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Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates.

The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels.

The molecular mechanisms underlying the enormous diversity of visual pigment wavelength sensitivities found in nature have been the focus of many molecular evolutionary studies, with particular attention to the short wavelength-sensitive 1 (SWS1) visual pigments that mediate vision in the ultraviolet to violet range of the electromagnetic spectrum. Over a decade of study has revealed that the remarkable extension of SWS1 absorption maxima (λ max ) into the ultraviolet occurs through a deprotonation of the Schiff base linkage of the retinal chromophore, a mechanism unique to this visual pigment type. In studies of visual ecology, there has been mounting interest in inferring visual sensitivity at short wavelengths, given the importance of UV signaling in courtship displays and other behaviors. Since experimentally determining spectral sensitivities can be both challenging and time-consuming, alternative strategies such as estimating λ max based on amino acids at sites known to affect spectral tuning are becoming increasingly common. However, these estimates should be made with knowledge of the limitations inherent in these approaches. Here, we provide an overview of the current literature on SWS1 site-directed mutagenesis spectral tuning studies, and discuss methodological caveats specific to the SWS1-type pigments. We focus particular attention on contrasting avian and mammalian SWS1 spectral tuning mechanisms, which are the best studied among vertebrates. We find that avian SWS1 visual pigment spectral tuning mechanisms are fairly consistent, and therefore more predictable in terms of wavelength absorption maxima, whereas mammalian pigments are not well suited to predictions of λ max from sequence data alone.

The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels.

The molecular mechanisms underlying the enormous diversity of visual pigment wavelength sensitivities found in nature have been the focus of many molecular evolutionary studies, with particular attention to the short wavelength-sensitive 1 (SWS1) visual pigments that mediate vision in the ultraviolet to violet range of the electromagnetic spectrum. Over a decade of study has revealed that the remarkable extension of SWS1 absorption maxima (λ max ) into the ultraviolet occurs through a deprotonation of the Schiff base linkage of the retinal chromophore, a mechanism unique to this visual pigment type. In studies of visual ecology, there has been mounting interest in inferring visual sensitivity at short wavelengths, given the importance of UV signaling in courtship displays and other behaviors. Since experimentally determining spectral sensitivities can be both challenging and time-consuming, alternative strategies such as estimating λ max based on amino acids at sites known to affect spectral tuning are becoming increasingly common. However, these estimates should be made with knowledge of the limitations inherent in these approaches. Here, we provide an overview of the current literature on SWS1 site-directed mutagenesis spectral tuning studies, and discuss methodological caveats specific to the SWS1-type pigments. We focus particular attention on contrasting avian and mammalian SWS1 spectral tuning mechanisms, which are the best studied among vertebrates. We find that avian SWS1 visual pigment spectral tuning mechanisms are fairly consistent, and therefore more predictable in terms of wavelength absorption maxima, whereas mammalian pigments are not well suited to predictions of λ max from sequence data alone.

Background One of the most striking features of avian vision is the variation in spectral sensitivity of the short wavelength sensitive (SWS1) opsins, which can be divided into two sub-types: violet- and UV- sensitive (VS & UVS). In birds, UVS has been found in both passerines and parrots, groups that were recently shown to be sister orders. While all parrots are thought to be UVS, recent evidence suggests some passerine lineages may also be VS. The great bowerbird (Chlamydera nuchalis) is a passerine notable for its courtship behaviours in which males build and decorate elaborate bower structures. Results The great bowerbird SWS1 sequence possesses an unusual residue combination at known spectral tuning sites that has not been previously investigated in mutagenesis experiments. In this study, the SWS1 opsin of C. nuchalis was expressed along with a series of spectral tuning mutants and ancestral passerine SWS1 pigments, allowing us to investigate spectral tuning mechanisms and explore the evolution of UV/violet sensitivity in early passerines and parrots. The expressed C. nuchalis SWS1 opsin was found to be a VS pigment, with a λmax of 403 nm. Bowerbird SWS1 mutants C86F, S90C, and C86S/S90C all shifted λmax into the UV, whereas C86S had no effect. Experimentally recreated ancestral passerine and parrot/passerine SWS1 pigments were both found to be VS, indicating that UV sensitivity evolved independently in passerines and parrots from a VS ancestor. Conclusions Our mutagenesis studies indicate that spectral tuning in C. nuchalis is mediated by mechanisms similar to those of other birds. Interestingly, our ancestral sequence reconstructions of SWS1 in landbird evolution suggest multiple transitions from VS to UVS, but no instances of the reverse. Our results not only provide a more precise prediction of where these spectral sensitivity shifts occurred, but also confirm the hypothesis that birds are an unusual exception among vertebrates where some descendants re-evolved UVS from a violet type ancestor. The re-evolution of UVS from a VS type pigment has not previously been predicted elsewhere in the vertebrate phylogeny.

This chapter discusses efficient experimental strategies to explore variation in ancestral sequence reconstructions. The experimental strategies are illustrated with two examples, ancestral rhodopsins in archosaurs and green fluorescent protein (GFP)-like proteins in corals.

Background Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. Results Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. Conclusion Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction.