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Accorsi A, Guo L, Marshall WF, Mommersteeg MTM, Nakajima YI. Extraordinary model systems for regeneration. Development 2024; 151:dev203083. [PMID: 39012059 DOI: 10.1242/dev.203083] [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] [Indexed: 07/17/2024]
Abstract
Regeneration is the remarkable phenomenon through which an organism can regrow lost or damaged parts with fully functional replacements, including complex anatomical structures, such as limbs. In 2019, Development launched its 'Model systems for regeneration' collection, a series of articles introducing some of the most popular model organisms for studying regeneration in vivo. To expand this topic further, this Perspective conveys the voices of five expert biologists from the field of regenerative biology, each of whom showcases some less well-known, but equally extraordinary, species for studying regeneration.
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Affiliation(s)
- Alice Accorsi
- University of California Davis, Department of Molecular and Cellular Biology, Davis, CA 95616, USA
| | - Longhua Guo
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Institute of Gerontology, Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wallace F Marshall
- Deptartment of Biochemistry & Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Mathilda T M Mommersteeg
- Institute of Developmental & Regenerative Medicine (IDRM), Department of Physiology, Anatomy & Genetics, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7TY, UK
| | - Yu-Ichiro Nakajima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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2
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Leclercq J, Torres-Paz J, Policarpo M, Agnès F, Rétaux S. Evolution of the regulation of developmental gene expression in blind Mexican cavefish. Development 2024; 151:dev202610. [PMID: 39007346 DOI: 10.1242/dev.202610] [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: 12/13/2023] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Developmental evolution and diversification of morphology can arise through changes in the regulation of gene expression or protein-coding sequence. To unravel mechanisms underlying early developmental evolution in cavefish of the species Astyanax mexicanus, we compared transcriptomes of surface-dwelling and blind cave-adapted morphs at the end of gastrulation. Twenty percent of the transcriptome was differentially expressed. Allelic expression ratios in cave X surface hybrids showed that cis-regulatory changes are the quasi-exclusive contributors to inter-morph variations in gene expression. Among a list of 108 genes with change at the cis-regulatory level, we explored the control of expression of rx3, which is a master eye gene. We discovered that cellular rx3 levels are cis-regulated in a cell-autonomous manner, whereas rx3 domain size depends on non-autonomous Wnt and Bmp signalling. These results highlight how uncoupled mechanisms and regulatory modules control developmental gene expression and shape morphological changes. Finally, a transcriptome-wide search for fixed coding mutations and differential exon use suggested that variations in coding sequence have a minor contribution. Thus, during early embryogenesis, changes in gene expression regulation are the main drivers of cavefish developmental evolution.
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Affiliation(s)
- Julien Leclercq
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Jorge Torres-Paz
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Maxime Policarpo
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - François Agnès
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
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3
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Farooqi IS, Xu Y. Translational potential of mouse models of human metabolic disease. Cell 2024; 187:4129-4143. [PMID: 39067442 DOI: 10.1016/j.cell.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/05/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
Obesity causes significant morbidity and mortality globally. Research in the last three decades has delivered a step-change in our understanding of the fundamental mechanisms that regulate energy homeostasis, building on foundational discoveries in mouse models of metabolic disease. However, not all findings made in rodents have translated to humans, hampering drug discovery in this field. Here, we review how studies in mice and humans have informed our current framework for understanding energy homeostasis, discuss their challenges and limitations, and offer a perspective on how human studies may play an increasingly important role in the discovery of disease mechanisms and identification of therapeutic targets in the future.
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Affiliation(s)
- I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Yong Xu
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Department of Molecular and Cellular Biology and Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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Warren WC, Rice ES, X M, Roback E, Keene A, Martin F, Ogeh D, Haggerty L, Carroll RA, McGaugh S, Rohner N. Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. G3 (BETHESDA, MD.) 2024; 14:jkae103. [PMID: 38771704 PMCID: PMC11304944 DOI: 10.1093/g3journal/jkae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024]
Abstract
The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Maggs X
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Emma Roback
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Alex Keene
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
- Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, KU Medical Center, Kansas City, KS 66160, USA
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Li W, Song J, Tu H, Jiang S, Pan B, Li J, Zhao Y, Chen L, Xu Q. Genome sequencing of Coryphaenoides yaquinae reveals convergent and lineage-specific molecular evolution in deep-sea adaptation. Mol Ecol Resour 2024; 24:e13989. [PMID: 38946220 DOI: 10.1111/1755-0998.13989] [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: 02/18/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes.
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Affiliation(s)
- Wenhao Li
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Jie Song
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Huaming Tu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Binbin Pan
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jiazhen Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Yongpeng Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Living Resource Sciences and Management, Shanghai Ocean University, Shanghai, China
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China
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Di Rosa V, Frigato E, Negrini P, Cristiano W, López-Olmeda JF, Rétaux S, Sánchez-Vázquez FJ, Foulkes NS, Bertolucci C. Sporadic feeding regulates robust food entrainable circadian clocks in blind cavefish. iScience 2024; 27:110171. [PMID: 38974965 PMCID: PMC11225386 DOI: 10.1016/j.isci.2024.110171] [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: 02/23/2024] [Revised: 04/14/2024] [Accepted: 05/31/2024] [Indexed: 07/09/2024] Open
Abstract
The circadian clock represents a key timing system entrained by various periodic signals that ensure synchronization with the environment. Many investigations have pointed to the existence of two distinct circadian oscillators: one regulated by the light-dark cycle and the other set by feeding time. Blind cavefish have evolved under extreme conditions where they completely lack light exposure and experience food deprivation. Here, we have investigated feeding regulated clocks in two cavefish species, the Somalian cavefish Phreatichthys andruzzii and the Mexican cavefish Astyanax mexicanus, in comparison with the surface-dwelling zebrafish Danio rerio. Our results reveal that feeding represents an extremely strong synchronizer for circadian locomotor rhythmicity in subterranean cavefish. Indeed, we showed that consuming just one meal every 4 days is sufficient to entrain circadian rhythmicity in both cavefish species, but not in zebrafish. These profound adaptations to an extreme environment provide insight into the connections between feeding and circadian clocks.
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Affiliation(s)
- Viviana Di Rosa
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Elena Frigato
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Pietro Negrini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Walter Cristiano
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Ecosystems and Health Unit, Environment and Health Department, Italian National Institute of Health, 00161 Rome, Italy
| | - Jose Fernando López-Olmeda
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Francisco Javier Sánchez-Vázquez
- Department of Physiology, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain
| | - Nicholas S. Foulkes
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
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Boggs TE, Gross JB. Gill morphology adapted to oxygen-limited caves in Astyanax mexicanus. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024. [PMID: 39031584 DOI: 10.1002/jez.2840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 07/22/2024]
Abstract
Sensing and acquiring dissolved oxygen is crucial for nearly all aquatic life. This may become even more vital as dissolved oxygen concentrations continue to decline in many aquatic environments. While certain phenotypes that enable fish to live in low oxygen have been characterized, adaptations that arise following sudden, drastic reductions in dissolved oxygen are relatively unknown. Here, we assessed the blind Mexican cavefish, Astyanax mexicanus, for alterations to gill morphology that may be adaptive for life in hypoxic caves. The Astyanax system provides the unique opportunity to compare gill morphology between stereotypical "surface" adapted morphotypes and obligate cave-dwelling conspecifics. While the surface environment is well-oxygenated, cavefish must cope with significantly reduced oxygen. We began by quantifying traditional morphological gill traits including filament number and length as well as lamellar density and height in surface fish and two distinct cave populations, Pachón and Tinaja. This enabled us to estimate total lamellar height, a proxy for gill surface area. We then used immunohistochemical staining to label 5-HT-positive neuroepithelial cells (NECs), which serve as key oxygen sensors in fish. We discovered an increase in gill surface area for both cavefish populations compared to surface, which may enable a higher capacity of oxygen acquisition. Additionally, we found more NECs in Pachón cavefish compared to both surface fish and Tinaja cavefish, suggesting certain selective pressures may be cave-specific. Collectively, this work provides evidence that cavefish have adapted to low oxygen conditions via alterations to gill morphology and oxygen sensing, and informs evolutionary mechanisms of rapid adaptation to dramatic, chronic hypoxia.
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Affiliation(s)
- Tyler E Boggs
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
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Choy S, Thakur S, Polyakov E, Abdelaziz J, Lloyd E, Enriquez M, Jayan N, Fily Y, McGaugh S, Keene AC, Kowalko JE. Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599419. [PMID: 38948816 PMCID: PMC11212897 DOI: 10.1101/2024.06.17.599419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Understanding the phenotypic consequences of naturally occurring genetic changes, as well as their impact on fitness, is fundamental to understanding how organisms adapt to an environment. This is critical when genetic variants have pleiotropic effects, as determining how each phenotype impacted by a gene contributes to fitness is essential to understand how and why traits have evolved. A striking example of a pleiotropic gene contributing to trait evolution is the oca2 gene, coding mutations in which underlie albinism and reductions of sleep in the blind Mexican cavefish, Astyanax mexicanus. Here, we characterize the effects of mutations in the oca2 gene on larval prey capture. We find that when conspecific surface fish with engineered mutations in the oca2 allele are hunting, they use cave-like, wide angle strikes to capture prey. However, unlike cavefish or surface fish in the dark, which rely on lateral line mediated hunting, oca2 mutant surface fish use vision when striking at prey from wide angles. Finally, we find that while oca2 mutant surface fish do not outcompete pigmented surface siblings in the dark, pigmented fish outcompete albino fish in the light. This raises the possibility that albinism is detrimental to larval feeding in a surface-like lighted environment, but does not have negative consequences for fish in cave-like, dark environments. Together, these results demonstrate that oca2 plays a role in larval feeding behavior in A. mexicanus. Further, they expand our understanding of the pleiotropic phenotypic consequences of oca2 in cavefish evolution.
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Affiliation(s)
- Stefan Choy
- Department of Biological Sciences, Lehigh University, Bethlehem, PA
| | - Sunishka Thakur
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Ellen Polyakov
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL
| | - Jennah Abdelaziz
- Department of Biological Sciences, Lehigh University, Bethlehem, PA
| | | | - Maya Enriquez
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Nikita Jayan
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL
| | - Yaouen Fily
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Alex C Keene
- Department of Biology, Texas A&M, College Station, TX
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Pozo-Morales M, Cobham AE, Centola C, McKinney MC, Liu P, Perazzolo C, Lefort A, Libert F, Bai H, Rohner N, Singh SP. Starvation-resistant cavefish reveal conserved mechanisms of starvation-induced hepatic lipotoxicity. Life Sci Alliance 2024; 7:e202302458. [PMID: 38467419 PMCID: PMC10927358 DOI: 10.26508/lsa.202302458] [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: 10/26/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Starvation causes the accumulation of lipid droplets in the liver, a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding, hepatic lipid accumulation (steatosis) during undernourishment can lead to lipotoxicity and atrophy of the liver. Here, we found that although surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation, the starvation-resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover, cavefish are resistant to liver atrophy during starvation, providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish, surface fish, and cavefish, we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Furthermore, down-regulation of FATP2 in Drosophila larvae inhibits the development of starvation-induced steatosis, suggesting the evolutionarily conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall, our study identifies a conserved, druggable target to protect the liver from atrophy during starvation.
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Affiliation(s)
- Macarena Pozo-Morales
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ansa E Cobham
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Cielo Centola
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Peiduo Liu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Camille Perazzolo
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anne Lefort
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Frédérick Libert
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sumeet Pal Singh
- https://ror.org/01r9htc13 IRIBHM, Université Libre de Bruxelles (ULB), Brussels, Belgium
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Pokrovac I, Rohner N, Pezer Ž. The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization. Mol Ecol 2024; 33:e17339. [PMID: 38556927 DOI: 10.1111/mec.17339] [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: 01/09/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.
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Affiliation(s)
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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Cobham AE, Rohner N. Unraveling stress resilience: Insights from adaptations to extreme environments by Astyanax mexicanus cavefish. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:178-188. [PMID: 38247307 DOI: 10.1002/jez.b.23238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/26/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Extreme environmental conditions have profound impacts on shaping the evolutionary trajectory of organisms. Exposure to these conditions elicits stress responses, that can trigger phenotypic changes in novel directions. The Mexican Tetra, Astyanax mexicanus, is an excellent model for understanding evolutionary mechanisms in response to extreme or new environments. This fish species consists of two morphs; the classical surface-dwelling fish and the blind cave-dwellers that inhabit dark and biodiversity-reduced ecosystems. In this review, we explore the specific stressors present in cave environments and examine the diverse adaptive strategies employed by cave populations to not only survive but thrive as successful colonizers. By analyzing the evolutionary responses of A. mexicanus, we gain valuable insights into the genetic, physiological, and behavioral adaptations that enable organisms to flourish under challenging environmental conditions.
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Affiliation(s)
- Ansa E Cobham
- Stowers Institute for Medical Research, Missouri, Kansas City, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Missouri, Kansas City, USA
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, Missouri, USA
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Biswas T, Rajendran N, Hassan H, Li H, Zhao C, Rohner N. 3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:301-312. [PMID: 38192038 PMCID: PMC11060904 DOI: 10.1002/jez.b.23236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/26/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024]
Abstract
In vitro assays are crucial tools for gaining detailed insights into various biological processes, including metabolism. Cave morphs of the river-dwelling fish species, Astyanax mexicanus, have adapted their metabolism allowing them to thrive in the biodiversity-deprived and nutrient-limited environment of caves. Liver-derived cells from the cave and river morphs of A. mexicanus have proven to be excellent in vitro resources to better understand the unique metabolism of these fish. However, the current 2D cultures have not fully captured the complex metabolic profile of the Astyanax liver. It is known that 3D culturing can modulate the transcriptomic state of cells when compared to its 2D monolayer culture. Therefore, to broaden the possibilities of the in vitro system by modeling a wider gamut of metabolic pathways, we cultured the liver-derived Astyanax cells of both surface and cavefish into 3D spheroids. We successfully established 3D cultures at various cell seeding densities for several weeks and characterized the resultant transcriptomic and metabolic variations. We found that the 3D cultured Astyanax cells exhibit an altered transcriptomic profile and consequently represent a wider range of metabolic pathways, including cell cycle changes and antioxidant activities, associated with liver functioning as compared to its monolayer culture. Enzymatic assay measuring antioxidants in 2D culture and 3D spheroids also revealed enhanced antioxidative capacity of 3D cultured spheroids, in line with the differential gene expression data. Additionally, the spheroids also exhibited surface and cave-specific metabolic signatures, making it a suitable system for evolutionary studies associated with cave adaptation. Notably, cavefish derived spheroids enriched for genes responding to xenobiotic stimulus, while the ones from surface enriched for immune response, both of which resonated with known physiologically adaptations associated with each morph. Taken together, the liver-derived spheroids prove to be a promising in vitro model for widening our understanding of metabolism in A. mexicanus and of vertebrates in general.
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Affiliation(s)
- Tathagata Biswas
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Naresh Rajendran
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Huzaifa Hassan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, KS 66103, USA
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13
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Riddle MR, Nguyen NK, Nave M, Peuß R, Maldonado E, Rohner N, Tabin CJ. Host evolution shapes gut microbiome composition in Astyanax mexicanus. Ecol Evol 2024; 14:e11192. [PMID: 38571802 PMCID: PMC10985381 DOI: 10.1002/ece3.11192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
The ecological and genetic changes that underlie the evolution of host-microbe interactions remain elusive, primarily due to challenges in disentangling the variables that alter microbiome composition. To understand the impact of host habitat, host genetics, and evolutionary history on microbial community structure, we examined gut microbiomes of river- and three cave-adapted morphotypes of the Mexican tetra, Astyanax mexicanus, in their natural environments and under controlled laboratory conditions. Field-collected samples were dominated by very few taxa and showed considerable interindividual variation. We found that lab-reared fish exhibited increased microbiome richness and distinct composition compared to their wild counterparts, underscoring the significant influence of habitat. Most notably, however, we found that morphotypes reared on the same diet throughout life developed distinct microbiomes suggesting that genetic loci resulting from cavefish evolution shape microbiome composition. We observed stable differences in Fusobacteriota abundance between morphotypes and demonstrated that this could be used as a trait for quantitative trait loci mapping to uncover the genetic basis of microbial community structure.
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Affiliation(s)
| | | | | | - Robert Peuß
- Institute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
| | - Ernesto Maldonado
- Institute of Marine Sciences and LimnologyUniversidad Nacional Autonoma de Mexico, UNAMPuerto MorelosMexico
| | - Nicolas Rohner
- Stowers Institute for Medical ResearchKansas CityMissouriUSA
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14
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Huang L, Deng X, Yang X, Tang Z, Fan S, Zhou Z, Tao M, Liu S. Cloning, distribution, and effects of growth regulation of MC3R and MC4R in red crucian carp ( Carassius auratus red var.). Front Endocrinol (Lausanne) 2024; 14:1310000. [PMID: 38322156 PMCID: PMC10846643 DOI: 10.3389/fendo.2023.1310000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/27/2023] [Indexed: 02/08/2024] Open
Abstract
Background Melanocortin-3 and -4 receptors (MC3R and MC4R), G protein-coupled receptors, play vital roles in the regulation of energy homeostasis. To understand the functions of mc3r and mc4r in the energy homeostasis of red crucian carp (Carassius auratus red var., RCC), we cloned mc3r and mc4r, analyzed the tissue expression and localization of the genes, and investigated the effects of knockout of mc3r (mc3r +/-) and mc4r (mc4r +/-) in RCC. Results The full-length cDNAs of RCC mc3r and mc4r were 1459 base pairs (bp) and 1894 bp, respectively. qRT-PCR indicated that mc3r and mc4r were profusely expressed in the brain, but lower expressed in the periphery tissues. ISH revealed that mc3r and mc4r were located in NPP, NPO, NAPv, NSC, NAT, NRL, NLTl, and NLTp of the brain, suggesting that mc3r and mc4r might regulate many physiological and behavioral aspects in RCC. To further verify the roles of mc3r and mc4r in energy homeostasis, the mc3r+/- and mc4r+/- fish were obtained by the CRISPR/Cas9 system. The average body weights, total lengths, body depths, and food intake of mc4r+/- fish were significantly higher than those of mc3r+/- and the normal wild-type (WT) fish, but there was no difference between the mc3r+/- and WT fish, indicating that the RCC phenotype and food intake were mainly influenced by mc4r but not mc3r. Interestingly, mc4r+/- fish displayed more visceral fat mass than mc3r+/- and WT fish, and mc3r+/- fish also exhibited slightly more visceral fat mass compared to WT. RNA-seq of the liver and muscle revealed that a large number of differentially expressed genes (DEGs) differed in WT vs. mc3r+/-, WT vs. mc4r+/-, and mc3r+/- vs. mc4r+/-, mainly related to lipid, glucose, and energy metabolism. The KEGG enrichment analysis revealed that DEGs were mainly enriched in pathways such as steroid biosynthesis, fatty acid metabolism, fatty acid biosynthesis, glycolysis/gluconeogenesis, wnt signaling pathway, PPAR signaling pathway, and MAPK signaling pathway, thereby affecting lipid accumulation and growth. Conclusion In conclusion, these results will assist in the further investigation of the molecular mechanisms in which MC3R and MC4R were involved in the regulation of energy homeostasis in fish.
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Affiliation(s)
| | | | | | | | | | | | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
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15
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Pozo-Morales M, Cobham AE, Centola C, McKinney MC, Liu P, Perazzolo C, Lefort A, Libert F, Bai H, Rohner N, Singh SP. Starvation resistant cavefish reveal conserved mechanisms of starvation-induced hepatic lipotoxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574986. [PMID: 38260657 PMCID: PMC10802416 DOI: 10.1101/2024.01.10.574986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Starvation causes the accumulation of lipid droplets in the liver, a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding, hepatic lipid accumulation (steatosis) during undernourishment can lead to lipotoxicity and atrophy of the liver. Here, we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation, the starvation-resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover, cavefish are resistant to liver atrophy during starvation, providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish, surface fish, and cavefish, we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further, down-regulation of FATP2 in drosophila larvae inhibits the development of starvation-induced steatosis, suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall, our study identifies a conserved, druggable target to protect the liver from atrophy during starvation.
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Affiliation(s)
- Macarena Pozo-Morales
- IRIBHM, Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Ansa E Cobham
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Cielo Centola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Peiduo Liu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Camille Perazzolo
- IRIBHM, Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Anne Lefort
- IRIBHM, Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Frédérick Libert
- IRIBHM, Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Sumeet Pal Singh
- IRIBHM, Université Libre de Bruxelles (ULB), Route de Lennik 808, 1070 Brussels, Belgium
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16
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Zhu W, Chang L, Shi S, Lu N, Du S, Li J, Jiang J, Wang B. Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity. THE ISME JOURNAL 2024; 18:wrad009. [PMID: 38365235 PMCID: PMC10811740 DOI: 10.1093/ismejo/wrad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 02/18/2024]
Abstract
Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.
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Affiliation(s)
- Wei Zhu
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Liming Chang
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Shengchao Shi
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Ningning Lu
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Simeng Du
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Jiatang Li
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Jianping Jiang
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
| | - Bin Wang
- Chinese Academy of Sciences Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
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17
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Swaminathan A, Xia F, Rohner N. From darkness to discovery: evolutionary, adaptive, and translational genetic insights from cavefish. Trends Genet 2024; 40:24-38. [PMID: 38707509 PMCID: PMC11068324 DOI: 10.1016/j.tig.2023.10.002] [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] [Indexed: 05/07/2024]
Abstract
How genotype determines phenotype is a well-explored question, but genotype-environment interactions and their heritable impact on phenotype over the course of evolution are not as thoroughly investigated. The fish Astyanax mexicanus, consisting of surface and cave ecotypes, is an ideal emerging model to study the genetic basis of adaptation to new environments. This model has permitted quantitative trait locus mapping and whole-genome comparisons to identify the genetic bases of traits such as albinism and insulin resistance and has helped to better understand fundamental evolutionary mechanisms. In this review, we summarize recent advances in A. mexicanus genetics and discuss their broader impact on the fields of adaptation and evolutionary genetics.
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Affiliation(s)
| | - Fanning Xia
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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18
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Schartl M, Lu Y. Validity of Xiphophorus fish as models for human disease. Dis Model Mech 2024; 17:dmm050382. [PMID: 38299666 PMCID: PMC10855230 DOI: 10.1242/dmm.050382] [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] [Indexed: 02/02/2024] Open
Abstract
Platyfish and swordtails of the genus Xiphophorus provide a well-established model for melanoma research and have become well known for this feature. Recently, modelling approaches for other human diseases in Xiphophorus have been developed or are emerging. This Review provides a comprehensive summary of these models and discusses how findings from basic biological and molecular studies and their translation to medical research demonstrate that Xiphophorus models have face, construct and predictive validity for studying a broad array of human diseases. These models can thus improve our understanding of disease mechanisms to benefit patients.
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Affiliation(s)
- Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
- Developmental Biochemistry, Theodor-Boveri Institute, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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19
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Xu DM, He S, Liang XF, Wu JQ, Wang QL, Jia XD. Regulatory effect of NK homeobox 1 (NKX2.1) on melanocortin 4 receptor (Mc4r) promoter in Mandarin fish. J Cell Physiol 2023; 238:2867-2878. [PMID: 37850660 DOI: 10.1002/jcp.31139] [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: 06/29/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
The melanocortin 4 receptor (MC4R) is a G protein-coupled transporter that mediates the regulation of thyroid hormones and leptin on energy balance and food intake. However, the mechanisms of transcriptional regulation of Mc4r by thyroid hormone and leptin in fish have been rarely reported. The messenger RNA expression of Mc4r gene was significantly higher in brain than those in other tissues of mandarin fish. We analyzed the structure and function of a 2029 bp sequence of Mc4r promoter. Meanwhile, overexpression of NKX2.1 and incubation with leptin significantly increased Mc4r promoter activity, but triiodothyronine showed the opposite effect. In addition, mutations in the NKX2.1 binding site abolished not only the activation of Mc4r promoter activity by leptin but also the inhibitory effect of thyroid hormones on Mc4r promoter activity. In summary, these results suggested that thyroid hormones and leptin might regulate the transcriptional expression of Mc4r through NKX2.1.
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Affiliation(s)
- Di-Mei Xu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Shan He
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Jia-Qi Wu
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Qiu-Ling Wang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Xiao-Dan Jia
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University, Wuhan, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
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20
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Warren WC, Rice ES, Maggs X, Roback E, Keene A, Martin F, Ogeh D, Haggerty L, Carroll RA, McGaugh S, Rohner N. Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567450. [PMID: 38014157 PMCID: PMC10680795 DOI: 10.1101/2023.11.16.567450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
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Affiliation(s)
- Wesley C. Warren
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO
| | - Edward S. Rice
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
| | - X Maggs
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
| | - Emma Roback
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN
| | - Alex Keene
- Department of Biology, Texas AM University, College Station, TX
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Denye Ogeh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rachel A. Carroll
- Department of Animal Sciences, Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO
| | - Suzanne McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, KU Medical Center, Kansas City, KS
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21
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Liu R, Friedrich M, Hemmen K, Jansen K, Adolfi MC, Schartl M, Heinze KG. Dimerization of melanocortin 4 receptor controls puberty onset and body size polymorphism. Front Endocrinol (Lausanne) 2023; 14:1267590. [PMID: 38027153 PMCID: PMC10667928 DOI: 10.3389/fendo.2023.1267590] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Xiphophorus fish exhibit a clear phenotypic polymorphism in puberty onset and reproductive strategies of males. In X. nigrensis and X. multilineatus, puberty onset is genetically determined and linked to a melanocortin 4 receptor (Mc4r) polymorphism of wild-type and mutant alleles on the sex chromosomes. We hypothesized that Mc4r mutant alleles act on wild-type alleles by a dominant negative effect through receptor dimerization, leading to differential intracellular signaling and effector gene activation. Depending on signaling strength, the onset of puberty either occurs early or is delayed. Here, we show by Förster Resonance Energy Transfer (FRET) that wild-type Xiphophorus Mc4r monomers can form homodimers, but also heterodimers with mutant receptors resulting in compromised signaling which explains the reduced Mc4r signaling in large males. Thus, hetero- vs. homo- dimerization seems to be the key molecular mechanism for the polymorphism in puberty onset and body size in male fish.
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Affiliation(s)
- Ruiqi Liu
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
- Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Mike Friedrich
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Katherina Hemmen
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Kerstin Jansen
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Mateus C. Adolfi
- Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States
| | - Katrin G. Heinze
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
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22
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Iwashita M, Tran A, Garcia M, Cashon J, Burbano D, Salgado V, Hasegawa M, Balmilero-Unciano R, Politan K, Wong M, Lee RWY, Yoshizawa M. Metabolic shift toward ketosis in asocial cavefish increases social-like affinity. BMC Biol 2023; 21:219. [PMID: 37840141 PMCID: PMC10577988 DOI: 10.1186/s12915-023-01725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023] Open
Abstract
BACKGROUND Social affinity and collective behavior are nearly ubiquitous in the animal kingdom, but many lineages feature evolutionarily asocial species. These solitary species may have evolved to conserve energy in food-sparse environments. However, the mechanism by which metabolic shifts regulate social affinity is not well investigated. RESULTS In this study, we used the Mexican tetra (Astyanax mexicanus), which features riverine sighted surface (surface fish) and cave-dwelling populations (cavefish), to address the impact of metabolic shifts on asociality and other cave-associated behaviors in cavefish, including repetitive turning, sleeplessness, swimming longer distances, and enhanced foraging behavior. After 1 month of ketosis-inducing ketogenic diet feeding, asocial cavefish exhibited significantly higher social affinity, whereas social affinity regressed in cavefish fed the standard diet. The ketogenic diet also reduced repetitive turning and swimming in cavefish. No major behavioral shifts were found regarding sleeplessness and foraging behavior, suggesting that other evolved behaviors are not largely regulated by ketosis. We further examined the effects of the ketogenic diet via supplementation with exogenous ketone bodies, revealing that ketone bodies are pivotal molecules positively associated with social affinity. CONCLUSIONS Our study indicated that fish that evolved to be asocial remain capable of exhibiting social affinity under ketosis, possibly linking the seasonal food availability and sociality.
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Affiliation(s)
- Motoko Iwashita
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Amity Tran
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Marianne Garcia
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Jia Cashon
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Devanne Burbano
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Vanessa Salgado
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Malia Hasegawa
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | | | - Kaylah Politan
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA
| | - Miki Wong
- Nā Pu'uwai Native Hawaiian Healthcare System, Kaunakakai, HI, 96748, USA
- Nutrition Services Department, Shriners Hospitals for Children, Honolulu, HI, 96826, USA
| | - Ryan W Y Lee
- Medical Staff Department, Shriners Hospitals for Children, Honolulu, HI, 96826, USA
| | - Masato Yoshizawa
- School of Life Sciences, University of Hawai'I at Mānoa, Honolulu, HI, 96822, USA.
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23
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Ponnimbaduge Perera P, Perez Guerra D, Riddle MR. The Mexican Tetra, Astyanax mexicanus, as a Model System in Cell and Developmental Biology. Annu Rev Cell Dev Biol 2023; 39:23-44. [PMID: 37437210 DOI: 10.1146/annurev-cellbio-012023-014003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Our understanding of cell and developmental biology has been greatly aided by a focus on a small number of model organisms. However, we are now in an era where techniques to investigate gene function can be applied across phyla, allowing scientists to explore the diversity and flexibility of developmental mechanisms and gain a deeper understanding of life. Researchers comparing the eyeless cave-adapted Mexican tetra, Astyanax mexicanus, with its river-dwelling counterpart are revealing how the development of the eyes, pigment, brain, cranium, blood, and digestive system evolves as animals adapt to new environments. Breakthroughs in our understanding of the genetic and developmental basis of regressive and constructive trait evolution have come from A. mexicanus research. They include understanding the types of mutations that alter traits, which cellular and developmental processes they affect, and how they lead to pleiotropy. We review recent progress in the field and highlight areas for future investigations that include evolution of sex differentiation, neural crest development, and metabolic regulation of embryogenesis.
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Affiliation(s)
| | | | - Misty R Riddle
- Department of Biology, University of Nevada, Reno, Nevada, USA;
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24
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Powers AK, Hyacinthe C, Riddle MR, Kim YK, Amaismeier A, Thiel K, Martineau B, Ferrante E, Moran RL, McGaugh SE, Boggs TE, Gross JB, Tabin CJ. Genetic mapping of craniofacial traits in the Mexican tetra reveals loci associated with bite differences between cave and surface fish. BMC Ecol Evol 2023; 23:41. [PMID: 37626324 PMCID: PMC10463419 DOI: 10.1186/s12862-023-02149-3] [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: 01/04/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The Mexican tetra, Astyanax mexicanus, includes interfertile surface-dwelling and cave-dwelling morphs, enabling powerful studies aimed at uncovering genes involved in the evolution of cave-associated traits. Compared to surface fish, cavefish harbor several extreme traits within their skull, such as a protruding lower jaw, a wider gape, and an increase in tooth number. These features are highly variable between individual cavefish and even across different cavefish populations. RESULTS To investigate these traits, we created a novel feeding behavior assay wherein bite impressions could be obtained. We determined that fish with an underbite leave larger bite impressions with an increase in the number of tooth marks. Capitalizing on the ability to produce hybrids from surface and cavefish crosses, we investigated genes underlying these segregating orofacial traits by performing Quantitative Trait Loci (QTL) analysis with F2 hybrids. We discovered significant QTL for bite (underbite vs. overbite) that mapped to a single region of the Astyanax genome. Within this genomic region, multiple genes exhibit coding region mutations, some with known roles in bone development. Further, we determined that there is evidence that this genomic region is under natural selection. CONCLUSIONS This work highlights cavefish as a valuable genetic model for orofacial patterning and will provide insight into the genetic regulators of jaw and tooth development.
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Affiliation(s)
- Amanda K Powers
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Carole Hyacinthe
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Misty R Riddle
- Department of Biology, University of Nevada, Reno, 1664 N. Virginia St., Reno, NV, 89557, USA
| | - Young Kwang Kim
- Harvard School of Dental Medicine, 188 Longwood Ave., Boston, MA, 02115, USA
| | - Alleigh Amaismeier
- Department of Biology, Xavier University, 3800 Victory Pkwy., Cincinnati, OH, 45207, USA
| | - Kathryn Thiel
- Department of Biology, Xavier University, 3800 Victory Pkwy., Cincinnati, OH, 45207, USA
| | - Brian Martineau
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Emma Ferrante
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Rachel L Moran
- Department of Biology, Texas A & M University, 100 Butler Hall, College Station, TX, 77843, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota, 1500 Gortner Ave., Saint Paul, MN, 55108, USA
| | - Tyler E Boggs
- Department of Biological Sciences, University of Cincinnati, 312 College Dr., Cincinnati, OH, 45221, USA
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, 312 College Dr., Cincinnati, OH, 45221, USA
| | - Clifford J Tabin
- Department of Genetics, Blavatnik Institute at Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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25
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Liu Y, Liu T, Wang Y, Liu J, Liu B, Gong L, Lü Z, Liu L. Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae). Int J Mol Sci 2023; 24:12892. [PMID: 37629073 PMCID: PMC10454203 DOI: 10.3390/ijms241612892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts.
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Affiliation(s)
- Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China
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26
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Ji RL, Liu T, Hou ZS, Wen HS, Tao YX. Divergent Pharmacology and Biased Signaling of the Four Melanocortin-4 Receptor Isoforms in Rainbow Trout ( Oncorhynchus mykiss). Biomolecules 2023; 13:1248. [PMID: 37627313 PMCID: PMC10452266 DOI: 10.3390/biom13081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The melanocortin-4 receptor (MC4R) is essential for the modulation of energy balance and reproduction in both fish and mammals. Rainbow trout (Oncorhynchus mykiss) has been extensively studied in various fields and provides a unique opportunity to investigate divergent physiological roles of paralogues. Herein we identified four trout mc4r (mc4ra1, mc4ra2, mc4rb1, and mc4rb2) genes. Four trout Mc4rs (omMc4rs) were homologous to those of teleost and mammalian MC4Rs. Multiple sequence alignments, a phylogenetic tree, chromosomal synteny analyses, and pharmacological studies showed that trout mc4r genes may have undergone different evolutionary processes. All four trout Mc4rs bound to two peptide agonists and elevated intracellular cAMP levels dose-dependently. High basal cAMP levels were observed at two omMc4rs, which were decreased by Agouti-related peptide. Only omMc4rb2 was constitutively active in the ERK1/2 signaling pathway. Ipsen 5i, ML00253764, and MCL0020 were biased allosteric modulators of omMc4rb1 with selective activation upon ERK1/2 signaling. ML00253764 behaved as an allosteric agonist in Gs-cAMP signaling of omMc4rb2. This study will lay the foundation for future physiological studies of various mc4r paralogs and reveal the evolution of MC4R in vertebrates.
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Affiliation(s)
- Ren-Lei Ji
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (R.-L.J.); (T.L.)
| | - Ting Liu
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (R.-L.J.); (T.L.)
| | - Zhi-Shuai Hou
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (R.-L.J.); (T.L.)
| | - Hai-Shen Wen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266100, China;
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (R.-L.J.); (T.L.)
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27
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Batista da Silva I, Aciole Barbosa D, Kavalco KF, Nunes LR, Pasa R, Menegidio FB. Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae). Sci Rep 2023; 13:12051. [PMID: 37491348 PMCID: PMC10368750 DOI: 10.1038/s41598-023-34198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/25/2023] [Indexed: 07/27/2023] Open
Abstract
Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo's eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.
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Affiliation(s)
- Iuri Batista da Silva
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - David Aciole Barbosa
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - Luiz R Nunes
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | - Rubens Pasa
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil.
| | - Fabiano B Menegidio
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil.
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28
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Čupić M, Marčić Z, Lukić M, Gračan R, Bilandžija H. The first cavefish in the Dinaric Karst? Cave colonization made possible by phenotypic plasticity in Telestes karsticus. Zool Res 2023; 44:821-833. [PMID: 37464939 PMCID: PMC10415781 DOI: 10.24272/j.issn.2095-8137.2022.528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/30/2023] [Indexed: 07/20/2023] Open
Abstract
Cave animals are an excellent model system for studying adaptive evolution. At present, however, little is known about the mechanisms that enable surface colonizers to survive in the challenging environment of caves. One possibility is that these species have the necessary genetic background to respond with plastic changes to the pressures of underground habitats. To gain insight into this process, we conducted a comparative study with the fish species Telestes karsticus, which occurs in a hydrological system consisting of an interconnected stream and a cave. Results showed that T. karsticus resided year-round and spawned in Sušik cave, making it the first known cavefish in the Dinaric Karst. Cave and surface populations differed in morphological and physiological characteristics, as well as in patterns of gene expression without any evidence of genetic divergence. To test whether observed trait differences were plastic or genetic, we placed adult fish from both populations under light/dark or constant dark conditions. Common laboratory conditions erased all morphometric differences between the two morphs, suggesting phenotypic plasticity is driving the divergence of shape and size in wild fish. Lighter pigmentation and increased fat deposition exhibited by cave individuals were also observed in surface fish kept in the dark in the laboratory. Our study also revealed that specialized cave traits were not solely attributed to developmental plasticity, but also arose from adult responses, including acclimatization. Thus, we conclude that T. karsticus can adapt to cave conditions, with phenotypic plasticity playing an important role in the process of cave colonization.
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Affiliation(s)
- Mateo Čupić
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia
| | - Zoran Marčić
- Department of Biology, Faculty of Science, Zagreb 10000, Croatia
| | - Marko Lukić
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia
- Croatian Biospeleological Society, Zagreb 10000, Croatia
| | - Romana Gračan
- Department of Biology, Faculty of Science, Zagreb 10000, Croatia
| | - Helena Bilandžija
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10000, Croatia
- Croatian Biospeleological Society, Zagreb 10000, Croatia. E-mail:
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29
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Swanson NE, Gluesenkamp AG, Donny AE, Mcgaugh SE. Developmental environment contributes to rapid trait shifts among newly colonized subterranean habitats. Zool Res 2023; 44:808-820. [PMID: 37464938 PMCID: PMC10415762 DOI: 10.24272/j.issn.2095-8137.2022.488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
Recent colonization of extreme environments provides unique opportunities to study the early steps of adaptation and the potential for rapid convergent evolution. However, phenotypic shifts during recent colonization may also be due to plasticity in response to changes in the rearing environment. Here, we analyzed a suite of morphological and behavioral traits in paired surface, subterranean, and facultatively subterranean Mexican tetras ( Astyanax mexicanus) from recent introductions in two separate watersheds outside of their native range. We found a variety of phenotypic and behavioral shifts between subterranean and surface populations that are similar to those observed in relatively ancient populations in Mexico. Despite this rapid morphological divergence, we found that most of these trait differences were due to plasticity in response to rearing environments. While most trait assays in common-garden, lab-raised fish indicated that phenotypic shifts in wild fish were the result of plasticity, we also found evidence of genetic control in several traits present in subterranean populations. Interestingly, wall-following behavior, an important subterranean foraging behavior, was greater in lab-born subterranean fish than in lab-born surface fish, suggesting rapid divergence of this trait between subterranean and surface populations. Thus, this study sheds light on the early steps of subterranean evolution, identifies potential rapid behavioral evolution, and suggests that plasticity in traits involving exploratory behavior may facilitate subterranean colonization.
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Affiliation(s)
- Nathan E Swanson
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697-2525, USA. E-mail:
| | - Andrew G Gluesenkamp
- Center for Conservation and Research, San Antonio Zoo, San Antonio, Texas 78212, USA
| | - Alexandra E Donny
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Suzanne E Mcgaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA. E-mail:
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30
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Espinasa L, Diamant R, Vinepinsky E, Espinasa M. Evolutionary modifications of Astyanax larval prey capture (LPC) in a dark environment. Zool Res 2023; 44:750-760. [PMID: 37464932 PMCID: PMC10415770 DOI: 10.24272/j.issn.2095-8137.2022.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Feeding strategies of an organism depend on the multimodal sensory processing that most efficiently integrates available visual, chemosensory, and/or mechanoreceptive cues as part of their environmental adaptation. The blind cavefish morph of Astyanax mexicanus has developed sensory-dependent behaviors to find food more efficiently than their eyed, surface-morph counterparts while in darkness. In the absence of light, adult cavefish have evolved enhanced behaviors, such as vibration attraction behavior (VAB), and changes in feeding angle. Here, we identified evolved differences in cavefish larval prey capture (LPC) behavior. In the dark, LPC is more efficient in cavefish than in surface fish. Furthermore, different cave populations express laterality in their LPC and strike towards prey preferentially located on their left or right sides. This suggests the occurrence, to some extent, of divergent LPC evolution among cave populations. While LPC can be triggered exclusively by a vibration stimulus in both surface and cavefish, we provide evidence that LPC is, at least partially, a multimodal sensory process different from adult VAB. We also found that a lack of food may exacerbate the laterality of LPC. Thus, we proposed a mathematical model for explaining laterality based on a balance between: (1) enlarged range of foraging field (behavioral or perceptive) due to asymmetry, (2) food abundance, and (3) disadvantages caused by laterality (unequal lateral hydrodynamic resistance when swimming, allocation of resources for the brain and receptors, and predator escape).
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Affiliation(s)
- Luis Espinasa
- School of Science, Marist College, Poughkeepsie, NY 12601, USA. E-mail:
| | - Ruth Diamant
- Depto. de Física, Universidad Autónoma Metropolitana - Iztapalapa, Ciudad de México C.P. 09310, México
| | - Ehud Vinepinsky
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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31
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Borowsky R. Selection Maintains the Phenotypic Divergence of Cave and Surface Fish. Am Nat 2023; 202:55-63. [PMID: 37384766 DOI: 10.1086/724661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractGenetic divergence in the presence of gene flow has been well documented, but there is little information on the specific factors maintaining divergence. The present study investigates this in the Mexican tetra (Astyanax mexicanus), an excellent model for studying this question because surface and cave populations differ markedly in phenotype and genotype but are interfertile. Previous population studies documented significant gene flow among cave and surface populations, but they focused on analyses of neutral markers whose evolutionary dynamics likely differ from those of genes involved in cave adaptation. The present study advances our understanding of this question by focusing specifically on the genetics responsible for eye and pigmentation reduction, signature traits of cave populations. Direct observations of two cave populations over the course of 63 years verify that surface fish frequently move into the caves and even hybridize with the cave fish. Importantly, however, historical records show that surface alleles for pigmentation and eye size do not persist but are rapidly eliminated from the cave gene pool. It has been argued that regression of eyes and pigmentation was driven by drift, but the results of this study suggest that strong selection actively eliminates surface alleles from the cave populations.
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32
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Rohner N. The cavefish Astyanax mexicanus. Nat Methods 2023; 20:948-950. [PMID: 37434002 DOI: 10.1038/s41592-023-01916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
- Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA.
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33
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Biswas T, Rajendran N, Hassan H, Zhao C, Rohner N. 3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544423. [PMID: 37333136 PMCID: PMC10274882 DOI: 10.1101/2023.06.09.544423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In vitro assays are crucial tools for gaining detailed insights into various biological processes, including metabolism. Cave morphs of the river-dwelling fish species, Astyanax mexicanus, have adapted their metabolism allowing them to thrive in the biodiversity-deprived and nutrient-limited environment of caves. Liver-derived cells from the cave and river morphs of Astyanax mexicanus have proven to be excellent in vitro resources to better understand the unique metabolism of these fish. However, the current 2D cultures have not fully captured the complex metabolic profile of the Astyanax liver. It is known that 3D culturing can modulate the transcriptomic state of cells when compared to its 2D monolayer culture. Therefore, in order to broaden the possibilities of the in vitro system by modeling a wider gamut of metabolic pathways, we cultured the liver-derived Astyanax cells of both surface and cavefish into 3D spheroids. We successfully established 3D cultures at various cell seeding densities for several weeks and characterized the resultant transcriptomic and metabolic variations. We found that the 3D cultured Astyanax cells represent a wider range of metabolic pathways, including cell cycle changes and antioxidant activities, associated with liver functioning as compared to its monolayer culture. Additionally, the spheroids also exhibited surface and cave-specific metabolic signatures, making it a suitable system for evolutionary studies associated with cave adaptation. Taken together, the liver-derived spheroids prove to be a promising in vitro model for widening our understanding of metabolism in Astyanax mexicanus and of vertebrates in general.
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Affiliation(s)
- Tathagata Biswas
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Naresh Rajendran
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Huzaifa Hassan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, KS 66103, USA
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Rajendran N, Deng F, Wang Y, Kenzior O, Krishnan J, Biswas T, Parmely T, Rohner N, Zhao C. Establishment, Long-Term Maintenance, and Characterization of Primary Liver Cells from Astyanax mexicanus. Curr Protoc 2023; 3:e736. [PMID: 37068186 DOI: 10.1002/cpz1.736] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The tetra fish species Astyanax mexicanus comprises two morphotypes: cavefish that live in caves and surface fish that inhabit rivers and lakes. Because cavefish have adapted to the nutrient-poor conditions in their habitat whereas the surface fish populations can be used as a proxy for the ancestral condition, this species has become a powerful model system for understanding genetic variation underlying metabolic adaptation. The liver plays a critical role in glucose and fat metabolism in the body and hence is an important tissue for studying altered metabolism in health and disease. Cavefish morphs of A. mexicanus have been shown to develop fatty livers and exhibit massive differences in gene expression and chromatin architecture. Primary cell lines from various tissues have become invaluable tools for biochemical, toxicology, and cell biology experiments, as well as genetic and genomic analyses. To enhance the utility of the model system by enabling an expanded set of biochemical and in vitro experiments, we developed protocols for the isolation and maintenance of primary liver cells from A. mexicanus surface fish and cavefish. We also describe methods that can be used for primary cell characterization, including cloning, characterization of cell growth pattern, and lentivirus transduction. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Primary culture of liver cells Support Protocol 1: Maintenance of A. mexicanus primary liver cells Support Protocol 2: Banking of A. mexicanus primary liver cells Support Protocol 3: Recovery of A. mexicanus primary liver cells Support Protocol 4: Primary liver cell cloning Support Protocol 5: Characterization of A. mexicanus primary liver cell growth pattern Basic Protocol 2: Lentiviral transduction of A. mexicanus primary liver cells.
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Affiliation(s)
| | - Fengyan Deng
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Yan Wang
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Olga Kenzior
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Jaya Krishnan
- Stowers Institute for Medical Research, Kansas City, Missouri
- Present address: Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Tari Parmely
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri
- Department of Cell Biology & Physiology, University of Kansas Medical Center, Kansas City, Kansas
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, Missouri
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Rodas LR, Sarbu SM, Bancila R, Price D, Fišer Ž, Protas M. Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod, Asellus aquaticus. Evol Dev 2023; 25:137-152. [PMID: 36755467 DOI: 10.1111/ede.12428] [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: 09/27/2022] [Revised: 12/14/2022] [Accepted: 01/07/2023] [Indexed: 02/10/2023]
Abstract
Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F2 crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.
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Affiliation(s)
- Lizet R Rodas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Serban M Sarbu
- Department of Biospeleology and Karst Edaphobiology, "Emil Racoviţă" Institute of Speleology of Romanian Academy of Sciences, Bucharest, Romania.,Department of Biological Sciences, California State University, Chico, California, USA
| | - Raluca Bancila
- Department of Biospeleology and Karst Edaphobiology, "Emil Racoviţă" Institute of Speleology of Romanian Academy of Sciences, Bucharest, Romania
| | - Devon Price
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
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36
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Yu HX, Li Y, Zhong DB, Ren X, Mo HL, Jiang ZB, Yu JJ, Xiong DM, Liu HX, Wang LX. The interaction of MC3R and MC4R with MRAP2a in rainbow trout (Oncorhynchus mykiss). FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:61-74. [PMID: 36525144 DOI: 10.1007/s10695-022-01159-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Melanocortin 3 and 4 receptors are two important neural G protein-coupled receptors that regulate energy homeostasis in vertebrates. Melanocortin receptor accessory protein 2 (MRAP2) is also involved in the regulation of food intake and body weight as a variable regulator of melanocortin receptors. Rainbow trout (Oncorhynchus mykiss) is a valuable cold-water fish cultured worldwide. In the rainbow trout model, we cloned and identified mrap2a, a paralog of mrap2. Rainbow trout mrap2a consisted of a 690 bp ORF and was expected to encode a putative protein of 229 amino acids. The qPCR results showed that rainbow trout mrap2a was expressed at high levels in brain tissue similar to mc3r and mc4r. In addition, co-immunoprecipitation verified that MRAP2a interacts with MC3R and MC4R in vitro and that MRAP2a is involved in and regulates the constitutive activity and signaling of MC3R and MC4R. MRAP2a reduced constitutive and agonist-stimulated cAMP levels of MC3R; furthermore, MRAP2a increased constitutive ERK1/2 activation but reduced ligand-induced stimulation at high levels of expression. For MC4R, MRAP2a showed decreased cAMP basal activity but increased agonist-stimulated cAMP signaling and increased ACTH ligand sensitivity. However, MRAP2a failed to affect MC4R constitutive activity and agonist-induced ERK1/2 signaling. Undoubtedly, our study will have great significance for revealing the conserved role of MC4R and MC3R signaling in teleost fish, especially in cold-water fish growth and energy homeostasis.
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Affiliation(s)
- Hui-Xia Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - De-Bin Zhong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Ren
- Meixian Aquaculture Farm of Shitouhe Reservoir Administration, Xianyang, 712000, Shaanxi, China
| | - Hao-Lin Mo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ze-Bin Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jia-Jia Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dong-Mei Xiong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hai-Xia Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Li-Xin Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Olsen L, Levy M, Medley JK, Hassan H, Miller B, Alexander R, Wilcock E, Yi K, Florens L, Weaver K, McKinney SA, Peuß R, Persons J, Kenzior A, Maldonado E, Delventhal K, Gluesenkamp A, Mager E, Coughlin D, Rohner N. Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility. Proc Natl Acad Sci U S A 2023; 120:e2204427120. [PMID: 36693105 PMCID: PMC9945943 DOI: 10.1073/pnas.2204427120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 11/15/2022] [Indexed: 01/25/2023] Open
Abstract
Physical inactivity is a scourge to human health, promoting metabolic disease and muscle wasting. Interestingly, multiple ecological niches have relaxed investment into physical activity, providing an evolutionary perspective into the effect of adaptive physical inactivity on tissue homeostasis. One such example, the Mexican cavefish Astyanax mexicanus, has lost moderate-to-vigorous activity following cave colonization, reaching basal swim speeds ~3.7-fold slower than their river-dwelling counterpart. This change in behavior is accompanied by a marked shift in body composition, decreasing total muscle mass and increasing fat mass. This shift persisted at the single muscle fiber level via increased lipid and sugar accumulation at the expense of myofibrillar volume. Transcriptomic analysis of laboratory-reared and wild-caught cavefish indicated that this shift is driven by increased expression of pparγ-the master regulator of adipogenesis-with a simultaneous decrease in fast myosin heavy chain expression. Ex vivo and in vivo analysis confirmed that these investment strategies come with a functional trade-off, decreasing cavefish muscle fiber shortening velocity, time to maximal force, and ultimately maximal swimming speed. Despite this, cavefish displayed a striking degree of muscular endurance, reaching maximal swim speeds ~3.5-fold faster than their basal swim speeds. Multi-omic analysis suggested metabolic reprogramming, specifically phosphorylation of Pgm1-Threonine 19, as a key component enhancing cavefish glycogen metabolism and sustained muscle contraction. Collectively, we reveal broad skeletal muscle changes following cave colonization, displaying an adaptive skeletal muscle phenotype reminiscent to mammalian disuse and high-fat models while simultaneously maintaining a unique capacity for sustained muscle contraction via enhanced glycogen metabolism.
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Affiliation(s)
- Luke Olsen
- Stowers Institute for Medical Research, Kansas City, MO64110
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS66160
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - J. Kyle Medley
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Huzaifa Hassan
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Brandon Miller
- Stowers Institute for Medical Research, Kansas City, MO64110
| | | | - Emma Wilcock
- Department of Biology, Widener University, Chester, PA19013
| | - Kexi Yi
- Stowers Institute for Medical Research, Kansas City, MO64110
| | | | - Kyle Weaver
- Stowers Institute for Medical Research, Kansas City, MO64110
| | | | - Robert Peuß
- Institute for Evolution and Biodiversity, University of Münster, Münster48149, Germany
| | - Jenna Persons
- Stowers Institute for Medical Research, Kansas City, MO64110
| | | | - Ernesto Maldonado
- EvoDevo Research Group, Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo77580, Mexico
| | - Kym Delventhal
- Stowers Institute for Medical Research, Kansas City, MO64110
| | - Andrew Gluesenkamp
- Center for Conservation and Research, San Antonio Zoo, San Antonio, TX78212
| | - Edward Mager
- Department of Biological Sciences, Advanced Environmental Research Institute, University of North Texas, Denton, TX76203
| | - David Coughlin
- Department of Biology, Widener University, Chester, PA19013
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO64110
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS66160
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Li ZL, Buck M. A proteome-scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics. Proteins 2023; 91:3-15. [PMID: 36053994 PMCID: PMC10087973 DOI: 10.1002/prot.26404] [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: 01/23/2022] [Revised: 07/06/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence. Here, we present a simple way to analyze the difference in amino acid occurrence by comparing highly homologous proteins on a subproteome level between several vertebrate model organisms. Specifically, we use this method to identify a pattern of amino acid conservation as well as a shift in amino acid occurrence between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, this general analysis and a specific example further establish a broad correlation, if not likely connection between the thermal adaptation of protein sequences and two of their physical features: on average a change in their protein dynamics and, even more strongly, in their solvation. For poikilotherms, such as frog and fish, the lower body temperature is expected to increase the protein-protein interaction due to a decrease in protein internal dynamics. In order to counteract the tendency for enhanced binding caused by low temperatures, poikilotherms enhance the solvation of their proteins by favoring polar amino acids. This feature appears to dominate over possible changes in dynamics for some proteins. The results suggest that a general trend for amino acid choice is part of the mechanism for thermoadaptation of vertebrate organisms at the molecular level.
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Affiliation(s)
- Zhen-Lu Li
- School of Life Science, Tianjin University, Tianjin, China.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Departments of Pharmacology and of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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Kuhn J, Azari S, Volkoff H. Effects of temperature on food intake and the expression of appetite regulators in three Characidae fish: The black-skirted tetra (Gymnocorymbus ternetzi), neon tetra (Paracheirodon innesi) and Mexican cavefish (Astyanax mexicanus). Comp Biochem Physiol A Mol Integr Physiol 2023; 275:111333. [PMID: 36244591 DOI: 10.1016/j.cbpa.2022.111333] [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: 07/27/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/07/2022]
Abstract
The Characidae family of fish is composed of commercially important species for which little is known about the regulation of feeding. Fish are ectotherms so that their body temperature fluctuates with the temperature of the surrounding water. Changes in water temperature can thus have major effects on the physiology of fish, in particular their feeding. The mechanisms by which appetite is influenced by changes in temperatures in fish remain unclear. In this study, we examined the effects of temperature on feeding behavior, food intake and the expression of appetite regulators in three characid fish (black tetra, neon tetra and cavefish) by submitting them to four different temperatures for 2 weeks (20°C, 24°C, 28°C, 32°C). In all species, food intake increased with increasing temperature. In neon and black tetras, increasing temperatures decreased expressions of orexin and leptin and increased that of cocaine and amphetamine regulated transcript (CART). In cavefish, temperature had no effect on brain orexin, leptin or CART. In all three species, higher temperatures induced increases in intestine expression of cholecystokinin (CCK), but no effects were seen for intestine ghrelin and peptide YY expressions. Our results show that temperature affects feeding in Characidae fish and induces species-specific changes in the expression of appetite regulators.
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Affiliation(s)
- Jannik Kuhn
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada; Hochschule Mannheim University, Mannheim 68163, Germany
| | - Sepideh Azari
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Helene Volkoff
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Evolution of left-right asymmetry in the sensory system and foraging behavior during adaptation to food-sparse cave environments. BMC Biol 2022; 20:295. [PMID: 36575431 PMCID: PMC9795734 DOI: 10.1186/s12915-022-01501-1] [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: 07/28/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Laterality in relation to behavior and sensory systems is found commonly in a variety of animal taxa. Despite the advantages conferred by laterality (e.g., the startle response and complex motor activities), little is known about the evolution of laterality and its plasticity in response to ecological demands. In the present study, a comparative study model, the Mexican tetra (Astyanax mexicanus), composed of two morphotypes, i.e., riverine surface fish and cave-dwelling cavefish, was used to address the relationship between environment and laterality. RESULTS The use of a machine learning-based fish posture detection system and sensory ablation revealed that the left cranial lateral line significantly supports one type of foraging behavior, i.e., vibration attraction behavior, in one cave population. Additionally, left-right asymmetric approaches toward a vibrating rod became symmetrical after fasting in one cave population but not in the other populations. CONCLUSION Based on these findings, we propose a model explaining how the observed sensory laterality and behavioral shift could help adaptation in terms of the tradeoff in energy gain and loss during foraging according to differences in food availability among caves.
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Zhao Q, Shao F, Li Y, Yi SV, Peng Z. Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes. Mol Ecol 2022; 31:5831-5845. [PMID: 36125323 PMCID: PMC9828065 DOI: 10.1111/mec.16700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.
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Affiliation(s)
- Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Department of Laboratory Animal Science, College of Basic Medical SciencesArmy Medical University (Third Military Medical University)ChongqingChina
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina
| | - Yanping Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Key Laboratory of Sichuan Province for Fish Conservation and Utilization in the Upper Reaches of the Yangtze RiverNeijiang Normal University College of Life SciencesNeijiangChina
| | - Soojin V. Yi
- Department of Ecology, Evolution and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)Southwest University School of Life SciencesChongqingChina,Academy of Plateau Science and SustainabilityQinghai Normal UniversityXiningChina
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Yuan XC, Tao YX. Ligands for Melanocortin Receptors: Beyond Melanocyte-Stimulating Hormones and Adrenocorticotropin. Biomolecules 2022; 12:biom12101407. [PMID: 36291616 PMCID: PMC9599618 DOI: 10.3390/biom12101407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The discovery of melanocortins in 1916 has resulted in more than 100 years of research focused on these peptides. Extensive studies have elucidated well-established functions of melanocortins mediated by cell surface receptors, including MSHR (melanocyte-stimulating hormone receptor) and ACTHR (adrenocorticotropin receptor). Subsequently, three additional melanocortin receptors (MCRs) were identified. Among these five MCRs, MC3R and MC4R are expressed primarily in the central nervous system, and are therefore referred to as the neural MCRs. Since the central melanocortin system plays important roles in regulating energy homeostasis, targeting neural MCRs is emerging as a therapeutic approach for treating metabolic conditions such as obesity and cachexia. Early efforts modifying endogenous ligands resulted in the development of many potent and selective ligands. This review focuses on the ligands for neural MCRs, including classical ligands (MSH and agouti-related peptide), nonclassical ligands (lipocalin 2, β-defensin, small molecules, and pharmacoperones), and clinically approved ligands (ACTH, setmelanotide, bremelanotide, and several repurposed drugs).
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Affiliation(s)
- Xiao-Chen Yuan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230061, China
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- Correspondence:
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Espinasa L, Collins E, Ornelas García CP, Rétaux S, Rohner N, Rutkowski J. Divergent evolutionary pathways for aggression and territoriality in Astyanax cavefish. SUBTERRANEAN BIOLOGY 2022. [DOI: 10.3897/subtbiol.73.79318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The surface morph of the Mexican tetra fish (Astyanax mexicanus) exhibits strong territoriality behavior and high levels of aggression. In contrast, the eyeless cave-adapted morph from Sierra de El Abra, México, rarely are aggressive and have totally lost the territorial behavior. These behaviors are part of what has been called the cavefish behavioral syndrome. Here, we report that several Astyanax cave populations of Sierra de Guatemala, unlike those reported for the Sierra de El Abra cave populations, display significant territoriality and aggression when confined into a reduced space. We discuss divergent evolutionary trajectories in terms of agonistic behavior for cavefish populations inhabiting different mountain ranges.
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Krishnan J, Wang Y, Kenzior O, Hassan H, Olsen L, Tsuchiya D, Kenzior A, Peuß R, Xiong S, Wang Y, Zhao C, Rohner N. Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation. Sci Rep 2022; 12:10115. [PMID: 35710938 PMCID: PMC9203785 DOI: 10.1038/s41598-022-14507-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/08/2022] [Indexed: 12/02/2022] Open
Abstract
Cell lines have become an integral resource and tool for conducting biological experiments ever since the Hela cell line was first developed (Scherer et al. in J Exp Med 97:695–710, 1953). They not only allow detailed investigation of molecular pathways but are faster and more cost-effective than most in vivo approaches. The last decade saw many emerging model systems strengthening basic science research. However, lack of genetic and molecular tools in these newer systems pose many obstacles. Astyanax mexicanus is proving to be an interesting new model system for understanding metabolic adaptation. To further enhance the utility of this system, we developed liver-derived cell lines from both surface-dwelling and cave-dwelling morphotypes. In this study, we provide detailed methodology of the derivation process along with comprehensive biochemical and molecular characterization of the cell lines, which reflect key metabolic traits of cavefish adaptation. We anticipate these cell lines to become a useful resource for the Astyanax community as well as researchers investigating fish biology, comparative physiology, and metabolism.
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Affiliation(s)
- Jaya Krishnan
- Stowers Institute for Medical Research, Kansas City, MO, USA.
| | - Yan Wang
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Olga Kenzior
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Huzaifa Hassan
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Luke Olsen
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Robert Peuß
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Shaolei Xiong
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Genetics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Chongbei Zhao
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA. .,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
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45
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Medley JK, Persons J, Biswas T, Olsen L, Peuß R, Krishnan J, Xiong S, Rohner N. The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites. eLife 2022; 11:74539. [PMID: 35703366 PMCID: PMC9200406 DOI: 10.7554/elife.74539] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 04/27/2022] [Indexed: 12/16/2022] Open
Abstract
Insights from organisms, which have evolved natural strategies for promoting survivability under extreme environmental pressures, may help guide future research into novel approaches for enhancing human longevity. The cave-adapted Mexican tetra, Astyanax mexicanus, has attracted interest as a model system for metabolic resilience, a term we use to denote the property of maintaining health and longevity under conditions that would be highly deleterious in other organisms (Figure 1). Cave-dwelling populations of Mexican tetra exhibit elevated blood glucose, insulin resistance and hypertrophic visceral adipocytes compared to surface-dwelling counterparts. However, cavefish appear to avoid pathologies typically associated with these conditions, such as accumulation of advanced-glycation-end-products (AGEs) and chronic tissue inflammation. The metabolic strategies underlying the resilience properties of A. mexicanus cavefish, and how they relate to environmental challenges of the cave environment, are poorly understood. Here, we provide an untargeted metabolomics study of long- and short-term fasting in two A. mexicanus cave populations and one surface population. We find that, although the metabolome of cavefish bears many similarities with pathological conditions such as metabolic syndrome, cavefish also exhibit features not commonly associated with a pathological condition, and in some cases considered indicative of an overall robust metabolic condition. These include a reduction in cholesteryl esters and intermediates of protein glycation, and an increase in antioxidants and metabolites associated with hypoxia and longevity. This work suggests that certain metabolic features associated with human pathologies are either not intrinsically harmful, or can be counteracted by reciprocal adaptations. We provide a transparent pipeline for reproducing our analysis and a Shiny app for other researchers to explore and visualize our dataset.
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Affiliation(s)
- J Kyle Medley
- Stowers Institute for Medical Research, Kansas City, United States
| | - Jenna Persons
- Stowers Institute for Medical Research, Kansas City, United States
| | - Tathagata Biswas
- Stowers Institute for Medical Research, Kansas City, United States
| | - Luke Olsen
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
| | - Robert Peuß
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
| | - Jaya Krishnan
- Stowers Institute for Medical Research, Kansas City, United States
| | - Shaolei Xiong
- Stowers Institute for Medical Research, Kansas City, United States
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, United States
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46
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Tao YX. Mutations in melanocortin-4 receptor: From fish to men. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:215-257. [PMID: 35595350 DOI: 10.1016/bs.pmbts.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Melanocortin-4 receptor (MC4R), expressed abundantly in the hypothalamus, is a critical regulator of energy homeostasis, including both food intake and energy expenditure. Shortly after the publication in 1997 of the Mc4r knockout phenotypes in mice, including increased food intake and severe obesity, the first mutations in MC4R were reported in humans in 1998. Studies in the subsequent two decades have established MC4R mutation as the most common monogenic form of obesity, especially in early-onset severe obesity. Studies in animals, from fish to mammals, have established the conserved physiological roles of MC4R in all vertebrates in regulating energy balance. Drug targeting MC4R has been recently approved for treating morbid genetic obesity. How the MC4R can be exploited for animal production is highly worthy of active investigation.
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Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.
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47
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Lunghi E, Bilandžija H. Longevity in Cave Animals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.874123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An extraordinary longevity has been observed in some cave species, and this raised the hypothesis that a longer lifespan may be considered one of the characteristic traits of these animals. However, only a few cave species have been studied thus far, and a firm conclusion remains to be drawn. Here we review the available knowledge on the longevity of subterranean species, point out the limitations of previous studies, and provide suggestions for future studies to answer important questions regarding the longevity in cave animals, its adaptive value and the related promoting factors. We also argue that studying the longevity in cave animals will contribute to the field of aging, especially to understanding the evolution of this phenomenon.
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48
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Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish. Nat Genet 2022; 54:684-693. [PMID: 35551306 DOI: 10.1038/s41588-022-01049-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Cis-regulatory changes are key drivers of adaptative evolution. However, their contribution to the metabolic adaptation of organisms is not well understood. Here, we used a unique vertebrate model, Astyanax mexicanus-different morphotypes of which survive in nutrient-rich surface and nutrient-deprived cave waters-to uncover gene regulatory networks underlying metabolic adaptation. We performed genome-wide epigenetic profiling in the liver tissues of Astyanax and found that many of the identified cis-regulatory elements (CREs) have genetically diverged and have differential chromatin features between surface and cave morphotypes, while retaining remarkably similar regulatory signatures between independently derived cave populations. One such CRE in the hpdb gene harbors a genomic deletion in cavefish that abolishes IRF2 repressor binding and derepresses enhancer activity in reporter assays. Selection of this mutation in multiple independent cave populations supports its importance in cave adaptation, and provides novel molecular insights into the evolutionary trade-off between loss of pigmentation and adaptation to food-deprived caves.
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49
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Xiong S, Wang W, Kenzior A, Olsen L, Krishnan J, Persons J, Medley K, Peuß R, Wang Y, Chen S, Zhang N, Thomas N, Miles JM, Alvarado AS, Rohner N. Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity. Curr Biol 2022; 32:2272-2280.e6. [PMID: 35390280 DOI: 10.1016/j.cub.2022.03.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 12/18/2022]
Abstract
Nutrient availability varies seasonally and spatially in the wild. While many animals, such as hibernating animals or migrating birds, evolved strategies to overcome periods of nutrient scarcity,1,2 the cellular mechanisms of these strategies are poorly understood. Cave environments represent an example of nutrient-deprived environments, since the lack of sunlight and therefore primary energy production drastically diminishes the nutrient availability.3 Here, we used Astyanax mexicanus, which includes river-dwelling surface fish and cave-adapted cavefish populations, to study the genetic adaptation to nutrient limitations.4-9 We show that cavefish populations store large amounts of fat in different body regions when fed ad libitum in the lab. We found higher expression of lipogenesis genes in cavefish livers when fed the same amount of food as surface fish, suggesting an improved ability of cavefish to use lipogenesis to convert available energy into triglycerides for storage into adipose tissue.10-12 Moreover, the lipid metabolism regulator, peroxisome proliferator-activated receptor γ (Pparγ), is upregulated at both transcript and protein levels in cavefish livers. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that Pparγ binds cavefish promoter regions of genes to a higher extent than surface fish and inhibiting Pparγ in vivo decreases fat accumulation in A. mexicanus. Finally, we identified nonsense mutations in per2, a known repressor of Pparγ, providing a possible regulatory mechanism of Pparγ in cavefish. Taken together, our study reveals that upregulated Pparγ promotes higher levels of lipogenesis in the liver and contributes to higher body fat accumulation in cavefish populations, an important adaptation to nutrient-limited environments.
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Affiliation(s)
- Shaolei Xiong
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Howard Hughes Medical Institute, Kansas City, MO 64110, USA; National Institute of Biological Sciences, Beijing 102206, China
| | | | - Luke Olsen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular & Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jaya Krishnan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jenna Persons
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Kyle Medley
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Robert Peuß
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ning Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Nancy Thomas
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - John M Miles
- Department of Medicine, Division of Metabolism, Endocrinology & Genetics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Howard Hughes Medical Institute, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular & Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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50
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Moran RL, Jaggard JB, Roback EY, Kenzior A, Rohner N, Kowalko JE, Ornelas-García CP, McGaugh SE, Keene AC. Hybridization underlies localized trait evolution in cavefish. iScience 2022; 25:103778. [PMID: 35146393 PMCID: PMC8819016 DOI: 10.1016/j.isci.2022.103778] [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: 08/05/2021] [Revised: 09/13/2021] [Accepted: 01/12/2022] [Indexed: 11/04/2022] Open
Abstract
Introgressive hybridization may play an integral role in local adaptation and speciation (Taylor and Larson, 2019). In the Mexican tetra Astyanax mexicanus, cave populations have repeatedly evolved traits including eye loss, sleep loss, and albinism. Of the 30 caves inhabited by A. mexicanus, Chica cave is unique because it contains multiple pools inhabited by putative hybrids between surface and cave populations (Mitchell et al., 1977), providing an opportunity to investigate the impact of hybridization on complex trait evolution. We show that hybridization between cave and surface populations may contribute to localized variation in traits associated with cave evolution, including pigmentation, eye development, and sleep. We also uncover an example of convergent evolution in a circadian clock gene in multiple cavefish lineages and burrowing mammals, suggesting a shared genetic mechanism underlying circadian disruption in subterranean vertebrates. Our results provide insight into the role of hybridization in facilitating phenotypic evolution. Hybridization leads to a localized difference in sleep duration within a single cave Genomic analysis identifies coding differences in Cry1A across cave pools Changes in Cry1A appear to be conserved in cavefish and burrowing mammals
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