Molecular evolution of vertebrate visual pigments

Yokoyama, Shozo

doi:10.1016/s1350-9462(00)00002-1

Cited by 534 publications

(589 citation statements)

References 177 publications

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“…Among vertebrates, most fishes, amphibians, reptiles, and birds have well‐developed color vision (Bowmaker, 1998; Kawamura, 2011; Yokoyama, 2000). Light colors are perceived by photopigments in cone cells in the retina of the eye (Yokoyama & Starmer, 1996).…”

Section: Introductionmentioning

confidence: 99%

“…Slight differences in opsin structure enable light to be optimally absorbed at different wavelengths. In bony fishes, the opsin repertoire differs among species (Gojobori & Innan, 2009; Yokoyama, 2000). Generally, the surface‐dwelling species, which habit the luminous superficial area of water, have a large cone opsin repertoire, as seen in zebrafish ( Danio rerio ) (Chinen, Hamaoka, Yamada, & Kawamura, 2003), medaka ( Oryzias latipes ) (Matsumoto, Fukamachi, Mitani, & Kawamura, 2006), and guppy ( Poecilia reticulata ) (Kawamura et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

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Green‐shifting ofSWS2A opsin sensitivity and loss of function ofRH2‐A opsin in flounders, genusVerasper

Kasagi

Mizusawa

Takahashi

2017

Ecology and Evolution

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We identified visual opsin genes for three flounder species, including the spotted halibut (Verasper variegatus), slime flounder (Microstomus achne), and Japanese flounder (Paralichthys olivaceus). Structure and function of opsins for the three species were characterized together with those of the barfin flounder (V. moseri) that we previously reported. All four flounder species possessed five basic opsin genes, including lws, sws1, sws2, rh1, and rh2. Specific features were observed in rh2 and sws2. The rh2‐a, one of the three subtypes of rh2, was absent in the genome of V. variegatus and pseudogenized in V. moseri. Moreover, rh2‐a mRNA was not detected in M. achne and P. olivaceus, despite the presence of a functional reading frame. Analyses of the maximum absorption spectra (λmax) estimated by in vitro reconstitution indicated that SWS2A of M. achne (451.9 nm) and P. olivaceus (465.6 nm) were blue‐sensitive, whereas in V. variegatus (485.4 nm), it was green‐sensitive and comparable to V. moseri (482.3 nm). Our results indicate that although the four flounder species possess a similar opsin gene repertoire, the SWS2A opsin of the genus Verasper is functionally green‐sensitive, while its overall structure remains conserved as a blue‐sensitive opsin. Further, the rh2‐a function seems to have been reduced during the evolution of flounders. λmax values of predicted ancestral SWS2A of Pleuronectiformes and Pleuronectidae was 465.4 and 462.4 nm, respectively, indicating that these were blue‐sensitive. Thus, the green‐sensitive SWS2A is estimated to be arisen in ancestral Verasper genus. It is suggested that the sensitivity shift of SWS2A from blue to green may have compensated functional reduction in RH2‐A.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Green‐shifting ofSWS2A opsin sensitivity and loss of function ofRH2‐A opsin in flounders, genusVerasper

Kasagi

Mizusawa

Takahashi

2017

Ecology and Evolution

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“…This spectral difference can be explained fully by three amino acid differences between the two pigments: A164 (alanine at residue 164, residue numbers hereafter follow those in bovine rhodopsin), F261 (phenylalanine 261), and A269 (alanine 269) in the gecko pigment and S164, Y261, and T269 in the chameleon pigment (e.g. Yokoyama, 2000aYokoyama, , 2002.…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleon

Takenaka

Yokoyama

2007

Gene

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At present, molecular bases of spectral tuning in rhodopsin-like (RH2) pigments are not well understood. Here, we have constructed the RH2 pigments of nocturnal Tokay gecko (Gekko gekko) and diurnal American chameleon (Anolis carolinensis) as well as chimeras between them. The RH2 pigments of the gecko and chameleon reconstituted with 11-cis-retinal had the wavelengths of maximal absorption (λ max 's) of 467 and 496 nm, respectively. Chimeric pigment analyses indicated that 76-86%, 14-24%, and 10% of the spectral difference between them could be explained by amino acid differences in transmembrane (TM) helices I~IV, V~VII, and amino acid interactions between the two segments, respectively. Evolutionary and mutagenesis analyses revealed that the λ max 's of the gecko and chameleon pigments diverged from each other not only by S49A (serine to alanine replacement at residue 49), S49F (serine to phenylalanine), L52M (leucine to methionine), D83N (aspartic acid to asparagine), M86T (methionine to thereonine), and T97A (threonine to alanine) but also by other amino acid replacements that cause minor λ max -shifts individually.

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“…The opsin is covalently linked to the retinal chromophore by a Schiff base linkage at lysine residue 296 located in the seventh TM domain (residue numbers are according to those in bovine rhodopsin) (Yokoyama 2000). The retinal visual pigments in vertebrates are classified into five evolutionarily distinct groups: RH1 (rhodopsin), RH2 (RH1-like or green), SWS1 (short wavelength-sensitive type 1 or UV-blue), SWS2 (short wavelength-sensitive type 2 or blue), and M/LWS (middleto-long wavelength-sensitive or red-green) (Yokoyama 2000). The RH1 pigment is responsible for dim vision, while the other four groups of visual pigments are responsible for color vision.…”

Section: Introductionmentioning

confidence: 99%

“…The RH1 pigment is responsible for dim vision, while the other four groups of visual pigments are responsible for color vision. The phylogenetic relationship of these pigments is considered as ((((RH1, RH2), SWS2), SWS1), M/LWS) (Yokoyama 2000).…”

Section: Introductionmentioning

confidence: 99%

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

Gan

2009

J Mol Evol

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We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genusSinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocketforming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

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Molecular evolution of vertebrate visual pigments

Cited by 534 publications

References 177 publications

Green‐shifting ofSWS2A opsin sensitivity and loss of function ofRH2‐A opsin in flounders, genusVerasper

Green‐shifting ofSWS2A opsin sensitivity and loss of function ofRH2‐A opsin in flounders, genusVerasper

Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleon

Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

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