Visual Pigment Genes: Evolution

Shozo Yokoyama, Syracuse University, Syracuse, New York, USA

Published online: May 2008

DOI: 10.1002/9780470015902.a0006148.pub2

More than 100 visual pigment genes have been cloned from a diverse range of vertebrates. Comparative sequence analyses of these genes and in vitro assays of engineered visual pigments have been used to elucidate not only the molecular bases of color vision but also the processes of adaptive evolution at the molecular level.

Keywords: opsins; visual pigments; absorption spectra; mutagenesis; adaptive evolution

Figure 1. Structures of visual pigment genes, where exons and introns are represented by black boxes and horizontal lines respectively. The numbers after P refer to max. For Malawi fish pigments, Dc and Mz denote Dimidiochromis compressiceps and Metriaclima zebra respectively. Malawi fish-Dc (P536), Malawi fish-Mz (P533), Malawi fish-2A-Dc (P447), Malawi fish-2B-Dc (P488), Malawi fish-Dc (P368), Malawi fish-Dc (P569), marmoset (P561), marmoset (P553) and marmoset (P539) pigment genes are from GenBank (accession nos. AF247121, AF247122, AF247113, AF247118, AF191220, AF247125, AB046549s1–s6, AB046555s1–s6 and AB046561s1–s6 respectively). For other genes, see Yokoyama (2000). The gene duplication of the human P530 and P560 genes occurred some 30 million years (MY) ago (Nathans et al., 1986). Two human (P560) genes have intron 1 length polymorphism, one of them being 2 kb longer than the other. Af: African; LWS/MWS: long wavelength- and middle wavelength-sensitive; RH1: rhodopsins; RH2: RH1-like; SWS1: short wavelength-sensitive type 1; SWS2: SWS type 2.
Figure 2. Phylogenetic tree for the vertebrate visual pigments by applying the neighbor-joining method (Saitou and Nei, 1987) to their amino acid sequences. Ind. coelacanth (P485) and Ind. coelacanth (P478) are from Indonesian coelacanth (Latimeria menadoensis). Salamander (P431), bull frog (P432) and mole rat (P534) pigments are from GenBank (accession nos. AF038946, AB010085 and AF139726 respectively). Blackbird (P360) is from red-winged blackbird (Agelaius pheniceus). For other sequences, see Yokoyama (2000). The arrow indicates the root of the phylogenetic tree. The bar at the bottom indicates evolutionary distance measured as the number of amino acid replacements per site.
Figure 3. Secondary structure of bovine RH1 opsin, showing naturally occurring amino acid mutations that cause more than 5 nm of max shift. The model is based on Palczewski et al. (2000). Open square, filled square and filled circles indicate the amino acid sites that are involved mainly in the spectral tuning of SWS1, LWS/MWS and RH1/RH2 pigments respectively (see Yokoyama et al., 2000; Shi et al., 2001).
close
 References
    Fasick JI, Applebury ML and Oprian DD (2002) Spectral tuning in the mammalian short-wavelength sensitive cone pigments. Biochemistry 41: 6860–6865.
    Nathans J (1999) The evolution and physiology of human color vision: insights from molecular genetic studies of visual pigments. Neuron 24: 299–312.
    Nathans J, Thomas D and Hogness DS (1986) Molecular genetics of human color vision: the genes encoding blue, green, and red pigments. Science 232: 193–201.
    Neitz M and Neitz J (1995) Numbers and ratios of visual pigment genes for normal red–green color vision. Science 267: 1013–1016.
    Neitz J, Neitz M and Kainz PM (1996) Visual pigment gene structure and the severity of color vision defects. Science 274: 801–803.
    Palczewski K, Kumasaka T, Hori T et al. (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289: 739–745.
    Saitou N and Nei M (1987) The neighbor-joining method: a new method for estimating phylogenetic trees. Molecular Biology and Evolution 4: 406–425.
    Shi Y, Radlwimmer FB and Yokoyama S (2001) Molecular genetics and the evolution of ultraviolet vision in vertebrates. Proceedings of the National Academy of Sciences of the USA 98: 11731–11736.
    Wilkie SE, Robinson PR, Cronin TW et al. (2000) Spectral tuning of avian violet- and ultraviolet-sensitive visual pigments. Biochemistry 39: 7895–7901.
    Winderickx J, Lindsey DT, Sanocki E et al. (1992) Polymorphism in red photopigment underlies variation in colour matching. Nature 356: 431–433.
    Yokoyama S (2000) Molecular evolution of vertebrate visual pigments. Progress in Retinal and Eye Research 19: 385–419.
    Yokoyama S and Radlwimmer FB (2001) The molecular genetics and evolution of red and green color vision in vertebrates. Genetics 158: 1697–1710.
    Yokoyama S, Radlwimmer FB and Blow NS (2000) Ultraviolet pigments in birds evolved from violet pigments by a single amino acid change. Proceedings of National Academy of Sciences of the USA 97: 7366–7371.
    Yokoyama S, Zhang H, Radlwimmer FB and Blow NS (1999) Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). Proceedings of National Academy of Sciences of the USA 96: 6279–6284.
 Further Reading
    Ebrey T and Koutalos Y (2001) Vertebrate photoreceptors. Progress in Retinal and Eye Research 20: 49–94.
    Fernald RD (2006) Casting a genetic light on the evolution of eyes. Science 313: 194–1918.
    Kochendoerfer GG, Lin SW, Sakmar TP and Mathies RA (1999) How color visual pigments are tuned. Trends in Biochemical Sciences 24: 300–305.
    Nathans J (1990) Determinants of visual pigment absorbance: role of changed amino acids in the putative transmembrane segments. Biochemistry 29: 937–942.
    Sharpe LT, Stockman A, Jagle H et al. (1998) Red, green and red–green hybrid pigments in the human retina: correlations between deduced protein sequences and psychophysically measured spectral sensitivities. Journal of Neuroscience 18: 10053–10069.
    Yokoyama S (2002) Molecular evolution of color vision in vertebartes. Gene 300: 69–78.

Related Sub-Topics:

Molecular Evolution | Protein Evolution | Evolution of Coding and Functional Modules
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Visual Pigment Genes: Evolution
 
How to Cite close
Yokoyama, Shozo(May 2008) Visual Pigment Genes: Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006148.pub2]