1
|
An X, Mao L, Wang Y, Xu Q, Liu X, Zhang S, Qiao Z, Li B, Li F, Kuang Z, Wan N, Liang X, Duan Q, Feng Z, Yang X, Liu S, Nevo E, Liu J, Storz JF, Li K. Genomic structural variation is associated with hypoxia adaptation in high-altitude zokors. Nat Ecol Evol 2024; 8:339-351. [PMID: 38195998 DOI: 10.1038/s41559-023-02275-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
Zokors, an Asiatic group of subterranean rodents, originated in lowlands and colonized high-elevational zones following the uplift of the Qinghai-Tibet plateau about 3.6 million years ago. Zokors live at high elevation in subterranean burrows and experience hypobaric hypoxia, including both hypoxia (low oxygen concentration) and hypercapnia (elevated partial pressure of CO2). Here we report a genomic analysis of six zokor species (genus Eospalax) with different elevational ranges to identify structural variants (deletions and inversions) that may have contributed to high-elevation adaptation. Based on an assembly of a chromosome-level genome of the high-elevation species, Eospalax baileyi, we identified 18 large inversions that distinguished this species from congeners native to lower elevations. Small-scale structural variants in the introns of EGLN1, HIF1A, HSF1 and SFTPD of E. baileyi were associated with the upregulated expression of those genes. A rearrangement on chromosome 1 was associated with altered chromatin accessibility, leading to modified gene expression profiles of key genes involved in the physiological response to hypoxia. Multigene families that underwent copy-number expansions in E. baileyi were enriched for autophagy, HIF1 signalling and immune response. E. baileyi show a significantly larger lung mass than those of other Eospalax species. These findings highlight the key role of structural variants underlying hypoxia adaptation of high-elevation species in Eospalax.
Collapse
Affiliation(s)
- Xuan An
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Leyan Mao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yinjia Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qinqin Xu
- Department of Medical Oncology, Qinghai Provincial People's Hospital, Xining, China
| | - Xi Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhenglei Qiao
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Bowen Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Fang Li
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Zhuoran Kuang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Na Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolong Liang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qijiao Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhilong Feng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojie Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Sanyuan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA.
| | - Kexin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
| |
Collapse
|
2
|
Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023; 14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023] Open
Abstract
Hyaluronic acid is a major component of extracellular matrix which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (Heterocephalus glaber) contains abundant high-molecular-mass hyaluronic acid in its tissues, which contributes to this species' cancer resistance and possibly to its longevity. Here we report that abundant high-molecular-mass hyaluronic acid is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These subterranean mammalian species accumulate abundant high-molecular-mass hyaluronic acid by regulating the expression of genes involved in hyaluronic acid degradation and synthesis and contain unique mutations in these genes. The abundant high-molecular-mass hyaluronic acid may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic conditions. Our work suggests that high-molecular-mass hyaluronic acid has evolved with subterranean lifestyle.
Collapse
Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Zhizhong Zheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yandong Xu
- Department of Physiology and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 301158, China
| | - Eric Hillpot
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Yifei S Lin
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Frances T Zakusilo
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - J Yuyang Lu
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Seyed Ali Biashad
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
- Department of Medicine, University of Rochester School of Medicine, Rochester, NY, 14627, USA.
| |
Collapse
|
3
|
Parey E, Fernandez-Aroca D, Frost S, Uribarren A, Park TJ, Zöttl M, St John Smith E, Berthelot C, Villar D. Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits. Genome Res 2023; 33:1513-1526. [PMID: 37625847 PMCID: PMC10620049 DOI: 10.1101/gr.277715.123] [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: 01/18/2023] [Accepted: 08/24/2023] [Indexed: 08/27/2023]
Abstract
Changes in gene regulation are thought to underlie most phenotypic differences between species. For subterranean rodents such as the naked mole-rat, proposed phenotypic adaptations include hypoxia tolerance, metabolic changes, and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the naked mole-rat, the mole-rat clade, or are also present in other mammals. Here, we investigate regulatory evolution in the heart and liver from two African mole-rat species and two rodent outgroups using genome-wide epigenomic profiling. First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole-rat adaptations in metabolic and functional pathways and suggest candidate genetic loci that may underlie mole-rat innovations. Second, we evaluated ancestral and species-specific regulatory changes in the study phylogeny and report several candidate pathways experiencing stepwise remodeling during the evolution of mole-rats, such as the insulin and hypoxia response pathways. Third, we report nonorthologous regulatory elements overlap with lineage-specific repetitive elements and appear to modify metabolic pathways by rewiring of HNF4 and RAR/RXR transcription factor binding sites in mole-rats. These comparative analyses reveal how mole-rat regulatory evolution informs previously reported phenotypic adaptations. Moreover, the phylogenetic modeling framework we propose here improves upon the state of the art by addressing known limitations of inter-species comparisons of epigenomic profiles and has broad implications in the field of comparative functional genomics.
Collapse
Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Diego Fernandez-Aroca
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
| | - Stephanie Frost
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom
| | - Ainhoa Uribarren
- Cambridge Institute, Cancer Research UK and University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Thomas J Park
- Department of Biological Sciences and Laboratory of Integrative Neuroscience, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Markus Zöttl
- Department of Biology and Environmental Science, Linnaeus University, 44054 Kalmar, Sweden
| | - Ewan St John Smith
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
| | - Camille Berthelot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France;
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, INSERM UA12, Comparative Functional Genomics Group, F-75015 Paris, France
| | - Diego Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, United Kingdom;
| |
Collapse
|
4
|
Zhao Y, Zheng Z, Zhang Z, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of High-Molecular-Mass Hyaluronic Acid is Associated with Subterranean Lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539764. [PMID: 37215017 PMCID: PMC10197608 DOI: 10.1101/2023.05.08.539764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hyaluronic acid (HA) is a major component of extracellular matrix (ECM) which plays an important role in development, cellular response to injury and inflammation, cell migration, and cancer. The naked mole-rat (NMR, Heterocephalus glaber ) contains abundant high-molecular-mass HA (HMM-HA) in its tissues, which contributes to this species' cancer resistance and possibly longevity. Here we report that abundant HMM-HA is found in a wide range of subterranean mammalian species, but not in phylogenetically related aboveground species. These species accumulate abundant HMM-HA by regulating the expression of genes involved in HA degradation and synthesis and contain unique mutations in these genes. The abundant high molecular weight HA may benefit the adaptation to subterranean environment by increasing skin elasticity and protecting from oxidative stress due to hypoxic subterranean environment. HMM-HA may also be coopted to confer cancer resistance and longevity to subterranean mammals. Our work suggests that HMM-HA has evolved with subterranean lifestyle.
Collapse
|
5
|
Luo H, Luo S, Fang W, Lin Q, Chen X, Zhou X. Genomic insight into the nocturnal adaptation of the black-crowned night heron (Nycticorax nycticorax). BMC Genomics 2022; 23:683. [PMID: 36192687 PMCID: PMC9531477 DOI: 10.1186/s12864-022-08904-y] [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] [Received: 05/05/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The black-crowned night heron (Nycticorax nycticorax) is an ardeid bird successfully adapted to the nocturnal environment. Previous studies had indicated that the eyes of the night herons have evolved several specialized morphological traits favoring nocturnal vision. However, the molecular mechanisms of the nocturnal vision adaptation of night herons remained inattentions. In this study, the whole genome of N. nycticorax was sequenced and comparative analyses were performed on the vision-related and olfactory receptor (OR) genes to understand the molecular mechanisms of the visual and olfactory adaptation of night herons. RESULTS The results indicated that a number of vision genes were under positive or relaxed selection in N. nycticorax, whereas a number of other vision genes were under relaxed or intensified selection in the boat-billed heron (Cochlearius cochlearius), which suggested that the two species adapt to nocturnality with different genetic mechanisms. The different selections acting on vision genes are probably associated with the enlargement of eye size and the enhancement of visual sensitivity in night herons. The analyses on olfactory receptor (OR) genes indicated that the total number of OR genes in the genomes of N. nycticorax and C. cochlearius were about half those in the little egret (Egretta garzetta), whereas the diversity of their OR genes was not remarkably different. Additionally, the number of expressed OR genes in the transcriptomes of N. nycticorax was also fewer than that in E. garzetta. These results suggest a reduced olfactory capability in night herons compared with E. garzetta. CONCLUSIONS Our results provided evidence that several vision genes of the night herons were subjected to different natural selections, which can contribute to a better understanding of the genetic mechanisms of visual adaptions of the night heron. In addition, the finding of the reduced number of total and expressed OR genes in night herons may reflect a trade-off between olfaction and vision.
Collapse
Affiliation(s)
- Haoran Luo
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Site Luo
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China.
| |
Collapse
|
6
|
Convergent evolution of a genomic rearrangement may explain cancer resistance in hystrico- and sciuromorpha rodents. NPJ Aging Mech Dis 2021; 7:20. [PMID: 34471123 PMCID: PMC8410860 DOI: 10.1038/s41514-021-00072-9] [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: 10/22/2020] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.
Collapse
|
7
|
Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A. Alternative Animal Models of Aging Research. Front Mol Biosci 2021; 8:660959. [PMID: 34079817 PMCID: PMC8166319 DOI: 10.3389/fmolb.2021.660959] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/08/2021] [Indexed: 12/23/2022] Open
Abstract
Most research on mechanisms of aging is being conducted in a very limited number of classical model species, i.e., laboratory mouse (Mus musculus), rat (Rattus norvegicus domestica), the common fruit fly (Drosophila melanogaster) and roundworm (Caenorhabditis elegans). The obvious advantages of using these models are access to resources such as strains with known genetic properties, high-quality genomic and transcriptomic sequencing data, versatile experimental manipulation capabilities including well-established genome editing tools, as well as extensive experience in husbandry. However, this approach may introduce interpretation biases due to the specific characteristics of the investigated species, which may lead to inappropriate, or even false, generalization. For example, it is still unclear to what extent knowledge of aging mechanisms gained in short-lived model organisms is transferable to long-lived species such as humans. In addition, other specific adaptations favoring a long and healthy life from the immense evolutionary toolbox may be entirely missed. In this review, we summarize the specific characteristics of emerging animal models that have attracted the attention of gerontologists, we provide an overview of the available data and resources related to these models, and we summarize important insights gained from them in recent years. The models presented include short-lived ones such as killifish (Nothobranchius furzeri), long-lived ones such as primates (Callithrix jacchus, Cebus imitator, Macaca mulatta), bathyergid mole-rats (Heterocephalus glaber, Fukomys spp.), bats (Myotis spp.), birds, olms (Proteus anguinus), turtles, greenland sharks, bivalves (Arctica islandica), and potentially non-aging ones such as Hydra and Planaria.
Collapse
Affiliation(s)
- Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ekaterina Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Stan Braude
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Alessandro Cellerino
- Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Central Animal Laboratory, University Hospital Essen, Essen, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, Berlin, Germany
| | - Andreas Hoeflich
- Division Signal Transduction, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Eva Terzibasi Tozzini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxim Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Skulachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| |
Collapse
|
8
|
The Somatosensory World of the African Naked Mole-Rat. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1319:197-220. [PMID: 34424517 DOI: 10.1007/978-3-030-65943-1_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The naked mole-rat (Heterocephalus glaber) is famous for its longevity and unusual physiology. This eusocial species that lives in highly ordered and hierarchical colonies with a single breeding queen, also discovered secrets enabling somewhat pain-free living around 20 million years ago. Unlike most mammals, naked mole-rats do not feel the burn of chili pepper's active ingredient, capsaicin, nor the sting of acid. Indeed, by accumulating mutations in genes encoding proteins that are only now being exploited as targets for new pain therapies (the nerve growth factor receptor TrkA and voltage-gated sodium channel, NaV1.7), this species mastered the art of analgesia before humans evolved. Recently, we have identified pain-insensitivity as a trait shared by several closely related African mole-rat species. In this chapter we will show how African mole-rats have evolved pain insensitivity as well as discussing what the proximate factors may have been that led to the evolution of pain-free traits.
Collapse
|
9
|
Social Evolution in African Mole-Rats - A Comparative Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1319:1-33. [PMID: 34424511 DOI: 10.1007/978-3-030-65943-1_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The African mole-rat superfamily are a unique group of subterranean rodents that are remarkable for their adaptations to a subterranean lifestyle and their range in sociality, spanning strictly solitary species to the naked mole-rat, the most social of all rodents. Widely distributed through sub-Saharan Africa their occurrence is associated with the presence of food resources in the form of underground roots, bulbs and tubers, which form their staple diet. African mole-rats have an ancient Oligocene/Eocene origin, with the naked mole-rat, the extant species with the earliest divergence from the common ancestor of the clade. As a consequence of its early evolution the naked mole-rat appears to have acquired many extraordinary biological features, even when compared with other mole-rats. Molecular phylogenies indicate that complex sociality and cooperative breeding has been convergently gained and/or lost more than once among African mole-rats, making them a fascinating group for comparative studies of social evolution. Ultimately, ecological constraints on digging and finding food have played a role in increasing cooperative behavior and social complexity, from what was most likely a monogamous ancestor living in family groups. Phylogenetically controlled comparisons suggest that proximate control of their lifestyle shows both conservation and divergence in the underlying mechanisms.
Collapse
|
10
|
Pyott SJ, van Tuinen M, Screven LA, Schrode KM, Bai JP, Barone CM, Price SD, Lysakowski A, Sanderford M, Kumar S, Santos-Sacchi J, Lauer AM, Park TJ. Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats. Curr Biol 2020; 30:4329-4341.e4. [PMID: 32888484 DOI: 10.1016/j.cub.2020.08.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
Abstract
Naked mole-rats are highly vocal, eusocial, subterranean rodents with, counterintuitively, poor hearing. The causes underlying their altered hearing are unknown. Moreover, whether altered hearing is degenerate or adaptive to their unique lifestyles is controversial. We used various methods to identify the factors contributing to altered hearing in naked and the related Damaraland mole-rats and to examine whether these alterations result from relaxed or adaptive selection. Remarkably, we found that cochlear amplification was absent from both species despite normal prestin function in outer hair cells isolated from naked mole-rats. Instead, loss of cochlear amplification appears to result from abnormal hair bundle morphologies observed in both species. By exploiting a well-curated deafness phenotype-genotype database, we identified amino acid substitutions consistent with abnormal hair bundle morphology and reduced hearing sensitivity. Amino acid substitutions were found in unique groups of six hair bundle link proteins. Molecular evolutionary analyses revealed shifts in selection pressure at both the gene and the codon level for five of these six hair bundle link proteins. Substitutions in three of these proteins are associated exclusively with altered hearing. Altogether, our findings identify the likely mechanism of altered hearing in African mole-rats, making them the only identified mammals naturally lacking cochlear amplification. Moreover, our findings suggest that altered hearing in African mole-rats is adaptive, perhaps tailoring hearing to eusocial and subterranean lifestyles. Finally, our work reveals multiple, unique evolutionary trajectories in African mole-rat hearing and establishes species members as naturally occurring disease models to investigate human hearing loss.
Collapse
Affiliation(s)
- Sonja J Pyott
- University Medical Center Groningen and University of Groningen, Department of Otorhinolaryngology and Head/Neck Surgery, 9713GZ Groningen, the Netherlands.
| | - Marcel van Tuinen
- University Medical Center Groningen and University of Groningen, Department of Otorhinolaryngology and Head/Neck Surgery, 9713GZ Groningen, the Netherlands
| | - Laurel A Screven
- Johns Hopkins School of Medicine, Department of Otolaryngology, Baltimore, MD 21205, USA
| | - Katrina M Schrode
- Johns Hopkins School of Medicine, Department of Otolaryngology, Baltimore, MD 21205, USA
| | - Jun-Ping Bai
- Yale University School of Medicine, Department of Neurology, 333 Cedar Street, New Haven, CT 06510, USA
| | - Catherine M Barone
- University of Illinois at Chicago, Department of Biological Sciences, Chicago, IL 60612, USA
| | - Steven D Price
- University of Illinois at Chicago, Department of Anatomy and Cell Biology, Chicago, IL 60612, USA
| | - Anna Lysakowski
- University of Illinois at Chicago, Department of Anatomy and Cell Biology, Chicago, IL 60612, USA
| | - Maxwell Sanderford
- Temple University, Institute for Genomics and Evolutionary Medicine and Department of Biology, Philadelphia, PA 19122, USA
| | - Sudhir Kumar
- Temple University, Institute for Genomics and Evolutionary Medicine and Department of Biology, Philadelphia, PA 19122, USA; King Abdulaziz University, Center for Excellence in Genome Medicine and Research, Jeddah, Saudi Arabia
| | - Joseph Santos-Sacchi
- Yale University School of Medicine, Department of Surgery (Otolaryngology) and Department of Neuroscience and Cellular and Molecular Physiology, 333 Cedar Street, New Haven, CT 06510, USA
| | - Amanda M Lauer
- Johns Hopkins School of Medicine, Department of Otolaryngology, Baltimore, MD 21205, USA
| | - Thomas J Park
- University of Illinois at Chicago, Department of Biological Sciences, Chicago, IL 60612, USA
| |
Collapse
|
11
|
Lopes-Marques M, Serrano C, Cardoso AR, Salazar R, Seixas S, Amorim A, Azevedo L, Prata MJ. GBA3: a polymorphic pseudogene in humans that experienced repeated gene loss during mammalian evolution. Sci Rep 2020; 10:11565. [PMID: 32665690 PMCID: PMC7360587 DOI: 10.1038/s41598-020-68106-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/03/2020] [Indexed: 11/18/2022] Open
Abstract
The gene encoding the cytosolic β-glucosidase GBA3 shows pseudogenization due to a truncated allele (rs358231) that is polymorphic in humans. Since this enzyme is involved in the transformation of many plant β-glycosides, this particular case of gene loss may have been influenced by dietary adaptations during evolution. In humans, apart from the inactivating allele, we found that GBA3 accumulated additional damaging mutations, implying an extensive GBA3 loss. The allelic distribution of loss-of-function alleles revealed significant differences between human populations which can be partially related with their staple diet. The analysis of mammalian orthologs disclosed that GBA3 underwent at least nine pseudogenization events. Most events of pseudogenization occurred in carnivorous lineages, suggesting a possible link to a β-glycoside poor diet. However, GBA3 was also lost in omnivorous and herbivorous species, hinting that the physiological role of GBA3 is not fully understood and other unknown causes may underlie GBA3 pseudogenization. Such possibility relies upon a putative role in sialic acid biology, where GBA3 participates in a cellular network involving NEU2 and CMAH. Overall, our data shows that the recurrent loss of GBA3 in mammals is likely to represent an evolutionary endpoint of the relaxation of selective constraints triggered by diet-related factors.
Collapse
Affiliation(s)
- Monica Lopes-Marques
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Catarina Serrano
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Ana R. Cardoso
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Renato Salazar
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
| | - Susana Seixas
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
| | - António Amorim
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Luisa Azevedo
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Prata
- i3S- Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| |
Collapse
|
12
|
Shepard A, Kissil JL. The use of non-traditional models in the study of cancer resistance-the case of the naked mole rat. Oncogene 2020; 39:5083-5097. [PMID: 32535616 DOI: 10.1038/s41388-020-1355-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Non-traditional model organisms are typically defined as any model the deviates from the typical laboratory animals, such as mouse, rat, and worm. These models are becoming increasingly important in human disease research, such as cancer, as they often display unusual biological features. Naked mole rats (NMRs) are currently one of the most popular non-traditional model, particularly in the longevity and cancer research fields. NMRs display an exceptionally long lifespan (~30 years), yet have been observed to display a low incidence of cancer, making them excellent candidates for understanding endogenous cancer resistance mechanisms. Over the past decade, many potential resistance mechanisms have been characterized. These include unique biological mechanisms involved in genome stability, protein stability, oxidative metabolism, and other cellular mechanisms such as cell cycle regulation and senescence. This review aims to summarize the many identified cancer resistance mechanisms to understand some of the main hypotheses that have thus far been generated. Many of these proposed mechanisms remain to be fully characterized or confirmed in vivo, giving the field a direction to grow and further understand the complex biology displayed by the NMR.
Collapse
Affiliation(s)
- Alyssa Shepard
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Joseph L Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
| |
Collapse
|
13
|
Smith ESJ, Park TJ, Lewin GR. Independent evolution of pain insensitivity in African mole-rats: origins and mechanisms. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020; 206:313-325. [PMID: 32206859 PMCID: PMC7192887 DOI: 10.1007/s00359-020-01414-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/10/2020] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
The naked mole-rat (Heterocephalus glaber) is famous for its longevity and unusual physiology. This eusocial species that lives in highly ordered and hierarchical colonies with a single breeding queen, also discovered secrets enabling somewhat pain-free living around 20 million years ago. Unlike most mammals, naked mole-rats do not feel the burn of chili pepper's active ingredient, capsaicin, nor the sting of acid. Indeed, by accumulating mutations in genes encoding proteins that are only now being exploited as targets for new pain therapies (the nerve growth factor receptor TrkA and voltage-gated sodium channel, NaV1.7), this species mastered the art of analgesia before humans evolved. Recently, we have identified pain insensitivity as a trait shared by several closely related African mole-rat species. One of these African mole-rats, the Highveld mole-rat (Cryptomys hottentotus pretoriae), is uniquely completely impervious and pain free when confronted with electrophilic compounds that activate the TRPA1 ion channel. The Highveld mole-rat has evolved a biophysical mechanism to shut down the activation of sensory neurons that drive pain. In this review, we will show how mole-rats have evolved pain insensitivity as well as discussing what the proximate factors may have been that led to the evolution of pain-free traits.
Collapse
Affiliation(s)
- Ewan St John Smith
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK
| | - Thomas J Park
- Laboratory of Integrative Neuroscience, Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Gary R Lewin
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Robert-Rössle Str. 10, D-13125, Berlin, Germany.
| |
Collapse
|
14
|
Cox PG, Faulkes CG, Bennett NC. Masticatory musculature of the African mole-rats (Rodentia: Bathyergidae). PeerJ 2020; 8:e8847. [PMID: 32231887 PMCID: PMC7100595 DOI: 10.7717/peerj.8847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/03/2020] [Indexed: 12/22/2022] Open
Abstract
The Bathyergidae, commonly known as blesmols or African mole-rats, is a family of rodents well-known for their subterranean lifestyle and tunnelling behaviour. Four of the five extant bathyergid genera (Cryptomys, Fukomys, Georychus and Heliophobius) are chisel-tooth diggers, that is they dig through soil with their enlarged incisors, whereas the remaining genus (Bathyergus) is a scratch-digger, only using its forelimbs for burrowing. Heterocephalus glaber, the naked mole-rat, is also a chisel-tooth digger and was until recently included within the Bathyergidae (as the most basally branching genus), but has now been placed by some researchers into its own family, the Heterocephalidae. Given the importance of the masticatory apparatus in habitat construction in this group, knowledge and understanding of the morphology and arrangement of the jaw-closing muscles in Bathyergidae is vital for future functional analyses. Here, we use diffusible iodine-based contrast-enhanced microCT to reveal and describe the muscles of mastication in representative specimens of each genus of bathyergid mole-rat and to compare them to the previously described musculature of the naked mole-rat. In all bathyergids, as in all rodents, the masseter muscle is the most dominant component of the masticatory musculature. However, the temporalis is also a relatively large muscle, a condition normally associated with sciuromorphous rodents. Unlike their hystricomorphous relatives, the bathyergids do not show an extension of the masseter through the infraorbital foramen on to the rostrum (other than a very slight protrusion in Cryptomys and Fukomys). Thus, morphologically, bathyergids are protrogomorphous, although this is thought to be secondarily derived rather than retained from ancestral rodents. Overall, the relative proportions of the jaw-closing muscles were found to be fairly consistent between genera except in Bathyergus, which was found to have an enlarged superficial masseter and relatively smaller pterygoid muscles. It is concluded that these differences may be a reflection of the behaviour of Bathyergus which, uniquely in the family, does not use its incisors for digging.
Collapse
Affiliation(s)
- Philip G Cox
- Department of Archaeology and Hull York Medical School, University of York, York, UK
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
15
|
Eigenbrod O, Debus KY, Reznick J, Bennett NC, Sánchez-Carranza O, Omerbašić D, Hart DW, Barker AJ, Zhong W, Lutermann H, Katandukila JV, Mgode G, Park TJ, Lewin GR. Rapid molecular evolution of pain insensitivity in multiple African rodents. Science 2019; 364:852-859. [PMID: 31147513 DOI: 10.1126/science.aau0236] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 04/25/2019] [Indexed: 12/19/2022]
Abstract
Noxious substances, called algogens, cause pain and are used as defensive weapons by plants and stinging insects. We identified four previously unknown instances of algogen-insensitivity by screening eight African rodent species related to the naked mole-rat with the painful substances capsaicin, acid (hydrogen chloride, pH 3.5), and allyl isothiocyanate (AITC). Using RNA sequencing, we traced the emergence of sequence variants in transduction channels, like transient receptor potential channel TRPA1 and voltage-gated sodium channel Nav1.7, that accompany algogen insensitivity. In addition, the AITC-insensitive highveld mole-rat exhibited overexpression of the leak channel NALCN (sodium leak channel, nonselective), ablating AITC detection by nociceptors. These molecular changes likely rendered highveld mole-rats immune to the stings of the Natal droptail ant. Our study reveals how evolution can be used as a discovery tool to find molecular mechanisms that shut down pain.
Collapse
Affiliation(s)
- Ole Eigenbrod
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Karlien Y Debus
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jane Reznick
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Oscar Sánchez-Carranza
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Damir Omerbašić
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Daniel W Hart
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Alison J Barker
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Wei Zhong
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Heike Lutermann
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa
| | - Jestina V Katandukila
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, Republic of South Africa.,University of Dar es Salaam, College of Natural and Applied Sciences, Department of Zoology and Wildlife Conservation, P.O. Box 35064, Dar es Salaam, Tanzania
| | - Georgies Mgode
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Thomas J Park
- Laboratory of Integrative Neuroscience, Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Gary R Lewin
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
16
|
Visser JH, Bennett NC, Jansen van Vuuren B. Phylogeny and biogeography of the African Bathyergidae: a review of patterns and processes. PeerJ 2019; 7:e7730. [PMID: 31637115 PMCID: PMC6798870 DOI: 10.7717/peerj.7730] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/23/2019] [Indexed: 12/18/2022] Open
Abstract
Background We review genealogical relationships, biogeographic patterns and broad historical drivers of speciation within the Bathyergidae, a group of endemic African rodents, as well as identify key taxa which need further research. Methods We sourced comparable cytochrome b sequence data (comparable data available for all members for the Family) and geographic information for all six genera of the African subterranean rodent. This information was combined into the most comprehensive and geographically representative evolutionary study for the Bathyergidae to date. Results Species richness within the Bathyergidae appears to be underestimated, with undescribed taxa in five of the six genera. Biogeographic patterns suggest large historical distributions, which were repeatedly fragmented by major landscape changes (especially rifting, uplift and drainage evolution) since the Miocene. Aside from vicariant events, other factors (ecological specialization, population-level responses and climatic change) may have been instrumental in driving divergences in the Bathyergidae. As such, adaptive differences may exist among both populations and species across their discrete ranges, driving independent evolutionary trajectories among taxa. In addition, highly fragmented distributions of divergent (and often relict) lineages indicates the possibility of narrow endemics restricted to diminishing suitable habitats. From this, it is clear that a systematic revision of the Bathyergidae is necessary; such a revision should include comprehensive sampling of all putative taxa, the addition of genomic information to assess adaptive differences, as well as ecological information.
Collapse
Affiliation(s)
- Jacobus H Visser
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, Gauteng Province, South Africa
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Pretoria, Gauteng Province, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, Gauteng Province, South Africa
| |
Collapse
|
17
|
Torres-Sánchez M, Gower DJ, Alvarez-Ponce D, Creevey CJ, Wilkinson M, San Mauro D. What lies beneath? Molecular evolution during the radiation of caecilian amphibians. BMC Genomics 2019; 20:354. [PMID: 31072350 PMCID: PMC6507065 DOI: 10.1186/s12864-019-5694-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022] Open
Abstract
Background Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates. Electronic supplementary material The online version of this article (10.1186/s12864-019-5694-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- María Torres-Sánchez
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain. .,Present address: Department of Neuroscience, Spinal Cord and Brain Injury Research Center & Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, 40536, USA.
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | | | - Christopher J Creevey
- Institute for Global Food Security, Queen's University Belfast, University Road, Belfast, BT7 1NN, Northern Ireland, UK
| | - Mark Wilkinson
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
| | - Diego San Mauro
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, 28040, Madrid, Spain
| |
Collapse
|
18
|
Simões BF, Foley NM, Hughes GM, Zhao H, Zhang S, Rossiter SJ, Teeling EC. As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Mol Biol Evol 2019; 36:54-68. [PMID: 30476197 PMCID: PMC6340466 DOI: 10.1093/molbev/msy192] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
Collapse
Affiliation(s)
- Bruno F Simões
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- School of Earth Science, University of Bristol, Bristol, United Kingdom
- School of Biological Science, The University of Adelaide, South Australia, Australia
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Graham M Hughes
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| |
Collapse
|
19
|
Walcher J, Ojeda‐Alonso J, Haseleu J, Oosthuizen MK, Rowe AH, Bennett NC, Lewin GR. Specialized mechanoreceptor systems in rodent glabrous skin. J Physiol 2018; 596:4995-5016. [PMID: 30132906 PMCID: PMC6187043 DOI: 10.1113/jp276608] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/20/2018] [Indexed: 01/17/2023] Open
Abstract
KEY POINTS An ex vivo preparation was developed to record from single sensory fibres innervating the glabrous skin of the mouse forepaw. The density of mechanoreceptor innervation of the forepaw glabrous skin was found to be three times higher than that of hindpaw glabrous skin. Rapidly adapting mechanoreceptors that innervate Meissner's corpuscles were severalfold more responsive to slowly moving stimuli in the forepaw compared to those innervating hindpaw skin. We found a distinct group of small hairs in the centre of the mouse hindpaw glabrous skin that were exclusively innervated by directionally sensitive D-hair receptors. The directional sensitivity, but not the end-organ anatomy, were the opposite to D-hair receptors in the hairy skin. Glabrous skin hairs in the hindpaw are not ubiquitous in rodents, but occur in African and North American species that diverged more than 65 million years ago. ABSTRACT Rodents use their forepaws to actively interact with their tactile environment. Studies on the physiology and anatomy of glabrous skin that makes up the majority of the forepaw are almost non-existent in the mouse. Here we developed a preparation to record from single sensory fibres of the forepaw and compared anatomical and physiological receptor properties to those of the hindpaw glabrous and hairy skin. We found that the mouse forepaw skin is equipped with a very high density of mechanoreceptors; >3 times more than hindpaw glabrous skin. In addition, rapidly adapting mechanoreceptors that innervate Meissner's corpuscles of the forepaw were severalfold more sensitive to slowly moving mechanical stimuli compared to their counterparts in the hindpaw glabrous skin. All other mechanoreceptor types as well as myelinated nociceptors had physiological properties that were invariant regardless of which skin area they occupied. We discovered a novel D-hair receptor innervating a small group of hairs in the middle of the hindpaw glabrous skin in mice. These glabrous skin D-hair receptors were direction sensitive albeit with an orientation sensitivity opposite to that described for hairy skin D-hair receptors. Glabrous skin hairs do not occur in all rodents, but are present in North American and African rodent species that diverged more than 65 million years ago. The function of these specialized hairs is unknown, but they are nevertheless evolutionarily very ancient. Our study reveals novel physiological specializations of mechanoreceptors in the glabrous skin that likely evolved to facilitate tactile exploration.
Collapse
Affiliation(s)
- Jan Walcher
- Max‐Delbrück Centre for Molecular MedicineDepartment of NeuroscienceRobert‐Rössle Str. 1013125Berlin‐BuchGermany
| | - Julia Ojeda‐Alonso
- Max‐Delbrück Centre for Molecular MedicineDepartment of NeuroscienceRobert‐Rössle Str. 1013125Berlin‐BuchGermany
| | - Julia Haseleu
- Max‐Delbrück Centre for Molecular MedicineDepartment of NeuroscienceRobert‐Rössle Str. 1013125Berlin‐BuchGermany
| | - Maria K. Oosthuizen
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaRepublic of South Africa
| | - Ashlee H. Rowe
- Department of Biology and Program in Cellular and Behavioral NeurobiologyUniversity of OklahomaNormanOKUSA
| | - Nigel C. Bennett
- Department of Zoology and EntomologyUniversity of PretoriaPretoriaRepublic of South Africa
| | - Gary R. Lewin
- Max‐Delbrück Centre for Molecular MedicineDepartment of NeuroscienceRobert‐Rössle Str. 1013125Berlin‐BuchGermany
- Excellence Cluster NeurocureCharité Universitätsmedizin10117BerlinGermany
| |
Collapse
|
20
|
Davies KTJ, Bennett NC, Faulkes CG, Rossiter SJ. Limited Evidence for Parallel Molecular Adaptations Associated with the Subterranean Niche in Mammals: A Comparative Study of Three Superorders. Mol Biol Evol 2018; 35:2544-2559. [PMID: 30137400 PMCID: PMC6188548 DOI: 10.1093/molbev/msy161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Among mammals, several lineages have independently adapted to a subterranean niche and possess similar phenotypic traits for burrowing (e.g., cylindrical bodies, short limbs, and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, and the absence of light. In contrast, almost nothing is known regarding molecular adaptations in other subterranean lineages (e.g., true moles and golden moles). Therefore, the extent to which the recurrent phenotypic adaptations of divergent subterranean taxa have arisen via parallel routes of molecular evolution remains untested. To address these issues, we analyzed ∼8,000 loci in 15 representative subterranean taxa of four independent transitions to an underground niche for signatures of positive selection and convergent amino acid substitutions. Complementary analyses were performed in nonsubterranean "control" taxa to assess the biological significance of results. We found comparable numbers of positively selected genes in each of the four subterranean groups; however, correspondence in terms of gene identity between gene sets was low. Furthermore, we did not detect evidence of more convergent amino acids among subterranean species pairs compared with levels found between nonsubterranean controls. Comparisons with nonsubterranean taxa also revealed loci either under positive selection or with convergent substitutions, with similar functional enrichment (e.g., cell adhesion, immune response, and coagulation). Given the limited indication that positive selection and convergence occurred in the same loci, we conclude that selection may have acted on different loci across subterranean mammal lineages to produce similar phenotypes.
Collapse
Affiliation(s)
- Kalina T J Davies
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nigel C Bennett
- Department of Zoology & Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Chris G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, London, United Kingdom
| |
Collapse
|
21
|
Tavares WC, Seuánez HN. Changes in selection intensity on the mitogenome of subterranean and fossorial rodents respective to aboveground species. Mamm Genome 2018; 29:353-363. [DOI: 10.1007/s00335-018-9748-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022]
|
22
|
Albuquerque TAF, Drummond do Val L, Doherty A, de Magalhães JP. From humans to hydra: patterns of cancer across the tree of life. Biol Rev Camb Philos Soc 2018; 93:1715-1734. [PMID: 29663630 PMCID: PMC6055669 DOI: 10.1111/brv.12415] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/18/2018] [Accepted: 03/21/2018] [Indexed: 12/25/2022]
Abstract
Cancer is a disease of multicellularity; it originates when cells become dysregulated due to mutations and grow out of control, invading other tissues and provoking discomfort, disability, and eventually death. Human life expectancy has greatly increased in the last two centuries, and consequently so has the incidence of cancer. However, how cancer patterns in humans compare to those of other species remains largely unknown. In this review, we search for clues about cancer and its evolutionary underpinnings across the tree of life. We discuss data from a wide range of species, drawing comparisons with humans when adequate, and interpret our findings from an evolutionary perspective. We conclude that certain cancers are uniquely common in humans, such as lung, prostate, and testicular cancer; while others are common across many species. Lymphomas appear in almost every animal analysed, including in young animals, which may be related to pathogens imposing selection on the immune system. Cancers unique to humans may be due to our modern environment or may be evolutionary accidents: random events in the evolution of our species. Finally, we find that cancer‐resistant animals such as whales and mole‐rats have evolved cellular mechanisms that help them avoid neoplasia, and we argue that there are multiple natural routes to cancer resistance.
Collapse
Affiliation(s)
- Thales A F Albuquerque
- Escola Superior de Ciências da Saúde, SMHN Quadra 03 conjunto A, Bloco 1 Edifício Fepecs CEP 70, 710-907, Brasilia, Brazil
| | - Luisa Drummond do Val
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Room 281, 6 West Derby Street, Liverpool, L7 8TX, U.K
| | - Aoife Doherty
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Room 281, 6 West Derby Street, Liverpool, L7 8TX, U.K
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, William Henry Duncan Building, Room 281, 6 West Derby Street, Liverpool, L7 8TX, U.K
| |
Collapse
|
23
|
Sahm A, Bens M, Szafranski K, Holtze S, Groth M, Görlach M, Calkhoven C, Müller C, Schwab M, Kraus J, Kestler HA, Cellerino A, Burda H, Hildebrandt T, Dammann P, Platzer M. Long-lived rodents reveal signatures of positive selection in genes associated with lifespan. PLoS Genet 2018; 14:e1007272. [PMID: 29570707 PMCID: PMC5884551 DOI: 10.1371/journal.pgen.1007272] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/04/2018] [Accepted: 02/22/2018] [Indexed: 12/11/2022] Open
Abstract
The genetics of lifespan determination is poorly understood. Most research has been done on short-lived animals and it is unclear if these insights can be transferred to long-lived mammals like humans. Some African mole-rats (Bathyergidae) have life expectancies that are multiple times higher than similar sized and phylogenetically closely related rodents. To gain new insights into genetic mechanisms determining mammalian lifespans, we obtained genomic and transcriptomic data from 17 rodent species and scanned eleven evolutionary branches associated with the evolution of enhanced longevity for positively selected genes (PSGs). Indicating relevance for aging, the set of 250 identified PSGs showed in liver of long-lived naked mole-rats and short-lived rats an expression pattern that fits the antagonistic pleiotropy theory of aging. Moreover, we found the PSGs to be enriched for genes known to be related to aging. Among these enrichments were “cellular respiration” and “metal ion homeostasis”, as well as functional terms associated with processes regulated by the mTOR pathway: translation, autophagy and inflammation. Remarkably, among PSGs are RHEB, a regulator of mTOR, and IGF1, both central components of aging-relevant pathways, as well as genes yet unknown to be aging-associated but representing convincing functional candidates, e.g. RHEBL1, AMHR2, PSMG1 and AGER. Exemplary protein homology modeling suggests functional consequences for amino acid changes under positive selection. Therefore, we conclude that our results provide a meaningful resource for follow-up studies to mechanistically link identified genes and amino acids under positive selection to aging and lifespan determination. As an adaption to different environments rodents have evolved a wide range of lifespans. While most rodents are short-lived, along several phylogenetic branches long-lived species evolved. This provided us a unique opportunity to search for genes that are associated with enhanced longevity in mammals. Towards this, we computationally compared gene sequences of exceptional long-lived rodent species (like the naked mole-rat and chinchilla) and short-lived rodents (like rat and mouse) and identified those which evolved exceptional fast. As natural selection acts in parallel on a multitude of phenotypes, only a subset of the identified genes is probably associated with enhanced longevity. Applying several tests, we ensured that the dataset is related to aging. We conclude that lifespan extension in rodents can be attributed to changes in their defense against free radicals, iron homeostasis as well as cellular respiration and translation as central parts of the growth program. This confirms aging theories assuming a tradeoff between fast growth and long lifespan. Moreover, our study offers a meaningful resource of targets, i.e. genes and specific positions therein, for functional follow-up studies on their potential roles in the determination of lifespan–regardless whether they are currently known to be aging-related or not.
Collapse
Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- * E-mail:
| | - Martin Bens
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marco Groth
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| | - Cornelis Calkhoven
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Christine Müller
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Matthias Schwab
- Department of Neurology; Jena University Hospital-Friedrich Schiller University, Jena, Germany
| | - Johann Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A. Kestler
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Alessandro Cellerino
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
- Laboratory of Biology Bio@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Hynek Burda
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Thomas Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging–Fritz Lipmann Institute, Jena, Germany
| |
Collapse
|
24
|
Omerbašić D, Smith ESJ, Moroni M, Homfeld J, Eigenbrod O, Bennett NC, Reznick J, Faulkes CG, Selbach M, Lewin GR. Hypofunctional TrkA Accounts for the Absence of Pain Sensitization in the African Naked Mole-Rat. Cell Rep 2017; 17:748-758. [PMID: 27732851 PMCID: PMC5081396 DOI: 10.1016/j.celrep.2016.09.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/23/2016] [Accepted: 09/13/2016] [Indexed: 12/21/2022] Open
Abstract
The naked mole-rat is a subterranean rodent lacking several pain behaviors found in humans, rats, and mice. For example, nerve growth factor (NGF), an important mediator of pain sensitization, fails to produce thermal hyperalgesia in naked mole-rats. The sensitization of capsaicin-sensitive TRPV1 ion channels is necessary for NGF-induced hyperalgesia, but naked mole-rats have fully functional TRPV1 channels. We show that exposing isolated naked mole-rat nociceptors to NGF does not sensitize TRPV1. However, the naked mole-rat NGF receptor TrkA displays a reduced ability to engage signal transduction pathways that sensitize TRPV1. Between one- and three-amino-acid substitutions in the kinase domain of the naked mole-rat TrkA are sufficient to render the receptor hypofunctional, and this is associated with the absence of heat hyperalgesia. Our data suggest that evolution has selected for a TrkA variant that abolishes a robust nociceptive behavior in this species but is still compatible with species fitness. TRPV1 ion channels in naked mole-rat nociceptors are not sensitized by NGF Naked mole-rat TRPV1 channels are sensitized by NGF in mouse nociceptors NGF activation of naked mole-rat TrkA receptors does not sensitize TRPV1 One to three amino acids in the naked mole-rat TrkA receptors may render it hypofunctional
Collapse
Affiliation(s)
- Damir Omerbašić
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Proteome Dynamics Group, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ewan St J Smith
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Mirko Moroni
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Johanna Homfeld
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ole Eigenbrod
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Nigel C Bennett
- Department of Zoology and Entomology, University of Pretoria, Pretoria, Hatfield 0028, Republic of South Africa
| | - Jane Reznick
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matthias Selbach
- Proteome Dynamics Group, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Gary R Lewin
- Molecular Physiology of Somatic Sensation, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany; Excellence Cluster Neurocure, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
| |
Collapse
|
25
|
Sahm A, Bens M, Platzer M, Szafranski K. PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes. Nucleic Acids Res 2017; 45:e100. [PMID: 28334822 PMCID: PMC5499814 DOI: 10.1093/nar/gkx179] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/09/2017] [Indexed: 11/12/2022] Open
Abstract
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software. We developed the software tool PosiGene that (i) detects positively selected genes (PSGs) on genome-scale, (ii) allows analysis of specific evolutionary branches, (iii) can be used in arbitrary species contexts and (iv) offers visualization of the results for further manual validation and biological interpretation. We exemplify PosiGene's performance using simulated and real data. In the simulated data approach, we determined a false positive rate <1%. With real data, we found that 68.4% of the PSGs detected by PosiGene, were shared by at least one previous study that used the same set of species. PosiGene is a user-friendly, reliable tool for reproducible genome-wide identification of PSGs and freely available at https://github.com/gengit/PosiGene.
Collapse
Affiliation(s)
- Arne Sahm
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Martin Bens
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| | - Karol Szafranski
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
| |
Collapse
|
26
|
Petruseva IO, Evdokimov AN, Lavrik OI. Genome Stability Maintenance in Naked Mole-Rat. Acta Naturae 2017; 9:31-41. [PMID: 29340215 PMCID: PMC5762826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Indexed: 11/02/2022] Open
Abstract
The naked mole-rat (Heterocephalus glaber) is one of the most promising models used to study genome maintenance systems, including the effective repair of damage to DNA. The naked mole-rat is the longest lived rodent species, which is extraordinarily resistant to cancer and has a number of other unique phenotypic traits. For at least 80% of its lifespan, this animal shows no signs of aging or any increased likelihood of death and retains the ability to reproduce. The naked mole-rat draws the heightened attention of researchers who study the molecular basis of lengthy lifespan and cancer resistance. Despite the fact that the naked mole-rat lives under genotoxic stress conditions (oxidative, etc.), the main characteristics of its genome and proteome are a high stability and effective functioning. Replicative senescence in the somatic cells of naked mole-rats is missing, while an additional p53/pRb-dependent mechanism of early contact inhibition has been revealed in its fibroblasts, which controls cell proliferation and its mechanism of arf-dependent aging. The unique traits of phenotypic and molecular adaptations found in the naked mole-rat speak to a high stability and effective functioning of the molecular machinery that counteract damage accumulation in its genome. This review analyzes existing results in the study of the molecular basis of longevity and high cancer resistance in naked mole-rats.
Collapse
Affiliation(s)
- I. O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 8, Novosibirsk, 630090, Russia
| | - A. N. Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 8, Novosibirsk, 630090, Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 8, Novosibirsk, 630090, Russia
- Novosibirsk State University, Ministry of education and science, Pirogova Str. 1, Novosibirsk, 630090 , Russia
- Altai State University, Ministry of education and science, Lenina Ave. 61, Barnaul, 656049, Russia
| |
Collapse
|
27
|
Weber RE, Jarvis JUM, Fago A, Bennett NC. O 2 binding and CO 2 sensitivity in haemoglobins of subterranean African mole rats. ACTA ACUST UNITED AC 2017; 220:3939-3948. [PMID: 28851819 DOI: 10.1242/jeb.160457] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/23/2017] [Indexed: 01/05/2023]
Abstract
Inhabiting deep and sealed subterranean burrows, mole rats exhibit a remarkable suite of specializations, including eusociality (living in colonies with single breeding queens), extraordinary longevity, cancer immunity and poikilothermy, and extreme tolerance of hypoxia and hypercapnia. With little information available on adjustments in haemoglobin (Hb) function that may mitigate the impact of exogenous and endogenous constraints on the uptake and internal transport of O2, we measured haematological characteristics, as well as Hb-O2 binding affinity and sensitivity to pH (Bohr effect), CO2, temperature and 2,3-diphosphoglycerate (DPG, the major allosteric modulator of Hb-O2 affinity in red blood cells) in four social and two solitary species of African mole rats (family Bathyergidae) originating from different biomes and soil types across Central and Southern Africa. We found no consistent patterns in haematocrit (Hct) and blood and red cell DPG and Hb concentrations or in intrinsic Hb-O2 affinity and its sensitivity to pH and DPG that correlate with burrowing, sociality and soil type. However, the results reveal low specific (pH independent) effects of CO2 on Hb-O2 affinity compared with humans that predictably safeguard pulmonary loading under hypoxic and hypercapnic burrow conditions. The O2 binding characteristics are discussed in relation to available information on the primary structure of Hbs from adult and developmental stages of mammals subjected to hypoxia and hypercapnia and the molecular mechanisms underlying functional variation in rodent Hbs.
Collapse
Affiliation(s)
- Roy E Weber
- Department of Bioscience, Aarhus University, C.F. Møllers Alle 3, Aarhus C 8000, Denmark
| | | | - Angela Fago
- Department of Bioscience, Aarhus University, C.F. Møllers Alle 3, Aarhus C 8000, Denmark
| | - Nigel C Bennett
- Zoology and Entomology Department, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| |
Collapse
|
28
|
Sahm A, Bens M, Platzer M, Cellerino A. Parallel evolution of genes controlling mitonuclear balance in short-lived annual fishes. Aging Cell 2017; 16:488-496. [PMID: 28295945 PMCID: PMC5418189 DOI: 10.1111/acel.12577] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2016] [Indexed: 12/15/2022] Open
Abstract
The current molecular understanding of the aging process derives almost exclusively from the study of random or targeted single‐gene mutations in highly inbred laboratory species, mostly invertebrates. Little information is available as to the genetic mechanisms responsible for natural lifespan variation and the evolution of lifespan, especially in vertebrates. Here, we investigated the pattern of positive selection in annual (i.e., short‐lived) and nonannual (i.e., longer‐lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan). We identified genes under positive selection in all steps of mitochondrial biogenesis: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes, and electron transport chain. Signs of paralleled evolution (i.e., evolution in more than one branch of Nothobranchius phylogeny) are observed in four out of five steps. Moreover, some genes under positive selection in Nothobranchius are under positive selection also in long‐lived mammals such as bats and mole‐rats. Complexes of the respiratory chain are formed in a coordinates multistep process where nuclearly and mitochondrially encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance, and experimental manipulations of mitonuclear balance can increase longevity of laboratory species. Our data strongly indicate that these genes are also casually linked to evolution lifespan in vertebrates.
Collapse
Affiliation(s)
- Arne Sahm
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Martin Bens
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Matthias Platzer
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
| | - Alessandro Cellerino
- Leibniz Insitute on Ageing; Fritz-Lipmann Institute; Jena 07745 Germany
- Bio@SNS; Scuola Normale Superiore; Pisa 56124 Italy
| |
Collapse
|
29
|
Faulkes CG, Mgode GF, Archer EK, Bennett NC. Relic populations of Fukomys mole-rats in Tanzania: description of two new species F. livingstoni sp. nov. and F. hanangensis sp. nov. PeerJ 2017; 5:e3214. [PMID: 28462027 PMCID: PMC5410139 DOI: 10.7717/peerj.3214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/21/2017] [Indexed: 11/22/2022] Open
Abstract
Previous studies of African mole-rats of the genera Heliophobius and Fukomys (Bathyergidae) in the regions of East and south central Africa have revealed a diversity of species and vicariant populations, with patterns of distribution having been influenced by the geological process of rifting and changing patterns of drainage of major river systems. This has resulted in most of the extant members of the genus Fukomys being distributed west of the main Rift Valley. However, a small number of isolated populations are known to occur east of the African Rift Valley in Tanzania, where Heliophobius is the most common bathyergid rodent. We conducted morphological, craniometric and phylogenetic analysis of mitochondrial cytochrome b (cyt b) sequences of two allopatric populations of Tanzanian mole-rats (genus Fukomys) at Ujiji and around Mount Hanang, in comparison with both geographically adjacent and more distant populations of Fukomys. Our results reveal two distinct evolutionary lineages, forming clades that constitute previously unnamed species. Here, we formally describe and designate these new species F. livingstoni and F. hanangensis respectively. Molecular clock-based estimates of divergence times, together with maximum likelihood inference of biogeographic range evolution, offers strong support for the hypothesis that vicariance in the Western Rift Valley and the drainage patterns of major river systems has subdivided populations of mole-rats. More recent climatic changes and tectonic activity in the “Mbeya triple junction” and Rungwe volcanic province between Lakes Rukwa and Nyasa have played a role in further isolation of these extra-limital populations of Fukomys in Tanzania.
Collapse
Affiliation(s)
- Chris G Faulkes
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Georgies F Mgode
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Elizabeth K Archer
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Nigel C Bennett
- Department of Zoology & Entomology, University of Pretoria, Pretoria, Gauteng, South Africa
| |
Collapse
|
30
|
Roberts WR, Roalson EH. Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae). BMC Genomics 2017; 18:240. [PMID: 28320315 PMCID: PMC5359931 DOI: 10.1186/s12864-017-3623-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 03/11/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae). RESULTS The assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species. CONCLUSIONS The floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.
Collapse
Affiliation(s)
- Wade R. Roberts
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164-1030 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236 USA
| | - Eric H. Roalson
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164-1030 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236 USA
| |
Collapse
|
31
|
Lewis KN, Soifer I, Melamud E, Roy M, McIsaac RS, Hibbs M, Buffenstein R. Unraveling the message: insights into comparative genomics of the naked mole-rat. Mamm Genome 2016; 27:259-78. [PMID: 27364349 PMCID: PMC4935753 DOI: 10.1007/s00335-016-9648-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/09/2016] [Indexed: 12/21/2022]
Abstract
Animals have evolved to survive, and even thrive, in different environments. Genetic adaptations may have indirectly created phenotypes that also resulted in a longer lifespan. One example of this phenomenon is the preternaturally long-lived naked mole-rat. This strictly subterranean rodent tolerates hypoxia, hypercapnia, and soil-based toxins. Naked mole-rats also exhibit pronounced resistance to cancer and an attenuated decline of many physiological characteristics that often decline as mammals age. Elucidating mechanisms that give rise to their unique phenotypes will lead to better understanding of subterranean ecophysiology and biology of aging. Comparative genomics could be a useful tool in this regard. Since the publication of a naked mole-rat genome assembly in 2011, analyses of genomic and transcriptomic data have enabled a clearer understanding of mole-rat evolutionary history and suggested molecular pathways (e.g., NRF2-signaling activation and DNA damage repair mechanisms) that may explain the extraordinarily longevity and unique health traits of this species. However, careful scrutiny and re-analysis suggest that some identified features result from incorrect or imprecise annotation and assembly of the naked mole-rat genome: in addition, some of these conclusions (e.g., genes involved in cancer resistance and hairlessness) are rejected when the analysis includes additional, more closely related species. We describe how the combination of better study design, improved genomic sequencing techniques, and new bioinformatic and data analytical tools will improve comparative genomics and ultimately bridge the gap between traditional model and nonmodel organisms.
Collapse
Affiliation(s)
- Kaitlyn N Lewis
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Ilya Soifer
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Eugene Melamud
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Margaret Roy
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - R Scott McIsaac
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA
| | - Matthew Hibbs
- Computer Science Department, Trinity University, San Antonio, TX, 78212, USA
| | - Rochelle Buffenstein
- Calico Life Sciences LLC, 1170 Veterans Blvd, South San Francisco, CA, 94080, USA.
| |
Collapse
|