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Guo B, Sun Y, Wang Y, Zhang Y, Zheng Y, Xu S, Yang G, Ren W. Evolutionary genetics of pulmonary anatomical adaptations in deep-diving cetaceans. BMC Genomics 2024; 25:339. [PMID: 38575860 PMCID: PMC10993460 DOI: 10.1186/s12864-024-10263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Cetaceans, having experienced prolonged adaptation to aquatic environments, have undergone evolutionary changes in their respiratory systems. This process of evolution has resulted in the emergence of distinctive phenotypic traits, notably the abundance of elastic fibers and thickened alveolar walls in their lungs, which may facilitate alveolar collapse during diving. This structure helps selective exchange of oxygen and carbon dioxide, while minimizing nitrogen exchange, thereby reducing the risk of DCS. Nevertheless, the scientific inquiry into the mechanisms through which these unique phenotypic characteristics govern the diving behavior of marine mammals, including cetaceans, remains unresolved. RESULTS This study entails an evolutionary analysis of 42 genes associated with pulmonary fibrosis across 45 mammalian species. Twenty-one genes in cetaceans exhibited accelerated evolution, featuring specific amino acid substitutions in 14 of them. Primarily linked to the development of the respiratory system and lung morphological construction, these genes play a crucial role. Moreover, among marine mammals, we identified eight genes undergoing positive selection, and the evolutionary rates of three genes significantly correlated with diving depth. Specifically, the SFTPC gene exhibited convergent amino acid substitutions. Through in vitro cellular experiments, we illustrated that convergent amino acid site mutations in SFTPC contribute positively to pulmonary fibrosis in marine mammals, and the presence of this phenotype can induce deep alveolar collapse during diving, thereby reducing the risk of DCS during diving. CONCLUSIONS The study unveils pivotal genetic signals in cetaceans and other marine mammals, arising through evolution. These genetic signals may influence lung characteristics in marine mammals and have been linked to a reduced risk of developing DCS. Moreover, the research serves as a valuable reference for delving deeper into human diving physiology.
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Affiliation(s)
- Boxiong Guo
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yixuan Sun
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yuehua Wang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Ya Zhang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yu Zheng
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
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2
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Gemmell P, Sackton TB, Edwards SV, Liu JS. A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution. PLoS Comput Biol 2024; 20:e1011995. [PMID: 38656999 PMCID: PMC11078400 DOI: 10.1371/journal.pcbi.1011995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/08/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Genomes contain conserved non-coding sequences that perform important biological functions, such as gene regulation. We present a phylogenetic method, PhyloAcc-C, that associates nucleotide substitution rates with changes in a continuous trait of interest. The method takes as input a multiple sequence alignment of conserved elements, continuous trait data observed in extant species, and a background phylogeny and substitution process. Gibbs sampling is used to assign rate categories (background, conserved, accelerated) to lineages and explore whether the assigned rate categories are associated with increases or decreases in the rate of trait evolution. We test our method using simulations and then illustrate its application using mammalian body size and lifespan data previously analyzed with respect to protein coding genes. Like other studies, we find processes such as tumor suppression, telomere maintenance, and p53 regulation to be related to changes in longevity and body size. In addition, we also find that skeletal genes, and developmental processes, such as sprouting angiogenesis, are relevant.
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Affiliation(s)
- Patrick Gemmell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy B. Sackton
- FAS Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jun S. Liu
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
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3
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Mu J, Lin Q, Liang Y. An update on the effects of food-derived active peptides on the intestinal microecology. Crit Rev Food Sci Nutr 2023; 63:11625-11639. [PMID: 35791779 DOI: 10.1080/10408398.2022.2094889] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The intestinal microecology is a research hotspot, and neologisms related to the gut such as gut-brain axis, gut-lung axis, gut-bone axis, gut-skin axis, gut-renal axis, and gut-liver axis have emerged from recent research. Meticulous investigation has discovered that food-derived active peptides (FDAPs) are bioactive substances that optimize the structure of the gut microbiota to improve human health. However, few reviews have summarized and emphasized the nutritional value of FDAPs and their mechanisms of action in regulating the composition of the gut microbiota. We aim to provide an update on the latest research on FDAPs by comparing, summarizing, and discussing the potential food sources of FDAPs, their physiological functions, and regulatory effects on the intestinal microecology. The key findings are that few studies have analyzed the potential mechanisms and molecular pathways through which FDAPs maintain intestinal microecological homeostasis. We found that an imbalance in the ratio of Bacteroidetes and Firmicutes in the gut microbiota and abnormal production of short-chain fatty acids are key to the occurrence and development of various diseases. This review provides theoretical support for future comprehensive research on the digestion, distribution, metabolism, and excretion of FDAPs and the mechanisms underlying the interactions between FDAPs and the intestinal microecology.
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Affiliation(s)
- Jianfei Mu
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Qinlu Lin
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ying Liang
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
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4
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Huang Z, Jiang C, Gu J, Uvizl M, Power S, Douglas D, Kacprzyk J. Duplications of Human Longevity-Associated Genes Across Placental Mammals. Genome Biol Evol 2023; 15:evad186. [PMID: 37831410 PMCID: PMC10588791 DOI: 10.1093/gbe/evad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
Natural selection has shaped a wide range of lifespans across mammals, with a few long-lived species showing negligible signs of ageing. Approaches used to elucidate the genetic mechanisms underlying mammalian longevity usually involve phylogenetic selection tests on candidate genes, detections of convergent amino acid changes in long-lived lineages, analyses of differential gene expression between age cohorts or species, and measurements of age-related epigenetic changes. However, the link between gene duplication and evolution of mammalian longevity has not been widely investigated. Here, we explored the association between gene duplication and mammalian lifespan by analyzing 287 human longevity-associated genes across 37 placental mammals. We estimated that the expansion rate of these genes is eight times higher than their contraction rate across these 37 species. Using phylogenetic approaches, we identified 43 genes whose duplication levels are significantly correlated with longevity quotients (False Discovery Rate (FDR) < 0.05). In particular, the strong correlation observed for four genes (CREBBP, PIK3R1, HELLS, FOXM1) appears to be driven mainly by their high duplication levels in two ageing extremists, the naked mole rat (Heterocephalus glaber) and the greater mouse-eared bat (Myotis myotis). Further sequence and expression analyses suggest that the gene PIK3R1 may have undergone a convergent duplication event, whereby the similar region of its coding sequence was independently duplicated multiple times in both of these long-lived species. Collectively, this study identified several candidate genes whose duplications may underlie the extreme longevity in mammals, and highlighted the potential role of gene duplication in the evolution of mammalian long lifespans.
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Affiliation(s)
- Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Chongyi Jiang
- Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Jiayun Gu
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Marek Uvizl
- Department of Zoology, National Museum, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Declan Douglas
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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5
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Barteri F, Valenzuela A, Farré X, de Juan D, Muntané G, Esteve-Altava B, Navarro A. CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions. Bioinformatics 2023; 39:btad623. [PMID: 37846039 PMCID: PMC10598582 DOI: 10.1093/bioinformatics/btad623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/04/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023] Open
Abstract
MOTIVATION Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes. RESULTS Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user. AVAILABILITY AND IMPLEMENTATION CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples.
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Affiliation(s)
- Fabio Barteri
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C/ Wellington 30, Barcelona 08006, Spain
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C/ Wellington 30, Barcelona 08006, Spain
| | - Xavier Farré
- Genomes for Life-GCAT Lab, GermanTrias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Badalona 08916, Spain
| | - David de Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
| | - Gerard Muntané
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), Hospital Universitari Institut Pere Mata, Universitat Rovira i Virgili. Avda. Josep Laporte, 2 – Planta 0 – E2 color taronja, Reus 43204, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0. Madrid 28029, Spain
| | - Borja Esteve-Altava
- European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. C. Doctor Aiguader 88, Barcelona 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C/ Wellington 30, Barcelona 08006, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Lluís Companys 23, Barcelona 08010, Spain
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C. Doctor Aiguader N88, Barcelona 08003, Spain
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6
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Igoshin AV, Yudin NS, Romashov GA, Larkin DM. A Multibreed Genome-Wide Association Study for Cattle Leukocyte Telomere Length. Genes (Basel) 2023; 14:1596. [PMID: 37628647 PMCID: PMC10454124 DOI: 10.3390/genes14081596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Telomeres are terminal DNA regions of chromosomes that prevent chromosomal fusion and degradation during cell division. In cattle, leukocyte telomere length (LTL) is associated with longevity, productive lifespan, and disease susceptibility. However, the genetic basis of LTL in this species is less studied than in humans. In this study, we utilized the whole-genome resequencing data of 239 animals from 17 cattle breeds for computational leukocyte telomere length estimation and subsequent genome-wide association study of LTL. As a result, we identified 42 significant SNPs, of which eight were found in seven genes (EXOC6B, PTPRD, RPS6KC1, NSL1, AGBL1, ENSBTAG00000052188, and GPC1) when using covariates for two major breed groups (Turano-Mongolian and European). Association analysis with covariates for breed effect detected 63 SNPs, including 13 in five genes (EXOC6B, PTPRD, RPS6KC1, ENSBTAG00000040318, and NELL1). The PTPRD gene, demonstrating the top signal in analysis with breed effect, was previously associated with leukocyte telomere length in cattle and likely is involved in the mechanism of alternative lengthening of telomeres. The single nucleotide variants found could be tested for marker-assisted selection to improve telomere-length-associated traits.
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Affiliation(s)
- Alexander V. Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Nikolay S. Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Grigorii A. Romashov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Denis M. Larkin
- Royal Veterinary College, University of London, London NW1 0TU, UK
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7
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Bapteste E, Huneman P, Keller L, Teulière J, Lopez P, Teeling EC, Lindner AB, Baudisch A, Ludington WB, Franceschi C. Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life. Ageing Res Rev 2023; 89:101982. [PMID: 37321383 PMCID: PMC10771319 DOI: 10.1016/j.arr.2023.101982] [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: 04/14/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored. The Mutation Accumulation theory and the Antagonistic Pleiotropy theory were developed under the traditional framework of population genetics, and therefore are logically centred on the ageing of individuals within a population. The Disposable Soma theory, based on principles of optimising physiology, mainly explains ageing within a species. Consequently, current leading evolutionary theories of ageing do not explicitly model the countless interspecific and ecological interactions, such as symbioses and host-microbiomes associations, increasingly recognized to shape organismal evolution across the Web of Life. Moreover, the development of network modelling supporting a deeper understanding on the molecular interactions associated with ageing within and between organisms is also bringing forward new questions regarding how and why molecular pathways associated with ageing evolved. Here, we take an evolutionary perspective to examine the effects of organismal interactions on ageing across different levels of biological organisation, and consider the impact of surrounding and nested systems on organismal ageing. We also apply this perspective to suggest open issues with potential to expand the standard evolutionary theories of ageing.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS/ Université Paris I Sorbonne), Paris, France
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
| | - Annette Baudisch
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, 5230 Odense M, Denmark
| | - William B Ludington
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; Department of Applied Mathematics and Laboratory of Systems Medicine of Aging, Lobachevsky University, Nizhny Novgorod 603950, Russia
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8
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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles. Animals (Basel) 2023; 13:ani13030471. [PMID: 36766360 PMCID: PMC9913427 DOI: 10.3390/ani13030471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.
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9
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Teulière J, Bernard C, Corel E, Lapointe FJ, Martens J, Lopez P, Bapteste E. Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals. GeroScience 2022; 45:1059-1080. [PMID: 36508078 PMCID: PMC9886728 DOI: 10.1007/s11357-022-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
The genetic roots of the diverse paces and shapes of ageing and of the large variations in longevity observed across the tree of life are poorly understood. Indeed, pathways associated with ageing/longevity are incompletely known, both in terms of their constitutive genes/proteins and of their molecular interactions. Moreover, there is limited overlap between the genes constituting these pathways across mammals. Yet, dedicated comparative analyses might still unravel evolutionarily conserved, important pathways associated with longevity or ageing. Here, we used an original strategy with a double evolutionary and systemic focus to analyse protein interactions associated with ageing or longevity during the evolution of five species of Opisthokonta. We ranked these proteins and interactions based on their evolutionary conservation and centrality in past and present protein-protein interaction (PPI) networks, providing a big systemic picture of the evolution of ageing and longevity pathways that identified which pathways emerged in which Opisthokonta lineages, were conserved, and/or central. We confirmed that longevity/ageing-associated proteins (LAPs), be they pro- or anti-longevity, are highly central in extant PPI, consistently with the antagonistic pleiotropy theory of ageing, and identified key antagonistic regulators of ageing/longevity, 52 of which with homologues in humans. While some highly central LAPs were evolutionarily conserved for over a billion years, we report a clear transition in the functionally important components of ageing/longevity within bilaterians. We also predicted 487 novel evolutionarily conserved LAPs in humans, 54% of which are more central than mTOR, and 138 of which are druggable, defining new potential targets for anti-ageing treatments in humans.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eduardo Corel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- grid.14848.310000 0001 2292 3357Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC Canada
| | - Johannes Martens
- Sciences, Normes, Démocratie (SND), Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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10
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Equivocal evidence for a link between megalencephaly-related genes and primate brain size evolution. Sci Rep 2022; 12:10902. [PMID: 35764790 PMCID: PMC9239989 DOI: 10.1038/s41598-022-12953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/19/2022] [Indexed: 11/08/2022] Open
Abstract
A large brain is a defining feature of modern humans, and much work has been dedicated to exploring the molecular underpinnings of this trait. Although numerous studies have focused on genes associated with human microcephaly, no studies have explicitly focused on genes associated with megalencephaly. Here, we investigate 16 candidate genes that have been linked to megalencephaly to determine if: (1) megalencephaly-associated genes evolved under positive selection across primates; and (2) selection pressure on megalencephaly-associated genes is linked to primate brain size. We found evidence for positive selection for only one gene, OFD1, with 1.8% of the sites estimated to have dN/dS values greater than 1; however, we did not detect a relationship between selection pressure on this gene and brain size across species, suggesting that selection for changes to non-brain size traits drove evolutionary changes to this gene. In fact, our primary analyses did not identify significant associations between selection pressure and brain size for any candidate genes. While we did detect positive associations for two genes (GPC3 and TBC1D7) when two phyletic dwarfs (i.e., species that underwent recent evolutionary decreases in brain size) were excluded, these associations did not withstand FDR correction. Overall, these results suggest that sequence alterations to megalencephaly-associated genes may have played little to no role in primate brain size evolution, possibly due to the highly pleiotropic effects of these genes. Future comparative studies of gene expression levels may provide further insights. This study enhances our understanding of the genetic underpinnings of brain size evolution in primates and identifies candidate genes that merit further exploration.
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11
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Font-Porterias N, McNelis MG, Comas D, Hlusko LJ. Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals. Integr Org Biol 2022; 4:obac018. [PMID: 35874492 PMCID: PMC9299678 DOI: 10.1093/iob/obac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/13/2022] Open
Abstract
Synopsis The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation. Spanish La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.
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Affiliation(s)
- Neus Font-Porterias
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Madeline G McNelis
- Department of Integrative Biology, University of California Berkeley , California , USA
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Institut de Biologia Evolutiva (UPF-CSIC) , Barcelona , Spain
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley , California , USA
- National Research Center on Human Evolution (CENIEH) , Burgos , Spain
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12
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Conte M, Giuliani C, Chiariello A, Iannuzzi V, Franceschi C, Salvioli S. GDF15, an emerging key player in human aging. Ageing Res Rev 2022; 75:101569. [PMID: 35051643 DOI: 10.1016/j.arr.2022.101569] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/14/2022] [Indexed: 12/20/2022]
Abstract
Growth differentiation factor 15 (GDF15) is recently emerging not only as a stress-related mitokine, but also as a key player in the aging process, being one of the most up-regulated protein with age and associated with a variety of age-related diseases (ARDs). Many data indicate that GDF15 has protective roles in several tissues during different stress and aging, thus playing a beneficial role in apparent contrast with the observed association with many ARDs. A possible detrimental role for this protein is then hypothesized to emerge with age. Therefore, GDF15 can be considered as a pleiotropic factor with beneficial activities that can turn detrimental in old age possibly when it is chronically elevated. In this review, we summarize the current knowledge on the biology of GDF15 during aging. We also propose GDF15 as a part of a dormancy program, where it may play a role as a mediator of defense processes aimed to protect from inflammatory damage and other stresses, according to the life history theory.
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Affiliation(s)
- Maria Conte
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy.
| | - Cristina Giuliani
- Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy; Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Antonio Chiariello
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Vincenzo Iannuzzi
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy; Interdepartmental Centre "Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate)", University of Bologna, Bologna, Italy
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13
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Wheeler LC, Walker JF, Ng J, Deanna R, Dunbar-Wallis A, Backes A, Pezzi PH, Palchetti MV, Robertson HM, Monaghan A, Brandão de Freitas L, Barboza GE, Moyroud E, Smith SD. Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway. Mol Biol Evol 2022; 39:6536971. [PMID: 35212724 PMCID: PMC8911815 DOI: 10.1093/molbev/msac044] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix–loop–helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.
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Affiliation(s)
- Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Joseph F Walker
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Rocío Deanna
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334.,Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
| | - Amy Dunbar-Wallis
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Alice Backes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Pedro H Pezzi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - M Virginia Palchetti
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
| | - Holly M Robertson
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Andrew Monaghan
- Research Computing,University of Colorado, 3100 Marine Street, 597 UCB Boulder, CO 80303
| | - Loreta Brandão de Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina.,Facultad de Ciencias Químicas, Universidad Nacional de Córdoba,Haya de la Torre y Medina Allende, Córdoba, Argentina
| | - Edwige Moyroud
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
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14
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Chai S, Tian R, Xu S, Ren W, Yang G. Evolution of Fertilization-Related Genes Provides Insights Into Reproductive Health in Natural Ascrotal Mammals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.828325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cryptorchidism is the failure of one or both testes to descend into the bottom of the scrotum. This common congenital malformation in humans and domestic animals is the best characterized risk factor for abnormal sperm functions and infertility. However, current treatment approaches for cryptorchidism do not ensure paternity in all cases. Some lineages of mammals (such as elephants and cetaceans) have natural ascrotal testes (i.e., undescended or incompletely descended testes) and normal sperm motility and fertility, providing an opportunity to understand the genetic basis of cryptorchidism. In this study, we showed that genes associated with sperm motility and competition/fertility in ascrotal mammals experienced frequent, strong selective pressure. The fixation of specific amino acids and positive selection in ascrotal mammals could affect the physicochemical properties and functions of fertilization-related proteins. In a comparison between mammals with undescended testes and incompletely descended testes, discrepancies in genes showing evidence for adaptive evolution and in functional enrichment suggested that multiple molecular mechanisms contribute to the maintenance of fertility in the challenging testicular environment. Our findings revealed substantial heterogeneity in the divergence of fertilization-related genes between natural scrotal and ascrotal mammals and provide insight into molecular mechanisms underlying normal sperm motility and competition in natural ascrotal mammals. We provide a detailed theoretical basis for understanding the pathology of cryptorchidism from a molecular evolutionary perspective. This study may contribute to the establishment of diagnostic and therapeutic targets for sperm motility and fertility disorders due to congenital cryptorchidism in humans and domestic animals.
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15
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BMI, Blood Pressure, and Plasma Lipids among Centenarians and Their Offspring. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3836247. [PMID: 35096109 PMCID: PMC8794670 DOI: 10.1155/2022/3836247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/30/2021] [Indexed: 11/20/2022]
Abstract
Background The burden of cardiovascular diseases (CVDs) is increasing substantially due to population growth and aging. Determining effective prevention and understanding the underlying mechanisms remain desirable pursuits for increasing the quality of life. As centenarians and their offspring may have genetic advantages, they may present with healthier cardiovascular-related profiles. Methods We launched a cross-sectional household-based survey of centenarian families, including 253 centenarians, 217 centenarian offspring, and 116 offspring spouses without centenarian parents from county-level Chinese longevity city Rugao. Among offspring and offspring spouses were the following arrangements: 101 paired offspring and offspring spouses who lived together, 116 unpaired offspring, and 16 unpaired spouses. We investigated their cardiovascular-related health status including waist circumference, body mass index (BMI), blood pressure, and plasma lipids and compared results among centenarians, centenarian offspring, and offspring spouses. Results Centenarians ranged from 99 to 109 years with a median age of 100 years. Centenarian offspring, with a median age of 70 years, and offspring spouses, with a median age of 69 years, shared similar age. Results of blood pressure, plasma lipid levels, and BMI displayed no significant difference between centenarian offspring and offspring spouses. However, centenarians appeared to have lower waist circumference, BMI, TC, LDL-C, TG, and diastolic blood pressure but higher levels of systolic blood pressure (p < 0.05). Multivariate analysis showed the prevalence of obesity, hypertension, and dyslipidemia was similar between centenarian offspring and offspring spouses, while centenarians appeared to have a lower prevalence of obesity and a higher prevalence of hypertension (p < 0.05). Conclusions Centenarians and centenarian offspring did not present healthier BMI, blood pressure, or plasma lipids than offspring spouses. Further research on longevity and cardiovascular diseases are desirable.
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16
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Sun (孙迪) D, Chai (柴思敏) S, Huang (黄鑫) X, Wang (王滢莹) Y, Xiao (肖琳琳) L, Xu (徐士霞) S, Yang (杨光) G. Novel Genomic Insights into Body Size Evolution in Cetaceans and a Resolution of Peto’s Paradox. Am Nat 2022; 199:E28-E42. [DOI: 10.1086/717768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Di Sun (孙迪)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Simin Chai (柴思敏)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Xin Huang (黄鑫)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yingying Wang (王滢莹)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Linlin Xiao (肖琳琳)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Shixia Xu (徐士霞)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Guang Yang (杨光)
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
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17
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Tejada-Martinez D, Avelar RA, Lopes I, Zhang B, Novoa G, de Magalhães JP, Trizzino M. Positive selection and enhancer evolution shaped lifespan and body mass in great apes. Mol Biol Evol 2021; 39:6491260. [PMID: 34971383 PMCID: PMC8837823 DOI: 10.1093/molbev/msab369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on over ten thousand genes, including ∼1,500 previously associated with lifespan, and additional ∼9,000 for which an association with longevity has never been suggested. We analyzed dN/dS rates, positive selection, gene expression (RNA-seq) and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan and body mass we identified 276 genes whose rate of evolution positively correlates with maximum lifespan in primates. Further, we identified 5 genes, important for tumor suppression, adaptive immunity, metastasis and inflammation, under positive selection exclusively in the great ape lineage. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that 8% of ∼1,500 genes previously associated with longevity are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel "ape-specific" enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE-Vntr-Alus (SVAs). In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.
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Affiliation(s)
- Daniela Tejada-Martinez
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Inês Lopes
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Bruce Zhang
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Guy Novoa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
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18
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Chai S, Huang X, Wu T, Xu S, Ren W, Yang G. Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals. BMC Genomics 2021; 22:763. [PMID: 34702182 PMCID: PMC8547080 DOI: 10.1186/s12864-021-08084-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear. RESULTS In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy. CONCLUSIONS Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the "cooling hypothesis", which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the "training hypothesis", which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.
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Affiliation(s)
- Simin Chai
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Xin Huang
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Tianzhen Wu
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Shixia Xu
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Wenhua Ren
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Guang Yang
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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Carlsson H, Ivimey-Cook E, Duxbury EML, Edden N, Sales K, Maklakov AA. Ageing as "early-life inertia": Disentangling life-history trade-offs along a lifetime of an individual. Evol Lett 2021; 5:551-564. [PMID: 34621540 PMCID: PMC8484722 DOI: 10.1002/evl3.254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/19/2021] [Accepted: 08/13/2021] [Indexed: 11/10/2022] Open
Abstract
The theory that ageing evolves because of competitive resource allocation between the soma and the germline has been challenged by studies showing that somatic maintenance can be improved without impairing reproduction. However, it has been suggested that cost‐free improvement in somatic maintenance is possible only under a narrow range of benign conditions. Here, we show that experimental downregulation of insulin/IGF‐1 signaling (IIS) in C. elegans nematodes, a robustly reproducible life span‐ and health span‐extending treatment, reduces fitness in a complex variable environment when initiated during development but does not reduce fitness when initiated in adulthood. Thus, our results show that the costs and benefits of reduced IIS can be uncoupled when organisms inhabit variable environments, and, therefore, do not provide support for the resource allocation theory. Our findings support the theory that the force of natural selection on gene expression in evolutionarily conserved signaling pathways that shape life‐history traits declines after the onset of reproduction resulting in organismal senescence.
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Affiliation(s)
- Hanne Carlsson
- School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom
| | - Edward Ivimey-Cook
- School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom
| | - Elizabeth M L Duxbury
- School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom
| | - Nathan Edden
- School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom
| | - Kris Sales
- School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom
| | - Alexei A Maklakov
- School of Biological Sciences University of East Anglia Norwich NR4 7TJ United Kingdom
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20
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Podder A, Raju A, Schork NJ. Cross-Species and Human Inter-Tissue Network Analysis of Genes Implicated in Longevity and Aging Reveal Strong Support for Nutrient Sensing. Front Genet 2021; 12:719713. [PMID: 34512728 PMCID: PMC8430347 DOI: 10.3389/fgene.2021.719713] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/10/2021] [Indexed: 12/22/2022] Open
Abstract
Intensive research efforts have been undertaken to slow human aging and therefore potentially delay the onset of age-related diseases. These efforts have generated an enormous amount of high-throughput data covering different levels in the physiologic hierarchy, e.g., genetic, epigenetic, transcriptomic, proteomic, and metabolomic, etc. We gathered 15 independent sources of information about genes potentially involved in human longevity and lifespan (N = 5836) and subjected them to various integrated analyses. Many of these genes were initially identified in non-human species, and we investigated their orthologs in three non-human species [i.e., mice (N = 967), fruit fly (N = 449), and worm (N = 411)] for further analysis. We characterized experimentally determined protein-protein interaction networks (PPIN) involving each species' genes from 9 known protein databases and studied the enriched biological pathways among the individually constructed PPINs. We observed three important signaling pathways: FoxO signaling, mTOR signaling, and autophagy to be common and highly enriched in all four species (p-value ≤ 0.001). Our study implies that the interaction of proteins involved in the mechanistic target of rapamycin (mTOR) signaling pathway is somewhat limited to each species or that a "rewiring" of specific networks has taken place over time. To corroborate our findings, we repeated our analysis in 43 different human tissues. We investigated conserved modules in various tissue-specific PPINs of the longevity-associated genes based upon their protein expression. This analysis also revealed mTOR signaling as shared biological processes across four different human tissue-specific PPINs for liver, heart, skeletal muscle, and adipose tissue. Further, we explored our results' translational potential by assessing the protein interactions with all the reported drugs and compounds that have been experimentally verified to promote longevity in the three-comparator species. We observed that the target proteins of the FDA-approved drug rapamycin (a known inhibitor of mTOR) were conserved across all four species. Drugs like melatonin and metformin exhibited shared targets with rapamycin in the human PPIN. The detailed information about the curated gene list, cross-species orthologs, PPIN, and pathways was assembled in an interactive data visualization portal using RStudio's Shiny framework (https://agingnetwork.shinyapps.io/frontiers/).
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Affiliation(s)
- Avijit Podder
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Anish Raju
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Nicholas J. Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, United States
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21
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Farré X, Molina R, Barteri F, Timmers PRHJ, Joshi PK, Oliva B, Acosta S, Esteve-Altava B, Navarro A, Muntané G. Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span. Mol Biol Evol 2021; 38:4948-4961. [PMID: 34297086 PMCID: PMC8557403 DOI: 10.1093/molbev/msab219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The enormous mammal's lifespan variation is the result of each species' adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, species lifespans and longevity of individuals, are in part shared across the tree of life. Here, we compared protein-coding regions across the mammalian phylogeny to detect individual amino acid (AA) changes shared by the most long-lived mammals and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 AA in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (P = 0.003). These genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 AA showed a significant association with maximum lifespan in a phylogenetic test. Interestingly, most of the detected AA positions do not vary in extant human populations (81.2%) or have allele frequencies below 1% (99.78%). Consequently, almost none of these putatively important variants could have been detected by genome-wide association studies. Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected, successfully demonstrating for the first time that comparative genomics can be used to enhance interpretation of human genome-wide association studies. Finally, we show that the human longevity-associated proteins are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan.
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Affiliation(s)
- Xavier Farré
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Ruben Molina
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabio Barteri
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul R H J Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom,Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Baldomero Oliva
- Structural Bioinformatics Lab, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sandra Acosta
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
| | - Borja Esteve-Altava
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain
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22
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The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proc Natl Acad Sci U S A 2021; 118:2010632118. [PMID: 33574059 PMCID: PMC7896301 DOI: 10.1073/pnas.2010632118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Surviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark human characteristics. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our method to generate high- and low-coverage genomes from noninvasive biomaterials. Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator. Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
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23
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Plasma methionine metabolic profile is associated with longevity in mammals. Commun Biol 2021; 4:725. [PMID: 34117367 PMCID: PMC8196171 DOI: 10.1038/s42003-021-02254-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 05/20/2021] [Indexed: 01/28/2023] Open
Abstract
Methionine metabolism arises as a key target to elucidate the molecular adaptations underlying animal longevity due to the negative association between longevity and methionine content. The present study follows a comparative approach to analyse plasma methionine metabolic profile using a LC-MS/MS platform from 11 mammalian species with a longevity ranging from 3.5 to 120 years. Our findings demonstrate the existence of a species-specific plasma profile for methionine metabolism associated with longevity characterised by: i) reduced methionine, cystathionine and choline; ii) increased non-polar amino acids; iii) reduced succinate and malate; and iv) increased carnitine. Our results support the existence of plasma longevity features that might respond to an optimised energetic metabolism and intracellular structures found in long-lived species. Mota-Martorell and colleagues use a comparative metabolomics approach to examine plasma metabolite levels associated with methionine metabolism in 11 mammalian species. They identify species specific plasma profiles indicative of a link between lifetime longevity and methionine metabolism.
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24
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Huang X, Sun D, Wu T, Liu X, Xu S, Yang G. Genomic insights into body size evolution in Carnivora support Peto's paradox. BMC Genomics 2021; 22:429. [PMID: 34107880 PMCID: PMC8191207 DOI: 10.1186/s12864-021-07732-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
Background The range of body sizes in Carnivora is unparalleled in any other mammalian order—the heaviest species is 130,000 times heavier than the lightest and the longest species is 50 times longer than the shortest. However, the molecular mechanisms underlying these huge differences in body size have not been explored. Results Herein, we performed a comparative genomics analysis of 20 carnivores to explore the evolutionary basis of the order’s great variations in body size. Phylogenetic generalized least squares (PGLS) revealed that 337 genes were significantly related to both head body length and body mass; these genes were defined as body size associated genes (BSAGs). Fourteen positively-related BSAGs were found to be associated with obesity, and three of these were under rapid evolution in the extremely large carnivores, suggesting that these obesity-related BSAGs might have driven the body size expansion in carnivores. Interestingly, 100 BSAGs were statistically significantly enriched in cancer control in carnivores, and 15 of which were found to be under rapid evolution in extremely large carnivores. These results suggested that large carnivores might have evolved an effective mechanism to resist cancer, which could be regarded as molecular evidence to support Peto’s paradox. For small carnivores, we identified 15 rapidly evolving genes and found six genes with fixed amino acid changes that were reported to reduce body size. Conclusions This study brings new insights into the molecular mechanisms that drove the diversifying evolution of body size in carnivores, and provides new target genes for exploring the mysteries of body size evolution in mammals. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07732-w.
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Affiliation(s)
- Xin Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Tianzhen Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Xing Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
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25
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Treaster S, Karasik D, Harris MP. Footprints in the Sand: Deep Taxonomic Comparisons in Vertebrate Genomics to Unveil the Genetic Programs of Human Longevity. Front Genet 2021; 12:678073. [PMID: 34163529 PMCID: PMC8215702 DOI: 10.3389/fgene.2021.678073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/12/2021] [Indexed: 01/09/2023] Open
Abstract
With the modern quality, quantity, and availability of genomic sequencing across species, as well as across the expanse of human populations, we can screen for shared signatures underlying longevity and lifespan. Knowledge of these mechanisms would be medically invaluable in combating aging and age-related diseases. The diversity of longevities across vertebrates is an opportunity to look for patterns of genetic variation that may signal how this life history property is regulated, and ultimately how it can be modulated. Variation in human longevity provides a unique window to look for cases of extreme lifespan within a population, as well as associations across populations for factors that influence capacity to live longer. Current large cohort studies support the use of population level analyses to identify key factors associating with human lifespan. These studies are powerful in concept, but have demonstrated limited ability to resolve signals from background variation. In parallel, the expanding catalog of sequencing and annotation from diverse species, some of which have evolved longevities well past a human lifespan, provides independent cases to look at the genomic signatures of longevity. Recent comparative genomic work has shown promise in finding shared mechanisms associating with longevity among distantly related vertebrate groups. Given the genetic constraints between vertebrates, we posit that a combination of approaches, of parallel meta-analysis of human longevity along with refined analysis of other vertebrate clades having exceptional longevity, will aid in resolving key regulators of enhanced lifespan that have proven to be elusive when analyzed in isolation.
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Affiliation(s)
- Stephen Treaster
- Department of Orthopaedics, Boston Children's Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Ramat Gan, Israel.,Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, United States
| | - Matthew P Harris
- Department of Orthopaedics, Boston Children's Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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26
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Molecular evolution and the decline of purifying selection with age. Nat Commun 2021; 12:2657. [PMID: 33976227 PMCID: PMC8113359 DOI: 10.1038/s41467-021-22981-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Life history theory predicts that the intensity of selection declines with age, and this trend should impact how genes expressed at different ages evolve. Here we find consistent relationships between a gene’s age of expression and patterns of molecular evolution in two mammals (the human Homo sapiens and the mouse Mus musculus) and two insects (the malaria mosquito Anopheles gambiae and the fruit fly Drosophila melanogaster). When expressed later in life, genes fix nonsynonymous mutations more frequently, are more polymorphic for nonsynonymous mutations, and have shorter evolutionary lifespans, relative to those expressed early. The latter pattern is explained by a simple evolutionary model. Further, early-expressed genes tend to be enriched in similar gene ontology terms across species, while late-expressed genes show no such consistency. In humans, late-expressed genes are more likely to be linked to cancer and to segregate for dominant disease-causing mutations. Last, the effective strength of selection (Nes) decreases and the fraction of beneficial mutations increases with a gene’s age of expression. These results are consistent with the diminishing efficacy of purifying selection with age, as proposed by Medawar’s classic hypothesis for the evolution of senescence, and provide links between life history theory and molecular evolution. A fundamental principle of evolutionary theory is that the force of natural selection is weaker on traits expressed late in life relative to traits expressed early. Here, the authors find strong and consistent patterns of molecular evolution reflecting this principle in four species of animals, including humans.
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27
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Genetic variation between long-lived versus short-lived bats illuminates the molecular signatures of longevity. Aging (Albany NY) 2021; 12:15962-15977. [PMID: 32674072 PMCID: PMC7485743 DOI: 10.18632/aging.103725] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/06/2020] [Indexed: 12/05/2022]
Abstract
Bats are the longest-lived mammals given their body size with majority of species exhibiting exceptional longevity. However, there are some short-lived species that do not exhibit extended lifespans. Here we conducted a comparative genomic and transcriptomic study on long-lived Myotis myotis (maximum lifespan = 37.1 years) and short-lived Molossus molossus (maximum lifespan = 5.6 years) to ascertain the genetic difference underlying their divergent longevities. Genome-wide selection tests on 12,467 single-copy genes between M. myotis and M. molossus revealed only three genes (CCDC175, FATE1 and MLKL) that exhibited significant positive selection. Although 97.96% of 12,467 genes underwent purifying selection, we observed a significant heterogeneity in their expression patterns. Using a linear mixed model, we obtained expression of 2,086 genes that may truly represent the genetic difference between M. myotis and M. molossus. Expression analysis indicated that long-lived M. myotis exhibited a transcriptomic profile of enhanced DNA repair and autophagy pathways, compared to M. molossus. Further investigation of the longevity-associated genes suggested that long-lived M. myotis have naturally evolved a diminished anti-longevity transcriptomic profile. Together with observations from other long-lived species, our results suggest that heightened DNA repair and autophagy activity may represent a universal mechanism to achieve longevity in long-lived mammals.
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28
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Rocha JL, Godinho R, Brito JC, Nielsen R. Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation. Trends Ecol Evol 2021; 36:637-650. [PMID: 33863602 DOI: 10.1016/j.tree.2021.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Deserts are among the harshest environments on Earth. The multiple ages of different deserts and their global distribution provide a unique opportunity to study repeated adaptation at different timescales. Here, we summarize recent genomic research on the genetic mechanisms underlying desert adaptations in mammals. Several studies on different desert mammals show large overlap in functional classes of genes and pathways, consistent with the complexity and variety of phenotypes associated with desert adaptation to water and food scarcity and extreme temperatures. However, studies of desert adaptation are also challenged by a lack of accurate genotype-phenotype-environment maps. We encourage development of systems that facilitate functional analyses, but also acknowledge the need for more studies on a wider variety of desert mammals.
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Affiliation(s)
- Joana L Rocha
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; Department of Zoology, University of Johannesburg, PO Box 534, Auckland Park 2006, South Africa
| | - José C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Rasmus Nielsen
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA 94820, USA; Globe Institute, University of Copenhagen, DK-1165 Copenhagen, Denmark.
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29
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Kacprzyk J, Locatelli AG, Hughes GM, Huang Z, Clarke M, Gorbunova V, Sacchi C, Stewart GS, Teeling EC. Evolution of mammalian longevity: age-related increase in autophagy in bats compared to other mammals. Aging (Albany NY) 2021; 13:7998-8025. [PMID: 33744862 PMCID: PMC8034928 DOI: 10.18632/aging.202852] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/05/2021] [Indexed: 12/30/2022]
Abstract
Autophagy maintains cellular homeostasis and its dysfunction has been implicated in aging. Bats are the longest-lived mammals for their size, but the molecular mechanisms underlying their extended healthspan are not well understood. Here, drawing on >8 years of mark-recapture field studies, we report the first longitudinal analysis of autophagy regulation in bats. Mining of published population level aging blood transcriptomes (M. myotis, mouse and human) highlighted a unique increase of autophagy related transcripts with age in bats, but not in other mammals. This bat-specific increase in autophagy transcripts was recapitulated by the western blot determination of the autophagy marker, LC3II/I ratio, in skin primary fibroblasts (Myotis myotis,Pipistrellus kuhlii, mouse), that also showed an increase with age in both bat species. Further phylogenomic selection pressure analyses across eutherian mammals (n=70 taxa; 274 genes) uncovered 10 autophagy-associated genes under selective pressure in bat lineages. These molecular adaptations potentially mediate the exceptional age-related increase of autophagy signalling in bats, which may contribute to their longer healthspans.
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Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Andrea G. Locatelli
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Present Institutional Address: Division of Genetics and Cell Biology, Fondazione Centro San Raffaele, Via Olgettina, Milano 6020132, Italy
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Clarke
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Carlotta Sacchi
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gavin S. Stewart
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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30
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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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31
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Franceschi C, Garagnani P, Olivieri F, Salvioli S, Giuliani C. The Contextualized Genetics of Human Longevity: JACC Focus Seminar. J Am Coll Cardiol 2020; 75:968-979. [PMID: 32130932 DOI: 10.1016/j.jacc.2019.12.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022]
Abstract
The genetics of human longevity has long been studied, and in this regard, centenarians represent a very informative model. Centenarians are characterized by 2 main features: 1) the capability to avoid or postpone the major age-related diseases; and 2) a high level of heterogeneity of their phenotype. The first suggests that longevity and resistance to diseases are mediated by shared mechanisms, the latter that many strategies can be used to become long lived, likely as a result of variable genome-environment interactions. The authors suggest that the complexity of genome-environment interactions must be considered within an evolutionary and ecological perspective and that the concept of "risk allele" is highly context dependent, changing with age, time, and geography. Genes involved in both longevity and cardiovascular diseases, taken as a paradigmatic example of age-related diseases, as well as other emerging topics in genetics of longevity, such as micro-ribonucleic acid (miRNA) genetics, polygenic risk scores, environmental pollutants, and somatic mutations are discussed.
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Affiliation(s)
- Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; Department of Applied Mathematics, Institute of Information Technology, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod-National Research University, Nizhny Novgorod, Russia.
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Fabiola Olivieri
- Laboratory of Experimental Pathology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy; Center of Clinical Pathology and Regenerative Therapy, IRCCS INRCA, Ancona, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
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Zhou M, Zhang L, Yang Q, Yan C, Jiang P, Lan Y, Wang J, Tang R, He M, Lei G, Sun P, Su N, Price M, Li J, Lin F, Yue B, Fan Z. Age-related gene expression and DNA methylation changes in rhesus macaque. Genomics 2020; 112:5147-5156. [DOI: 10.1016/j.ygeno.2020.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
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33
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Mota-Martorell N, Jove M, Pradas I, Berdún R, Sanchez I, Naudi A, Gari E, Barja G, Pamplona R. Gene expression and regulatory factors of the mechanistic target of rapamycin (mTOR) complex 1 predict mammalian longevity. GeroScience 2020; 42:1157-1173. [PMID: 32578071 PMCID: PMC7434991 DOI: 10.1007/s11357-020-00210-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/01/2020] [Indexed: 01/17/2023] Open
Abstract
Species longevity varies significantly across animal species, but the underlying molecular mechanisms remain poorly understood. Recent studies and omics approaches suggest that phenotypic traits of longevity could converge in the mammalian target of rapamycin (mTOR) signalling pathway. The present study focuses on the comparative approach in heart tissue from 8 mammalian species with a ML ranging from 3.5 to 46 years. Gene expression, protein content, and concentration of regulatory metabolites of the mTOR complex 1 (mTORC1) were measured using droplet digital PCR, western blot, and mass spectrometry, respectively. Our results demonstrate (1) the existence of differences in species-specific gene expression and protein content of mTORC1, (2) that the achievement of a high longevity phenotype correlates with decreased and inhibited mTORC1, (3) a decreased content of mTORC1 activators in long-lived animals, and (4) that these differences are independent of phylogeny. Our findings, taken together, support an important role for mTORC1 downregulation in the evolution of long-lived mammals.
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Affiliation(s)
- Natalia Mota-Martorell
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain
| | - Mariona Jove
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain
| | - Irene Pradas
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain
| | - Rebeca Berdún
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain
| | - Isabel Sanchez
- Proteomics and Genomics Unit, University of Lleida, 25198, Lleida, Catalonia, Spain
| | - Alba Naudi
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain
| | - Eloi Gari
- Department of Basic Medical Sciences, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain
| | - Gustavo Barja
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid (UCM), 28040, Madrid, Spain.
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-Lleida Biomedical Research Institute (UdL-IRBLleida), 25198, Lleida, Catalonia, Spain.
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Branching out: what omics can tell us about primate evolution. Curr Opin Genet Dev 2020; 62:65-71. [DOI: 10.1016/j.gde.2020.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022]
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Smith SD, Pennell MW, Dunn CW, Edwards SV. Phylogenetics is the New Genetics (for Most of Biodiversity). Trends Ecol Evol 2020; 35:415-425. [DOI: 10.1016/j.tree.2020.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
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Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
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Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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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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Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
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The dynamic nature of ageing: novel findings, therapeutic avenues and medical interventions. ANTHROPOLOGICAL REVIEW 2020. [DOI: 10.2478/anre-2020-0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ageing is one of the most complex and difficult problems for humans to face and for science to solve. Although human senescence was viewed as a passive and uncontrollable process of deterioration over time with little or no genetic regulation, the concept that ageing is caused by both genetic and environmental factors is now generally accepted, even though it remains difficult to distinguish between ageing sensu stricto and the effects of age-related diseases. Empirical data show that mechanisms of ageing are highly conserved during evolution. Moreover, it has been established that there are specific molecular ‘instructions’ for ageing, which suggests that a better understanding of the molecular biology of ageing will open new possibilities regarding future interventions. The complexity of ageing diminishes the possibility that any general theory will completely explain this metaphenomenon. Likewise, it is highly unlikely that any medication can stop or reverse human senescence. Nevertheless, ageing as a dynamic and malleable metaphenomenon can be modulated by a variety of influences. The concept of the shrinkage of the homeodynamic space with age, i.e. homeostenosis, is especially interesting and intriguing as it shows that novel therapeutic approaches and rational strategies can help delay the onset of the ageing-associated pathologies by enhancing the homeodynamic capabilities of the body. The aim of this article is to present current data from evolutionary and molecular gerontology and discuss them within the ambit of this review which is devoted to the dynamic, emergent and plastic nature of human ageing and implications for future interventions.
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40
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Kowalczyk A, Partha R, Clark NL, Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan. eLife 2020; 9:e51089. [PMID: 32043462 PMCID: PMC7012612 DOI: 10.7554/elife.51089] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
Although lifespan in mammals varies over 100-fold, the precise evolutionary mechanisms underlying variation in longevity remain unknown. Species-specific genetic changes have been observed in long-lived species including the naked mole-rat, bats, and the bowhead whale, but these adaptations do not generalize to other mammals. We present a novel method to identify associations between rates of protein evolution and continuous phenotypes across the entire mammalian phylogeny. Unlike previous analyses that focused on individual species, we treat absolute and relative longevity as quantitative traits and demonstrate that these lifespan traits affect the evolutionary constraint on hundreds of genes. Specifically, we find that genes related to cell cycle, DNA repair, cell death, the IGF1 pathway, and immunity are under increased evolutionary constraint in large and long-lived mammals. For mammals exceptionally long-lived for their body size, we find increased constraint in inflammation, DNA repair, and NFKB-related pathways. Strikingly, these pathways have considerable overlap with those that have been previously reported to have potentially adaptive changes in single-species studies, and thus would be expected to show decreased constraint in our analysis. This unexpected finding of increased constraint in many longevity-associated pathways underscores the power of our quantitative approach to detect patterns that generalize across the mammalian phylogeny.
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Affiliation(s)
- Amanda Kowalczyk
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational BiologyPittsburghUnited States
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
| | - Raghavendran Partha
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational BiologyPittsburghUnited States
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
| | - Nathan L Clark
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
- Pittsburgh Center for Evolutionary Biology and MedicineUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Maria Chikina
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
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41
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The molecular mechanisms associated with PIN7, a protein-protein interaction network of seven pleiotropic proteins. J Theor Biol 2020; 487:110124. [DOI: 10.1016/j.jtbi.2019.110124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
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42
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Abstract
Between the 1930s and 1950s, scientists developed key principles of population genetics to try and explain the aging process. Almost a century later, these aging theories, including antagonistic pleiotropy and mutation accumulation, have been experimentally validated in animals. Although the theories have been much harder to test in humans despite research dating back to the 1970s, recent research is closing this evidence gap. Here we examine the strength of evidence for antagonistic pleiotropy in humans, one of the leading evolutionary explanations for the retention of genetic risk variation for non-communicable diseases. We discuss the analytical tools and types of data that are used to test for patterns of antagonistic pleiotropy and provide a primer of evolutionary theory on types of selection as a guide for understanding this mechanism and how it may manifest in other diseases. We find an abundance of non-experimental evidence for antagonistic pleiotropy in many diseases. In some cases, several studies have independently found corroborating evidence for this mechanism in the same or related sets of diseases including cancer and neurodegenerative diseases. Recent studies also suggest antagonistic pleiotropy may be involved in cardiovascular disease and diabetes. There are also compelling examples of disease risk variants that confer fitness benefits ranging from resistance to other diseases or survival in extreme environments. This provides increasingly strong support for the theory that antagonistic pleiotropic variants have enabled improved fitness but have been traded for higher burden of disease later in life. Future research in this field is required to better understand how this mechanism influences contemporary disease and possible consequences for their treatment.
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Rubanov LI, Zaraisky AG, Shilovsky GA, Seliverstov AV, Zverkov OA, Lyubetsky VA. Screening for mouse genes lost in mammals with long lifespans. BioData Min 2019; 12:20. [PMID: 31728160 PMCID: PMC6842137 DOI: 10.1186/s13040-019-0208-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/25/2019] [Indexed: 12/23/2022] Open
Abstract
Background Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate species can be due, among other things, to the loss of particular genes that are present in short-lived species of the same orders. These genes can also explain the widely different rates of aging among diverse species as well as why similarly sized rodents or primates sometimes have anomalous life expectancies (e.g., naked mole-rats and humans). Here, we consider the gene loss in the context of the prediction of Williams’ theory that concerns the reallocation of physiological resources of an organism between active reproduction (r-strategy) and self-maintenance (K-strategy). We have identified such lost genes using an original computer-aided approach; the software considers the loss of a gene as disruptions in gene orthology, local gene synteny or both. Results A method and software identifying the genes that are absent from a predefined set of species but present in another predefined set of species are suggested. Examples of such pairs of sets include long-lived vs short-lived, homeothermic vs poikilothermic, amniotic vs anamniotic, aquatic vs terrestrial, and neotenic vs nonneotenic species, among others. Species are included in one of two sets according to the property of interest, such as longevity or homeothermy. The program is universal towards these pairs, i.e., towards the underlying property, although the sets should include species with quality genome assemblies. Here, the proposed method was applied to study the longevity of Euarchontoglires species. It largely predicted genes that are highly expressed in the testis, epididymis, uterus, mammary glands, and the vomeronasal and other reproduction-related organs. This agrees with Williams’ theory that hypothesizes a species transition from r-strategy to K-strategy. For instance, the method predicts the mouse gene Smpd5, which has an expression level 20 times greater in the testis than in organs unrelated to reproduction as experimentally demonstrated elsewhere. At the same time, its paralog Smpd3 is not predicted by the program and is widely expressed in many organs not specifically related to reproduction. Conclusions The method and program, which were applied here to screen for gene losses that can accompany increased lifespan, were also applied to study reduced regenerative capacity and development of the telencephalon, neoteny, etc. Some of these results have been carefully tested experimentally. Therefore, we assume that the method is widely applicable.
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Affiliation(s)
- Lev I Rubanov
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Andrey G Zaraisky
- 2Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (IBCH RAS) 16/10, Miklukho-Maklaya str., Moscow, 117997 Russia
| | - Gregory A Shilovsky
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Alexandr V Seliverstov
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Oleg A Zverkov
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
| | - Vassily A Lyubetsky
- 1Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute) IITP RAS, 19 build. 1 Bolshoy Karetny per., Moscow, 127051 Russia
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44
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de Magalhães JP, Wang J. The fog of genetics: what is known, unknown and unknowable in the genetics of complex traits and diseases. EMBO Rep 2019; 20:e48054. [PMID: 31633864 DOI: 10.15252/embr.201948054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A major task for genetics is searching for genetic variants associated with disease. But we may well be missing a large number of "unknown unknown" alleles in the "fog of genetics".
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Affiliation(s)
- João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Jingwei Wang
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.,Wellcome Sanger Institute, Hinxton, UK
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45
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Abstract
The field of aging research has progressed significantly over the past decades. Exogenously and endogenously inflicted molecular damage ranging from genotoxic to organellar damage drives the aging process. Repair mechanisms and compensatory responses counteract the detrimental consequences of the various damage types. Here, we discuss recent progress in understanding cellular mechanisms and interconnections between signaling pathways that control longevity. We summarize cell-autonomous and non-cell-autonomous mechanisms that impact the cellular and organismal aging process
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Affiliation(s)
- Robert Bayersdorf
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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46
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Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, Edwards SV. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180248. [PMID: 31154982 PMCID: PMC6560268 DOI: 10.1098/rstb.2018.0248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, University of Texas Arlington, Arlington, TX 76019, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - João F. R. Tonini
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Kathrin Näpflin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Flavia Termignoni-Garcia
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Torres
- Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
- Department of Geological Sciences, The University of Texas at Austin, Austin, MA 78712, USA
| | - Frank Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY 10024, USA
| | - Julia A. Clarke
- Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
- Department of Geological Sciences, The University of Texas at Austin, Austin, MA 78712, USA
| | | | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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47
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Hu Z, Sackton TB, Edwards SV, Liu JS. Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees. Mol Biol Evol 2019; 36:1086-1100. [PMID: 30851112 PMCID: PMC6501877 DOI: 10.1093/molbev/msz049] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.
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Affiliation(s)
- Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA
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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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49
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Dansereau G, Wey TW, Legault V, Brunet MA, Kemnitz JW, Ferrucci L, Cohen AA. Conservation of physiological dysregulation signatures of aging across primates. Aging Cell 2019; 18:e12925. [PMID: 30746836 PMCID: PMC6413749 DOI: 10.1111/acel.12925] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/14/2018] [Accepted: 01/24/2019] [Indexed: 12/14/2022] Open
Abstract
Two major goals in the current biology of aging are to identify general mechanisms underlying the aging process and to explain species differences in aging. Recent research in humans suggests that one important driver of aging is dysregulation, the progressive loss of homeostasis in complex biological networks. Yet, there is a lack of comparative data for this hypothesis, and we do not know whether dysregulation is widely associated with aging or how well signals of homeostasis are conserved. To address this knowledge gap, we use unusually detailed longitudinal biomarker data from 10 species of nonhuman primates housed in research centers and data from two human populations to test the hypotheses that (a) greater dysregulation is associated with aging across primates and (b) physiological states characterizing homeostasis are conserved across primates to degrees associated with phylogenetic proximity. To evaluate dysregulation, we employed a multivariate distance measure, calculated from sets of biomarkers, that is associated with aging and mortality in human populations. Dysregulation scores positively correlated with age and risk of mortality in most nonhuman primates studied, and signals of homeostatic state were significantly conserved across species, declining with phylogenetic distance. Our study provides the first broad demonstration of physiological dysregulation associated with aging and mortality risk in multiple nonhuman primates. Our results also imply that emergent signals of homeostasis are evolutionarily conserved, although with notable variation among species, and suggest promising directions for future comparative studies on dysregulation and the aging process.
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Affiliation(s)
- Gabriel Dansereau
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
| | - Tina W. Wey
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
| | - Véronique Legault
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
| | - Marie A. Brunet
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
- Department of Biochemistry; University of Sherbrooke; Sherbrooke Quebec Canada
- PROTEO; Quebec Network for Research on Protein Function, Structure, and Engineering; Quebec Canada
| | - Joseph W. Kemnitz
- Department of Cell and Regenerative Biology; University of Wisconsin; School of Medicine and Public Health; Madison Wisconsin
- Wisconsin National Primate Research Center; University of Wisconsin-Madison; Madison Wisconsin
| | - Luigi Ferrucci
- Translational Gerontology Branch, Longitudinal Studies Section; National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital; Baltimore Maryland
| | - Alan A. Cohen
- Groupe de recherche PRIMUS, Department of Family Medicine; University of Sherbrooke; Sherbrooke Quebec Canada
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