A second visual rhodopsin gene,rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes

Abstract

Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1. We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1. These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.

Visual pigment evolution in Characiformes: the dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning

“…In addition, we also found another TGD surviving opsin product of a RH1 duplication: RH1-2. We confirmed this as the surviving duplicates clustered with the known RH1-2 opsins of Cypriniformes (Morrow et al 2011; Morrow et al 2017) (Fig. 2), however their functionality remains unknown.…”

Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding

“…In Actinopterygians, the rhodopsin gene generally occurs in two copies, homologous to other vertebrates. One copy, rh1, is an intronless retrogene that does not recombine anymore with other opsins and has proven useful for fish identification and phylogeny (Fitzgibbon et al, 1995;Chen et al, 2003;Lin et al, 2017;Morrow et al, 2017).…”

Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication

“…Origin of these rho , namely fw-rho for freshwater and ds-rho for deep-sea in this study, is clearly the result of a gene duplication event [ 29 ], but when the event occurred remains unsolved. From the deep-branching phylogeny of rhodopsin and related genes in fish, the duplicate genes might be derivatives of TSD, but previous studies have not yielded a clear conclusion [ 19 , 39 , 40 ]. The timing of TSD is estimated to predate the occurrences of Elopomorpha and Osteoglossomorpha, and postdate the divergence between Teleostei and Holostei (gar and bowfin) (Fig.…”