Green‐shifting of SWS2A opsin sensitivity and loss of function of RH2‐A opsin in flounders, genus Verasper

Abstract

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.

Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)

“…It may enhance color vision and contribute to prey detection in the bluish ocean [10]. Based on the loss of RH2A function in the genus Verasper [11] and our results showing low expression levels of RH2B2 and pairs of RH2A, we deduce that RH2B1 and RH2C are the major RH2 genes in turbot. Furthermore, the retention of RH2C is an adaptation of turbot to the spectral environment in the deep sea due to its short-shift of λ max .…”

“…To identify the visual opsin gene repertoire of turbot, zebrafish opsin sequences were used as BLASTp query sequences with e-value < 10 -10 , and they were downloaded from the chromosome of the [11,28,44,45]. Phylogenetic relationships among the visual opsin nucleotide sequences were inferred using MEGA 7 software [46] by applying the neighbor-joining method [47] and maximum composite likelihood model algorithm [48].…”

“…The cone opsin genes derived from two rounds of whole genome duplication [6]. It is believed that after several additional duplication events, diverse opsin repertoires were maintained among different species [7][8][9][10][11][12]. RH2 and LWS duplication events were most prevalent in ray-finned fish, and tandem duplication seems to have produced more duplicates [13].…”

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

“…In some cases, only minor changes in the amino acid sequence have resulted in major changes in the λ max value, as was demonstrated for the A269T (Amino acid numbering in this study is based upon bovine RH1 sequence numbering; S1 Fig ) change in the Sws2a opsin of the spotted flounder ( Verasper variegatus ) that resulted in a photopigment that is sensitive to longer wavelengths (i.e. λ max = 485 nm instead of 466 nm) [ 23 ].…”

“…There is great interest in understanding the evolutionary, as well as the molecular mechanisms, that underlie the diversity of visual photopigments and their spectral peak absorbances. In general, there are two main experimental techniques for defining the λ max value of visual photopigments, namely microspectrophotometry, which analyzes the spectral profile of photoreceptors directly, but only with fresh retinas, and spectral tuning site substitutions cannot be studied in isolation [ 24 ] or in vitro regeneration [ 2 , 23 , 25 – 27 ]. The latter is a popular, yet highly specialized and labor-intensive, approach that has been used to deduce the spectral properties of photopigments in isolation from wildtype and inferred ancestral protein sequences, followed by reconstitution with chromophore (usually 11- cis retinal) and experimental measurement of absorbance from 200–800 nm [ 25 , 28 – 31 ].…”