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Hill BG, Shiva S, Ballinger S, Zhang J, Darley-Usmar VM. Bioenergetics and translational metabolism: implications for genetics, physiology and precision medicine. Biol Chem 2019; 401:3-29. [PMID: 31815377 PMCID: PMC6944318 DOI: 10.1515/hsz-2019-0268] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/24/2019] [Indexed: 12/25/2022]
Abstract
It is now becoming clear that human metabolism is extremely plastic and varies substantially between healthy individuals. Understanding the biochemistry that underlies this physiology will enable personalized clinical interventions related to metabolism. Mitochondrial quality control and the detailed mechanisms of mitochondrial energy generation are central to understanding susceptibility to pathologies associated with aging including cancer, cardiac and neurodegenerative diseases. A precision medicine approach is also needed to evaluate the impact of exercise or caloric restriction on health. In this review, we discuss how technical advances in assessing mitochondrial genetics, cellular bioenergetics and metabolomics offer new insights into developing metabolism-based clinical tests and metabolotherapies. We discuss informatics approaches, which can define the bioenergetic-metabolite interactome and how this can help define healthy energetics. We propose that a personalized medicine approach that integrates metabolism and bioenergetics with physiologic parameters is central for understanding the pathophysiology of diseases with a metabolic etiology. New approaches that measure energetics and metabolomics from cells isolated from human blood or tissues can be of diagnostic and prognostic value to precision medicine. This is particularly significant with the development of new metabolotherapies, such as mitochondrial transplantation, which could help treat complex metabolic diseases.
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Affiliation(s)
- Bradford G. Hill
- Envirome Institute, Diabetes and Obesity Center, Department of Medicine, University of Louisville, Louisville, KY 40202
| | - Sruti Shiva
- Department of Pharmacology & Chemical Biology, Vascular Medicine Institute, Center for Metabolism & Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15143
| | - Scott Ballinger
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Jianhua Zhang
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294
- Department of Veteran Affairs Medical Center, Birmingham, AL 35294
| | - Victor M. Darley-Usmar
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294
- Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL 35294
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Dubie JJ, Caraway AR, Stout MM, Katju V, Bergthorsson U. The conflict within: origin, proliferation and persistence of a spontaneously arising selfish mitochondrial genome. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190174. [PMID: 31787044 DOI: 10.1098/rstb.2019.0174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial genomes can sustain mutations that are simultaneously detrimental to individual fitness and yet, can proliferate within individuals owing to a replicative advantage. We analysed the fitness effects and population dynamics of a mitochondrial genome containing a novel 499 bp deletion in the cytochrome b(1) (ctb-1) gene (Δctb-1) encoding the cytochrome b of complex III in Caenorhabditis elegans. Δctb-1 reached a high heteroplasmic frequency of 96% in one experimental line during a mutation accumulation experiment and was linked to additional spontaneous mutations in nd5 and tRNA-Asn. The Δctb-1 mutant mitotype imposed a significant fitness cost including a 65% and 52% reduction in productivity and competitive fitness, respectively, relative to individuals bearing wild-type (WT) mitochondria. Deletion-bearing worms were rapidly purged within a few generations when competed against WT mitochondrial DNA (mtDNA) bearing worms in experimental populations. By contrast, the Δctb-1 mitotype was able to persist in large populations comprising heteroplasmic individuals only, although the average intracellular frequency of Δctb-1 exhibited a slow decline owing to competition among individuals bearing different frequencies of the heteroplasmy. Within experimental lines subjected to severe population bottlenecks (n = 1), the relative intracellular frequency of Δctb-1 increased, which is a hallmark of selfish drive. A positive correlation between Δctb-1 and WT mtDNA copy-number suggests a mechanism that increases total mtDNA per se, and does not discern the Δctb-1 mitotype from the WT mtDNA. This study demonstrates the selfish nature of the Δctb-1 mitotype, given its transmission advantage and substantial fitness load for the host, and highlights the importance of population size for the population dynamics of selfish mtDNA. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Joseph James Dubie
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - Avery Robert Caraway
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - McKenna Margaret Stout
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Parkway, College Station, TX 77845, USA
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Parr N, Wilkes M, Hawkes LA. Natural Climbers: Insights from Avian Physiology at High Altitude. High Alt Med Biol 2019; 20:427-437. [DOI: 10.1089/ham.2019.0032] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nicole Parr
- College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall, United Kingdom
| | - Matt Wilkes
- Centre for Altitude Space and Extreme Environment Medicine, Institute of Sport, Exercise and Health, London, United Kingdom
| | - Lucy Alice Hawkes
- Hatherly Laboratories, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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55
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Sun S, Sha Z, Wang Y. The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications. Ecol Evol 2019; 9:12390-12407. [PMID: 31788185 PMCID: PMC6875667 DOI: 10.1002/ece3.5542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication-random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.
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Affiliation(s)
- Shao'e Sun
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Zhongli Sha
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yanrong Wang
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
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Zhang D, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Li WX, Wang GT. Evidence for Adaptive Selection in the Mitogenome of a Mesoparasitic Monogenean Flatworm Enterogyrus malmbergi. Genes (Basel) 2019; 10:genes10110863. [PMID: 31671638 PMCID: PMC6896049 DOI: 10.3390/genes10110863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/26/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Whereas a majority of monogenean flatworms are ectoparasitic, i.e., parasitize on external surfaces (mainly gills) of their fish hosts, Enterogyrus species (subfamily Ancyrocephalinae) are mesoparasitic, i.e., parasitize in the stomach of the host. As there are numerous drastic differences between these two environments (including lower oxygen availability), we hypothesized that this life-history innovation might have produced adaptive pressures on the energy metabolism, which is partially encoded by the mitochondrial genome (OXPHOS). To test this hypothesis, we sequenced mitochondrial genomes of two Ancyrocephalinae species: mesoparasitic E. malmbergi and ectoparasitic Ancyrocephalus mogurndae. The mitogenomic architecture of E. malmbergi is mostly standard for monogeneans, but that of A. mogurndae exhibits some unique features: missing trnL2 gene, very low AT content (60%), a non-canonical start codon of the nad2 gene, and exceptionally long tandem-repeats in the non-coding region (253 bp). Phylogenetic analyses produced paraphyletic Ancyrocephalinae (with embedded Dactylogyrinae), but with low support values. Selective pressure (PAML and HYPHY) and protein structure analyses all found evidence for adaptive evolution in cox2 and cox3 genes of the mesoparasitic E. malmbergi. These findings tentatively support our hypothesis of adaptive evolution driven by life-history innovations in the mitogenome of this species. However, as only one stomach-inhabiting mesoparasitic monogenean was available for this analysis, our findings should be corroborated on a larger number of mesoparasitic monogeneans and by physiological studies.
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Affiliation(s)
- Dong Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Shan G Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | | | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China.
| | - Rong Chen
- Bio-Transduction Lab, Wuhan 430075, China.
| | - Wen X Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | - Gui T Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
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Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives. Sci Data 2019; 6:192. [PMID: 31586122 PMCID: PMC6778140 DOI: 10.1038/s41597-019-0204-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022] Open
Abstract
Animals that lived at high altitudes have evolved distinctive physiological traits that allow them to tolerate extreme high-altitude environment, including higher hemoglobin concentration, increased oxygen saturation of blood and a high energy metabolism. Although previous investigations performed plenty of comparison between high- and low-altitude mammals at the level of morphology, physiology and genomics, mechanism underlying high-altitude adaptation remains largely unknown. Few studies provided comparative analyses in high-altitude adaptation, such as parallel analysis in multiple species. In this study, we generated high-quality small RNA sequencing data for six tissues (heart, liver, spleen, lung, kidney and muscle) from low- and high-altitude populations of four typical livestock animals, and identified comparable numbers of miRNAs in each species. This dataset will provide valuable information for understanding the molecular mechanism of high-altitude adaptation in vertebrates.
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58
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Storz JF, Scott GR. Life Ascending: Mechanism and Process in Physiological Adaptation to High-Altitude Hypoxia. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019; 50:503-526. [PMID: 33033467 DOI: 10.1146/annurev-ecolsys-110218-025014] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To cope with the reduced availability of O2 at high altitude, air-breathing vertebrates have evolved myriad adjustments in the cardiorespiratory system to match tissue O2 delivery with metabolic O2 demand. We explain how changes at interacting steps of the O2 transport pathway contribute to plastic and evolved changes in whole-animal aerobic performance under hypoxia. In vertebrates native to high altitude, enhancements of aerobic performance under hypoxia are attributable to a combination of environmentally induced and evolved changes in multiple steps of the pathway. Additionally, evidence suggests that many high-altitude natives have evolved mechanisms for attenuating maladaptive acclimatization responses to hypoxia, resulting in counter-gradient patterns of altitudinal variation for key physiological phenotypes. For traits that exhibit counteracting environmental and genetic effects, evolved changes in phenotype may be cryptic under field conditions and can only be revealed by rearing representatives of high-and low-altitude populations under standardized environmental conditions to control for plasticity.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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Zhou C, James JG, Xu Y, Tu H, He X, Wen Q, Price M, Yang N, Wu Y, Ran J, Meng Y, Yue B. Genome-wide analysis sheds light on the high-altitude adaptation of the buff-throated partridge (Tetraophasis szechenyii). Mol Genet Genomics 2019; 295:31-46. [PMID: 31414227 DOI: 10.1007/s00438-019-01601-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022]
Abstract
The buff-throated partridge (Tetraophasis szechenyii) is a hypoxia-tolerant bird living in an extremely inhospitable high-altitude environment, which has high ultraviolet (UV) radiation as well as a low oxygen supply when compared with low-altitude areas. To further understand the molecular genetic mechanisms of the high-altitude adaptation of the buff-throated partridges, we de novo assembled the complete genome of the buff-throated partridge. Comparative genomics revealed that positively selected hypoxia-related genes in the buff-throated partridge were distributed in the HIF-1 signaling pathway (map04066), response to hypoxia (GO:0001666), response to oxygen-containing compound (GO:1901700), ATP binding (GO:0005524), and angiogenesis (GO:0001525). Of these positively selected hypoxia-related genes, one positively selected gene (LONP1) had one buff-throated partridge-specific missense mutation which was classified as deleterious by PolyPhen-2. Moreover, positively selected genes in the buff-throated partridge were enriched in cellular response to DNA damage stimulus (corrected P value: 0.028006) and DNA repair (corrected P value: 0.044549), which was related to the increased exposure of the buff-throated partridge to UV radiation. Compared with other avian genomes, the buff-throated partridge showed expansion in genes associated with steroid hormone receptor activity and contractions in genes related to immune and olfactory perception. Furthermore, comparisons between the buff-throated partridge genome and red junglefowl genome revealed a conserved genome structure and provided strong evidence of the sibling relationship between Tetraophasis and Lophophorus. Our data and analysis contributed to the study of Phasianidae evolutionary history and provided new insights into the potential adaptation mechanisms to the high altitude employed by the buff-throated partridge.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jake George James
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yu Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, People's Republic of China
| | - Hongmei Tu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xingcheng He
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Qinchao Wen
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Megan Price
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, People's Republic of China
| | - Yongjie Wu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jianghong Ran
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yang Meng
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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Zhu W, Meng Q, Zhang H, Wang ML, Li X, Wang HT, Zhou GL, Miao L, Qin QL, Zhang JH. Metabolomics reveals the key role of oxygen metabolism in heat susceptibility of an alpine-dwelling ghost moth, Thitarodes xiaojinensis (Lepidoptera: Hepialidae). INSECT SCIENCE 2019; 26:695-710. [PMID: 29790270 DOI: 10.1111/1744-7917.12605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/11/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Ghost moths inhabiting the alpine meadows of the Tibetan Plateau are cold-adapted stenothermal organisms that are susceptible to heat (dead within 7 days at 27 °C exposure). Exploring the metabolic basis of their heat susceptibility would extend our understanding of the thermal biology of alpine-dwelling invertebrates. Here, gas chromatography-mass spectrometry-based metabolomics was combined with physiological and transcriptional approaches to determine the metabolic mechanisms of heat susceptibility in Thitarodes xiaojinensis larvae. The metabolomics results showed that 27 °C heat stress impaired the Krebs cycle and lipolysis in T. xiaojinensis larvae, as demonstrated by the accumulation of intermediary metabolites. In addition, carbohydrate reserves were highly and exclusively consumed, and an anaerobic product, lactate, accumulated. This evidence suggested a strong reliance on glycolysis to anaerobically generate energy. The respiration rate and enzymatic activity test results indicated a deficiency in O2 metabolism; in addition, the Krebs cycle capacity was not decreased, and the metabolic flux through aerobic pathways was limited. These findings were further supported by the occurrence of hypoxia symptoms in midgut mitochondria (vacuolation and swelling) and increased transcription of hypoxia-induced factor 1-α. Overall, heat stress caused O2 limitation and depressed the overall intensity of aerobic metabolism in ghost moths, and less efficient anaerobic glycolysis was activated to sustain their energy supply. As carbohydrates were depleted, the energy supply became deficient. Our study presents a comprehensive metabolic explanation for the heat susceptibility of ghost moths and reveals the relationship between O2 metabolism and heat susceptibility in these larvae.
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Affiliation(s)
- Wei Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qian Meng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huan Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Meng-Long Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xuan Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Tuo Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gui-Ling Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Miao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi-Lian Qin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ji-Hong Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Zhang D, Zou H, Hua CJ, Li WX, Mahboob S, Al-Ghanim KA, Al-Misned F, Jakovlić I, Wang GT. Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda. Genome Biol Evol 2019; 11:1797-1812. [PMID: 31192351 PMCID: PMC6601869 DOI: 10.1093/gbe/evz121] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2019] [Indexed: 01/04/2023] Open
Abstract
The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Cong-Jie Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
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62
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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63
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
Abstract
Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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64
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Storz JF, Cheviron ZA, McClelland GB, Scott GR. Evolution of physiological performance capacities and environmental adaptation: insights from high-elevation deer mice ( Peromyscus maniculatus). J Mammal 2019; 100:910-922. [PMID: 31138949 DOI: 10.1093/jmammal/gyy173] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
Analysis of variation in whole-animal performance can shed light on causal connections between specific traits, integrated physiological capacities, and Darwinian fitness. Here, we review and synthesize information on naturally occurring variation in physiological performance capacities and how it relates to environmental adaptation in deer mice (Peromyscus maniculatus). We discuss how evolved changes in aerobic exercise capacity and thermogenic capacity have contributed to adaptation to high elevations. Comparative work on deer mice at high and low elevations has revealed evolved differences in aerobic performance capacities in hypoxia. Highland deer mice have consistently higher aerobic performance capacities under hypoxia relative to lowland natives, consistent with the idea that it is beneficial to have a higher maximal metabolic rate (as measured by the maximal rate of O2 consumption, VO2max) in an environment characterized by lower air temperatures and lower O2 availability. Observed differences in aerobic performance capacities between highland and lowland deer mice stem from changes in numerous subordinate traits that alter the flux capacity of the O2-transport system, the oxidative capacity of tissue mitochondria, and the relationship between O2 consumption and ATP synthesis. Many such changes in physiological phenotype are associated with hypoxia-induced changes in gene expression. Research on natural variation in whole-animal performance forms a nexus between physiological ecology and evolutionary biology that requires insight into the natural history of the study species.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | | | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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65
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Banguera-Hinestroza E, Ferrada E, Sawall Y, Flot JF. Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. Genes (Basel) 2019; 10:E324. [PMID: 31035578 PMCID: PMC6562464 DOI: 10.3390/genes10050324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/15/2023] Open
Abstract
More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.
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Affiliation(s)
- Eulalia Banguera-Hinestroza
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
| | - Evandro Ferrada
- Center for Genomics and Bioinformatics, Universidad Mayor, Santiago, Chile.
| | - Yvonne Sawall
- Coral Reef Ecology, Bermuda Institute of Ocean Sciences (BIOS), St.George's GE 01, Bermuda.
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
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66
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Twort VG, Newcomb RD, Buckley TR. New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci. Genome Biol Evol 2019; 11:1293-1306. [PMID: 30957857 PMCID: PMC6486805 DOI: 10.1093/gbe/evz070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2019] [Indexed: 01/01/2023] Open
Abstract
Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best-hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of ortholog ratios of synonymous to nonsynonymous amino acid changes found 83 genes that are under positive selection for at least one codon. A wide variety of Gene Ontology terms, enzymes, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways are represented among these genes. In particular, enzymes involved in oxidative phosphorylation, melanin synthesis, and free-radical scavenging are represented, consistent with physiological and metabolic changes that are associated with adaptation to alpine environments. Structural alignment of the transcripts with the most codons under positive selection revealed that the majority of sites are surface residues, and therefore have the potential to influence the thermostability of the enzyme, with the exception of prophenoloxidase where two residues near the active site are under selection. These proteins provide interesting candidates for further analysis of protein evolution.
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Affiliation(s)
- Victoria G Twort
- School of Biological Sciences, University of Auckland, New Zealand.,Manaaki Whenua - Landcare Research, Auckland, New Zealand.,Department of Biology, Lund University, Lund, Sweden
| | - Richard D Newcomb
- School of Biological Sciences, University of Auckland, New Zealand.,The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R Buckley
- School of Biological Sciences, University of Auckland, New Zealand.,Manaaki Whenua - Landcare Research, Auckland, New Zealand
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67
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Mao X, Shi Y, Liang X, Cai M, Yang X, Chen S, Jia X, Wang J, Hu S, Lai S. Genetic diversities of MT-ND3 and MT-ND4L genes are associated with high-altitude adaptation. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1544040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xudong Mao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaohu Liang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingcheng Cai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xue Yang
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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68
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Shen X, Pu Z, Chen X, Murphy RW, Shen Y. Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes. Front Genet 2019; 10:925. [PMID: 31632444 PMCID: PMC6785628 DOI: 10.3389/fgene.2019.00925] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/04/2019] [Indexed: 02/05/2023] Open
Abstract
Deep seas have extremely harsh conditions including high hydrostatic pressure, total darkness, cold, and little food and oxygen. The adaptations of fishes to deep-sea environment apparently have occurred independently many times. The genetic basis of adaptation for obtaining their energy remains unknown. Mitochondria play a central role in aerobic respiration. Analyses of the available 2,161 complete mitochondrial genomes of 1,042 fishes, including 115 deep-sea species, detect signals of positive selection in mitochondrial genes in nine branches of deep-sea fishes. Aerobic metabolism yields much more energy per unit of source material than anaerobic metabolism. The adaptive evolution of the mtDNA may reflect that aerobic metabolism plays a more important role than anaerobic metabolism in deep-sea fishes, whose energy sources (food) are extremely limited. This strategy maximizes the usage of energy sources. Eleven mitochondrial genes have convergent/parallel amino acid changes between branches of deep-sea fishes. Thus, these amino acid sites may be functionally important in the acquisition of energy, and reflect convergent evolution during their independent invasion of the harsh deep-sea ecological niche.
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Affiliation(s)
- Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou, China
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
- *Correspondence: Yongyi Shen,
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69
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Solari KA, Ramakrishnan U, Hadly EA. Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient. PLoS One 2018; 13:e0207936. [PMID: 30540800 PMCID: PMC6291101 DOI: 10.1371/journal.pone.0207936] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 11/08/2018] [Indexed: 01/25/2023] Open
Abstract
Species are shifting their ranges due to climate change, many moving to cooler and higher locations. However, with elevation increase comes oxygen decline, potentially limiting a species’ ability to track its environment depending on what mechanisms it has available to compensate for hypoxic stress. Pikas (Family Ochotonidae), cold-specialist small mammal species, are already undergoing elevational range shifts. We collected RNA samples from one population of Ochotona roylei in the western Himalaya at three sites– 3,600, 4,000, and 5,000 meters–and found no evidence of significant population genetic structure nor positive selection among sites. However, out of over 10,000 expressed transcripts, 26 were significantly upregulated at the 5,000 m site and were significantly enriched for pathways consistent with physiological compensation for limited oxygen. These results suggest that differences in gene expression may play a key role in enabling hypoxia tolerance on this local scale, indicating elevational flexibility that may facilitate successful range shifts in response to climate change.
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Affiliation(s)
- Katherine A. Solari
- Department of Biology, Stanford University, Stanford, California, United States of America
- Woods Institute for the Environment, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bangalore, India
- Program for Conservation Genomics, Stanford University, Stanford, California, United States of America
| | - Elizabeth A. Hadly
- Department of Biology, Stanford University, Stanford, California, United States of America
- Woods Institute for the Environment, Stanford University, Stanford, California, United States of America
- Program for Conservation Genomics, Stanford University, Stanford, California, United States of America
- Center for Innovation in Global Health, Stanford University, Stanford, California, United States of America
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70
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Solari KA, Hadly EA. Evolution for extreme living: variation in mitochondrial cytochrome c oxidase genes correlated with elevation in pikas (genus Ochotona). Integr Zool 2018; 13:517-535. [PMID: 29851233 DOI: 10.1111/1749-4877.12332] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The genus Ochotona (pikas) is a clade of cold-tolerant lagomorphs that includes many high-elevation species. Pikas offer a unique opportunity to study adaptations and potential limitations of an ecologically important mammal to high-elevation hypoxia. We analyzed the evolution of 3 mitochondrial genes encoding the catalytic core of cytochrome c oxidase (COX) in 10 pika species occupying elevations from sea level to 5000 m. COX is an enzyme highly reliant on oxygen and essential for cell function. One amino acid property, the equilibrium constant (ionization of COOH), was found to be under selection in the overall protein complex. We observed a strong relationship between the net value change in this property and the elevation each species occupies, with higher-elevation species having potentially more efficient proteins. We also found evidence of selection in low-elevation species for potentially less efficient COX, perhaps trading efficiency for heat production in the absence of hypoxia. Our results suggest that different pika species may have evolved elevation-specific COX proteins, specialization that may indicate limitations in their ability to shift their elevational ranges in response to future climate change.
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Affiliation(s)
| | - Elizabeth A Hadly
- Department of Biology, Stanford University, Stanford, California, USA.,Woods Institute for the Environment, Stanford University, Stanford, California, USA.,Program for Conservation Genomics, Stanford University, Stanford, California, USA
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71
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McClelland GB, Scott GR. Evolved Mechanisms of Aerobic Performance and Hypoxia Resistance in High-Altitude Natives. Annu Rev Physiol 2018; 81:561-583. [PMID: 30256727 DOI: 10.1146/annurev-physiol-021317-121527] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparative physiology studies of high-altitude species provide an exceptional opportunity to understand naturally evolved mechanisms of hypoxia resistance. Aerobic capacity (VO2max) is a critical performance trait under positive selection in some high-altitude taxa, and several high-altitude natives have evolved to resist the depressive effects of hypoxia on VO2max. This is associated with enhanced flux capacity through the O2 transport cascade and attenuation of the maladaptive responses to chronic hypoxia that can impair O2 transport. Some highlanders exhibit elevated rates of carbohydrate oxidation during exercise, taking advantage of its high ATP yield per mole of O2. Certain highland native animals have also evolved more oxidative muscles and can sustain high rates of lipid oxidation to support thermogenesis. The underlying mechanisms include regulatory adjustments of metabolic pathways and to gene expression networks. Therefore, the evolution of hypoxia resistance in high-altitude natives involves integrated functional changes in the pathways for O2 and substrate delivery and utilization by mitochondria.
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Affiliation(s)
- Grant B McClelland
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada;
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada;
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72
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Liu R, Jin L, Long K, Tang Q, Ma J, Wang X, Zhu L, Jiang A, Tang G, Jiang Y, Li X, Li M. Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:847-851. [PMID: 33474342 PMCID: PMC7799994 DOI: 10.1080/23802359.2018.1501285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
High-altitude inhospitable environments impose a formidable life challenge for the local animals. Training and exposure to high-altitude environments produce both distinct physiological and phenotypic characteristics. The mitochondrion, an organelle crucial for the energy production, plays an important role in hypoxia adaptation. In this study, we investigated the mitochondrial DNA (mtDNA) polymorphism and copy number variation between the population pairs from distinct altitudes across the multi-species. Higher mitochondrial DNA control region's genetic diversity is conspicuous in high-altitude animals versus low-altitude relatives. We also found an accordant decrease of mtDNA copy number in most of the tissues from high-altitude animals. Compared to mammals, chickens have significantly distinct mitogenomic characteristics, and more significant changes in the skeletal muscle mtDNA copy number between high- and low-altitude individuals. Our study catches a snapshot of the biological similarities and differences in the mitochondrial high-altitude acclimation across the species.
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Affiliation(s)
- Rui Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jideng Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - An'an Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yanzhi Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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73
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Beckman EJ, Benham PM, Cheviron ZA, Witt C. Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins. Mol Ecol 2018; 27:4350-4367. [DOI: 10.1111/mec.14795] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Elizabeth J. Beckman
- Division of Biological Sciences University of Montana Missoula Montana
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
| | - Phred M. Benham
- Division of Biological Sciences University of Montana Missoula Montana
| | | | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
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74
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Yuan ML, Zhang QL, Zhang L, Jia CL, Li XP, Yang XZ, Feng RQ. Mitochondrial phylogeny, divergence history and high-altitude adaptation of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) inhabiting the Tibetan Plateau. Mol Phylogenet Evol 2018; 122:116-124. [DOI: 10.1016/j.ympev.2018.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/26/2017] [Accepted: 01/20/2018] [Indexed: 11/16/2022]
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75
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Jochmans-Lemoine A, Revollo S, Villalpando G, Valverde I, Gonzales M, Laouafa S, Soliz J, Joseph V. Divergent Mitochondrial Antioxidant Activities and Lung Alveolar Architecture in the Lungs of Rats and Mice at High Altitude. Front Physiol 2018; 9:311. [PMID: 29670534 PMCID: PMC5893716 DOI: 10.3389/fphys.2018.00311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/14/2018] [Indexed: 01/22/2023] Open
Abstract
Compared with mice, adult rats living at 3,600 m above sea level (SL—La Paz, Bolivia) have high hematocrit, signs of pulmonary hypertension, and low lung volume with reduced alveolar surface area. This phenotype is associated with chronic mountain sickness in humans living at high altitude (HA). We tested the hypothesis that this phenotype is associated with impaired gas exchange and oxidative stress in the lungs. We used rats and mice (3 months old) living at HA (La Paz) and SL (Quebec City, Canada) to measure arterial oxygen saturation under graded levels of hypoxia (by pulse oximetry), the alveolar surface area in lung slices and the activity of pro- (NADPH and xanthine oxidases—NOX and XO) and anti- (superoxide dismutase, and glutathione peroxidase—SOD and GPx) oxidant enzymes in cytosolic and mitochondrial lung protein extracts. HA rats have a lower arterial oxygen saturation and reduced alveolar surface area compared to HA mice and SL rats. Enzymatic activities (NOX, XO, SOD, and GPx) in the cytosol were similar between HA and SL animals, but SOD and GPx activities in the mitochondria were 2–3 times higher in HA vs. SL rats, and only marginally higher in HA mice vs. SL mice. Furthermore, the maximum activity of cytochrome oxidase-c (COX) measured in mitochondrial lung extracts was also 2 times higher in HA rats compared with SL rats, while there was only a small increase in HA mice vs. SL mice. Interestingly, compared with SL controls, alterations in lung morphology are not observed for young rats at HA (15 days after birth), and enzymatic activities are only slightly altered. These results suggest that rats living at HA have a gradual reduction of their alveolar surface area beyond the postnatal period. We can speculate that the elevation of SOD, GPx, and COX activities in the lung mitochondria are not sufficient to compensate for oxidative stress, leading to damage of the lung tissue in rats.
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Affiliation(s)
- Alexandra Jochmans-Lemoine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, QC, Canada
| | - Susana Revollo
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, QC, Canada
| | - Gabriella Villalpando
- Instituto Boliviano de Biologia de Altura, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Ibana Valverde
- Instituto Boliviano de Biologia de Altura, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Marcelino Gonzales
- Instituto Boliviano de Biologia de Altura, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Sofien Laouafa
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, QC, Canada.,Centre National de la Recherche Scientifique, UMR 5023, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Jorge Soliz
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, QC, Canada
| | - Vincent Joseph
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec City, QC, Canada
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Hawkes LA, Batbayar N, Butler PJ, Chua B, Frappell PB, Meir JU, Milsom WK, Natsagdorj T, Parr N, Scott GR, Takekawa JY, WikeIski M, Witt MJ, Bishop CM. Do Bar-Headed Geese Train for High Altitude Flights? Integr Comp Biol 2018; 57:240-251. [PMID: 28859401 DOI: 10.1093/icb/icx068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
SYNOPSIS Exercise at high altitude is extremely challenging, largely due to hypobaric hypoxia (low oxygen levels brought about by low air pressure). In humans, the maximal rate of oxygen consumption decreases with increasing altitude, supporting progressively poorer performance. Bar-headed geese (Anser indicus) are renowned high altitude migrants and, although they appear to minimize altitude during migration where possible, they must fly over the Tibetan Plateau (mean altitude 4800 m) for much of their annual migration. This requires considerable cardiovascular effort, but no study has assessed the extent to which bar-headed geese may train prior to migration for long distances, or for high altitudes. Using implanted loggers that recorded heart rate, acceleration, pressure, and temperature, we found no evidence of training for migration in bar-headed geese. Geese showed no significant change in summed activity per day or maximal activity per day. There was also no significant change in maximum heart rate per day or minimum resting heart rate, which may be evidence of an increase in cardiac stroke volume if all other variables were to remain the same. We discuss the strategies used by bar-headed geese in the context of training undertaken by human mountaineers when preparing for high altitude, noting the differences between their respective cardiovascular physiology.
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Affiliation(s)
- Lucy A Hawkes
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall TR10?9FE, UK
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Bayanzurkh District, Ulaanbataar 210351, Mongolia
| | - Patrick J Butler
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15?2TT, UK
| | - Beverley Chua
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | - Peter B Frappell
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | | - William K Milsom
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
| | | | - Nicole Parr
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Cornwall TR10?9FE, UK
| | - Graham R Scott
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 3K1
| | - John Y Takekawa
- Audubon California, Richardson Bay Audubon Center and Sanctuary, Tiburon, CA 94920, USA
| | - Martin WikeIski
- Max Planck Institute for Ornithology, D-82319 Seewiesen, Germany.,Department of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Matthew J Witt
- College of Life and Environmental Sciences, University of Exeter, Environment and Sustainability Institute, Penryn Campus, Cornwall TR10?9FE, UK
| | - Charles M Bishop
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57?2UW, UK
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77
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Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet. Sci Rep 2018; 8:4671. [PMID: 29549310 PMCID: PMC5856782 DOI: 10.1038/s41598-018-22483-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/30/2018] [Indexed: 11/20/2022] Open
Abstract
Animals living at high altitudes have evolved distinct phenotypic and genotypic adaptations against stressful environments. We studied the adaptive patterns of altitudinal stresses on transcriptome turnover in subterranean plateau zokors (Myospalax baileyi) in the high-altitude Qinghai-Tibetan Plateau. Transcriptomes of zokors from three populations with distinct altitudes and ecologies (Low: 2846 m, Middle: 3282 m, High: 3,714 m) were sequenced and compared. Phylogenetic and principal component analyses classified them into three divergent altitudinal population clusters. Genetic polymorphisms showed that the population at H, approaching the uppermost species boundary, harbors the highest genetic polymorphism. Moreover, 1056 highly up-regulated UniGenes were identified from M to H. Gene ontologies reveal genes like EPAS1 and COX1 were overexpressed under hypoxia conditions. EPAS1, EGLN1, and COX1 were convergent in high-altitude adaptation against stresses in other species. The fixation indices (FST and GST)-based outlier analysis identified 191 and 211 genes, highly differentiated among L, M, and H. We observed adaptive transcriptome changes in Myospalax baileyi, across a few hundred meters, near the uppermost species boundary, regardless of their relatively stable underground burrows’ microclimate. The highly variant genes identified in Myospalax were involved in hypoxia tolerance, hypercapnia tolerance, ATP-pathway energetics, and temperature changes.
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78
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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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79
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Zhang QL, Yang XZ, Zhang L, Feng RQ, Zhu QH, Chen JY, Yuan ML. Adaptive evidence of mitochondrial genomes in Dolycoris baccarum (Hemiptera: Pentatomidae) to divergent altitude environments. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [PMID: 29521177 DOI: 10.1080/24701394.2018.1446951] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl). All the 37 mitochondrial genes were highly conserved and under purifying selection, except for two mitochondrial protein-coding genes (MPCGs) (atp6 and nad5) that showed positively selected signatures. We therefore further examined non-synonymous substitutions in atp6 and nad5, by sequencing more individuals from three populations with different altitudes. We found that these non-synonymous substitutions were polymorphic in these populations, likely due to relaxed selection constraints in different altitudes. Purifying selection in all mitochondrial genes may be due to their functional importance for the precision of ATP production usually. Length difference in mitochondrial control regions between DBHC and DBQY was also conversed at the population level, indicating that sequence size adjustments in control region may be associated with adaptation to divergent altitudes. Quantitatively real-time PCR analysis for 12 MPCGs showed that gene expression patterns had a significant change between the two populations, suggesting that expression levels of MPCGs could be modulated by divergent environmental pressures (e.g. oxygen content and ambient temperature). These results provided an important guide for further uncovering genetic mechanisms of ecological adaptation in insects.
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Affiliation(s)
- Qi-Lin Zhang
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China.,b State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science , Nanjing University , Nanjing , China
| | - Xing-Zhuo Yang
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China
| | - Li Zhang
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China
| | - Run-Qiu Feng
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China
| | | | - Jun-Yuan Chen
- b State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science , Nanjing University , Nanjing , China
| | - Ming-Long Yuan
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China.,d Key Laboratory of Grassland Livestock Industry Innovation , Ministry of Agriculture , Lanzhou , China
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80
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Pamenter ME, Lau GY, Richards JG, Milsom WK. Naked mole rat brain mitochondria electron transport system flux and H + leak are reduced during acute hypoxia. ACTA ACUST UNITED AC 2018; 221:jeb.171397. [PMID: 29361591 DOI: 10.1242/jeb.171397] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Mitochondrial respiration and ATP production are compromised by hypoxia. Naked mole rats (NMRs) are among the most hypoxia-tolerant mammals and reduce metabolic rate in hypoxic environments; however, little is known regarding mitochondrial function during in vivo hypoxia exposure in this species. To address this knowledge gap, we asked whether the function of NMR brain mitochondria exhibits metabolic plasticity during acute hypoxia. Respirometry was utilized to assess whole-animal oxygen consumption rates and high-resolution respirometry was utilized to assess electron transport system (ETS) function in saponin-permeabilized NMR brain. We found that NMR whole-animal oxygen consumption rate reversibly decreased by ∼85% in acute hypoxia (4 h at 3% O2). Similarly, relative to untreated controls, permeabilized brain respiratory flux through the ETS was decreased by ∼90% in acutely hypoxic animals. Relative to carbonyl cyanide p-trifluoro-methoxyphenylhydrazone-uncoupled total ETS flux, this functional decrease was observed equally across all components of the ETS except for complex IV (cytochrome c oxidase), at which flux was further reduced, supporting a regulatory role for this enzyme during acute hypoxia. The maximum enzymatic capacities of ETS complexes I-V were not altered by acute hypoxia; however, the mitochondrial H+ gradient decreased in step with the decrease in ETS respiration. Taken together, our results indicate that NMR brain ETS flux and H+ leak are reduced in a balanced and regulated fashion during acute hypoxia. Changes in NMR mitochondrial metabolic plasticity mirror whole-animal metabolic responses to hypoxia.
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Affiliation(s)
- Matthew E Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada K1N 6N5 .,Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
| | - Gigi Y Lau
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Jeffrey G Richards
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - William K Milsom
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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81
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Lamb AM, Gan HM, Greening C, Joseph L, Lee Y, Morán‐Ordóñez A, Sunnucks P, Pavlova A. Climate‐driven mitochondrial selection: A test in Australian songbirds. Mol Ecol 2018; 27:898-918. [DOI: 10.1111/mec.14488] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Annika Mae Lamb
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Han Ming Gan
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds Vic. Australia
| | - Chris Greening
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections Canberra ACT Australia
| | - Yin Peng Lee
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
| | - Alejandra Morán‐Ordóñez
- InForest Joint Research Unit (CTFC‐CREAF) Forest Science Centre of Catalonia Solsona Catalonia Spain
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Vic. Australia
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82
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York JM, Scadeng M, McCracken KG, Milsom WK. Respiratory mechanics and morphology of Tibetan and Andean high-altitude geese with divergent life histories. ACTA ACUST UNITED AC 2018; 221:jeb.170738. [PMID: 29180602 DOI: 10.1242/jeb.170738] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022]
Abstract
High-altitude bar-headed geese (Anser indicus) and Andean geese (Chloephaga melanoptera) have been shown to preferentially increase tidal volume over breathing frequency when increasing ventilation during exposure to hypoxia. Increasing tidal volume is a more effective breathing strategy but is also thought to be more mechanically and metabolically expensive. We asked whether there might be differences in the mechanics or morphology of the respiratory systems of high-altitude transient bar-headed geese and high-altitude resident Andean geese that could minimize the cost of breathing more deeply. We compared these two species with a low-altitude migratory species, the barnacle goose (Branta leucopsis). We ventilated anesthetized birds to measure mechanical properties of the respiratory system and used CT scans to quantify respiratory morphology. We found that the respiratory system of Andean geese was disproportionately larger than that of the other two species, allowing use of a deeper breathing strategy for the same energetic cost. The relative size of the respiratory system, especially the caudal air sacs, of bar-headed geese was also larger than that of barnacle geese. However, when normalized to respiratory system size, the mechanical cost of breathing did not differ significantly among these three species, indicating that deeper breathing is enabled by morphological but not mechanical differences between species. The metabolic cost of breathing was estimated to be <1% of basal metabolic rate at rest in normoxia. Because of differences in the magnitude of the ventilatory response, the cost of breathing was estimated to increase 7- to 10-fold in bar-headed and barnacle geese in severe hypoxia, but less than 1-fold in Andean geese exposed to the same low atmospheric PO2.
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Affiliation(s)
- Julia M York
- University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
| | - Miriam Scadeng
- University of California San Diego, Department of Radiology, Center for Functional MRI, 9500 Gilman Drive 0677, La Jolla, CA, USA 92093
| | - Kevin G McCracken
- University of Miami, Department of Biology, Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, and Human Genetics and Genomics - Miller School of Medicine, Coral Gables, FL, 33146, USA
| | - William K Milsom
- University of British Columbia, Department of Zoology, 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
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83
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Lau GY, Richards JG. Interspecific variation in brain mitochondrial complex I and II capacity and ROS emission in marine sculpins. J Exp Biol 2018; 222:jeb.189407. [DOI: 10.1242/jeb.189407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/29/2018] [Indexed: 12/29/2022]
Abstract
Environmental hypoxia presents a metabolic challenge for animals because it inhibits mitochondrial respiration and can lead to the generation of reactive oxygen species (ROS). We investigated the interplay between O2 use for aerobic respiration and ROS generation among sculpin fishes (Cottidae, Actinopterygii) that are known to vary in whole-animal hypoxia tolerance. We hypothesized that mitochondria from hypoxia tolerant sculpins would show more efficient O2 use with a higher phosphorylation efficiency and lower ROS emission. We showed that brain mitochondria from more hypoxia tolerant sculpins had lower complex I and higher complex II flux capacities compared with less hypoxia tolerant sculpins, but these differences were not related to variation in phosphorylation efficiency (ADP/O) or mitochondrial coupling (respiratory control ratio). The hypoxia tolerant sculpin had higher mitochondrial H2O2 emission per O2 consumed (H2O2/O2) under oligomycin-induced state 4 conditions compared to less hypoxia tolerant sculpin. An in vitro redox challenge experiment revealed species differences in how well mitochondria defend their glutathione redox status when challenged with high levels of reduced glutathione, but the redox challenge elicited the same H2O2/O2 in all species. Furthermore, in vitro anoxia-recovery lowered absolute H2O2 emission (H2O2/mg mitochondrial protein) in all species and negatively impacted state 3 respiration rates in some species, but the responses were not related to hypoxia tolerance. Overall, we clearly demonstrate a relationship between hypoxia tolerance and complex I and II flux capacities in sculpins, but the differences in complex flux capacity do not appear to be directly related to variation in ROS metabolism.
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Affiliation(s)
- Gigi Y. Lau
- Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, B.C., Canada, V6T 1Z4
| | - Jeffrey G. Richards
- Department of Zoology, The University of British Columbia, 6270 University Boulevard, Vancouver, B.C., Canada, V6T 1Z4
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84
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Snelling EP, Maloney SK, Farrell AP, Meyer LCR, Izwan A, Fuller A, Mitchell D, Haw A, Costello MA, Seymour RS. Scaling of morphology and ultrastructure of hearts among wild African antelope. J Exp Biol 2018; 221:jeb.184713. [DOI: 10.1242/jeb.184713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/29/2018] [Indexed: 11/20/2022]
Abstract
The hearts of smaller mammals tend to operate at higher mass-specific mechanical work rates than those of larger mammals. The ultrastructural characteristics of the heart that allow for such variation in work rate still is largely unknown. We have used perfusion-fixation, transmission electron microscopy and stereology to assess the morphology and anatomical aerobic power density of the heart as a function of body mass across six species of wild African antelope differing by approximately 20-fold in body mass. The survival of wild antelope, as prey animals, depends on competent cardiovascular performance. We found that relative heart mass (g kg−1 body mass) decreases with body mass according to a power equation with an exponent of –0.12±0.07 (± 95% CI) (P=0.0027). Likewise, capillary length density (km cm−3 of cardiomyocyte), mitochondrial volume density (fraction of cardiomyocyte), and mitochondrial inner membrane surface density (m2 cm−3 of mitochondria) also decrease with body mass with exponents of –0.17±0.16 (P=0.039), –0.06±0.05 (P=0.018), and –0.07±0.05 (P=0.015), respectively, trends likely to be associated with the greater mass-specific mechanical work rates of the hearts in smaller antelope. Finally, we found proportionality between quantitative characteristics of a structure responsible for the delivery of oxygen (total capillary length) and those of a structure that ultimately uses that oxygen (total mitochondrial inner membrane surface area), which provides support for the economic principle of symmorphosis at the cellular level of the oxygen cascade in an aerobic organ.
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Affiliation(s)
- Edward P. Snelling
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane K. Maloney
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Anthony P. Farrell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leith C. R. Meyer
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paraclinical Sciences, University of Pretoria, Pretoria, South Africa
| | - Adian Izwan
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Andrea Fuller
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- Department of Paraclinical Sciences, University of Pretoria, Pretoria, South Africa
| | - Duncan Mitchell
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Anna Haw
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mary-Ann Costello
- Central Animal Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Roger S. Seymour
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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85
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Graham AM, Lavretsky P, Muñoz-Fuentes V, Green AJ, Wilson RE, McCracken KG. Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes. Genome Biol Evol 2018; 10:14-32. [PMID: 29211852 PMCID: PMC5757641 DOI: 10.1093/gbe/evx253] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2017] [Indexed: 12/30/2022] Open
Abstract
Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A. f. oxyptera) are locally adapted to the Andean environment and mostly allopatric from low-altitude birds (A. f. flavirostris); however, there is occasional gene flow across altitudinal gradients. In this study, we used next-generation sequencing to explore genetic patterns associated with high-altitude adaptation in speckled teal populations, as well as the extent to which the balance between selection and migration have affected genetic architecture. We identified a set of loci with allele frequencies strongly correlated with altitude, including those involved in the insulin-like signaling pathway, bone morphogenesis, oxidative phosphorylation, responders to hypoxia-induced DNA damage, and feedback loops to the hypoxia-inducible factor pathway. These same outlier loci were found to have depressed gene flow estimates, as well as being highly concentrated on the Z-chromosome. Our results suggest a multifactorial response to life at high altitudes through an array of interconnected pathways that are likely under positive selection and whose genetic components seem to be providing an effective genomic barrier to interbreeding, potentially functioning as an avenue for population divergence and speciation.
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Affiliation(s)
| | | | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Andy J Green
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Robert E Wilson
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska, Fairbanks
| | - Kevin G McCracken
- Department of Biology, University of Miami
- Institute of Arctic Biology and University of Alaska Museum, University of Alaska, Fairbanks
- Rosenstiel School of Marine and Atmospheric Sciences, University of Miami
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine
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86
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Lan D, Xiong X, Ji W, Li J, Mipam TD, Ai Y, Chai Z. Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs. Genetica 2017; 146:151-160. [DOI: 10.1007/s10709-017-0005-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/26/2017] [Indexed: 11/29/2022]
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87
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Butler PJ. The physiological basis of bird flight. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0384. [PMID: 27528774 DOI: 10.1098/rstb.2015.0384] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 11/12/2022] Open
Abstract
Flapping flight is energetically more costly than running, although it is less costly to fly a given body mass a given distance per unit time than it is for a similar mass to run the same distance per unit time. This is mainly because birds can fly faster than they can run. Oxygen transfer and transport are enhanced in migrating birds compared with those in non-migrators: at the gas-exchange regions of the lungs the effective area is greater and the diffusion distance smaller. Also, migrating birds have larger hearts and haemoglobin concentrations in the blood, and capillary density in the flight muscles tends to be higher. Species like bar-headed geese migrate at high altitudes, where the availability of oxygen is reduced and the energy cost of flapping flight increased compared with those at sea level. Physiological adaptations to these conditions include haemoglobin with a higher affinity for oxygen than that in lowland birds, a greater effective ventilation of the gas-exchange surface of the lungs and a greater capillary-to-muscle fibre ratio. Migrating birds use fatty acids as their source of energy, so they have to be transported at a sufficient rate to meet the high demand. Since fatty acids are insoluble in water, birds maintain high concentrations of fatty acid-binding proteins to transport fatty acids across the cell membrane and within the cytoplasm. The concentrations of these proteins, together with that of a key enzyme in the β-oxidation of fatty acids, increase before migration.This article is part of the themed issue 'Moving in a moving medium: new perspectives on flight'.
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Affiliation(s)
- Patrick J Butler
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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88
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Intraspecific variation and plasticity in mitochondrial oxygen binding affinity as a response to environmental temperature. Sci Rep 2017; 7:16238. [PMID: 29176558 PMCID: PMC5701142 DOI: 10.1038/s41598-017-16598-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/15/2017] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial function has been suggested to underlie constraints on whole-organism aerobic performance and associated hypoxia and thermal tolerance limits, but most studies have focused on measures of maximum mitochondrial capacity. Here we investigated whether variation in mitochondrial oxygen kinetics could contribute to local adaptation and plasticity in response to temperature using two subspecies of the Atlantic killifish (Fundulus heteroclitus) acclimated to a range of temperatures (5, 15, and 33 °C). The southern subspecies of F. heteroclitus, which has superior thermal and hypoxia tolerances compared to the northern subspecies, exhibited lower mitochondrial O2 P50 (higher O2 affinity). Acclimation to thermal extremes (5 or 33 °C) altered mitochondrial O2 P50 in both subspecies consistent with the effects of thermal acclimation on whole-organism thermal tolerance limits. We also examined differences between subspecies and thermal acclimation effects on whole-blood Hb O2-P50 to assess whether variation in oxygen delivery is involved in these responses. In contrast to the clear differences between subspecies in mitochondrial O2-P50 there were no differences in whole-blood Hb-O2 P50 between subspecies. Taken together these findings support a general role for mitochondrial oxygen kinetics in differentiating whole-organism aerobic performance and thus in influencing species responses to environmental change.
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89
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Lau GY, Mandic M, Richards JG. Evolution of Cytochrome c Oxidase in Hypoxia Tolerant Sculpins (Cottidae, Actinopterygii). Mol Biol Evol 2017; 34:2153-2162. [PMID: 28655155 DOI: 10.1093/molbev/msx179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Vertebrate hypoxia tolerance can emerge from modifications to the oxygen (O2) transport cascade, but whether there is adaptive variation to O2 binding at the terminus of this cascade, mitochondrial cytochrome c oxidase (COX), is not known. In order to address the hypothesis that hypoxia tolerance is associated with enhanced O2 binding by mitochondria we undertook a comparative analysis of COX O2 kinetics across species of intertidal sculpins (Cottidae, Actinopterygii) that vary in hypoxia tolerance. Our analysis revealed a significant relationship between hypoxia tolerance (critical O2 tension of O2 consumption rate; Pcrit), mitochondrial O2 binding affinity (O2 tension at which mitochondrial respiration was half maximal; P50), and COX O2-binding affinity (apparent Michaelis-Menten constant for O2 binding to COX; Km,app O2). The more hypoxia tolerant species had both a lower mitochondrial P50 and lower COX Km,app O2, facilitating the maintenance of mitochondrial function to a lower O2 tension than in hypoxia intolerant species. Additionally, hypoxia tolerant species had a lower overall COX Vmax but higher mitochondrial COX respiration rate when expressed relative to maximal electron transport system respiration rate. In silico analyses of the COX3 subunit postulated as the entry point for O2 into the COX protein catalytic core, points to variation in COX3 protein stability (estimated as free energy of unfolding) contributing to the variation in COX Km,app O2. We propose that interactions between COX3 and cardiolipin at four amino acid positions along the same alpha-helix forming the COX3 v-cleft represent likely determinants of interspecific differences in COX Km,app O2.
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Affiliation(s)
- Gigi Y Lau
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Milica Mandic
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
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90
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Mu H, Sun J, Cheung SG, Fang L, Zhou H, Luan T, Zhang H, Wong CKC, Qiu JW. Comparative proteomics and codon substitution analysis reveal mechanisms of differential resistance to hypoxia in congeneric snails. J Proteomics 2017; 172:36-48. [PMID: 29122728 DOI: 10.1016/j.jprot.2017.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/21/2017] [Accepted: 11/01/2017] [Indexed: 12/01/2022]
Abstract
Although high-throughput proteomics has been widely applied to study mechanisms of environmental adaptation, the conclusions from studies that are based on one species can be confounded by phylogeny. We compare the freshwater snail Pomacea canaliculata (a notorious invasive species) and its congener Pomacea diffusa (a non-invasive species) to understand the molecular mechanisms of their differential resistance to hypoxia. A 72-h acute exposure experiment showed that P. canaliculata is more tolerant to hypoxia than P. diffusa. The two species were then exposed to three levels of dissolved oxygen (6.7, 2.0 and 1.0mgL-1) for 8h, and their gill proteins were analyzed using iTRAQ-coupled LC-MS/MS. The two species showed striking differences in protein expression profiles, with the more hypoxia tolerant P. canaliculata having more up-regulated proteins in signal transduction and down-regulated proteins in glycolysis and the tricarboxylic acid cycle. Evolutionary analysis revealed five orthologous genes encoding differentially expressed proteins having clear signal of positive selection, indicating selection has acted on some of the hypoxia responsive genes. Our case study has highlighted the potential of integrated proteomics and comparative evolutionary analysis for understanding the genetic basis of adaptation to global environmental change in non-model species. SIGNIFICANCE Rapid globalization in recent decades has greatly facilitated species introduction around the world. Successfully established introduced species, so-called invasive species, have threatened the invaded ecosystems. There has been substantial interest in studying how invasive species respond to extreme environmental conditions because the results can help not only predict their range of expansion and manage their impact, but also may reveal the adaptive mechanisms underlying their invasiveness. Our study has adopted a comparative approach to study the differential physiological and proteomic responses of two congeneric snails to various hypoxic conditions, as well as codon substitution analysis at transcriptomic level to detect signals of positive selection in hypoxia-responsive genes. The integrated physiological, proteomic and transcriptomic approach can be applied in other non-model species to understand the molecular mechanisms of adaptation to global environmental change.
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Affiliation(s)
- Huawei Mu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jin Sun
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Siu Gin Cheung
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Ling Fang
- Instrumental Analysis and Research Center, Sun Yat-Sen University, Guangzhou, PR China
| | - Haiyun Zhou
- Instrumental Analysis and Research Center, Sun Yat-Sen University, Guangzhou, PR China
| | - Tiangang Luan
- Instrumental Analysis and Research Center, Sun Yat-Sen University, Guangzhou, PR China; MOE Key Laboratory of Aquatic Product Safety, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Huoming Zhang
- Biosciences Core Laboratory, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
| | - Chris K C Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
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91
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Fetterman JL, Sammy MJ, Ballinger SW. Mitochondrial toxicity of tobacco smoke and air pollution. Toxicology 2017; 391:18-33. [PMID: 28838641 PMCID: PMC5681398 DOI: 10.1016/j.tox.2017.08.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Jessica L Fetterman
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, United States
| | - Melissa J Sammy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama, Birmingham, AL, United States
| | - Scott W Ballinger
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama, Birmingham, AL, United States.
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92
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Mohandesan E, Fitak RR, Corander J, Yadamsuren A, Chuluunbat B, Abdelhadi O, Raziq A, Nagy P, Stalder G, Walzer C, Faye B, Burger PA. Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels. Sci Rep 2017; 7:9970. [PMID: 28855525 PMCID: PMC5577142 DOI: 10.1038/s41598-017-08995-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/14/2017] [Indexed: 01/05/2023] Open
Abstract
The genus Camelus is an interesting model to study adaptive evolution in the mitochondrial genome, as the three extant Old World camel species inhabit hot and low-altitude as well as cold and high-altitude deserts. We sequenced 24 camel mitogenomes and combined them with three previously published sequences to study the role of natural selection under different environmental pressure, and to advance our understanding of the evolutionary history of the genus Camelus. We confirmed the heterogeneity of divergence across different components of the electron transport system. Lineage-specific analysis of mitochondrial protein evolution revealed a significant effect of purifying selection in the concatenated protein-coding genes in domestic Bactrian camels. The estimated dN/dS < 1 in the concatenated protein-coding genes suggested purifying selection as driving force for shaping mitogenome diversity in camels. Additional analyses of the functional divergence in amino acid changes between species-specific lineages indicated fixed substitutions in various genes, with radical effects on the physicochemical properties of the protein products. The evolutionary time estimates revealed a divergence between domestic and wild Bactrian camels around 1.1 [0.58-1.8] million years ago (mya). This has major implications for the conservation and management of the critically endangered wild species, Camelus ferus.
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Affiliation(s)
- Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.
- Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
- Institute for Molecular Evolution and Development, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - Robert R Fitak
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, N-0317, Oslo, Norway
- Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Helsinki, Finland
| | - Adiya Yadamsuren
- Mammalian Ecology Laboratory, Institute of Biology, Mongolian Academy of Sciences, Peace avenue-54b, Bayanzurh district, Ulaanbaatar, 210351, Mongolia
| | - Battsetseg Chuluunbat
- Laboratory of Genetics, Institute of Biology, Mongolian Academy of Sciences, Peace avenue-54b, Bayanzurh district, Ulaanbaatar, 210351, Mongolia
| | - Omer Abdelhadi
- University of Khartoum, Department for Meat Sciences, Khartoum, Sudan
| | - Abdul Raziq
- Lasbela University of Agriculture, Water and Marine Sciences, Regional Cooperation for Development (RCD) Highway, Uthal, Pakistan
| | - Peter Nagy
- Farm and Veterinary Department, Emirates Industry for Camel Milk and Products, PO Box 294239, Dubai, Umm Nahad, United Arab Emirates
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
| | - Chris Walzer
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
- International Takhi Group - Mongolia, Baigal Ordon, Ulaanbaatar, Mongolia
| | - Bernard Faye
- CIRAD-ES, UMR 112, Campus International de Baillarguet, TA C/112A, 34398, Montpellier, France
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.
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93
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Laguë SL. High-altitude champions: birds that live and migrate at altitude. J Appl Physiol (1985) 2017; 123:942-950. [PMID: 28839002 DOI: 10.1152/japplphysiol.00110.2017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 08/09/2017] [Accepted: 08/14/2017] [Indexed: 11/22/2022] Open
Abstract
High altitude is physiologically challenging for vertebrate life for many reasons, including hypoxia (low environmental oxygen); yet, many birds thrive at altitude. Compared with mammals, birds have additional enhancements to their oxygen transport cascade, the conceptual series of steps responsible for acquiring oxygen from the environment and transporting it to the mitochondria. These adaptations have allowed them to inhabit a number of high-altitude regions. Waterfowl are a taxon prolific at altitude. This minireview explores the physiological responses of high-altitude waterfowl (geese and ducks), comparing the strategies of lifelong high-altitude residents to those of transient high-altitude performers, providing insight into how birds champion high-altitude life. In particular, this review highlights and contrasts the physiological hypoxia responses of bar-headed geese (Anser indicus), birds that migrate biannually through the Himalayas (4,500-6,500 m), and Andean geese (Chloephaga melanoptera), lifelong residents of the Andes (4,000-5,500 m). These two species exhibit markedly different ventilatory and cardiovascular strategies for coping with hypoxia: bar-headed geese robustly increase convective oxygen transport elements (i.e., heart rate and total ventilation) whereas Andean geese rely predominantly on enhancements that are likely morphological in origin (i.e., increases in lung oxygen diffusion and cardiac stroke volume). The minireview compares the short- and long-term cardiovascular and ventilatory trade-offs of these different physiological strategies and offers hypotheses surrounding their origins. It also draws parallels to high-altitude human physiology and research, and identifies a number of areas of further research. The field of high-altitude avian physiology offers a unique and broadly applicable insight into physiological enhancements in hypoxia.
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94
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Tate KB, Ivy CM, Velotta JP, Storz JF, McClelland GB, Cheviron ZA, Scott GR. Circulatory mechanisms underlying adaptive increases in thermogenic capacity in high-altitude deer mice. ACTA ACUST UNITED AC 2017; 220:3616-3620. [PMID: 28839010 DOI: 10.1242/jeb.164491] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/18/2017] [Indexed: 01/08/2023]
Abstract
We examined the circulatory mechanisms underlying adaptive increases in thermogenic capacity in deer mice (Peromyscus maniculatus) native to the cold hypoxic environment at high altitudes. Deer mice from high- and low-altitude populations were born and raised in captivity to adulthood, and then acclimated to normoxia or hypobaric hypoxia (simulating hypoxia at ∼4300 m). Thermogenic capacity [maximal O2 consumption (V̇O2,max), during cold exposure] was measured in hypoxia, along with arterial O2 saturation (SaO2 ) and heart rate (fH). Hypoxia acclimation increased V̇O2,max by a greater magnitude in highlanders than in lowlanders. Highlanders also had higher SaO2 and extracted more O2 from the blood per heartbeat (O2 pulse=V̇O2,max/fH). Hypoxia acclimation increased fH, O2 pulse and capillary density in the left ventricle of the heart. Our results suggest that adaptive increases in thermogenic capacity involve integrated functional changes across the O2 cascade that augment O2 circulation and extraction from the blood.
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Affiliation(s)
- Kevin B Tate
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.,School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Catherine M Ivy
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Jonathan P Velotta
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Grant B McClelland
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
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95
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Su Y, Li D, Gaur U, Chen B, Zhao X, Wang Y, Yin H, Zhu Q. The comparison of blood characteristics in low- and high-altitude chickens. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1355272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yuan Su
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Uma Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Binlong Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Xiaoling Zhao
- Department of Animal Science, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, China
| | - Qing Zhu
- Department of Animal Science, Sichuan Agricultural University, Chengdu, Sichuan Province, China
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96
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Liu X, Zhang P, Zhang G, Li S, Zhang L, Xu Z, Ma T, Li D. A Comparison of Genetic Diversity of COX-III Gene in Lowland Chickens and Tibetan Chickens. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8064613. [PMID: 28758122 PMCID: PMC5512117 DOI: 10.1155/2017/8064613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/03/2017] [Accepted: 05/25/2017] [Indexed: 11/18/2022]
Abstract
To obtain a full understanding of the genetic diversity of the cytochrome oxidase III gene (COX-III) and its association with high altitude adaptation in Tibetan chickens, we sequenced COX-III in 12 chicken populations (155 Tibetan chickens and 145 other domestic chickens). We identified a total of 11 single nucleotide polymorphisms (SNPs) and 12 haplotypes (Ha1-Ha12). Low genetic diversity (haplotype diversity = 0.531 ± 0.087, nucleotide diversity = 0.00125) was detected for COX-III, and haplotype diversity of Tibetan chicken populations (0.750 ± 0.018) was markedly higher than lowland chicken populations (0.570 ± 0.028). Obvious genetic differentiation (nucleotide divergence = 0.092~0.339) and conspicuous gene communication (gene flow = 0.33~32.22) among 12 populations suggested that Tianfu black-bone fowl (white feather) was possibly introduced from Tibetan chicken. SNP m.10587 T>C affects the specific functions of the COX enzyme. Haplotype Ha3 was found in Tibetan chickens, and SNP m.10115G>A caused an amino acid substitution (Val62Ile) associated with phospholipid binding, while mutations m.10017C>A and m.10555G>A and the previously reported SNP m.10065T>C reduced the hydropathy index to some extent. Together, this indicates that the mitochondrial membrane is more hydrophobic in Tibetan chickens.
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Affiliation(s)
- Xueqin Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Pu Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gongying Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Sichen Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Long Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongxian Xu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tianyuan Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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97
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Koch EL, Neiber MT, Walther F, Hausdorf B. High gene flow despite opposite chirality in hybrid zones between enantiomorphic door snails. Mol Ecol 2017; 26:3998-4012. [DOI: 10.1111/mec.14159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/12/2017] [Accepted: 04/19/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Eva L. Koch
- Center of Natural History; Zoological Museum; University of Hamburg; Hamburg Germany
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - Marco T. Neiber
- Center of Natural History; Zoological Museum; University of Hamburg; Hamburg Germany
| | - Frank Walther
- Center of Natural History; Zoological Museum; University of Hamburg; Hamburg Germany
| | - Bernhard Hausdorf
- Center of Natural History; Zoological Museum; University of Hamburg; Hamburg Germany
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98
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Shi Y, Hu Y, Wang J, Elzo MA, Yang X, Lai S. Genetic diversities of MT-ND1 and MT-ND2 genes are associated with high-altitude adaptation in yak. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:485-494. [PMID: 28366030 DOI: 10.1080/24701394.2017.1307976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Tibetan yak (Bos grunniens) inhabiting the Qinghai-Tibet Plateau (QTP) where the average altitude is 4000 m, is specially adapted to live at these altitudes. Conversely, cattle (B. taurus) has been found to suffer from high-altitude hypertension or heart failure when exposed to these high altitudes. Two mitochondrial genes, MT-ND1 and MT-ND2, encode two subunits of NADH dehydrogenase play an essential role in the electron transport chain of oxidative phosphorylation (OXPHOS). We sequenced these two mitochondrial genes in two bovine groups (70 Tibetan yaks and 70 Xuanhan cattle) and downloaded 300 sequences of B. taurus (cattle), 93 sequences of B. grunniens (domestic yak), and 2 sequences of B. mutus (wild yak) from NCBI to increase our understanding of the mechanisms of adaptability to hypoxia at high altitudes in yaks compared to cattle. MT-ND1 SNP m.3907 C > T, present in all Tibetan yaks, was positively associated with high-altitude adaptation (p < .0006). Specially, mutation m.3638 A > G present in all cattle, resulting in the termination of transcription, was negatively associated with high-altitude adaptation (p < .0006). Additionally, MT-ND2 SNPs m.4351 G > A and m.5218 C > T also showed positive associations with high-altitude adaptation (p < .0004). MT-ND1 haplotypes H2, H3, H4, H6, and H7 showed positive associations but haplotype H20 had a negative association with high-altitude adaptation (p < .0008). Similarly, MT-ND2 haplotypes Ha1 Ha8, Ha10, and Ha11 were positively associated whereas haplotype Ha2 was negatively associated with adaptability to high-altitudes (p < .0008). Thus, MT-ND1 and MT-ND2 can be considered as candidate genes associated with adaptation to high-altitude environments.
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Affiliation(s)
- Yu Shi
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Yongsong Hu
- b Chengdu Agricultural College , Chengdu , Sichuan , China
| | - Jie Wang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
| | - Mauricio A Elzo
- c Department of Animal Science , University of Florida , Gainesville , FL, USA
| | - Xue Yang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China.,d Chengdu Academy of Agriculture and Forestry Sciences , Chengdu , China
| | - Songjia Lai
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China
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99
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Wang J, Shi Y, Elzo MA, Dang S, Jia X, Lai S. Genetic diversity of ATP8 and ATP6 genes is associated with high-altitude adaptation in yak. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:385-393. [PMID: 28306370 DOI: 10.1080/24701394.2017.1285292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ATP synthase 8 (ATP8) and ATPase synthase 6 (ATP6) play an important role in mitochondrial ATPase assembly. Mutations in either of these units could affect the ATP processing and the respiration chain in mitochondria. To find out if there were differences in gene diversity between Tibetan yaks and domestic cattle, we sequenced the ATP8 and ATP6 genes in 66 Tibetan yaks and 81 domestic cattle. We identified 20 SNPs in the ATP8 gene and 60 SNPs in the ATP6 gene. Ten SNPs detected in ATP8 were probably positively associated with high-altitude adaptation, of which SNPs m.8164 G > A, m.8210 G > A, m.8231 C > T and m. 8249 C > T resulted in amino acid changes. Similarly, SNPs m.8308A > G, m.8370A > C, m.8514G > A of ATP6 also appeared to be associated with high-altitude adaptability. Specifically, m.8308 A > G, located in the overlap region, might bring in a conserved region found in cytochrome b561 which play an important role in iron regulation, thus it might help the Tibetan yaks with this mutation to utilize rare oxygen efficiently. Considering all mutations, three of eight haplotypes identified in gene ATP8 were present only in Tibetan yaks, and six (H3 to H8) out of 21 haplotypes (H1 to H21) in gene ATP6 were restricted to Tibetan yaks. Haplotypes present only in Tibetan yaks could be positively associated with high-altitude adaptation.
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Affiliation(s)
- Jie Wang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Yu Shi
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Mauricio A Elzo
- b Department of Animal Sciences , University of Florida , Gainesville , FL , USA
| | - Shuzhang Dang
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Xianbo Jia
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
| | - Songjia Lai
- a College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , Sichuan , China
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100
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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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