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York JM. Temperature activated transient receptor potential ion channels from Antarctic fishes. Open Biol 2023; 13:230215. [PMID: 37848053 PMCID: PMC10581778 DOI: 10.1098/rsob.230215] [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: 07/05/2023] [Accepted: 09/01/2023] [Indexed: 10/19/2023] Open
Abstract
Antarctic notothenioid fishes (cryonotothenioids) live in waters that range between -1.86°C and an extreme maximum +4°C. Evidence suggests these fish sense temperature peripherally, but the molecular mechanism of temperature sensation in unknown. Previous work identified transient receptor potential (TRP) channels TRPA1b, TRPM4 and TRPV1a as the top candidates for temperature sensors. Here, cryonotothenioid TRPA1b and TRPV1a are characterized using Xenopus oocyte electrophysiology. TRPA1b and TRPV1a showed heat-evoked currents with Q10s of 11.1 ± 2.2 and 20.5 ± 2.4, respectively. Unexpectedly, heat activation occurred at a threshold of 22.9 ± 1.3°C for TRPA1b and 32.1 ± 0.6°C for TRPV1a. These fish have not experienced such temperatures for at least 15 Myr. Either (1) another molecular mechanism underlies temperature sensation, (2) these fishes do not sense temperatures below these thresholds despite having lethal limits as low as 5°C, or (3) native cellular conditions modify the TRP channels to function at relevant temperatures. The effects of osmolytes, pH, oxidation, phosphorylation, lipids and accessory proteins were tested. No conditions shifted the activity range of TRPV1a. Oxidation in combination with reduced cholesterol significantly dropped activation threshold of TRPA1b to 11.3 ± 2.3°C, it is hypothesized the effect may be due to lipid raft disruption.
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Affiliation(s)
- Julia M. York
- Department of Integrative Biology, Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
- School of Integrative Biology, University of Illinois Urbana–Champaign, Urbana, Illinois, USA
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Cheng CHC, Rivera-Colón AG, Minhas BF, Wilson L, Rayamajhi N, Vargas-Chacoff L, Catchen JM. Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus-The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes (Basel) 2023; 14:1196. [PMID: 37372376 DOI: 10.3390/genes14061196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus' phylogenetic position. We additionally curated E. maclovinus' repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.
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Affiliation(s)
- Chi-Hing Christina Cheng
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Bushra Fazal Minhas
- Informatics Program, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Loralee Wilson
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Niraj Rayamajhi
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Luis Vargas-Chacoff
- Laboratorio de Fisiología de Peces, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia 5090000, Chile
- Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia 5090000, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Universidad Austral de Chile, Valdivia 5090000, Chile
| | - Julian M Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
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Rivera-Colón AG, Rayamajhi N, Minhas BF, Madrigal G, Bilyk KT, Yoon V, Hüne M, Gregory S, Cheng CHC, Catchen JM. Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Mol Biol Evol 2023; 40:7035026. [PMID: 36806940 PMCID: PMC9985337 DOI: 10.1093/molbev/msad029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.
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Affiliation(s)
- Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Niraj Rayamajhi
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL
| | | | - Giovanni Madrigal
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Kevin T Bilyk
- Department of Biology, Montclair State University, Montclair, NJ
| | - Veronica Yoon
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Mathias Hüne
- Centro de Investigación para la Conservación de los Ecosistemas Australes, Punta Arenas, Chile
| | - Susan Gregory
- British Antarctic Survey, Cambridge, United Kingdom.,Government of South Georgia and the South Sandwich Islands, Stanley, Falklands
| | - C H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL
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Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA. How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member. Mol Biol Evol 2023; 40:6993039. [PMID: 36656997 PMCID: PMC9897032 DOI: 10.1093/molbev/msad014] [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: 10/07/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.
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Affiliation(s)
| | - Michael W Vandewege
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Catalina Meléndez
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Charlotte Luchsinger
- Department of Physiology, School of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Luis Vargas-Chacoff
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Applied Biochemistry Laboratory, Facultad de Ciencias Veterinarias, Instituto de Farmacología y Morfofisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Cheril Tapia-Rojas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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Cvetkovska M, Vakulenko G, Smith DR, Zhang X, Hüner NPA. Temperature stress in psychrophilic green microalgae: Minireview. PHYSIOLOGIA PLANTARUM 2022; 174:e13811. [PMID: 36309822 DOI: 10.1111/ppl.13811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Photosynthetic algae are the main primary producers in polar regions, form the basis of polar food webs, and are responsible for a significant portion of global carbon fixation. Many cold-water algae are psychrophiles that thrive in the cold but cannot grow at moderate temperatures (≥20°C). Polar regions are at risk of rapid warming caused by climate change, and the sensitivity of psychrophilic algae to rising temperatures makes them, and the ecosystems they inhabit, particularly vulnerable. Recent research on the Antarctic psychrophile Chlamydomonas priscuii, an emerging algal model, has revealed unique adaptations to life in the permanent cold. Additionally, genome sequencing of C. priscuii and its relative Chlamydomonas sp. ICE-L has given rise to a plethora of computational tools that can help elucidate the genetic basis of psychrophily. This minireview summarizes new advances in characterizing the heat stress responses in psychrophilic algae and examines their extraordinary sensitivity to temperature increases. Further research in this field will help determine the impact of climate change on psychrophiles from threatened polar environments.
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Affiliation(s)
- Marina Cvetkovska
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Galyna Vakulenko
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - David R Smith
- Department of Biology, University of Western Ontario, London, Canada
| | - Xi Zhang
- Institute for Comparative Genomics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Norman P A Hüner
- Department of Biology, University of Western Ontario, London, Canada
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Daane JM, William Detrich H. Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective. Annu Rev Anim Biosci 2021; 10:39-62. [PMID: 34748709 DOI: 10.1146/annurev-animal-081221-064325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antarctic notothenioid fishes are the classic example of vertebrate adaptive radiation in a marine environment. Notothenioids diversified from a single common ancestor ∼25 Mya to more than 140 species today, and they represent ∼90% of fish biomass on the continental shelf of Antarctica. As they diversified in the cold Southern Ocean, notothenioids evolved numerous traits, including osteopenia, anemia, cardiomegaly, dyslipidemia, and aglomerular kidneys, that are beneficial or tolerated in their environment but are pathological in humans. Thus, notothenioids are models for understanding adaptive radiations, physiological and biochemical adaptations to extreme environments, and genetic mechanisms of human disease. Since 2014, 16 notothenioid genomes have been published, which enable a first-pass holistic analysis of the notothenioid radiation and the genetic underpinnings of novel notothenioid traits. Here, we review the notothenioid radiation from a genomic perspective and integrate our insights with recent observations from other fish radiations. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
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