1
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Zhou X, Lian P, Liu H, Wang Y, Zhou M, Feng Z. Causal Associations between Gut Microbiota and Different Types of Dyslipidemia: A Two-Sample Mendelian Randomization Study. Nutrients 2023; 15:4445. [PMID: 37892520 PMCID: PMC10609956 DOI: 10.3390/nu15204445] [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: 09/14/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The determination of a causal association between gut microbiota and a range of dyslipidemia remains uncertain. To clarify these associations, we employed a two-sample Mendelian randomization (MR) analysis utilizing the inverse-variance weighted (IVW) method. This comprehensive analysis investigated the genetic variants that exhibited a significant association (p < 5 × 10-8) with 129 distinct gut microbiota genera and their potential link to different types of dyslipidemia. The results indicated a potential causal association between 22 gut microbiota genera and dyslipidemia in humans. Furthermore, these findings suggested that the impact of gut microbiota on dyslipidemia regulation is dependent on the specific phylum, family, and genus. Bacillota phylum demonstrated the greatest diversity, with 15 distinct genera distributed among eight families. Notably, gut microbiota-derived from the Lachnospiraceae and Lactobacillaceae families exhibit statistically significant associations with lipid levels that contribute to overall health (p < 0.05). The sensitivity analysis indicated that our findings possess robustness (p > 0.05). The findings of our investigation provide compelling evidence that substantiates a causal association between the gut microbiota and dyslipidemia in the human body. It is noteworthy to highlight the significant influence of the Bacillota phylum as a crucial regulator of lipid levels, and the families Lachnospiraceae and Lactobacillaceae should be recognized as probiotics that significantly contribute to this metabolic process.
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Affiliation(s)
| | | | | | | | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.Z.); (P.L.); (H.L.); (Y.W.)
| | - Zhijun Feng
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou 510515, China; (X.Z.); (P.L.); (H.L.); (Y.W.)
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2
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Bedbrook CN, Nath RD, Nagvekar R, Deisseroth K, Brunet A. Rapid and precise genome engineering in a naturally short-lived vertebrate. eLife 2023; 12:80639. [PMID: 37191291 DOI: 10.7554/elife.80639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here, we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci in order to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.
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Affiliation(s)
- Claire N Bedbrook
- Department of Genetics, Stanford University, Stanford, United States
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, United States
| | - Rahul Nagvekar
- Department of Genetics, Stanford University, Stanford, United States
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, United States
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, United States
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, United States
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3
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Neuronal Phenotype of col4a1 and col25a1: An Intriguing Hypothesis in Vertebrates Brain Aging. Int J Mol Sci 2022; 23:ijms23031778. [PMID: 35163698 PMCID: PMC8836537 DOI: 10.3390/ijms23031778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/11/2022] Open
Abstract
Collagens are the most abundant proteins in vertebrates and constitute the major components of the extracellular matrix. Collagens play an important and multifaceted role in the development and functioning of the nervous system and undergo structural remodeling and quantitative modifications during aging. Here, we investigated the age-dependent regulation of col4a1 and col25a1 in the brain of the short-lived vertebrate Nothobranchius furzeri, a powerful model organism for aging research due to its natural fast-aging process and further characterized typical hallmarks of brain aging in this species. We showed that col4a1 and col25a1 are relatively well conserved during vertebrate evolution, and their expression significantly increases in the brain of N. furzeri upon aging. Noteworthy, we report that both col4a1 and col25a1 are expressed in cells with a neuronal phenotype, unlike what has already been documented in mammalian brain, in which only col25a1 is considered a neuronal marker, whereas col4a1 seems to be expressed only in endothelial cells. Overall, our findings encourage further investigation on the role of col4a1 and col25a1 in the biology of the vertebrate brain as well as the onset of aging and neurodegenerative diseases.
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4
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Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A. Alternative Animal Models of Aging Research. Front Mol Biosci 2021; 8:660959. [PMID: 34079817 PMCID: PMC8166319 DOI: 10.3389/fmolb.2021.660959] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.
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Affiliation(s)
- Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ekaterina Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stan Braude
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Alessandro Cellerino
- Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Central Animal Laboratory, University Hospital Essen, Essen, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Andreas Hoeflich
- Division Signal Transduction, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Eva Terzibasi Tozzini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxim Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
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5
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Van Houcke J, Mariën V, Zandecki C, Seuntjens E, Ayana R, Arckens L. Modeling Neuroregeneration and Neurorepair in an Aging Context: The Power of a Teleost Model. Front Cell Dev Biol 2021; 9:619197. [PMID: 33816468 PMCID: PMC8012675 DOI: 10.3389/fcell.2021.619197] [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: 10/19/2020] [Accepted: 02/19/2021] [Indexed: 01/10/2023] Open
Abstract
Aging increases the risk for neurodegenerative disease and brain trauma, both leading to irreversible and multifaceted deficits that impose a clear societal and economic burden onto the growing world population. Despite tremendous research efforts, there are still no treatments available that can fully restore brain function, which would imply neuroregeneration. In the adult mammalian brain, neuroregeneration is naturally limited, even more so in an aging context. In view of the significant influence of aging on (late-onset) neurological disease, it is a critical factor in future research. This review discusses the use of a non-standard gerontology model, the teleost brain, for studying the impact of aging on neurorepair. Teleost fish share a vertebrate physiology with mammals, including mammalian-like aging, but in contrast to mammals have a high capacity for regeneration. Moreover, access to large mutagenesis screens empowers these teleost species to fill the gap between established invertebrate and rodent models. As such, we here highlight opportunities to decode the factor age in relation to neurorepair, and we propose the use of teleost fish, and in particular killifish, to fuel new research in the neuro-gerontology field.
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Affiliation(s)
- Jolien Van Houcke
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Valerie Mariën
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Caroline Zandecki
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium.,Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Eve Seuntjens
- Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Brain Institute, Leuven, Belgium
| | - Rajagopal Ayana
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium.,Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium
| | - Lutgarde Arckens
- Laboratory of Neuroplasticity and Neuroproteomics, Department of Biology, KU Leuven, Leuven, Belgium.,Leuven Brain Institute, Leuven, Belgium
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6
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Pamplona R, Jové M, Mota-Martorell N, Barja G. Is the NDUFV2 subunit of the hydrophilic complex I domain a key determinant of animal longevity? FEBS J 2021; 288:6652-6673. [PMID: 33455045 DOI: 10.1111/febs.15714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/02/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022]
Abstract
Complex I, a component of the electron transport chain, plays a central functional role in cell bioenergetics and the biology of free radicals. The structural and functional N module of complex I is one of the main sites of the generation of free radicals. The NDUFV2 subunit/N1a cluster is a component of this module. Furthermore, the rate of free radical production is linked to animal longevity. In this review, we explore the hypothesis that NDUFV2 is the only conserved core subunit designed with a regulatory function to ensure correct electron transfer and free radical production, that low gene expression and protein abundance of the NDUFV2 subunit is an evolutionary adaptation needed to achieve a longevity phenotype, and that these features are determinants of the lower free radical generation at the mitochondrial level and a slower rate of aging of long-lived animals.
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Affiliation(s)
- Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Spain
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
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7
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Terzibasi Tozzini E, Cellerino A. Nothobranchius annual killifishes. EvoDevo 2020; 11:25. [PMID: 33323125 PMCID: PMC7739477 DOI: 10.1186/s13227-020-00170-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Annual fishes of the genus Nothobranchius inhabit ephemeral habitats in Eastern and Southeastern Africa. Their life cycle is characterized by very rapid maturation, a posthatch lifespan of a few weeks to months and embryonic diapause to survive the dry season. The species N. furzeri holds the record of the fastest-maturing vertebrate and of the vertebrate with the shortest captive lifespan and is emerging as model organism in biomedical research, evolutionary biology, and developmental biology. Extensive characterization of age-related phenotypes in the laboratory and of ecology, distribution, and demography in the wild are available. Species/populations from habitats differing in precipitation intensity show parallel evolution of lifespan and age-related traits that conform to the classical theories on aging. Genome sequencing and the establishment of CRISPR/Cas9 techniques made this species particularly attractive to investigate the effects genetic and non-genetic intervention on lifespan and aging-related phenotypes. At the same time, annual fishes are a very interesting subject for comparative approaches, including genomics, transcriptomics, and proteomics. The N. furzeri community is highly diverse and rapidly expanding and organizes a biannual meeting.
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Affiliation(s)
| | - Alessandro Cellerino
- Scuola Normale Superiore, Pisa, Italy. .,Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.
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8
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van der Rijt S, Molenaars M, McIntyre RL, Janssens GE, Houtkooper RH. Integrating the Hallmarks of Aging Throughout the Tree of Life: A Focus on Mitochondrial Dysfunction. Front Cell Dev Biol 2020; 8:594416. [PMID: 33324647 PMCID: PMC7726203 DOI: 10.3389/fcell.2020.594416] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Since the identification and definition of the hallmarks of aging, these aspects of molecular and cellular decline have been most often described as isolated or distinct mechanisms. However, there is significant evidence demonstrating interplay between most of these hallmarks and that they have the capacity to influence and regulate one another. These interactions are demonstrable across the tree of life, yet not all aspects are conserved. Here, we describe an integrative view on the hallmarks of aging by using the hallmark "mitochondrial dysfunction" as a focus point, and illustrate its capacity to both influence and be influenced by the other hallmarks of aging. We discuss the effects of mitochondrial pathways involved in aging, such as oxidative phosphorylation, mitochondrial dynamics, mitochondrial protein synthesis, mitophagy, reactive oxygen species and mitochondrial DNA damage in relation to each of the primary, antagonistic and integrative hallmarks. We discuss the similarities and differences in these interactions throughout the tree of life, and speculate how speciation may play a role in the variation in these mechanisms. We propose that the hallmarks are critically intertwined, and that mapping the full extent of these interactions would be of significant benefit to the aging research community.
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Affiliation(s)
- Sanne van der Rijt
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rebecca L McIntyre
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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9
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de Costa J, Barja G, Almaida-Pagan PF. Membrane peroxidation index and maximum lifespan are negatively correlated in fish of the genus Nothobranchius. J Exp Biol 2020; 223:jeb224063. [PMID: 32366693 DOI: 10.1242/jeb.224063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/22/2020] [Indexed: 11/20/2022]
Abstract
The lipid composition of cell membranes is linked to metabolic rate and lifespan in mammals and birds but very little information is available for fish. In this study, three fish species of the short-lived annual genus Nothobranchius with different maximum lifespan potential (MLSP) and the longer-lived outgroup species Aphyosemion australe were studied to test whether they conform to the predictions of the longevity-homeoviscous adaptation (LHA) theory of ageing. Lipid analyses were performed in whole-fish samples and the peroxidation index (PIn) for every phospholipid (PL) class and for the whole membrane was calculated. Total PL content was significantly lower in A. australe and N. korthausae, the two species with the highest MLSP, and a negative correlation between membrane total PIn and fish MLSP was found, meaning that the longer-lived fish species have more saturated membranes and, therefore, a lower susceptibility to oxidative damage, as the LHA theory posits.
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Affiliation(s)
- Jorge de Costa
- Chronobiology Lab, Department of Physiology, Faculty of Biology, University of Murcia, Mare Nostrum Campus, IUIE, IMIB-Arrixaca, 30100 Murcia, Spain
- Ciber Fragilidad y Envejecimiento Saludable (CIBERFES), 28029 Madrid, Spain
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Pedro F Almaida-Pagan
- Chronobiology Lab, Department of Physiology, Faculty of Biology, University of Murcia, Mare Nostrum Campus, IUIE, IMIB-Arrixaca, 30100 Murcia, Spain
- Ciber Fragilidad y Envejecimiento Saludable (CIBERFES), 28029 Madrid, Spain
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10
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Mota-Martorell N, Jove M, Pradas I, Sanchez I, Gómez J, Naudi A, Barja G, Pamplona R. Low abundance of NDUFV2 and NDUFS4 subunits of the hydrophilic complex I domain and VDAC1 predicts mammalian longevity. Redox Biol 2020; 34:101539. [PMID: 32353747 PMCID: PMC7191849 DOI: 10.1016/j.redox.2020.101539] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 01/14/2023] Open
Abstract
Mitochondrial reactive oxygen species (ROS) production, specifically at complex I (Cx I), has been widely suggested to be one of the determinants of species longevity. The present study follows a comparative approach to analyse complex I in heart tissue from 8 mammalian species with a longevity ranging from 3.5 to 46 years. Gene expression and protein content of selected Cx I subunits were analysed using droplet digital PCR (ddPCR) and western blot, respectively. Our results demonstrate: 1) the existence of species-specific differences in gene expression and protein content of Cx I in relation to longevity; 2) the achievement of a longevity phenotype is associated with low protein abundance of subunits NDUFV2 and NDUFS4 from the matrix hydrophilic domain of Cx I; and 3) long-lived mammals show also lower levels of VDAC (voltage-dependent anion channel) amount. These differences could be associated with the lower mitochondrial ROS production and slower aging rate of long-lived animals and, unexpectedly, with a low content of the mitochondrial permeability transition pore in these species. There are species-specific differences in gene expression and protein content of Cx I. The achievement of a longevity phenotype is associated with low protein abundance of subunits NDUFV2 and NDUFS4 from the matrix hydrophilic domain of Cx I. Long-lived mammals show also lower levels of VDAC (voltage-dependent anion channel) amount. These differences can be causally associated with the aging rate of long-lived animals.
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Affiliation(s)
- Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Mariona Jove
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Irene Pradas
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Isabel Sanchez
- Proteomics and Genomics Unit, University of Lleida, Lleida, Catalonia, Spain.
| | - José Gómez
- Department of Biology and Geology, Physics and Inorganic Chemistry, University Rey Juan Carlos I, ESCET-Campus de Móstoles, Móstoles, Madrid, Spain.
| | - Alba Naudi
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain.
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), Lleida, Catalonia, Spain.
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11
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Sahm A, Almaida-Pagán P, Bens M, Mutalipassi M, Lucas-Sánchez A, de Costa Ruiz J, Görlach M, Cellerino A. Analysis of the coding sequences of clownfish reveals molecular convergence in the evolution of lifespan. BMC Evol Biol 2019; 19:89. [PMID: 30975078 PMCID: PMC6460853 DOI: 10.1186/s12862-019-1409-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 03/10/2019] [Indexed: 01/12/2023] Open
Abstract
Background Standard evolutionary theories of aging postulate that reduced extrinsic mortality leads to evolution of longevity. Clownfishes of the genus Amphiprion live in a symbiotic relationship with sea anemones that provide protection from predators. We performed a survey and identified at least two species with a lifespan of over 20 years. Given their small size and ease of captive reproduction, clownfish lend themselves as experimental models of exceptional longevity. To identify genetic correlates of exceptional longevity, we sequenced the transcriptomes of Amphiprion percula and A. clarkii and performed a scan for positively-selected genes (PSGs). Results The PSGs that we identified in the last common clownfish ancestor were compared with PSGs detected in long-lived mole rats and short-lived killifishes revealing convergent evolution in processes such as mitochondrial biogenesis. Among individual genes, the Mitochondrial Transcription Termination Factor 1 (MTERF1), was positively-selected in all three clades, whereas the Glutathione S-Transferase Kappa 1 (GSTK1) was under positive selection in two independent clades. For the latter, homology modelling strongly suggested that positive selection targeted enzymatically important residues. Conclusions These results indicate that specific pathways were recruited in independent lineages evolving an exceptionally extended or shortened lifespan and point to mito-nuclear balance as a key factor. Electronic supplementary material The online version of this article (10.1186/s12862-019-1409-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | | | - Martin Bens
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | | | | | | | - Matthias Görlach
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Alessandro Cellerino
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany. .,Bio@SNS, Scuola Normale Superiore, Pisa, Italy.
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12
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Singh PP, Demmitt BA, Nath RD, Brunet A. The Genetics of Aging: A Vertebrate Perspective. Cell 2019; 177:200-220. [PMID: 30901541 PMCID: PMC7592626 DOI: 10.1016/j.cell.2019.02.038] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
Aging negatively impacts vitality and health. Many genetic pathways that regulate aging were discovered in invertebrates. However, the genetics of aging is more complex in vertebrates because of their specialized systems. This Review discusses advances in the genetic regulation of aging in vertebrates from work in mice, humans, and organisms with exceptional lifespans. We highlight challenges for the future, including sex-dependent differences in lifespan and the interplay between genes and environment. We also discuss how the identification of reliable biomarkers of age and development of new vertebrate models can be leveraged for personalized interventions to counter aging and age-related diseases.
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Affiliation(s)
- Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford, CA 94305, USA.
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13
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Sahm A, Cellerino A. (Anti-)parallel evolution of lifespan. Aging (Albany NY) 2019; 9:2018-2019. [PMID: 29074821 PMCID: PMC5680550 DOI: 10.18632/aging.101314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/25/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Arne Sahm
- Lebniz Insitute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Alessandro Cellerino
- Lebniz Insitute on Aging, Fritz Lipmann Institute, Jena, Germany.,Bio@SNS, Scuola Normale Superiore, Pisa, Italy
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14
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Davies KTJ, Bennett NC, Faulkes CG, Rossiter SJ. Limited Evidence for Parallel Molecular Adaptations Associated with the Subterranean Niche in Mammals: A Comparative Study of Three Superorders. Mol Biol Evol 2018; 35:2544-2559. [PMID: 30137400 PMCID: PMC6188548 DOI: 10.1093/molbev/msy161] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Among mammals, several lineages have independently adapted to a subterranean niche and possess similar phenotypic traits for burrowing (e.g., cylindrical bodies, short limbs, and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, and the absence of light. In contrast, almost nothing is known regarding molecular adaptations in other subterranean lineages (e.g., true moles and golden moles). Therefore, the extent to which the recurrent phenotypic adaptations of divergent subterranean taxa have arisen via parallel routes of molecular evolution remains untested. To address these issues, we analyzed ∼8,000 loci in 15 representative subterranean taxa of four independent transitions to an underground niche for signatures of positive selection and convergent amino acid substitutions. Complementary analyses were performed in nonsubterranean "control" taxa to assess the biological significance of results. We found comparable numbers of positively selected genes in each of the four subterranean groups; however, correspondence in terms of gene identity between gene sets was low. Furthermore, we did not detect evidence of more convergent amino acids among subterranean species pairs compared with levels found between nonsubterranean controls. Comparisons with nonsubterranean taxa also revealed loci either under positive selection or with convergent substitutions, with similar functional enrichment (e.g., cell adhesion, immune response, and coagulation). Given the limited indication that positive selection and convergence occurred in the same loci, we conclude that selection may have acted on different loci across subterranean mammal lineages to produce similar phenotypes.
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Affiliation(s)
- Kalina T J Davies
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nigel C Bennett
- Department of Zoology & Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Chris G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
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15
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Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging. BMC Biol 2018; 16:82. [PMID: 30068331 PMCID: PMC6090990 DOI: 10.1186/s12915-018-0547-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/28/2018] [Indexed: 12/04/2022] Open
Abstract
Background Mammals display a wide range of variation in their lifespan. Investigating the molecular networks that distinguish long- from short-lived species has proven useful to identify determinants of longevity. Here, we compared the livers of young and old long-lived naked mole-rats (NMRs) and the phylogenetically closely related, shorter-lived, guinea pigs using an integrated omics approach. Results We found that NMR livers display a unique expression pattern of mitochondrial proteins that results in distinct metabolic features of their mitochondria. For instance, we observed a generally reduced respiration rate associated with lower protein levels of respiratory chain components, particularly complex I, and increased capacity to utilize fatty acids. Interestingly, we show that the same molecular networks are affected during aging in both NMRs and humans, supporting a direct link to the extraordinary longevity of both species. Finally, we identified a novel detoxification pathway linked to longevity and validated it experimentally in the nematode Caenorhabditis elegans. Conclusions Our work demonstrates the benefits of integrating proteomic and transcriptomic data to perform cross-species comparisons of longevity-associated networks. Using a multispecies approach, we show at the molecular level that livers of NMRs display progressive age-dependent changes that recapitulate typical signatures of aging despite the negligible senescence and extraordinary longevity of these rodents. Electronic supplementary material The online version of this article (10.1186/s12915-018-0547-y) contains supplementary material, which is available to authorized users.
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16
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Sahm A, Bens M, Szafranski K, Holtze S, Groth M, Görlach M, Calkhoven C, Müller C, Schwab M, Kraus J, Kestler HA, Cellerino A, Burda H, Hildebrandt T, Dammann P, Platzer M. Long-lived rodents reveal signatures of positive selection in genes associated with lifespan. PLoS Genet 2018; 14:e1007272. [PMID: 29570707 PMCID: PMC5884551 DOI: 10.1371/journal.pgen.1007272] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/04/2018] [Accepted: 02/22/2018] [Indexed: 12/11/2022] Open
Abstract
The genetics of lifespan determination is poorly understood. Most research has been done on short-lived animals and it is unclear if these insights can be transferred to long-lived mammals like humans. Some African mole-rats (Bathyergidae) have life expectancies that are multiple times higher than similar sized and phylogenetically closely related rodents. To gain new insights into genetic mechanisms determining mammalian lifespans, we obtained genomic and transcriptomic data from 17 rodent species and scanned eleven evolutionary branches associated with the evolution of enhanced longevity for positively selected genes (PSGs). Indicating relevance for aging, the set of 250 identified PSGs showed in liver of long-lived naked mole-rats and short-lived rats an expression pattern that fits the antagonistic pleiotropy theory of aging. Moreover, we found the PSGs to be enriched for genes known to be related to aging. Among these enrichments were “cellular respiration” and “metal ion homeostasis”, as well as functional terms associated with processes regulated by the mTOR pathway: translation, autophagy and inflammation. Remarkably, among PSGs are RHEB, a regulator of mTOR, and IGF1, both central components of aging-relevant pathways, as well as genes yet unknown to be aging-associated but representing convincing functional candidates, e.g. RHEBL1, AMHR2, PSMG1 and AGER. Exemplary protein homology modeling suggests functional consequences for amino acid changes under positive selection. Therefore, we conclude that our results provide a meaningful resource for follow-up studies to mechanistically link identified genes and amino acids under positive selection to aging and lifespan determination. As an adaption to different environments rodents have evolved a wide range of lifespans. While most rodents are short-lived, along several phylogenetic branches long-lived species evolved. This provided us a unique opportunity to search for genes that are associated with enhanced longevity in mammals. Towards this, we computationally compared gene sequences of exceptional long-lived rodent species (like the naked mole-rat and chinchilla) and short-lived rodents (like rat and mouse) and identified those which evolved exceptional fast. As natural selection acts in parallel on a multitude of phenotypes, only a subset of the identified genes is probably associated with enhanced longevity. Applying several tests, we ensured that the dataset is related to aging. We conclude that lifespan extension in rodents can be attributed to changes in their defense against free radicals, iron homeostasis as well as cellular respiration and translation as central parts of the growth program. This confirms aging theories assuming a tradeoff between fast growth and long lifespan. Moreover, our study offers a meaningful resource of targets, i.e. genes and specific positions therein, for functional follow-up studies on their potential roles in the determination of lifespan–regardless whether they are currently known to be aging-related or not.
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Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- * E-mail:
| | - Martin Bens
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marco Groth
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Cornelis Calkhoven
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Christine Müller
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Matthias Schwab
- Department of Neurology; Jena University Hospital-Friedrich Schiller University, Jena, Germany
| | - Johann Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A. Kestler
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Alessandro Cellerino
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- Laboratory of Biology Bio@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Hynek Burda
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Thomas Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
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17
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Wagner JT, Singh PP, Romney AL, Riggs CL, Minx P, Woll SC, Roush J, Warren WC, Brunet A, Podrabsky JE. The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development. BMC Genomics 2018; 19:155. [PMID: 29463212 PMCID: PMC5819677 DOI: 10.1186/s12864-018-4539-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/12/2018] [Indexed: 11/21/2022] Open
Abstract
Background The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system. Results We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection. Conclusion The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4539-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Josiah T Wagner
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA. .,Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon, USA.
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Amie L Romney
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Claire L Riggs
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Patrick Minx
- McDonnell Genome Institute at Washington University, St Louis, Missouri, USA
| | - Steven C Woll
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Jake Roush
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Wesley C Warren
- McDonnell Genome Institute at Washington University, St Louis, Missouri, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, California, USA.,Glenn Center for the Biology of Aging, Stanford, California, USA
| | - Jason E Podrabsky
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
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18
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Sahm A, Bens M, Platzer M, Szafranski K. PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes. Nucleic Acids Res 2017; 45:e100. [PMID: 28334822 PMCID: PMC5499814 DOI: 10.1093/nar/gkx179] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/09/2017] [Indexed: 11/12/2022] Open
Abstract
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software. We developed the software tool PosiGene that (i) detects positively selected genes (PSGs) on genome-scale, (ii) allows analysis of specific evolutionary branches, (iii) can be used in arbitrary species contexts and (iv) offers visualization of the results for further manual validation and biological interpretation. We exemplify PosiGene's performance using simulated and real data. In the simulated data approach, we determined a false positive rate <1%. With real data, we found that 68.4% of the PSGs detected by PosiGene, were shared by at least one previous study that used the same set of species. PosiGene is a user-friendly, reliable tool for reproducible genome-wide identification of PSGs and freely available at https://github.com/gengit/PosiGene.
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Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Martin Bens
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
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19
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Ma S, Gladyshev VN. Molecular signatures of longevity: Insights from cross-species comparative studies. Semin Cell Dev Biol 2017; 70:190-203. [PMID: 28800931 PMCID: PMC5807068 DOI: 10.1016/j.semcdb.2017.08.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/31/2017] [Accepted: 08/03/2017] [Indexed: 01/26/2023]
Abstract
Much of the current research on longevity focuses on the aging process within a single species. Several molecular players (e.g. IGF1 and MTOR), pharmacological compounds (e.g. rapamycin and metformin), and dietary approaches (e.g. calorie restriction and methionine restriction) have been shown to be important in regulating and modestly extending lifespan in model organisms. On the other hand, natural lifespan varies much more significantly across species. Within mammals alone, maximum lifespan differs more than 100 fold, but the underlying regulatory mechanisms remain poorly understood. Recent comparative studies are beginning to shed light on the molecular signatures associated with exceptional longevity. These include genome sequencing of microbats, naked mole rat, blind mole rat, bowhead whale and African turquoise killifish, and comparative analyses of gene expression, metabolites, lipids and ions across multiple mammalian species. Together, they point towards several putative strategies for lifespan regulation and cancer resistance, as well as the pathways and metabolites associated with longevity variation. In particular, longevity may be achieved by both lineage-specific adaptations and common mechanisms that apply across the species. Comparing the resulting cross-species molecular signatures with the within-species lifespan extension strategies will improve our understanding of mechanisms of longevity control and provide a starting point for novel and effective interventions.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Biology of Aging, Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119234, Russia.
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20
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21
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What modulates animal longevity? Fast and slow aging in bivalves as a model for the study of lifespan. Semin Cell Dev Biol 2017; 70:130-140. [PMID: 28778411 DOI: 10.1016/j.semcdb.2017.07.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022]
Abstract
Delineating the physiological and biochemical causes of aging process in the animal kingdom is a highly active area of research not only because of potential benefits for human health but also because aging process is related to life history strategies (growth and reproduction) and to responses of organisms to environmental conditions and stress. In this synthesis, we advocate studying bivalve species as models for revealing the determinants of species divergences in maximal longevity. This taxonomic group includes the longest living metazoan on earth (Arctica islandica), which insures the widest range of maximum life span when shorter living species are also included in the comparative model. This model can also be useful for uncovering factors modulating the pace of aging in given species by taking advantages of the wide disparity of lifespan among different populations of the same species. For example, maximal lifespan in different populations of A islandica range from approximately 36 years to over 500 years. In the last 15 years, research has revealed that either regulation or tolerance to oxidative stress is tightly correlated to longevity in this group which support further investigations on this taxon to unveil putative mechanistic links between Reactive Oxygen Species and aging process.
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22
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Yu J, Hu F, Dossa K, Wang Z, Ke T. Genome-wide analysis of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization. BMC Genomics 2017. [PMID: 28645261 PMCID: PMC5481917 DOI: 10.1186/s12864-017-3844-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to conserved domains identified in their amino acid sequences, these glycosyltransferases can be classified into a single UDP-glycosyltransferase (UGT) 1 superfamily. Results We performed genome-wide comparative analysis of UGT genes to trace evolutionary history in algae, bryophytes, pteridophytes, and angiosperms; then, we further investigated the expansion mechanisms and function characterization of UGT gene families in Brassica rapa and Brassica oleracea. Using Hidden Markov Model search, we identified 3, 21, 140, 200, 115, 147, and 147 UGTs in Chlamydomonas reinhardtii, Physcomitrella patens, Selaginella moellendorffii, Oryza sativa, Arabidopsis thaliana, B. rapa, and B. oleracea, respectively. Phylogenetic analysis revealed that UGT80 gene family is an ancient gene family, which is shared by all plants and UGT74 gene family is shared by ferns and angiosperms, but the remaining UGT gene families were shared by angiosperms. In dicot lineage, UGTs among three species were classified into three subgroups containing 3, 6, and 12 UGT gene families. Analysis of chromosomal distribution indicates that 98.6 and 71.4% of UGTs were located on B. rapa and B. oleracea pseudo-molecules, respectively. Expansion mechanism analyses uncovered that whole genome duplication event exerted larger influence than tandem duplication on expansion of UGT gene families in B. rapa, and B. oleracea. Analysis of selection forces of UGT orthologous gene pairs in B. rapa, and B. oleracea compared to A. thaliana suggested that orthologous genes in B. rapa, and B. oleracea have undergone negative selection, but there were no significant differences between A. thaliana –B. rapa and A. thaliana –B. oleracea lineages. Our comparisons of expression profiling illustrated that UGTs in B. rapa performed more discrete expression patterns than these in B. oleracea indicating stronger function divergence. Combing with phylogeny and expression analysis, the UGTs in B. rapa and B. oleracea experienced parallel evolution after they diverged from a common ancestor. Conclusion We first traced the evolutionary history of UGT gene families in plants and revealed its evolutionary and functional characterization of UGTs in B. rapa, and B. oleracea. This study provides novel insights into the evolutionary history and functional divergence of important traits or phenotype-related gene families in plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3844-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingyin Yu
- Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang, 473061, China.,Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Fan Hu
- Third Institute of Oceanography, State Oceanic Administration, Fujian, 361005, China
| | - Komivi Dossa
- Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang, 473061, China.,Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Zhaokai Wang
- Third Institute of Oceanography, State Oceanic Administration, Fujian, 361005, China.
| | - Tao Ke
- Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang, 473061, China.
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23
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Sahm A, Bens M, Platzer M, Cellerino A. Parallel evolution of genes controlling mitonuclear balance in short-lived annual fishes. Aging Cell 2017; 16:488-496. [PMID: 28295945 PMCID: PMC5418189 DOI: 10.1111/acel.12577] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2016] [Indexed: 12/15/2022] Open
Abstract
The current molecular understanding of the aging process derives almost exclusively from the study of random or targeted single‐gene mutations in highly inbred laboratory species, mostly invertebrates. Little information is available as to the genetic mechanisms responsible for natural lifespan variation and the evolution of lifespan, especially in vertebrates. Here, we investigated the pattern of positive selection in annual (i.e., short‐lived) and nonannual (i.e., longer‐lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan). We identified genes under positive selection in all steps of mitochondrial biogenesis: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes, and electron transport chain. Signs of paralleled evolution (i.e., evolution in more than one branch of Nothobranchius phylogeny) are observed in four out of five steps. Moreover, some genes under positive selection in Nothobranchius are under positive selection also in long‐lived mammals such as bats and mole‐rats. Complexes of the respiratory chain are formed in a coordinates multistep process where nuclearly and mitochondrially encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance, and experimental manipulations of mitonuclear balance can increase longevity of laboratory species. Our data strongly indicate that these genes are also casually linked to evolution lifespan in vertebrates.
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Affiliation(s)
- Arne Sahm
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Martin Bens
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Matthias Platzer
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Alessandro Cellerino
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
- Bio@SNS; Scuola Normale Superiore; Pisa 56124 Italy
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