
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong Zhang
- Department of Biology, University of Nevada, Reno, Reno, NV, United States
| |
Collapse
|
48
|
Dobler R, Dowling DK, Morrow EH, Reinhardt K. A systematic review and meta-analysis reveals pervasive effects of germline mitochondrial replacement on components of health. Hum Reprod Update 2019; 24:519-534. [PMID: 29757366 DOI: 10.1093/humupd/dmy018] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 05/03/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Mitochondrial replacement, a form of nuclear transfer, has been proposed as a germline therapy to prevent the transmission of mitochondrial diseases. Mitochondrial replacement therapy has been licensed for clinical application in the UK, and already carried out in other countries, but little is known about negative or unintended effects on the health of offspring born using this technique. OBJECTIVE AND RATIONALE Studies in invertebrate models have used techniques that achieve mitochondrial replacement to create offspring with novel combinations of mitochondrial and nuclear genotype. These have demonstrated that the creation of novel mitochondrial-nuclear interactions can lead to alterations in offspring characteristics, such as development rates, fertility and longevity. However, it is currently unclear whether such interactions could similarly affect the outcomes of vertebrate biomedical studies, which have sought to assess the efficacy of the replacement therapy. SEARCH METHODS This systematic review addresses whether the effects of mitochondrial replacement on offspring characteristics differ in magnitude between biological (conducted on invertebrate models, with an ecological or evolutionary focus) and biomedical studies (conducted on vertebrate models, with a clinical focus). Studies were selected based on a key-word search in 'Web of Science', complemented by backward searches of reviews on the topic of mitochondrial-nuclear (mito-nuclear) interactions. In total, 43 of the resulting 116 publications identified in the search contained reliable data to estimate effect sizes of mitochondrial replacement. We found no evidence of publication bias when examining effect-size estimates across sample sizes. OUTCOMES Mitochondrial replacement consistently altered the phenotype, with significant effects at several levels of organismal performance and health, including gene expression, anatomy, metabolism and life-history. Biomedical and biological studies, while differing in the methods used to achieve mitochondrial replacement, showed only marginally significant differences in effect-size estimates (-0.233 [CI: -0.495 to -0.011]), with larger effect-size estimates in biomedical studies (0.697 [CI: 0.450-0.956]) than biological studies (0.462 [CI: 0.287-0.688]). Humans showed stronger effects than other species. Effects of mitochondrial replacement were also stronger in species with a higher basal metabolic rate. Based on our results, we conducted the first formal risk analysis of mitochondrial replacement, and conservatively estimate negative effects in at least one in every 130 resulting offspring born to the therapy. WIDER IMPLICATIONS Our findings suggest that mitochondrial replacement may routinely affect offspring characteristics across a wide array of animal species, and that such effects are likely to extend to humans. Studies in invertebrate models have confirmed mito-nuclear interactions as the underpinning cause of organismal effects following mitochondrial replacement. This therefore suggests that mito-nuclear interactions are also likely to be contributing to effects seen in biomedical studies, on vertebrate models, whose effect sizes exceeded those of biological studies. Our results advocate the use of safeguards that could offset any negative effects (defining any unintended effect as being negative) mediated by mito-nuclear interactions following mitochondrial replacement in humans, such as mitochondrial genetic matching between donor and recipient. Our results also suggest that further research into the molecular nature of mito-nuclear interactions would be beneficial in refining the clinical application of mitochondrial replacement, and in establishing what degree of variation between donor and patient mitochondrial DNA haplotypes is acceptable to ensure 'haplotype matching'.
Collapse
Affiliation(s)
- Ralph Dobler
- Applied Zoology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Edward H Morrow
- Evolution, Behaviour and Environment Group, School of Life Sciences, University of Sussex, Brighton, UK
| | - Klaus Reinhardt
- Applied Zoology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, Germany
| |
Collapse
|
49
|
Palozzi JM, Jeedigunta SP, Hurd TR. Mitochondrial DNA Purifying Selection in Mammals and Invertebrates. J Mol Biol 2018; 430:4834-4848. [DOI: 10.1016/j.jmb.2018.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/20/2018] [Accepted: 10/25/2018] [Indexed: 01/19/2023]
|
50
|
Koch RE, Phillips JM, Camus MF, Dowling DK. Maternal age effects on fecundity and offspring egg-to-adult viability are not affected by mitochondrial haplotype. Ecol Evol 2018; 8:10722-10732. [PMID: 30519401 PMCID: PMC6262919 DOI: 10.1002/ece3.4516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 01/07/2023] Open
Abstract
While numerous studies have demonstrated that mitochondrial genetic variation can shape organismal phenotype, the level of contribution the mitochondrial genotype makes to life-history phenotype across the life course remains unknown. Furthermore, a clear technical bias has emerged in studies of mitochondrial effects on reproduction, with many studies conducted on males, but few on females. Here, we apply a classic prediction of the evolutionary theory of aging to the mitochondrial genome, predicting the declining force of natural selection with age will have facilitated the accumulation of mtDNA mutations that confer late-life effects on female reproductive performance. This should lead to increased levels of mitochondrial genetic variation on reproduction at later-life stages. We tested this hypothesis using thirteen strains of Drosophila melanogaster that each possessed a different mitochondrial haplotype in an otherwise standard nuclear genetic background. We measured fecundity and egg-to-adult viability of females over five different age classes ranging from early to late life and quantified the survival of females throughout this time period. We found no significant variation across mitochondrial haplotypes for the reproductive traits, and no mitochondrial effect on the slope of decline in these traits with increasing age. However, we observed that flies that died earlier in the experiment experienced steeper declines in the reproductive traits prior to death, and we also identified maternal and grandparental age effects on the measured traits. These results suggest the mitochondrial variation does not make a key contribution to shaping the reproductive performance of females.
Collapse
Affiliation(s)
- Rebecca E. Koch
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - James M. Phillips
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| | - M. Florencia Camus
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
- Department of Genetics, Evolution and EnvironmentUniversity CollegeLondonUK
| | - Damian K. Dowling
- School of Biological SciencesMonash UniversityClaytonVictoriaAustralia
| |
Collapse
|