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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [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: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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2
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Camus MF, Inwongwan S. Mitonuclear interactions modulate nutritional preference. Biol Lett 2023; 19:20230375. [PMID: 38053364 PMCID: PMC10698477 DOI: 10.1098/rsbl.2023.0375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
In nature, organisms are faced with constant nutritional options which fuel key life-history traits. Studies have shown that species can actively make nutritional decisions based on internal and external cues. Metabolism itself is underpinned by complex genomic interactions involving components from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled. Given the complicated nature of metabolism, it is not well understood how nutritional choices are affected by mitonuclear interactions. This is under the rationale that changes in genomic interactions will affect metabolic flux and change physiological requirements. To this end we used a large Drosophila mitonuclear genetic panel, comprising nine isogenic nuclear genomes coupled to nine mitochondrial haplotypes, giving a total of 81 different mitonuclear genotypes. We use a capillary-based feeding assay to screen this panel for dietary preference between carbohydrate and protein. We find significant mitonuclear interactions modulating nutritional choices, with these epistatic interactions also being dependent on sex. Our findings support the notion that complex genomic interactions can place a constraint on metabolic flux. This work gives us deeper insights into how key metabolic interactions can have broad implications on behaviour.
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Affiliation(s)
- M. Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sahutchai Inwongwan
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Deep Technology in Beekeeping and Bee Products for Sustainable Development Goals, Chiang Mai University, Chiang Mai, Thailand
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3
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Dobson AJ, Voigt S, Kumpitsch L, Langer L, Voigt E, Ibrahim R, Dowling DK, Reinhardt K. Mitonuclear interactions shape both direct and parental effects of diet on fitness and involve a SNP in mitoribosomal 16s rRNA. PLoS Biol 2023; 21:e3002218. [PMID: 37603597 PMCID: PMC10441796 DOI: 10.1371/journal.pbio.3002218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 06/28/2023] [Indexed: 08/23/2023] Open
Abstract
Nutrition is a primary determinant of health, but responses to nutrition vary with genotype. Epistasis between mitochondrial and nuclear genomes may cause some of this variation, but which mitochondrial loci and nutrients participate in complex gene-by-gene-by-diet interactions? Furthermore, it remains unknown whether mitonuclear epistasis is involved only in the immediate responses to changes in diet, or whether mitonuclear genotype might modulate sensitivity to variation in parental nutrition, to shape intergenerational fitness responses. Here, in Drosophila melanogaster, we show that mitonuclear epistasis shapes fitness responses to variation in dietary lipids and amino acids. We also show that mitonuclear genotype modulates the parental effect of dietary lipid and amino acid variation on offspring fitness. Effect sizes for the interactions between diet, mitogenotype, and nucleogenotype were equal to or greater than the main effect of diet for some traits, suggesting that dietary impacts cannot be understood without first accounting for these interactions. Associating phenotype to mtDNA variation in a subset of populations implicated a C/T polymorphism in mt:lrRNA, which encodes the 16S rRNA of the mitochondrial ribosome. This association suggests that directionally different responses to dietary changes can result from variants on mtDNA that do not change protein coding sequence, dependent on epistatic interactions with variation in the nuclear genome.
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Affiliation(s)
- Adam J. Dobson
- School of Molecular Biosciences, University of Glasgow, Glasgow, United Kingdom
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Susanne Voigt
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Luisa Kumpitsch
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Lucas Langer
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Emmely Voigt
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Rita Ibrahim
- School of Molecular Biosciences, University of Glasgow, Glasgow, United Kingdom
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Klaus Reinhardt
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
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4
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Vila-Sanjurjo A, Mallo N, Atkins JF, Elson JL, Smith PM. Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease? Front Physiol 2023; 14:1082953. [PMID: 37457031 PMCID: PMC10349377 DOI: 10.3389/fphys.2023.1082953] [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: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 07/18/2023] Open
Abstract
Altered mito-ribosomal fidelity is an important and insufficiently understood causative agent of mitochondrial dysfunction. Its pathogenic effects are particularly well-known in the case of mitochondrially induced deafness, due to the existence of the, so called, ototoxic variants at positions 847C (m.1494C) and 908A (m.1555A) of 12S mitochondrial (mt-) rRNA. It was shown long ago that the deleterious effects of these variants could remain dormant until an external stimulus triggered their pathogenicity. Yet, the link from the fidelity defect at the mito-ribosomal level to its phenotypic manifestation remained obscure. Recent work with fidelity-impaired mito-ribosomes, carrying error-prone and hyper-accurate mutations in mito-ribosomal proteins, have started to reveal the complexities of the phenotypic manifestation of mito-ribosomal fidelity defects, leading to a new understanding of mtDNA disease. While much needs to be done to arrive to a clear picture of how defects at the level of mito-ribosomal translation eventually result in the complex patterns of disease observed in patients, the current evidence indicates that altered mito-ribosome function, even at very low levels, may become highly pathogenic. The aims of this review are three-fold. First, we compare the molecular details associated with mito-ribosomal fidelity to those of general ribosomal fidelity. Second, we gather information on the cellular and organismal phenotypes associated with defective translational fidelity in order to provide the necessary grounds for an understanding of the phenotypic manifestation of defective mito-ribosomal fidelity. Finally, the results of recent experiments directly tackling mito-ribosomal fidelity are reviewed and future paths of investigation are discussed.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - John F Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Cork, Ireland
| | - Joanna L Elson
- The Bioscience Institute, Newcastle University, Newcastle uponTyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, Scotland, United Kingdom
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5
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Dowling DK, Wolff JN. Evolutionary genetics of the mitochondrial genome: insights from Drosophila. Genetics 2023:7160843. [PMID: 37171259 DOI: 10.1093/genetics/iyad036] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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
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6
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Sarmah D, Sarkar A, Datta A, Ghosh B, Rana N, Sahu S, Gupta V, Thongire V, Chaudhary A, Vadak N, Kaur H, Raut S, Singh U, Borah A, Bhattacharya P. Cardiolipin-Mediated Alleviation of Mitochondrial Dysfunction Is a Neuroprotective Effect of Statin in Animal Model of Ischemic Stroke. ACS Chem Neurosci 2023; 14:709-724. [PMID: 36706354 DOI: 10.1021/acschemneuro.2c00645] [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: 01/28/2023] Open
Abstract
In clinical settings, the benefit of statin for stroke is debatable as regular statin users may suffer from myalgia, statin-associated myopathy (SAM), and rarely rhabdomyolysis. Studies suggest that patients on statin therapy show lesser vulnerability toward ischemic stroke and post-stroke frailty. Both pre- and post-treatment benefits of statin have been reported as evident by its neuroprotective effects in both cases. As mitochondrial dysfunction following stroke is the fulcrum for neuronal death, we hereby explore the role of statin in alleviating mitochondrial dysfunction by regulating the mitochondrial dynamics. In the present study, we intend to evaluate the role of statin in modulating cardiolipin-mediated mitochondrial functionality and further providing a therapeutic rationale for repurposing statins either as preventive or an adjunctive therapy for stroke.
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Affiliation(s)
- Deepaneeta Sarmah
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Abhishek Sarkar
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Aishika Datta
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Bijoyani Ghosh
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Nikita Rana
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Shubhrakanta Sahu
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Vishal Gupta
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Vrushali Thongire
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Antra Chaudhary
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Namrata Vadak
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Harpreet Kaur
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Swapnil Raut
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Upasna Singh
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Anupom Borah
- Cellular and Molecular Neurobiology Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, Assam 788011, India
| | - Pallab Bhattacharya
- Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, Gujarat 382355, India
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7
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Towarnicki SG, Youngson NA, Corley SM, St. John JC, Melvin RG, Turner N, Morris MJ, Ballard JWO. Ancestral dietary change alters the development of Drosophila larvae through MAPK signalling. Fly (Austin) 2022; 16:299-311. [PMID: 35765944 PMCID: PMC9354765 DOI: 10.1080/19336934.2022.2088032] [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] [Indexed: 01/05/2023] Open
Abstract
Studies in a broad range of animal species have revealed phenotypes that are caused by ancestral life experiences, including stress and diet. Ancestral dietary macronutrient composition and quantity (over- and under-nutrition) have been shown to alter descendent growth, metabolism and behaviour. Molecules have been identified in gametes that are changed by ancestral diet and are required for transgenerational effects. However, there is less understanding of the developmental pathways altered by inherited molecules during the period between fertilization and adulthood. To investigate this non-genetic inheritance, we exposed great grand-parental and grand-parental generations to defined protein to carbohydrate (P:C) dietary ratios. Descendent developmental timing was consistently faster in the period between the embryonic and pupal stages when ancestors had a higher P:C ratio diet. Transcriptional analysis revealed extensive and long-lasting changes to the MAPK signalling pathway, which controls growth rate through the regulation of ribosomal RNA transcription. Pharmacological inhibition of both MAPK and rRNA pathways recapitulated the ancestral diet-induced developmental changes. This work provides insight into non-genetic inheritance between fertilization and adulthood.
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Affiliation(s)
- Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Neil A. Youngson
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia,The Institute of Hepatology, The Foundation for Liver Research, London, UK
| | - Susan M. Corley
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Jus C. St. John
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Richard G. Melvin
- Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia
| | - Nigel Turner
- The Institute of Hepatology, The Foundation for Liver Research, London, UK
| | - Margaret J. Morris
- The Institute of Hepatology, The Foundation for Liver Research, London, UK
| | - J. William O. Ballard
- Department of Environment and Genetics, La Trobe University, Melbourne, VIC, Australia,Department of Ecology, Environment and Evolution, School of Life Sciences, Victoria 3086, La Trobe University, Melbourne, VIC, Australia,CONTACT J. William O. Ballard Department of Environment and Genetics, SABE, La Trobe University, Bundoora, VIC3086, Australia
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8
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Jacobs HT, Ballard JWO. What physiological role(s) does the alternative oxidase perform in animals? BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148556. [PMID: 35367450 DOI: 10.1016/j.bbabio.2022.148556] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Although the alternative oxidase, AOX, was known to be widespread in the animal kingdom by 2004, its exact physiological role in animals remains poorly understood. Here we present what evidence has accumulated thus far, indicating that it may play a role in enabling animals to resist various kinds of stress, including toxins, abnormal oxygen or nutrient levels, protein unfolding, dessication and pathogen attack. Much of our knowledge comes from studies in model organisms, where any benefits from exogenously expressed AOX may be masked by its unregulated expression, which may itself be stressful. The further question arises as to why AOX has been lost from some major crown groups, namely vertebrates, insects and cephalopods, if it plays important roles favouring the survival of other animals. We conclude by presenting some speculative ideas addressing this question, and an outline of how it might be approached experimentally.
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Affiliation(s)
- Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - J William O Ballard
- Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
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9
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Zhan B, Shen J. Mitochondria and their potential role in acute lung injury (Review). Exp Ther Med 2022; 24:479. [PMID: 35761815 PMCID: PMC9214601 DOI: 10.3892/etm.2022.11406] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/16/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Biao Zhan
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
| | - Jie Shen
- Center of Emergency and Critical Medicine, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
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10
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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.
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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.
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11
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Pravenec M, Šilhavý J, Mlejnek P, Šimáková M, Mráček T, Pecinová A, Tauchmannová K, Hütl M, Malínská H, Kazdová L, Neckář J, Kolář F, Žurmanová J, Novotný J, Houštěk J. Conplastic strains for identification of retrograde effects of mitochondrial dna variation on cardiometabolic traits in the spontaneously hypertensive rat. Physiol Res 2021; 70:S471-S484. [DOI: 10.33549/physiolres.934740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial retrograde signaling is a pathway of communication from mitochondria to the nucleus. Recently, natural mitochondrial genome (mtDNA) polymorphisms (haplogroups) received increasing attention in the pathophysiology of human common diseases. However, retrograde effects of mtDNA variants on such traits are difficult to study in humans. The conplastic strains represent key animal models to elucidate regulatory roles of mtDNA haplogroups on defined nuclear genome background. To analyze the relationship between mtDNA variants and cardiometabolic traits, we derived a set of rat conplastic strains (SHR-mtBN, SHR-mtF344 and SHR-mtLEW), harboring all major mtDNA haplotypes present in common inbred strains on the nuclear background of the spontaneously hypertensive rat (SHR). The BN, F344 and LEW mtDNA differ from the SHR in multiple amino acid substitutions in protein coding genes and also in variants of tRNA and rRNA genes. Different mtDNA haplotypes were found to predispose to various sets of cardiometabolic phenotypes which provided evidence for significant retrograde effects of mtDNA in the SHR. In the future, these animals could be used to decipher individual biochemical components involved in the retrograde signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - J Houštěk
- Institute of Physiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic. ,
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12
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Klink GV, O'Keefe H, Gogna A, Bazykin GA, Elson JL. A broad comparative genomics approach to understanding the pathogenicity of Complex I mutations. Sci Rep 2021; 11:19578. [PMID: 34599203 PMCID: PMC8486755 DOI: 10.1038/s41598-021-98360-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Disease caused by mutations of mitochondrial DNA (mtDNA) are highly variable in both presentation and penetrance. Over the last 30 years, clinical recognition of this group of diseases has increased. It has been suggested that haplogroup background could influence the penetrance and presentation of disease-causing mutations; however, to date there is only one well-established example of such an effect: the increased penetrance of two Complex I Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducts the most extensive investigation to date into the importance of haplogroup context in the pathogenicity of mtDNA mutations in Complex I. We searched for proven human point mutations across more than 900 metazoans finding human disease-causing mutations and potential masking variants. We found more than a half of human pathogenic variants as compensated pathogenic deviations (CPD) in at least in one animal species from our multiple sequence alignments. Some variants were found in many species, and some were even the most prevalent amino acids across our dataset. Variants were also found in other primates, and in such cases, we looked for non-human amino acids in sites with high probability to interact with the CPD in folded protein. Using this "local interactions" approach allowed us to find potential masking substitutions in other amino acid sites. We suggest that the masking variants might arise in humans, resulting in variability of mutation effect in our species.
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Affiliation(s)
- Galya V Klink
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Hannah O'Keefe
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amrita Gogna
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Georgii A Bazykin
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation.
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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13
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Fenton A, Camus MF, Hurst GDD. Positive selection on mitochondria may eliminate heritable microbes from arthropod populations. Proc Biol Sci 2021; 288:20211735. [PMID: 34583583 PMCID: PMC8488761 DOI: 10.1098/rspb.2021.1735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Diverse eukaryotic taxa carry facultative heritable symbionts, microbes that are passed from mother to offspring. These symbionts are coinherited with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria, but with currently unknown consequences for symbiont evolution. We therefore employed a population genetic mean field framework to model the impact of selection on mitochondrial DNA (mtDNA) upon symbiont frequency for three generic scenarios of host–symbiont interaction. Our models predict that direct selection on mtDNA can drive symbionts out of the population where a positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, by contrast, the positively selected mtDNA mutation occurs in a symbiont-infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. We conclude that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA.
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Affiliation(s)
- Andy Fenton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - M Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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14
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Gabor CR, Kivlin SN, Hua J, Bickford N, Reiskind MOB, Wright TF. Understanding Organismal Capacity to Respond to Anthropogenic Change: Barriers and Solutions. Integr Comp Biol 2021; 61:2132-2144. [PMID: 34279616 DOI: 10.1093/icb/icab162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/15/2021] [Accepted: 07/13/2021] [Indexed: 11/14/2022] Open
Abstract
Global environmental changes induced by human activities are forcing organisms to respond at an unprecedented pace. At present we have only a limited understanding of why some species possess the capacity to respond to these changes while others do not. We introduce the concept of multidimensional phenospace as an organizing construct to understanding organismal evolutionary responses to environmental change. We then describe five barriers that currently challenge our ability to understand these responses: 1) Understanding the parameters of environmental change and their fitness effects, 2) Mapping and integrating phenotypic and genotypic variation, 3) Understanding whether changes in phenospace are heritable, 4) Predicting consistency of genotype to phenotype patterns across space and time, and 5) Determining which traits should be prioritized to understand organismal response to environmental change. For each we suggest one or more solutions that would help us surmount the barrier and improve our ability to predict, and eventually manipulate, organismal capacity to respond to anthropogenic change. Additionally, we provide examples of target species that could be useful to examine interactions between phenotypic plasticity and adaptive evolution in changing phenospace.
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Affiliation(s)
- Caitlin R Gabor
- Department of Biology, Population and Conservation Biology Group, Texas State University, San Marcos, TX, 78666, USA.,The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, 78666, USA
| | - Stephanie N Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN, 37996, USA
| | - Jessica Hua
- Biological Sciences Department, Binghamton University (SUNY), Binghamton, NY, 13902, USA
| | - Nate Bickford
- Biology Department, Colorado State University Pueblo, Pueblo, CO 81003, USA
| | | | - Timothy F Wright
- Biology Department, New Mexico State University, Las Cruces, NM, 88003, USA
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15
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Friesen CR, Wilson M, Rollings N, Sudyka J, Giraudeau M, Whittington CM, Olsson M. Exercise training has morph-specific effects on telomere, body condition and growth dynamics in a color-polymorphic lizard. J Exp Biol 2021; 224:jeb.242164. [PMID: 33785504 DOI: 10.1242/jeb.242164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
Abstract
Alternative reproductive tactics (ARTs) are correlated suites of sexually selected traits that are likely to impose differential physiological costs on different individuals. While moderate activity might be beneficial, animals living in the wild often work at the margins of their resources and performance limits. Individuals using ARTs may have divergent capacities for activity. When pushed beyond their respective capacities, they may experience condition loss, oxidative stress, and molecular damage that must be repaired with limited resources. We used the Australian painted dragon lizard that exhibits color polymorphism as a model to experimentally test the effect of exercise on body condition, growth, reactive oxygen species (ROS) and telomere dynamics - a potential marker of stress and aging and a correlate of longevity. For most males, ROS levels tended to be lower with greater exercise; however, males with yellow throat patches - or bibs - had higher ROS levels than non-bibbed males. At the highest level of exercise, bibbed males exhibited telomere loss, while non-bibbed males gained telomere length; the opposite pattern was observed in the no-exercise controls. Growth was positively related to food intake but negatively correlated with telomere length at the end of the experiment. Body condition was not related to food intake but was positively correlated with increases in telomere length. These results, along with our previous work, suggest that aggressive - territory holding - bibbed males suffer physiological costs that may reduce longevity compared with non-bibbed males with superior postcopulatory traits.
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Affiliation(s)
- Christopher R Friesen
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW 2522, Australia.,Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Mark Wilson
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Nicky Rollings
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Joanna Sudyka
- Institute of Environmental Sciences, Jagiellonian University, 30-060 Krakow, Poland
| | - Mathieu Giraudeau
- CREEC, UMR IRD 224-CNRS 5290-Université de Montpellier, F34394 Montpellier, France.,CREES Centre for Research on the Ecology and Evolution of Disease, 34394 Montpellier, France
| | - Camilla M Whittington
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Mats Olsson
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW 2522, Australia.,Department of Biological & Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
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16
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Carnegie L, Reuter M, Fowler K, Lane N, Camus MF. Mother's curse is pervasive across a large mitonuclear Drosophila panel. Evol Lett 2021; 5:230-239. [PMID: 34136271 PMCID: PMC8190446 DOI: 10.1002/evl3.221] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/18/2021] [Accepted: 02/11/2021] [Indexed: 01/16/2023] Open
Abstract
The maternal inheritance of mitochondrial genomes entails a sex‐specific selective sieve, whereby mutations in mitochondrial DNA can only respond to selection acting on females. In theory, this enables male‐harming mutations to accumulate in mitochondrial genomes as long as they are neutral, beneficial, or only slightly deleterious to females. Ultimately, this bias could drive the evolution of male‐specific mitochondrial mutation loads, an idea known as mother's curse. Earlier work on this hypothesis has mainly used small Drosophila panels, in which naturally sourced mitochondrial genomes were coupled to an isogenic nuclear background. The lack of nuclear genetic variation in these designs has precluded robust generalization. Here, we test the predictions of mother's curse using a large Drosophila mitonuclear genetic panel, comprising nine isogenic nuclear genomes coupled to nine mitochondrial haplotypes, giving a total of 81 different mitonuclear genotypes. Following a predictive framework, we tested the mother's curse hypothesis by screening our panel for wing size. This trait is tightly correlated with overall body size and is sexually dimorphic in Drosophila. Moreover, growth is heavily reliant on metabolism and mitochondrial function, making wing size an ideal trait for the study of the impact of mitochondrial variation. We detect high levels of mitonuclear epistasis, and more importantly, we report that mitochondrial genetic variance is larger in male than female Drosophila for eight out of the nine nuclear genetic backgrounds used. These results demonstrate that the maternal inheritance of mitochondrial DNA does indeed modulate male life history traits in a more generalisable way than previously demonstrated.
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Affiliation(s)
- Lorcan Carnegie
- Research Department of Genetics, Evolution and Environment University College London London WC1E 6BT United Kingdom
| | - Max Reuter
- Research Department of Genetics, Evolution and Environment University College London London WC1E 6BT United Kingdom
| | - Kevin Fowler
- Research Department of Genetics, Evolution and Environment University College London London WC1E 6BT United Kingdom
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment University College London London WC1E 6BT United Kingdom
| | - M Florencia Camus
- Research Department of Genetics, Evolution and Environment University College London London WC1E 6BT United Kingdom
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17
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Vila-Sanjurjo A, Smith PM, Elson JL. Heterologous Inferential Analysis (HIA) and Other Emerging Concepts: In Understanding Mitochondrial Variation In Pathogenesis: There is no More Low-Hanging Fruit. Methods Mol Biol 2021; 2277:203-245. [PMID: 34080154 DOI: 10.1007/978-1-0716-1270-5_14] [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] [Indexed: 06/12/2023]
Abstract
Here we summarize our latest efforts to elucidate the role of mtDNA variants affecting the mitochondrial translation machinery, namely variants mapping to the mt-rRNA and mt-tRNA genes. Evidence is accumulating to suggest that the cellular response to interference with mitochondrial translation is different from that occurring as a result of mutations in genes encoding OXPHOS proteins. As a result, it appears safe to state that a complete view of mitochondrial disease will not be obtained until we understand the effect of mt-rRNA and mt-tRNA variants on mitochondrial protein synthesis. Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis (HIA ) that can be used to make predictions concerning the disruptive potential of a large subset of mt-rRNA variants. We have used HIA to explore the mutational landscape of 12S and 16S mt-rRNA genes. Our HIA studies include a thorough classification of all rare variants reported in the literature as well as others obtained from studies performed in collaboration with physicians. HIA has also been used with non-mammalian mt-rRNA genes to elucidate how mitotypes influence the interaction of the individual and the environment. Regarding mt-tRNA variations, rapidly growing evidence shows that the spectrum of mutations causing mitochondrial disease might differ between the different mitochondrial haplogroups seen in human populations.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Departamento de Bioloxía, Facultade de Ciencias, Centro de Investigacións en Ciencias Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain.
| | - Paul M Smith
- Department of Paediatrics, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Joanna L Elson
- Biosciences Institute Newcastle, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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18
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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.
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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
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19
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Mitochondria, the gut microbiome and ROS. Cell Signal 2020; 75:109737. [PMID: 32810578 DOI: 10.1016/j.cellsig.2020.109737] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
In this review, we discuss the connections between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). We examine the mitochondrion as an endosymbiotic organelle that is a hub for energy production, signaling, and cell homeostasis. Maintaining a diverse gut microbiome is generally associated with organismal fitness, intestinal health and resistance to environmental stress. In contrast, gut microbiome imbalance, termed dysbiosis, is linked to a reduction in organismal well-being. ROS are essential signaling molecules but can be damaging when present in excess. Increasing ROS levels have been shown to influence human health, homeostasis of gut cells, and the gastrointestinal microbial community's biodiversity. Reciprocally, gut microbes can affect ROS levels, mitochondrial homeostasis, and host health. We propose that mechanistic understanding of the suite of bi-directional interactions between mitochondria and the gut microbiome will facilitate innovative interdisciplinary studies examining evolutionary divergence and provide novel treatments and therapeutics for disease. GLOSS: In this review, we focus on the nexus between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). Mitochondria are a cell organelle that is derived from an ancestral alpha-proteobacteria. They generate around 80% of the adenosine triphosphate that an organism needs to function and release a range of signaling molecules essential for cellular homeostasis. The gut microbiome is a suite of microorganisms that are commensal, symbiotic and pathogenic to their host. ROS are one predominant group of essential signaling molecules that can be harmful in excess. We suggest that the mitochondria- microbiome nexus is a frontier of research that has cross-disciplinary benefits in understanding genetic divergence and human well-being.
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20
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Bai Y, Carrillo JA, Li Y, He Y, Song J. Diet induced the change of mtDNA copy number and metabolism in Angus cattle. J Anim Sci Biotechnol 2020; 11:84. [PMID: 32699629 PMCID: PMC7372754 DOI: 10.1186/s40104-020-00482-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
Background Grass-fed and grain-fed Angus cattle differ in the diet regimes. However, the intricate mechanisms of different beef quality and other phenotypes induced by diet differences are still unclear. Diet affects mitochondrial function and dynamic behavior in response to changes in energy demand and supply. In this study, we examined the mtDNA copy number, mitochondria-related genes expression, and metabolic biomarkers in grass-fed and grain-fed Angus cattle. Results We found that the grass-fed group had a higher mtDNA copy number than the grain-fed group. Among different tissues, the mtDNA copy number was the highest in the liver than muscle, rumen, and spleen. Based on the transcriptome of the four tissues, a lower expression of mtDNA-encoded genes in the grass-fed group compared to the grain-fed group was discovered. For the mitochondria-related nuclear genes, however, most of them were significantly down-regulated in the muscle of the grass-fed group and up-regulated in the other three tissues. In which, COX6A2, POLG2, PPIF, DCN, and NDUFA12, involving in ATP synthesis, mitochondrial replication, transcription, and maintenance, might contribute to the alterations of mtDNA copy number and gene expression. Meanwhile, 40 and 23 metabolic biomarkers were identified in the blood and muscle of the grain-fed group compared to a grass-fed group, respectively. Integrated analysis of the altered metabolites and gene expression revealed the high expression level of MDH1 in the grain-fed group might contribute to the mitochondrial NADH oxidation and spermidine metabolism for adapting the deletion mtDNA copy number. Conclusions Overall, the study may provide further deep insight into the adaptive and regulatory modulations of the mitochondrial function in response to different feeding systems in Angus cattle.
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Affiliation(s)
- Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056038 China.,Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - José A Carrillo
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA.,Council on Dairy Cattle Breeding, Bowie, MD 20716 USA
| | - Yaokun Li
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Yanghua He
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA.,Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822 USA
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742 USA
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21
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Perez-Matos MC, Mair WB. Predicting longevity responses to dietary restriction: A stepping stone toward precision geroscience. PLoS Genet 2020; 16:e1008833. [PMID: 32644994 PMCID: PMC7347097 DOI: 10.1371/journal.pgen.1008833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Maria C. Perez-Matos
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - William B. Mair
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
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22
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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.
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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
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23
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Sukhorukov VS, Voronkova AS, Litvinova NA, Baranich TI, Illarioshkin SN. The Role of Mitochondrial DNA Individuality in the Pathogenesis of Parkinson’s Disease. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420040146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Towarnicki SG, Kok LM, Ballard JWO. Yin and Yang of mitochondrial ROS in Drosophila. JOURNAL OF INSECT PHYSIOLOGY 2020; 122:104022. [PMID: 32045573 DOI: 10.1016/j.jinsphys.2020.104022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/12/2019] [Accepted: 02/07/2020] [Indexed: 06/10/2023]
Abstract
In this study, we test the hypothesis that Drosophila larvae producing mildly elevated levels of endogenous mitochondrial reactive oxygen species (ROS) benefit in stressful environmental conditions due to the priming of antioxidant responses. Reactive oxygen species (ROS) are produced as a by-product of oxidative phosphorylation and may be elevated when mutations decrease the efficiency of ATP production. In moderation, ROS are necessary for cell signaling and organismal health, but in excess can damage DNA, proteins, and lipids. We utilize two Drosophila melanogaster strains (Dahomey and Alstonville) that share the same nuclear genetic background but differ in their mitochondrial DNA haplotypes. Previously, we reported that Dahomey larvae harboring the V161L ND4 mtDNA mutation have reduced proton pumping and higher levels of mitochondrial ROS than Alstonville larvae when they are fed a 1:2 protein: carbohydrate (P:C) diet. Here, we explore the potential for mitochondrial ROS to provide resistance to dietary stressors by feeding larvae 1:2 P:C food supplemented with ethanol or hydrogen peroxide (H2O2). When fed a diet supplemented with ethanol or H2O2, Dahomey develop more quickly than Alstonville into larger pupae, while Alstonville developed faster on the control. Dahomey larvae displayed higher antioxidant capacity than Alstonville on all diets, with mitochondrial H2O2 levels unchanged after the addition of stressors. Addition of stressors to the diet did not affect the mitochondrial functions of Dahomey larvae as measured by mitochondrial membrane potential, respiratory control ratio, or larval survival after bacterial challenge. In contrast, Alstonville larvae developed slower, had lower pupal weight, higher cytosolic H2O2, and had reduced mitochondrial functions. Further, Alstonville larvae fed the ethanol treated diet had lower survival after bacterial infection than those fed the control diet. Surprisingly, they had greater survival when fed diet with H2O2 indicating a mitotype by stressor interaction that influences the immune response. Overall, these data suggest that elevated mitochondrial ROS in Dahomey can result in greater antioxidant capacity that prevents oxidative damage from exogenous stressors and may be a conserved response to high ethanol found in rotting fruit.
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Affiliation(s)
- Samuel G Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Leanne M Kok
- Saxion University of Applied Sciences Maarten Harpertszoon Tromplaan 28, 7513 AB Enschede, The Netherlands.
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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25
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Camus MF, Moore J, Reuter M. Nutritional geometry of mitochondrial genetic effects on male fertility. Biol Lett 2020; 16:20190891. [PMID: 32097597 DOI: 10.1098/rsbl.2019.0891] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Organismal fitness is partly determined by how well the nutritional intake matches sex-specific metabolic requirements. Metabolism itself is underpinned by complex genomic interactions involving products from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled, processes vital for fuelling reproduction. Given the complicated nature of metabolism, it is not well understood how the functioning of these two genomes is modulated by nutrients. Here we use nutritional geometry techniques on Drosophila lines that only differ in their mtDNA, with the aim to understand if there is nutrient-dependent mitochondrial genetic variance for male reproduction. We first find genetic variance for diet consumption, indicating that flies are consuming different amounts of food to meet new physiological requirements. We then find an interaction between mtDNA and diet for fitness, suggesting that the mtDNA plays a role in modulating diet-dependent fitness. Our results enhance our basic understanding of nutritional health and our chimeric genomes.
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Affiliation(s)
- M F Camus
- Research Department of Genetics, Evolution and Environment, University College, Gower Street, London WC1E 6BT, UK
| | - J Moore
- Research Department of Genetics, Evolution and Environment, University College, Gower Street, London WC1E 6BT, UK
| | - M Reuter
- Research Department of Genetics, Evolution and Environment, University College, Gower Street, London WC1E 6BT, UK
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26
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Camus MF, O'Leary M, Reuter M, Lane N. Impact of mitonuclear interactions on life-history responses to diet. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190416. [PMID: 31787037 DOI: 10.1098/rstb.2019.0416] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are central to both energy metabolism and biosynthesis. Mitochondrial function could therefore influence resource allocation. Critically, mitochondrial function depends on interactions between proteins encoded by the mitochondrial and nuclear genomes. Severe incompatibilities between these genomes can have pervasive effects on both fitness and longevity. How milder deficits in mitochondrial function affect life-history trade-offs is less well understood. Here, we analyse how mitonuclear interactions affect the trade-off between fecundity and longevity in Drosophila melanogaster. We consider a panel of 10 different mitochondrial DNA haplotypes against two contrasting nuclear backgrounds (w1118 (WE) and Zim53 (ZIM)) in response to high-protein versus standard diet. We report strikingly different responses between the two nuclear backgrounds. WE females have higher fecundity and decreased longevity on high protein. ZIM females have much greater fecundity and shorter lifespan than WE flies on standard diet. High protein doubled their fecundity with no effect on longevity. Mitochondrial haplotype reflected nuclear life-history trade-offs, with a negative correlation between longevity and fecundity in WE flies and no correlation in ZIM flies. Mitonuclear interactions had substantial effects but did not reflect genetic distance between mitochondrial haplotypes. We conclude that mitonuclear interactions can have significant impact on life-history trade-offs, but their effects are not predictable by relatedness. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- M Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Michael O'Leary
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Max Reuter
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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27
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Rand DM, Mossman JA. Mitonuclear conflict and cooperation govern the integration of genotypes, phenotypes and environments. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190188. [PMID: 31787039 PMCID: PMC6939372 DOI: 10.1098/rstb.2019.0188] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mitonuclear genome is the most successful co-evolved mutualism in the history of life on Earth. The cross-talk between the mitochondrial and nuclear genomes has been shaped by conflict and cooperation for more than 1.5 billion years, yet this system has adapted to countless genomic reorganizations by each partner, and done so under changing environments that have placed dramatic biochemical and physiological pressures on evolving lineages. From putative anaerobic origins, mitochondria emerged as the defining aerobic organelle. During this transition, the two genomes resolved rules for sex determination and transmission that made uniparental inheritance the dominant, but not a universal pattern. Mitochondria are much more than energy-producing organelles and play crucial roles in nutrient and stress signalling that can alter how nuclear genes are expressed as phenotypes. All of these interactions are examples of genotype-by-environment (GxE) interactions, gene-by-gene (GxG) interactions (epistasis) or more generally context-dependent effects on the link between genotype and phenotype. We provide evidence from our own studies in Drosophila, and from those of other systems, that mitonuclear interactions—either conflicting or cooperative—are common features of GxE and GxG. We argue that mitonuclear interactions are an important model for how to better understand the pervasive context-dependent effects underlying the architecture of complex phenotypes. Future research in this area should focus on the quantitative genetic concept of effect size to place mitochondrial links to phenotype in a proper context. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
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28
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Dong W, Dobler R, Dowling DK, Moussian B. The cuticle inward barrier in Drosophila melanogaster is shaped by mitochondrial and nuclear genotypes and a sex-specific effect of diet. PeerJ 2019; 7:e7802. [PMID: 31592352 PMCID: PMC6779114 DOI: 10.7717/peerj.7802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 08/31/2019] [Indexed: 01/23/2023] Open
Abstract
An important role of the insect cuticle is to prevent wetting (i.e., permeation of water) and also to prevent penetration of potentially harmful substances. This barrier function mainly depends on the hydrophobic cuticle surface composed of lipids including cuticular hydrocarbons (CHCs). We investigated to what extent the cuticle inward barrier function depends on the genotype, comprising mitochondrial and nuclear genes in the fruit fly Drosophila melanogaster, and investigated the contribution of interactions between mitochondrial and nuclear genotypes (mito-nuclear interactions) on this function. In addition, we assessed the effects of nutrition and sex on the cuticle barrier function. Based on a dye penetration assay, we find that cuticle barrier function varies across three fly lines that were captured from geographically separated regions in three continents. Testing different combinations of mito-nuclear genotypes, we show that the inward barrier efficiency is modulated by the nuclear and mitochondrial genomes independently. We also find an interaction between diet and sex. Our findings provide new insights into the regulation of cuticle inward barrier function in nature.
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Affiliation(s)
- Wei Dong
- Institute of Applied Biology, Shanxi University, Taiyuan, China.,Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Ralph Dobler
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Bernard Moussian
- Institute of Applied Biology, Shanxi University, Taiyuan, China.,Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany.,Université Côte d'Azur, CNRS-Inserm, iBV, Parc Valrose, Nice, France
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29
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Mitochondria in the signaling pathways that control longevity and health span. Ageing Res Rev 2019; 54:100940. [PMID: 31415807 PMCID: PMC7479635 DOI: 10.1016/j.arr.2019.100940] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022]
Abstract
Genetic and pharmacological intervention studies have identified evolutionarily conserved and functionally interconnected networks of cellular energy homeostasis, nutrient-sensing, and genome damage response signaling pathways, as prominent regulators of longevity and health span in various species. Mitochondria are the primary sites of ATP production and are key players in several other important cellular processes. Mitochondrial dysfunction diminishes tissue and organ functional performance and is a commonly considered feature of the aging process. Here we review the evidence that through reciprocal and multilevel functional interactions, mitochondria are implicated in the lifespan modulation function of these pathways, which altogether constitute a highly dynamic and complex system that controls the aging process. An important characteristic of these pathways is their extensive crosstalk and apparent malleability to modification by non-invasive pharmacological, dietary, and lifestyle interventions, with promising effects on lifespan and health span in animal models and potentially also in humans.
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30
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Saari S, Kemppainen E, Tuomela T, Oliveira MT, Dufour E, Jacobs HT. Alternative oxidase confers nutritional limitation on Drosophila development. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2019; 331:341-356. [PMID: 31218852 PMCID: PMC6617715 DOI: 10.1002/jez.2274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/12/2019] [Accepted: 05/17/2019] [Indexed: 11/12/2022]
Abstract
The mitochondrial alternative oxidase, AOX, present in most eukaryotes apart from vertebrates and insects, catalyzes the direct oxidation of ubiquinol by oxygen, by‐passing the terminal proton‐motive steps of the respiratory chain. Its physiological role is not fully understood, but it is proposed to buffer stresses in the respiratory chain similar to those encountered in mitochondrial diseases in humans. Previously, we found that the ubiquitous expression of AOX from Ciona intestinalis in
Drosophila perturbs the development of flies cultured under low‐nutrient conditions (media containing only glucose and yeast). Here we tested the effects of a wide range of nutritional supplements on
Drosophila development, to gain insight into the physiological mechanism underlying this developmental failure. On low‐nutrient medium, larvae contained decreased amounts of triglycerides, lactate, and pyruvate, irrespective of AOX expression. Complex food supplements, including treacle (molasses), restored normal development to AOX‐expressing flies, but many individual additives did not. Inhibition of AOX by treacle extract was excluded as a mechanism, since the supplement did not alter the enzymatic activity of AOX in vitro. Furthermore, antibiotics did not influence the organismal phenotype, indicating that commensal microbes were not involved. Fractionation of treacle identified a water‐soluble fraction with low solubility in ethanol, rich in lactate and tricarboxylic acid cycle intermediates, which contained the critical activity. We propose that the partial activation of AOX during metamorphosis impairs the efficient use of stored metabolites, resulting in developmental failure. Drosophila expressing the alternative oxidase are unable to complete pupal development if reared on low‐nutrient medium. Additional nutrients are needed, to replace those normally manufactured cataplerotically.
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Affiliation(s)
- Sina Saari
- Faculty of Medicine and Health Technology and Tampere University Hospital, Tampere University, Tampere, Finland
| | - Esko Kemppainen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Tea Tuomela
- Faculty of Medicine and Health Technology and Tampere University Hospital, Tampere University, Tampere, Finland
| | - Marcos T Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Eric Dufour
- Faculty of Medicine and Health Technology and Tampere University Hospital, Tampere University, Tampere, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Health Technology and Tampere University Hospital, Tampere University, Tampere, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Exogenous Factors May Differentially Influence the Selective Costs of mtDNA Mutations. CELLULAR AND MOLECULAR BASIS OF MITOCHONDRIAL INHERITANCE 2019; 231:51-74. [DOI: 10.1007/102_2018_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Towarnicki SG, Ballard JWO. Mitotype Interacts With Diet to Influence Longevity, Fitness, and Mitochondrial Functions in Adult Female Drosophila. Front Genet 2018; 9:593. [PMID: 30555517 PMCID: PMC6284043 DOI: 10.3389/fgene.2018.00593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/15/2018] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and the dietary macronutrient ratio are known to influence a wide range of phenotypic traits including longevity, fitness and energy production. Commonly mtDNA mutations are posited to be selectively neutral or reduce fitness and, to date, no selectively advantageous mtDNA mutations have been experimentally demonstrated in adult female Drosophila. Here we propose that a ND V161L mutation interacted with diets differing in their macronutrient ratios to influence organismal physiology and mitochondrial traits, but further studies are required to definitively show no linked mtDNA mutations are functionally significant. We utilized two mtDNA types (mitotypes) fed either a 1:2 Protein: Carbohydrate (P:C) or 1:16 P:C diet. When fed the former diet, Dahomey females harboring the V161L mitotype lived longer than those with the Alstonville mitotype and had higher climbing, basal reactive oxygen species (ROS) and elevated glutathione S-transferase E1 expression. The short lived Alstonville females ate more, had higher walking speed and elevated mitochondrial functions as suggested by respiratory control ratio (RCR), mtDNA copy number and expression of mitochondrial transcription termination factor 3. In contrast, Dahomey females fed 1:16 P:C were shorter lived, had higher fecundity, walking speed and mitochondrial functions. They had reduced climbing. This result suggests that mtDNA cannot be assumed to be a strictly neutral evolutionary marker when the dietary macronutrient ratio of a species varies over time and space and supports the hypothesis that mtDNA diversity may reflect the amount of time since the last selective sweep rather than strictly demographic processes.
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Affiliation(s)
| | - J. William O. Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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