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Ruiz-Orera J, Miller DC, Greiner J, Genehr C, Grammatikaki A, Blachut S, Mbebi J, Patone G, Myronova A, Adami E, Dewani N, Liang N, Hummel O, Muecke MB, Hildebrandt TB, Fritsch G, Schrade L, Zimmermann WH, Kondova I, Diecke S, van Heesch S, Hübner N. Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts. NATURE CARDIOVASCULAR RESEARCH 2024:10.1038/s44161-024-00544-7. [PMID: 39317836 DOI: 10.1038/s44161-024-00544-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 08/28/2024] [Indexed: 09/26/2024]
Abstract
Evolutionary innovations can be driven by changes in the rates of RNA translation and the emergence of new genes and small open reading frames (sORFs). In this study, we characterized the transcriptional and translational landscape of the hearts of four primate and two rodent species through integrative ribosome and transcriptomic profiling, including adult left ventricle tissues and induced pluripotent stem cell-derived cardiomyocyte cell cultures. We show here that the translational efficiencies of subunits of the mitochondrial oxidative phosphorylation chain complexes IV and V evolved rapidly across mammalian evolution. Moreover, we discovered hundreds of species-specific and lineage-specific genomic innovations that emerged during primate evolution in the heart, including 551 genes, 504 sORFs and 76 evolutionarily conserved genes displaying human-specific cardiac-enriched expression. Overall, our work describes the evolutionary processes and mechanisms that have shaped cardiac transcription and translation in recent primate evolution and sheds light on how these can contribute to cardiac development and disease.
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Affiliation(s)
- Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
| | - Duncan C Miller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Pluripotent Stem Cells, Berlin, Germany
| | - Johannes Greiner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Carolin Genehr
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Pluripotent Stem Cells, Berlin, Germany
| | - Aliki Grammatikaki
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jeanne Mbebi
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Anna Myronova
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Nikita Dewani
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ning Liang
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michael B Muecke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Freie Universitaet Berlin, Berlin, Germany
| | - Guido Fritsch
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Lisa Schrade
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Wolfram H Zimmermann
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Lower Saxony, Göttingen, Germany
- DZNE (German Center for Neurodegenerative Diseases), Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Göttingen, Germany
| | - Ivanela Kondova
- Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Pluripotent Stem Cells, Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.
- Charité-Universitätsmedizin, Berlin, Germany.
- Helmholtz Institute for Translational AngioCardioScience (HI-TAC) of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) at Heidelberg University, Heidelberg, Germany.
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Burgstaller JP, Chiaratti MR. Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease. Methods Mol Biol 2023; 2647:83-104. [PMID: 37041330 DOI: 10.1007/978-1-0716-3064-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Mitochondria are indispensable power plants of eukaryotic cells that also act as a major biochemical hub. As such, mitochondrial dysfunction, which can originate from mutations in the mitochondrial genome (mtDNA), may impair organism fitness and lead to severe diseases in humans. MtDNA is a multi-copy, highly polymorphic genome that is uniparentally transmitted through the maternal line. Several mechanisms act in the germline to counteract heteroplasmy (i.e., coexistence of two or more mtDNA variants) and prevent expansion of mtDNA mutations. However, reproductive biotechnologies such as cloning by nuclear transfer can disrupt mtDNA inheritance, resulting in new genetic combinations that may be unstable and have physiological consequences. Here, we review the current understanding of mitochondrial inheritance, with emphasis on its pattern in animals and human embryos generated by nuclear transfer.
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Affiliation(s)
- Jörg P Burgstaller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
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3
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [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] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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4
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Stewart JB. Current progress with mammalian models of mitochondrial DNA disease. J Inherit Metab Dis 2021; 44:325-342. [PMID: 33099782 DOI: 10.1002/jimd.12324] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial disorders make up a large class of heritable diseases that cause a broad array of different human pathologies. They can affect many different organ systems, or display very specific tissue presentation, and can lead to illness either in childhood or later in life. While the over 1200 genes encoded in the nuclear DNA play an important role in human mitochondrial disease, it has been known for over 30 years that mutations of the mitochondria's own small, multicopy DNA chromosome (mtDNA) can lead to heritable human diseases. Unfortunately, animal mtDNA has resisted transgenic and directed genome editing technologies until quite recently. As such, animal models to aid in our understanding of these diseases, and to explore preclinical therapeutic research have been quite rare. This review will discuss the unusual properties of animal mitochondria that have hindered the generation of animal models. It will also discuss the existing mammalian models of human mtDNA disease, describe the methods employed in their generation, and will discuss recent advances in the targeting of DNA-manipulating enzymes to the mitochondria and how these may be employed to generate new models.
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Affiliation(s)
- James Bruce Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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5
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Mitochondrial metabolism assessment of lycaon-dog fetuses in interspecies somatic cell nuclear transfer. Theriogenology 2021; 165:18-27. [PMID: 33611171 DOI: 10.1016/j.theriogenology.2021.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/06/2021] [Accepted: 01/16/2021] [Indexed: 12/16/2022]
Abstract
Many studies have reported that interspecies somatic cell nuclear transfer (iSCNT) is considered the prominent method in preserving endangered animals. However, the development rate of iSCNT embryos is low, and there are limited studies on the molecular mechanism of the iSCNT process. This study evaluated the developmental potential of interspecies lycaon (Lycaon pictus)-dog embryos and assessed the mitochondrial content and metabolism of the produced cloned lycaon-dog fetus. Of 678 collected oocytes, 516 were subjected to nuclear transfer, and 419 reconstructed embryos with male lycaon fibroblasts were transferred into 27 surrogates. Of 720 oocytes, 568 were subjected to nuclear transfer and 469 reconstructed embryos with female lycaon fibroblasts were transferred into 31 surrogates. Two recipients who received female reconstructed embryos were identified as pregnant at 30 days. However, fetal retardation with no cardiac activity was observed at 46 days. Microsatellite analysis confirmed that the cloned lycaon-dog fetus was genetically identical to the lycaon donor cell, whereas mitochondrial sequencing analysis revealed that oocyte donor dogs transmitted their mtDNA. We assessed the oxygen consumption rate and mitochondrial content of the aborted lycaon-dog fetus to shed some light on the aborted fetus's cellular metabolism. The oxygen consumption rates in the lycaon-dog fetal fibroblasts were lower than those in adult dog, lycaon and cloned dog fetal fibroblasts. Furthermore, lycaon-dog fetal fibroblasts showed decreased proportions of live and active mitochondria compared with other groups. Overall, we hypothesized that nuclear-mitochondrial incompatibility affects pyruvate metabolism and that these processes cause intrauterine fetal death.
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Abstract
The study of the mitochondrial DNA (mtDNA) has been hampered by the lack of methods to genetically manipulate the mitochondrial genome in living animal cells. This limitation has been partially alleviated by the ability to transfer mitochondria (and their mtDNAs) from one cell into another, as long as they are from the same species. This is done by isolating mtDNA-containing cytoplasts and fusing these to cells lacking mtDNA. This transmitochondrial cytoplasmic hybrid (cybrid) technology has helped the field understand the mechanism of several pathogenic mutations. In this chapter, we describe procedures to obtain transmitochondrial cybrids.
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Affiliation(s)
- Sandra R Bacman
- Department of Neurology, University of Miami School of Medicine, Miami, FL, United States
| | - Nadee Nissanka
- Department of Neurology, University of Miami School of Medicine, Miami, FL, United States
| | - Carlos T Moraes
- Department of Neurology, University of Miami School of Medicine, Miami, FL, United States.
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7
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Wang Q, Lu W, Yang J, Jiang L, Zhang Q, Kan X, Yang X. Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:27-36. [DOI: 10.1016/j.cbd.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
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8
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Angers B, Chapdelaine V, Deremiens L, Vergilino R, Leung C, Doucet SL, Glémet H, Angers A. Gene flow prevents mitonuclear co-adaptation: A comparative portrait of sympatric wild types and cybrids in the fish Chrosomus eos. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 27:77-84. [PMID: 29986214 DOI: 10.1016/j.cbd.2018.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/26/2022]
Abstract
Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges. Such diversity provides a useful system for in situ assessment of allospecific mtDNA effects. We determined genetic, epigenetic and transcriptomic variation as well as mitochondrial enzymatic activity (complex IV) changes among wild types and cybrids either in sympatry or allopatry. Wild types and cybrids did not segregate spatially within a lake. Moreover, no significant genetic differentiation was detected among wild types and cybrids indicating sustained gene flow. Mitochondrial complex IV activity was higher for cybrids in both sympatry and allopatry while no difference was detected among cybrid haplotypes. Epigenetic and transcriptomic analyses revealed only subtle differences between sympatric wild types and cybrids compared to differences between sites. Altogether, these results indicate a limited influence of allospecific mtDNA in nuclear gene expression when controlling for genetic and environmental effects. The absence of a reproductive barrier between wild types and cybrids results in random association of either C. eos or C. neogaeus mtDNA with C. eos nDNA at each generation, and prevents mitonuclear co-adaptation in sympatry.
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Affiliation(s)
- Bernard Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada.
| | - Vincent Chapdelaine
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Léo Deremiens
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Roland Vergilino
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Christelle Leung
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Simon-Luc Doucet
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Hélène Glémet
- Department of environmental sciences, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - Annie Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
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Lang SA, Saglam N, Kawash J, Shain DH. Punctuated invasion of water, ice, snow and terrestrial ecozones by segmented worms (Oligochaeta: Enchytraeidae: Mesenchytraeus). Proc Biol Sci 2018; 284:rspb.2017.1081. [PMID: 29021169 DOI: 10.1098/rspb.2017.1081] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/11/2017] [Indexed: 11/12/2022] Open
Abstract
Segmented worms (Annelida) are among the most successful animal inhabitants of extreme environments worldwide. An unusual group of enchytraeid oligochaetes of genus Mesenchytraeus are abundant in the Pacific northwestern region of North America and occupy geographically proximal ecozones ranging from low elevation rainforests and waterways to high altitude glaciers. Along this altitudinal transect, Mesenchytraeus representatives from disparate habitat types were collected and subjected to deep mitochondrial and nuclear phylogenetic analyses. Our data identify significant topological discordance among gene trees, and near equivalent interspecific divergence levels indicative of a rapid radiation event. Collectively, our results identify a Mesenchytraeus 'explosion' coincident with mountain building in the Pacific northwestern region that gave rise to closely related aquatic, ice, snow and terrestrial worms.
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Affiliation(s)
- Shirley A Lang
- Rowan University Graduate School of Biomedical Sciences at SOM, Stratford, NJ 08084, USA
| | - Naim Saglam
- Department of Aquaculture and Fish Diseases, Faculty of Fisheries, Firat University, 23119 Elazig, Turkey
| | - Joseph Kawash
- Department of Biology, Rutgers The State University of New Jersey, Camden, NJ 08102, USA
| | - Daniel H Shain
- Department of Biology, Rutgers The State University of New Jersey, Camden, NJ 08102, USA
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Sun S, Li Q, Kong L, Yu H. Limited locomotive ability relaxed selective constraints on molluscs mitochondrial genomes. Sci Rep 2017; 7:10628. [PMID: 28878314 PMCID: PMC5587578 DOI: 10.1038/s41598-017-11117-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/18/2017] [Indexed: 01/13/2023] Open
Abstract
Mollusca are the second largest phylum in the animal kingdom with different types of locomotion. Some molluscs are poor-migrating, while others are free-moving or fast-swimming. Most of the energy required for locomotion is provided by mitochondria via oxidative phosphorylation. Here, we conduct a comparative genomic analysis of 256 molluscs complete mitochondrial genomes and evaluate the role of energetic functional constraints on the protein-coding genes, providing a new insight into mitochondrial DNA (mtDNA) evolution. The weakly locomotive molluscs, compared to strongly locomotive molluscs, show significantly higher Ka/Ks ratio, which suggest they accumulated more nonsynonymous mutations in mtDNA and have experienced more relaxed evolutionary constraints. Eleven protein-coding genes (CoxI, CoxII, ATP6, Cytb, ND1-6, ND4L) show significant difference for Ka/Ks ratios between the strongly and weakly locomotive groups. The relaxation of selective constraints on Atp8 arise in the common ancestor of bivalves, and the further relaxation occurred in marine bivalves lineage. Our study thus demonstrates that selective constraints relevant to locomotive ability play an essential role in evolution of molluscs mtDNA.
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Affiliation(s)
- Shao'e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
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11
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Wang J, Xiang H, Liu L, Kong M, Yin T, Zhao X. Mitochondrial haplotypes influence metabolic traits across bovine inter- and intra-species cybrids. Sci Rep 2017. [PMID: 28646188 PMCID: PMC5482896 DOI: 10.1038/s41598-017-04457-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In bovine species, mitochondrial DNA polymorphisms and their correlation to productive or reproductive performances have been widely reported across breeds and individuals. However, experimental evidence of this correlation has never been provided. In order to identify differences among bovine mtDNA haplotypes, transmitochondrial cybrids were generated, with the nucleus from MAC-T cell line, derived from a Holstein dairy cow (Bos taurus) and mitochondria from either primary cell line derived from a domestic Chinese native beef Luxi cattle breed or central Asian domestic yak (Bos grunniens). Yak primary cells illustrated a stronger metabolic capacity than that of Luxi. However, all yak cybrid parameters illustrated a drop in relative yak mtDNA compared to Luxi mtDNA, in line with a mitonuclear imbalance in yak interspecies cybrid. Luxi has 250 divergent variations relative to the mitogenome of Holsteins. In cybrids there were generally higher rates of oxygen consumption (OCR) and extracellular acidification (ECAR), and lower mRNA expression levels of nuclear-encoded mitochondrial genes, potentially reflecting active energy metabolism and cellular stress resistance. The results demonstrate that functional differences exist between bovine cybrid cells. While cybrid viability was similar between Holstein and Luxi breeds, the mitonuclear mismatch caused a marked metabolic dysfunction in cattle:yak cybrid species.
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Affiliation(s)
- Jikun Wang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Hai Xiang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Langqing Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Minghua Kong
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Tao Yin
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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12
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Incompatibility between Nuclear and Mitochondrial Genomes Contributes to an Interspecies Reproductive Barrier. Cell Metab 2016; 24:283-94. [PMID: 27425585 PMCID: PMC4981548 DOI: 10.1016/j.cmet.2016.06.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/29/2016] [Accepted: 06/17/2016] [Indexed: 11/22/2022]
Abstract
Vertebrate cells carry two different genomes, nuclear (nDNA) and mitochondrial (mtDNA), both encoding proteins involved in oxidative phosphorylation. Because of the extensive interactions, adaptive coevolution of the two genomes must occur to ensure normal mitochondrial function. To investigate whether incompatibilities between these two genomes could contribute to interspecies reproductive barriers, we performed reciprocal mtDNA replacement (MR) in zygotes between widely divergent Mus m. domesticus (B6) and conplastic Mus m. musculus (PWD) mice. Transfer of MR1 cybrid embryos (B6nDNA-PWDmtDNA) supported normal development of F1 offspring with reduced male fertility but unaffected reproductive fitness in females. Furthermore, donor PWD mtDNA was faithfully transmitted through the germline into F2 and F3 generations. In contrast, reciprocal MR2 (PWDnDNA-B6mtDNA) produced high embryonic loss and stillborn rates, suggesting an association between mitochondrial function and infertility. These results strongly suggest that functional incompatibility between nuclear and mitochondrial genomes contributes to interspecies reproductive isolation in mammals.
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13
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Wolters JF, Chiu K, Fiumera HL. Population structure of mitochondrial genomes in Saccharomyces cerevisiae. BMC Genomics 2015; 16:451. [PMID: 26062918 PMCID: PMC4464245 DOI: 10.1186/s12864-015-1664-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
Background Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences. Results To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae. Conclusions Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John F Wolters
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
| | - Kenneth Chiu
- Computer Science Department, Binghamton University, Binghamton, NY, USA.
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
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14
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Mitochondrial-nuclear epistasis contributes to phenotypic variation and coadaptation in natural isolates of Saccharomyces cerevisiae. Genetics 2014; 198:1251-65. [PMID: 25164882 DOI: 10.1534/genetics.114.168575] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mitochondria are essential multifunctional organelles whose metabolic functions, biogenesis, and maintenance are controlled through genetic interactions between mitochondrial and nuclear genomes. In natural populations, mitochondrial efficiencies may be impacted by epistatic interactions between naturally segregating genome variants. The extent that mitochondrial-nuclear epistasis contributes to the phenotypic variation present in nature is unknown. We have systematically replaced mitochondrial DNAs in a collection of divergent Saccharomyces cerevisiae yeast isolates and quantified the effects on growth rates in a variety of environments. We found that mitochondrial-nuclear interactions significantly affected growth rates and explained a substantial proportion of the phenotypic variances under some environmental conditions. Naturally occurring mitochondrial-nuclear genome combinations were more likely to provide growth advantages, but genetic distance could not predict the effects of epistasis. Interruption of naturally occurring mitochondrial-nuclear genome combinations increased endogenous reactive oxygen species in several strains to levels that were not always proportional to growth rate differences. Our results demonstrate that interactions between mitochondrial and nuclear genomes generate phenotypic diversity in natural populations of yeasts and that coadaptation of intergenomic interactions likely occurs quickly within the specific niches that yeast occupy. This study reveals the importance of considering allelic interactions between mitochondrial and nuclear genomes when investigating evolutionary relationships and mapping the genetic basis underlying complex traits.
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Yu G, Tian J, Yin J, Li Q, Zhao X. Incompatibility of nucleus and mitochondria causes xenomitochondrial cybrid unviable across human, mouse, and pig cells. Anim Biotechnol 2014; 25:139-49. [PMID: 24555799 DOI: 10.1080/10495398.2013.841709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The nucleus and mitochondria are on correlative dependence; they interact in the process of protein transportation and energy metabolism. The compatibility of nucleus and mitochondria is essential for interspecies somatic cell nuclear transfer (iSCNT) and xenomitochondrial cybrid. In order to test the compatibility of nucleus and mitochondria among human, mouse, and pig cells, we compared the performances of cybrids that fused inter- and intra-species. The ρ0 cells from human and pig cell lines were created as nucleus donors which were transfected with GFP-neo for cell selective system in advance, and mitochondria donor cells were labeled by Mitochondria-RFP. Human and mouse platelets were also used as a mitochondrial donor. Results indicated that all interspecies cybrids declined to die in 2-4 d after the cell fusion in the selection medium, while intraspecies cybrid cells survived and formed stable clones. As a conclusion, the incompatibility between nucleus and mitochondria is the critical factor for the formation of interspecies cybrids.
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Affiliation(s)
- Guanghui Yu
- a National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology , China Agricultural University , Beijing , China
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Yuan J, Zhu Q, Liu B. Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes. PLoS One 2014; 9:e84330. [PMID: 24465405 PMCID: PMC3896360 DOI: 10.1371/journal.pone.0084330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/14/2013] [Indexed: 12/29/2022] Open
Abstract
The evolutionary history of living species is usually inferred through the phylogenetic analysis of molecular and morphological information using various mathematical models. New challenges in phylogenetic analysis are centered mostly on the search for accurate and efficient methods to handle the huge amounts of sequence data generated from newer genome sequencing. The next major challenge is the determination of relationships between the evolution of structural elements and their functional implementation, which is largely ignored in previous analyses. Here, we described the discovery of structural elements in metazoan mitochondrial genomes, termed key K-strings, that can serve as a basis for phylogenetic tree construction. Although comprising only a small fraction (0.73%) of all K-strings, these key K-strings are pivotal to the tree construction because they allow for a significant reduction in the computational time required to construct phylogenetic trees, and more importantly, they make significant improvement to the results of phylogenetic inference. The trees constructed from the key K-strings were consistent overall to our current view of metazoan phylogeny and exhibited a more rational topology than the trees constructed by using other conventional methods. Surprisingly, the key K-strings tended to accumulate in the conserved regions of the original sequences, which were most likely due to strong selection pressure. Furthermore, the special structural features of the key K-strings should have some potential applications in the study of the structures and functions relationship of proteins and in the determination of evolutionary trajectory of species. The novelty and potential importance of key K-strings lead us to believe that they are essential evolutionary elements. As such, they may play important roles in the process of species evolution and their physical existence. Further studies could lead to discoveries regarding the relationship between evolution and processes of speciation.
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Affiliation(s)
- Jianbo Yuan
- Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | | | - Bin Liu
- Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Bacman SR, Williams SL, Pinto M, Moraes CT. The use of mitochondria-targeted endonucleases to manipulate mtDNA. Methods Enzymol 2014; 547:373-97. [PMID: 25416366 DOI: 10.1016/b978-0-12-801415-8.00018-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For more than a decade, mitochondria-targeted nucleases have been used to promote double-strand breaks in the mitochondrial genome. This was done in mitochondrial DNA (mtDNA) homoplasmic systems, where all mtDNA molecules can be affected, to create models of mitochondrial deficiencies. Alternatively, they were also used in a heteroplasmic model, where only a subset of the mtDNA molecules were substrates for cleavage. The latter approach showed that mitochondrial-targeted nucleases can reduce mtDNA haplotype loads in affected tissues, with clear implications for the treatment of patients with mitochondrial diseases. In the last few years, designer nucleases, such as ZFN and TALEN, have been adapted to cleave mtDNA, greatly expanding the potential therapeutic use. This chapter describes the techniques and approaches used to test these designer enzymes.
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Affiliation(s)
- Sandra R Bacman
- Department of Neurology, University of Miami School of Medicine, Miami, Florida, USA
| | - Sion L Williams
- Department of Neurology, University of Miami School of Medicine, Miami, Florida, USA
| | - Milena Pinto
- Department of Neurology, University of Miami School of Medicine, Miami, Florida, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami School of Medicine, Miami, Florida, USA.
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MacFabe DF. Short-chain fatty acid fermentation products of the gut microbiome: implications in autism spectrum disorders. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2012; 23:19260. [PMID: 23990817 PMCID: PMC3747729 DOI: 10.3402/mehd.v23i0.19260] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent evidence suggests potential, but unproven, links between dietary, metabolic, infective, and gastrointestinal factors and the behavioral exacerbations and remissions of autism spectrum disorders (ASDs). Propionic acid (PPA) and its related short-chain fatty acids (SCFAs) are fermentation products of ASD-associated bacteria (Clostridia, Bacteriodetes, Desulfovibrio). SCFAs represent a group of compounds derived from the host microbiome that are plausibly linked to ASDs and can induce widespread effects on gut, brain, and behavior. Intraventricular administration of PPA and SCFAs in rats induces abnormal motor movements, repetitive interests, electrographic changes, cognitive deficits, perseveration, and impaired social interactions. The brain tissue of PPA-treated rats shows a number of ASD-linked neurochemical changes, including innate neuroinflammation, increased oxidative stress, glutathione depletion, and altered phospholipid/acylcarnitine profiles. These directly or indirectly contribute to acquired mitochondrial dysfunction via impairment in carnitine-dependent pathways, consistent with findings in patients with ASDs. Of note, common antibiotics may impair carnitine-dependent processes by altering gut flora favoring PPA-producing bacteria and by directly inhibiting carnitine transport across the gut. Human populations that are partial metabolizers of PPA are more common than previously thought. PPA has further bioactive effects on neurotransmitter systems, intracellular acidification/calcium release, fatty acid metabolism, gap junction gating, immune function, and alteration of gene expression that warrant further exploration. These findings are consistent with the symptoms and proposed underlying mechanisms of ASDs and support the use of PPA infusions in rats as a valid animal model of the condition. Collectively, this offers further support that gut-derived factors, such as dietary or enteric bacterially produced SCFAs, may be plausible environmental agents that can trigger ASDs or ASD-related behaviors and deserve further exploration in basic science, agriculture, and clinical medicine.
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Affiliation(s)
- Derrick F. MacFabe
- Director: The Kilee Patchell-Evans Autism Research Group, Departments of Psychology (Neuroscience) and Psychiatry, Division of Developmental Disabilities, Lawson Research Institute, University of Western Ontario, London, ON, Canada, N6A 5C2
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Evans ML, Bernatchez L. Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological divergence. J Evol Biol 2012; 25:1823-34. [PMID: 22830417 DOI: 10.1111/j.1420-9101.2012.02570.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/31/2012] [Indexed: 12/31/2022]
Abstract
Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved 'dwarf' and 'normal' sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with the five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further studies are now needed to evaluate the contribution of genetically vs. plasticity driven variation in transcription associated with this critical physiological pathway.
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Affiliation(s)
- M L Evans
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada.
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Pacheu-Grau D, Gómez-Durán A, López-Gallardo E, Pinós T, Andreu AL, López-Pérez MJ, Montoya J, Ruiz-Pesini E. 'Progress' renders detrimental an ancient mitochondrial DNA genetic variant. Hum Mol Genet 2011; 20:4224-31. [PMID: 21828074 DOI: 10.1093/hmg/ddr350] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A human mitochondrial DNA (mtDNA) transition, m.1555A>G, in the 12S rRNA gene causes non-syndromic hearing loss. However, this pathological mutation is the wild-type allele in orangutan mtDNA. Here we rule out different genetic factors as the reason for its fixation in orangutans and show that aminoglycosides negatively affect the oxidative phosphorylation function by decreasing the synthesis of mtDNA-encoded proteins and the amount and activity of respiratory complex IV. These drugs also diminish the growth rate of orangutan cells. The m.1555G nucleotide is also the wild-type allele in other mammal species and they might be at risk of suffering a mitochondrial disorder if treated with aminoglycosides. Therefore, pharmacogenomic approaches should be used to confirm this possibility. These observations are important for human health. Due to the fact that old age and high frequency are criteria widely used in mitochondrial medicine to rule out a genetic change as being a pathological mutation, our results prevent against simplistic genetic approaches that do not consider the potential effect of environmental conditions. Hence, these results suggest that some ancient and highly frequent human population polymorphisms, such as those defining mtDNA haplogroups, in mitochondrial rRNA genes can be deleterious in association with new environmental conditions. Therefore, as the discovery of ribosomal antibiotics has allowed to fight infectious diseases and this breakthrough can be considered an important scientific advance or 'progress', our results suggest that 'progress' can also have a negative counterpart and render detrimental many of these mtDNA genotypes.
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Affiliation(s)
- David Pacheu-Grau
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
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Evolution and disease converge in the mitochondrion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1099-104. [DOI: 10.1016/j.bbabio.2010.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 12/31/2009] [Accepted: 01/07/2010] [Indexed: 11/18/2022]
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Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci U S A 2010; 107:8666-71. [PMID: 20421465 DOI: 10.1073/pnas.0912613107] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.
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24
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Yu X, Wester-Rosenlöf L, Gimsa U, Holzhueter SA, Marques A, Jonas L, Hagenow K, Kunz M, Nizze H, Tiedge M, Holmdahl R, Ibrahim SM. The mtDNA nt7778 G/T polymorphism affects autoimmune diseases and reproductive performance in the mouse. Hum Mol Genet 2009; 18:4689-98. [PMID: 19759059 DOI: 10.1093/hmg/ddp432] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondria are organelles of all nucleated cells, and variations in mtDNA sequence affect a wide spectrum of human diseases. However, animal models for mtDNA-associated diseases are rare, making it challenging to explore mechanisms underlying the contribution of mitochondria. Here, we identify a polymorphism in the mitochondrial genome, G-to-T at position 7778, which results in an aspartic acid-to-tyrosine (D-Y) substitution in the fifth amino acid of the highly conserved N-terminus of ATP synthase 8 (ATP8). Using a series of conplastic strains we show that this polymorphism increases susceptibility to multiple autoimmune diseases, including collagen-induced arthritis, autoimmune diabetes, nephritis and autoimmune pancreatitis. In addition, it impairs reproductive performance in females, but only in the MRL/MpJ strain. We also demonstrate that the mtAtp8 polymorphism alters mitochondrial performance, increasing H(2)O(2) production and affecting mitochondrial structure. Functional analysis reveals that the polymorphism increase the CD4 T cell adaptive potential to an oxidative phosphorylation impaired condition. Our findings provide direct experimental evidence for the role of mitochondria in autoimmunity and reproduction.
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Affiliation(s)
- Xinhua Yu
- Section of Immunogenetics, University of Rostock, Rostock, Germany
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Shen X, Ma X, Ren J, Zhao F. A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta. BMC Genomics 2009; 10:136. [PMID: 19327168 PMCID: PMC2667193 DOI: 10.1186/1471-2164-10-136] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 03/28/2009] [Indexed: 11/18/2022] Open
Abstract
Background There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.
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Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science, Huaihai Institute of Technology, Lianyungang 222005, PR China.
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Sun Z, Ma L, Murphy RW, Zhang X, Huang D. Factors affecting mito-nuclear codon usage interactions in the OXPHOS system of Drosophila melanogaster. J Genet Genomics 2008; 35:729-35. [DOI: 10.1016/s1673-8527(08)60228-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 10/17/2008] [Accepted: 10/20/2008] [Indexed: 11/27/2022]
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The use of common mitochondrial variants to detect and characterise population structure in the Australian population: implications for genome-wide association studies. Eur J Hum Genet 2008; 16:1396-403. [DOI: 10.1038/ejhg.2008.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Bilal E, Rabadan R, Alexe G, Fuku N, Ueno H, Nishigaki Y, Fujita Y, Ito M, Arai Y, Hirose N, Ruckenstein A, Bhanot G, Tanaka M. Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan. PLoS One 2008; 3:e2421. [PMID: 18545700 PMCID: PMC2408726 DOI: 10.1371/journal.pone.0002421] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 04/25/2008] [Indexed: 01/09/2023] Open
Abstract
We report results from the analysis of complete mitochondrial DNA (mtDNA) sequences from 112 Japanese semi-supercentenarians (aged above 105 years) combined with previously published data from 96 patients in each of three non-disease phenotypes: centenarians (99-105 years of age), healthy non-obese males, obese young males and four disease phenotypes, diabetics with and without angiopathy, and Alzheimer's and Parkinson's disease patients. We analyze the correlation between mitochondrial polymorphisms and the longevity phenotype using two different methods. We first use an exhaustive algorithm to identify all maximal patterns of polymorphisms shared by at least five individuals and define a significance score for enrichment of the patterns in each phenotype relative to healthy normals. Our study confirms the correlations observed in a previous study showing enrichment of a hierarchy of haplogroups in the D clade for longevity. For the extreme longevity phenotype we see a single statistically significant signal: a progressive enrichment of certain "beneficial" patterns in centenarians and semi-supercentenarians in the D4a haplogroup. We then use Principal Component Spectral Analysis of the SNP-SNP Covariance Matrix to compare the measured eigenvalues to a Null distribution of eigenvalues on Gaussian datasets to determine whether the correlations in the data (due to longevity) arises from some property of the mutations themselves or whether they are due to population structure. The conclusion is that the correlations are entirely due to population structure (phylogenetic tree). We find no signal for a functional mtDNA SNP correlated with longevity. The fact that the correlations are from the population structure suggests that hitch-hiking on autosomal events is a possible explanation for the observed correlations.
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Affiliation(s)
- Erhan Bilal
- BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Raul Rabadan
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
| | - Gabriela Alexe
- Computational Biology and Bioinformatics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Noriyuki Fuku
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Hitomi Ueno
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Yutaka Nishigaki
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Yasunori Fujita
- Department of Longevity and Aging Research, Gifu International Institute of Biotechnology, Kakamigahara, Gifu, Japan
| | - Masafumi Ito
- Department of Longevity and Aging Research, Gifu International Institute of Biotechnology, Kakamigahara, Gifu, Japan
| | - Yasumichi Arai
- Department of Geriatric Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Nobuyoshi Hirose
- Department of Geriatric Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Andrei Ruckenstein
- Department of Physics, Boston University, Boston, Massachusetts, United States of America
| | - Gyan Bhanot
- BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, United States of America
| | - Masashi Tanaka
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
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Casanova MF, Tillquist CR. Encephalization, emergent properties, and psychiatry: a minicolumnar perspective. Neuroscientist 2007; 14:101-18. [PMID: 17971507 DOI: 10.1177/1073858407309091] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The focus of the authors' attention is the consequence of brain growth understood in terms of the development of networks of cortical cell minicolumns, the elemental information-processing units of the brain. The authors view cortical growth, encephalization, and the emergence of higher cognitive functions in humans as the consequence of an increase in the number of minicolumns and their connections. Encephalization has proceeded via weak linkages of canonical circuits, which facilitate the emergence of novel cortical functions. In addition to reframing the evolution of mind, this perspective provides a conceptual framework for a better understanding of the origin and maladaptive nature of certain psychiatric conditions.
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Affiliation(s)
- Manuel F Casanova
- Department of Psychiatry and Behavioral Sciences, University of Louisville, Louisville, KY 40292, USA.
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30
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Kessler D, Papatheodorou P, Stratmann T, Dian EA, Hartmann-Fatu C, Rassow J, Bayer P, Mueller JW. The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae. BMC Biol 2007; 5:37. [PMID: 17875217 PMCID: PMC2031878 DOI: 10.1186/1741-7007-5-37] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 09/17/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The parvulin-type peptidyl prolyl cis/trans isomerase Par14 is highly conserved in all metazoans. The recently identified parvulin Par17 contains an additional N-terminal domain whose occurrence and function was the focus of the present study. RESULTS Based on the observation that the human genome encodes Par17, but bovine and rodent genomes do not, Par17 exon sequences from 10 different primate species were cloned and sequenced. Par17 is encoded in the genomes of Hominidae species including humans, but is absent from other mammalian species. In contrast to Par14, endogenous Par17 was found in mitochondrial and membrane fractions of human cell lysates. Fluorescence of EGFP fusions of Par17, but not Par14, co-localized with mitochondrial staining. Par14 and Par17 associated with isolated human, rat and yeast mitochondria at low salt concentrations, but only the Par17 mitochondrial association was resistant to higher salt concentrations. Par17 was imported into mitochondria in a time and membrane potential-dependent manner, where it reached the mitochondrial matrix. Moreover, Par17 was shown to bind to double-stranded DNA under physiological salt conditions. CONCLUSION Taken together, the DNA binding parvulin Par17 is targeted to the mitochondrial matrix by the most recently evolved mitochondrial prepeptide known to date, thus adding a novel protein constituent to the mitochondrial proteome of Hominidae.
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Affiliation(s)
- Daniel Kessler
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Tina Stratmann
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elke Andrea Dian
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Cristina Hartmann-Fatu
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joachim Rassow
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonathan Wolf Mueller
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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Ingman M, Gyllensten U. Rate variation between mitochondrial domains and adaptive evolution in humans. Hum Mol Genet 2007; 16:2281-7. [PMID: 17617636 DOI: 10.1093/hmg/ddm180] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It has been proposed that as a result of human adaptation to different climates, mitochondrial genes have been affected by natural selection. To further study the selective pressure on human mitochondrial DNA, we have analysed polymorphism at the gene, domain and nucleotide site level in four geographic regions. The ratio of non-synonymous relative to synonymous substitutions is elevated for ATP6 in North Asia, ND3 in Africa and cytb in Europe relative to other mitochondrial genes. In addition, non-synonymous substitutions appear nearly five times more frequently outside core functional domains as compared with within functional domains. Therefore, a large part of the rate variation between mitochondrial genes is explained by differences in the length of the functional domain relative to the length of the gene. The accumulation of non-synonymous substitutions in the ATP6 gene among sequences from North Asia has been a gradual process over many thousands of years, consistent with relaxed purifying selection rather than recent strong selective sweeps. It is not necessary to invoke adaptive selection to explain the pattern of polymorphism in mitochondrial genes, when the most parsimonious explanation is relaxed purifying selection and the action of genetic drift.
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Affiliation(s)
- Max Ingman
- Department of Genetics and Pathology, University of Uppsala, Sweden.
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Affiliation(s)
- Sandra R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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Yoon YG, Haug CL, Koob MD. Interspecies mitochondrial fusion between mouse and human mitochondria is rapid and efficient. Mitochondrion 2006; 7:223-9. [PMID: 17251069 PMCID: PMC2693707 DOI: 10.1016/j.mito.2006.11.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2006] [Revised: 11/28/2006] [Accepted: 11/30/2006] [Indexed: 10/23/2022]
Abstract
A detailed molecular understanding of mitochondrial fusion and fission in mammalian cells is rapidly emerging. In this report, we demonstrate for the first time cross-species mitochondrial fusion between distantly related species using green and red fluorescent proteins targeted to the mitochondrial matrix. We found that mouse mitochondria were able to efficiently fuse to unmodified mitochondria of human cells and that the contents of the mitochondrial matrix were completely mixed in less than 4h. We also observed that mitochondria from the mtDNA-less (rho(0)) mouse cells can homogeneously fuse to the mitochondria of human cells. We were, however, unable to maintain human mitochondrial DNA in the mouse cells. These results indicate that mitochondrial fusion proteins in mouse and human cells have enough functional homology to mediate efficient cross-species mitochondrial fusion, but mouse nuclear and human mitochondrial genomes have not retained functional compatibility with one another.
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Affiliation(s)
| | | | - Michael D. Koob
- Corresponding author. Tel.: +1 612 626 6516; fax: +1 612 626 7031. E-mail address: (M.D. Koob)
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Rottenberg H. Longevity and the evolution of the mitochondrial DNA-coded proteins in mammals. Mech Ageing Dev 2006; 127:748-60. [PMID: 16876233 DOI: 10.1016/j.mad.2006.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 12/22/2005] [Accepted: 06/12/2006] [Indexed: 10/24/2022]
Abstract
The amino acids sequences of the mitochondrial DNA-coded peptides of placental mammals evolved at different rates in different branches of the mammalian phylogenetic tree. Adaptive selection was suggested to account for the faster evolution of some mitochondrial DNA-coded proteins in several branches of the mammalian tree, but the driving force(s) for the accelerated evolution has not been elucidated. Mitochondria generate reactive oxygen species (ROS) that appear to constrain the life span of many species. Therefore, I tested the hypothesis that the evolution of mammalian longevity drives the accelerated evolution of mitochondrial DNA-coded peptides. Using rodents as an outgroup for a clad that included most placental mammals (excluding rodents and hedgehogs) the computed rates of amino acid substitution per site were positively correlated with genus longevity (maximal observed averaged life span) for most of the mitochondrial DNA-coded peptides. The substitution per site of ATP6, the proton conducting subunit of ATPsynthase, CYTB, the core subunit of ubiquinone oxidoreductase that participate in both electron and proton transport, and ND3, a subunit of NADH dehydrogenase, showed the strongest correlations with longevity. Additional confirmation for the hypothesis was obtained by the observation that the genetic distances between placental mammals species that belong to different orders are positively correlated with the sum of longevities of the species pairs. The substitutions per site for the entire amino acid sequence coded by the heavy strand mtDNA were also positively correlated with the average longevities of the placental mammals orders. These results support the hypothesis that the evolution of longevity in mammals drove the accelerated evolution of mtDNA-coded peptide. It is suggested that, in mammals, adaptive selection of mutations that decrease the rate of production of reactive oxygen species, directly or indirectly (e.g. by increasing proton leak), increases longevity.
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Affiliation(s)
- Hagai Rottenberg
- New Hope Biomedical R&D, 23 W. Bridge Street, New Hope, PA 18938, USA.
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Rawson PD, Burton RS. Molecular Evolution at the Cytochrome Oxidase Subunit 2 Gene Among Divergent Populations of the Intertidal Copepod, Tigriopus californicus. J Mol Evol 2006; 62:753-64. [PMID: 16752213 DOI: 10.1007/s00239-005-0074-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 01/23/2006] [Indexed: 11/28/2022]
Abstract
The cytochrome c oxidase subunit 2 gene (COII) encodes a highly conserved protein that is directly responsible for the initial transfer of electrons from cytochrome c to cytochrome c oxidase (COX) crucial to the production of ATP during cellular respiration. Despite its integral role in electron transport, we have observed extensive intraspecific nucleotide and amino acid variation among 26 full-length COII sequences sampled from seven populations of the marine copepod, Tigriopus californicus. Although intrapopulation divergence was virtually nonexistent, interpopulation divergence at the COII locus was nearly 20% at the nucleotide level, including 38 nonsynonymous substitutions. Given the high degree of interaction between the cytochrome c oxidase subunit 2 protein (COX2) and the nuclear-encoded subunits of COX and cytochrome c (CYC), we hypothesized that some codons in the COII gene are likely to be under positive selection in order to compensate for amino acid substitutions in other subunits. Estimates of the ratio of nonsynonymous to synonymous substitution (omega), obtained using a series of maximum likelihood models of codon substitution, indicated that the majority of codons in T. californicus COII are under strong purifying selection (omega << 1), while approximately 4% of the sites in this gene appear to evolve under relaxed selective constraint (omega = 1). A branch-site maximum likelihood model identified three sites that may have experienced positive selection within the central California sequence clade in our COII phylogeny; these results are consistent with previous studies showing functional and fitness consequences among interpopulation hybrids between central and northern California populations.
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Affiliation(s)
- Paul D Rawson
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA.
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