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Schott RK, Fujita MK, Streicher JW, Gower DJ, Thomas KN, Loew ER, Bamba Kaya AG, Bittencourt-Silva GB, Guillherme Becker C, Cisneros-Heredia D, Clulow S, Davila M, Firneno TJ, Haddad CFB, Janssenswillen S, Labisko J, Maddock ST, Mahony M, Martins RA, Michaels CJ, Mitchell NJ, Portik DM, Prates I, Roelants K, Roelke C, Tobi E, Woolfolk M, Bell RC. Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments. Mol Biol Evol 2024; 41:msae049. [PMID: 38573520 PMCID: PMC10994157 DOI: 10.1093/molbev/msae049] [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: 09/12/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.
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Affiliation(s)
- Ryan K Schott
- Department of Biology and Centre for Vision Research, York University, Toronto, Ontario, Canada
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Matthew K Fujita
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | | | | | - Kate N Thomas
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
- Natural History Museum, London, UK
| | - Ellis R Loew
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | | | - C Guillherme Becker
- Department of Biology and One Health Microbiome Center, Center for Infectious Disease Dynamics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Diego Cisneros-Heredia
- Laboratorio de Zoología Terrestre, Instituto de Biodiversidad Tropical IBIOTROP, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Simon Clulow
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mateo Davila
- Laboratorio de Zoología Terrestre, Instituto de Biodiversidad Tropical IBIOTROP, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Thomas J Firneno
- Department of Biological Sciences, University of Denver, Denver, USA
| | - Célio F B Haddad
- Department of Biodiversity and Center of Aquaculture—CAUNESP, I.B., São Paulo State University, Rio Claro, São Paulo, Brazil
| | - Sunita Janssenswillen
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jim Labisko
- Natural History Museum, London, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
| | - Simon T Maddock
- Natural History Museum, London, UK
- Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Michael Mahony
- Department of Biological Sciences, The University of Newcastle, Newcastle 2308, Australia
| | - Renato A Martins
- Programa de Pós-graduação em Conservação da Fauna, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | - Nicola J Mitchell
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Daniel M Portik
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Ivan Prates
- Department of Biology, Lund University, Lund, Sweden
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Corey Roelke
- Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Center for Conservation and Sustainability, Smithsonian National Zoo and Conservation Biology Institute, Gamba, Gabon
| | - Maya Woolfolk
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
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2
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Papadogiannis V, Hockman D, Mercurio S, Ramsay C, Hintze M, Patthey C, Streit A, Shimeld SM. Evolution of the expression and regulation of the nuclear hormone receptor ERR gene family in the chordate lineage. Dev Biol 2023; 504:12-24. [PMID: 37696353 DOI: 10.1016/j.ydbio.2023.09.003] [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: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/09/2023] [Indexed: 09/13/2023]
Abstract
The Estrogen Related Receptor (ERR) nuclear hormone receptor genes have a wide diversity of roles in vertebrate development. In embryos, ERR genes are expressed in several tissues, including the central and peripheral nervous systems. Here we seek to establish the evolutionary history of chordate ERR genes, their expression and their regulation. We examine ERR expression in mollusc, amphioxus and sea squirt embryos, finding the single ERR orthologue is expressed in the nervous system in all three, with muscle expression also found in the two chordates. We show that most jawed vertebrates and lampreys have four ERR paralogues, and that vertebrate ERR genes were ancestrally linked to Estrogen Receptor genes. One of the lamprey paralogues shares conserved expression domains with jawed vertebrate ERRγ in the embryonic vestibuloacoustic ganglion, eye, brain and spinal cord. Hypothesising that conserved expression derives from conserved regulation, we identify a suite of pan-vertebrate conserved non-coding sequences in ERR introns. We use transgenesis in lamprey and chicken embryos to show that these sequences are regulatory and drive reporter gene expression in the nervous system. Our data suggest an ancient association between ERR and the nervous system, including expression in cells associated with photosensation and mechanosensation. This includes the origin in the vertebrate common ancestor of a suite of regulatory elements in the 3' introns that drove nervous system expression and have been conserved from this point onwards.
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Affiliation(s)
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Silvia Mercurio
- Department of Environmental Science and Policy, Università Degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Claire Ramsay
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Mark Hintze
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Cedric Patthey
- Department of Radiosciences, Umeå University, 901 85, Umeå, Sweden
| | - Andrea Streit
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Sebastian M Shimeld
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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3
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [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: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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Cellular and Molecular Mechanisms of Pathogenesis Underlying Inherited Retinal Dystrophies. Biomolecules 2023; 13:biom13020271. [PMID: 36830640 PMCID: PMC9953031 DOI: 10.3390/biom13020271] [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: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are congenital retinal degenerative diseases that have various inheritance patterns, including dominant, recessive, X-linked, and mitochondrial. These diseases are most often the result of defects in rod and/or cone photoreceptor and retinal pigment epithelium function, development, or both. The genes associated with these diseases, when mutated, produce altered protein products that have downstream effects in pathways critical to vision, including phototransduction, the visual cycle, photoreceptor development, cellular respiration, and retinal homeostasis. The aim of this manuscript is to provide a comprehensive review of the underlying molecular mechanisms of pathogenesis of IRDs by delving into many of the genes associated with IRD development, their protein products, and the pathways interrupted by genetic mutation.
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Lagman D, Haines HJ, Abalo XM, Larhammar D. Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates. PLoS One 2022; 17:e0279548. [PMID: 36584110 PMCID: PMC9803222 DOI: 10.1371/journal.pone.0279548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in metazoans and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.
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Affiliation(s)
- David Lagman
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Helen J. Haines
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Xesús M. Abalo
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
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6
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Kon T, Fukuta K, Chen Z, Kon-Nanjo K, Suzuki K, Ishikawa M, Tanaka H, Burgess SM, Noguchi H, Toyoda A, Omori Y. Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization. Commun Biol 2022; 5:1404. [PMID: 36572749 PMCID: PMC9792465 DOI: 10.1038/s42003-022-04351-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.
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Affiliation(s)
- Tetsuo Kon
- grid.419056.f0000 0004 1793 2541Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan ,grid.10420.370000 0001 2286 1424Present Address: Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Kentaro Fukuta
- grid.418987.b0000 0004 1764 2181Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
| | - Zelin Chen
- grid.280128.10000 0001 2233 9230Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD USA ,grid.9227.e0000000119573309Present Address: CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Koto Kon-Nanjo
- grid.10420.370000 0001 2286 1424Department of Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Kota Suzuki
- Yatomi Station, Aichi Fisheries Research Institute, Yatomi, Japan
| | | | | | - Shawn M. Burgess
- grid.280128.10000 0001 2233 9230Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD USA
| | - Hideki Noguchi
- grid.418987.b0000 0004 1764 2181Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan ,grid.288127.60000 0004 0466 9350Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- grid.288127.60000 0004 0466 9350Advanced Genomics Center, National Institute of Genetics, Mishima, Japan ,grid.288127.60000 0004 0466 9350Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Yoshihiro Omori
- grid.419056.f0000 0004 1793 2541Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan
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Lamb TD. Photoreceptor physiology and evolution: cellular and molecular basis of rod and cone phototransduction. J Physiol 2022; 600:4585-4601. [PMID: 35412676 PMCID: PMC9790638 DOI: 10.1113/jp282058] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/29/2022] [Indexed: 12/30/2022] Open
Abstract
The detection of light in the vertebrate retina utilizes a duplex system of closely related rod and cone photoreceptors: cones respond extremely rapidly, and operate at 'photopic' levels of illumination, from moonlight upwards; rods respond much more slowly, thereby obtaining greater sensitivity, and function effectively only at 'scotopic' levels of moonlight and lower. Rods and cones employ distinct isoforms of many of the proteins in the phototransduction cascade, and they thereby represent a unique evolutionary system, whereby the same process (the detection of light) uses a distinct set of genes in two classes of cell. The molecular mechanisms of phototransduction activation are described, and the classical quantitative predictions for the onset phase of the electrical response to light are developed. Recent work predicting the recovery phase of the rod's response to intense flashes is then presented, that provides an accurate account of the time that the response spends in saturation. Importantly, this also provides a new estimate for the rate at which a single rhodopsin activates molecules of the G-protein, transducin, that is substantially higher than other estimates in the literature. Finally, the evolutionary origin of the phototransduction proteins in rods and cones is examined, and it is shown that most of the rod/cone differences were established at the first of the two rounds of whole-genome duplication more than 500 million years ago.
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Affiliation(s)
- Trevor D. Lamb
- Eccles Institute of NeuroscienceJohn Curtin School of Medical ResearchThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
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8
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White ND, Batz ZA, Braun EL, Braun MJ, Carleton KL, Kimball RT, Swaroop A. A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution. Mol Ecol Resour 2021; 22:587-601. [PMID: 34652059 DOI: 10.1111/1755-0998.13496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.
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Affiliation(s)
- Noor D White
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA
| | - Zachary A Batz
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Karen L Carleton
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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9
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Wada S, Kawano-Yamashita E, Sugihara T, Tamotsu S, Koyanagi M, Terakita A. Insights into the evolutionary origin of the pineal color discrimination mechanism from the river lamprey. BMC Biol 2021; 19:188. [PMID: 34526036 PMCID: PMC8444496 DOI: 10.1186/s12915-021-01121-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Background Pineal-related organs in cyclostomes, teleosts, amphibians, and reptiles exhibit color opponency, generating antagonistic neural responses to different wavelengths of light and thereby sensory information about its “color”. Our previous studies suggested that in zebrafish and iguana pineal-related organs, a single photoreceptor cell expressing both UV-sensitive parapinopsin and green-sensitive parietopsin generates color opponency in a “one-cell system.” However, it remains unknown to what degree these opsins and the single cell-based mechanism in the pineal color opponency are conserved throughout non-mammalian vertebrates. Results We found that in the lamprey pineal organ, the two opsins are conserved but that, in contrast to the situation in other vertebrate pineal-related organs, they are expressed in separate photoreceptor cells. Intracellular electrophysiological recordings demonstrated that the parietopsin-expressing photoreceptor cells with Go-type G protein evoke a depolarizing response to visible light. Additionally, spectroscopic analyses revealed that parietopsin with 11-cis 3-dehydroretinal has an absorption maximum at ~570 nm, which is in approximate agreement with the wavelength (~560 nm) that produces the maximum rate of neural firing in pineal ganglion cells exposed to visible light. The vesicular glutamate transporter is localized at both the parietopsin- and parapinopsin-expressing photoreceptor terminals, suggesting that both types of photoreceptor cells use glutamate as a transmitter. Retrograde tracing of the pineal ganglion cells revealed that the terminal of the parietopsin-expressing cells is located close enough to form a neural connection with the ganglion cells, which is similar to our previous observation for the parapinopsin-expressing photoreceptor cells and the ganglion cells. In sum, our observations point to a “two-cell system” in which parietopsin and parapinopsin, expressed separately in two different types of photoreceptor cells, contribute to the generation of color opponency in the pineal ganglion cells. Conclusion Our results indicate that the jawless vertebrate, lamprey, employs a system for color opponency that differes from that described previously in jawed vertebrates. From a physiological viewpoint, we propose an evolutionary insight, the emergence of pineal “one-cell system” from the ancestral “multiple (two)-cell system,” showing the opposite evolutionary direction to that of the ocular color opponency. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01121-1.
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Affiliation(s)
- Seiji Wada
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, 558-8585, Japan
| | - Emi Kawano-Yamashita
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan.,Department of Chemistry, Biology and Environmental Science, Faculty of Science, Nara Women's University, Nara, 630-8506, Japan
| | - Tomohiro Sugihara
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan
| | - Satoshi Tamotsu
- Department of Chemistry, Biology and Environmental Science, Faculty of Science, Nara Women's University, Nara, 630-8506, Japan
| | - Mitsumasa Koyanagi
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, 558-8585, Japan
| | - Akihisa Terakita
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, 558-8585, Japan. .,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, 558-8585, Japan.
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10
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Gesemann M, Neuhauss SCF. Selective Gene Loss of Visual and Olfactory Guanylyl Cyclase Genes Following the Two Rounds of Vertebrate-Specific Whole-Genome Duplications. Genome Biol Evol 2021; 12:2153-2167. [PMID: 32915957 PMCID: PMC7674705 DOI: 10.1093/gbe/evaa192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2020] [Indexed: 12/12/2022] Open
Abstract
Photoreceptors convey visual information and come in two flavors; dim-light and bright-light dedicated rod and cones. Both cell types feature highly specialized phototransduction cascades that convert photonic energy into intracellular signals. Although a substantial amount of phototransduction gene ohnologs are expressed either in rods or cones, visual guanylyl cyclases (GCs) involved in the calcium (Ca2+) dependent feedback regulation of phototransduction are neither rod nor cone specific. The co-existence of visual GCs in both photoreceptor types suggests that specialization of these ohnologs occurred despite their overlapping expression. Here, we analyze gene retention and inactivation patterns of vertebrate visual and closely related olfactory GCs following two rounds (2R) of vertebrate-specific whole-genome duplication events (2R WGD). Although eutherians generally use two visual and one olfactory GC, independent inactivation occurred in some lineages. Sauropsids (birds, lizards, snakes, turtles, and crocodiles) generally have only one visual GC (GC-E). Additionally, turtles (testodes) also lost the olfactory GC (GC-D). Pseudogenization in mammals occurred in specific species/families likely according to functional needs (i.e., many species with reduced vision only have GC-E). Likewise, some species not relying on scent marks lack GC-D, the olfactory GC enzyme. Interestingly, in the case of fish, no species can be found with fewer than three (two visual and one olfactory) genes and the teleost-specific 3R WGD can increase this number to up to five. This suggests that vision in fish now requires at least two visual GCs.
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Affiliation(s)
- Matthias Gesemann
- Institute of Molecular Life Sciences, University of Zurich, Switzerland
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11
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Distinct Opsin 3 ( Opn3) Expression in the Developing Nervous System during Mammalian Embryogenesis. eNeuro 2021; 8:ENEURO.0141-21.2021. [PMID: 34417283 PMCID: PMC8445036 DOI: 10.1523/eneuro.0141-21.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Opsin 3 (Opn3) is highly expressed in the adult brain, however, information for spatial and temporal expression patterns during embryogenesis is significantly lacking. Here, an Opn3-eGFP reporter mouse line was used to monitor cell body expression and axonal projections during embryonic and early postnatal to adult stages. By applying 2D and 3D fluorescence imaging techniques, we have identified the onset of Opn3 expression, which predominantly occurred during embryonic stages, in various structures during brain/head development. In addition, this study defines over twenty Opn3-eGFP-positive neural structures never reported before. Opn3-eGFP was first observed at E9.5 in neural regions, including the ganglia that will ultimately form the trigeminal, facial and vestibulocochlear cranial nerves (CNs). As development proceeds, expanded Opn3-eGFP expression coincided with the formation and maturation of critical components of the central and peripheral nervous systems (CNS, PNS), including various motor-sensory tracts, such as the dorsal column-medial lemniscus (DCML) sensory tract, and olfactory, acoustic, and optic tracts. The widespread, yet distinct, detection of Opn3-eGFP already at early embryonic stages suggests that Opn3 might play important functional roles in the developing brain and spinal cord to regulate multiple motor and sensory circuitry systems, including proprioception, nociception, ocular movement, and olfaction, as well as memory, mood, and emotion. This study presents a crucial blueprint from which to investigate autonomic and cognitive opsin-dependent neural development and resultant behaviors under physiological and pathophysiological conditions.
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12
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Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:33-59. [PMID: 34170501 DOI: 10.1007/5584_2021_649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The photoreceptor phosphodiesterase (PDE6) is a member of large family of Class I phosphodiesterases responsible for hydrolyzing the second messengers cAMP and cGMP. PDE6 consists of two catalytic subunits and two inhibitory subunits that form a tetrameric protein. PDE6 is a peripheral membrane protein that is localized to the signal-transducing compartment of rod and cone photoreceptors. As the central effector enzyme of the G-protein coupled visual transduction pathway, activation of PDE6 catalysis causes a rapid decrease in cGMP levels that results in closure of cGMP-gated ion channels in the photoreceptor plasma membrane. Because of its importance in the phototransduction pathway, mutations in PDE6 genes result in various retinal diseases that currently lack therapeutic treatment strategies due to inadequate knowledge of the structure, function, and regulation of this enzyme. This review focuses on recent progress in understanding the structure of the regulatory and catalytic domains of the PDE6 holoenzyme, the central role of the multi-functional inhibitory γ-subunit, the mechanism of activation by the heterotrimeric G protein, transducin, and future directions for pharmacological interventions to treat retinal degenerative diseases arising from mutations in the PDE6 genes.
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13
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Dong EM, Allison WT. Vertebrate features revealed in the rudimentary eye of the Pacific hagfish ( Eptatretus stoutii). Proc Biol Sci 2021; 288:20202187. [PMID: 33434464 DOI: 10.1098/rspb.2020.2187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hagfish eyes are markedly basic compared to the eyes of other vertebrates, lacking a pigmented epithelium, a lens and a retinal architecture built of three cell layers: the photoreceptors, interneurons and ganglion cells. Concomitant with hagfish belonging to the earliest-branching vertebrate group (the jawless Agnathans), this lack of derived characters has prompted competing interpretations that hagfish eyes represent either a transitional form in the early evolution of vertebrate vision, or a regression from a previously elaborate organ. Here, we show the hagfish retina is not extensively degenerating during its ontogeny, but instead grows throughout life via a recognizable PAX6+ ciliary marginal zone. The retina has a distinct layer of photoreceptor cells that appear to homogeneously express a single opsin of the RH1 rod opsin class. The epithelium that encompasses these photoreceptors is striking because it lacks the melanin pigment that is universally associated with animal vision; notwithstanding, we suggest this epithelium is a homologue of gnathosome retinal pigment epithelium (RPE) based on its robust expression of RPE65 and its engulfment of photoreceptor outer segments. We infer that the hagfish retina is not entirely rudimentary in its wiring, despite lacking a morphologically distinct layer of interneurons: multiple populations of cells exist in the hagfish inner retina and subsets of these express markers of vertebrate retinal interneurons. Overall, these data clarify Agnathan retinal homologies, reveal characters that now appear to be ubiquitous across the eyes of vertebrates, and refine interpretations of early vertebrate visual system evolution.
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Affiliation(s)
- Emily M Dong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T7Y 1C4
| | - W Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T7Y 1C4
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14
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Warrington RE, Davies WIL, Hemmi JM, Hart NS, Potter IC, Collin SP, Hunt DM. Visual opsin expression and morphological characterization of retinal photoreceptors in the pouched lamprey (Geotria australis, Gray). J Comp Neurol 2020; 529:2265-2282. [PMID: 33336375 DOI: 10.1002/cne.25092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/09/2022]
Abstract
Lampreys are extant members of the agnathan (jawless) vertebrates that diverged ~500 million years ago, during a critical stage of vertebrate evolution when image-forming eyes first emerged. Among lamprey species assessed thus far, the retina of the southern hemisphere pouched lamprey, Geotria australis, is unique, in that it possesses morphologically distinct photoreceptors and expresses five visual photopigments. This study focused on determining the number of different photoreceptors present in the retina of G. australis and whether each cell type expresses a single opsin class. Five photoreceptor subtypes were identified based on ultrastructure and differential expression of one of each of the five different visual opsin classes (lws, sws1, sws2, rh1, and rh2) known to be expressed in the retina. This suggests, therefore, that the retina of G. australis possesses five spectrally and morphologically distinct photoreceptors, with the potential for complex color vision. Each photoreceptor subtype was shown to have a specific spatial distribution in the retina, which is potentially associated with changes in spectral radiance across different lines of sight. These results suggest that there have been strong selection pressures for G. australis to maintain broad spectral sensitivity for the brightly lit surface waters that this species inhabits during its marine phase. These findings provide important insights into the functional anatomy of the early vertebrate retina and the selection pressures that may have led to the evolution of complex color vision.
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Affiliation(s)
- Rachael E Warrington
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA.,School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Wayne I L Davies
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia.,Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia.,School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Jan M Hemmi
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Nathan S Hart
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia.,Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Ian C Potter
- Centre for Sustainable Aquatic Ecosystems, Murdoch University, Perth, Western Australia, Australia
| | - Shaun P Collin
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia.,School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - David M Hunt
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
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15
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Accelerated evolution and positive selection of rhodopsin in Tibetan loaches living in high altitude. Int J Biol Macromol 2020; 165:2598-2606. [PMID: 33470199 DOI: 10.1016/j.ijbiomac.2020.10.151] [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: 07/31/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 11/22/2022]
Abstract
Rhodopsin (RH1), the temperature-sensitive visual pigment, attained cold adaptation by functional trade-offs between protein stability and activity. Recent studies suggested convergent selection pressures drove cold adaptation of rhodopsin in high altitude catfishes through nonparallel molecular mechanisms. Here, we tested whether the similar shift occurred in RH1 of Tibetan loaches on the Qinghai-Tibet Plateau (QTP) by investigating the molecular evolution and potential effect on function of RH1. We sequenced RH1 from 27 Triplophysa species, and four lowland loaches and combined these data with published sequences. Tests using a series of models of molecular evolution resulted in strong evidence for accelerated evolution and positive selection in Triplophysa RH1. Three positively selected sites were near key functional domains modulating nonspectral properties of rhodopsin, substitutions of which were likely to compensate for cold-induced decrease in rhodopsin kinetics in cold environments. Moreover, although accelerated evolutionary rates in Tibetan loaches was convergent with those in high altitude catfishes, the sites under positive selection were nonoverlapping. Our findings provide evidence for convergent shift in selection pressures of RH1 in high altitude fish during the ecological transition to cold environment of the QTP.
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16
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Yamaguchi K, Koyanagi M, Kuraku S. Visual and nonvisual opsin genes of sharks and other nonosteichthyan vertebrates: Genomic exploration of underwater photoreception. J Evol Biol 2020; 34:968-976. [DOI: 10.1111/jeb.13730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Kazuaki Yamaguchi
- Laboratory for Phyloinformatics RIKEN Center for Biosystems Dynamics Research (BDR) Kobe Japan
| | - Mitsumasa Koyanagi
- Department of Biology and Geosciences Graduate School of Science Osaka City University Osaka Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics RIKEN Center for Biosystems Dynamics Research (BDR) Kobe Japan
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17
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Hart NS, Lamb TD, Patel HR, Chuah A, Natoli RC, Hudson NJ, Cutmore SC, Davies WIL, Collin SP, Hunt DM. Visual Opsin Diversity in Sharks and Rays. Mol Biol Evol 2020; 37:811-827. [PMID: 31770430 DOI: 10.1093/molbev/msz269] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.
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Affiliation(s)
- Nathan S Hart
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Hardip R Patel
- Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Riccardo C Natoli
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Nicholas J Hudson
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Scott C Cutmore
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Wayne I L Davies
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Shaun P Collin
- School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - David M Hunt
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, The University of Western Australia, Crawley, WA, Australia
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18
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Espíndola-Hernández P, Mueller JC, Carrete M, Boerno S, Kempenaers B. Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls. Genome Biol Evol 2020; 12:1895-1908. [PMID: 32770228 PMCID: PMC7566403 DOI: 10.1093/gbe/evaa166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism, and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of 20 bird genomes, including 11 owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm, and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.
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Affiliation(s)
- Pamela Espíndola-Hernández
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Martina Carrete
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, Sevilla, Spain
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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19
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The non-visual opsins expressed in deep brain neurons projecting to the retina in lampreys. Sci Rep 2020; 10:9669. [PMID: 32541666 PMCID: PMC7295746 DOI: 10.1038/s41598-020-66679-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/26/2020] [Indexed: 11/23/2022] Open
Abstract
In lower vertebrates, brain photoreceptor cells express vertebrate-specific non-visual opsins. We previously revealed that a pineal-related organ-specific opsin, parapinopsin, is UV-sensitive and allows pineal wavelength discrimination in lampreys and teleost. The Australian pouched lamprey was recently reported as having two parapinopsin-related genes. We demonstrate that a parapinopsin-like opsin from the Japanese river lamprey exhibits different molecular properties and distribution than parapinopsin. This opsin activates Gi-type G protein in a mammalian cell culture assay in a light-dependent manner. Heterologous action spectroscopy revealed that the opsin forms a violet to blue-sensitive pigment. Interestingly, the opsin is co-localised with green-sensitive P-opsin in the cells of the M5 nucleus of Schober (M5NS) in the mesencephalon of the river and brook lamprey. Some opsins-containing cells of the river lamprey have cilia and others an axon projecting to the retina. The opsins of the brook lamprey are co-localised in the cilia of centrifugal neurons projecting to the retina, suggesting that cells expressing the parapinopsin-like opsin and P-opsin are sensitive to violet to green light. Moreover, we found neural connections between M5NS cells expressing the opsins and the retina. These findings suggest that the retinal activity might be modulated by brain photoreception.
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20
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Davies KTJ, Yohe LR, Almonte J, Sánchez MKR, Rengifo EM, Dumont ER, Sears KE, Dávalos LM, Rossiter SJ. Foraging shifts and visual preadaptation in ecologically diverse bats. Mol Ecol 2020; 29:1839-1859. [PMID: 32293071 DOI: 10.1111/mec.15445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/28/2020] [Accepted: 03/31/2020] [Indexed: 12/11/2022]
Abstract
Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative contribution of molecular adaptations, measured by positive and relaxed selection, acting on eye-expressed genes associated with shifts to new adaptive zones in ecologically diverse bats from the superfamily Noctilionoidea. Collectively, noctilionoids display remarkable ecological breadth, from highly divergent echolocation to flight strategies linked to specialized insectivory, the parallel evolution of diverse plant-based diets (e.g., nectar, pollen and fruit) from ancestral insectivory, and-unusually for echolocating bats-often have large, well-developed eyes. We report contrasting levels of positive selection in genes associated with the development, maintenance and scope of visual function, tracing back to the origins of noctilionoids and Phyllostomidae (the bat family with most dietary diversity), instead of during shifts to novel diets. Generalized plant visiting was not associated with exceptional molecular adaptation, and exploration of these novel niches took place in an ancestral phyllostomid genetic background. In contrast, evidence for positive selection in vision genes was found at subsequent shifts to either nectarivory or frugivory. Thus, neotropical noctilionoids that use visual cues for identifying food and roosts, as well as for orientation, were effectively preadapted, with subsequent molecular adaptations in nectar-feeding lineages and the subfamily Stenodermatinae of fig-eating bats fine-tuning pre-existing visual adaptations for specialized purposes.
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Affiliation(s)
- Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA.,Department of Geology & Geophysics, Yale University, New Haven, CT, USA
| | - Jesus Almonte
- Independent Scientist, Santo Domingo, Dominican Republic
| | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Elizabeth R Dumont
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, USA.,Consortium for Inter-Disciplinary Environmental Research, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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21
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Lamb TD. Evolution of the genes mediating phototransduction in rod and cone photoreceptors. Prog Retin Eye Res 2019; 76:100823. [PMID: 31790748 DOI: 10.1016/j.preteyeres.2019.100823] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022]
Abstract
This paper reviews current knowledge of the evolution of the multiple genes encoding proteins that mediate the process of phototransduction in rod and cone photoreceptors of vertebrates. The approach primarily involves molecular phylogenetic analysis of phototransduction protein sequences, combined with analysis of the syntenic arrangement of the genes. At least 35 of these phototransduction genes appear to reside on no more than five paralogons - paralogous regions that each arose from a common ancestral region. Furthermore, it appears that such paralogs arose through quadruplication during the two rounds of genome duplication (2R WGD) that occurred in a chordate ancestor prior to the vertebrate radiation, probably around 600 millions years ago. For several components of the phototransduction cascade, it is shown that distinct isoforms already existed prior to WGD, with the likely implication that separate classes of scotopic and photopic photoreceptor cells had already evolved by that stage. The subsequent quadruplication of the entire genome then permitted the refinement of multiple distinct protein isoforms in rods and cones. A unified picture of the likely pattern and approximate timing of all the important gene duplications is synthesised, and the implications for our understanding of the evolution of rod and cone phototransduction are presented.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
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22
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Fain GL. Lamprey vision: Photoreceptors and organization of the retina. Semin Cell Dev Biol 2019; 106:5-11. [PMID: 31711759 DOI: 10.1016/j.semcdb.2019.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 01/22/2023]
Abstract
The lamprey is an important non-model vertebrate because it is an agnathan or jawless vertebrate and belongs to the superclass cyclostomata, a group that split off from the rest of the vertebrates 500 million years ago. Investigation of the lamprey retina may therefore reveal attributes of visual function that were characteristic of even the most primitive vertebrates. The rod and cone photoreceptors are a striking example, because the biochemistry and physiology of phototransduction is remarkably similar between lamprey and the rest of the vertebrates, including mammals. The fundamental mechanism of light sensation seems therefore to have emerged very early in the evolution of vertebrates in the late Cambrian. Some other characteristics of the retina are also similar and may be very old, but other features such as the morphology of ganglion cells are rather different in lamprey and other vertebrates. Even these differences may provide new insight into the various mechanisms vertebrates use for visual detection.
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Affiliation(s)
- Gordon L Fain
- Department of Ophthalmology, Jules Stein Eye Institute, UCLA School of Medicine, University of California, Los Angeles, 90095-7000, United States; Department of Ophthalmology, Jules Stein Eye Institute, UCLA School of Medicine, University of California, Los Angeles, 90095-7000,United States.
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23
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Wang X, Plachetzki DC, Cote RH. The N termini of the inhibitory γ-subunits of phosphodiesterase-6 (PDE6) from rod and cone photoreceptors differentially regulate transducin-mediated PDE6 activation. J Biol Chem 2019; 294:8351-8360. [PMID: 30962282 DOI: 10.1074/jbc.ra119.007520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/02/2019] [Indexed: 12/26/2022] Open
Abstract
Phosphodiesterase-6 (PDE6) plays a central role in both rod and cone phototransduction pathways. In the dark, PDE6 activity is suppressed by its inhibitory γ-subunit (Pγ). Rhodopsin-catalyzed activation of the G protein transducin relieves this inhibition and enhances PDE6 catalysis. We hypothesized that amino acid sequence differences between rod- and cone-specific Pγs underlie transducin's ability to more effectively activate cone-specific PDE6 than rod PDE6. To test this, we analyzed rod and cone Pγ sequences from all major vertebrate and cyclostome lineages and found that rod Pγ loci are far more conserved than cone Pγ sequences and that most of the sequence differences are located in the N-terminal region. Next we reconstituted rod PDE6 catalytic dimer (Pαβ) with various rod or cone Pγ variants and analyzed PDE6 activation upon addition of the activated transducin α-subunit (Gtα*-GTPγS). This analysis revealed a rod-specific Pγ motif (amino acids 9-18) that reduces the ability of Gtα*-GTPγS to activate the reconstituted PDE6. In cone Pγ, Asn-13 and Gln-14 significantly enhanced Gtα*-GTPγS activation of cone Pγ truncation variants. Moreover, we observed that the first four amino acids of either rod or cone Pγ contribute to Gtα*-GTPγS-mediated activation of PDE6. We conclude that physiological differences between rod and cone photoreceptor light responsiveness can be partially ascribed to ancient, highly conserved amino acid differences in the N-terminal regions of Pγ isoforms, demonstrating for the first time a functional role for this region of Pγ in the differential activation of rod and cone PDE6 by transducin.
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Affiliation(s)
- Xin Wang
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - David C Plachetzki
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - Rick H Cote
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824.
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24
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Pinto BJ, Card DC, Castoe TA, Diaz RE, Nielsen SV, Trainor PA, Gamble T. The transcriptome of the veiled chameleon (Chamaeleo calyptratus): A resource for studying the evolution and development of vertebrates. Dev Dyn 2019; 248:702-708. [PMID: 30839129 DOI: 10.1002/dvdy.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo-devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking. METHODS To address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) and whole embryos at three distinct developmental stages. We used these data to assemble a largely complete de novo transcriptome consisting of only 82 952 transcripts. In addition, a majority of assembled transcripts (67%) were successfully annotated. RESULTS We then demonstrated the utility of these data in the context of studying visual system evolution by examining the content of veiled chameleon opsin genes to show that chameleons possess all five ancestral tetrapod opsins. CONCLUSION We present this de novo, annotated, multi-tissue transcriptome assembly for the Veiled Chameleon, Chamaeleo calyptratus, as a resource to address a range of evolutionary and developmental questions. The associated raw reads and final annotated transcriptome assembly are freely available for use on NCBI and Figshare, respectively.
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Affiliation(s)
- Brendan J Pinto
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin
| | - Daren C Card
- Department of Biology, The University of Texas at Arlington, Arlington, Texas
| | - Todd A Castoe
- Department of Biology, The University of Texas at Arlington, Arlington, Texas
| | - Raul E Diaz
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana.,Natural History Museum of Los Angeles County, Los Angeles, California
| | - Stuart V Nielsen
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin
| | - Paul A Trainor
- Department of Anatomy & Cell Biology, Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin.,Milwaukee Public Museum, Milwaukee, Wisconsin.,Bell Museum of Natural History, University of Minnesota, St Paul, Minnesota
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25
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Lamb TD, Patel HR, Chuah A, Hunt DM. Evolution of the shut-off steps of vertebrate phototransduction. Open Biol 2019; 8:rsob.170232. [PMID: 29321241 PMCID: PMC5795056 DOI: 10.1098/rsob.170232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
Different isoforms of the genes involved in phototransduction are expressed in vertebrate rod and cone photoreceptors, providing a unique example of parallel evolution via gene duplication. In this study, we determine the molecular phylogeny of the proteins underlying the shut-off steps of phototransduction in the agnathan and jawed vertebrate lineages. For the G-protein receptor kinases (GRKs), the GRK1 and GRK7 divisions arose prior to the divergence of tunicates, with further expansion during the two rounds of whole-genome duplication (2R); subsequently, jawed and agnathan vertebrates retained different subsets of three isoforms of GRK. For the arrestins, gene expansion occurred during 2R. Importantly, both for GRKs and arrestins, the respective rod isoforms did not emerge until the second round of 2R, just prior to the separation of jawed and agnathan vertebrates. For the triplet of proteins mediating shut-off of the G-protein transducin, RGS9 diverged from RGS11, probably at the second round of 2R, whereas Gβ5 and R9AP appear not to have undergone 2R expansion. Overall, our analysis provides a description of the duplications and losses of phototransduction shut-off genes that occurred during the transition from a chordate with only cone-like photoreceptors to an ancestral vertebrate with both cone- and rod-like photoreceptors.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Australian Capital Territory 2600, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, The Australian National University, Australian Capital Territory 2600, Australia
| | - Aaron Chuah
- Genome Discovery Unit, John Curtin School of Medical Research, The Australian National University, Australian Capital Territory 2600, Australia
| | - David M Hunt
- The Lions Eye Institute, The University of Western Australia, Western Australia 6009, Australia.,School of Biological Sciences, The University of Western Australia, Western Australia 6009, Australia
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26
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Castiglione GM, Chang BS. Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision. eLife 2018; 7:35957. [PMID: 30362942 PMCID: PMC6203435 DOI: 10.7554/elife.35957] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022] Open
Abstract
Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.
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Affiliation(s)
- Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Belinda Sw Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
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27
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Lamb TD, Hunt DM. Evolution of the calcium feedback steps of vertebrate phototransduction. Open Biol 2018; 8:180119. [PMID: 30257895 PMCID: PMC6170504 DOI: 10.1098/rsob.180119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/29/2018] [Indexed: 01/11/2023] Open
Abstract
We examined the genes encoding the proteins that mediate the Ca-feedback regulatory system in vertebrate rod and cone phototransduction. These proteins comprise four families: recoverin/visinin, the guanylyl cyclase activating proteins (GCAPs), the guanylyl cyclases (GCs) and the sodium/calcium-potassium exchangers (NCKXs). We identified a paralogon containing at least 36 phototransduction genes from at least fourteen families, including all four of the families involved in the Ca-feedback loop (recoverin/visinin, GCAPs, GCs and NCKXs). By combining analyses of gene synteny with analyses of the molecular phylogeny for each of these four families of genes for Ca-feedback regulation, we have established the likely pattern of gene duplications and losses underlying the expansion of isoforms, both before and during the two rounds of whole-genome duplication (2R WGD) that occurred in early vertebrate evolution. Furthermore, by combining our results with earlier evidence on the timing of duplication of the visual G-protein receptor kinase genes, we propose that specialization of proto-vertebrate photoreceptor cells for operation at high and low light intensities preceded the emergence of rhodopsin, which occurred during 2R WGD.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Australian Capital Territory 2600, Australia
| | - David M Hunt
- Centre for Ophthalmology and Visual Science, The Lions Eye Institute, The University of Western Australia, Western Australia 6009, Australia
- School of Biological Sciences, The University of Western Australia, Western Australia 6009, Australia
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28
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Lokits AD, Indrischek H, Meiler J, Hamm HE, Stadler PF. Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa. BMC Evol Biol 2018; 18:51. [PMID: 29642851 PMCID: PMC5896119 DOI: 10.1186/s12862-018-1147-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/06/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Heterotrimeric G proteins are fundamental signaling proteins composed of three subunits, Gα and a Gβγ dimer. The role of Gα as a molecular switch is critical for transmitting and amplifying intracellular signaling cascades initiated by an activated G protein Coupled Receptor (GPCR). Despite their biochemical and therapeutic importance, the study of G protein evolution has been limited to the scope of a few model organisms. Furthermore, of the five primary Gα subfamilies, the underlying gene structure of only two families has been thoroughly investigated outside of Mammalia evolution. Therefore our understanding of Gα emergence and evolution across phylogeny remains incomplete. RESULTS We have computationally identified the presence and absence of every Gα gene (GNA-) across all major branches of Deuterostomia and evaluated the conservation of the underlying exon-intron structures across these phylogenetic groups. We provide evidence of mutually exclusive exon inclusion through alternative splicing in specific lineages. Variations of splice site conservation and isoforms were found for several paralogs which coincide with conserved, putative motifs of DNA-/RNA-binding proteins. In addition to our curated gene annotations, within Primates, we identified 15 retrotranspositions, many of which have undergone pseudogenization. Most importantly, we find numerous deviations from previous findings regarding the presence and absence of individual GNA- genes, nuanced differences in phyla-specific gene copy numbers, novel paralog duplications and subsequent intron gain and loss events. CONCLUSIONS Our curated annotations allow us to draw more accurate inferences regarding the emergence of all Gα family members across Metazoa and to present a new, updated theory of Gα evolution. Leveraging this, our results are critical for gaining new insights into the co-evolution of the Gα subunit and its many protein binding partners, especially therapeutically relevant G protein - GPCR signaling pathways which radiated in Vertebrata evolution.
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Affiliation(s)
- A. D. Lokits
- 0000 0001 2264 7217grid.152326.1Neuroscience Program, Vanderbilt University, Nashville, TN USA ,0000 0001 2264 7217grid.152326.1Center for Structural Biology, Vanderbilt University, Nashville, TN USA
| | - H. Indrischek
- 0000 0001 2230 9752grid.9647.cBioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany ,0000 0001 2230 9752grid.9647.cComputational EvoDevo Group, Bioinformatics Department, Leipzig University, Leipzig, Germany
| | - J. Meiler
- 0000 0001 2264 7217grid.152326.1Center for Structural Biology, Vanderbilt University, Nashville, TN USA ,0000 0001 2264 7217grid.152326.1Chemistry Department, Vanderbilt University, Nashville, TN USA
| | - H. E. Hamm
- 0000 0004 1936 9916grid.412807.8Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN USA
| | - P. F. Stadler
- 0000 0001 2230 9752grid.9647.cBioinformatics Group, Department of Computer Science, Leipzig University, Leipzig, Germany ,0000 0001 0674 042Xgrid.5254.6Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark ,0000 0001 2286 1424grid.10420.37Institute for Theoretical Chemistry, University of Vienna, Wien, Austria ,0000 0001 2230 9752grid.9647.cIZBI-Interdisciplinary Center for Bioinformatics and LIFE-Leipzig Research Center for Civilization Diseases and Competence Center for Scalable Data Services and Solutions, University Leipzig, Leipzig, Germany ,grid.419532.8Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany ,0000 0001 1941 1940grid.209665.eSanta Fe Institute, Santa Fe, NM USA
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29
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Castiglione GM, Schott RK, Hauser FE, Chang BSW. Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms. Evolution 2018; 72:170-186. [DOI: 10.1111/evo.13396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/02/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Gianni M. Castiglione
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Ryan K. Schott
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Belinda S. W. Chang
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
- Centre for the Analysis of Genome Evolution and Function; University of Toronto; Toronto Ontario M5S 3B2 Canada
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30
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Lin JJ, Wang FY, Li WH, Wang TY. The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation. Sci Rep 2017; 7:15568. [PMID: 29138475 PMCID: PMC5686071 DOI: 10.1038/s41598-017-15868-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/03/2017] [Indexed: 01/25/2023] Open
Abstract
We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes. For cone opsin genes, the rhodopsin-like (Rh2) and long-wave-sensitive (LWS) genes showed great variation in N among species, ranging from 0 to 5 and from 0 to 4, respectively. The two short-wave-sensitive genes, SWS1 and SWS2, were lost in 23 and 6 species, respectively. The syntenies involving LWS, SWS2 and Rh2 underwent complex changes, while the evolution of the other opsin gene syntenies was much simpler. Evolutionary adaptation in tuning sites under different living environments was discussed. Our study provides a detailed view of opsin gene gains and losses, synteny changes and tuning site changes during ray-finned fish evolution.
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Affiliation(s)
- Jinn-Jy Lin
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, 852, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan. .,Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, 60637, USA.
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
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31
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Insights into visual pigment adaptation and diversity from model ecological and evolutionary systems. Curr Opin Genet Dev 2017; 47:110-120. [PMID: 29102895 DOI: 10.1016/j.gde.2017.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/18/2017] [Accepted: 09/29/2017] [Indexed: 01/07/2023]
Abstract
Sensory systems provide valuable insight into the evolution of molecular mechanisms underlying organismal anatomy, physiology, and behaviour. Visual pigments, which mediate the first step in visual transduction, offer a unique window into the relationship between molecular variation and visual performance, and enhance our understanding of how ecology, life history, and physiology may shape genetic variation across a variety of organisms. Here we review recent work investigating vertebrate visual pigments from a number of perspectives. Opsin gene duplication, loss, differential expression, structural variation, and the physiological context in which they operate, have profoundly shaped the visual capabilities of vertebrates adapting to novel environments. We note the importance of conceptual frameworks in investigating visual pigment diversity in vertebrates, highlighting key examples including evolutionary transitions between different photic environments, major shifts in life history evolution and ecology, evolutionary innovations in visual system anatomy and physiology, as well as shifts in visually mediated behaviours and behavioural ecology. We emphasize the utility of studying visual pigment evolution in the context of these different perspectives, and demonstrate how the integrative approaches discussed in this review contribute to a better understanding of the underlying molecular processes mediating adaptation in sensory systems, and the contexts in which they occur.
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32
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Musser JM, Arendt D. Loss and gain of cone types in vertebrate ciliary photoreceptor evolution. Dev Biol 2017; 431:26-35. [DOI: 10.1016/j.ydbio.2017.08.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 01/09/2023]
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33
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de Busserolles F, Cortesi F, Helvik JV, Davies WIL, Templin RM, Sullivan RKP, Michell CT, Mountford JK, Collin SP, Irigoien X, Kaartvedt S, Marshall J. Pushing the limits of photoreception in twilight conditions: The rod-like cone retina of the deep-sea pearlsides. SCIENCE ADVANCES 2017; 3:eaao4709. [PMID: 29134201 PMCID: PMC5677336 DOI: 10.1126/sciadv.aao4709] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
Most vertebrates have a duplex retina comprising two photoreceptor types, rods for dim-light (scotopic) vision and cones for bright-light (photopic) and color vision. However, deep-sea fishes are only active in dim-light conditions; hence, most species have lost their cones in favor of a simplex retina composed exclusively of rods. Although the pearlsides, Maurolicus spp., have such a pure rod retina, their behavior is at odds with this simplex visual system. Contrary to other deep-sea fishes, pearlsides are mostly active during dusk and dawn close to the surface, where light levels are intermediate (twilight or mesopic) and require the use of both rod and cone photoreceptors. This study elucidates this paradox by demonstrating that the pearlside retina does not have rod photoreceptors only; instead, it is composed almost exclusively of transmuted cone photoreceptors. These transmuted cells combine the morphological characteristics of a rod photoreceptor with a cone opsin and a cone phototransduction cascade to form a unique photoreceptor type, a rod-like cone, specifically tuned to the light conditions of the pearlsides' habitat (blue-shifted light at mesopic intensities). Combining properties of both rods and cones into a single cell type, instead of using two photoreceptor types that do not function at their full potential under mesopic conditions, is likely to be the most efficient and economical solution to optimize visual performance. These results challenge the standing paradigm of the function and evolution of the vertebrate duplex retina and emphasize the need for a more comprehensive evaluation of visual systems in general.
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Affiliation(s)
- Fanny de Busserolles
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jon Vidar Helvik
- Department of Biology, University of Bergen, Bergen 5020, Norway
| | - Wayne I. L. Davies
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Rachel M. Templin
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert K. P. Sullivan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Craig T. Michell
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistokatu 7, FI-80101 Joensuu, Finland
| | - Jessica K. Mountford
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Shaun P. Collin
- The Oceans Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
- School of Biological Science, The University of Western Australia, Crawley, Western Australia 6009, Australia
- Lions Eye Institute, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Xabier Irigoien
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Marine Research, AZTI - Tecnalia, Herrera Kaia, Portualdea z/g, 20110 Pasaia (Gipuzkoa), Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Stein Kaartvedt
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | - Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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34
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Morshedian A, Toomey MB, Pollock GE, Frederiksen R, Enright JM, McCormick SD, Cornwall MC, Fain GL, Corbo JC. Cambrian origin of the CYP27C1-mediated vitamin A 1-to-A 2 switch, a key mechanism of vertebrate sensory plasticity. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170362. [PMID: 28791166 PMCID: PMC5541561 DOI: 10.1098/rsos.170362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/07/2017] [Indexed: 05/16/2023]
Abstract
The spectral composition of ambient light varies across both space and time. Many species of jawed vertebrates adapt to this variation by tuning the sensitivity of their photoreceptors via the expression of CYP27C1, an enzyme that converts vitamin A1 into vitamin A2, thereby shifting the ratio of vitamin A1-based rhodopsin to red-shifted vitamin A2-based porphyropsin in the eye. Here, we show that the sea lamprey (Petromyzon marinus), a jawless vertebrate that diverged from jawed vertebrates during the Cambrian period (approx. 500 Ma), dynamically shifts its photoreceptor spectral sensitivity via vitamin A1-to-A2 chromophore exchange as it transitions between photically divergent aquatic habitats. We further show that this shift correlates with high-level expression of the lamprey orthologue of CYP27C1, specifically in the retinal pigment epithelium as in jawed vertebrates. Our results suggest that the CYP27C1-mediated vitamin A1-to-A2 switch is an evolutionarily ancient mechanism of sensory plasticity that appeared not long after the origin of vertebrates.
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Affiliation(s)
- Ala Morshedian
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew B. Toomey
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Gabriel E. Pollock
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Rikard Frederiksen
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jennifer M. Enright
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Stephen D. McCormick
- Conte Anadromous Fish Research Laboratory, US Geological Survey, Leetown Science Center, Turners Falls, MA 01370, USA
| | - M. Carter Cornwall
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Gordon L. Fain
- Department of Ophthalmology and Jules Stein Eye Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Authors for correspondence: Gordon L. Fain e-mail:
| | - Joseph C. Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
- Authors for correspondence: Joseph C. Corbo e-mail:
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35
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Abstract
High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.
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Morshedian A, Fain GL. Light adaptation and the evolution of vertebrate photoreceptors. J Physiol 2017; 595:4947-4960. [PMID: 28488783 DOI: 10.1113/jp274211] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/02/2017] [Indexed: 11/08/2022] Open
Abstract
KEY POINTS Lamprey are cyclostomes, a group of vertebrates that diverged from lines leading to jawed vertebrates (including mammals) in the late Cambrian, 500 million years ago. It may therefore be possible to infer properties of photoreceptors in early vertebrate progenitors by comparing lamprey to other vertebrates. We show that lamprey rods and cones respond to light much like rods and cones in amphibians and mammals. They operate over a similar range of light intensities and adapt to backgrounds and bleaches nearly identically. These correspondences are pervasive and detailed; they argue for the presence of rods and cones very early in the evolution of vertebrates with properties much like those of rods and cones in existing vertebrate species. ABSTRACT The earliest vertebrates were agnathans - fish-like organisms without jaws, which first appeared near the end of the Cambrian radiation. One group of agnathans became cyclostomes, which include lamprey and hagfish. Other agnathans gave rise to jawed vertebrates or gnathostomes, the group including all other existing vertebrate species. Because cyclostomes diverged from other vertebrates 500 million years ago, it may be possible to infer some of the properties of the retina of early vertebrate progenitors by comparing lamprey to other vertebrates. We have previously shown that rods and cones in lamprey respond to light much like photoreceptors in other vertebrates and have a similar sensitivity. We now show that these affinities are even closer. Both rods and cones adapt to background light and to bleaches in a manner almost identical to other vertebrate photoreceptors. The operating range in darkness is nearly the same in lamprey and in amphibian or mammalian rods and cones; moreover background light shifts response-intensity curves downward and to the right over a similar range of ambient intensities. Rods show increment saturation at about the same intensity as mammalian rods, and cones never saturate. Bleaches decrease sensitivity in part by loss of quantum catch and in part by opsin activation of transduction. These correspondences are so numerous and pervasive that they are unlikely to result from convergent evolution but argue instead that early vertebrate progenitors of both cyclostomes and mammals had photoreceptors much like our own.
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Affiliation(s)
- Ala Morshedian
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095-7239, USA
| | - Gordon L Fain
- Department of Integrative Biology and Physiology, UCLA, Los Angeles, CA, 90095-7239, USA.,Jules Stein Eye Institute, UCLA School of Medicine, Los Angeles, CA, 90095-7000, USA
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Koyanagi M, Kawano-Yamashita E, Wada S, Terakita A. Vertebrate Bistable Pigment Parapinopsin: Implications for Emergence of Visual Signaling and Neofunctionalization of Non-visual Pigment. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Lamb TD, Hunt DM. Evolution of the vertebrate phototransduction cascade activation steps. Dev Biol 2017; 431:77-92. [PMID: 28347645 DOI: 10.1016/j.ydbio.2017.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/28/2017] [Accepted: 03/20/2017] [Indexed: 02/06/2023]
Abstract
We examine the molecular phylogeny of the proteins underlying the activation steps of vertebrate phototransduction, for both agnathan and jawed vertebrate taxa. We expand the number of taxa analysed and we update the alignment and tree building methodology from a previous analysis. For each of the four primary components (the G-protein transducin alpha subunit, GαT, the cyclic GMP phosphodiesterase, PDE6, and the alpha and beta subunits of the cGMP-gated ion channel, CNGC), the phylogenies appear consistent with expansion from an ancestral proto-vertebrate cascade during two rounds of whole-genome duplication followed by divergence of the agnathan and jawed vertebrate lineages. In each case, we consider possible scenarios for the underlying gene duplications and losses, and we apply relevant constraints to the tree construction. From tests of the topology of the resulting trees, we obtain a scenario for the expansion of each component during 2R that accurately fits the observations. Similar analysis of the visual opsins indicates that the only expansion to have occurred during 2R was the formation of Rh1 and Rh2. Finally, we propose a hypothetical scenario for the conversion of an ancestral chordate cascade into the proto-vertebrate phototransduction cascade, prior to whole-genome duplication. Together, our models provide a plausible account for the origin and expansion of the vertebrate phototransduction cascade.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, ACT 2600, Australia.
| | - David M Hunt
- The Lions Eye Institute, The University of Western Australia, WA 6009, Australia; School of Biological Sciences, The University of Western Australia, WA 6009, Australia
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Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors. Sci Rep 2016; 6:33578. [PMID: 27645106 PMCID: PMC5028738 DOI: 10.1038/srep33578] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/31/2016] [Indexed: 01/06/2023] Open
Abstract
Owls (Strigiformes) represent a fascinating group of birds that are the ecological night-time counterparts to diurnal raptors (Accipitriformes). The nocturnality of owls, unusual within birds, has favored an exceptional visual system that is highly tuned for hunting at night, yet the molecular basis for this adaptation is lacking. Here, using a comparative evolutionary analysis of 120 vision genes obtained by retinal transcriptome sequencing, we found strong positive selection for low-light vision genes in owls, which contributes to their remarkable nocturnal vision. Not surprisingly, we detected gene loss of the violet/ultraviolet-sensitive opsin (SWS1) in all owls we studied, but two other color vision genes, the red-sensitive LWS and the blue-sensitive SWS2, were found to be under strong positive selection, which may be linked to the spectral tunings of these genes toward maximizing photon absorption in crepuscular conditions. We also detected the only other positively selected genes associated with motion detection in falcons and positively selected genes associated with bright-light vision and eye protection in other diurnal raptors (Accipitriformes). Our results suggest the adaptive evolution of vision genes reflect differentiated activity time and distinct hunting behaviors.
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