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Selleghin-Veiga G, Magpali L, Picorelli A, Silva FA, Ramos E, Nery MF. Breathing Air and Living Underwater: Molecular Evolution of Genes Related to Antioxidant Response in Cetaceans and Pinnipeds. J Mol Evol 2024; 92:300-316. [PMID: 38735005 DOI: 10.1007/s00239-024-10170-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 04/05/2024] [Indexed: 05/13/2024]
Abstract
Cetaceans and pinnipeds are lineages of mammals that have independently returned to the aquatic environment, acquiring varying degrees of dependence on it while sharing adaptations for underwater living. Here, we focused on one critical adaptation from both groups, their ability to withstand the ischemia and reperfusion experienced during apnea diving, which can lead to the production of reactive oxygen species (ROS) and subsequent oxidative damage. Previous studies have shown that cetaceans and pinnipeds possess efficient antioxidant enzymes that protect against ROS. In this study, we investigated the molecular evolution of key antioxidant enzyme genes (CAT, GPX3, GSR, PRDX1, PRDX3, and SOD1) and the ROS-producing gene XDH, in cetaceans and pinnipeds lineages. We used the ratio of non-synonymous (dN) to synonymous (dS) substitutions as a measure to identify signatures of adaptive molecular evolution in these genes within and between the two lineages. Additionally, we performed protein modeling and variant impact analyzes to assess the functional consequences of observed mutations. Our findings revealed distinct selective regimes between aquatic and terrestrial mammals in five of the examined genes, including divergences within cetacean and pinniped lineages, between ancestral and recent lineages and between crowns groups. We identified specific sites under positive selection unique to Cetacea and Pinnipedia, with one site showing evidence of convergent evolution in species known for their long and deep-diving capacities. Notably, many sites under adaptive selection exhibited radical changes in amino acid properties, with some being damaging mutations in human variations, but with no apparent detrimental impacts on aquatic mammals. In conclusion, our study provides insights into the adaptive changes that have occurred in the antioxidant systems of aquatic mammals throughout their evolutionary history. We observed both distinctive features within each group of Cetacea and Pinnipedia and instances of convergence. These findings highlight the dynamic nature of the antioxidant system in response to challenges of the aquatic environment and provide a foundation for further investigations into the molecular mechanisms underlying these adaptations.
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Affiliation(s)
- Giovanna Selleghin-Veiga
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
| | - Letícia Magpali
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Agnello Picorelli
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Felipe A Silva
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| | - Elisa Ramos
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Mariana F Nery
- Laboratório de Genômica Evolutiva, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil.
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Wang QP, Luo CY, Xu XH, Hu WX, Gai YL, Gong YJ, Mu Y. Adaptive evolution of antioxidase-related genes in hypoxia-tolerant mammals. Front Genet 2024; 15:1315677. [PMID: 38725483 PMCID: PMC11079137 DOI: 10.3389/fgene.2024.1315677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/20/2024] [Indexed: 05/12/2024] Open
Abstract
To cope with the damage from oxidative stress caused by hypoxia, mammals have evolved a series of physiological and biochemical traits, including antioxidant ability. Although numerous research studies about the mechanisms of hypoxia evolution have been reported, the molecular mechanisms of antioxidase-related genes in mammals living in different environments are yet to be completely understood. In this study, we constructed a dataset comprising 7 antioxidase-related genes (CAT, SOD1, SOD2, SOD3, GPX1, GPX2, and GPX3) from 43 mammalian species to implement evolutionary analysis. The results showed that six genes (CAT, SOD1, SOD2, SOD3, GPX1, and GPX3) have undergone divergent evolution based on the free-ratio (M1) model. Furthermore, multi-ratio model analyses uncovered the divergent evolution between hypoxic and non-hypoxic lineages, as well as various hypoxic lineages. In addition, the branch-site model identified 9 positively selected branches in 6 genes (CAT, SOD1, SOD2, SOD3, GPX2, and GPX3) that contained 35 positively selected sites, among which 31 positively selected sites were identified in hypoxia-tolerant branches, accounting for 89% of the total number of positively selected sites. Interestingly, 65 parallel/convergent sites were identified in the 7 genes. In summary, antioxidase-related genes are subjected to different selective pressures among hypoxia-tolerant species living in different habitats. This study provides a valuable insight into the molecular evolution of antioxidase-related genes in hypoxia evolution in mammals.
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Affiliation(s)
- Qiu-Ping Wang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Chao-Yang Luo
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Xiong-Hui Xu
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Wen-Xian Hu
- Erhai Watershed Ecological Environment Quality Testing Engineering Research Center of Yunnan Provincial Universities, Erhai Research Institute, West Yunnan University of Applied Sciences, Dali, Yunnan, China
| | - Yu-Lin Gai
- Colledge of Life Science, China West Normal University, Nanchong, Sichuan, China
| | - You-Jing Gong
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region from Dali University, Dali, Yunnan, China
| | - Yuan Mu
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- The Provincial Innovation Team of Biodiversity Conservation and Utility of the Three Parallel Rivers Region from Dali University, Dali, Yunnan, China
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Yépez Y, Marcano-Ruiz M, Bortolini MC. Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance. Genet Mol Biol 2024; 46:e20230140. [PMID: 38252060 PMCID: PMC10802827 DOI: 10.1590/1678-4685-gmb-2023-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 12/06/2023] [Indexed: 01/23/2024] Open
Abstract
Aquatic mammals (marine and freshwater species) share significant and similar adaptations, enabling them to tolerate hypoxia during regular breath-hold diving. Despite the established importance of HIF1A, a master regulator in the molecular mechanism of hypoxia response, and other associated genes, their role in the evolutionary adaptation of aquatic mammals is not fully understood. In this study, we investigated this topic by employing a candidate gene approach to analyze 11 critical genes involved in the HIF1A signaling pathway in aquatic mammals. Our gene analyses included evaluating positive and negative selection, relaxation or constriction of selection, and molecular convergence compared to other terrestrial mammals, including subterranean mammals. Evidence of selection suggested a significant role of negative selection, as well as relaxation of the selective regime in cetaceans for most of these genes. We found that the glutamine 68 variant in the HIF3α protein is unique to cetaceans and initial evaluations indicated a destabilizing effect on protein structure. However, further analyses are necessary to evaluate its functional impact and adaptive relevance in this taxon.
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Affiliation(s)
- Yuri Yépez
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Mariana Marcano-Ruiz
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
| | - Maria Cátira Bortolini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Humana e Molecular, Porto Alegre, RS, Brazil
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Hewitt OH, Degnan SM. Distribution and diversity of ROS-generating enzymes across the animal kingdom, with a focus on sponges (Porifera). BMC Biol 2022; 20:212. [PMID: 36175868 PMCID: PMC9524095 DOI: 10.1186/s12915-022-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reactive derivatives of oxygen (reactive oxygen species; ROS) are essential in signalling networks of all aerobic life. Redox signalling, based on cascades of oxidation-reduction reactions, is an evolutionarily ancient mechanism that uses ROS to regulate an array of vital cellular processes. Hydrogen peroxide (H2O2) and superoxide anion (O2•-) are employed as signalling molecules that alter the oxidation state of atoms, inhibiting or activating gene activity. Here, we conduct metazoan-wide comparative genomic assessments of the two enzyme families, superoxide dismutase (SOD) and NADPH oxidases (NOX), that generate H2O2 and/or O2•- in animals. RESULTS Using the genomes of 19 metazoan species representing 10 phyla, we expand significantly on previous surveys of these two ancient enzyme families. We find that the diversity and distribution of both the SOD and NOX enzyme families comprise some conserved members but also vary considerably across phyletic animal lineages. For example, there is substantial NOX gene loss in the ctenophore Mnemiopsis leidyi and divergent SOD isoforms in the bilaterians D. melanogaster and C. elegans. We focus particularly on the sponges (phylum Porifera), a sister group to all other metazoans, from which these enzymes have not previously been described. Within Porifera, we find a unique calcium-regulated NOX, the widespread radiation of an atypical member of CuZnSOD named Rsod, and a novel endoplasmic reticulum MnSOD that is prevalent across aquatic metazoans. CONCLUSIONS Considering the precise, spatiotemporal specificity of redox signalling, our findings highlight the value of expanding redox research across a greater diversity of organisms to better understand the functional roles of these ancient enzymes within a universally important signalling mechanism.
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Affiliation(s)
- Olivia H Hewitt
- School of Biological Sciences and Centre for Marine Science, University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Sandie M Degnan
- School of Biological Sciences and Centre for Marine Science, University of Queensland, St Lucia, QLD, 4072, Australia
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