1
|
Ferreira RC, Rodrigues CR, Broach JR, Briones MRS. Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals. Int J Mol Sci 2024; 25:3785. [PMID: 38612593 PMCID: PMC11012180 DOI: 10.3390/ijms25073785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.
Collapse
Affiliation(s)
- Renata C. Ferreira
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - Camila R. Rodrigues
- Graduate Program in Microbiology and Immunology, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| | - James R. Broach
- Department of Biochemistry, Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA;
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Federal University of São Paulo, São Paulo 04039032, SP, Brazil;
| |
Collapse
|
2
|
Edmands S. Mother's Curse effects on lifespan and aging. FRONTIERS IN AGING 2024; 5:1361396. [PMID: 38523670 PMCID: PMC10957651 DOI: 10.3389/fragi.2024.1361396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
The Mother's Curse hypothesis posits that mothers curse their sons with harmful mitochondria, because maternal mitochondrial inheritance makes selection blind to mitochondrial mutations that harm only males. As a result, mitochondrial function may be evolutionarily optimized for females. This is an attractive explanation for ubiquitous sex differences in lifespan and aging, given the prevalence of maternal mitochondrial inheritance and the established relationship between mitochondria and aging. This review outlines patterns expected under the hypothesis, and traits most likely to be affected, chiefly those that are sexually dimorphic and energy intensive. A survey of the literature shows that evidence for Mother's Curse is limited to a few taxonomic groups, with the strongest support coming from experimental crosses in Drosophila. Much of the evidence comes from studies of fertility, which is expected to be particularly vulnerable to male-harming mitochondrial mutations, but studies of lifespan and aging also show evidence of Mother's Curse effects. Despite some very compelling studies supporting the hypothesis, the evidence is quite patchy overall, with contradictory results even found for the same traits in the same taxa. Reasons for this scarcity of evidence are discussed, including nuclear compensation, factors opposing male-specific mutation load, effects of interspecific hybridization, context dependency and demographic effects. Mother's Curse effects may indeed contribute to sex differences, but the complexity of other contributing factors make Mother's Curse a poor general predictor of sex-specific lifespan and aging.
Collapse
Affiliation(s)
- Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
3
|
Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
Collapse
Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
| |
Collapse
|
4
|
Zhang Y, Li H, Wang Y, Nie M, Zhang K, Pan J, Zhang Y, Ye Z, Zufall RA, Lynch M, Long H. Mitogenomic architecture and evolution of the soil ciliates Colpoda. mSystems 2024; 9:e0116123. [PMID: 38259100 PMCID: PMC10878089 DOI: 10.1128/msystems.01161-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024] Open
Abstract
Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.
Collapse
Affiliation(s)
- Yuanyuan Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Haichao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Yaohai Wang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Mu Nie
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Kexin Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Jiao Pan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Yu Zhang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province, China
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Hongan Long
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| |
Collapse
|
5
|
Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
Collapse
Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
6
|
Camus MF, Inwongwan S. Mitonuclear interactions modulate nutritional preference. Biol Lett 2023; 19:20230375. [PMID: 38053364 PMCID: PMC10698477 DOI: 10.1098/rsbl.2023.0375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023] Open
Abstract
In nature, organisms are faced with constant nutritional options which fuel key life-history traits. Studies have shown that species can actively make nutritional decisions based on internal and external cues. Metabolism itself is underpinned by complex genomic interactions involving components from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled. Given the complicated nature of metabolism, it is not well understood how nutritional choices are affected by mitonuclear interactions. This is under the rationale that changes in genomic interactions will affect metabolic flux and change physiological requirements. To this end we used a large Drosophila mitonuclear genetic panel, comprising nine isogenic nuclear genomes coupled to nine mitochondrial haplotypes, giving a total of 81 different mitonuclear genotypes. We use a capillary-based feeding assay to screen this panel for dietary preference between carbohydrate and protein. We find significant mitonuclear interactions modulating nutritional choices, with these epistatic interactions also being dependent on sex. Our findings support the notion that complex genomic interactions can place a constraint on metabolic flux. This work gives us deeper insights into how key metabolic interactions can have broad implications on behaviour.
Collapse
Affiliation(s)
- M. Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sahutchai Inwongwan
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Deep Technology in Beekeeping and Bee Products for Sustainable Development Goals, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
7
|
Long H, Johri P, Gout JF, Ni J, Hao Y, Licknack T, Wang Y, Pan J, Jiménez-Marín B, Lynch M. Paramecium Genetics, Genomics, and Evolution. Annu Rev Genet 2023; 57:391-410. [PMID: 38012024 DOI: 10.1146/annurev-genet-071819-104035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The ciliate genus Paramecium served as one of the first model systems in microbial eukaryotic genetics, contributing much to the early understanding of phenomena as diverse as genome rearrangement, cryptic speciation, cytoplasmic inheritance, and endosymbiosis, as well as more recently to the evolution of mating types, introns, and roles of small RNAs in DNA processing. Substantial progress has recently been made in the area of comparative and population genomics. Paramecium species combine some of the lowest known mutation rates with some of the largest known effective populations, along with likely very high recombination rates, thereby harboring a population-genetic environment that promotes an exceptionally efficient capacity for selection. As a consequence, the genomes are extraordinarily streamlined, with very small intergenic regions combined with small numbers of tiny introns. The subject of the bulk of Paramecium research, the ancient Paramecium aurelia species complex, is descended from two whole-genome duplication events that retain high degrees of synteny, thereby providing an exceptional platform for studying the fates of duplicate genes. Despite having a common ancestor dating to several hundred million years ago, the known descendant species are morphologically indistinguishable, raising significant questions about the common view that gene duplications lead to the origins of evolutionary novelties.
Collapse
Affiliation(s)
- Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, Shandong Province, China
| | - Parul Johri
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jean-Francois Gout
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Jiahao Ni
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Timothy Licknack
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Yaohai Wang
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Jiao Pan
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China;
| | - Berenice Jiménez-Marín
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA;
| |
Collapse
|
8
|
Zwonitzer KD, Iverson ENK, Sterling JE, Weaver RJ, Maclaine BA, Havird JC. Disentangling Positive Selection from Relaxed Selection in Animal Mitochondrial Genomes. Am Nat 2023; 202:E121-E129. [PMID: 37792916 PMCID: PMC10955554 DOI: 10.1086/725805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractDisentangling different types of selection is a common goal in molecular evolution. Elevated dN/dS ratios (the ratio of nonsynonymous to synonymous substitution rates) in focal lineages are often interpreted as signs of positive selection. Paradoxically, relaxed purifying selection can also result in elevated dN/dS ratios, but tests to distinguish these two causes are seldomly implemented. Here, we reevaluated seven case studies describing elevated dN/dS ratios in animal mitochondrial DNA (mtDNA) and their accompanying hypotheses regarding selection. They included flightless lineages versus flighted lineages in birds, bats, and insects and physiological adaptations in snakes, two groups of electric fishes, and primates. We found that elevated dN/dS ratios were often not caused by the predicted mechanism, and we sometimes found strong support for the opposite mechanism. We discuss reasons why energetic hypotheses may be confounded by other selective forces acting on mtDNA and caution against overinterpreting singular molecular signals, including elevated dN/dS ratios.
Collapse
Affiliation(s)
- Kendra D. Zwonitzer
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Erik N. K. Iverson
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Jess E. Sterling
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Ryan J. Weaver
- Department of Ecology, Evolution, and Organismal Biology and Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa 50011
| | - Bradley A. Maclaine
- Department of Human Development and Family Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
9
|
Archetti M. Soft selection reduces loss of heterozygosity in asexual reproduction. J Evol Biol 2023; 36:1313-1327. [PMID: 37584223 DOI: 10.1111/jeb.14209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023]
Abstract
The adaptive value of sexual reproduction is still debated in evolutionary theory. It has been proposed that the advantage of sexual reproduction over asexual reproduction is to promote genetic diversity, to prevent the accumulation of harmful mutations or to preserve heterozygosity. Since these hypothetical advantages depend on the type of asexual reproduction, understanding how selection affects the taxonomic distribution of each type could help us discriminate between existing hypotheses. Here, I argue that soft selection, competition among embryos or offspring in selection arenas prior to the hard selection of the adult phase, reduces loss of heterozygosity in certain types of asexual reproduction. Since loss of heterozygosity leads to the unmasking of recessive deleterious mutations in the progeny of asexual individuals, soft selection facilitates the evolution of these types of asexual reproduction. Using a population genetics model, I calculate how loss of heterozygosity affects fitness for different types of apomixis and automixis, and I show that soft selection significantly reduces loss of heterozygosity, hence increases fitness, in apomixis with suppression of the first meiotic division and in automixis with central fusion, the most common types of asexual reproduction. Therefore, if sexual reproduction evolved to preserve heterozygosity, soft selection should be associated with these types of asexual reproduction. I discuss the evidence for this prediction and how this and other observations on the distribution of different types of asexual reproduction in nature is consistent with the heterozygosity hypothesis.
Collapse
Affiliation(s)
- Marco Archetti
- Department of Biology, W210 MSC, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
10
|
Bracewell RR, Stillman JH, Dahlhoff EP, Smeds E, Chatla K, Bachtrog D, Williams C, Rank NE. A chromosome-scale genome assembly and evaluation of mtDNA variation in the willow leaf beetle Chrysomela aeneicollis. G3 (BETHESDA, MD.) 2023; 13:jkad106. [PMID: 37178174 PMCID: PMC10320752 DOI: 10.1093/g3journal/jkad106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/08/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700-3,500 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here, we report a chromosome-scale genome assembly alongside a complete mitochondrial genome and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology with Tribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein-coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
Collapse
Affiliation(s)
- Ryan R Bracewell
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathon H Stillman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | | | - Elliott Smeds
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caroline Williams
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan E Rank
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| |
Collapse
|
11
|
Klucnika A, Mu P, Jezek J, McCormack M, Di Y, Bradshaw CR, Ma H. REC drives recombination to repair double-strand breaks in animal mtDNA. J Cell Biol 2023; 222:e202201137. [PMID: 36355348 PMCID: PMC9652705 DOI: 10.1083/jcb.202201137] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Mechanisms that safeguard mitochondrial DNA (mtDNA) limit the accumulation of mutations linked to mitochondrial and age-related diseases. Yet, pathways that repair double-strand breaks (DSBs) in animal mitochondria are poorly understood. By performing a candidate screen for mtDNA repair proteins, we identify that REC-an MCM helicase that drives meiotic recombination in the nucleus-also localizes to mitochondria in Drosophila. We show that REC repairs mtDNA DSBs by homologous recombination in somatic and germline tissues. Moreover, REC prevents age-associated mtDNA mutations. We further show that MCM8, the human ortholog of REC, also localizes to mitochondria and limits the accumulation of mtDNA mutations. This study provides mechanistic insight into animal mtDNA recombination and demonstrates its importance in safeguarding mtDNA during ageing and evolution.
Collapse
Affiliation(s)
- Anna Klucnika
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Peiqiang Mu
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jan Jezek
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthew McCormack
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ying Di
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Hansong Ma
- Wellcome/Cancer Research UK Gurdon Institute, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| |
Collapse
|
12
|
Weaver RJ, Rabinowitz S, Thueson K, Havird JC. Genomic Signatures of Mitonuclear Coevolution in Mammals. Mol Biol Evol 2022; 39:6775223. [PMID: 36288802 PMCID: PMC9641969 DOI: 10.1093/molbev/msac233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) and nuclear-encoded proteins are integrated in aerobic respiration, requiring co-functionality among gene products from fundamentally different genomes. Different evolutionary rates, inheritance mechanisms, and selection pressures set the stage for incompatibilities between interacting products of the two genomes. The mitonuclear coevolution hypothesis posits that incompatibilities may be avoided if evolution in one genome selects for complementary changes in interacting genes encoded by the other genome. Nuclear compensation, in which deleterious mtDNA changes are offset by compensatory nuclear changes, is often invoked as the primary mechanism for mitonuclear coevolution. Yet, direct evidence supporting nuclear compensation is rare. Here, we used data from 58 mammalian species representing eight orders to show strong correlations between evolutionary rates of mt and nuclear-encoded mt-targeted (N-mt) proteins, but not between mt and non-mt-targeted nuclear proteins, providing strong support for mitonuclear coevolution across mammals. N-mt genes with direct mt interactions also showed the strongest correlations. Although most N-mt genes had elevated dN/dS ratios compared to mt genes (as predicted under nuclear compensation), N-mt sites in close contact with mt proteins were not overrepresented for signs of positive selection compared to noncontact N-mt sites (contrary to predictions of nuclear compensation). Furthermore, temporal patterns of N-mt and mt amino acid substitutions did not support predictions of nuclear compensation, even in positively selected, functionally important residues with direct mitonuclear contacts. Overall, our results strongly support mitonuclear coevolution across ∼170 million years of mammalian evolution but fail to support nuclear compensation as the major mode of mitonuclear coevolution.
Collapse
Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA.,Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA
| | | | - Kiley Thueson
- Department of Integrative Biology, University of Texas, Austin, TX
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX
| |
Collapse
|
13
|
Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification. Proc Natl Acad Sci U S A 2022; 119:e2206076119. [PMID: 36260744 PMCID: PMC9618123 DOI: 10.1073/pnas.2206076119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Although interactions between the cytoplasmic and nuclear genomes occurred during diversification of many plants, the evolutionary conflicts due to cytonuclear interactions are poorly understood in crop breeding. Here, we constructed a pan-mitogenome and identified chimeric open reading frames (ORFs) generated by extensive structural variations (SVs). Meanwhile, short reads from 184 accessions of citrus species were combined to construct three variation maps for the nuclear, mitochondrial, and chloroplast genomes. The population genomic data showed discordant topologies between the cytoplasmic and nuclear genomes because of differences in mutation rates and levels of heteroplasmy from paternal leakage. An analysis of species-specific SVs indicated that mitochondrial heteroplasmy was common and that chloroplast heteroplasmy was undetectable. Interestingly, we found a prominent divergence in the mitogenomes and the highest genetic load in the, which may provide the basis for cytoplasmic male sterility (CMS) and thus influence the reshuffling of the cytoplasmic and nuclear genomes during hybridization. Using cytoplasmic replacement experiments, we identified a type of species-specific CMS in mandarin related to two chimeric mitochondrial genes. Our analyses indicate that cytoplasmic genomes from mandarin have rarely been maintained in hybrids and that paternal leakage produced very low levels of mitochondrial heteroplasmy in mandarin. A genome-wide association study (GWAS) provided evidence for three nuclear genes that encode pentatricopeptide repeat (PPR) proteins contributing to the cytonuclear interactions in the Citrus genus. Our study demonstrates the occurrence of evolutionary conflicts between cytoplasmic and nuclear genomes in citrus and has important implications for genetics and breeding.
Collapse
|
14
|
Moradi N, Ohadian Moghadam S, Heidarzadeh S. Application of next-generation sequencing in the diagnosis of gastric cancer. Scand J Gastroenterol 2022; 57:842-855. [PMID: 35293278 DOI: 10.1080/00365521.2022.2041717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.
Collapse
Affiliation(s)
- Narges Moradi
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| |
Collapse
|
15
|
Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
Collapse
Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
| |
Collapse
|
16
|
Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
Collapse
|
17
|
Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis. Nat Commun 2022; 13:651. [PMID: 35115503 PMCID: PMC8814026 DOI: 10.1038/s41467-022-28272-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Sustained mitochondrial fitness relies on coordinated biogenesis and clearance. Both processes are regulated by constant targeting of proteins into the organelle. Thus, mitochondrial protein import sets the pace for mitochondrial abundance and function. However, our understanding of mitochondrial protein translocation as a regulator of longevity remains enigmatic. Here, we targeted the main protein import translocases and assessed their contribution to mitochondrial abundance and organismal physiology. We find that reduction in cellular mitochondrial load through mitochondrial protein import system suppression, referred to as MitoMISS, elicits a distinct longevity paradigm. We show that MitoMISS triggers the mitochondrial unfolded protein response, orchestrating an adaptive reprogramming of metabolism. Glycolysis and de novo serine biosynthesis are causatively linked to longevity, whilst mitochondrial chaperone induction is dispensable for lifespan extension. Our findings extent the pro-longevity role of UPRmt and provide insight, relevant to the metabolic alterations that promote or undermine survival and longevity. Mitochondrial function is linked to lifespan. Here the authors show that inhibition of mitochondrial protein import leads to a reduction in mitochondrial abundance and extends lifespan in Caenorhabditis elegans via activation of glycolysis and de novo serine biosynthesis.
Collapse
|
18
|
Mishra A, Forche A, Anderson MZ. Parasexuality of Candida Species. Front Cell Infect Microbiol 2021; 11:796929. [PMID: 34966696 PMCID: PMC8711763 DOI: 10.3389/fcimb.2021.796929] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/19/2021] [Indexed: 12/03/2022] Open
Abstract
While most fungi have the ability to reproduce sexually, multiple independent lineages have lost meiosis and developed parasexual cycles in its place. Emergence of parasexual cycles is particularly prominent in medically relevant fungi from the CUG paraphyletic group of Candida species. Since the discovery of parasex in C. albicans roughly two decades ago, it has served as the model for Candida species. Importantly, parasex in C. albicans retains hallmarks of meiosis including genetic recombination and chromosome segregation, making it a potential driver of genetic diversity. Furthermore, key meiotic genes play similar roles in C. albicans parasex and highlights parallels between these processes. Yet, the evolutionary role of parasex in Candida adaptation and the extent of resulting genotypic and phenotypic diversity remain as key knowledge gaps in this facultative reproductive program. Here, we present our current understanding of parasex, the mechanisms governing its regulation, and its relevance to Candida biology.
Collapse
Affiliation(s)
- Abhishek Mishra
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, ME, United States
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
19
|
Kelly S. The economics of organellar gene loss and endosymbiotic gene transfer. Genome Biol 2021; 22:345. [PMID: 34930424 PMCID: PMC8686548 DOI: 10.1186/s13059-021-02567-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/06/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. RESULTS Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell. CONCLUSION Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.
Collapse
Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| |
Collapse
|
20
|
Mitochondrial Oxidative Stress-A Causative Factor and Therapeutic Target in Many Diseases. Int J Mol Sci 2021; 22:ijms222413384. [PMID: 34948180 PMCID: PMC8707347 DOI: 10.3390/ijms222413384] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 02/07/2023] Open
Abstract
The excessive formation of reactive oxygen species (ROS) and impairment of defensive antioxidant systems leads to a condition known as oxidative stress. The main source of free radicals responsible for oxidative stress is mitochondrial respiration. The deleterious effects of ROS on cellular biomolecules, including DNA, is a well-known phenomenon that can disrupt mitochondrial function and contribute to cellular damage and death, and the subsequent development of various disease processes. In this review, we summarize the most important findings that implicated mitochondrial oxidative stress in a wide variety of pathologies from Alzheimer disease (AD) to autoimmune type 1 diabetes. This review also discusses attempts to affect oxidative stress as a therapeutic avenue.
Collapse
|
21
|
Khan KA. Genetic diversity and phylogenetic relationship among the western and the Asian honey bees based on two mitochondrial gene segments (COI and ND5). Saudi J Biol Sci 2021; 28:6853-6860. [PMID: 34866985 PMCID: PMC8626216 DOI: 10.1016/j.sjbs.2021.07.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 11/25/2022] Open
Abstract
The Asian honey bee species i.e., Apis cerana (the eastern honey bee), A. dorsata (the giant honey bee), and the western or European honey bee (A. mellifera) collected from Pakistan were studied using partial sequences from two mitochondrial genes (i) the Cytochrome c oxidase I (COI) and (ii) the mitochondrially encoded NADH dehydrogenase 5 (ND5) and then compared with other honey bees sequences (already submitted from different countries around the globe) obtained after the national center for biotechnology information (NCBI). DNA sequences were analyzed employing molecular evolutionary genetics analysis and Kimura 2-parameter model, neighbor-joining method was applied to investigate phylogenetic relationships, and DNA sequence polymorphism was applied to measure the genetic diversity within the genus Apis. The phylogenetic analyses yielded consistent results. Based on COI gene fragment in two Asian and European honey bee species from Pakistan and from other countries showed considerable genetic diversity levels and deviation among the species. While in contrast the phylogenetic analyses based on ND5 gene fragment in Asian and European honey bee species from Pakistan and other countries showed comparatively higher genetic diversity indices and variations than the COI gene. So, in the genus Apis, the mitochondrial ND5 region has shown the possibility to answer the interactions among species. A further detailed work (by linking the analysis of other genomic and mitochondrial genes) is required for good quality solution to establish the concise genetic diversity and interaction among the Apis species. The objective of this study was to explore the extent of genetic differences and phylogenetic links among the three kinds of honey bee species from Pakistan and comparing them with other bee species around the globe.
Collapse
Affiliation(s)
- Khalid Ali Khan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| |
Collapse
|
22
|
Rodríguez E, Grover Thomas F, Camus MF, Lane N. Mitonuclear Interactions Produce Diverging Responses to Mild Stress in Drosophila Larvae. Front Genet 2021; 12:734255. [PMID: 34603395 PMCID: PMC8482813 DOI: 10.3389/fgene.2021.734255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial function depends on direct interactions between respiratory proteins encoded by genes in two genomes, mitochondrial and nuclear, which evolve in very different ways. Serious incompatibilities between these genomes can have severe effects on development, fitness and viability. The effect of subtle mitonuclear mismatches has received less attention, especially when subject to mild physiological stress. Here, we investigate how two distinct physiological stresses, metabolic stress (high-protein diet) and redox stress [the glutathione precursor N-acetyl cysteine (NAC)], affect development time, egg-to-adult viability, and the mitochondrial physiology of Drosophila larvae with an isogenic nuclear background set against three mitochondrial DNA (mtDNA) haplotypes: one coevolved (WT) and two slightly mismatched (COX and BAR). Larvae fed the high-protein diet developed faster and had greater viability in all haplotypes. The opposite was true of NAC-fed flies, especially those with the COX haplotype. Unexpectedly, the slightly mismatched BAR larvae developed fastest and were the most viable on both treatments, as well as control diets. These changes in larval development were linked to a shift to complex I-driven mitochondrial respiration in all haplotypes on the high-protein diet. In contrast, NAC increased respiration in COX larvae but drove a shift toward oxidation of proline and succinate. The flux of reactive oxygen species was increased in COX larvae treated with NAC and was associated with an increase in mtDNA copy number. Our results support the notion that subtle mitonuclear mismatches can lead to diverging responses to mild physiological stress, undermining fitness in some cases, but surprisingly improving outcomes in other ostensibly mismatched fly lines.
Collapse
Affiliation(s)
- Enrique Rodríguez
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Finley Grover Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - M Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| |
Collapse
|
23
|
Piccinini G, Iannello M, Puccio G, Plazzi F, Havird JC, Ghiselli F. Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves. Mol Biol Evol 2021; 38:2597-2614. [PMID: 33616640 PMCID: PMC8136519 DOI: 10.1093/molbev/msab054] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the “nuclear compensation hypothesis,” a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with “doubly uniparental” mtDNA inheritance. Our data showed strong and clear signals of mitonuclear coevolution. NuOXPHOS subunits had concordant topologies with mtOXPHOS subunits, contrary to previous phylogenies based on nuclear genes lacking mt interactions. Evolutionary rates between mt and nuOXPHOS subunits were also highly correlated compared with non-OXPHO-interacting nuclear genes. Nuclear subunits of chimeric OXPHOS complexes (I, III, IV, and V) also had higher dN/dS ratios than Complex II, which is formed exclusively by nuDNA-encoded subunits. However, we did not find evidence of nuclear compensation: mitochondria-encoded subunits showed similar dN/dS ratios compared with nuclear-encoded subunits, contrary to most previously studied bilaterian animals. Moreover, no site-specific signals of compensatory positive selection were detected in nuOXPHOS genes. Our analyses extend the evidence for mitonuclear coevolution to a new taxonomic group, but we propose a reconsideration of the nuclear compensation hypothesis.
Collapse
Affiliation(s)
- Giovanni Piccinini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| |
Collapse
|
24
|
Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen DE, Hoff KJ, Nachweide S, Romoth L, Walden KKO, Guigo R, Stanke M, Narzisi G, Yandell M, Robertson HM, Koeniger N, Chantawannakul P, Schatz MC, Worley KC, Robinson GE, Elsik CG, Rueppell O. The genomic basis of evolutionary differentiation among honey bees. Genome Res 2021; 31:1203-1215. [PMID: 33947700 PMCID: PMC8256857 DOI: 10.1101/gr.272310.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.
Collapse
Affiliation(s)
- Bertrand Fouks
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, 48149 Münster, Germany
| | - Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California 95161, USA
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Hung N Nguyen
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Jacob Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
| | - Francisco Camara
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Daniel Ence
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Katharina J Hoff
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Stefanie Nachweide
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Lars Romoth
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Mario Stanke
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | | | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nikolaus Koeniger
- Department of Behavioral Physiology and Sociobiology (Zoology II), University of Würzburg, 97074 Würzburg, Germany
| | - Panuwan Chantawannakul
- Environmental Science Research Center (ESRC) and Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gene E Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christine G Elsik
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| |
Collapse
|
25
|
Neice AA, McRae SB. An eDNA diagnostic test to detect a rare, secretive marsh bird. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
|
26
|
Lopez KA, McDiarmid CS, Griffith SC, Lovette IJ, Hooper DM. Evaluating evidence of mitonuclear incompatibilities with the sex chromosomes in an avian hybrid zone. Evolution 2021; 75:1395-1414. [PMID: 33908624 DOI: 10.1111/evo.14243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 02/15/2021] [Accepted: 04/11/2021] [Indexed: 12/13/2022]
Abstract
The exploration of hybrid zones and the intergenomic conflicts exposed through hybridization provide windows into the processes of divergence and speciation. Sex chromosomes and mitonuclear incompatibilities have strong associations with the genetics of hybrid dysfunction. In ZW sex-determining systems, maternal co-inheritance of the mitochondrial and W chromosomes immediately exposes incompatibilities between these maternal contributions of one species and the Z chromosome of another. We analyze mitochondrial and Z chromosome admixture in the long-tailed finch (Poephila acuticauda) of Australia, where hybridizing subspecies differ prominently in Z chromosome genotype and in bill color, yet the respective centers of geographic admixture for these two traits are offset by 350 km. We report two well-defined mitochondrial clades that diverged ∼0.5 million years ago. Mitochondrial contact is geographically co-located within a hybrid zone of Z chromosome admixture and is displaced from bill color admixture by nearly 400 km. Consistent with Haldane's rule expectations, hybrid zone females are significantly less likely than males to carry an admixed Z chromosome or have mismatched Z-mitochondrial genotypes. Furthermore, there are significantly fewer than expected mitonuclear mismatches in hybrid zone females and paternal backcross males. Results suggest a potential for mitonuclear/sex chromosome incompatibilities in the emergence of reproductive isolation in this system.
Collapse
Affiliation(s)
- Kelsie A Lopez
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Callum S McDiarmid
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
| | - Daniel M Hooper
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA.,Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| |
Collapse
|
27
|
Chak STC, Baeza JA, Barden P. Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps. Mol Biol Evol 2021; 38:1372-1383. [PMID: 33211078 PMCID: PMC8480187 DOI: 10.1093/molbev/msaa297] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm-lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits-extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.
Collapse
Affiliation(s)
- Solomon T C Chak
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Department of Biological Sciences, SUNY College at Old Westbury, Old Westbury, NY
| | - Juan Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC
- Smithsonian Institution, Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
| |
Collapse
|
28
|
Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
Collapse
Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
| |
Collapse
|
29
|
Zia A, Farkhondeh T, Pourbagher-Shahri AM, Samarghandian S. The Roles of mitochondrial dysfunction and Reactive Oxygen Species in Aging and Senescence. Curr Mol Med 2021; 22:37-49. [PMID: 33602082 DOI: 10.2174/1566524021666210218112616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 11/22/2022]
Abstract
The aging process deteriorates organs' function at different levels, causing its progressive decline to resist stress, damage, and disease. In addition to alterations in metabolic control and gene expression, the rate of aging has been connected with the generation of high amounts of Reactive Oxygen Species (ROS). The essential perspective in free radical biology is that reactive oxygen species (ROS) and free radicals are toxic, mostly cause direct biological damage to targets, and are thus a major cause of oxidative stress. Different enzymatic and non-enzymatic compounds in the cells have roles in neutralizing this toxicity. Oxidative damage in aging is mostly high in particular molecular targets, such as mitochondrial DNA and aconitase, and oxidative stress in mitochondria can cause tissue aging across intrinsic apoptosis. Mitochondria's function and morphology are impaired through aging, following a decrease in the membrane potential by an increase in peroxide generation and size of the organelles. Telomeres may be the significant trigger of replicative senescence. Oxidative stress accelerates telomere loss, whereas antioxidants slow it down. Oxidative stress is a crucial modulator of telomere shortening, and that telomere-driven replicative senescence is mainly a stress response. The age-linked mitochondrial DNA mutation and protein dysfunction aggregate in some organs like the brain and skeletal muscle, thus contributing considerably to these post-mitotic tissues' aging. The aging process is mostly due to accumulated damage done by harmful species in some macromolecules such proteins, DNA, and lipids. The degradation of non-functional, oxidized proteins is a crucial part of the antioxidant defenses of cells, in which the clearance of these proteins occurs through autophagy in the cells, which is known as mitophagy for mitochondria.
Collapse
Affiliation(s)
- Aliabbas Zia
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran. Iran
| | - Tahereh Farkhondeh
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand. Iran
| | | | - Saeed Samarghandian
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur. Iran
| |
Collapse
|
30
|
Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Syst Biol 2021; 70:908-921. [PMID: 33410870 DOI: 10.1093/sysbio/syaa085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (T. canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and T. umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.
Collapse
Affiliation(s)
- Brice A J Sarver
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
| | | | - David Sneddon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho.,UC-Davis Genome Center, Davis, California
| | | | | | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana.,Wildlife Biology Program, University of Montana, Missoula, Montana
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
| |
Collapse
|
31
|
Kraft DW, Conklin EE, Barba EW, Hutchinson M, Toonen RJ, Forsman ZH, Bowen BW. Genomics versus mtDNA for resolving stock structure in the silky shark ( Carcharhinus falciformis). PeerJ 2020; 8:e10186. [PMID: 33150082 PMCID: PMC7585369 DOI: 10.7717/peerj.10186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.
Collapse
Affiliation(s)
- Derek W. Kraft
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Emily E. Conklin
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Evan W. Barba
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Melanie Hutchinson
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
- Joint Institute of Marine and Atmospheric Research, Pacific Islands Fisheries Science Center, NOAA, University of Hawai’i, Honolulu, HI, USA
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Zac H. Forsman
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Brian W. Bowen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| |
Collapse
|
32
|
Aljasmi FA, Vijayan R, Sudalaimuthuasari N, Souid AK, Karuvantevida N, Almaskari R, Mohammed Abdul Kader H, Kundu B, Michel Hazzouri K, Amiri KMA. Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population. Genes (Basel) 2020; 11:genes11080876. [PMID: 32752197 PMCID: PMC7464197 DOI: 10.3390/genes11080876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.
Collapse
Affiliation(s)
- Fatma A Aljasmi
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Ranjit Vijayan
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Abdul-Kader Souid
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Raja Almaskari
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Biduth Kundu
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled M A Amiri
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| |
Collapse
|
33
|
Mitochondria, spermatogenesis, and male infertility - An update. Mitochondrion 2020; 54:26-40. [PMID: 32534048 DOI: 10.1016/j.mito.2020.06.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/14/2022]
Abstract
The incorporation of mitochondria in the eukaryotic cell is one of the most enigmatic events in the course of evolution. This important organelle was thought to be only the powerhouse of the cell, but was later learnt to perform many other indispensable functions in the cell. Two major contributions of mitochondria in spermatogenesis concern energy production and apoptosis. Apart from this, mitochondria also participate in a number of other processes affecting spermatogenesis and fertility. Mitochondria in sperm are arranged in the periphery of the tail microtubules to serve to energy demand for motility. Apart from this, the role of mitochondria in germ cell proliferation, mitotic regulation, and the elimination of germ cells by apoptosis are now well recognized. Eventually, mutations in the mitochondrial genome have been reported in male infertility, particularly in sluggish sperm (asthenozoospermia); however, heteroplasmy in the mtDNA and a complex interplay between the nucleus and mitochondria affect their penetrance. In this article, we have provided an update on the role of mitochondria in various events of spermatogenesis and male fertility and on the correlation of mitochondrial DNA mutations with male infertility.
Collapse
|
34
|
Sreedhar A, Aguilera-Aguirre L, Singh KK. Mitochondria in skin health, aging, and disease. Cell Death Dis 2020; 11:444. [PMID: 32518230 PMCID: PMC7283348 DOI: 10.1038/s41419-020-2649-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 02/08/2023]
Abstract
The skin is a high turnover organ, and its constant renewal depends on the rapid proliferation of its progenitor cells. The energy requirement for these metabolically active cells is met by mitochondrial respiration, an ATP generating process driven by a series of protein complexes collectively known as the electron transport chain (ETC) that is located on the inner membrane of the mitochondria. However, reactive oxygen species (ROS) like superoxide, singlet oxygen, peroxides are inevitably produced during respiration and disrupt macromolecular and cellular structures if not quenched by the antioxidant system. The oxidative damage caused by mitochondrial ROS production has been established as the molecular basis of multiple pathophysiological conditions, including aging and cancer. Not surprisingly, the mitochondria are the primary organelle affected during chronological and UV-induced skin aging, the phenotypic manifestations of which are the direct consequence of mitochondrial dysfunction. Also, deletions and other aberrations in the mitochondrial DNA (mtDNA) are frequent in photo-aged skin and skin cancer lesions. Recent studies have revealed a more innate role of the mitochondria in maintaining skin homeostasis and pigmentation, which are affected when the essential mitochondrial functions are impaired. Some common and rare skin disorders have a mitochondrial involvement and include dermal manifestations of primary mitochondrial diseases as well as congenital skin diseases caused by damaged mitochondria. With studies increasingly supporting the close association between mitochondria and skin health, its therapeutic targeting in the skin-either via an ATP production boost or free radical scavenging-has gained attention from clinicians and aestheticians alike. Numerous bioactive compounds have been identified that improve mitochondrial functions and have proved effective against aged and diseased skin. In this review, we discuss the essential role of mitochondria in regulating normal and abnormal skin physiology and the possibility of targeting this organelle in various skin disorders.
Collapse
Affiliation(s)
| | | | - Keshav K Singh
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
- Integartive Center For Aging Research and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| |
Collapse
|
35
|
Xiao F, Li M, Wang J, Liu J, Li J, Fang H, Lyu J, Shen L. Association between mitochondrial DNA haplogroup variation and coronary artery disease. Nutr Metab Cardiovasc Dis 2020; 30:960-966. [PMID: 32402592 DOI: 10.1016/j.numecd.2020.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/01/2020] [Accepted: 03/10/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND AIMS Mitochondrial DNA (mtDNA) haplogroups have been associated with the development of coronary artery disease (CAD) in European populations. However, the specific mtDNA haplogroups associated with CAD have not been investigated in Chinese populations. METHODS AND RESULTS Here, we carried out a case-control study including 1036 and 481 CAD patients and 973 and 511 geographically matched asymptomatic control subjects in southern and northern China, respectively. After adjusting for age and gender, our results indicated that mtDNA haplogroups are not associated with the occurrence of CAD and its subcategories, acute coronary syndromes and stable coronary heart disease, in both southern and northern Chinese populations. By focusing on the southern Chinese population, we further revealed that mtDNA haplogroups are not associated with CAD severity. Type 2 diabetes (T2D) and hypertension are two key driving factors for the development of CAD, nonetheless, we found that the frequencies of the 12 studied mtDNA haplogroups did not differ between patients with and without T2D or hypertension. CONCLUSION mtDNA haplogroups are not associated with the occurrence of CAD or its subcategories in Chinese populations. Other factors such as environment and nuclear genetic background may contribute to the occurrence of CAD.
Collapse
Affiliation(s)
- Fangyi Xiao
- Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meinan Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junyi Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiangtao Liu
- Department of Orthopedics Surgery, Ningbo HwaMei Hospital, University of Chinese Academy of Science, Ningbo, Zhejiang, China
| | - Jin Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China; College of Laboratory Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Lijun Shen
- Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| |
Collapse
|
36
|
Durairajanayagam D, Singh D, Agarwal A, Henkel R. Causes and consequences of sperm mitochondrial dysfunction. Andrologia 2020; 53:e13666. [PMID: 32510691 DOI: 10.1111/and.13666] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria have multiple functions, including synthesis of adenine triphosphate, production of reactive oxygen species, calcium signalling, thermogenesis and apoptosis. Mitochondria have a significant contribution in regulating the various physiological aspects of reproductive function, from spermatogenesis up to fertilisation. Mitochondrial functionality and intact mitochondrial membrane potential are a pre-requisite for sperm motility, hyperactivation, capacitation, acrosin activity, acrosome reaction and DNA integrity. Optimal mitochondrial activity is therefore crucial for human sperm function and semen quality. However, the precise role of mitochondria in spermatozoa remains to be fully explored. Defects in sperm mitochondrial function severely impair the maintenance of energy production required for sperm motility and may be an underlying cause of asthenozoospermia. Sperm mtDNA is susceptible to oxidative damage and mutations that could compromise sperm function leading to infertility. Males with abnormal semen parameters have increased mtDNA copy number and reduced mtDNA integrity. This review discusses the role of mitochondria in sperm function, along with the causes and impact of its dysfunction on male fertility. Greater understanding of sperm mitochondrial function and its correlation with sperm quality could provide further insights into their contribution in the assessment of the infertile male.
Collapse
Affiliation(s)
- Damayanthi Durairajanayagam
- Department of Physiology, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, Sungai Buloh, Malaysia
| | - Dipty Singh
- Department of Neuroendocrinology, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive Health (NIRRH), Mumbai, India
| | - Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Ralf Henkel
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.,Department of Medical Bioscience, Faculty of Natural Science, University of the Western Cape, Belville, South Africa
| |
Collapse
|
37
|
Rolling-Circle Replication in Mitochondrial DNA Inheritance: Scientific Evidence and Significance from Yeast to Human Cells. Genes (Basel) 2020; 11:genes11050514. [PMID: 32384722 PMCID: PMC7288456 DOI: 10.3390/genes11050514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/23/2022] Open
Abstract
Studies of mitochondrial (mt)DNA replication, which forms the basis of mitochondrial inheritance, have demonstrated that a rolling-circle replication mode exists in yeasts and human cells. In yeast, rolling-circle mtDNA replication mediated by homologous recombination is the predominant pathway for replication of wild-type mtDNA. In human cells, reactive oxygen species (ROS) induce rolling-circle replication to produce concatemers, linear tandem multimers linked by head-to-tail unit-sized mtDNA that promote restoration of homoplasmy from heteroplasmy. The event occurs ahead of mtDNA replication mechanisms observed in mammalian cells, especially under higher ROS load, as newly synthesized mtDNA is concatemeric in hydrogen peroxide-treated human cells. Rolling-circle replication holds promise for treatment of mtDNA heteroplasmy-attributed diseases, which are regarded as incurable. This review highlights the potential therapeutic value of rolling-circle mtDNA replication.
Collapse
|
38
|
Molenaars M, Daniels EG, Meurs A, Janssens GE, Houtkooper RH. Mitochondrial cross-compartmental signalling to maintain proteostasis and longevity. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190414. [PMID: 32362258 DOI: 10.1098/rstb.2019.0414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lifespan in eukaryotic species can be prolonged by shifting from cellular states favouring growth to those favouring maintenance and stress resistance. For instance, perturbations in mitochondrial oxidative phosphorylation (OXPHOS) can shift cells into this latter state and extend lifespan. Because mitochondria rely on proteins synthesized from nuclear as well as mitochondrial DNA, they need to constantly send and receive messages from other compartments of the cell in order to function properly and maintain homeostasis, and lifespan extension is often dependent on this cross-compartmental signalling. Here, we describe the mechanisms of bi-directional mitochondrial cross-compartmental signalling resulting in proteostasis and longevity. These proteostasis mechanisms are highly context-dependent, governed by the origin and extent of stress. Furthermore, we discuss the translatability of these mechanisms and explore therapeutic developments, such as the antibiotic studies targeting mitochondria or mitochondria-derived peptides as therapies for age-related diseases such as neurodegeneration and cancer. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
Collapse
Affiliation(s)
- Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Eileen G Daniels
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Amber Meurs
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, The Netherlands
| |
Collapse
|
39
|
Cavalcante GC, Magalhães L, Ribeiro-dos-Santos Â, Vidal AF. Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity. Int J Mol Sci 2020; 21:E1838. [PMID: 32155913 PMCID: PMC7084767 DOI: 10.3390/ijms21051838] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are organelles responsible for several functions involved in cellular balance, including energy generation and apoptosis. For decades now, it has been well-known that mitochondria have their own genetic material (mitochondrial DNA), which is different from nuclear DNA in many ways. More recently, studies indicated that, much like nuclear DNA, mitochondrial DNA is regulated by epigenetic factors, particularly DNA methylation and non-coding RNAs (ncRNAs). This field is now called mitoepigenetics. Additionally, it has also been established that nucleus and mitochondria are constantly communicating to each other to regulate different cellular pathways. However, little is known about the mechanisms underlying mitoepigenetics and nuclei-mitochondria communication, and also about the involvement of the ncRNAs in mitochondrial functions and related diseases. In this context, this review presents the state-of-the-art knowledge, focusing on ncRNAs as new players in mitoepigenetic regulation and discussing future perspectives of these fields.
Collapse
Affiliation(s)
- Giovanna C. Cavalcante
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Researches, Federal University of Pará, Rua dos Mundurucus, 4487, 66073-005 Belém, PA, Brazil
| | - Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| |
Collapse
|
40
|
Evolving mtDNA populations within cells. Biochem Soc Trans 2020; 47:1367-1382. [PMID: 31484687 PMCID: PMC6824680 DOI: 10.1042/bst20190238] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular mtDNA populations, changing cell-to-cell distributions, means, and variances of mutant mtDNA load over time. As mtDNA mutant load has nonlinear effects on cell functionality, and cell functionality has nonlinear effects on tissue performance, these statistics of cellular mtDNA populations play vital roles in health, disease, and inheritance. This mini review will describe some of the better-known ways in which these populations change over time in different organisms, highlighting the importance of quantitatively understanding both mutant load mean and variance. Due to length constraints, we cannot attempt to be comprehensive but hope to provide useful links to some of the many excellent studies on these topics.
Collapse
|
41
|
Havird JC, McConie HJ. Sexually Antagonistic Mitonuclear Coevolution in Duplicate Oxidative Phosphorylation Genes. Integr Comp Biol 2020; 59:864-874. [PMID: 30942855 DOI: 10.1093/icb/icz021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Mitochondrial function is critical in eukaryotes. To maintain an adequate supply of energy, precise interactions must be maintained between nuclear- and mitochondrial-encoded gene products. Such interactions are paramount in chimeric enzymes such as the oxidative phosphorylation (OXPHOS) complexes. Mutualistic coevolution between the two genomes has therefore been suggested to be a critical, ubiquitous feature of eukaryotes that acts to maintain cellular function. However, mitochondrial genomes can also act selfishly and increase their own transmission at the expense of organismal function. For example, male-harming mutations are predisposed to accumulate in mitochondrial genomes due to their maternal inheritance ("mother's curse"). Here, we investigate sexually antagonistic mitonuclear coevolution in nuclear-encoded OXPHOS paralogs from mammals and Drosophila. These duplicate genes are highly divergent but must interact with the same set of mitochondrial-encoded genes. Many such paralogs show testis-specific expression, prompting previous hypotheses suggesting they may have evolved under selection to counteract male-harming mitochondrial mutations. We found increased rates of evolution in OXPHOS paralogs with testis-specific expression in mammals and Drosophila, supporting this hypothesis. However, further analyses suggested such patterns may be due to relaxed, not positive selection, especially in Drosophila. Structural data also suggest that mitonuclear interactions do not play a major role in the evolution of many OXPHOS paralogs in a consistent way. In conclusion, no single OXPHOS paralog met all our criteria for being under selection to counteract male-harming mitochondrial mutations. We discuss alternative explanations for the drastic patterns of evolution in these genes, including mutualistic mitonuclear coevolution, adaptive subfunctionalization after gene duplication, and relaxed selection on OXPHOS in male tissues.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hunter J McConie
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
42
|
Tobler M, Barts N, Greenway R. Mitochondria and the Origin of Species: Bridging Genetic and Ecological Perspectives on Speciation Processes. Integr Comp Biol 2020; 59:900-911. [PMID: 31004483 DOI: 10.1093/icb/icz025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria have been known to be involved in speciation through the generation of Dobzhansky-Muller incompatibilities, where functionally neutral co-evolution between mitochondrial and nuclear genomes can cause dysfunction when alleles are recombined in hybrids. We propose that adaptive mitochondrial divergence between populations can not only produce intrinsic (Dobzhansky-Muller) incompatibilities, but could also contribute to reproductive isolation through natural and sexual selection against migrants, post-mating prezygotic isolation, as well as by causing extrinsic reductions in hybrid fitness. We describe how these reproductive isolating barriers can potentially arise through adaptive divergence of mitochondrial function in the absence of mito-nuclear coevolution, a departure from more established views. While a role for mitochondria in the speciation process appears promising, we also highlight critical gaps of knowledge: (1) many systems with a potential for mitochondrially-mediated reproductive isolation lack crucial evidence directly linking reproductive isolation and mitochondrial function; (2) it often remains to be seen if mitochondrial barriers are a driver or a consequence of reproductive isolation; (3) the presence of substantial gene flow in the presence of mito-nuclear incompatibilities raises questions whether such incompatibilities are strong enough to drive speciation to completion; and (4) it remains to be tested how mitochondrial effects on reproductive isolation compare when multiple mechanisms of reproductive isolation coincide. We hope this perspective and the proposed research plans help to inform future studies of mitochondrial adaptation in a manner that links genotypic changes to phenotypic adaptations, fitness, and reproductive isolation in natural systems, helping to clarify the importance of mitochondria in the formation and maintenance of biological diversity.
Collapse
Affiliation(s)
- M Tobler
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - N Barts
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - R Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
43
|
Koutsovoulos GD, Marques E, Arguel M, Duret L, Machado ACZ, Carneiro RMDG, Kozlowski DK, Bailly‐Bechet M, Castagnone‐Sereno P, Albuquerque EVS, Danchin EGJ. Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest. Evol Appl 2020; 13:442-457. [PMID: 31993088 PMCID: PMC6976969 DOI: 10.1111/eva.12881] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The root-knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four "host races" had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4-gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro-economic challenges.
Collapse
Affiliation(s)
| | - Eder Marques
- Embrapa Recursos Genéticos e BiotecnologiaBrasíliaBrazil
| | | | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558CNRSUniversité Lyon 1Université de LyonVilleurbanneFrance
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Repetti SI, Jackson CJ, Judd LM, Wick RR, Holt KE, Verbruggen H. The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PeerJ 2020; 8:e8273. [PMID: 31915577 PMCID: PMC6944098 DOI: 10.7717/peerj.8273] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
Collapse
Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | | | - Louise M Judd
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
45
|
Whole mitochondrial genome sequencing highlights mitochondrial impact in gastric cancer. Sci Rep 2019; 9:15716. [PMID: 31673122 PMCID: PMC6823544 DOI: 10.1038/s41598-019-51951-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are organelles that perform major roles in cellular operation. Thus, alterations in mitochondrial genome (mtGenome) may lead to mitochondrial dysfunction and cellular deregulation, influencing carcinogenesis. Gastric cancer (GC) is one of the most incident and mortal types of cancer in Brazil, particularly in the Amazon region. Here, we sequenced and compared the whole mtGenome extracted from FFPE tissue samples of GC patients (tumor and internal control – IC) and cancer-free individuals (external control – EC) from this region. We found 3-fold more variants and up to 9-fold more heteroplasmic regions in tumor when compared to paired IC samples. Moreover, tumor presented more heteroplasmic variants when compared to EC, while IC and EC showed no significant difference when compared to each other. Tumor also presented substantially more variants in the following regions: MT-RNR1, MT-ND5, MT-ND4, MT-ND2, MT-DLOOP1 and MT-CO1. In addition, our haplogroup results indicate an association of Native American ancestry (particularly haplogroup C) to gastric cancer development. To the best of our knowledge, this is the first study to sequence the whole mtGenome from FFPE samples and to apply mtGenome analysis in association to GC in Brazil.
Collapse
|
46
|
Arias-Robledo G, Wall R, Szpila K, Shpeley D, Whitworth T, Stark T, King R, Stevens J. Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:218-230. [PMID: 31667085 PMCID: PMC6812060 DOI: 10.1016/j.ijppaw.2019.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 11/16/2022]
Abstract
Lucilia (Diptera: Calliphoridae) is a genus of blowflies comprised largely of saprophagous and facultative parasites of livestock. Lucilia bufonivora, however, exhibits a unique form of obligate parasitism of amphibians, typically affecting wild hosts. The evolutionary route by which amphibian myiasis arose, however, is not well understood due to the low phylogenetic resolution in existing nuclear DNA phylogenies. Furthermore, the timing of when specificity for amphibian hosts arose in L. bufonivora is also unknown. In addition, this species was recently reported for the first time in North America (Canada) and, to date, no molecular studies have analysed the evolutionary relationships between individuals from Eastern and Western hemispheres. To provide broader insights into the evolution of the amphibian parasitic life history trait and to estimate when the trait first arose, a time-scaled phylogeny was inferred from a concatenated data set comprising mtDNA, nDNA and non-coding rDNA (COX1, per and ITS2 respectively). Specimens from Canada, the UK, Poland, Switzerland, the Netherlands and Germany were analysed, as well as individuals from its sister taxa, the saprophage Lucilia silvarum and a Nearctic species also implicated in amphibian myiasis, Lucilia elongata. Obligate amphibian parasitism appears to have arisen ~4 mya, likely as a result of niche displacement of a saprophagous/facultative parasite ancestor. Consistent paraphyly of L. bufonivora with respect to L. elongata across single-gene phylogenies and high mtDNA genetic distances between Nearctic and Palearctic individuals suggest on-going cryptic speciation facilitated by geographical isolation. These findings suggest that recent reports of L. bufonivora in the Nearctic do not constitute a recent introduction, but instead suggest that it remained unrecorded due to taxonomic confusion and low abundance. This is the first study to confirm the involvement of L. bufonivora in amphibian myiasis in Canada using DNA-based identification methods. Within Lucilia, a small genus of blowflies mostly comprised of carrion-breeding species, obligate parasitism for amphibians evolved around 4 mya. Geographic isolation between Nearctic and Palearctic lineages is facilitating on-going cryptic speciation of Lucilia bufonivora. First positive identification of L. bufonivora from two confirmed cases of amphibian myiasis in North America.
Collapse
Affiliation(s)
- G. Arias-Robledo
- Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
- School of Biological Sciences, University of Bristol, UK
- Corresponding author. College of Life and Environmental Sciences, University of Exeter, Prince of Wales Rd, Exeter, EX4 4PS, UK.
| | - R. Wall
- School of Biological Sciences, University of Bristol, UK
| | - K. Szpila
- Department of Ecology and Biogeography, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - D. Shpeley
- E.H. Strickland Entomological Museum, Department of Biological Sciences, University of Alberta, Canada
| | - T. Whitworth
- Department of Entomology, Washington State University, Pullman, USA
| | - T. Stark
- Reptile, Amphibian and Fish Conservation Netherlands (RAVON), Nijmegen, the Netherlands
| | - R.A. King
- Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| | - J.R. Stevens
- Biosciences, College of Life and Environmental Sciences, University of Exeter, UK
| |
Collapse
|
47
|
Feng B, Wang K, Yang Y, Wang G, Zhang H, Liu Y, Jiang K. Ultrasensitive recognition of AP sites in DNA at the single-cell level: one molecular rotor sequentially self-regulated to form multiple different stable conformations. Chem Sci 2019; 10:10373-10380. [PMID: 32110326 PMCID: PMC6988597 DOI: 10.1039/c9sc04140k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/20/2019] [Indexed: 01/22/2023] Open
Abstract
Molecular rotors self-regulate their conformations to emit different ultrasensitive recognition signals for AP sites in DNA at the single-cell level.
The AP site is a primary form of DNA damage. Its presence alters the genetic structure and eventually causes malignant diseases. AP sites generally present a high-speed dynamic change in the DNA sequence. Thus, precisely recognizing AP sites is difficult, especially at the single-cell level. To address this issue, we provide a broad-spectrum strategy to design a group of molecular rotors, that is, a series of nonfluorescent 2-(4-vinylbenzylidene)malononitrile derivatives (BMN-Fluors), which constantly display molecular rotation in a free state. Interestingly, after activating the relevant specific-recognition reaction (i.e., hydrolysis reaction of benzylidenemalononitrile) only in the AP-site cavity within a short time (approximately 300 s), each of these molecules can be fixed into this cavity and can sequentially self-regulate to form different stable conformations in accordance with the cavity size. The different stable conformations possess various HOMO–LUMO energy gaps in their excited state. This condition enables the AP site to emit different fluorescence signals at various wavelengths. Given the different self-regulation abilities of the conformations, the series of molecules, BMN-Fluors, can emit different types of signals, including an “OFF–ON” single-channel signal, a “ratio” double-channel signal, and even a precise multichannel signal. Among the BMN-Fluors derivatives, d1-BMN can sequentially self-regulate to form five stable conformations, thereby resulting in the emission of a five-channel signal for different AP sites in situ. Thus, d1-BMN can be used as a probe to ultrasensitively recognize the AP site with precise fluorescent signals at the single-cell level. This design strategy can be generalized to develop additional single-channel to multichannel signal probes to recognize other specific sites in DNA sequences in living organisms.
Collapse
Affiliation(s)
- Beidou Feng
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Kui Wang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Yonggang Yang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Ge Wang
- Xinxiang Medical University , Xinxiang 453000 , P. R. China
| | - Hua Zhang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Yufang Liu
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| | - Kai Jiang
- Henan Key Laboratory of Green Chemical Media and Reactions , Ministry of Education , Key Laboratory of Green Chemical Media and Reactions; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals , Henan Key Laboratory of Organic Functional Molecules and Drug Innovation , School of Chemistry and Chemical Engineering , School of Environment , College of Physics and Materials Science , Henan Normal University , Xinxiang 453007 , China .
| |
Collapse
|
48
|
Johri P, Marinov GK, Doak TG, Lynch M. Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. Genome Biol Evol 2019; 11:1398-1416. [PMID: 30980669 PMCID: PMC6505448 DOI: 10.1093/gbe/evz081] [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: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
The evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across 13 highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ∼20% to ∼40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.
Collapse
Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington
| | - Georgi K Marinov
- Department of Biology, Indiana University, Bloomington.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington.,National Center for Genome Analysis Support, Indiana University, Bloomington
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington.,Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe
| |
Collapse
|
49
|
Tahmasebi S, Khoutorsky A, Mathews MB, Sonenberg N. Translation deregulation in human disease. Nat Rev Mol Cell Biol 2019; 19:791-807. [PMID: 30038383 DOI: 10.1038/s41580-018-0034-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Advances in sequencing and high-throughput techniques have provided an unprecedented opportunity to interrogate human diseases on a genome-wide scale. The list of disease-causing mutations is expanding rapidly, and mutations affecting mRNA translation are no exception. Translation (protein synthesis) is one of the most complex processes in the cell. The orchestrated action of ribosomes, tRNAs and numerous translation factors decodes the information contained in mRNA into a polypeptide chain. The intricate nature of this process renders it susceptible to deregulation at multiple levels. In this Review, we summarize current evidence of translation deregulation in human diseases other than cancer. We discuss translation-related diseases on the basis of the molecular aberration that underpins their pathogenesis (including tRNA dysfunction, ribosomopathies, deregulation of the integrated stress response and deregulation of the mTOR pathway) and describe how deregulation of translation generates the phenotypic variability observed in these disorders.
Collapse
Affiliation(s)
- Soroush Tahmasebi
- Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada. .,Department of Biochemistry, McGill University, Montreal, Quebec, Canada. .,Department of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA.
| | - Arkady Khoutorsky
- Department of Anesthesia and Alan Edwards Centre for Research on Pain, McGill University, Montreal, Canada
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada. .,Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
| |
Collapse
|
50
|
Yan Z, Ye G, Werren JH. Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects. Mol Biol Evol 2019; 36:1022-1036. [PMID: 30785203 DOI: 10.1093/molbev/msz036] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex.
Collapse
Affiliation(s)
- Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Department of Biology, University of Rochester, Rochester, NY
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY
| |
Collapse
|