1
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Krivenko OV, Kuleshova ON, Baiandina IS. Light sensitivity in Beroidae ctenophores: Insights from laboratory studies and genomics. Comp Biochem Physiol A Mol Integr Physiol 2024; 296:111694. [PMID: 38992417 DOI: 10.1016/j.cbpa.2024.111694] [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: 01/24/2024] [Revised: 06/05/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Light detection underlies a variety of animal behaviors, including those related to spatial orientation, feeding, avoidance of predators, and reproduction. Ctenophores are likely the oldest animal group in which light sensitivity based on opsins evolved, so they may still have the ancestral molecular mechanisms for photoreception. However, knowledge about ctenophore photosensitivity, associated morphological structures, molecular mechanisms involved, and behavioral reactions is limited and fragmented. We present the initial experiments on the responses of adult Beroe ovata to high-intensity light exposure with different spectra and photosensitivity in various parts of the animal's body. Ctenophores have shown a consistent behavioral response when their aboral organ is exposed to a household-grade laser in the violet spectrum. To investigate the genes responsible for the photosensitivity of Beroidae, we have analyzed transcriptome and genome-wide datasets. We identified three opsins in Beroe that are homologous to those found in Mnemiopsis leidyi (Lobata) and Pleurobrachia bachei (Cydippida). These opsins form clades Ctenopsin1, 2, and 3, respectively. Ctenopsin3 is significantly distinct from other ctenophore opsins and clustered outside the main animal opsin groups. The Ctenopsin1 and Ctenopsin2 groups are sister clusters within the canonical animal opsin tree. These two groups could have originated from gene duplication in the common ancestor of the species we studied and then developed independently in different lineages of Ctenophores. So far, there is no evidence of additional expansion of the opsin family in ctenophore evolution. The involvement of ctenophore opsins in photoreception is discussed by analyzing their protein structures.
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Affiliation(s)
- Olga V Krivenko
- Laboratory of functional genomics, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Moscow, Russia.
| | - Olga N Kuleshova
- Laboratory of functional genomics, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Moscow, Russia
| | - Iuliia S Baiandina
- Laboratory of functional genomics, A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, Moscow, Russia
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2
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Wijayaratna D, Sacchetta F, Pedraza-González L, Fanelli F, Sugihara T, Koyanagi M, Piyawardana S, Ghotra K, Thotamune W, Terakita A, Olivucci M, Karunarathne A. In-silico predicted mouse melanopsins with blue spectral shifts deliver efficient subcellular signaling. Cell Commun Signal 2024; 22:394. [PMID: 39118111 PMCID: PMC11312219 DOI: 10.1186/s12964-024-01753-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Melanopsin is a photopigment belonging to the G Protein-Coupled Receptor (GPCR) family expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) and responsible for a variety of processes. The bistability and, thus, the possibility to function under low retinal availability would make melanopsin a powerful optogenetic tool. Here, we aim to utilize mouse melanopsin to trigger macrophage migration by its subcellular optical activation with localized blue light, while simultaneously imaging the migration with red light. To reduce melanopsin's red light sensitivity, we employ a combination of in silico structure prediction and automated quantum mechanics/molecular mechanics modeling to predict minimally invasive mutations to shift its absorption spectrum towards the shorter wavelength region of the visible spectrum without compromising the signaling efficiency. The results demonstrate that it is possible to achieve melanopsin mutants that resist red light-induced activation but are activated by blue light and display properties indicating preserved bistability. Using the A333T mutant, we show that the blue light-induced subcellular melanopsin activation triggers localized PIP3 generation and macrophage migration, which we imaged using red light, demonstrating the optogenetic utility of minimally engineered melanopsins.
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Affiliation(s)
| | - Filippo Sacchetta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Francesca Fanelli
- Department of Life Sciences, Dulbecco Telethon Institute, University of Modena and Reggio Emilia, Modena, I-41125, Italy
| | - Tomohiro Sugihara
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
| | - Mitsumasa Koyanagi
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Senuri Piyawardana
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Kiran Ghotra
- Department of Biology, Siena Heights University, Adrian, MI, 49221, USA
| | - Waruna Thotamune
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA
| | - Akihisa Terakita
- Department of Biology, Osaka Metropolitan University, O 3-3-138 Sugimoto, Sumiyoshi-Ku, Osaka, 558-8585, Japan
- The OMU Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka, Japan
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Ajith Karunarathne
- Department of Chemistry, Saint Louis University, Saint Louis, MO, 63103, USA.
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3
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Lin JJ, Wang FY, Chung WY, Wang TY. The genomic evolution of visual opsin genes in amphibians. Vision Res 2024; 222:108447. [PMID: 38906036 DOI: 10.1016/j.visres.2024.108447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/23/2024]
Abstract
Among tetrapod (terrestrial) vertebrates, amphibians remain more closely tied to an amphibious lifestyle than amniotes, and their visual opsin genes may be adapted to this lifestyle. Previous studies have discussed physiological, morphological, and molecular changes in the evolution of amphibian vision. We predicted the locations of the visual opsin genes, their neighboring genes, and the tuning sites of the visual opsins, in 39 amphibian genomes. We found that all of the examined genomes lacked the Rh2 gene. The caecilian genomes have further lost the SWS1 and SWS2 genes; only the Rh1 and LWS genes were retained. The loss of the SWS1 and SWS2 genes in caecilians may be correlated with their cryptic lifestyles. The opsin gene syntenies were predicted to be highly similar to those of other bony vertebrates. Moreover, dual syntenies were identified in allotetraploid Xenopus laevis and X. borealis. Tuning site analysis showed that only some Caudata species might have UV vision. In addition, the S164A that occurred several times in LWS evolution might either functionally compensate for the Rh2 gene loss or fine-tuning visual adaptation. Our study provides the first genomic evidence for a caecilian LWS gene and a genomic viewpoint of visual opsin genes by reviewing the gains and losses of visual opsin genes, the rearrangement of syntenies, and the alteration of spectral tuning in the course of amphibians' evolution.
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Affiliation(s)
- Jinn-Jy Lin
- National Center for High-performance Computing, National Applied Research Laboratories, Hsinchu, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan
| | - Wen-Yu Chung
- Department of Computer Science and Information Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
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4
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Wan YC, Navarrete Méndez MJ, O'Connell LA, Uricchio LH, Roland AB, Maan ME, Ron SR, Betancourth-Cundar M, Pie MR, Howell KA, Richards-Zawacki CL, Cummings ME, Cannatella DC, Santos JC, Tarvin RD. Selection on Visual Opsin Genes in Diurnal Neotropical Frogs and Loss of the SWS2 Opsin in Poison Frogs. Mol Biol Evol 2023; 40:msad206. [PMID: 37791477 PMCID: PMC10548314 DOI: 10.1093/molbev/msad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here, we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: Atelopus), and pumpkin toadlets (Brachycephalidae: Brachycephalus). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their behavior. Our analyses show that assessments of opsin diversification in across taxa could expand our understanding of the role of sensory system evolution in ecological adaptation.
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Affiliation(s)
- Yin Chen Wan
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - María José Navarrete Méndez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Lawrence H Uricchio
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Biology, Tufts University, Medford, MA, USA
| | - Alexandre-Benoit Roland
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), UMR5169 CNRS, Toulouse University, Toulouse, France
| | - Martine E Maan
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Santiago R Ron
- Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Marcio R Pie
- Department of Zoology, Universidade Federal do Paraná, Curitiba, Brazil
- Biology Department, Edge Hill University, Ormskirk, United Kingdom
| | - Kimberly A Howell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Molly E Cummings
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - David C Cannatella
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Biodiversity Center, University of Texas at Austin, Austin, TX, USA
| | - Juan C Santos
- Department of Biological Sciences, St. John's University, New York City, NY, USA
| | - Rebecca D Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
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5
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Corredor VH, Hauzman E, Gonçalves ADS, Ventura DF. Genetic characterization of the visual pigments of the red-eared turtle (Trachemys scripta elegans) and computational predictions of the spectral sensitivity. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2022. [DOI: 10.1016/j.jpap.2022.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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6
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Huang Z, He T, Zhang J, Du C. Red light irradiation as an intervention for myopia. Indian J Ophthalmol 2022; 70:3198-3201. [PMID: 36018087 DOI: 10.4103/ijo.ijo_15_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Myopia is one of the main causes of visual impairment worldwide. Preventing myopia and providing myopia-related interventions are of paramount importance. Based on a thorough review of the available literature, we conclude that red light irradiation can produce hyperopia, resulting in myopia prevention and control. Further, we suggest that red light irradiation may be a powerful tool for myopia prevention and control in the future. At the same time, red light has a protective effect on the cornea and retina at the cellular level, suggesting that red light irradiation may be a safe and effective modality for delaying myopia. Therefore, this form of irradiation is expected to play an important role in the prevention and control of myopia. However, more studies are needed to enhance the current state of knowledge and inform medical guidelines more comprehensively.
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Affiliation(s)
- Zhu Huang
- Department of Ophthalmology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ting He
- Department of Ophthalmology, The Forth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Junna Zhang
- Department of Ophthalmology, The Forth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Chixin Du
- Department of Ophthalmology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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7
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Smedley GD, McElroy KE, Feller KD, Serb JM. Additive and epistatic effects influence spectral tuning in molluscan retinochrome opsin. J Exp Biol 2022; 225:275511. [DOI: 10.1242/jeb.242929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
The relationship between genotype and phenotype is nontrivial due to often complex molecular pathways that make it difficult to unambiguously relate phenotypes to specific genotypes. Photopigments, an opsin apoprotein bound to a light-absorbing chromophore, present an opportunity to directly relate the amino acid sequence to an absorbance peak phenotype (λmax). We examined this relationship by conducting a series of site-directed mutagenesis experiments of retinochrome, a non-visual opsin, from two closely related species: the common bay scallop, Argopecten irradians, and the king scallop, Pecten maximus. Using protein folding models, we identified three amino acid sites of likely functional importance and expressed mutated retinochrome proteins in vitro. Our results show that the mutation of amino acids lining the opsin binding pocket are responsible for fine spectral tuning, or small changes in the λmax of these light sensitive proteins Mutations resulted in a blue or red shift as predicted, but with dissimilar magnitudes. Shifts ranged from a 16 nm blue shift to a 12 nm red shift from the wild-type λmax. These mutations do not show an additive effect, but rather suggests the presence of epistatic interactions. This work highlights the importance of binding pocket shape in the evolution of spectral tuning and builds on our ability to relate genotypic changes to phenotypes in an emerging model for opsin functional analysis.
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Affiliation(s)
- G. Dalton Smedley
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Kyle E. McElroy
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | - Kathryn D. Feller
- Department of Biological Sciences, Union College, Schenectady, New York, USA
| | - Jeanne M. Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
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8
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Hauzman E, Pierotti MER, Bhattacharyya N, Tashiro JH, Yovanovich CAM, Campos PF, Ventura DF, Chang BSW. Simultaneous expression of UV and violet SWS1 opsins expands the visual palette in a group of freshwater snakes. Mol Biol Evol 2021; 38:5225-5240. [PMID: 34562092 PMCID: PMC8662652 DOI: 10.1093/molbev/msab285] [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] [Indexed: 11/13/2022] Open
Abstract
Snakes are known to express a rod visual opsin and two cone opsins, only (SWS1, LWS), a reduced palette resulting from their supposedly fossorial origins. Dipsadid snakes in the genus Helicops are highly visual predators that successfully invaded freshwater habitats from ancestral terrestrial-only habitats. Here, we report the first case of multiple SWS1 visual pigments in a vertebrate, simultaneously expressed in different photoreceptors and conferring both UV and violet sensitivity to Helicops snakes. Molecular analysis and in vitro expression confirmed the presence of two functional SWS1 opsins, likely the result of recent gene duplication. Evolutionary analyses indicate that each sws1 variant has undergone different evolutionary paths with strong purifying selection acting on the UV-sensitive copy and dN/dS ∼1 on the violet-sensitive copy. Site-directed mutagenesis points to the functional role of a single amino acid substitution, Phe86Val, in the large spectral shift between UV and violet opsins. In addition, higher densities of photoreceptors and SWS1 cones in the ventral retina suggest improved acuity in the upper visual field possibly correlated with visually guided behaviors. The expanded visual opsin repertoire and specialized retinal architecture are likely to improve photon uptake in underwater and terrestrial environments, and provide the neural substrate for a gain in chromatic discrimination, potentially conferring unique color vision in the UV–violet range. Our findings highlight the innovative solutions undertaken by a highly specialized lineage to tackle the challenges imposed by the invasion of novel photic environments and the extraordinary diversity of evolutionary trajectories taken by visual opsin-based perception in vertebrates.
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Affiliation(s)
- Einat Hauzman
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Michele E R Pierotti
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Nihar Bhattacharyya
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Juliana H Tashiro
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, São Paulo, Brazil
| | - Carola A M Yovanovich
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Pollyanna F Campos
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Dora F Ventura
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Belinda S W Chang
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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9
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Xu P, Zhao C, You X, Yang F, Chen J, Ruan Z, Gu R, Xu J, Bian C, Shi Q. Draft Genome of the Mirrorwing Flyingfish ( Hirundichthys speculiger). Front Genet 2021; 12:695700. [PMID: 34306036 PMCID: PMC8294118 DOI: 10.3389/fgene.2021.695700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/03/2021] [Indexed: 12/04/2022] Open
Affiliation(s)
- Pengwei Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chenxi Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinxin You
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Fan Yang
- Marine Geological Department, Marine Geological Survey Institute of Hainan Province, Haikou, China
| | - Jieming Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Zhiqiang Ruan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Ruobo Gu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Junmin Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Chao Bian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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10
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Zheng S, Shao F, Tao W, Liu Z, Long J, Wang X, Zhang S, Zhao Q, Carleton KL, Kocher TD, Jin L, Wang Z, Peng Z, Wang D, Zhang Y. Chromosome-level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles. Mol Ecol Resour 2021; 21:1575-1592. [PMID: 33503304 DOI: 10.1111/1755-0998.13338] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 01/07/2023]
Abstract
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.
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Affiliation(s)
- Shuqing Zheng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhilong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Juan Long
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Xiaoshuang Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Shuai Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Key Laboratory of Aquatic Science of Chongqing, Southwest University, Chongqing, P. R. China
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11
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Upton BA, Díaz NM, Gordon SA, Van Gelder RN, Buhr ED, Lang RA. Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins. J Biol Rhythms 2021; 36:109-126. [PMID: 33765865 PMCID: PMC8058843 DOI: 10.1177/0748730421999870] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animals have evolved light-sensitive G protein-coupled receptors, known as opsins, to detect coherent and ambient light for visual and nonvisual functions. These opsins have evolved to satisfy the particular lighting niches of the organisms that express them. While many unique patterns of evolution have been identified in mammals for rod and cone opsins, far less is known about the atypical mammalian opsins. Using genomic data from over 400 mammalian species from 22 orders, unique patterns of evolution for each mammalian opsins were identified, including photoisomerases, RGR-opsin (RGR) and peropsin (RRH), as well as atypical opsins, encephalopsin (OPN3), melanopsin (OPN4), and neuropsin (OPN5). The results demonstrate that OPN5 and rhodopsin show extreme conservation across all mammalian lineages. The cone opsins, SWS1 and LWS, and the nonvisual opsins, OPN3 and RRH, demonstrate a moderate degree of sequence conservation relative to other opsins, with some instances of lineage-specific gene loss. Finally, the photoisomerase, RGR, and the best-studied atypical opsin, OPN4, have high sequence diversity within mammals. These conservation patterns are maintained in human populations. Importantly, all mammalian opsins retain key amino acid residues important for conjugation to retinal-based chromophores, permitting light sensitivity. These patterns of evolution are discussed along with known functions of each atypical opsin, such as in circadian or metabolic physiology, to provide insight into the observed patterns of evolutionary constraint.
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Affiliation(s)
- Brian A. Upton
- Visual Systems Group, Abrahamson Pediatric Eye Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Center for Chronobiology, Division of Pediatric Ophthalmology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Molecular & Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Nicolás M. Díaz
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington
| | - Shannon A. Gordon
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington
| | - Russell N. Van Gelder
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington
- Departments of Biological Structure and Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Ethan D. Buhr
- Department of Ophthalmology, University of Washington School of Medicine, Seattle, Washington
| | - Richard A. Lang
- Visual Systems Group, Abrahamson Pediatric Eye Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Center for Chronobiology, Division of Pediatric Ophthalmology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, Ohio
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12
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Mantovani V, Hauzman E, Corredor VH, Goulart PRK, Galvão O, Talebi M, Pessoa DMA, Soares JGM, Fiorani M, Gattass R, Fix Ventura D, Bonci DMO. Genetic variability of the sws1 cone opsin gene among New World monkeys. Am J Primatol 2020; 82:e23199. [PMID: 32990997 DOI: 10.1002/ajp.23199] [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: 03/12/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Vision is a major sense for Primates and the ability to perceive colors has great importance for the species ecology and behavior. Visual processing begins with the activation of the visual opsins in the retina, and the spectral absorption peaks are highly variable among species. In most Primates, LWS/MWS opsins are responsible for sensitivity to long/middle wavelengths within the visible light spectrum, and SWS1 opsins provide sensitivity to short wavelengths, in the violet region of the spectrum. In this study, we aimed to investigate the genetic variation on the sws1 opsin gene of New World monkeys (NWM) and search for amino acid substitutions that might be associated with the different color vision phenotypes described for a few species. We sequenced the exon 1 of the sws1 opsin gene of seven species from the families Callitrichidae, Cebidae, and Atelidae, and searched for variation at the spectral tuning sites 46, 49, 52, 86, 90, 93, 114, 116, and 118. Among the known spectral tuning sites, only residue 114 was variable. To investigate whether other residues have a functional role in the SWS1 absorption peak, we performed computational modeling of wild-type SWS1 and mutants A50I and A50V, found naturally among the species investigated. Although in silico analysis did not show any visible effect caused by these substitutions, it is possible that interactions of residue 50 with other sites might have some effect in the spectral shifts in the order of ~14 nm, found among the NWM. We also performed phylogenetic reconstruction of the sws1 gene, which partially recovered the species phylogeny. Further studies will be important to uncover the mutations responsible for the phenotypic variability of the SWS1 of NWM, and how spectral tuning may be associated with specific ecological features such as preferred food items and habitat use.
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Affiliation(s)
- Viviani Mantovani
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Vitor H Corredor
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo R K Goulart
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Olavo Galvão
- Núcleo de Teoria de Pesquisa do Comportamento, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Mauricio Talebi
- Departamento de Ciências Ambientais, Universidade Federal de São Paulo, Campus Diadema, São Paulo, São Paulo, Brazil
| | - Daniel M A Pessoa
- Departamento de Fisiologia e Comportamento, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Juliana G M Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mario Fiorani
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo Gattass
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Daniela M O Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, São Paulo, Brazil.,Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
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13
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Abstract
Abstract
Knowledge of a species’ visual system has far reaching implications that affect our understanding of a species’ ecology and evolutionary history. As a model taxon, the heteromyid rodent genus Dipodomys has been valuable in elucidating patterns and mechanisms in biomechanics, ecology, adaptive physiology, biogeography, and more. Although studied extensively, the visual system of Dipodomys has not been described beyond anecdotal mention of their large eyes. Here, the transmittance parameters of the cornea and lens of Ord’s kangaroo rat (Dipodomys ordii) were analyzed and photoreceptor proteins (opsins) expressed in the retina were identified with immunohistochemical (IHC) labeling. Retina maps were constructed to illustrate the relative densities of photoreceptor cells expressing short wavelength (SWS1) opsins, middle/long wavelength (MW/LW) opsins, and rhodopsin (RH1). The retina of D. ordii has variable densities of SWS1 opsin with the highest density being ventral to the optic nerve, high density of MW/LW opsin, and uniform distribution and high density of RH1 across the retina. Our results suggest that D. ordii has a UV-sensitive visual system. Composition and densities of MW/LW- and SWS1-expressing cells resemble that of a crepuscular/diurnal species thereby supporting previous authors who have reported such activity patterns. Uniform retinal distribution of RH1 indicates visual acuity at night, also confirming the paradigm of D. ordii as primarily a nocturnal species and suggesting visual acuity at all times of the day in the species. These results demonstrate not only that the species is capable of UV vision and has a retina characteristic of a diurnal mammal, but that many previously unknown photic niche selective advantages likely have shaped the evolution and ecology of this model taxon.
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Affiliation(s)
- Brandon McDonald
- Cameron University, Department of Agriculture, Biology, and Health Sciences, Lawton, OK, USA
| | - Bryce Geiger
- Cameron University, Department of Agriculture, Biology, and Health Sciences, Lawton, OK, USA
| | - Sarah Vrla
- Cameron University, Department of Agriculture, Biology, and Health Sciences, Lawton, OK, USA
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14
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Simões BF, Gower DJ, Rasmussen AR, Sarker MAR, Fry GC, Casewell NR, Harrison RA, Hart NS, Partridge JC, Hunt DM, Chang BS, Pisani D, Sanders KL. Spectral Diversification and Trans-Species Allelic Polymorphism during the Land-to-Sea Transition in Snakes. Curr Biol 2020; 30:2608-2615.e4. [PMID: 32470360 DOI: 10.1016/j.cub.2020.04.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 11/16/2022]
Abstract
Snakes are descended from highly visual lizards [1] but have limited (probably dichromatic) color vision attributed to a dim-light lifestyle of early snakes [2-4]. The living species of front-fanged elapids, however, are ecologically very diverse, with ∼300 terrestrial species (cobras, taipans, etc.) and ∼60 fully marine sea snakes, plus eight independently marine, amphibious sea kraits [1]. Here, we investigate the evolution of spectral sensitivity in elapids by analyzing their opsin genes (which are responsible for sensitivity to UV and visible light), retinal photoreceptors, and ocular lenses. We found that sea snakes underwent rapid adaptive diversification of their visual pigments when compared with their terrestrial and amphibious relatives. The three opsins present in snakes (SWS1, LWS, and RH1) have evolved under positive selection in elapids, and in sea snakes they have undergone multiple shifts in spectral sensitivity toward the longer wavelengths that dominate below the sea surface. Several relatively distantly related Hydrophis sea snakes are polymorphic for shortwave sensitive visual pigment encoded by alleles of SWS1. This spectral site polymorphism is expected to confer expanded "UV-blue" spectral sensitivity and is estimated to have persisted twice as long as the predicted survival time for selectively neutral nuclear alleles. We suggest that this polymorphism is adaptively maintained across Hydrophis species via balancing selection, similarly to the LWS polymorphism that confers allelic trichromacy in some primates. Diving sea snakes thus appear to share parallel mechanisms of color vision diversification with fruit-eating primates.
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Affiliation(s)
- Bruno F Simões
- University of Plymouth, School of Biological and Marine Sciences, Drake Circus, Plymouth PL4 8AA, United Kingdom; University of Bristol, School of Biological Sciences and School of Earth Sciences, Tyndall Avenue, Bristol BS8 1TG, United Kingdom; The University of Adelaide, School of Biological Sciences, North Terrace, Adelaide, South Australia 5005, Australia.
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Arne R Rasmussen
- The Royal Danish Academy of Fine Arts, School of Architecture, Design and Conservation, Philip de Langes Allé, 1435 Copenhagen K, Denmark
| | - Mohammad A R Sarker
- University of Dhaka, Department of Zoology, Curzon Hall Campus, Dhaka 1000, Bangladesh
| | - Gary C Fry
- CSIRO Oceans and Atmosphere, Queensland Biosciences Precinct, St Lucia, Queensland 4072, Australia
| | - Nicholas R Casewell
- Liverpool School of Tropical Medicine, Centre for Snakebite Research & Interventions, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Robert A Harrison
- Liverpool School of Tropical Medicine, Centre for Snakebite Research & Interventions, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Nathan S Hart
- Macquarie University, Department of Biological Sciences, North Ryde, Sydney, New South Wales 2109, Australia
| | - Julian C Partridge
- The University of Western Australia, Oceans Institute, Crawley, Perth, Western Australia 6009, Australia
| | - David M Hunt
- The University of Western Australia, School of Biological Sciences, Crawley, Perth, Western Australia 6009, Australia; The Lions Eye Institute, Centre for Ophthalmology and Visual Science, Nedlands, Perth, Western Australia 6009, Australia
| | - Belinda S Chang
- University of Toronto, Departments of Ecology & Evolutionary, Cell & Systems Biology, Willcocks Street, Toronto M5S 3G5, Canada
| | - Davide Pisani
- University of Bristol, School of Biological Sciences and School of Earth Sciences, Tyndall Avenue, Bristol BS8 1TG, United Kingdom
| | - Kate L Sanders
- The University of Adelaide, School of Biological Sciences, North Terrace, Adelaide, South Australia 5005, Australia; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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15
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Allen AE, Mouland JW, Rodgers J, Baño-Otálora B, Douglas RH, Jeffery G, Vugler AA, Brown TM, Lucas RJ. Spectral sensitivity of cone vision in the diurnal murid Rhabdomys pumilio. J Exp Biol 2020; 223:jeb215368. [PMID: 32371443 PMCID: PMC7272338 DOI: 10.1242/jeb.215368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/20/2020] [Indexed: 01/14/2023]
Abstract
An animal's temporal niche - the time of day at which it is active - is known to drive a variety of adaptations in the visual system. These include variations in the topography, spectral sensitivity and density of retinal photoreceptors, and changes in the eye's gross anatomy and spectral transmission characteristics. We have characterised visual spectral sensitivity in the murid rodent Rhabdomys pumilio (the four-striped grass mouse), which is in the same family as (nocturnal) mice and rats but exhibits a strong diurnal niche. As is common in diurnal species, the R. pumilio lens acts as a long-pass spectral filter, providing limited transmission of light <400 nm. Conversely, we found strong sequence homologies with the R. pumilio SWS and MWS opsins and those of related nocturnal species (mice and rats) whose SWS opsins are maximally sensitive in the near-UV. We continued to assess in vivo spectral sensitivity of cone vision using electroretinography and multi-channel recordings from the visual thalamus. These revealed that responses across the human visible range could be adequately described by those of a single pigment (assumed to be MWS opsin) maximally sensitive at ∼500 nm, but that sensitivity in the near-UV required inclusion of a second pigment whose peak sensitivity lay well into the UV range (λmax<400 nm, probably ∼360 nm). We therefore conclude that, despite the UV-filtering effects of the lens, R. pumilio retains an SWS pigment with a UV-A λmax In effect, this somewhat paradoxical combination of long-pass lens and UV-A λmax results in narrow-band sensitivity for SWS cone pathways in the UV-A range.
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Affiliation(s)
- Annette E Allen
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Joshua W Mouland
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Jessica Rodgers
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Beatriz Baño-Otálora
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Ronald H Douglas
- Department of Optometry and Visual Science, City, University of London, London, EC1V 0HB, UK
| | - Glen Jeffery
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Anthony A Vugler
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Timothy M Brown
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Robert J Lucas
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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16
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Hauzman E. Adaptations and evolutionary trajectories of the snake rod and cone photoreceptors. Semin Cell Dev Biol 2020; 106:86-93. [PMID: 32359892 DOI: 10.1016/j.semcdb.2020.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 10/24/2022]
Abstract
Most vertebrates have duplex retinas, with two classes of photoreceptors, rods and cones. In the group of Snakes, however, distinct patterns of retinal morphology are associated with transitions between diurnal-nocturnal habits and reflect important adaptations of their visual system. Pure-cone, pure-rod and duplex retinas were described in different species, and this variability led Gordon Walls (1934) to formulate the transmutation theory, which suggests that rods and cones are not fixed entities, but can assume transitional states. Three opsin genes are expressed in retinas of most snake species, lws, rh1, and sws1, and recent studies have shown that the rhodopsin gene, rh1, is expressed in pure-cone retinas of diurnal snakes. This expression raised many questions about the nature of transmutation and functional aspects of the rhodopsin in a cone-like photoreceptor. Extreme differences in the retinal architecture of diurnal and nocturnal snakes also highlight the complexity of adaptations of their visual structures, which might have contributed to the adaptive radiation of this group and will be discussed in this review.
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Affiliation(s)
- Einat Hauzman
- Department of Experimental Psychology, Psychology Institute, University of São Paulo, Av. Professor Mello Moraes, 1721, Bloco A - D9. Butantã, São Paulo, CEP. 05508-030, Brazil.
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17
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18
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Duytschaever G, Janiak MC, Ong PS, Wells K, Dominy NJ, Melin AD. Opsin genes of select treeshrews resolve ancestral character states within Scandentia. ROYAL SOCIETY OPEN SCIENCE 2019; 6:182037. [PMID: 31183134 PMCID: PMC6502361 DOI: 10.1098/rsos.182037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed treeshrew (Dendrogale melanura). The opsin, by inference, is red-shifted by ca 6 nm with an inferred peak sensitivity of 561 nm. It is tempting to view this trait as a novel visual adaptation; however, the genetic and functional diversity of visual pigments in treeshrews is unresolved outside of Borneo. Here, we report gene sequences from the northern smooth-tailed treeshrew (Dendrogale murina) and the Mindanao treeshrew (Tupaia everetti, the senior synonym of Urogale everetti). We found that the opsin genes are under purifying selection and that D. murina shares the same substitution as its congener, a result that distinguishes Dendrogale from other treeshrews, including T. everetti. We discuss the implications of opsin functional variation in light of limited knowledge about the visual ecology of smooth-tailed treeshrews.
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Affiliation(s)
- Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C. Janiak
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Perry S. Ong
- Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines
| | - Konstans Wells
- Department of Biosciences, Swansea University, Wales, UK
| | - Nathaniel J. Dominy
- Department of Anthropology, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
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19
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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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20
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Gower DJ, Sampaio FL, Peichl L, Wagner HJ, Loew ER, Mclamb W, Douglas RH, Orlov N, Grace MS, Hart NS, Hunt DM, Partridge JC, Simões BF. Evolution of the eyes of vipers with and without infrared-sensing pit organs. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- David J Gower
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Filipa L Sampaio
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Leo Peichl
- Max Planck Institute for Brain Research, Germany
- Dr. Senckenbergische Anatomie, Goethe University Frankfurt, Germany
| | | | - Ellis R Loew
- Department of Biomedical Sciences, Cornell University, USA
| | - William Mclamb
- Department of Biological Sciences, Florida Institute of Technology, and Center for the Advancement of Science in Space, Melbourne, FL, USA
| | - Ronald H Douglas
- Department of Life Sciences, The Natural History Museum, London, UK
- Department of Optometry and Visual Science, City, University of London, London, UK
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, Russia
| | - Michael S Grace
- College of Science, Florida Institute of Technology, Melbourne, FL, USA
| | - Nathan S Hart
- Department of Biological Sciences, Macquarie University, Australia
| | - David M Hunt
- School of Biological Sciences, The University of Western Australia, Australia
- Centre for Ophthalmology and Vision Science, Lions Eye Institute, The University of Western Australia, Perth, Australia
| | - Julian C Partridge
- School of Biological Sciences, The University of Western Australia, Australia
- Oceans Institute, The University of Western Australia, Perth, WA, Australia
| | - Bruno F Simões
- Department of Life Sciences, The Natural History Museum, London, UK
- School of Earth Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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21
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Bittencourt GB, Hauzman E, Bonci DMO, Ventura DF. Photoreceptors morphology and genetics of the visual pigments of Bothrops jararaca and Crotalus durissus terrificus (Serpentes, Viperidae). Vision Res 2019; 158:72-77. [PMID: 30826356 DOI: 10.1016/j.visres.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/11/2019] [Accepted: 02/24/2019] [Indexed: 10/27/2022]
Abstract
Snakes inhabit a great variety of habitats, whose spectral quality of light may vary a lot and influence specific adaptations of their visual system. In this study, we investigated the genetics of the visual opsins and the morphology of retinal photoreceptors, of two nocturnal snakes from the Viperidae family, Bothrops jararaca and Crotalus durissus terrificus, which inhabit preferentially the Atlantic Rain Forest and the Brazilian Savannah, respectively. Total RNA was extracted from homogenized retinas and converted to cDNA. The opsin genes expressed in snake retinas, LWS, RH1, and SWS1, were amplified by polymerase chain reactions (PCRs) and sequenced. The absorption peak (λmax) of the opsins were estimated based on amino acids located at specific spectral tuning sites. Photoreceptor cell populations were analyzed using immunohistochemistry with anti-opsin antibodies. Results showed the same morphological cell populations and same opsins absorption peaks, in both viperid species: double and single cones with LWS photopigment and λmax at ∼555 nm; single cones with SWS1 photopigment and λmax at ∼360 nm; and rods with the rhodopsin RH1 photopigment and λmax at ∼500 nm. The results indicate adaptations to nocturnal habit in both species despite the differences in habitat, and the possibility of a dichromatic color vision at photopic conditions.
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Affiliation(s)
- Guido Barbieri Bittencourt
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil
| | - Einat Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil; Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, Brazil.
| | - Daniela Maria Oliveira Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil; Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Dora Fix Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, São Paulo, Brazil; Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, Brazil
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22
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Kries K, Barros MAS, Duytschaever G, Orkin JD, Janiak MC, Pessoa DMA, Melin AD. Colour vision variation in leaf-nosed bats (Phyllostomidae): Links to cave roosting and dietary specialization. Mol Ecol 2018; 27:3627-3640. [PMID: 30059176 DOI: 10.1111/mec.14818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
Abstract
Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf-nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali). OPN1LW genes appear intact for all species, and predicted spectral tuning of long-wavelength opsins varied among lineages. OPN1SW genes appear intact and under purifying selection for Myotis lavali and most phyllostomid bats, with two exceptions: (a) We found evidence of ancient OPN1SW pseudogenization in the vampire bat lineage, and loss-of-function mutations in all three species of extant vampire bats; (b) we additionally found a recent, independently derived OPN1SW pseudogene in Lonchophylla mordax, a cave-roosting species. These mutations in leaf-nosed bats are independent of the OPN1SW pseudogenization events previously reported in Yinpterochiropterans. Therefore, the evolution of monochromacy (complete colour blindness) has occurred in both suborders of bats and under various evolutionary drivers; we find independent support for the hypothesis that obligate cave roosting drives colour vision loss. We additionally suggest that haematophagous dietary specialization and corresponding selection on nonvisual senses led to loss of colour vision through evolutionary sensory trade-off. Our results underscore the evolutionary plasticity of opsins among nocturnal mammals.
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Affiliation(s)
- Kelly Kries
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri
| | - Marília A S Barros
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, New Jersey
| | - Daniel M A Pessoa
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Visual pigment genes and absorbance spectra in the Japanese sardine Sardinops melanostictus (Teleostei: Clupeiformes). Comp Biochem Physiol B Biochem Mol Biol 2018; 218:54-63. [DOI: 10.1016/j.cbpb.2018.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/17/2018] [Accepted: 02/23/2018] [Indexed: 11/20/2022]
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24
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Srinivasan S, Fernández-Sampedro MA, Morillo M, Ramon E, Jiménez-Rosés M, Cordomí A, Garriga P. Human Blue Cone Opsin Regeneration Involves Secondary Retinal Binding with Analog Specificity. Biophys J 2018; 114:1285-1294. [PMID: 29590586 PMCID: PMC5883618 DOI: 10.1016/j.bpj.2018.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigments.
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Affiliation(s)
| | | | | | - Eva Ramon
- Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Mireia Jiménez-Rosés
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Garriga
- Universitat Politècnica de Catalunya, Terrassa, Spain.
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25
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Borges R, Johnson WE, O'Brien SJ, Gomes C, Heesy CP, Antunes A. Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments. BMC Genomics 2018; 19:121. [PMID: 29402215 PMCID: PMC5800076 DOI: 10.1186/s12864-017-4417-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/22/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Based on evolutionary patterns of the vertebrate eye, Walls (1942) hypothesized that early placental mammals evolved primarily in nocturnal habitats. However, not only Eutheria, but all mammals show photic characteristics (i.e. dichromatic vision, rod-dominated retina) suggestive of a scotopic eye design. RESULTS Here, we used integrative comparative genomic and phylogenetic methodologies employing the photoreceptive opsin gene family in 154 mammals to test the likelihood of a nocturnal period in the emergence of all mammals. We showed that mammals possess genomic patterns concordant with a nocturnal ancestry. The loss of the RH2, VA, PARA, PARIE and OPN4x opsins in all mammals led us to advance a probable and most-parsimonious hypothesis of a global nocturnal bottleneck that explains the loss of these genes in the emerging lineage (> > 215.5 million years ago). In addition, ancestral character reconstruction analyses provided strong evidence that ancestral mammals possessed a nocturnal lifestyle, ultra-violet-sensitive vision, low visual acuity and low orbit convergence (i.e. panoramic vision). CONCLUSIONS Overall, this study provides insight into the evolutionary history of the mammalian eye while discussing important ecological aspects of the photic paleo-environments ancestral mammals have occupied.
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Affiliation(s)
- Rui Borges
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia, 199004
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, 8000, North Ocean Drive, Ft Lauderdale, 33004, Florida, USA
| | - Cidália Gomes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
- ICBAS, Institute of the Biomedical Sciences of Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Christopher P Heesy
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, 19555 N. 59th avenue, Glendale, AZ, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal.
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26
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Hauzman E, Bonci DMO, Suárez-Villota EY, Neitz M, Ventura DF. Daily activity patterns influence retinal morphology, signatures of selection, and spectral tuning of opsin genes in colubrid snakes. BMC Evol Biol 2017; 17:249. [PMID: 29228925 PMCID: PMC5725783 DOI: 10.1186/s12862-017-1110-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/06/2017] [Indexed: 11/10/2022] Open
Abstract
Background Morphological divergences of snake retinal structure point to complex evolutionary processes and adaptations. The Colubridae family has a remarkable variety of retinal structure that can range from all-cone and all-rod to duplex (cone/rod) retinas. To explore whether nocturnal versus diurnal activity is responsible for constraints on molecular evolution and plays a role in visual opsin spectral tuning of colubrids, we carried out molecular evolution analyses of the visual opsin genes LWS, RH1, and SWS1 from 17 species and performed morphological analyses. Results Phylogenetic reconstructions of the RH1 and LWS recovered major clades characterized by primarily diurnal or primarily nocturnal activity patterns, in contrast with the topology for SWS1, which is very similar to the species tree. We found stronger signals of purifying selection along diurnal and nocturnal lineages for RH1 and SWS1, respectively. A blue-shift of the RH1 spectral peak is associated with diurnal habits. Spectral tuning of cone opsins did not differ among diurnal and nocturnal species. Retinas of nocturnal colubrids had many rows of photoreceptor nuclei, with large numbers of rods, labeled by wheat germ agglutinin (WGA), and two types of cones: large cones sensitive to long/medium wavelengths (L/M) and small cones sensitive to ultra-violet/violet wavelengths (UV/VS). In contrast, retinas of diurnal species had only one row of photoreceptor nuclei, with four types of cones: large and double L/M cones, small UV/VS cones, and a second group of small cones, labeled by WGA. Conclusions For LWS gene, selection tests did not confirm different constraints related to activity pattern. For SWS1, stronger purifying selection in nocturnal lineages indicates divergent evolutionary pressures related to the activity pattern, and the importance of the short wavelength sensitivity at low light condition. Activity pattern has a clear influence on the signatures of selection and spectral tuning of RH1, with stronger purifying selection in diurnal lineages, which indicates selective pressure to preserve rhodopsin structure and function in pure-cone retinas. We suggest that the presence of four cone types in primarily diurnal colubrids might be related to the gain of color discrimination capacity. Electronic supplementary material The online version of this article (10.1186/s12862-017-1110-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- E Hauzman
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes 1721 Bloco A Sala D9 - Butantã, São Paulo, SP, CEP 05508-030, Brazil. .,Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil.
| | - D M O Bonci
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes 1721 Bloco A Sala D9 - Butantã, São Paulo, SP, CEP 05508-030, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil
| | - E Y Suárez-Villota
- Instituto de Ciencias Marinas y Limnólogicas, Universidad Austral de Chile, Edificio Emilio Pugin, Campus Isla Teja S/N, 5110236, Valdivia, Chile.,Laboratório de Ecologia e Evolução, Instituto Butantan, São Paulo, Brazil
| | - M Neitz
- Department of Opthalmology, University of Washington, 750 Republican Street, Box 358058, Seattle, WA, 98109, USA
| | - D F Ventura
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Professor Mello Moraes 1721 Bloco A Sala D9 - Butantã, São Paulo, SP, CEP 05508-030, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, São Paulo, Brazil
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27
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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: 62] [Impact Index Per Article: 8.9] [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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28
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Nandamuri SP, Yourick MR, Carleton KL. Adult plasticity in African cichlids: Rapid changes in opsin expression in response to environmental light differences. Mol Ecol 2017; 26:6036-6052. [PMID: 28926160 DOI: 10.1111/mec.14357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 08/01/2017] [Accepted: 08/14/2017] [Indexed: 01/09/2023]
Abstract
Phenotypic plasticity allows organisms to adapt quickly to local environmental conditions and could facilitate adaptive radiations. Cichlids have recently undergone an adaptive radiation in Lake Malawi where they inhabit diverse light environments and tune their visual sensitivity through differences in cone opsin expression. While cichlid opsin expression is known to be plastic over development, whether adults remain plastic is unknown. Adult plasticity in visual tuning could play a role in cichlid radiations by enabling survival in changing environments and facilitating invasion into novel environments. Here we examine the existence of and temporal changes in adult visual plasticity of two closely related species. In complementary experiments, wild adult Metriaclima mbenji from Lake Malawi were moved to the lab under UV-deficient fluorescent lighting; while lab raised M. benetos were placed under UV-rich lighting designed to mimic light conditions in the wild. Surprisingly, adult cichlids in both experiments showed significant changes in the expression of the UV-sensitive single cone opsin, SWS1, in only 3 days. Modeling quantum catches in the light environments revealed a possible link between the light available to the SWS1 visual pigment and SWS1 expression. We conclude that adult cichlids can undergo rapid and significant changes in opsin expression in response to environmental light shifts that are relevant to their habitat and evolutionary history in Lake Malawi. This could have contributed to the rapid divergence characteristic of these fantastic fishes.
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Affiliation(s)
| | - Miranda R Yourick
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
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29
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Carvalho LS, Pessoa DMA, Mountford JK, Davies WIL, Hunt DM. The Genetic and Evolutionary Drives behind Primate Color Vision. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Melin AD, Wells K, Moritz GL, Kistler L, Orkin JD, Timm RM, Bernard H, Lakim MB, Perry GH, Kawamura S, Dominy NJ. Euarchontan Opsin Variation Brings New Focus to Primate Origins. Mol Biol Evol 2016; 33:1029-41. [PMID: 26739880 PMCID: PMC4776711 DOI: 10.1093/molbev/msv346] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology, Dartmouth College, Hanover, NH Department of Anthropology and Archaeology, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB
| | - Konstans Wells
- Environmental Futures Research Institute, Griffith University, Brisbane, QLD, Australia
| | - Gillian L Moritz
- Department of Biological Sciences, Class of 1978 Life Sciences Center, Dartmouth College, Hanover, NH Department of Evolutionary Anthropology, Duke University
| | - Logan Kistler
- Departments of Anthropology and Biology, Pennsylvania State University School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, United Kingdom
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB Department of Anthropology, Washington University in St. Louis
| | - Robert M Timm
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Maklarin B Lakim
- Sabah Parks, Lot 45 & 46 KK Times Square Coastal Highway, Kota Kinabalu, Sabah, Malaysia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, Hanover, NH Department of Biological Sciences, Class of 1978 Life Sciences Center, Dartmouth College, Hanover, NH
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31
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Yokoyama S, Tada T, Liu Y, Faggionato D, Altun A. A simple method for studying the molecular mechanisms of ultraviolet and violet reception in vertebrates. BMC Evol Biol 2016; 16:64. [PMID: 27001075 PMCID: PMC4802639 DOI: 10.1186/s12862-016-0637-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/16/2016] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Many vertebrate species use ultraviolet (UV) reception for such basic behaviors as foraging and mating, but many others switched to violet reception and improved their visual resolution. The respective phenotypes are regulated by the short wavelength-sensitive (SWS1) pigments that absorb light maximally (λmax) at ~360 and 395-440 nm. Because of strong epistatic interactions, the biological significance of the extensive mutagenesis results on the molecular basis of spectral tuning in SWS1 pigments and the mechanisms of their phenotypic adaptations remains uncertain. RESULTS The magnitudes of the λmax-shifts caused by mutations in a present-day SWS1 pigment and by the corresponding forward mutations in its ancestral pigment are often dramatically different. To resolve these mutagenesis results, the A/B ratio, in which A and B are the areas formed by amino acids at sites 90, 113 and 118 and by those at sites 86, 90 and 118 and 295, respectively, becomes indispensable. Then, all critical mutations that generated the λmax of a SWS1 pigment can be identified by establishing that 1) the difference between the λmax of the ancestral pigment with these mutations and that of the present-day pigment is small (3 ~ 5 nm, depending on the entire λmax-shift) and 2) the difference between the corresponding A/B ratios is < 0.002. CONCLUSION Molecular adaptation has been studied mostly by using comparative sequence analyses. These statistical results provide biological hypotheses and need to be tested using experimental means. This is an opportune time to explore the currently available and new genetic systems and test these statistical hypotheses. Evaluating the λmaxs and A/B ratios of mutagenized present-day and their ancestral pigments, we now have a method to identify all critical mutations that are responsible for phenotypic adaptation of SWS1 pigments. The result also explains spectral tuning of the same pigments, a central unanswered question in phototransduction.
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Affiliation(s)
- Shozo Yokoyama
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - Takashi Tada
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Yang Liu
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | | | - Ahmet Altun
- Department of Physics, Fatih University, Istanbul, 34500, Turkey.,Department of Genetics and Bioengineering, Fatih University, Istanbul, 34500, Turkey
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33
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Morrow JM, Chang BSW. Comparative Mutagenesis Studies of Retinal Release in Light-Activated Zebrafish Rhodopsin Using Fluorescence Spectroscopy. Biochemistry 2015; 54:4507-18. [PMID: 26098991 DOI: 10.1021/bi501377b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rhodopsin is the visual pigment responsible for initiating scotopic (dim-light) vision in vetebrates. Once activated by light, release of all-trans-retinal from rhodopsin involves hydrolysis of the Schiff base linkage, followed by dissociation of retinal from the protein moiety. This kinetic process has been well studied in model systems such as bovine rhodopsin, but not in rhodopsins from cold-blooded animals, where physiological temperatures can vary considerably. Here, we characterize the rate of retinal release from light-activated rhodopsin in an ectotherm, zebrafish (Danio rerio), demonstrating in a fluorescence assay that this process occurs more than twice as fast as bovine rhodopsin at similar temperatures in 0.1% dodecyl maltoside. Using site-directed mutagenesis, we found that differences in retinal release rates can be attributed to a series of variable residues lining the retinal channel in three key structural motifs: an opening in metarhodopsin II between transmembrane helix 5 (TM5) and TM6, in TM3 near E122, and in the "retinal plug" formed by extracellular loop 2 (EL2). The majority of these sites are more proximal to the β-ionone ring of retinal than the Schiff base, indicating their influence on retinal release is more likely due to steric effects during retinal dissociation, rather than alterations to Schiff base stability. An Arrhenius plot of zebrafish rhodopsin was consistent with this model, inferring that the activation energy for Schiff base hydrolysis is similar to that of bovine rhodopsin. Functional variation at key sites identified in this study is consistent with the idea that retinal release might be an adaptive property of rhodopsin in vertebrates. Our study is one of the few investigating a nonmammalian rhodopsin, which will help establish a better understanding of the molecular mechanisms contributing to vision in cold-blooded vertebrates.
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34
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Dichromatic vision in a fruit bat with diurnal proclivities: the Samoan flying fox (Pteropus samoensis). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2014; 200:1015-22. [DOI: 10.1007/s00359-014-0951-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 09/26/2014] [Accepted: 10/01/2014] [Indexed: 11/25/2022]
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35
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Hauser FE, van Hazel I, Chang BSW. Spectral tuning in vertebrate short wavelength-sensitive 1 (SWS1) visual pigments: Can wavelength sensitivity be inferred from sequence data? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:529-39. [DOI: 10.1002/jez.b.22576] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/05/2014] [Accepted: 05/06/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Ilke van Hazel
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
| | - Belinda S. W. Chang
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario Canada
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario Canada
- Centre for the Analysis of Genome Evolution & Function; University of Toronto; Toronto Ontario Canada
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36
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Emerling CA, Springer MS. Eyes underground: regression of visual protein networks in subterranean mammals. Mol Phylogenet Evol 2014; 78:260-70. [PMID: 24859681 DOI: 10.1016/j.ympev.2014.05.016] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 04/26/2014] [Accepted: 05/05/2014] [Indexed: 11/26/2022]
Abstract
Regressive evolution involves the degeneration of formerly useful structures in a lineage over time, and may be accompanied by the molecular decay of phenotype-specific genes. The mammalian eye has repeatedly undergone degeneration in taxa that occupy dim-light environments including subterranean habitats. Here we assess whether a decrease in the amount of light that reaches the retina is associated with increased regression of retinal genes, whether the phototransduction and visual cycle pathways degrade in a predictable pattern, and if the timing of retinal gene loss is associated with the entrance of mammalian lineages into subterranean environments. Sequence data were obtained from the publically available genomes of the Cape golden mole (Chrysochloris asiatica), naked mole-rat (Heterocephalus glaber) and star-nosed mole (Condylura cristata) for 65 genes associated with phototransduction, the visual cycle, and other retinal functions. Gene sequences were inspected for inactivating mutations and, when present, pseudogene sequences were compared to sequences from subaerial outgroup species. To test whether retinal degeneration is correlated with historical entrances into subterranean environments, estimated dates of retinal gene inactivation were compared to the fossil record and phylogenetic inferences of ancestral fossoriality. Our results show that (1) lower levels of light available to the retina correspond with an increase in the number of retinal pseudogenes, (2) retinal protein networks generally degrade in a predictable manner, although the extensive loss of cone phototransduction genes in Heterocephalus raises further questions regarding SWS1-cone monochromacy versus functional rod monochromacy in this species, and (3) inactivation dates of retinal genes usually post-date inferred entrances into subterranean habitats.
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Affiliation(s)
- Christopher A Emerling
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
| | - Mark S Springer
- Department of Biology, University of California Riverside, 900 University Ave, Riverside, CA 92521, United States.
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Miyagi R, Terai Y. The diversity of male nuptial coloration leads to species diversity in Lake Victoria cichlids. Genes Genet Syst 2014; 88:145-53. [PMID: 24025243 DOI: 10.1266/ggs.88.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The amazing coloration shown by diverse cichlid fish not only fascinates aquarium keepers, but also receives great attention from biologists interested in speciation because of its recently-revealed role in their adaptive radiation in an African lake. We review the important role of coloration in the speciation and adaptive evolution of Lake Victoria cichlids, which have experienced adaptive radiation during a very short evolutionary period. Mature male cichlids display their colors during mate choice. The color of their skin reflects light, and the reflected light forms a color signal that is received by the visual system of females. The adaptive divergence of visual perceptions shapes and diverges colorations, to match the adapted visual perceptions. The divergence of visual perception and coloration indicates that the divergence of color signals causes reproductive isolation between species, and this process leads to speciation. Differences in color signals among coexisting species act to maintain reproductive isolation by preventing hybridization. Thus, the diversity of coloration has caused speciation and has maintained species diversity in Lake Victoria cichlids.
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Affiliation(s)
- Ryutaro Miyagi
- Department of Biological Sciences, Tokyo Metropolitan University
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38
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Douglas RH, Jeffery G. The spectral transmission of ocular media suggests ultraviolet sensitivity is widespread among mammals. Proc Biol Sci 2014; 281:20132995. [PMID: 24552839 PMCID: PMC4027392 DOI: 10.1098/rspb.2013.2995] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although ultraviolet (UV) sensitivity is widespread among animals it is considered rare in mammals, being restricted to the few species that have a visual pigment maximally sensitive (λmax) below 400 nm. However, even animals without such a pigment will be UV-sensitive if they have ocular media that transmit these wavelengths, as all visual pigments absorb significant amounts of UV if the energy level is sufficient. Although it is known that lenses of diurnal sciurid rodents, tree shrews and primates prevent UV from reaching the retina, the degree of UV transmission by ocular media of most other mammals without a visual pigment with λmax in the UV is unknown. We examined lenses of 38 mammalian species from 25 families in nine orders and observed large diversity in the degree of short-wavelength transmission. All species whose lenses removed short wavelengths had retinae specialized for high spatial resolution and relatively high cone numbers, suggesting that UV removal is primarily linked to increased acuity. Other mammals, however, such as hedgehogs, dogs, cats, ferrets and okapis had lenses transmitting significant amounts of UVA (315-400 nm), suggesting that they will be UV-sensitive even without a specific UV visual pigment.
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Affiliation(s)
- R H Douglas
- Department of Optometry and Visual Science, City University London, , Northampton Square, London EC1V 0HB, UK, Institute of Ophthalmology, University College London, , 11-43 Bath Street, London EC1V 9EL, UK
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39
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Knott B, Davies WIL, Carvalho LS, Berg ML, Buchanan KL, Bowmaker JK, Bennett ATD, Hunt DM. How parrots see their colours: novelty in the visual pigments of Platycercus elegans. J Exp Biol 2013; 216:4454-61. [DOI: 10.1242/jeb.094136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
Intraspecific differences in retinal physiology have been demonstrated in several vertebrate taxa and are often subject to adaptive evolution. Nonetheless, such differences are currently unknown in birds, despite variations in habitat, behaviour and visual stimuli that might influence spectral sensitivity. The parrot Platycercus elegans is a species complex with extreme plumage colour differences between (and sometimes within) subspecies, making it an ideal candidate for intraspecific differences in spectral sensitivity. Here, the visual pigments of P. elegans were fully characterised through molecular sequencing of five visual opsin genes and measurement of their absorbance spectra using microspectrophotometry. Three of the genes, LWS, SW1 and SWS2, encode for proteins similar to those found in other birds; however, both the RH1 and RH2 pigments had polypeptides with carboxyl termini of different lengths and unusual properties that are unknown previously for any vertebrate visual pigment. Specifically, multiple RH2 transcripts and protein variants (short, medium and long) were identified for the first time that are generated by alternative splicing of downstream coding and non-coding exons. Our work provides the first complete characterisation of the visual pigments of a parrot, perhaps the most colourful order of birds, and moreover suggests more variability in avian eyes than hitherto considered.
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Affiliation(s)
- Ben Knott
- Centre for Behavioural Biology, School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia
| | - Wayne I. L. Davies
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
- School of Animal Biology and UWA Oceans Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Livia S. Carvalho
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Mathew L. Berg
- Centre for Behavioural Biology, School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia
| | - Katherine L. Buchanan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - James K. Bowmaker
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Andrew T. D. Bennett
- Centre for Behavioural Biology, School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia
| | - David M. Hunt
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
- School of Animal Biology and UWA Oceans Institute, University of Western Australia, Perth, WA 6009, Australia
- Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia
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Retinal cone photoreceptors of the deer mouse Peromyscus maniculatus: development, topography, opsin expression and spectral tuning. PLoS One 2013; 8:e80910. [PMID: 24260509 PMCID: PMC3829927 DOI: 10.1371/journal.pone.0080910] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/09/2013] [Indexed: 11/19/2022] Open
Abstract
A quantitative analysis of photoreceptor properties was performed in the retina of the nocturnal deer mouse, Peromyscus maniculatus, using pigmented (wildtype) and albino animals. The aim was to establish whether the deer mouse is a more suitable model species than the house mouse for photoreceptor studies, and whether oculocutaneous albinism affects its photoreceptor properties. In retinal flatmounts, cone photoreceptors were identified by opsin immunostaining, and their numbers, spectral types, and distributions across the retina were determined. Rod photoreceptors were counted using differential interference contrast microscopy. Pigmented P. maniculatus have a rod-dominated retina with rod densities of about 450.000/mm2 and cone densities of 3000 - 6500/mm2. Two cone opsins, shortwave sensitive (S) and middle-to-longwave sensitive (M), are present and expressed in distinct cone types. Partial sequencing of the S opsin gene strongly supports UV sensitivity of the S cone visual pigment. The S cones constitute a 5-15% minority of the cones. Different from house mouse, S and M cone distributions do not have dorsoventral gradients, and coexpression of both opsins in single cones is exceptional (<2% of the cones). In albino P. maniculatus, rod densities are reduced by approximately 40% (270.000/mm2). Overall, cone density and the density of cones exclusively expressing S opsin are not significantly different from pigmented P. maniculatus. However, in albino retinas S opsin is coexpressed with M opsin in 60-90% of the cones and therefore the population of cones expressing only M opsin is significantly reduced to 5-25%. In conclusion, deer mouse cone properties largely conform to the general mammalian pattern, hence the deer mouse may be better suited than the house mouse for the study of certain basic cone properties, including the effects of albinism on cone opsin expression.
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Abstract
AbstractS cones expressing the short wavelength-sensitive type 1 (SWS1) class of visual pigment generally form only a minority type of cone photoreceptor within the vertebrate duplex retina. Hence, their primary role is in color vision, not in high acuity vision. In mammals, S cones may be present as a constant fraction of the cones across the retina, may be restricted to certain regions of the retina or may form a gradient across the retina, and in some species, there is coexpression of SWS1 and the long wavelength-sensitive (LWS) class of pigment in many cones. During retinal development, SWS1 opsin expression generally precedes that of LWS opsin, and evidence from genetic studies indicates that the S cone pathway may be the default pathway for cone development. With the notable exception of the cartilaginous fishes, where S cones appear to be absent, they are present in representative species from all other vertebrate classes. S cone loss is not, however, uncommon; they are absent from most aquatic mammals and from some but not all nocturnal terrestrial species. The peak spectral sensitivity of S cones depends on the spectral characteristics of the pigment present. Evidence from the study of agnathans and teleost fishes indicates that the ancestral vertebrate SWS1 pigment was ultraviolet (UV) sensitive with a peak around 360 nm, but this has shifted into the violet region of the spectrum (>380 nm) on many separate occasions during vertebrate evolution. In all cases, the shift was generated by just one or a few replacements in tuning-relevant residues. Only in the avian lineage has tuning moved in the opposite direction, with the reinvention of UV-sensitive pigments.
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Zhang T, Fu Y. A Phe-rich region in short-wavelength sensitive opsins is responsible for their aggregation in the absence of 11-cis-retinal. FEBS Lett 2013; 587:2430-4. [PMID: 23792161 DOI: 10.1016/j.febslet.2013.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 01/05/2023]
Abstract
Human blue and mouse S-opsin are prone to aggregation in the absence of 11-cis-retinal, which underlie the rapid cone degeneration in human patients and animal models of Leber congenital amaurosis (LCA). By in silico analysis and domain swapping experiments, we show that a Phe-rich region in short-wavelength sensitive (SWS) opsins, but not in medium/long-wavelength sensitive opsins, is responsible for SWS opsin aggregation. Mutagenesis studies suggest that Phe residues in this region are critical in mediating protein aggregation. Fusing the Phe-rich region of SWS opsins to GFP causes the latter to aggregate. Our findings suggest that new therapeutics can be designed to disrupt the Phe-rich region in preventing cone degeneration due to S-opsin aggregation in LCA.
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Affiliation(s)
- Tao Zhang
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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Moritz GL, Lim NTL, Neitz M, Peichl L, Dominy NJ. Expression and Evolution of Short Wavelength Sensitive Opsins in Colugos: A Nocturnal Lineage That Informs Debate on Primate Origins. Evol Biol 2013; 40:542-553. [PMID: 24293738 PMCID: PMC3832777 DOI: 10.1007/s11692-013-9230-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/29/2013] [Indexed: 11/25/2022]
Abstract
A nocturnal activity pattern is central to almost all hypotheses on the adaptive origins of primates. This enduring view has been challenged in recent years on the basis of variation in the opsin genes of nocturnal primates. A correspondence between the opsin genes and activity patterns of species in Euarchonta-the superordinal group that includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews)-could prove instructive, yet the basic biology of the dermopteran visual system is practically unknown. Here we show that the eye of the Sunda colugo (Galeopterus variegatus) lacks a tapetum lucidum and has an avascular retina, and we report on the expression and spectral sensitivity of cone photopigments. We found that Sunda colugos have intact short wavelength sensitive (S-) and long wavelength sensitive (L-) opsin genes, and that both opsins are expressed in cone photoreceptors of the retina. The inferred peak spectral sensitivities are 451 and 562 nm, respectively. In line with adaptation to nocturnal vision, cone densities are low. Surprisingly, a majority of S-cones coexpress some L-opsin. We also show that the ratio of rates of nonsynonymous to synonymous substitutions of exon 1 of the S-opsin gene is indicative of purifying selection. Taken together, our results suggest that natural selection has favored a functional S-opsin in a nocturnal lineage for at least 45 million years. Accordingly, a nocturnal activity pattern remains the most likely ancestral character state of euprimates.
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Affiliation(s)
- Gillian L. Moritz
- Department of Biological Sciences, Dartmouth College, The Class of 1978 Life Sciences Center, 78 College Street, Hanover, NH 03755 USA
| | - Norman T.-L. Lim
- Department of Wildlife, Fish and Conservation Biology, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Box 356485, 1959 NE Pacific Street, Seattle, WA 98195 USA
| | - Leo Peichl
- Max Planck Institute for Brain Research, Deutschordenstrasse 46, 60528 Frankfurt am Main, Germany
| | - Nathaniel J. Dominy
- Department of Biological Sciences, Dartmouth College, The Class of 1978 Life Sciences Center, 78 College Street, Hanover, NH 03755 USA
- Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH 03755 USA
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Ostrovsky MA. Molecular physiology of visual pigment rhodopsin. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2012. [DOI: 10.1134/s1990747812010084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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DAVIES WAYNEIL, COLLIN SHAUNP, HUNT DAVIDM. Molecular ecology and adaptation of visual photopigments in craniates. Mol Ecol 2012; 21:3121-58. [DOI: 10.1111/j.1365-294x.2012.05617.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Miyagi R, Terai Y, Aibara M, Sugawara T, Imai H, Tachida H, Mzighani SI, Okitsu T, Wada A, Okada N. Correlation between nuptial colors and visual sensitivities tuned by opsins leads to species richness in sympatric Lake Victoria cichlid fishes. Mol Biol Evol 2012; 29:3281-96. [PMID: 22617953 DOI: 10.1093/molbev/mss139] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reproductive isolation that prevents interspecific hybridization between closely related coexisting species maintains sympatric species diversity. One of the reproductive isolations is mate choice based on color signals (breeding color perceived by color vision). This is well known in several animal taxa, yet little is known about its genetic and molecular mechanism. Lake Victoria cichlid fishes are thought to be an example of sympatric species diversity. In the species inhabiting different light environments in rocky shore, speciation by sensory drive through color signals has been proposed by analyses of the long wavelength-sensitive (LWS) opsin gene and the male nuptial coloration. However, the genetic and molecular mechanism of how diversity of sympatric species occurring in the same habitat is maintained remains unknown. To address this issue, we determined nucleotide sequences of eight opsins of six sympatric species collected from a sandy-muddy shore--an ideal model system for studying sympatric species. Among eight opsins, the LWS and RH1 alleles were diversified and one particular allele is dominant or fixed in each species, and we propose that this is due to natural selection. The functions of their LWS alleles were also diversified as shown by absorption measurements of reconstituted visual pigments. To analyze the relationship between nuptial coloration and the absorption of LWS pigments, we systematically evaluated and defined nuptial coloration. We showed that the coloration was species specific with respect to hue and significantly differentiated by the index values of hue (dominant wavelength: λ(d)). The λ(d) value of the male nuptial coloration correlated with the absorption of LWS pigments from all the species, suggesting that reproductive isolation through mate choice using color signals may prevent sympatric interspecific hybridization, thereby maintaining the species diversity in sympatric species in Lake Victoria.
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Affiliation(s)
- Ryutaro Miyagi
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Chen MH, Kuemmel C, Birge RR, Knox BE. Rapid release of retinal from a cone visual pigment following photoactivation. Biochemistry 2012; 51:4117-25. [PMID: 22217337 DOI: 10.1021/bi201522h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As part of the visual cycle, the retinal chromophore in both rod and cone visual pigments undergoes reversible Schiff base hydrolysis and dissociation following photobleaching. We characterized light-activated release of retinal from a short-wavelength-sensitive cone pigment (VCOP) in 0.1% dodecyl maltoside using fluorescence spectroscopy. The half-time (t(1/2)) of release of retinal from VCOP was 7.1 s, 250-fold faster than that of rhodopsin. VCOP exhibited pH-dependent release kinetics, with the t(1/2) decreasing from 23 to 4 s with the pH decreasing from 4.1 to 8, respectively. However, the Arrhenius activation energy (E(a)) for VCOP derived from kinetic measurements between 4 and 20 °C was 17.4 kcal/mol, similar to the value of 18.5 kcal/mol for rhodopsin. There was a small kinetic isotope (D(2)O) effect in VCOP, but this effect was smaller than that observed in rhodopsin. Mutation of the primary Schiff base counterion (VCOP(D108A)) produced a pigment with an unprotonated chromophore (λ(max) = 360 nm) and dramatically slowed (t(1/2) ~ 6.8 min) light-dependent retinal release. Using homology modeling, a VCOP mutant with two substitutions (S85D and D108A) was designed to move the counterion one α-helical turn into the transmembrane region from the native position. This double mutant had a UV-visible absorption spectrum consistent with a protonated Schiff base (λ(max) = 420 nm). Moreover, the VCOP(S85D/D108A) mutant had retinal release kinetics (t(1/2) = 7 s) and an E(a) (18 kcal/mol) similar to those of the native pigment exhibiting no pH dependence. By contrast, the single mutant VCOP(S85D) had an ~3-fold decreased retinal release rate compared to that of the native pigment. Photoactivated VCOP(D108A) had kinetics comparable to those of a rhodopsin counterion mutant, Rho(E113Q), both requiring hydroxylamine to fully release retinal. These results demonstrate that the primary counterion of cone visual pigments is necessary for efficient Schiff base hydrolysis. We discuss how the large differences in retinal release rates between rod and cone visual pigments arise, not from inherent differences in the rate of Schiff base hydrolysis but rather from differences in the properties of noncovalent binding of the retinal chromophore to the protein.
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Affiliation(s)
- Min-Hsuan Chen
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, USA
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Mooney VL, Szundi I, Lewis JW, Yan ECY, Kliger DS. Schiff base protonation changes in Siberian hamster ultraviolet cone pigment photointermediates. Biochemistry 2012; 51:2630-7. [PMID: 22394396 DOI: 10.1021/bi300157r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular structure and function studies of vertebrate ultraviolet (UV) cone visual pigments are needed to understand the molecular evolution of these photoreceptors, which uniquely contain unprotonated Schiff base linkages between the 11-cis-retinal chromophore and the opsin proteins. In this study, the Siberian hamster ultraviolet cone pigment (SHUV) was expressed and purified in an n-dodecyl-β-D-maltoside suspension for optical characterization. Time-resolved absorbance measurements, over a spectral range from 300 to 700 nm, were taken for the purified pigment at time delays from 30 ns to 4.64 s after photoexcitation using 7 ns pulses of 355 nm light. The resulting data were fit globally to a sum of exponential functions after noise reduction using singular-value decomposition. Four exponentials best fit the data with lifetimes of 1.4 μs, 210 μs, 47 ms, and 1 s. The first photointermediate species characterized here is an equilibrated mixture similar to the one formed after rhodopsin's Batho intermediate decays into equilibrium with its successor, BSI. The extremely large red shift of the SHUV Batho component relative to the pigment suggests that SHUV Batho has a protonated Schiff base and that the SHUV cone pigment itself has an unprotonated Schiff base. In contrast to SHUV Batho, the portion of the equilibrated mixture's spectrum corresponding to SHUV BSI is well fit by a model spectrum with an unprotonated Schiff base. The spectra of the next two photointermediate species revealed that they both have unprotonated Schiff bases and suggest they are analogous to rhodopsin's Lumi I and Lumi II species. After decay of SHUV Lumi II, the correspondence with rhodopsin photointermediates breaks down and the next photointermediate, presumably including the G protein-activating species, is a mixture of protonated and unprotonated Schiff base photointermediate species.
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Affiliation(s)
- Victoria L Mooney
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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MELIN AMANDAD, MORITZ GILLIANL, FOSBURY ROBERTAE, KAWAMURA SHOJI, DOMINY NATHANIELJ. Why Aye-Ayes See Blue. Am J Primatol 2012; 74:185-92. [DOI: 10.1002/ajp.21996] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- AMANDA D. MELIN
- Department of Anthropology; Dartmouth College; Hanover; New Hampshire
| | - GILLIAN L. MORITZ
- Department of Biological Sciences; Dartmouth College; Hanover; New Hampshire
| | | | - SHOJI KAWAMURA
- Department of Integrated Bioscience; University of Tokyo; Kashiwa; Chiba; Japan
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Jacobs GH. The Evolution of Vertebrate Color Vision. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 739:156-72. [DOI: 10.1007/978-1-4614-1704-0_10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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