Figure 1.
A phylogenetic tree of 33 representative SWS1 pigments.
The numbers after P indicate the λmax values. Divergence times inferred using through the “TimeTree of Life” web server (www.Timetree.org) are shown at the bottom. Black and blue rectangles indicate UV- and blue-sensitive pigments, respectively.
Figure 2.
Absorption spectra of SWS1 pigments.
(A) AncBoreotheria S1 and T52F mutants. AncBoreotheria S1 has a λmax of 357 nm and is UV-sensitive, whereas the T52F mutant does not form a functional visual pigment. (B) Mouse S1 and T52F mutants. Both pigments have λmax values of 359 nm and are UV-sensitive. All of these pigments were regenerated by incubating the opsins with 11-cis-retinal (a gift from Dr. Rosalie K. Crouch and the National Eye Institute) and were purified using immobilized 1D4 (The Culture Center, Minneapolis, MN). UV visible spectra were recorded at 20°C using a Hitachi U-3000 dual beam spectrophotometer. Visual pigments were bleached for 3 min using a 60 W standard light bulb equipped with a Kodak Wratten #3 filter at a distance of 20 cm. Data were analyzed using Sigmaplot software (Jandel Scientific, San Rafael, CA).
Figure 3.
The tertiary structures of SWS1 pigments.
(A) A dehydrated model of AncBoreotheria S1 with SBR and protonated E113, which is located at the protein surface. (B) A hydrated model of AncBoreotheria S1 with PSBR, where E113 is located next the 11-cis-retinal. (C) Water channel connected to T52 of mouse S1. (D) Channel connected to V79 of mouse S1. Blue arrows indicate the directions of water movement. Black, blue, red and white molecules represent carbon, nitrogen, oxygen and hydrogen atoms, respectively. The structures of AncBoreotheria S1 and mouse S1 pigments were obtained by 1) applying homology modeling (Modeller 9v7, www.salilab.org/modeller) to bovine rhodopsin (pdb code: 1U19), 2) adding the missing hydrogen atoms, water molecules and 11-cis-retinal, and 3) optimizing them first at pure AMBER96 force field level (http://ambermd.org) and then using hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in the ONIOM electronic embedding scheme (QM = B3LYP/6–31G*; MM = AMBER).
Figure 4.
Patterns of amino acid replacements in human S1.
The evolutionary tree of representative mammalian SWS1 pigments, where black, blue and purple rectangles indicate UV-, blue- and their intermediate color-sensitive pigments, respectively (left panel) and their amino acid compositions (right panel). The rectangles surrounded by broken lines indicate their suspected color sensitivities. Amino acids in rectangle (right panel) indicate that they occurred once at that site, where the identical amino acid compositions of the primate pigments are highlighted by blue color and the four steps of amino acid replacements have been inferred from them (left panel). The numbers at different nodes indicate the divergence times, which have been estimated previously [27], [28].
Figure 5.
Eight most likely evolutionary paths used during the evolution of human S1.
Human S1 evolution starting either with T93P (in black lines) or with A114G (in broken lines) are shown separately. In the background, a total of 442 evolutionarily accessible trajectories are given. The eight trajectories are characterized by the gradual increase in their λmax values, consisting of each step with |Δλmax|<25 nm. The path in red shows the λmax values predicted by considering only epistatic interactions among the seven mutations. Δλmax values smaller (in blue) or larger (in orange) than 25 nm are distinguished.
Figure 6.
The θ values (|θ|>5 nm) that are generated by epistasis in AncBoreotheria S1.
The λmax values of the 127 SWS1 mutant pigments were expressed as that of AncBoreotheria S1 (λ) plus the effects of the appropriate single and multiple amino acid changes on the λmax-shift (denoted by a sum of θ values). These θ values were estimated by solving a total of 128 simultaneous linear equations with the ancestral λ and 127 mutant values. The individual effects of θ46, θ49, θ52, θ86, θ93, θ114 and θ118 are −2, −3, 0, 0, 2, 1 and 1 nm, respectively, and their roles in human S1 evolution are negligible compared with those of epistatic interactions. The graph shows the *P<0.05. **P<0.01.
Figure 7.
Evolutionary change in the wavelength discrimination by human ancestors.
Forty-five My ago, our ancestor possessed almost final product of human S1 and human L and could have achieved color vision of deuteranopes who do not have functional MWS pigment (represented by a discrimination function with black circles). This has changed to the color vision of trichromats with the three cone pigments (represented by a discrimination function with white circles) in the following 15 My. The arrow indicates this evolutionary change. The wavelength discrimination functions of deuteranope and trichromat data are those of A. W. G. in [48] and W. D. W. in [49], respectively.