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Robleto-Quesada J, Umaña-Blanco F, Solano-Barquero A, Allen J, Levi T, Gori F, Schnyder M, Rojas A. Seek, and you will find: Cryptic diversity of the cardiopulmonary nematode Angiostrongylus vasorum in the Americas. Acta Trop 2024; 258:107337. [PMID: 39098751 DOI: 10.1016/j.actatropica.2024.107337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/17/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
Angiostrongylus vasorum is a metastrongylid parasite infecting wild canids and domestic dogs. Its patchy distribution, high pathogenicity and taxonomical classification makes the evolutionary history of A. vasorum intriguing and important to study. First larval stages of A. vasorum were recovered from feces of two grey foxes, Urocyon cinereoargenteus, from Costa Rica. Sequencing and phylogenetic and haplotypic analyses of the ITS2, 18S and cytochrome oxidase subunit 1 (cox1) fragments were performed. Then p- and Nei´s genetic distance, nucleotide substitution rates and species delimitation analyses were conducted with cox1 data of the specimens collected herein and other Angiostrongylus spp. Cophylogenetic congruence and coevolutionary events of Angiostrongylus spp. and their hosts were evaluated using patristic and phenetic distances and maximum parsimony reconciliations. Specimens from Costa Rica clustered in a separate branch from European and Brazilian A. vasorum sequences in the phylogenetic and haplotype network analyses using the ITS2 and cox1 data. In addition, cox1 p-distance of the sequences derived from Costa Rica were up to 8.6 % different to the ones from Europe and Brazil, a finding mirrored in Nei´s genetic distance PCoA. Species delimitation analysis supported a separate group with the sequences from Costa Rica, suggesting that these worms may represent cryptic variants of A. vasorum, a new undescribed taxon or Angiocaulus raillieti, a synonym species of A. vasorum described in Brazil. Moreover, nucleotide substitution rates in A. vasorum were up to six times higher than in the congener Angiostrongylus cantonensis. This finding and the long time elapsed since the last common ancestor between both species may explain the larger diversity in A. vasorum. Finally, cophylogenetic congruence was observed between Angiostrongylus spp. and their hosts, with cospeciation events occurring at deeper taxonomic branching of host order. Altogether, our data suggest that the diversity of the genus Angiostrongylus is larger than expected, since additional species may be circulating in wild canids from the Americas.
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Affiliation(s)
- Joby Robleto-Quesada
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica 11501-2060
| | - Fabián Umaña-Blanco
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica 11501-2060
| | - Alberto Solano-Barquero
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica 11501-2060; Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica 11501-2060
| | - Jennifer Allen
- Department of Fisheries, Wildlife and Conservation Sciences Oregon State University, Oregon, United States of America
| | - Taal Levi
- Department of Fisheries, Wildlife and Conservation Sciences Oregon State University, Oregon, United States of America
| | - Francesca Gori
- Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland
| | - Manuela Schnyder
- Institute of Parasitology, University of Zurich, Winterthurerstrasse 266a, 8057 Zurich, Switzerland
| | - Alicia Rojas
- Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José, Costa Rica 11501-2060; Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica 11501-2060.
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2
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Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
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Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
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3
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Gao AW, Alam GE, Zhu Y, Li W, Katsyuba E, Sulc J, Li TY, Li X, Overmyer KA, Lalou A, Mouchiroud L, Sleiman MB, Cornaglia M, Morel JD, Houtkooper RH, Coon JJ, Auwerx J. High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575638. [PMID: 38293129 PMCID: PMC10827074 DOI: 10.1101/2024.01.15.575638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Lifespan is influenced by complex interactions between genetic and environmental factors. Studying those factors in model organisms of a single genetic background limits their translational value for humans. Here, we mapped lifespan determinants in 85 genetically diverse C. elegans recombinant intercross advanced inbred lines (RIAILs). We assessed molecular profiles - transcriptome, proteome, and lipidome - and life-history traits, including lifespan, development, growth dynamics, and reproduction. RIAILs exhibited large variations in lifespan, which positively correlated with developmental time. Among the top candidates obtained from multi-omics data integration and QTL mapping, we validated known and novel longevity modulators, including rict-1, gfm-1 and mltn-1. We translated their relevance to humans using UK Biobank data and showed that variants in RICTOR and GFM1 are associated with an elevated risk of age-related heart disease, dementia, diabetes, kidney, and liver diseases. We organized our dataset as a resource (https://lisp-lms.shinyapps.io/RIAILs/) that allows interactive explorations for new longevity targets.
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Affiliation(s)
- Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Weisha Li
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Elena Katsyuba
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Jonathan Sulc
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Terytty Y. Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Present address: State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Metabolic Remodeling and Health, Laboratory of Longevity and Metabolic Adaptations, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
| | - Amelia Lalou
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Laurent Mouchiroud
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Matteo Cornaglia
- Nagi Bioscience SA, EPFL Innovation Park, CH-1025 Saint-Sulpice, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Joshua J. Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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4
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Flowers S, Kothari R, Torres Cleuren YN, Alcorn MR, Ewe CK, Alok G, Fiallo SL, Joshi PM, Rothman JH. Regulation of defective mitochondrial DNA accumulation and transmission in C. elegans by the programmed cell death and aging pathways. eLife 2023; 12:e79725. [PMID: 37782016 PMCID: PMC10545429 DOI: 10.7554/elife.79725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/15/2023] [Indexed: 10/03/2023] Open
Abstract
The heteroplasmic state of eukaryotic cells allows for cryptic accumulation of defective mitochondrial genomes (mtDNA). 'Purifying selection' mechanisms operate to remove such dysfunctional mtDNAs. We found that activators of programmed cell death (PCD), including the CED-3 and CSP-1 caspases, the BH3-only protein CED-13, and PCD corpse engulfment factors, are required in C. elegans to attenuate germline abundance of a 3.1-kb mtDNA deletion mutation, uaDf5, which is normally stably maintained in heteroplasmy with wildtype mtDNA. In contrast, removal of CED-4/Apaf1 or a mutation in the CED-4-interacting prodomain of CED-3, do not increase accumulation of the defective mtDNA, suggesting induction of a non-canonical germline PCD mechanism or non-apoptotic action of the CED-13/caspase axis. We also found that the abundance of germline mtDNAuaDf5 reproducibly increases with age of the mothers. This effect is transmitted to the offspring of mothers, with only partial intergenerational removal of the defective mtDNA. In mutants with elevated mtDNAuaDf5 levels, this removal is enhanced in older mothers, suggesting an age-dependent mechanism of mtDNA quality control. Indeed, we found that both steady-state and age-dependent accumulation rates of uaDf5 are markedly decreased in long-lived, and increased in short-lived, mutants. These findings reveal that regulators of both PCD and the aging program are required for germline mtDNA quality control and its intergenerational transmission.
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Affiliation(s)
- Sagen Flowers
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Rushali Kothari
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Yamila N Torres Cleuren
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
- Computational Biology Unit, Institute for Informatics, University of BergenBergenNorway
| | - Melissa R Alcorn
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Geneva Alok
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Samantha L Fiallo
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Pradeep M Joshi
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa BarbaraSanta BarbaraUnited States
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5
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Wang JY, Zhang LH, Hong YH, Cai LN, Storey KB, Zhang JY, Zhang SS, Yu DN. How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures? Animals (Basel) 2023; 13:3015. [PMID: 37835622 PMCID: PMC10571990 DOI: 10.3390/ani13193015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.
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Affiliation(s)
- Jing-Yan Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou 325000, China
| | - Yue-Huan Hong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ling-Na Cai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Sheng Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Wuyanling National Nature Reserve, Wenzhou 325500, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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6
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Estes S, Dietz ZP, Katju V, Bergthorsson U. Evolutionary codependency: insights into the mitonuclear interaction landscape from experimental and wild Caenorhabditis nematodes. Curr Opin Genet Dev 2023; 81:102081. [PMID: 37421904 DOI: 10.1016/j.gde.2023.102081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Aided by new technologies, the upsurgence of research into mitochondrial genome biology during the past 15 years suggests that we have misunderstood, and perhaps dramatically underestimated, the ongoing biological and evolutionary significance of our long-time symbiotic partner. While we have begun to scratch the surface of several topics, many questions regarding the nature of mutation and selection in the mitochondrial genome, and the nature of its relationship to the nuclear genome, remain unanswered. Although best known for their contributions to studies of developmental and aging biology, Caenorhabditis nematodes are increasingly recognized as excellent model systems to advance understanding in these areas. We review recent discoveries with relevance to mitonuclear coevolution and conflict and offer several fertile areas for future work.
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Affiliation(s)
- Suzanne Estes
- Portland State University, Department of Biology, Portland, OR, USA.
| | - Zachary P Dietz
- Portland State University, Department of Biology, Portland, OR, USA
| | - Vaishali Katju
- Uppsala University, Department of Ecology and Genetics, 752 36 Uppsala, Sweden
| | - Ulfar Bergthorsson
- Uppsala University, Department of Ecology and Genetics, 752 36 Uppsala, Sweden
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7
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Zhu Y, Li Y, Wang Y, Wang L, Shi P, Du X, Zhang Y, Song Y, Zhu Z. Mitochondrial DNA polymorphisms in COX1 affect the lifespan of Caenorhabditis elegans through nuclear gene dct-15. Gene 2022; 845:146776. [PMID: 36063972 DOI: 10.1016/j.gene.2022.146776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/28/2022] [Accepted: 07/28/2022] [Indexed: 11/04/2022]
Abstract
Mutations in the mitochondrial DNA (mtDNA) are closely related to age and age-related complex diseases, but the exact regulatory mechanism of mtDNA natural variation or polymorphism and ageing remains unclear. Recently, nuclear genes that regulate mitochondrial functions and thereby influence ageing have been widely studied. In this study, the relationship between the retrograde communication from the mitochondria to the nucleus and its ultimate effect on ageing has been elucidated. This study found that the natural variations in COX1 of the mitochondria in the Caenorhabditis elegans population do not correlate with multiple phenotypes, except for a mild correlation with lifespan. After excluding the differences in the nuclear genome, the correlation between natural mitochondrial variation and lifespan increased significantly. Moreover, mtDNA variation downregulated the nuclear dct-15 gene expression, which consequently reduced the lifespan, development rate and motility of C. elegans. dct-15 mutations decreased mitochondria copy number but increased ATP content and mitochondrial ultrastructure. Thus, the results indicated that dct-15 interacted with the mitochondrial DNA polymorphisms in COX1 and is associated with ageing. Finally, bioinformatic analyses revealed that mtDNA variation regulated the structural constituent of the cuticle via dct-15 and suggested that the structural constituent of the cuticle could have an important role in the development and ageing processes. These results provide insights into the mtDNA mechanism that can alter the nuclear gene and thereby regulate ageing and ageing-related diseases.
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Affiliation(s)
- Yao Zhu
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Ying Li
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | | | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Peng Shi
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | - Xinze Du
- The First Clinical College, Xuzhou Medical University, Xuzhou, China
| | - Yingchun Zhang
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Yuanjian Song
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China.
| | - Zuobin Zhu
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Key Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, China.
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8
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Jin WT, Guan JY, Dai XY, Wu GJ, Zhang LP, Storey KB, Zhang JY, Zheng RQ, Yu DN. Mitochondrial gene expression in different organs of Hoplobatrachus rugulosus from China and Thailand under low-temperature stress. BMC ZOOL 2022; 7:24. [PMID: 37170336 PMCID: PMC10127437 DOI: 10.1186/s40850-022-00128-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/29/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Hoplobatrachus rugulosus (Anura: Dicroglossidae) is distributed in China and Thailand and the former can survive substantially lower temperatures than the latter. The mitochondrial genomes of the two subspecies also differ: Chinese tiger frogs (CT frogs) display two identical ND5 genes whereas Thai tiger frogs (TT frogs) have two different ND5 genes. Metabolism of ectotherms is very sensitive to temperature change and different organs have different demands on energy metabolism at low temperatures. Therefore, we conducted studies to understand: (1) the differences in mitochondrial gene expression of tiger frogs from China (CT frogs) versus Thailand (TT frogs); (2) the differences in mitochondrial gene expression of tiger frogs (CT and TT frogs) under short term 24 h hypothermia exposure at 25 °C and 8 °C; (3) the differences in mitochondrial gene expression in three organs (brain, liver and kidney) of CT and TT frogs.
Results
Utilizing RT-qPCR and comparing control groups at 25 °C with low temperature groups at 8 °C, we came to the following results. (1) At the same temperature, mitochondrial gene expression was significantly different in two subspecies. The transcript levels of two identical ND5 of CT frogs were observed to decrease significantly at low temperatures (P < 0.05) whereas the two different copies of ND5 in TT frogs were not. (2) Under low temperature stress, most of the genes in the brain, liver and kidney were down-regulated (except for COI and ATP6 measured in brain and COI measured in liver of CT frogs). (3) For both CT and TT frogs, the changes in overall pattern of mitochondrial gene expression in different organs under low temperature and normal temperature was brain > liver > kidney.
Conclusions
We mainly drew the following conclusions: (1) The differences in the structure and expression of the ND5 gene between CT and TT frogs could result in the different tolerances to low temperature stress. (2) At low temperatures, the transcript levels of most of mitochondrial protein-encoding genes were down-regulated, which could have a significant effect in reducing metabolic rate and supporting long term survival at low temperatures. (3) The expression pattern of mitochondrial genes in different organs was related to mitochondrial activity and mtDNA replication in different organs.
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Bever BW, Dietz ZP, Sullins JA, Montoya AM, Bergthorsson U, Katju V, Estes S. Mitonuclear Mismatch is Associated With Increased Male Frequency, Outcrossing, and Male Sperm Size in Experimentally-Evolved C. elegans. Front Genet 2022; 13:742272. [PMID: 35360860 PMCID: PMC8961728 DOI: 10.3389/fgene.2022.742272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
We provide a partial test of the mitonuclear sex hypothesis with the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested—nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant—and confirmed for a single line set (cox-1) that increased male frequency also resulted in successful outcrossing. We previously found the same result for lines evolved from another nuclear ETC mutant, gas-1. For several lines in the current experiment, however, male frequency declined to wildtype levels (near 0%) in later generations. Male frequency did not change in lines evolved from a wildtype control strain. Additional phenotypic assays of lines evolved from the mitochondrial cox-1 mutant indicated that evolution of high male frequency was accompanied by evolution of increased male sperm size and mating success with tester females, but that it did not translate into increased mating success with coevolved hermaphrodites. Rather, hermaphrodites’ self-crossed reproductive fitness increased, consistent with sexually antagonistic coevolution. In accordance with evolutionary theory, males and sexual outcrossing may be most beneficial to populations evolving from a state of low ancestral fitness (gas-1, as previously reported) and less beneficial or deleterious to those evolving from a state of higher ancestral fitness (cox-1). In support of this idea, the obligately outcrossing fog-2 V; cox-1 M lines exhibited no fitness evolution compared to their ancestor, while facultatively outcrossing lines showed slight upward evolution of fitness, and all but one of the obligately selfing xol-1 X; cox-1 M lines evolved substantially increased fitness—even beyond wildtype levels. This work provides a foundation to directly test the effect of reproductive mode on the evolutionary dynamics of mitonuclear genomes, as well as whether compensatory mutations (nuclear or mitochondrial) can rescue populations from mitochondrial dysfunction.
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Affiliation(s)
- Brent W. Bever
- Department of Biology, Portland State University, Portland, OR, United States
| | - Zachary P. Dietz
- Department of Biology, Portland State University, Portland, OR, United States
| | - Jennifer A. Sullins
- Department of Biology, Portland State University, Portland, OR, United States
| | - Ariana M. Montoya
- Department of Biology, Portland State University, Portland, OR, United States
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR, United States
- *Correspondence: Suzanne Estes,
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10
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Gao AW, El Alam G, Lalou A, Li TY, Molenaars M, Zhu Y, Overmyer KA, Shishkova E, Hof K, Bou Sleiman M, Houtkooper RH, Coon JJ, Auwerx J. Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains. iScience 2022; 25:103734. [PMID: 35118355 PMCID: PMC8792074 DOI: 10.1016/j.isci.2022.103734] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/02/2021] [Accepted: 12/31/2021] [Indexed: 11/28/2022] Open
Abstract
The mitochondrial unfolded protein response (UPRmt) is a promising pharmacological target for aging and age-related diseases. However, the integrative analysis of the impact of UPRmt activation on different signaling layers in animals with different genetic backgrounds is lacking. Here, we applied systems approaches to investigate the effect of UPRmt induced by doxycycline (Dox) on transcriptome, proteome, and lipidome in two genetically divergent worm strains, named N2 and CB4856. From the integrated omics datasets, we found that Dox prolongs lifespan of both worm strains through shared and strain-specific mechanisms. Specifically, Dox strongly impacts mitochondria, upregulates defense response, and lipid metabolism, while decreasing triglycerides. We further validated that lipid genes acs-2/20 and fat-7/6 were required for Dox-induced UPRmt and longevity in N2 and CB4856 worms, respectively. Our data have translational value as they indicate that the beneficial effects of Dox-induced UPRmt on lifespan are consistent across different genetic backgrounds through different regulators. Dox extends lifespan of N2 and CB4856 via shared and strain-specific mechanisms Dox controls mitochondria, defense responses, and lipid metabolism in both strains Dox-mediated longevity requires acs-2/20 in N2 and fat-7/6 in CB4856 worms
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Affiliation(s)
- Arwen W. Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Amélia Lalou
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, AZ, the Netherlands
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
| | - Kevin Hof
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, AZ, the Netherlands
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53515, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Corresponding author
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11
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Repetto SA, Quarroz Braghini J, Risso MG, Argüello LB, Batalla EI, Stecher DR, Sierra MF, Burgos JM, Radisic MV, González Cappa SM, Ruybal P. Molecular typing of Strongyloides stercoralis in Latin America, the clinical connection. Parasitology 2022; 149:24-34. [PMID: 35184784 PMCID: PMC11010477 DOI: 10.1017/s0031182021001517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/06/2021] [Accepted: 08/18/2021] [Indexed: 12/31/2022]
Abstract
This study analysed Strongyloides stercoralis genetic variability based on a 404 bp region of the cox1 gene from Latin-American samples in a clinical context including epidemiological, diagnosis and follow-up variables. A prospective, descriptive, observational study was conducted to evaluate clinical and parasitological evolution after ivermectin treatment of 41 patients infected with S. stercoralis. Reactivation of the disease was defined both by clinical symptoms appearance and/or direct larvae detection 30 days after treatment or later. We described 10 haplotypes organized in two clusters. Most frequent variants were also described in the Asian continent in human (HP24 and HP93) and canine (HP24) samples. Clinical presentation (intestinal, severe, cutaneous and asymptomatic), immunological status and eosinophil count were not associated with specific haplotypes or clusters. Nevertheless, presence of cluster 1 haplotypes during diagnosis increased the risk of reactivation with an odds ratio (OR) of 7.51 [confidence interval (CI) 95% 1.38–44.29, P = 0.026]. In contrast, reactivation probability was 83 times lower if cluster 2 (I152V mutation) was detected (OR = 0.17, CI 95% 0.02–0.80, P = 0.02). This is the first analysis of S. stercoralis cox1 diversity in the clinical context. Determination of clusters during the diagnosis could facilitate and improve the design of follow-up strategies to prevent severe reactivations of this chronic disease.
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Affiliation(s)
- Silvia Analía Repetto
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
- Universidad de Buenos Aires, Hospital de Clínicas “José de San Martín”, División Infectología, Buenos Aires, Argentina
| | - Juan Quarroz Braghini
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - Marikena Guadalupe Risso
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - Lisana Belén Argüello
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - Estela Inés Batalla
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - Daniel Ricardo Stecher
- Universidad de Buenos Aires, Hospital de Clínicas “José de San Martín”, División Infectología, Buenos Aires, Argentina
| | - Mariela Fernanda Sierra
- Universidad de Buenos Aires, Hospital de Clínicas “José de San Martín”, División Infectología, Buenos Aires, Argentina
| | - Juan Miguel Burgos
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Marcelo Víctor Radisic
- División de Enfermedades Infecciosas, Instituto de Nefrología/Nephrology, Buenos Aires, Argentina
| | - Stella Maris González Cappa
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
| | - Paula Ruybal
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Microbiología, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Buenos Aires, Argentina
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12
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Weitemier K, Penaluna BE, Hauck LL, Longway LJ, Garcia T, Cronn R. Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding. Mol Ecol 2021; 30:4970-4990. [PMID: 33594756 PMCID: PMC8597136 DOI: 10.1111/mec.15811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/23/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
Genetic diversity underpins species conservation and management goals, and ultimately determines a species' ability to adapt. Using freshwater environmental DNA (eDNA) samples, we examined mitochondrial genetic diversity using multigene metabarcode sequence data from four Oncorhynchus species across 16 sites in Oregon and northern California. Our multigene metabarcode panel included targets commonly used in population genetic NADH dehydrogenase 2 (ND2), phylogenetic cytochrome c oxidase subunit 1 (COI) and eDNA (12S ribosomal DNA) screening. The ND2 locus showed the greatest within-species haplotype diversity for all species, followed by COI and then 12S rDNA for all species except Oncorhynchus kisutch. Sequences recovered for O. clarkii clarkii were either identical to, or one mutation different from, previously characterized haplotypes (95.3% and 4.5% of reads, respectively). The greatest diversity in O. c. clarkii was among coastal watersheds, and subsets of this diversity were shared with fish in inland watersheds. However, coastal streams and the Umpqua River watershed appear to harbour unique haplotypes. Sequences from O. mykiss revealed a disjunction between the Willamette watershed and southern watersheds suggesting divergent histories. We also identified similarities between populations in the northern Deschutes and southern Klamath watersheds, consistent with previously hypothesized connections between the two via inland basins. Oncorhynchus kisutch was only identified in coastal streams and the Klamath River watershed, with most diversity concentrated in the coastal Coquille watershed. Oncorhynchus tshawytscha was only observed at one site, but contained multiple haplotypes at each locus. The characterization of genetic diversity at multiple loci expands the knowledge gained from eDNA sampling and provides crucial information for conservation actions and genetic management.
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Affiliation(s)
- Kevin Weitemier
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
| | - Brooke E. Penaluna
- U.S. Department of Agriculture, Forest ServicePacific Northwest Research StationCorvallisORUSA
| | - Laura L. Hauck
- U.S. Department of Agriculture, Forest ServicePacific Northwest Research StationCorvallisORUSA
| | - Lucas J. Longway
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
| | - Tiffany Garcia
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
| | - Richard Cronn
- U.S. Department of Agriculture, Forest ServicePacific Northwest Research StationCorvallisORUSA
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13
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Awadi A, Ben Slimen H, Schaschl H, Knauer F, Suchentrunk F. Positive selection on two mitochondrial coding genes and adaptation signals in hares (genus Lepus) from China. BMC Ecol Evol 2021; 21:100. [PMID: 34039261 PMCID: PMC8157742 DOI: 10.1186/s12862-021-01832-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection. RESULTS Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of Δ vibrational entropy energy between wild and mutant type. Moreover, our PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. Our statistical models indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgression, which is not uncommon in a number of hare species. CONCLUSIONS Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.
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Affiliation(s)
- Asma Awadi
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Beja, University of Jendouba, Jendouba, Tunisia
| | - Hichem Ben Slimen
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Beja, University of Jendouba, Jendouba, Tunisia
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Felix Knauer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, 1160 Vienna, Austria
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14
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Brown JA, Sammy MJ, Ballinger SW. An evolutionary, or "Mitocentric" perspective on cellular function and disease. Redox Biol 2020; 36:101568. [PMID: 32512469 PMCID: PMC7281786 DOI: 10.1016/j.redox.2020.101568] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
The incidence of common, metabolic diseases (e.g. obesity, cardiovascular disease, diabetes) with complex genetic etiology has been steadily increasing nationally and globally. While identification of a genetic model that explains susceptibility and risk for these diseases has been pursued over several decades, no clear paradigm has yet been found to disentangle the genetic basis of polygenic/complex disease development. Since the evolution of the eukaryotic cell involved a symbiotic interaction between the antecedents of the mitochondrion and nucleus (which itself is a genetic hybrid), we suggest that this history provides a rational basis for investigating whether genetic interaction and co-evolution of these genomes still exists. We propose that both mitochondrial and Mendelian, or "mito-Mendelian" genetics play a significant role in cell function, and thus disease risk. This paradigm contemplates the natural variation and co-evolution of both mitochondrial and nuclear DNA backgrounds on multiple mitochondrial functions that are discussed herein, including energy production, cell signaling and immune response, which collectively can influence disease development. At the nexus of these processes is the economy of mitochondrial metabolism, programmed by both mitochondrial and nuclear genomes.
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Affiliation(s)
- Jamelle A Brown
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Melissa J Sammy
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Scott W Ballinger
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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15
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Zhu Z, Li Y, Liang M, Wang L, Wang L, Rizak JD, Han C, Zhang W. piRNAs Regulated by Mitochondria Variation Linked With Reproduction and Aging in Caenorhabditis elegans. Front Genet 2020; 11:190. [PMID: 32269587 PMCID: PMC7111505 DOI: 10.3389/fgene.2020.00190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/17/2020] [Indexed: 12/20/2022] Open
Abstract
In Caenorhabditis elegans, the binding of Piwi protein to a non-coding RNA form, called piRNA, has been found to be important to both reproductive and aging processes. As the biosynthesis of piRNA is modulated by mitochondrial function, it is likely that the interaction between mitochondrial function and piRNA expression plays an unknown, yet important, role in reproductive and aging processes because both processes are known to be affected by declines in mitochondrial quality and activity. While the relationship between reproduction and longevity is not characterized in full, the optimality theory of aging and the disposable soma theory suggest that a trade-off between energy and resources is needed for reproductive and aging maintenance. In this study, the influence of mitochondrial variations, via a respiratory chain complex IV (COX1) polymorphism, on piRNA expression was examined in relation to the reproductive and aging outcomes of C. elegans. The COX1 polymorphism in mitochondria was found to affect the number of piRNAs expressed, the development of germ cells, and the length of the lifespan of the nematodes. Interestingly, more than two-thirds of the piRNA expression changes associated with the mitochondrial variation were found to also be affected by age. A gene ontology analysis of the altered piRNA species found that the piRNAs affected by mitochondrial variation and age were linked to genes known to have roles in reproductive and developmental function. Moreover, a piRNA-lncRNA-mRNA regulatory network based on the differential expression patterns of piRNA related to the mitochondrial variation was constructed to further identify potential gene targets with functional interactions. Similarly, this network identified genes involved in reproduction, development, and aging processes. These findings provide new insight into understanding how mitochondrial variations may regulate piRNA expression and may influence the underlying molecular mechanisms that affect reproduction and aging.
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Affiliation(s)
- Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Ying Li
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Mengyu Liang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Lei Wang
- Department of Histology and Embryology, Xuzhou Medical University, Xuzhou, China
| | - Liang Wang
- Department of Biochemistry, Xuzhou Medical University, Xuzhou, China
| | | | - Conghui Han
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Wenda Zhang
- Department of Genetics, Xuzhou Medical University, Xuzhou, China.,Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, China
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16
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Song Y, Wang Y, Li Y, Wang L, Zhang W, Cheng J, Zhu Y, Zhang H, Zhang Q, Niu H, zheng Y, Liang M, Deng M, Shi H, Wang H, Zhang F, Zhu Z. The whole transcriptome regulation as a function of mitochondrial polymorphisms and aging in Caenorhabditis elegans. Aging (Albany NY) 2020; 12:2453-2470. [PMID: 32019902 PMCID: PMC7041728 DOI: 10.18632/aging.102754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Recently, mitochondrial-nuclear interaction in aging has been widely studied. However, the nuclear genome controlled by natural mitochondrial variations that influence aging has not been comprehensively understood so far. We hypothesized that mitochondrial polymorphisms could play critical roles in the aging process, probably by regulation of the whole-transcriptome expression. Our results showed that mitochondria polymorphisms not only decreased the mitochondrial mass but also miRNA, lncRNA, mRNA, circRNA and metabolite profiles. Furthermore, most genes that are associated with mitochondria show age-related expression features (P = 3.58E-35). We also constructed a differentially expressed circRNA-lncRNA-miRNA-mRNA regulatory network and a ceRNA network affected by the mitochondrial variations. In addition, Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that the genes affected by the mitochondrial variation were enriched in metabolic activity. We finally constructed a multi-level regulatory network with aging which affected by the mitochondrial variation in Caenorhabditis elegans. The interactions between these genes and metabolites have great values for further aging research. In sum, our findings provide new evidence for understanding the molecular mechanisms of how mitochondria influence aging.
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Affiliation(s)
- Yuanjian Song
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Yuechen Wang
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Ying Li
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - WenDa Zhang
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Jing Cheng
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Yao Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Haoyu Zhang
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, China
| | - Qiang Zhang
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Haichen Niu
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Yingwei zheng
- Department of Biochemistry, Xuzhou Medical University, Xuzhou, China
| | - Mengyu Liang
- Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Mengqiong Deng
- Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Hao Shi
- Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Hao Wang
- Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Fang Zhang
- Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, China
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17
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Shtolz N, Mishmar D. The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00342] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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18
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Bilska-Zając E, Franssen F, Różycki M, Swart A, Karamon J, Sroka J, Zdybel J, Ziętek-Barszcz A, Cencek T. Intraspecific genetic variation in Trichinella spiralis and Trichinella britovi populations circulating in different geographical regions of Poland. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:101-112. [PMID: 31440446 PMCID: PMC6698805 DOI: 10.1016/j.ijppaw.2019.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 11/25/2022]
Abstract
Trichinella spiralis and Trichinella britovi are species of nematodes which are responsible for the majority of Trichinella infections in the world and the most prevalent in Poland. The most abundant species – T. spiralis, is considered to be more genetically homogeneous in Europe than T. britovi. The aim of the present study was to determine the genetic variability in T. spiralis and T. britovi populations based on nuclear 5S rDNA intergenic spacer region (5S rDNA) and cytochrome c oxidase 1 (COX1) gene sequences. For the study, 55 isolates of T. spiralis and 50 isolates of T. britovi isolated from wild boars, pigs, brown rat and a red fox were analyzed. Based on the analysis of both genes, the genetic variability within populations of T. spiralis and T. britovi differed. In T. spiralis, two single nucleotide polymorphisms (SNPs) were observed in the 612 bp 5S rDNA gene fragment, and one SNP was detected in the 700 bp COX1 gene fragment. In T. britovi, 17 single nucleotide variations (SNVs) were detected in the 5S rDNA gene fragment (among them 16 SNPs), while COX1 sequence analysis revealed the occurrence of 20 SNVs between the sequences tested (among them 19 SNPs). For the majority of T. spiralis isolates the investigated larvae presented uniform haplotypes. In contrast, most of the isolates of T. britovi consisted of larvae of different haplotypes. Geographical analysis showed that each region exhibited different haplotype composition and richness. Warmińsko-Mazurskie and Zachodniopomorskie regions were the richest in haplotypes (15 and 16 haplotypes, respectively). We used heatmaps showing a characteristic pattern for each region graphically. This may allow to differentiate regions based on the occurrence of particular haplotypes. Furthermore, a PCA analysis on the SNP level yielded biplots that show that certain haplotypes/genotypes are associated with (clusters of) regions. The genetic variability within the Polish T. britovi population is high. 5S rDNA and COX1 variability in T. spiralis is low compared to T. britovi. T. britovi variability may correlate to geographical origin. Heatmap and PCA analysis could be helpful analytical tool for epidemiological investigations.
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Affiliation(s)
- Ewa Bilska-Zając
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Frits Franssen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mirosław Różycki
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Arno Swart
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jacek Karamon
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Jacek Sroka
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Jolanta Zdybel
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Anna Ziętek-Barszcz
- Department of Epidemiology and Risk Assessment, National Veterinary Research InstitutePulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
| | - Tomasz Cencek
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute in Pulawy, Al. Partyzantow 57, 24-100, Pulawy, Poland
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19
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Zhu Z, Han X, Wang Y, Liu W, Lu Y, Xu C, Wang X, Hao L, Song Y, Huang S, Rizak JD, Li Y, Han C. Identification of Specific Nuclear Genetic Loci and Genes That Interact With the Mitochondrial Genome and Contribute to Fecundity in Caenorhabditis elegans. Front Genet 2019; 10:28. [PMID: 30778368 PMCID: PMC6369210 DOI: 10.3389/fgene.2019.00028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/17/2019] [Indexed: 12/16/2022] Open
Abstract
Previous studies have found that fecundity is a multigenic trait regulated, in part, by mitochondrial-nuclear (mit-n) genetic interactions. However, the identification of specific nuclear genetic loci or genes interacting with the mitochondrial genome and contributing to the quantitative trait fecundity is an unsolved issue. Here, a panel of recombinant inbred advanced intercrossed lines (RIAILs), established from a cross between the N2 and CB4856 strains of C. elegans, were used to characterize the underlying genetic basis of mit-n genetic interactions related to fecundity. Sixty-seven single nucleotide polymorphisms (SNPs) were identified by association mapping to be linked with fecundity among 115 SNPs linked to mitotype. This indicated significant epistatic effects between nuclear and mitochondria genetics on fecundity. In addition, two specific nuclear genetic loci interacting with the mitochondrial genome and contributing to fecundity were identified. A significant reduction in fecundity was observed in the RIAILs that carried CB4856 mitochondria and a N2 genotype at locus 1 or a CB4856 genotype at locus 2 relative to the wild-type strains. Then, a hybrid strain (CNC10) was established, which was bred as homoplasmic for the CB4856 mtDNA genome and N2 genotype at locus 1 in the CB4856 nuclear background. The mean fecundity of CNC10 was half the fecundity of the control strain. Several functional characteristics of the mitochondria in CNC10 were also influenced by mit-n interactions. Overall, experimental evidence was presented that specific nuclear genetic loci or genes have interactions with the mitochondrial genome and are associated with fecundity. In total, 18 genes were identified using integrative approaches to have interactions with the mitochondrial genome and to contribute to fecundity.
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Affiliation(s)
- Zuobin Zhu
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Xiaoxiao Han
- Center of Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuechen Wang
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Wei Liu
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Yue Lu
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Chang Xu
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Xitao Wang
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yuanjian Song
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Shi Huang
- School of Life Sciences, Xiangya Medical School, Central South University, Changsha, China
| | | | - Ying Li
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Conghui Han
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, China
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20
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Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT. Mitochondrial DNA and temperature tolerance in lager yeasts. SCIENCE ADVANCES 2019; 5:eaav1869. [PMID: 30729163 PMCID: PMC6353617 DOI: 10.1126/sciadv.aav1869] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/03/2019] [Indexed: 06/01/2023]
Abstract
A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Paterna, Valencia, Spain
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Xueying C. Li
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C. Fay
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
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21
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Abstract
Dipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.
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22
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Woodruff GC, Phillips PC. Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps. BMC Ecol 2018; 18:26. [PMID: 30129423 PMCID: PMC6102938 DOI: 10.1186/s12898-018-0182-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biotic interactions are ubiquitous and require information from ecology, evolutionary biology, and functional genetics in order to be understood. However, study systems that are amenable to investigations across such disparate fields are rare. Figs and fig wasps are a classic system for ecology and evolutionary biology with poor functional genetics; Caenorhabditis elegans is a classic system for functional genetics with poor ecology. In order to help bridge these disciplines, here we describe the natural history of a close relative of C. elegans, Caenorhabditis inopinata, that is associated with the fig Ficus septica and its pollinating Ceratosolen wasps. RESULTS To understand the natural context of fig-associated Caenorhabditis, fresh F. septica figs from four Okinawan islands were sampled, dissected, and observed under microscopy. C. inopinata was found in all islands where F. septica figs were found. C.i nopinata was routinely found in the fig interior and almost never observed on the outside surface. C. inopinata was only found in pollinated figs, and C. inopinata was more likely to be observed in figs with more foundress pollinating wasps. Actively reproducing C. inopinata dominated early phase figs, whereas late phase figs with emerging wasp progeny harbored C. inopinata dauer larvae. Additionally, C. inopinata was observed dismounting from Ceratosolen pollinating wasps that were placed on agar plates. C. inopinata was not found on non-pollinating, parasitic Philotrypesis wasps. Finally, C. inopinata was only observed in F. septica figs among five Okinawan Ficus species sampled. CONCLUSION These are the first detailed field observations of C. inopinata, and they suggest a natural history where this species proliferates in early phase F. septica figs and disperses from late phase figs on Ceratosolen pollinating fig wasps. While consistent with other examples of nematode diversification in the fig microcosm, the fig and wasp host specificity of C. inopinata is highly divergent from the life histories of its close relatives and frames hypotheses for future investigations. This natural co-occurrence of the fig/fig wasp and C. inopinata study systems sets the stage for an integrated research program that can help to explain the evolution of interspecific interactions.
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Affiliation(s)
- Gavin C Woodruff
- Forest Pathology Laboratory, Forestry and Forest Products Research Institute, Tsukuba, Japan.
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
| | - Patrick C Phillips
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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23
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Skibinski DOF, Ghiselli F, Diz AP, Milani L, Mullins JGL. Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System. Genome Biol Evol 2018; 9:3265-3281. [PMID: 29149282 PMCID: PMC5726481 DOI: 10.1093/gbe/evx235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2017] [Indexed: 12/27/2022] Open
Abstract
Many bivalve species have two types of mitochondrial DNA passed independently through the female line (F genome) and male line (M genome). Here we study the cytochrome oxidase I protein in such bivalve species and provide evidence for differences between the F and M proteins in amino acid property values, particularly relating to hydrophobicity and helicity. The magnitude of these differences varies between different regions of the protein and the change from the ancestor is most marked in the M protein. The observed changes occur in parallel and in the same direction in the different species studied. Two possible causes are considered, first relaxation of purifying selection with drift and second positive selection. These may operate in different ways in different regions of the protein. Many different amino acid substitutions contribute in a small way to the observed variation, but substitutions involving alanine and serine have a quantitatively large effect. Some of these substitutions are potential targets for phosphorylation and some are close to residues of functional importance in the catalytic mechanism. We propose that the observed changes in the F and M proteins might contribute to functional differences between them relating to ATP production and mitochondrial membrane potential with implications for sperm function.
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Affiliation(s)
- David O F Skibinski
- Institute of Life Science, Swansea University Medical School, United Kingdom
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Angel P Diz
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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24
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Abstract
Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mito-nuclear interactions. Recombinant mtDNAs were generated to determine fitness components within high- and low-fitness mtDNAs. Based on phenotypic distributions of isogenic strains containing recombinant mtDNAs, we found that multiple loci contributed to mitotype fitness differences. These mitochondrial loci interacted in epistatic, nonadditive ways in certain environmental conditions. Mito-mito epistasis (i.e., nonadditive interactions between mitochondrial loci) influenced fitness in progeny from four different crosses, suggesting that mito-mito epistasis is a widespread phenomenon in yeast and other systems with recombining mtDNAs. Furthermore, we found that interruption of coadapted mito-mito interactions produced recombinant mtDNAs with lower fitness. Our results demonstrate that mito-mito epistasis results in functional variation through mitochondrial recombination in fungi, providing modes for adaptive evolution and the generation of mito-mito incompatibilities.
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25
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Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C. Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Front Genet 2017; 8:25. [PMID: 28316610 PMCID: PMC5334354 DOI: 10.3389/fgene.2017.00025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
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Affiliation(s)
- Paul Sunnucks
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Hernán E. Morales
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
- Department of Marine Sciences, University of GothenburgGothenburg, Sweden
| | - Annika M. Lamb
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
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26
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Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab 2016; 24:91-103. [PMID: 27411011 PMCID: PMC5287496 DOI: 10.1016/j.cmet.2016.06.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/27/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023]
Abstract
Mutant mitochondrial genomes (mtDNA) can be viewed as selfish genetic elements that persist in a state of heteroplasmy despite having potentially deleterious metabolic consequences. We sought to study regulation of selfish mtDNA dynamics. We establish that the large 3.1-kb deletion-bearing mtDNA variant uaDf5 is a selfish genome in Caenorhabditis elegans. Next, we show that uaDf5 mutant mtDNA replicates in addition to, not at the expense of, wild-type mtDNA. These data suggest the existence of a homeostatic copy-number control that is exploited by uaDf5 to "hitchhike" to high frequency. We also observe activation of the mitochondrial unfolded protein response (UPR(mt)) in uaDf5 animals. Loss of UPR(mt) causes a decrease in uaDf5 frequency, whereas its constitutive activation increases uaDf5 levels. UPR(mt) activation protects uaDf5 from mitophagy. Taken together, we propose that mtDNA copy-number control and UPR(mt) represent two homeostatic response mechanisms that play important roles in regulating selfish mitochondrial genome dynamics.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Interdisciplinary Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Biological Sciences Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rama D Gangula
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon A Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA 6150, Australia
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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27
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Grosemans T, Morris K, Thomas WK, Rigaux A, Moens T, Derycke S. Mitogenomics reveals high synteny and long evolutionary histories of sympatric cryptic nematode species. Ecol Evol 2016; 6:1854-70. [PMID: 26933490 PMCID: PMC4760989 DOI: 10.1002/ece3.1975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/18/2015] [Accepted: 01/03/2016] [Indexed: 11/09/2022] Open
Abstract
Species with seemingly identical morphology but with distinct genetic differences are abundant in the marine environment and frequently co-occur in the same habitat. Such cryptic species are typically delineated using a limited number of mitochondrial and/or nuclear marker genes, which do not yield information on gene order and gene content of the genomes under consideration. We used next-generation sequencing to study the composition of the mitochondrial genomes of four sympatrically distributed cryptic species of the Litoditis marina species complex (PmI, PmII, PmIII, and PmIV). The ecology, biology, and natural occurrence of these four species are well known, but the evolutionary processes behind this cryptic speciation remain largely unknown. The gene order of the mitochondrial genomes of the four species was conserved, but differences in genome length, gene length, and codon usage were observed. The atp8 gene was lacking in all four species. Phylogenetic analyses confirm that PmI and PmIV are sister species and that PmIII diverged earliest. The most recent common ancestor of the four cryptic species was estimated to have diverged 16 MYA. Synonymous mutations outnumbered nonsynonymous changes in all protein-encoding genes, with the Complex IV genes (coxI-III) experiencing the strongest purifying selection. Our mitogenomic results show that morphologically similar species can have long evolutionary histories and that PmIII has several differences in genetic makeup compared to the three other species, which may explain why it is better adapted to higher temperatures than the other species.
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Affiliation(s)
- Tara Grosemans
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium
| | - Krystalynne Morris
- Department of Biochemistry and Molecular Biology Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Durham New Hampshire 03824
| | - William Kelley Thomas
- Department of Biochemistry and Molecular Biology Hubbard Center for Genome Studies University of New Hampshire 35 Colovos Road Durham New Hampshire 03824
| | - Annelien Rigaux
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium; CeMoFe University of Ghent Karel Lodewijk Ledeganckstraat 359000 Gent Belgium
| | - Tom Moens
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium
| | - Sofie Derycke
- Marine Biology Section Biology Department Faculty of Science University of Ghent Krijgslaan 281 (S8) 9000 Gent Belgium; Royal Belgian Institute of Natural Sciences (RBINS) OD Taxonomy and Phylogeny Vautierstraat 291000 Brussels Belgium
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28
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Zhu Z, Lu Q, Zeng F, Wang J, Huang S. Compatibility between mitochondrial and nuclear genomes correlates with the quantitative trait of lifespan in Caenorhabditis elegans. Sci Rep 2015; 5:17303. [PMID: 26601686 PMCID: PMC4658563 DOI: 10.1038/srep17303] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/28/2015] [Indexed: 12/12/2022] Open
Abstract
Mutations in mitochondrial genome have epistatic effects on organisms depending on
the nuclear background, but a role for the compatibility of mitochondrial-nuclear
genomes (mit-n) in the quantitative nature of a complex trait remains unexplored. We
studied a panel of recombinant inbred advanced intercrossed lines (RIAILs) of C.
elegans that were established from a cross between the N2 and HW strains. We
determined the HW nuclear genome content and the mitochondrial type (HW or N2) of
each RIAIL strain. We found that the degree of mit-n compatibility was correlated
with the lifespans but not the foraging behaviors of RIAILs. Several known
aging-associated QTLs individually showed no relationship with mitotypes but
collectively a weak trend consistent with a role in mit-n compatibility. By
association mapping, we identified 293 SNPs that showed linkage with lifespan and a
relationship with mitotypes consistent with a role in mit-n compatibility. We
further found an association between mit-n compatibility and several functional
characteristics of mitochondria as well as the expressions of genes involved in the
respiratory oxidation pathway. The results provide the first evidence implicating
mit-n compatibility in the quantitative nature of a complex trait, and may be
informative to certain evolutionary puzzles on hybrids.
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Affiliation(s)
- Zuobin Zhu
- State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Qing Lu
- State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Fangfang Zeng
- State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Junjing Wang
- State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
| | - Shi Huang
- State Key Laboratory of Medical Genetics, School of Life Sciences, Xiangya Medical School, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China
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