Evolution of Dim-Light and Color Vision Pigments

Yokoyama, Shozo

doi:10.1146/annurev.genom.9.081307.164228

Cited by 272 publications

(469 citation statements)

References 89 publications

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“…Only one site (56V, which correspond to site 49 of bovine rhodopsin), located in TM I region, has been investigated by functional study. Amino acid substitutions on this site can shift the k max of RH2 and SWS1 pigments, but this site is not in the list that can contribute to the k max shift of SWS2 (Yokoyama 2008). Interestingly, this position was invariably occupied by V in B copy of SWS2, except for B copy of C. auratus (occupied by I).…”

Section: Positive Selection Functional Diversification Of Duplicatedmentioning

confidence: 99%

“…At present, certain amino acid changes at a total of 28 critical sites are known to be able to modify the k max of various visual pigments during vertebrate evolution (reviewed by Yokoyama 2008). There are 12 sites (44, 46, 91, 94, 109, 116, 118, 122, 261, 265, 269, and 292) and 5 sites (164, 181, 261, 269, and 292) involved in spectral tuning of SWS2 pigments and M/LWS pigments, respectively.…”

Section: Site Inspectionsmentioning

confidence: 99%

“…These changes are located within or near the transmembrane segments, which can form a pocket for chromophores. The critical amino acid changes that shift k max s of visual pigments are summarized by Yokoyama (2008). The k max values of the M/LWS pigments are mostly determined by 5 aa residues at positions 164, 181, 261, 269, and 292 (numbered according to bovine rhodopsin), which is called ''five-sites'' rule and has correctly predicted the in vitroexpressed pigments of many mammals studied to date (Yokoyama 2000).…”

Section: Introductionmentioning

confidence: 98%

“…Visual sensitivities of vertebrates are tightly associated with ecological photoenvironments (Bowmaker 1995;Yokoyama 2008). For example, the cottoid fishes in Lake Baikal (the deepest lake in the world) and coelacanths in the deep sea alter their spectral sensitivities of cone and rod opsin to match with the available downwelling sunlight (Hunt et al 1996;Yokoyama and Tada 2000).…”

Section: Introductionmentioning

confidence: 99%

“…Thanks to site-directed mutagenesis and in vitro assay, now we can construct the chimeric and presumed ancestral pigments to study the effects of amino acid (aa) substitutions of specific residues on the k max values. Up to now, it is known that aa substitutions at 28 sites are involved in the spectral tuning of vertebrate visual pigments (Yokoyama 2008). These changes are located within or near the transmembrane segments, which can form a pocket for chromophores.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Positive Selection Functional Diversification Of Duplicatedmentioning

confidence: 99%

Section: Site Inspectionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Gan

2009

J Mol Evol

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Origin and adaptation of green‐sensitive (RH2) pigments in vertebrates

Yokoyama

Jia

2020

FEBS Open Bio

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One of the critical times for the survival of animals is twilight where the most abundant visible lights are between 400 and 550 nanometres (nm). Green‐sensitive RH2 pigments help nonmammalian vertebrate species to better discriminate wavelengths in this blue‐green region. Here, evaluation of the wavelengths of maximal absorption (λmaxs) of genetically engineered RH2 pigments representing 13 critical stages of vertebrate evolution revealed that the RH2 pigment of the most recent common ancestor of vertebrates had a λmax of 503 nm, while the 12 ancestral pigments exhibited an expanded range in λmaxs between 474 and 524 nm, and present‐day RH2 pigments have further expanded the range to ~ 450–530 nm. During vertebrate evolution, eight out of the 16 significant λmax shifts (or |Δλmax| ≥ 10 nm) of RH2 pigments identified were fully explained by the repeated mutations E122Q (twice), Q122E (thrice) and M207L (twice), and A292S (once). Our data indicated that the highly variable λmaxs of teleost RH2 pigments arose from gene duplications followed by accelerated amino acid substitution.

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Visual Pigment Evolution in Reptiles

Simões

Gower

2017

Encyclopedia of Life Sciences

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The long history and great ecological and morphological diversity of reptiles (all amniotes except mammals and birds) is matched by their visual system diversity. Although less known than in other amniotes, visual pigments have been studied in all extant reptile orders except Sphenodontia. There have been no additions to the five visual pigments present in the ancestral vertebrate, although there have been multiple independent losses. Crocodylians retain three visual pigments, many lizards as well as Testudines four or five and snakes one to three. Adaptive pigment evolution includes tuning site amino acid substitutions and switches between chromophore types that together generate ultraviolet to infrared spectral sensitivity. Reptiles present some of the best evidences of evolutionary rod–cone and cone–rod transmutation with, for example typically cone visual pigments expressed in rod‐like photoreceptors. Reptile visual pigments show evidence of substantial adaptive evolution, at least some of which is associated with major ecological shifts. Key Concepts Reptiles have no more than five visual pigments, as few as one and typically at least three. Up to four of the ancestral vertebrate visual pigments have been lost independently in different reptile lineages, and no visual opsin gene duplications have been identified so far. Testudines have between four and five visual pigments and a wide range of photoreceptor oil droplets, representing one of the most complex visual pigment systems in tetrapod vertebrates. Despite many of them being nocturnal, no rhodopsin 1 has been detected in geckos. No sws1 or rh2 opsin genes can be detected in genomic sequence data for crocodylians. Among squamates, some lizards have a mixture of A 1 and A 2 chromophores incorporated in their visual pigments, allowing a wide colour sensitivity, including infrared vision. In the green anole ( Anolis carolinensis ), only cone opsins have been reported (SWS1, SWS2, RH2 and LWS) in studies of the eye. However, a 515‐nm tuned rh1 rhodopsin gene occurs in the genome of this species. Extant snakes have lost two visual pigments (SWS2 and RH2), likely as an adaptation to a low light environment inhabited by a snake ancestor. Extreme burrowing in scolecophidians (blind, worm and thread snakes) is correlated with the loss of the SWS1 and LWS visual pigments and cones, rendering these snakes rod (RH1) monochromats. The expression of RH1, SWS1 and LWS pigments in snake lineages with seemingly all‐cone and all‐rod retinae suggests multiple transmutations from cone to rod and vice versa in snakes. Similar transmutations likely occurred in some lizards and perhaps crocodylians. Visual pigment spectral sensitivity in reptiles has been found to correlate with the light transmission properties of the ocular media (e.g. snakes) and photoreceptor oil droplets (e.g. testudines), that is the pigments are not sensitive to wavelengths of light filtered out by these structures.

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Evolution of Dim-Light and Color Vision Pigments

Cited by 272 publications

References 89 publications

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

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

Origin and adaptation of green‐sensitive (RH2) pigments in vertebrates

Visual Pigment Evolution in Reptiles

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