Shedding new light on opsin evolution

Abstract

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

Metazoan opsin evolution reveals a simple route to animal vision

“…Common problems with previous studies (1)(2)(3)(4) were the use of under-sampled data sets, substitution models that did not fit the data [precomputed empirical time reversible (GTR) matrices], and inadequate outgroup selection (as detailed earlier). To avoid such problems, we assembled three GPCR and opsin alignments scoring hundreds of sequences (Methods), and estimated alignment-specific GTR matrices.…”

“…ancestral character state reconstruction | Metazoa | protein evolution U nderstanding the origin and early evolution of vision at the molecular level has proven difficult (1)(2)(3)(4). Both Protostomia (e.g., Mollusca and Arthropoda) and Deuterostomia (e.g., Vertebrata) have eyes, and it is plausible that the last common ancestor of the Bilateria possessed simple eyespots and some limited ability to detect light (5).…”

“…Given that the opsins seem to be universally distributed within Neuralia (1,2,4,7,13), it is clear that, to understand the molecular foundations of vision, we must focus on the early branching metazoans: the Cnidaria, the Ctenophora, the Placozoa, and the sponges. Unfortunately, the phylogenetic relationships of the neuralian opsins are still debated (1)(2)(3)(4), and, as a consequence, the early history of gene duplications and deletions within this family is still unknown (SI Appendix, Fig. S1).…”

“…Usually there is an association between light receptors (i.e., the cells expressing these proteins) and specific opsin subfamilies, with the ciliary receptors expressing C and Go/RGR opsins, and the rhabdomeric receptors expressing R opsins (3,24). A fourth opsin subfamily was suggested by Plachetzki et al (1).…”

Evolution under pressure and the adaptation of visual pigment compressibility in deep-sea environments

“…Therefore, to investigate potential intrinsic changes that have evolved in GPCRs in high-pressure, deepsea environments, we obtained gene sequences of the transmembrane GPCR opsin from two independent taxonomic groups of marine animals: 122 species of teleost fish and 65 species of cephalopods, representing animals living at a wide range of depths. In fish we investigated the C-type rod opsin, Rh1, and in cephalopods the R-type opsin, representing the two main evolutionarily distinct groups of opsin proteins used in animal vision (Porter et al, 2012). Furthermore, each opsin amino acid sequence provides a convenient analytical way to calculate the adiabatic compressibility of the protein by using well-tested empirical relationships based on the individual physicochemical properties of each constituent amino acid (Gromiha and Ponnuswamy, 1993, and table 1 therein) (Table S1).…”