1
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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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2
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Aanen DK, van ’t Padje A, Auxier B. Longevity of Fungal Mycelia and Nuclear Quality Checks: a New Hypothesis for the Role of Clamp Connections in Dikaryons. Microbiol Mol Biol Rev 2023; 87:e0002221. [PMID: 37409939 PMCID: PMC10521366 DOI: 10.1128/mmbr.00022-21] [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] [Indexed: 07/07/2023] Open
Abstract
This paper addresses the stability of mycelial growth in fungi and differences between ascomycetes and basidiomycetes. Starting with general evolutionary theories of multicellularity and the role of sex, we then discuss individuality in fungi. Recent research has demonstrated the deleterious consequences of nucleus-level selection in fungal mycelia, favoring cheaters with a nucleus-level benefit during spore formation but a negative effect on mycelium-level fitness. Cheaters appear to generally be loss-of-fusion (LOF) mutants, with a higher propensity to form aerial hyphae developing into asexual spores. Since LOF mutants rely on heterokaryosis with wild-type nuclei, we argue that regular single-spore bottlenecks can efficiently select against such cheater mutants. We then zoom in on ecological differences between ascomycetes being typically fast-growing but short-lived with frequent asexual-spore bottlenecks and basidiomycetes being generally slow-growing but long-lived and usually without asexual-spore bottlenecks. We argue that these life history differences have coevolved with stricter nuclear quality checks in basidiomycetes. Specifically, we propose a new function for clamp connections, structures formed during the sexual stage in ascomycetes and basidiomycetes but during somatic growth only in basidiomycete dikaryons. During dikaryon cell division, the two haploid nuclei temporarily enter a monokaryotic phase, by alternatingly entering a retrograde-growing clamp cell, which subsequently fuses with the subapical cell to recover the dikaryotic cell. We hypothesize that clamp connections act as screening devices for nuclear quality, with both nuclei continuously testing each other for fusion ability, a test that LOF mutants will fail. By linking differences in longevity of the mycelial phase to ecology and stringency of nuclear quality checks, we propose that mycelia have a constant and low lifetime cheating risk, irrespective of their size and longevity.
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Affiliation(s)
- Duur K. Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Anouk van ’t Padje
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Benjamin Auxier
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
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3
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Scott TJ, Larsen TJ, Brock DA, Uhm SYS, Queller DC, Strassmann JE. Symbiotic bacteria, immune-like sentinel cells, and the response to pathogens in a social amoeba. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230727. [PMID: 37593719 PMCID: PMC10427822 DOI: 10.1098/rsos.230727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023]
Abstract
Some endosymbionts living within a host must modulate their hosts' immune systems in order to infect and persist. We studied the effect of a bacterial endosymbiont on a facultatively multicellular social amoeba host. Aggregates of the amoeba Dictyostelium discoideum contain a subpopulation of sentinel cells that function akin to the immune systems of more conventional multicellular organisms. Sentinel cells sequester and discard toxins from D. discoideum aggregates and may play a central role in defence against pathogens. We measured the number and functionality of sentinel cells in aggregates of D. discoideum infected by bacterial endosymbionts in the genus Paraburkholderia. Infected D. discoideum produced fewer and less functional sentinel cells, suggesting that Paraburkholderia may interfere with its host's immune system. Despite impaired sentinel cells, however, infected D. discoideum were less sensitive to ethidium bromide toxicity, suggesting that Paraburkholderia may also have a protective effect on its host. By contrast, D. discoideum infected by Paraburkholderia did not show differences in their sensitivity to two non-symbiotic pathogens. Our results expand previous work on yet another aspect of the complicated relationship between D. discoideum and Paraburkholderia, which has considerable potential as a model for the study of symbiosis.
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Affiliation(s)
- Trey J. Scott
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tyler J. Larsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Debra A. Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - So Yeon Stacey Uhm
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David C. Queller
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joan E. Strassmann
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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4
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Al Amir Dache Z, Thierry AR. Mitochondria-derived cell-to-cell communication. Cell Rep 2023; 42:112728. [PMID: 37440408 DOI: 10.1016/j.celrep.2023.112728] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 02/21/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
In addition to their intracellular mobility, mitochondria and their components can exist outside the cells from which they originate. As a result, they are capable of acting on non-parental distant cells and mediate intercellular communication in physiological conditions and in a variety of pathologies. It has recently been demonstrated that this horizontal transfer governs a wide range of biological processes, such as tissue homeostasis, the rescue of injured recipient cells, and tumorigenesis. In addition, due to mitochondria's bacterial ancestry, they and their components can be recognized as damage-associated molecular patterns (DAMPs) by the immune cells, leading to inflammation. Here, we provide an overview of the most current and significant findings concerning the different structures of extracellular mitochondria and their by-products and their functions in the physiological and pathological context. This account illustrates the ongoing expansion of our understanding of mitochondria's biological role and functions in mammalian organisms.
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Affiliation(s)
- Zahra Al Amir Dache
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France; INSERM U1316, CNRS UMR7057, Université Paris Cité, Paris, France
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France; ICM, Institut Régional du Cancer de Montpellier, 34298 Montpellier, France.
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5
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Radzvilavicius A. Beyond the "selfish mitochondrion" theory of uniparental inheritance: A unified theory based on mutational variance redistribution. Bioessays 2021; 43:e2100009. [PMID: 33729620 DOI: 10.1002/bies.202100009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/08/2022]
Abstract
"Selfish" gene theories have offered invaluable insight into eukaryotic genome evolution, but they can also be misleading. The "selfish mitochondrion" hypothesis, developed in the 90s explained uniparental organelle inheritance as a mechanism of conflict resolution, improving cooperation between genetically distinct compartments of the cell. But modern population genetic models provided a more general explanation for uniparental inheritance based on mutational variance redistribution, modulating the efficiency of both purifying and adaptive selection. Nevertheless, as reviewed here, "selfish" conflict theories still dominate the literature. While these hypotheses are rich in metaphor and highly intuitive, selective focus on only one type of mitochondrial mutation limits the generality of our understanding and hinders progress in mito-nuclear evolution theory. Recognizing that uniparental inheritance may have evolved-and is maintained across the eukaryotic tree of life-because of its influence on mutational variance and improved selection will only increase the generality of our evolutionary reasoning, retaining "selfish" conflict explanations as a special case of a much broader theory.
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Affiliation(s)
- Arunas Radzvilavicius
- Department of Philosophy and Charles Perkins Centre, University of Sydney, New South Wales, Australia
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6
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Liu H, Wang J, Wang D, Kong M, Ning C, Zhang X, Xiao J, Zhang X, Liu J, Zhao X. Cybrid Model Supports Mitochondrial Genetic Effect on Pig Litter Size. Front Genet 2020; 11:579382. [PMID: 33384712 PMCID: PMC7770168 DOI: 10.3389/fgene.2020.579382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/23/2020] [Indexed: 11/13/2022] Open
Abstract
In pigs, mitochondrial DNA (mtDNA) polymorphism and the correlation to reproductive performance across breeds and individuals have been largely reported, however, experimental proof has never been provided. In this study, we analyzed 807 sows for correlation of total number born (TNB) and mitotype, which presented the maximum of 1.73 piglets for mtDNA contribution. Cybrid models representing different mitotypes were generated for identification of the mtDNA effect. Results indicated significant differences on cellular and molecular characteristics among cybrids, including energy metabolic traits, mtDNA copy numbers and transcriptions, mRNA and protein expressions on mitochondrial biogenesis genes and reproduction-related genes. Referring to mitotypes, the cybrids with prolific mitotypes presented significantly higher oxygen consumption rate (OCR) productions, mtDNA transcriptions and copy numbers than those with common mitotypes, while both mRNA and protein expressions of PPARA, TFAM, ER1, ER2, and ESRRG in prolific cybrids were significantly higher than those with common mitotypes. Cybrid models reflected the mtDNA effect on pig litter size, suggesting the potential application of mtDNA polymorphism in pig selection and breeding practices.
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Affiliation(s)
- Hao Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, China
| | - Dan Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Minghua Kong
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chao Ning
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Xing Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
| | - Jinlong Xiao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
| | - Xin Zhang
- Wenshang Professor Workstation of China Agricultural University, Jining, China.,Jining Animal Husbandry Station, Jining, China
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xingbo Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Wenshang Professor Workstation of China Agricultural University, Jining, China
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7
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Karakaidos P, Rampias T. Mitonuclear Interactions in the Maintenance of Mitochondrial Integrity. Life (Basel) 2020; 10:life10090173. [PMID: 32878185 PMCID: PMC7555762 DOI: 10.3390/life10090173] [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: 08/03/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022] Open
Abstract
In eukaryotic cells, mitochondria originated in an α-proteobacterial endosymbiont. Although these organelles harbor their own genome, the large majority of genes, originally encoded in the endosymbiont, were either lost or transferred to the nucleus. As a consequence, mitochondria have become semi-autonomous and most of their processes require the import of nuclear-encoded components to be functional. Therefore, the mitochondrial-specific translation has evolved to be coordinated by mitonuclear interactions to respond to the energetic demands of the cell, acquiring unique and mosaic features. However, mitochondrial-DNA-encoded genes are essential for the assembly of the respiratory chain complexes. Impaired mitochondrial function due to oxidative damage and mutations has been associated with numerous human pathologies, the aging process, and cancer. In this review, we highlight the unique features of mitochondrial protein synthesis and provide a comprehensive insight into the mitonuclear crosstalk and its co-evolution, as well as the vulnerabilities of the animal mitochondrial genome.
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8
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Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer. Nat Commun 2020; 11:3059. [PMID: 32546718 PMCID: PMC7297733 DOI: 10.1038/s41467-020-16765-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/26/2020] [Indexed: 01/27/2023] Open
Abstract
Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for 'selfish' traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby 'selfish' positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells.
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9
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Chiaratti MR, Macabelli CH, Augusto Neto JD, Grejo MP, Pandey AK, Perecin F, Collado MD. Maternal transmission of mitochondrial diseases. Genet Mol Biol 2020; 43:e20190095. [PMID: 32141474 PMCID: PMC7197987 DOI: 10.1590/1678-4685-gmb-2019-0095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022] Open
Abstract
Given the major role of the mitochondrion in cellular homeostasis, dysfunctions of this organelle may lead to several common diseases in humans. Among these, maternal diseases linked to mitochondrial DNA (mtDNA) mutations are of special interest due to the unclear pattern of mitochondrial inheritance. Multiple copies of mtDNA are present in a cell, each encoding for 37 genes essential for mitochondrial function. In cases of mtDNA mutations, mitochondrial malfunctioning relies on mutation load, as mutant and wild-type molecules may co-exist within the cell. Since the mutation load associated with disease manifestation varies for different mutations and tissues, it is hard to predict the progeny phenotype based on mutation load in the progenitor. In addition, poorly understood mechanisms act in the female germline to prevent the accumulation of deleterious mtDNA in the following generations. In this review, we outline basic aspects of mitochondrial inheritance in mammals and how they may lead to maternally-inherited diseases. Furthermore, we discuss potential therapeutic strategies for these diseases, which may be used in the future to prevent their transmission.
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Affiliation(s)
- Marcos R Chiaratti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Carolina H Macabelli
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - José Djaci Augusto Neto
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Mateus Priolo Grejo
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Anand Kumar Pandey
- Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Felipe Perecin
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Morfofisiologia Molecular e Desenvolvimento, Pirassununga, SP, Brazil
| | - Maite Del Collado
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Morfofisiologia Molecular e Desenvolvimento, Pirassununga, SP, Brazil
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10
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Ghiselli F, Milani L. Linking the mitochondrial genotype to phenotype: a complex endeavour. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190169. [PMID: 31787041 DOI: 10.1098/rstb.2019.0169] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Finding causal links between genotype and phenotype is a major issue in biology, even more in mitochondrial biology. First of all, mitochondria form complex networks, undergoing fission and fusion and we do not know how such dynamics influence the distribution of mtDNA variants across the mitochondrial network and how they affect the phenotype. Second, the non-Mendelian inheritance of mitochondrial genes can have sex-specific effects and the mechanism of mitochondrial inheritance is still poorly understood, so it is not clear how selection and/or drift act on mtDNA genetic variation in each generation. Third, we still do not know how mtDNA expression is regulated; there is growing evidence for a convoluted mechanism that includes RNA editing, mRNA stability/turnover, post-transcriptional and post-translational modifications. Fourth, mitochondrial activity differs across species as a result of several interacting processes such as drift, adaptation, genotype-by-environment interactions, mitonuclear coevolution and epistasis. This issue will cover several aspects of mitochondrial biology along the path from genotype to phenotype, and it is subdivided into four sections focusing on mitochondrial genetic variation, on the relationship among mitochondria, germ line and sex, on the role of mitochondria in adaptation and phenotypic plasticity, and on some future perspectives in mitochondrial research. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy
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11
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Al Khatib I, Shutt TE. Advances Towards Therapeutic Approaches for mtDNA Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:217-246. [PMID: 31452143 DOI: 10.1007/978-981-13-8367-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondria maintain and express their own genome, referred to as mtDNA, which is required for proper mitochondrial function. While mutations in mtDNA can cause a heterogeneous array of disease phenotypes, there is currently no cure for this collection of diseases. Here, we will cover characteristics of the mitochondrial genome important for understanding the pathology associated with mtDNA mutations, and review recent approaches that are being developed to treat and prevent mtDNA disease. First, we will discuss mitochondrial replacement therapy (MRT), where mitochondria from a healthy donor replace maternal mitochondria harbouring mutant mtDNA. In addition to ethical concerns surrounding this procedure, MRT is only applicable in cases where the mother is known or suspected to carry mtDNA mutations. Thus, there remains a need for other strategies to treat patients with mtDNA disease. To this end, we will also discuss several alternative means to reduce the amount of mutant mtDNA present in cells. Such methods, referred to as heteroplasmy shifting, have proven successful in animal models. In particular, we will focus on the approach of targeting engineered endonucleases to specifically cleave mutant mtDNA. Together, these approaches offer hope to prevent the transmission of mtDNA disease and potentially reduce the impact of mtDNA mutations.
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Affiliation(s)
- Iman Al Khatib
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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12
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Iannello M, Puccio G, Piccinini G, Passamonti M, Ghiselli F. The dynamics of mito-nuclear coevolution: A perspective from bivalve species with two different mechanisms of mitochondrial inheritance. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Guglielmo Puccio
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Marco Passamonti
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences; University of Bologna; Bologna Italy
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13
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Chiaratti MR, Garcia BM, Carvalho KF, Macabelli CH, Ribeiro FKDS, Zangirolamo AF, Sarapião FD, Seneda MM, Meirelles FV, Guimarães FEG, Machado TS. Oocyte mitochondria: role on fertility and disease transmission. Anim Reprod 2018; 15:231-238. [PMID: 34178146 PMCID: PMC8202466 DOI: 10.21451/1984-3143-ar2018-0069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oocyte mitochondria are increased in number, smaller, and rounder in appearance than mitochondria in somatic cells. Moreover, mitochondrial numbers and activity are narrowly tied with oocyte quality because of the key role of mitochondria to oocyte maturation. During oocyte maturation, mitochondria display great mobility and cluster at specific sites to meet the high energy demand. Conversely, oocyte mitochondria are not required during early oogenesis as coupling with granulosa cells is sufficient to support gamete's needs. In part, this might be explained by the importance of protecting mitochondria from oxidative damage that result in mutations in mitochondrial DNA (mtDNA). Considering mitochondria are transmitted exclusively by the mother, oocytes with mtDNA mutations may lead to diseases in offspring. Thus, to counterbalance mutation expansion, the oocyte has developed specific mechanisms to filter out deleterious mtDNA molecules. Herein, we discuss the role of mitochondria on oocyte developmental potential and recent evidence supporting a purifying filter against deleterious mtDNA mutations in oocytes.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Bruna M Garcia
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Karen F Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Carolina H Macabelli
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | | | | | | | - Flávio V Meirelles
- Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil.,Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, SP, Brazil
| | | | - Thiago S Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.,Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
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14
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Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W, Burton RS. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat Ecol Evol 2018; 2:1250-1257. [DOI: 10.1038/s41559-018-0588-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
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15
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Chiaratti MR, Garcia BM, Carvalho KF, Machado TS, Ribeiro FKDS, Macabelli CH. The role of mitochondria in the female germline: Implications to fertility and inheritance of mitochondrial diseases. Cell Biol Int 2018; 42:711-724. [PMID: 29418047 DOI: 10.1002/cbin.10947] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/03/2018] [Indexed: 12/21/2022]
Abstract
Mitochondria play a fundamental role during development of the female germline. They are fragmented, round, and small. Despite these characteristics suggesting that they are inactive, there is accumulating evidence that mitochondrial dysfunctions are a major cause of infertility and generation of aneuploidies in humans. In addition, mitochondria and their own genomes (mitochondrial DNA-mtDNA) may become damaged with time, which might be one reason why aging leads to infertility. As a result, mitochondria have been proposed as an important target for evaluating oocyte and embryo quality, and developing treatments for female infertility. On the other hand, mutations in mtDNA may cause mitochondrial dysfunctions, leading to severe diseases that affect 1 in 4,300 people. Moreover, very low levels of mutated mtDNA seem to be present in every person worldwide. These may increase with time and associate with late-onset degenerative diseases such as Parkinson disease, Alzheimer disease, and common cancers. Mutations in mtDNA are transmitted down the maternal lineage, following a poorly understood pattern of inheritance. Recent findings have indicated existence in the female germline of a purifying filter against deleterious mtDNA variants. Although the underlying mechanism of this filter is largely unknown, it has been suggested to rely on autophagic degradation of dysfunctional mitochondria or selective replication/transmission of non-deleterious variants. Thus, understanding the mechanisms regulating mitochondrial inheritance is important both to improve diagnosis and develop therapeutic tools for preventing transmission of mtDNA-encoded diseases.
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Affiliation(s)
- Marcos Roberto Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil.,Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, 05508-270, Brazil
| | - Bruna Martins Garcia
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Karen Freire Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Thiago Simões Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil.,Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, 05508-270, Brazil
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16
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Konrad A, Thompson O, Waterston RH, Moerman DG, Keightley PD, Bergthorsson U, Katju V. Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size. Mol Biol Evol 2017; 34:1319-1334. [PMID: 28087770 DOI: 10.1093/molbev/msx051] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication.
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Affiliation(s)
- Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Owen Thompson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Donald G Moerman
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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17
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Rongvaux A. Innate immunity and tolerance toward mitochondria. Mitochondrion 2017; 41:14-20. [PMID: 29054471 DOI: 10.1016/j.mito.2017.10.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 01/19/2023]
Abstract
Mitochondria are intracellular organelles that originate from a bacterial symbiont, and they retain multiple features of this bacterial ancestry. The immune system evolved to detect the presence of invading pathogens, including bacteria, to eliminate them by a diversity of antimicrobial mechanisms and to mount long-term protective immunity. Due to their bacterial ancestry, mitochondria are sensed by the innate immune system, and trigger inflammatory responses comparable to those induced by pathogenic bacteria. In both cases, innate sensing mechanisms involve Toll-Like Receptors, Formyl Peptide Receptors, inflammasomes or the cGAS/STING pathway. Stressed mitochondria release mitochondrial molecules, such as cardiolipin and mitochondrial DNA, which are sensed as cellular damage potentially caused by infections. Recent research has identified several conditions in which mitochondrial stress-induced immunity is essential to effective antimicrobial defenses. But, in pathological conditions, the abnormal activation of the innate immune system by damaged mitochondria results in auto-inflammatory or autoimmune diseases. To prevent undesirable mitochondria-targeted responses, immune tolerance toward mitochondria must be established, involving regulation of mitophagy and mitochondrial permeability, as well as activation of specific nucleases and pro-apoptotic caspases. Overall, recent findings identify mitochondria as central in the induction of innate immunity, and provide new insights as to how immune responses to these multi-functional organelles might be exploited therapeutically in various disease states.
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Affiliation(s)
- Anthony Rongvaux
- Fred Hutchinson Cancer Research Center, Program in Immunology, Clinical Research Division, Seattle, WA 98109, United States; University of Washington School of Medicine, Department of Immunology, Seattle, WA 98109, United States.
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18
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Pawłowska E, Szczepanska J, Blasiak J. DNA2-An Important Player in DNA Damage Response or Just Another DNA Maintenance Protein? Int J Mol Sci 2017; 18:ijms18071562. [PMID: 28718810 PMCID: PMC5536050 DOI: 10.3390/ijms18071562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 02/01/2023] Open
Abstract
The human DNA2 (DNA replication helicase/nuclease 2) protein is expressed in both the nucleus and mitochondria, where it displays ATPase-dependent nuclease and helicase activities. DNA2 plays an important role in the removing of long flaps in DNA replication and long-patch base excision repair (LP-BER), interacting with the replication protein A (RPA) and the flap endonuclease 1 (FEN1). DNA2 can promote the restart of arrested replication fork along with Werner syndrome ATP-dependent helicase (WRN) and Bloom syndrome protein (BLM). In mitochondria, DNA2 can facilitate primer removal during strand-displacement replication. DNA2 is involved in DNA double strand (DSB) repair, in which it is complexed with BLM, RPA and MRN for DNA strand resection required for homologous recombination repair. DNA2 can be a major protein involved in the repair of complex DNA damage containing a DSB and a 5' adduct resulting from a chemical group bound to DNA 5' ends, created by ionizing radiation and several anticancer drugs, including etoposide, mitoxantrone and some anthracyclines. The role of DNA2 in telomere end maintenance and cell cycle regulation suggests its more general role in keeping genomic stability, which is impaired in cancer. Therefore DNA2 can be an attractive target in cancer therapy. This is supported by enhanced expression of DNA2 in many cancer cell lines with oncogene activation and premalignant cells. Therefore, DNA2 can be considered as a potential marker, useful in cancer therapy. DNA2, along with PARP1 inhibition, may be considered as a potential target for inducing synthetic lethality, a concept of killing tumor cells by targeting two essential genes.
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Affiliation(s)
- Elzbieta Pawłowska
- Department of Orthodontics, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
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19
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Wang J, Xiang H, Liu L, Kong M, Yin T, Zhao X. Mitochondrial haplotypes influence metabolic traits across bovine inter- and intra-species cybrids. Sci Rep 2017. [PMID: 28646188 PMCID: PMC5482896 DOI: 10.1038/s41598-017-04457-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In bovine species, mitochondrial DNA polymorphisms and their correlation to productive or reproductive performances have been widely reported across breeds and individuals. However, experimental evidence of this correlation has never been provided. In order to identify differences among bovine mtDNA haplotypes, transmitochondrial cybrids were generated, with the nucleus from MAC-T cell line, derived from a Holstein dairy cow (Bos taurus) and mitochondria from either primary cell line derived from a domestic Chinese native beef Luxi cattle breed or central Asian domestic yak (Bos grunniens). Yak primary cells illustrated a stronger metabolic capacity than that of Luxi. However, all yak cybrid parameters illustrated a drop in relative yak mtDNA compared to Luxi mtDNA, in line with a mitonuclear imbalance in yak interspecies cybrid. Luxi has 250 divergent variations relative to the mitogenome of Holsteins. In cybrids there were generally higher rates of oxygen consumption (OCR) and extracellular acidification (ECAR), and lower mRNA expression levels of nuclear-encoded mitochondrial genes, potentially reflecting active energy metabolism and cellular stress resistance. The results demonstrate that functional differences exist between bovine cybrid cells. While cybrid viability was similar between Holstein and Luxi breeds, the mitonuclear mismatch caused a marked metabolic dysfunction in cattle:yak cybrid species.
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Affiliation(s)
- Jikun Wang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Hai Xiang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Langqing Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Minghua Kong
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Tao Yin
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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20
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Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, Bhattacharya D. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ 2017; 5:e3319. [PMID: 28533967 PMCID: PMC5438590 DOI: 10.7717/peerj.3319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/15/2017] [Indexed: 11/20/2022] Open
Abstract
We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.
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Affiliation(s)
- Hollie M Putnam
- Hawai'i Institute of Marine Biology, Kaneohe, HI, United States of America.,Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States of America
| | - Diane K Adams
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States of America
| | - Ehud Zelzion
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
| | - Nicole E Wagner
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
| | - Huan Qiu
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
| | - Tali Mass
- Marine Biology Department, University of Haifa, Haifa, Israel
| | - Paul G Falkowski
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States of America.,Department of Earth and Planetary Sciences, Rutgers University, Piscataway, NJ, United States of America
| | - Ruth D Gates
- Hawai'i Institute of Marine Biology, Kaneohe, HI, United States of America
| | - Debashish Bhattacharya
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, United States of America
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21
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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22
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Khungwanmaythawee K, Sornjai W, Paemanee A, Jaratsittisin J, Fucharoen S, Svasti S, Lithanatudom P, Roytrakul S, Smith DR. Mitochondrial Changes in β0-Thalassemia/Hb E Disease. PLoS One 2016; 11:e0153831. [PMID: 27092778 PMCID: PMC4836671 DOI: 10.1371/journal.pone.0153831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/03/2016] [Indexed: 11/18/2022] Open
Abstract
The compound β°-thalassemia/Hb E hemoglobinopathy is characterized by an unusually large range of presentation from essentially asymptomatic to a severe transfusion dependent state. While a number of factors are known that moderate presentation, these factors do not account for the full spectrum of presentation. Mitochondria are subcellular organelles that are pivotal in a number of cellular processes including oxidative phosphorylation and apoptosis. A mitochondrial protein enriched proteome was determined and validated from erythroblasts from normal controls and β°-thalassemia/Hb E patients of different severities. Mitochondria were evaluated through the use of mitotracker staining, analysis of relative mitochondrial genome number and evaluation of mitochondrial gene expression in addition to assay of overall cellular redox status through the use of alamarBlue assays. Fifty differentially regulated mitochondrial proteins were identified. Mitotracker staining revealed significant differences in staining between normal control erythroblasts and those from β°-thalassemia/Hb E patients. Differences in relative mitochondria number and gene expression were seen primarily in day 10 cells. Significant differences were seen in redox status as evaluated by alamarBlue staining in newly isolated CD34+ cells. Mitochondria mediate oxidative phosphorylation and apoptosis, both of which are known to be dysregulated in differentiating erythrocytes from β°-thalassemia/Hb E patients. The evidence presented here suggest that there are inherent differences in these cells as early as the erythroid progenitor cell stage, and that maximum deficit is seen coincident with high levels of globin gene expression.
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Affiliation(s)
- Kornpat Khungwanmaythawee
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
| | - Wannapa Sornjai
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
| | - Atchara Paemanee
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Janejira Jaratsittisin
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
| | - Suthat Fucharoen
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
| | - Saovaros Svasti
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
| | - Pathrapol Lithanatudom
- Department of Biology, Faculty of Science, Chiang Mai University, 239 Huay Kaew Rd., Suthep, Muang, Chiang Mai, 50202, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Duncan R. Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya campus, 25/25 Phuttamontol Sai 4, Salaya, Nakorn Pathom, 73170, Thailand
- * E-mail: ;
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23
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Haig D. Intracellular evolution of mitochondrial DNA (mtDNA) and the tragedy of the cytoplasmic commons. Bioessays 2016; 38:549-55. [DOI: 10.1002/bies.201600003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA USA
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24
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Isakova EP, Deryabina YI, Leonovich OA, Zylkova MV, Biriukova IK. Study of the Accumulation of Rec A from Bacillus subtilis in the Mitochondria of a Recombinant Strain of the Yeast Yarovia lipolytica. APPL BIOCHEM MICRO+ 2016. [DOI: 10.1134/s0003683816020071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Wolff JN, Pichaud N, Camus MF, Côté G, Blier PU, Dowling DK. Evolutionary implications of mitochondrial genetic variation: mitochondrial genetic effects on OXPHOS respiration and mitochondrial quantity change with age and sex in fruit flies. J Evol Biol 2016; 29:736-47. [PMID: 26728607 DOI: 10.1111/jeb.12822] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/21/2015] [Accepted: 12/26/2015] [Indexed: 12/22/2022]
Abstract
The ancient acquisition of the mitochondrion into the ancestor of modern-day eukaryotes is thought to have been pivotal in facilitating the evolution of complex life. Mitochondria retain their own diminutive genome, with mitochondrial genes encoding core subunits involved in oxidative phosphorylation. Traditionally, it was assumed that there was little scope for genetic variation to accumulate and be maintained within the mitochondrial genome. However, in the past decade, mitochondrial genetic variation has been routinely tied to the expression of life-history traits such as fertility, development and longevity. To examine whether these broad-scale effects on life-history trait expression might ultimately find their root in mitochondrially mediated effects on core bioenergetic function, we measured the effects of genetic variation across twelve different mitochondrial haplotypes on respiratory capacity and mitochondrial quantity in the fruit fly, Drosophila melanogaster. We used strains of flies that differed only in their mitochondrial haplotype, and tested each sex separately at two different adult ages. Mitochondrial haplotypes affected both respiratory capacity and mitochondrial quantity. However, these effects were highly context-dependent, with the genetic effects contingent on both the sex and the age of the flies. These sex- and age-specific genetic effects are likely to resonate across the entire organismal life-history, providing insights into how mitochondrial genetic variation may contribute to sex-specific trajectories of life-history evolution.
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Affiliation(s)
- J N Wolff
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - N Pichaud
- Département de Chimie et Biochimie, Université de Moncton, Moncton, NB, Canada.,Départment de Biologie, Université du Québec de Rimouski, Rimouski, QC, Canada
| | - M F Camus
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - G Côté
- Départment de Biologie, Université du Québec de Rimouski, Rimouski, QC, Canada
| | - P U Blier
- Départment de Biologie, Université du Québec de Rimouski, Rimouski, QC, Canada
| | - D K Dowling
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
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26
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27
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Abstract
Various endogenous and environmental factors can cause mitochondrial DNA (mtDNA) damage. One of the reasons for enhanced mtDNA damage could be its proximity to the source of oxidants, and lack of histone-like protective proteins. Moreover, mitochondria contain inadequate DNA repair pathways, and, diminished DNA repair capacity may be one of the factors responsible for high mutation frequency of the mtDNA. mtDNA damage might cause impaired mitochondrial function, and, unrepaired mtDNA damage has been frequently linked with several diseases. Exploration of mitochondrial perspective of diseases might lead to a better understanding of several diseases, and will certainly open new avenues for detection, cure, and prevention of ailments.
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Affiliation(s)
- Gyanesh Singh
- School of Biotechnology and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - U C Pachouri
- School of Biotechnology and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Devika Chanu Khaidem
- School of Biotechnology and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Aman Kundu
- School of Biotechnology and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Chirag Chopra
- School of Biotechnology and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Pushplata Singh
- Department of Medicine, Punjab Institute of Medical Sciences, Jalandhar, Punjab, India
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28
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Phillips WS, Coleman-Hulbert AL, Weiss ES, Howe DK, Ping S, Wernick RI, Estes S, Denver DR. Selfish Mitochondrial DNA Proliferates and Diversifies in Small, but not Large, Experimental Populations of Caenorhabditis briggsae. Genome Biol Evol 2015; 7:2023-37. [PMID: 26108490 PMCID: PMC4524483 DOI: 10.1093/gbe/evv116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called “selfish” genetic elements will proliferate when the host effective population size (Ne) is small, but direct tests of this prediction remain few. We analyzed the evolutionary dynamics of deletion-containing mitochondrial DNA (ΔmtDNA) molecules, previously characterized as selfish elements, in six different natural strains of the nematode Caenorhabditis briggsae allowed to undergo experimental evolution in a range of population sizes (N = 1, 10, 100, and 1,000) for a maximum of 50 generations. Mitochondrial DNA (mtDNA) was analyzed for replicate lineages at each five-generation time point. Ten different ΔmtDNA molecule types were observed and characterized across generations in the experimental populations. Consistent with predictions from evolutionary theory, lab lines evolved in small-population sizes (e.g., nematode N = 1) were more susceptible to accumulation of high levels of preexisting ΔmtDNA compared with those evolved in larger populations. New ΔmtDNA elements were observed to increase in frequency and persist across time points, but almost exclusively at small population sizes. In some cases, ΔmtDNA levels decreased across generations when population size was large (nematode N = 1,000). Different natural strains of C. briggsae varied in their susceptibilities to ΔmtDNA accumulation, owing in part to preexisting compensatory mtDNA alleles in some strains that prevent deletion formation. This analysis directly demonstrates that the evolutionary trajectories of ΔmtDNA elements depend upon the population-genetic environments and molecular-genetic features of their hosts.
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Affiliation(s)
| | | | - Emily S Weiss
- Department of Integrative Biology, Oregon State University
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | - Sita Ping
- Department of Integrative Biology, Oregon State University
| | | | | | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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29
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Yeast model analysis of novel polymerase gamma variants found in patients with autosomal recessive mitochondrial disease. Hum Genet 2015; 134:951-66. [PMID: 26077851 PMCID: PMC4529462 DOI: 10.1007/s00439-015-1578-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022]
Abstract
Replication of the mitochondrial genome depends on the single DNA polymerase (pol gamma). Mutations in the POLG gene, encoding the catalytic subunit of the human polymerase gamma, have been linked to a wide variety of mitochondrial disorders that show remarkable heterogeneity, with more than 200 sequence variants, often very rare, found in patients. The pathogenicity and dominance status of many such mutations remain, however, unclear. Remarkable structural and functional conservation of human POLG and its S. cerevisiae ortholog (Mip1p) led to the development of many successful yeast models, enabling to study the phenotype of putative pathogenic mutations. In a group of patients with suspicion of mitochondrial pathology, we identified five novel POLG sequence variants, four of which (p.Arg869Ter, p.Gln968Glu, p.Thr1053Argfs*6, and p.Val1106Ala), together with one previously known but uncharacterised variant (p.Arg309Cys), were amenable to modelling in yeast. Familial analysis indicated causal relationship of these variants with disease, consistent with autosomal recessive inheritance. To investigate the effect of these sequence changes on mtDNA replication, we obtained the corresponding yeast mip1 alleles (Arg265Cys, Arg672Ter, Arg770Glu, Thr809Ter, and Val863Ala, respectively) and tested their effect on mitochondrial genome stability and replication fidelity. For three of them (Arg265Cys, Arg672Ter, and Thr809Ter), we observed a strong, partially dominant phenotype of a complete loss of functional mtDNA, whereas the remaining two led to partial mtDNA depletion and significant increase in point mutation frequencies. These results show good correlation with the severity of symptoms observed in patients and allow to establish these variants as pathogenic mutations.
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Isakova EP, Epova EY, Sekova VY, Trubnikova EV, Kudykina YK, Zylkova MV, Guseva MA, Deryabina YI. The engineering of a Yarrowia lipolytica yeast strain capable of homologous recombination of the mitochondrial genome. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815030096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Affiliation(s)
- Walter H. Moos
- SRI International; Menlo Park CA USA
- University of California; San Francisco CA USA
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Hough J, Ågren JA, Barrett SCH, Wright SI. Chromosomal distribution of cytonuclear genes in a dioecious plant with sex chromosomes. Genome Biol Evol 2014; 6:2439-43. [PMID: 25193309 PMCID: PMC4202333 DOI: 10.1093/gbe/evu197] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The coordination between nuclear and organellar genes is essential to many aspects of eukaryotic life, including basic metabolism, energy production, and ultimately, organismal fitness. Although nuclear genes are biparentally inherited, mitochondrial and chloroplast genes are almost exclusively maternally inherited, and this asymmetry may lead to a bias in the chromosomal distribution of nuclear genes whose products act in the mitochondria or chloroplasts. In particular, because X-linked genes have a higher probability of cotransmission with organellar genes (2/3) compared with autosomal genes (1/2), selection for coadaptation has been predicted to lead to an overrepresentation of nuclear-mitochondrial and nuclear-chloroplast genes on the X chromosome relative to autosomes. In contrast, the occurrence of sexually antagonistic organellar mutations might lead to selection for movement of cytonuclear genes from the X chromosome to autosomes to reduce male mutation load. Recent broad-scale comparative studies of N-mt distributions in animals have found evidence for these hypotheses in some species, but not others. Here, we use transcriptome sequences to conduct the first study of the chromosomal distribution of cytonuclear interacting genes in a plant species with sex chromosomes (Rumex hastatulus; Polygonaceae). We found no evidence of under- or overrepresentation of either N-mt or N-cp genes on the X chromosome, and thus no support for either the coadaptation or the sexual-conflict hypothesis. We discuss how our results from a species with recently evolved sex chromosomes fit into an emerging picture of the evolutionary forces governing the chromosomal distribution of nuclear-mitochondrial and nuclear-chloroplast genes.
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Affiliation(s)
- Josh Hough
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - J Arvid Ågren
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
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