1
|
Gerwin J, Torres-Dowdall J, Brown TF, Meyer A. Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes. J Mol Evol 2024:10.1007/s00239-024-10181-0. [PMID: 38861038 DOI: 10.1007/s00239-024-10181-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Gene duplication is one of the most important sources of novel genotypic diversity and the subsequent evolution of phenotypic diversity. Determining the evolutionary history and functional changes of duplicated genes is crucial for a comprehensive understanding of adaptive evolution. The evolutionary history of visual opsin genes is very dynamic, with repeated duplication events followed by sub- or neofunctionalization. While duplication of the green-sensitive opsins rh2 is common in teleost fish, fewer cases of multiple duplication events of the red-sensitive opsin lws are known. In this study, we investigate the visual opsin gene repertoire of the anabantoid fishes, focusing on the five lws opsin genes found in the genus Betta. We determine the evolutionary history of the lws opsin gene by taking advantage of whole-genome sequences of nine anabantoid species, including the newly assembled genome of Betta imbellis. Our results show that at least two independent duplications of lws occurred in the Betta lineage. The analysis of amino acid sequences of the lws paralogs of Betta revealed high levels of diversification in four of the seven transmembrane regions of the lws protein. Amino acid substitutions at two key-tuning sites are predicted to lead to differentiation of absorption maxima (λmax) between the paralogs within Betta. Finally, eye transcriptomics of B. splendens at different developmental stages revealed expression shifts between paralogs for all cone opsin classes. The lws genes are expressed according to their relative position in the lws opsin cluster throughout ontogeny. We conclude that temporal collinearity of lws expression might have facilitated subfunctionalization of lws in Betta and teleost opsins in general.
Collapse
Affiliation(s)
- Jan Gerwin
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany.
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Thomas F Brown
- Max Planck Institute of Molecular Cellular Biology and Genetics, Dresden, Germany
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany.
| |
Collapse
|
2
|
Musilova Z, Salzburger W, Cortesi F. The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function. Annu Rev Cell Dev Biol 2021; 37:441-468. [PMID: 34351785 DOI: 10.1146/annurev-cellbio-120219-024915] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Zuzana Musilova
- Department of Zoology, Charles University, Prague 128 44, Czech Republic;
| | | | - Fabio Cortesi
- Queensland Brain Institute, The University of Queensland, Brisbane 4072, Queensland, Australia;
| |
Collapse
|
3
|
Byun JH, Hyeon JY, Kim ES, Kim BH, Miyanishi H, Kagawa H, Takeuchi Y, Kim SJ, Takemura A, Hur SP. Gene expression patterns of novel visual and non-visual opsin families in immature and mature Japanese eel males. PeerJ 2020; 8:e8326. [PMID: 32149019 PMCID: PMC7049458 DOI: 10.7717/peerj.8326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 12/02/2019] [Indexed: 01/24/2023] Open
Abstract
This study was carried out to identify and estimate physiological function of a new type of opsin subfamily present in the retina and whole brain tissues of Japanese eel using RNA–Seq transcriptome method. A total of 18 opsin subfamilies were identified through RNA–seq. The visual opsin family included Rh2, SWS2, FWO, DSO, and Exo-Rhod. The non-visual opsin family included four types of melanopsin subfamily (Opn4x1, Opn4x2, Opn4m1, and Opn4m2), peropsin, two types of neuropsin subfamily (Opn5-like, Opn5), Opn3, three types of TMT opsin subfamily (TMT1, 2, 3), VA-opsin, and parapinopsin. In terms of changes in photoreceptor gene expression in the retina of sexually mature and immature male eels, DSO mRNA increased in the maturation group. Analysis of expression of opsin family gene in male eel brain before and after maturation revealed that DSO and SWS2 expression in terms of visual opsin mRNA increased in the sexually mature group. In terms of non-visual opsin mRNA, parapinopsin mRNA increased whereas that of TMT2 decreased in the fore-brain of the sexually mature group. The mRNA for parapinopsin increased in the mid-brain of the sexually mature group, whereas those of TMT1 and TMT3 increased in the hind-brain of the sexually mature group. DSO mRNA also increased in the retina after sexual maturation, and DSO and SWS2 mRNA increased in whole brain part, suggesting that DSO and SWS2 are closely related to sexual maturation.
Collapse
Affiliation(s)
- Jun-Hwan Byun
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Ji-Yeon Hyeon
- Jeju Research Institute, Korea Institute of Ocean Science & Technology, Jeju, Jeju, Republic of Korea.,Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Eun-Su Kim
- Jeju Research Institute, Korea Institute of Ocean Science & Technology, Jeju, Jeju, Republic of Korea.,Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Byeong-Hoon Kim
- Marine Science Institute, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Hiroshi Miyanishi
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadai-Nishi, Miyazaki, Japan
| | - Hirohiko Kagawa
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadai-Nishi, Miyazaki, Japan
| | - Yuki Takeuchi
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Se-Jae Kim
- Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Akihiro Takemura
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Sung-Pyo Hur
- Jeju Research Institute, Korea Institute of Ocean Science & Technology, Jeju, Jeju, Republic of Korea.,Department of Biology, Jeju National University, Jeju, Jeju, Republic of Korea
| |
Collapse
|
4
|
Musilova Z, Cortesi F, Matschiner M, Davies WIL, Patel JS, Stieb SM, de Busserolles F, Malmstrøm M, Tørresen OK, Brown CJ, Mountford JK, Hanel R, Stenkamp DL, Jakobsen KS, Carleton KL, Jentoft S, Marshall J, Salzburger W. Vision using multiple distinct rod opsins in deep-sea fishes. Science 2019; 364:588-592. [PMID: 31073066 DOI: 10.1126/science.aav4632] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/16/2019] [Indexed: 02/01/2023]
Abstract
Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.
Collapse
Affiliation(s)
- Zuzana Musilova
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland. .,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Fabio Cortesi
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland. .,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Matschiner
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland
| | - Wayne I L Davies
- UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia.,School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.,Lions Eye Institute, The University of Western Australia, Perth, WA, Australia.,Oceans Graduate School, The University of Western Australia, Perth, WA, Australia
| | - Jagdish Suresh Patel
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, USA.,Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Sara M Stieb
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,Center for Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Fanny de Busserolles
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.,Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Martin Malmstrøm
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Celeste J Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Jessica K Mountford
- UWA Oceans Institute, The University of Western Australia, Perth, WA, Australia.,School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.,Lions Eye Institute, The University of Western Australia, Perth, WA, Australia
| | - Reinhold Hanel
- Thünen Institute of Fisheries Ecology, Bremerhaven, Germany
| | | | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Justin Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland. .,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
5
|
Evolutionary history of teleost intron-containing and intron-less rhodopsin genes. Sci Rep 2019; 9:10653. [PMID: 31337799 PMCID: PMC6650399 DOI: 10.1038/s41598-019-47028-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/09/2019] [Indexed: 11/08/2022] Open
Abstract
Recent progress in whole genome sequencing has revealed that animals have various kinds of opsin genes for photoreception. Among them, most opsin genes have introns in their coding regions. However, it has been known for a long time that teleost retinas express intron-less rhodopsin genes, which are presumed to have been formed by retroduplication from an ancestral intron-containing rhodopsin gene. In addition, teleosts have an intron-containing rhodopsin gene (exo-rhodopsin) exclusively for pineal photoreception. In this study, to unravel the evolutionary origin of the two teleost rhodopsin genes, we analyzed the rhodopsin genes of non-teleost fishes in the Actinopterygii. The phylogenetic analysis of full-length sequences of bichir, sturgeon and gar rhodopsins revealed that retroduplication of the rhodopsin gene occurred after branching of the bichir lineage. In addition, analysis of the tissue distribution and the molecular properties of bichir, sturgeon and gar rhodopsins showed that the abundant and exclusive expression of intron-containing rhodopsin in the pineal gland and the short lifetime of its meta II intermediate, which leads to optimization for pineal photoreception, were achieved after branching of the gar lineage. Based on these results, we propose a stepwise evolutionary model of teleost intron-containing and intron-less rhodopsin genes.
Collapse
|
6
|
Chen JN, Samadi S, Chen WJ. Rhodopsin gene evolution in early teleost fishes. PLoS One 2018; 13:e0206918. [PMID: 30395593 PMCID: PMC6218077 DOI: 10.1371/journal.pone.0206918] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/22/2018] [Indexed: 01/03/2023] Open
Abstract
Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.
Collapse
Affiliation(s)
- Jhen-Nien Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Sarah Samadi
- Institute de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle–CNRS, Sorbonne Université, EPHE, Paris, France
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
7
|
Athanasiou D, Aguila M, Bellingham J, Li W, McCulley C, Reeves PJ, Cheetham ME. The molecular and cellular basis of rhodopsin retinitis pigmentosa reveals potential strategies for therapy. Prog Retin Eye Res 2018; 62:1-23. [PMID: 29042326 PMCID: PMC5779616 DOI: 10.1016/j.preteyeres.2017.10.002] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/03/2017] [Accepted: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Inherited mutations in the rod visual pigment, rhodopsin, cause the degenerative blinding condition, retinitis pigmentosa (RP). Over 150 different mutations in rhodopsin have been identified and, collectively, they are the most common cause of autosomal dominant RP (adRP). Mutations in rhodopsin are also associated with dominant congenital stationary night blindness (adCSNB) and, less frequently, recessive RP (arRP). Recessive RP is usually associated with loss of rhodopsin function, whereas the dominant conditions are a consequence of gain of function and/or dominant negative activity. The in-depth characterisation of many rhodopsin mutations has revealed that there are distinct consequences on the protein structure and function associated with different mutations. Here we categorise rhodopsin mutations into seven discrete classes; with defects ranging from misfolding and disruption of proteostasis, through mislocalisation and disrupted intracellular traffic to instability and altered function. Rhodopsin adRP offers a unique paradigm to understand how disturbances in photoreceptor homeostasis can lead to neuronal cell death. Furthermore, a wide range of therapies have been tested in rhodopsin RP, from gene therapy and gene editing to pharmacological interventions. The understanding of the disease mechanisms associated with rhodopsin RP and the development of targeted therapies offer the potential of treatment for this currently untreatable neurodegeneration.
Collapse
Affiliation(s)
| | - Monica Aguila
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - James Bellingham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Wenwen Li
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Caroline McCulley
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK.
| | | |
Collapse
|
8
|
Beaudry FEG, Iwanicki TW, Mariluz BRZ, Darnet S, Brinkmann H, Schneider P, Taylor JS. The non-visual opsins: eighteen in the ancestor of vertebrates, astonishing increase in ray-finned fish, and loss in amniotes. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:685-696. [DOI: 10.1002/jez.b.22773] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 12/20/2022]
Affiliation(s)
| | - Tom W. Iwanicki
- Department of Biology; University of Victoria; Victoria BC Canada
| | | | - Sylvain Darnet
- Instituto de Ciências Biológicas; Universidade Federal do Pará (UFPA); Campus do Guamá Belém PA Brazil
| | - Henner Brinkmann
- Microbial Ecology and Diversity Research; Leibniz Institute; DSMZ, Inhoffenstraße 7B Braunschweig Germany
| | - Patricia Schneider
- Instituto de Ciências Biológicas; Universidade Federal do Pará (UFPA); Campus do Guamá Belém PA Brazil
| | | |
Collapse
|
9
|
Morrow JM, Lazic S, Dixon Fox M, Kuo C, Schott RK, de A Gutierrez E, Santini F, Tropepe V, Chang BSW. A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes. ACTA ACUST UNITED AC 2016; 220:294-303. [PMID: 27811293 DOI: 10.1242/jeb.145953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022]
Abstract
Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1 We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1 These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.
Collapse
Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Savo Lazic
- Department of Molecular Genetics, University of Toronto, Toronto, Canada, M5S 1A8
| | - Monica Dixon Fox
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Claire Kuo
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Francesco Santini
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada, M5T 3A9.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5 .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| |
Collapse
|
10
|
Lagman D, Franzén IE, Eggert J, Larhammar D, Abalo XM. Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity. BMC Evol Biol 2016; 16:124. [PMID: 27296292 PMCID: PMC4906994 DOI: 10.1186/s12862-016-0695-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/01/2016] [Indexed: 02/25/2023] Open
Abstract
Background Phosphodiesterase 6 (PDE6) is a protein complex that hydrolyses cGMP and acts as the effector of the vertebrate phototransduction cascade. The PDE6 holoenzyme consists of catalytic and inhibitory subunits belonging to two unrelated gene families. Rods and cones express distinct genes from both families: PDE6A and PDE6B code for the catalytic and PDE6G the inhibitory subunits in rods while PDE6C codes for the catalytic and PDE6H the inhibitory subunits in cones. We performed phylogenetic and comparative synteny analyses for both gene families in genomes from a broad range of animals. Furthermore, gene expression was investigated in zebrafish. Results We found that both gene families expanded from one to three members in the two rounds of genome doubling (2R) that occurred at the base of vertebrate evolution. The PDE6 inhibitory subunit gene family appears to be unique to vertebrates and expanded further after the teleost-specific genome doubling (3R). We also describe a new family member that originated in 2R and has been lost in amniotes, which we have named pde6i. Zebrafish has retained two additional copies of the PDE6 inhibitory subunit genes after 3R that are highly conserved, have high amino acid sequence identity, are coexpressed in the same photoreceptor type as their amniote orthologs and, interestingly, show strikingly different daily oscillation in gene expression levels. Conclusions Together, these data suggest specialisation related to the adaptation to different light intensities during the day-night cycle, most likely maintaining the regulatory function of the PDE inhibitory subunits in the phototransduction cascade. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0695-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- David Lagman
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124, Uppsala, Sweden
| | - Ilkin E Franzén
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124, Uppsala, Sweden
| | - Joel Eggert
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124, Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124, Uppsala, Sweden
| | - Xesús M Abalo
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124, Uppsala, Sweden.
| |
Collapse
|
11
|
Feuda R, Marlétaz F, Bentley MA, Holland PWH. Conservation, Duplication, and Divergence of Five Opsin Genes in Insect Evolution. Genome Biol Evol 2016; 8:579-87. [PMID: 26865071 PMCID: PMC4824169 DOI: 10.1093/gbe/evw015] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Opsin proteins covalently bind to small molecular chromophores and each protein-chromophore complex is sensitive to particular wavelengths of light. Multiple opsins with different wavelength absorbance peaks are required for color vision. Comparing opsin responses is challenging at low light levels, explaining why color vision is often lost in nocturnal species. Here, we investigated opsin evolution in 27 phylogenetically diverse insect species including several transitions between photic niches (nocturnal, diurnal, and crepuscular). We find widespread conservation of five distinct opsin genes, more than commonly considered. These comprise one c-opsin plus four r-opsins (long wavelength sensitive or LWS, blue sensitive, ultra violet [UV] sensitive and the often overlooked Rh7 gene). Several recent opsin gene duplications are also detected. The diversity of opsin genes is consistent with color vision in diurnal, crepuscular, and nocturnal insects. Tests for positive selection in relation to photic niche reveal evidence for adaptive evolution in UV-sensitive opsins in day-flying insects in general, and in LWS opsins of day-flying Lepidoptera specifically.
Collapse
Affiliation(s)
- Roberto Feuda
- Department of Zoology, University of Oxford, United Kingdom
| | | | | | | |
Collapse
|
12
|
Brüning A, Hölker F, Franke S, Kleiner W, Kloas W. Impact of different colours of artificial light at night on melatonin rhythm and gene expression of gonadotropins in European perch. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 543:214-222. [PMID: 26584071 DOI: 10.1016/j.scitotenv.2015.11.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 05/10/2023]
Abstract
The distribution and intensity of artificial light at night, commonly referred to as light pollution, is consequently rising and progressively also ecological implications come to light. Low intensity light is known to suppress nocturnal melatonin production in several fish species. This study aims to examine the least suppressive light colour for melatonin excreted into the holding water and the influence of different light qualities and quantities in the night on gene expression of gonadotropins in fish. European perch (Perca fluviatilis) were exposed to light of different wavelengths during the night (blue, green, and red). Melatonin concentrations were measured from water samples every 3h during a 24h period. Gene expression of gonadotropins was measured in perch exposed to different light colours and was additionally examined for perch subjected to different intensities of white light (0 lx, 1 lx, 10 lx, 100 lx) during the night. All different light colours caused a significant drop of melatonin concentration; however, blue light was least suppressive. Gene expression of gonadotropins was not influenced by nocturnal light of different light colours, but in female perch gonadotropin expression was significantly reduced by white light already at the lowest level (1 lx). We conclude that artificial light with shorter wavelengths at night is less effective in disturbing biological rhythms of perch than longer wavelengths, coinciding with the light situation in freshwater habitats inhabited by perch. Different light colours in the night showed no significant effect on gonadotropin expression, but white light in the night can disturb reproductive traits already at very low light intensities. These findings indicate that light pollution has not only the potential to disturb the melatonin cycle but also the reproductive rhythm and may therefore have implications on whole species communities.
Collapse
Affiliation(s)
- Anika Brüning
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany.
| | - Franz Hölker
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany.
| | - Steffen Franke
- Leibniz Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany.
| | - Wibke Kleiner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany.
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany.
| |
Collapse
|
13
|
Davies WIL, Tamai TK, Zheng L, Fu JK, Rihel J, Foster RG, Whitmore D, Hankins MW. An extended family of novel vertebrate photopigments is widely expressed and displays a diversity of function. Genome Res 2015; 25:1666-79. [PMID: 26450929 PMCID: PMC4617963 DOI: 10.1101/gr.189886.115] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/15/2015] [Indexed: 11/24/2022]
Abstract
Light affects animal physiology and behavior more than simply through classical visual, image-forming pathways. Nonvisual photoreception regulates numerous biological systems, including circadian entrainment, DNA repair, metabolism, and behavior. However, for the majority of these processes, the photoreceptive molecules involved are unknown. Given the diversity of photophysiological responses, the question arises whether a single photopigment or a greater diversity of proteins within the opsin superfamily detect photic stimuli. Here, a functional genomics approach identified the full complement of photopigments in a highly light-sensitive model vertebrate, the zebrafish (Danio rerio), and characterized their tissue distribution, expression levels, and biochemical properties. The results presented here reveal the presence of 42 distinct genes encoding 10 classical visual photopigments and 32 nonvisual opsins, including 10 novel opsin genes comprising four new pigment classes. Consistent with the presence of light-entrainable circadian oscillators in zebrafish, all adult tissues examined expressed two or more opsins, including several novel opsins. Spectral and electrophysiological analyses of the new opsins demonstrate that they form functional photopigments, each with unique chromophore-binding and wavelength specificities. This study has revealed a remarkable number and diversity of photopigments in zebrafish, the largest number so far discovered for any vertebrate. Found in amphibians, reptiles, birds, and all three mammalian clades, most of these genes are not restricted to teleosts. Therefore, nonvisual light detection is far more complex than initially appreciated, which has significant biological implications in understanding photoreception in vertebrates.
Collapse
Affiliation(s)
- Wayne I L Davies
- School of Animal Biology and University of Western Australia Oceans Institute, University of Western Australia, Perth, Western Australia 6009, Australia; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - T Katherine Tamai
- Centre for Cell and Molecular Dynamics, Department of Cell and Developmental Biology, University College London, London, WC1E 6DE, United Kingdom
| | - Lei Zheng
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Josephine K Fu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, United Kingdom
| | - Russell G Foster
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - David Whitmore
- Centre for Cell and Molecular Dynamics, Department of Cell and Developmental Biology, University College London, London, WC1E 6DE, United Kingdom
| | - Mark W Hankins
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, United Kingdom
| |
Collapse
|
14
|
Eilertsen M, Drivenes O, Edvardsen RB, Bradley CA, Ebbesson LOE, Helvik JV. Exorhodopsin and melanopsin systems in the pineal complex and brain at early developmental stages of Atlantic halibut (Hippoglossus hippoglossus). J Comp Neurol 2014; 522:4003-22. [PMID: 25044160 DOI: 10.1002/cne.23652] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 01/05/2023]
Abstract
The complexity of the nonvisual photoreception systems in teleosts has just started to be appreciated, with colocalization of multiple photoreceptor types with unresolved functions. Here we describe an intricate expression pattern of melanopsins in early life stages of the marine flat fish Atlantic halibut (Hippoglossus hippoglossus), a period when the unpigmented brain is directly exposed to environmental photons. We show a refined and extensive expression of melanopsins in the halibut brain already at the time of hatching, long before the eyes are functional. We detect melanopsin in the habenula, suprachiasmatic nucleus, dorsal thalamus, and lateral tubular nucleus of first feeding larvae, suggesting conserved functions of the melanopsins in marine teleosts. The complex expression of melanopsins already at larval stages indicates the importance of nonvisual photoreception early in development. Most strikingly, we detect expression of both exorhodopsin and melanopsin in the pineal complex of halibut larvae. Double-fluorescence labeling showed that two clusters of melanopsin-positive cells are located lateral to the central rosette of exorhodopsin-positive cells. The localization of different photopigments in the pineal complex suggests that two parallel photoreceptor systems may be active. Furthermore, the dispersed melanopsin-positive cells in the spinal cord of halibut larvae at the time of hatching may be primary sensory cells or interneurons representing the first example of dispersed high-order photoreceptor cells. The appearance of nonvisual opsins early in the development of halibut provides an alternative model for studying the evolution and functional significance of nonvisual opsins.
Collapse
|
15
|
Lagman D, Ocampo Daza D, Widmark J, Abalo XM, Sundström G, Larhammar D. The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications. BMC Evol Biol 2013; 13:238. [PMID: 24180662 PMCID: PMC3826523 DOI: 10.1186/1471-2148-13-238] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1), these form the family of vertebrate visual opsins. Vertebrate genomes contain many multi-membered gene families that can largely be explained by the two rounds of whole genome duplication (WGD) in the vertebrate ancestor (2R) followed by a third round in the teleost ancestor (3R). Related chromosome regions resulting from WGD or block duplications are said to form a paralogon. We describe here a paralogon containing the genes for visual opsins, the G-protein alpha subunit families for transducin (GNAT) and adenylyl cyclase inhibition (GNAI), the oxytocin and vasopressin receptors (OT/VP-R), and the L-type voltage-gated calcium channels (CACNA1-L). RESULTS Sequence-based phylogenies and analyses of conserved synteny show that the above-mentioned gene families, and many neighboring gene families, expanded in the early vertebrate WGDs. This allows us to deduce the following evolutionary scenario: The vertebrate ancestor had a chromosome containing the genes for two visual opsins, one GNAT, one GNAI, two OT/VP-Rs and one CACNA1-L gene. This chromosome was quadrupled in 2R. Subsequent gene losses resulted in a set of five visual opsin genes, three GNAT and GNAI genes, six OT/VP-R genes and four CACNA1-L genes. These regions were duplicated again in 3R resulting in additional teleost genes for some of the families. Major chromosomal rearrangements have taken place in the teleost genomes. By comparison with the corresponding chromosomal regions in the spotted gar, which diverged prior to 3R, we could time these rearrangements to post-3R. CONCLUSIONS We present an extensive analysis of the paralogon housing the visual opsin, GNAT and GNAI, OT/VP-R, and CACNA1-L gene families. The combined data imply that the early vertebrate WGD events contributed to the evolution of vision and the other neuronal and neuroendocrine functions exerted by the proteins encoded by these gene families. In pouched lamprey all five visual opsin genes have previously been identified, suggesting that lampreys diverged from the jawed vertebrates after 2R.
Collapse
Affiliation(s)
- David Lagman
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Daniel Ocampo Daza
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Jenny Widmark
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Xesús M Abalo
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Görel Sundström
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
- Present address: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-75123 Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| |
Collapse
|
16
|
Magnoli D, Zichichi R, Laurà R, Guerrera MC, Campo S, de Carlos F, Suárez AÁ, Abbate F, Ciriaco E, Vega JA, Germanà A. Rhodopsin expression in the zebrafish pineal gland from larval to adult stage. Brain Res 2012; 1442:9-14. [DOI: 10.1016/j.brainres.2012.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/08/2011] [Accepted: 01/10/2012] [Indexed: 11/25/2022]
|
17
|
Davies WIL, Zheng L, Hughes S, Tamai TK, Turton M, Halford S, Foster RG, Whitmore D, Hankins MW. Functional diversity of melanopsins and their global expression in the teleost retina. Cell Mol Life Sci 2011; 68:4115-32. [PMID: 21833582 PMCID: PMC11114754 DOI: 10.1007/s00018-011-0785-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 06/29/2011] [Accepted: 07/19/2011] [Indexed: 12/19/2022]
Abstract
Melanopsin (OPN4) is an opsin photopigment that, in mammals, confers photosensitivity to retinal ganglion cells and regulates circadian entrainment and pupil constriction. In non-mammalian species, two forms of opn4 exist, and are classified into mammalian-like (m) and non-mammalian-like (x) clades. However, far less is understood of the function of this photopigment family. Here we identify in zebrafish five melanopsins (opn4m-1, opn4m-2, opn4m-3, opn4x-1 and opn4x-2), each encoding a full-length opsin G protein. All five genes are expressed in the adult retina in a largely non-overlapping pattern, as revealed by RNA in situ hybridisation and immunocytochemistry, with at least one melanopsin form present in all neuronal cell types, including cone photoreceptors. This raises the possibility that the teleost retina is globally light sensitive. Electrophysiological and spectrophotometric studies demonstrate that all five zebrafish melanopsins encode a functional photopigment with peak spectral sensitivities that range from 470 to 484 nm, with opn4m-1 and opn4m-3 displaying invertebrate-like bistability, where the retinal chromophore interchanges between cis- and trans-isomers in a light-dependent manner and remains within the opsin binding pocket. In contrast, opn4m-2, opn4x-1 and opn4x-2 are monostable and function more like classical vertebrate-like photopigments, where the chromophore is converted from 11-cis to all-trans retinal upon absorption of a photon, hydrolysed and exits from the binding pocket of the opsin. It is thought that all melanopsins exhibit an invertebrate-like bistability biochemistry. Our novel findings, however, reveal the presence of both invertebrate-like and vertebrate-like forms of melanopsin in the teleost retina, and indicate that photopigment bistability is not a universal property of the melanopsin family. The functional diversity of these teleost melanopsins, together with their widespread expression pattern within the retina, suggests that melanopsins confer global photosensitivity to the teleost retina and might allow for direct "fine-tuning" of retinal circuitry and physiology in the dynamic light environments found in aquatic habitats.
Collapse
Affiliation(s)
- Wayne I. L. Davies
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| | - Lei Zheng
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| | - Steven Hughes
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| | - T. Katherine Tamai
- Department of Cell and Developmental Biology, Centre for Cell and Molecular Dynamics, University College London, 21 University Street, London, WC1E 6DE UK
| | - Michael Turton
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| | - Russell G. Foster
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| | - David Whitmore
- Department of Cell and Developmental Biology, Centre for Cell and Molecular Dynamics, University College London, 21 University Street, London, WC1E 6DE UK
| | - Mark W. Hankins
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Levels 5-6 West Wing, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford, OX3 9DU UK
| |
Collapse
|
18
|
Tarttelin EE, Fransen MP, Edwards PC, Hankins MW, Schertler GFX, Vogel R, Lucas RJ, Bellingham J. Adaptation of pineal expressed teleost exo-rod opsin to non-image forming photoreception through enhanced Meta II decay. Cell Mol Life Sci 2011; 68:3713-23. [PMID: 21416149 PMCID: PMC3203999 DOI: 10.1007/s00018-011-0665-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/01/2011] [Accepted: 03/01/2011] [Indexed: 12/03/2022]
Abstract
Photoreception by vertebrates enables both image-forming vision and non-image-forming responses such as circadian photoentrainment. Over the recent years, distinct non-rod non-cone photopigments have been found to support circadian photoreception in diverse species. By allowing specialization to this sensory task a selective advantage is implied, but the nature of that specialization remains elusive. We have used the presence of distinct rod opsin genes specialized to either image-forming (retinal rod opsin) or non-image-forming (pineal exo-rod opsin) photoreception in ray-finned fish (Actinopterygii) to gain a unique insight into this problem. A comparison of biochemical features for these paralogous opsins in two model teleosts, Fugu pufferfish (Takifugu rubripes) and zebrafish (Danio rerio), reveals striking differences. While spectral sensitivity is largely unaltered by specialization to the pineal environment, in other aspects exo-rod opsins exhibit a behavior that is quite distinct from the cardinal features of the rod opsin family. While they display a similar thermal stability, they show a greater than tenfold reduction in the lifetime of the signaling active Meta II photoproduct. We show that these features reflect structural changes in retinal association domains of helices 3 and 5 but, interestingly, not at either of the two residues known to define these characteristics in cone opsins. Our findings suggest that the requirements of non-image-forming photoreception have lead exo-rod opsin to adopt a characteristic that seemingly favors efficient bleach recovery but not at the expense of absolute sensitivity.
Collapse
Affiliation(s)
- Emma E Tarttelin
- Faculty of Life Sciences, The University of Manchester, Manchester, UK
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Fu B, Chen M, Zou M, Long M, He S. The rapid generation of chimerical genes expanding protein diversity in zebrafish. BMC Genomics 2010; 11:657. [PMID: 21106061 PMCID: PMC3091775 DOI: 10.1186/1471-2164-11-657] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 11/24/2010] [Indexed: 12/03/2022] Open
Abstract
Background Variation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome. Results Here we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13×10-9 substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice. Conclusion There is compelling evidence that much of the extensive transcriptional activity of retrogenes does not represent transcriptional "noise" but indicates the functionality of these retrogenes. Our results indicate that retroposition created a large amount of new genes in the zebrafish genome, which has contributed significantly to the evolution of the fish genome.
Collapse
Affiliation(s)
- Beide Fu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P R China
| | | | | | | | | |
Collapse
|
20
|
|
21
|
Vera LM, Davie A, Taylor JF, Migaud H. Differential light intensity and spectral sensitivities of Atlantic salmon, European sea bass and Atlantic cod pineal glands ex vivo. Gen Comp Endocrinol 2010; 165:25-33. [PMID: 19501092 DOI: 10.1016/j.ygcen.2009.05.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 03/23/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
Photoperiod is perceived by pineal photoreceptors and transduced into rhythmic melatonin signals. These rhythms can be influenced by light intensity and spectral content. In this study we compared the light sensitivity of Atlantic salmon, European sea bass and Atlantic cod by testing ex vivo the effect of different intensities and narrow bandwidth lights on nocturnal melatonin suppression by isolated pineal glands in a flow-through culture system. Using combinations of neutral density and bandpass interference filters we tested a range of light intensities (ranging from 1.22x10(13) to 3.85x10(6) photons s(-1) cm(-2)) and three wavelengths of 80 nm width (472, 555 and 661 nm corresponding to blue, green and red, respectively). Results showed clear species specific light intensity and spectral sensitivities, with cod being from 100 to 1000 times more sensitive than sea bass and salmon. Regarding the influence of spectrum, red light was less efficient on suppressing melatonin than blue and green in salmon but results were not as clear in the two other species studied. Finally, the first evidence of relative photoreception in teleosts was obtained in cod suggesting that the definition of illuminance thresholds (day/night perception) would depend on the day intensity. Indeed, a single order of magnitude increase or decrease in day intensity was shown to elicit a significant shift in the intensity response curve of night-time melatonin suppression. Taken together, this study demonstrated species specific light intensity and spectral sensitivities within temperate teleosts.
Collapse
Affiliation(s)
- L M Vera
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | | | | |
Collapse
|
22
|
Larhammar D, Nordström K, Larsson TA. Evolution of vertebrate rod and cone phototransduction genes. Philos Trans R Soc Lond B Biol Sci 2009; 364:2867-80. [PMID: 19720650 DOI: 10.1098/rstb.2009.0077] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Vertebrate cones and rods in several cases use separate but related components for their signal transduction (opsins, G-proteins, ion channels, etc.). Some of these proteins are also used differentially in other cell types in the retina. Because cones, rods and other retinal cell types originated in early vertebrate evolution, it is of interest to see if their specific genes arose in the extensive gene duplications that took place in the ancestor of the jawed vertebrates (gnathostomes) by two tetraploidizations (genome doublings). The ancestor of teleost fishes subsequently underwent a third tetraploidization. Our previously reported analyses showed that several gene families in the vertebrate visual phototransduction cascade received new members in the basal tetraploidizations. We here expand these data with studies of additional gene families and vertebrate species. We conclude that no less than 10 of the 13 studied phototransduction gene families received additional members in the two basal vertebrate tetraploidizations. Also the remaining three families seem to have undergone duplications during the same time period but it is unclear if this happened as a result of the tetraploidizations. The implications of the many early vertebrate gene duplications for functional specialization of specific retinal cell types, particularly cones and rods, are discussed.
Collapse
Affiliation(s)
- Dan Larhammar
- Department of Neuroscience, Unit of Pharmacology, Uppsala University, SE-751 24 Uppsala, Sweden.
| | | | | |
Collapse
|
23
|
Davies WL, Carvalho LS, Tay BH, Brenner S, Hunt DM, Venkatesh B. Into the blue: gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii. Genome Res 2009; 19:415-26. [PMID: 19196633 DOI: 10.1101/gr.084509.108] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The cartilaginous fishes reside at the base of the gnathostome lineage as the oldest extant group of jawed vertebrates. Recently, the genome of the elephant shark, Callorhinchus milii, a chimaerid holocephalan, has been sequenced and therefore becomes the first cartilaginous fish to be analyzed in this way. The chimaeras have been largely neglected and very little is known about the visual systems of these fishes. By searching the elephant shark genome, we have identified gene fragments encoding a rod visual pigment, Rh1, and three cone visual pigments, the middle wavelength-sensitive or Rh2 pigment, and two isoforms of the long wavelength-sensitive or LWS pigment, LWS1 and LWS2, but no evidence for the two short wavelength-sensitive cone classes, SWS1 and SWS2. Expression of these genes in the retina was confirmed by RT-PCR. Full-length coding sequences were used for in vitro expression and gave the following peak absorbances: Rh1 496 nm, Rh2 442 nm, LWS1 499 nm, and LWS2 548 nm. Unusually, therefore, for a deep-sea fish, the elephant shark possesses cone pigments and the potential for trichromacy. Compared with other vertebrates, the elephant shark Rh2 and LWS1 pigments are the shortest wavelength-shifted pigments of their respective classes known to date. The mechanisms for this are discussed and we provide experimental evidence that the elephant shark LWS1 pigment uses a novel tuning mechanism to achieve the short wavelength shift to 499 nm, which inactivates the chloride-binding site. Our findings have important implications for the present knowledge of color vision evolution in early vertebrates.
Collapse
Affiliation(s)
- Wayne L Davies
- UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom
| | | | | | | | | | | |
Collapse
|
24
|
Ward MN, Churcher AM, Dick KJ, Laver CRJ, Owens GL, Polack MD, Ward PR, Breden F, Taylor JS. The molecular basis of color vision in colorful fish: four long wave-sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites. BMC Evol Biol 2008; 8:210. [PMID: 18638376 PMCID: PMC2527612 DOI: 10.1186/1471-2148-8-210] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 07/18/2008] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Comparisons of functionally important changes at the molecular level in model systems have identified key adaptations driving isolation and speciation. In cichlids, for example, long wavelength-sensitive (LWS) opsins appear to play a role in mate choice and male color variation within and among species. To test the hypothesis that the evolution of elaborate coloration in male guppies (Poecilia reticulata) is also associated with opsin gene diversity, we sequenced long wavelength-sensitive (LWS) opsin genes in six species of the family Poeciliidae. RESULTS Sequences of four LWS opsin genes were amplified from the guppy genome and from mRNA isolated from adult guppy eyes. Variation in expression was quantified using qPCR. Three of the four genes encode opsins predicted to be most sensitive to different wavelengths of light because they vary at key amino acid positions. This family of LWS opsin genes was produced by a diversity of duplication events. One, an intronless gene, was produced prior to the divergence of families Fundulidae and Poeciliidae. Between-gene PCR and DNA sequencing show that two of the guppy LWS opsins are linked in an inverted orientation. This inverted tandem duplication event occurred near the base of the poeciliid tree in the common ancestor of Poecilia and Xiphophorus. The fourth sequence has been uncovered only in the genus Poecilia. In the guppies surveyed here, this sequence is a hybrid, with the 5' end most similar to one of the tandem duplicates and the 3' end identical to the other. CONCLUSION Enhanced wavelength discrimination, a possible consequence of opsin gene duplication and divergence, might have been an evolutionary prerequisite for color-based sexual selection and have led to the extraordinary coloration now observed in male guppies and in many other poeciliids.
Collapse
Affiliation(s)
- Matthew N Ward
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Allison M Churcher
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Kevin J Dick
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Chris RJ Laver
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Greg L Owens
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Megan D Polack
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Pam R Ward
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| | - Felix Breden
- Simon Fraser University, Department of Biological Sciences, Burnaby, British Columbia, Canada
| | - John S Taylor
- University of Victoria, Department of Biology, Victoria, British Columbia, Canada
| |
Collapse
|
25
|
Bellingham J, Chaurasia SS, Melyan Z, Liu C, Cameron MA, Tarttelin EE, Iuvone PM, Hankins MW, Tosini G, Lucas RJ. Evolution of melanopsin photoreceptors: discovery and characterization of a new melanopsin in nonmammalian vertebrates. PLoS Biol 2006; 4:e254. [PMID: 16856781 PMCID: PMC1514791 DOI: 10.1371/journal.pbio.0040254] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 05/25/2006] [Indexed: 11/18/2022] Open
Abstract
In mammals, the melanopsin gene
(Opn4) encodes a sensory photopigment that underpins newly discovered inner retinal photoreceptors. Since its first discovery in
Xenopus laevis and subsequent description in humans and mice, melanopsin genes have been described in all vertebrate classes. Until now, all of these sequences have been considered representatives of a single orthologous gene (albeit with duplications in the teleost fish). Here, we describe the discovery and functional characterisation of a new melanopsin gene in fish, bird, and amphibian genomes, demonstrating that, in fact, the vertebrates have evolved two quite separate melanopsins. On the basis of sequence similarity, chromosomal localisation, and phylogeny, we identify our new melanopsins as the true orthologs of the melanopsin gene previously described in mammals and term this grouping
Opn4m. By contrast, the previously published melanopsin genes in nonmammalian vertebrates represent a separate branch of the melanopsin family which we term
Opn4x. RT-PCR analysis in chicken, zebrafish, and
Xenopus identifies expression of both
Opn4m and
Opn4x genes in tissues known to be photosensitive (eye, brain, and skin). In the day-14 chicken eye,
Opn4m mRNA is found in a subset of cells in the outer nuclear, inner nuclear, and ganglion cell layers, the vast majority of which also express
Opn4x. Importantly, we show that a representative of the new melanopsins (chicken
Opn4m) encodes a photosensory pigment capable of activating G protein signalling cascades in a light- and retinaldehyde-dependent manner under heterologous expression in Neuro-2a cells. A comprehensive in silico analysis of vertebrate genomes indicates that while most vertebrate species have both
Opn4m and
Opn4x genes, the latter is absent from eutherian and, possibly, marsupial mammals, lost in the course of their evolution as a result of chromosomal reorganisation. Thus, our findings show for the first time that nonmammalian vertebrates retain two quite separate melanopsin genes, while mammals have just one. These data raise important questions regarding the functional differences between Opn4x and Opn4m pigments, the associated adaptive advantages for most vertebrate species in retaining both melanopsins, and the implications for mammalian biology of lacking Opn4x.
A new melanopsin gene, identified in fish, bird, and amphibian genomes, is the true ortholog of the melanopsin gene previously described in mammals.
Collapse
Affiliation(s)
- James Bellingham
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Santillo S, Orlando P, De Petrocellis L, Cristino L, Guglielmotti V, Musio C. Evolving visual pigments: hints from the opsin-based proteins in a phylogenetically old "eyeless" invertebrate. Biosystems 2006; 86:3-17. [PMID: 16843587 DOI: 10.1016/j.biosystems.2006.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 03/23/2006] [Accepted: 03/27/2006] [Indexed: 10/24/2022]
Abstract
Visual pigments are photosensitive receptor proteins that trigger the transduction process producing the visual excitation once they have absorbed photons. In spite of the molecular and morpho-functional complexity that has characterized the development of animal eyes and eyeless photoreceptive systems, opsin-based protein family appears ubiquous along metazoan visual systems. Moreover, in addition to classic rhodopsin photoreceptors, all Metazoa have supplementary non-visual photosensitive structures, mainly located in the central nervous system, that sense light without forming an image and that rather regulate the organism's temporal physiology. The investigation of novel non-visual photopigments exerting extraretinal photoreception is a challenging field in vision research. Here we propose the cnidarian Hydra as a useful tool of investigation for molecular and functional differences between these pigment families. Hydra is the first metazoan owning a nervous system and it is an eyeless invertebrate showing only an extraocular photoreception, as it has no recognized visual or photosensitive structures. In this paper we provide an overview of the molecular and functional features of the opsin-based protein subfamilies and preliminary evidences in a phylogenetically old species of both image-forming and non-visual opsins. Then we give new insights on the molecular biology of Hydra photoreception and on the evolutionary pathways of visual pigments.
Collapse
Affiliation(s)
- Silvia Santillo
- Istituto di Cibernetica Eduardo Caianiello (ICIB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei, 34 Comprensorio A Olivetti, Pozzuoli (Napoli), Italy
| | | | | | | | | | | |
Collapse
|
27
|
Molecular and Cellular Regulation of Pineal Organ Responses. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1546-5098(06)25006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
28
|
Bowmaker JK, Wagner HJ. Pineal organs of deep-sea fish: photopigments and structure. ACTA ACUST UNITED AC 2004; 207:2379-87. [PMID: 15184510 DOI: 10.1242/jeb.01033] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have examined the morphology and photopigments of the pineal organs from a number of mesopelagic fish, including representatives of the hatchet fish (Sternoptychidae), scaly dragon-fish (Chauliodontidae) and bristlemouths (Gonostomidae). Although these fish were caught at depths of between 500 and 1000 m, the morphological organisation of their pineal organs is remarkably similar to that of surface-dwelling fish. Photoreceptor inner and outer segments protrude into the lumen of the pineal vesicle, and the outer segment is composed of a stack of up to 20 curved disks that form a cap-like cover over the inner segment. In all species, the pineal photopigment was spectrally distinct from the retinal rod pigment, with lambdamax displaced to longer wavelengths, between approximately 485 and 503 nm. We also investigated the pineal organ of the deep demersal eel, Synaphobranchus kaupi, caught at depths below 2000 m, which possesses a rod visual pigment with lambdamax at 478 nm, but the pineal pigment has lambdamax at approximately 515 nm. In one species of hatchet fish, Argyropelecus affinis, two spectral classes of pinealocyte were identified, both spectrally distinct from the retinal rod photopigment.
Collapse
Affiliation(s)
- James K Bowmaker
- Division of Visual Science, Institute of Ophthalmology, University College London, EC1V 9EL, UK.
| | | |
Collapse
|