E113 is required for the efficient photoisomerization of the unprotonated chromophore in a UV-absorbing visual pigment

The evolutionary history and spectral tuning of vertebrate visual opsins

Many animals depend on the sense of vision for survival. In eumetazoans, vision requires specialized, light-sensitive cells called photoreceptors. Light reaches the photoreceptors and triggers the excitation of light-detecting proteins called opsins. Here, we describe the story of visual opsin evolution from the ancestral bilaterian to the extant vertebrate lineages. We explain the mechanisms determining color vision of extant vertebrates, focusing on opsin gene losses, duplications, and the expression regulation of vertebrate opsins. We describe the sequence variation both within and between species that has tweaked the sensitivities of opsin proteins towards different wavelengths of light. We provide an extensive resource of wavelength sensitivities and mutations that have diverged light sensitivity in many vertebrate species and predict how these mutations were accumulated in each lineage based on parsimony. We suggest possible natural and sexual selection mechanisms underlying these spectral differences. Understanding how molecular changes allow for functional adaptation of animals to different environments is a major goal in the field, and therefore identifying mutations affecting vision and their relationship to photic selection pressures is imperative. The goal of this review is to provide a comprehensive overview of our current understanding of opsin evolution in vertebrates.

Vision adaptation in the laughing dove (Streptopelia senegalensis, Linnaeus, 1766) inferred from structural, ultrastructural, and genetic characterization

Neuroanatomy of the retina reflects adaptation and acclimation for dark and light conditions. Retinal cells and genes must be functionally adjusted to various environmental luminosities. Opsins are brilliant molecules to assess the adaptations at the genetic and phenotypic levels. Photic adaptations may reveal new mechanisms that enhance vision abilities. Through the investigation of histological, ultrastructural constituents of the whole retinal layers, and the sequencing of shortwave length sensitive opsin 1 (SWS1) of the laughing dove (Streptopelia senegalensis), the current study confirms the plasticity of the retina in response to the natural photic conditions. Retinal pigmented epithelium has plentiful melanosomes, signifying a highly adapted eye for maximum light perception and protection. Variously colored oil droplets signify high color vision ability. Stratified outer nuclear layer with many Müller cells suggests high sensitivity to dim conditions and high retinal regeneration. The penetration of outer limiting membrane by photoreceptor nuclei and Müller cell microvilli could minimize the light reflection. Oligodendrocytes establish thick myelination demanded for a keen visual acuity. A functional violet sensitive SWS1 with crucial Ser90 is presumed. Molecular phylogeny showed a secondary loss as color vision was shifted back from ultraviolet (UV) sensitivity to the ancestral avian violet sensitivity, thus improving visual resolution. However, SWS1 has some UV sensitive residues. These findings implicate not only spectral adaptations with high color vision ability and acuity but also photoinduced structural reorganizations. Further studies are needed to assess the secrets between photons and the structural genes.

Transcriptome analysis of phototransduction-related genes in tentacles of the sea cucumber Apostichopus japonicus

The sea cucumber Apostichopus japonicus (Selenka)is a typical nocturnal echinoderm, which is believed to be almost completely dependent on light intensity for the regulation of endogenous rhythms. Under conditions of high light intensity, this species shows clear evidence of light avoidance behavior, seeking out shaded areas of reef in which to reside. In this study, we performed RNA-Seq analysis to examine the tentacle transcriptome of A. japonicus specimens that had been subjected to dark and light (5 min and 1 h) conditions. We specifically focused on detecting genes involved in opsin-based light perception, including opsins and members of phototransduction-related pathways. On the basis of comparisons with both vertebrate and invertebrate phototransduction pathways, we determined that components of two of the main metazoan phototransduction pathways were altered in response to illumination. Among the key phototransduction-related genes in tentacles, we identified retinol dehydrogenase, members of the dehydrogenase/reductase family, and myosin III, and also detected a pair of visual pigment-like receptors, peropsin and peropsin-like, the homologous genes of which are believed to have the same function but show opposite expression patterns in response to different light environments. In general, the up-regulation of key genes in sea cucumber exposed to illumination indicated that the tentacles can respond to differences in the light environment at the molecular level.

Atomic and molecular analysis highlights the biophysics of unprotonated and protonated retinal in UV and scotopic vision

Unprotonated (UR) and protonated (PR) retinal have marked atomic and molecular differences in cis and trans configurations. In conclusion, UR and PR uphold UV and light vision through their different biophysical properties.

Kinetics of thermal activation of an ultraviolet cone pigment

Visual pigments can be thermally activated via isomerization of the retinyl chromophore and hydrolysis of the Schiff base (SB) through which the retinyl chromophore is bound to the opsin protein. Here, we present the first combined experimental and theoretical study of the thermal activation of a Siberian hamster ultraviolet (SHUV) pigment. We measured the rates of thermal isomerization and hydrolysis in the SHUV pigment and bovine rhodopsin. We found that these rates were significantly faster in the UV pigment than in rhodopsin due to the difference in the structural and electrostatic effects surrounding the unprotonated Schiff base (USB) retinyl chromophore in the UV pigment. Theoretical (DFT-QM/MM) calculations of the cis-trans thermal isomerization revealed a barrier of ∼23 kcal/mol for the USB retinyl chromophore in SHUV compared to ∼40 kcal/mol for protonated Schiff base (PSB) chromophore in rhodopsin. The lower barrier for thermal isomerization in the SHUV pigment is attributed to the (i) lessening of the steric restraints near the β-ionone ring and SB ends of the chromophore, (ii) displacement of the transmembrane helix 6 (TM6) away from the binding pocket toward TM5 due to absence of the salt bridge between the USB and the protonated E113 residue, and (iii) change in orientation of the hydrogen-bonding networks (HBNs) in the extracellular loop 2 (EII). The results in comparing thermal stability of UV cone pigment and rhodopsin provide insight into molecular evolution of vertebrate visual pigments in achieving low discrete dark noise and high photosensitivity in rod pigments for dim-light vision.

Photochemical nature of parietopsin

Parietopsin is a nonvisual green light-sensitive opsin closely related to vertebrate visual opsins and was originally identified in lizard parietal eye photoreceptor cells. To obtain insight into the functional diversity of opsins, we investigated by UV-visible absorption spectroscopy the molecular properties of parietopsin and its mutants exogenously expressed in cultured cells and compared the properties to those of vertebrate and invertebrate visual opsins. Our mutational analysis revealed that the counterion in parietopsin is the glutamic acid (Glu) in the second extracellular loop, corresponding to Glu181 in bovine rhodopsin. This arrangement is characteristic of invertebrate rather than vertebrate visual opsins. The photosensitivity and the molar extinction coefficient of parietopsin were also lower than those of vertebrate visual opsins, features likewise characteristic of invertebrate visual opsins. On the other hand, irradiation of parietopsin yielded meta-I, meta-II, and meta-III intermediates after batho and lumi intermediates, similar to vertebrate visual opsins. The pH-dependent equilibrium profile between meta-I and meta-II intermediates was, however, similar to that between acid and alkaline metarhodopsins in invertebrate visual opsins. Thus, parietopsin behaves as an "evolutionary intermediate" between invertebrate and vertebrate visual opsins.

Multiple functions of Schiff base counterion in rhodopsins

In rhodopsins, visible-light absorption is achieved by the protonation of the chromophore Schiff base. The Schiff base proton is stabilized by the negative charge of an amino acid residue called the Schiff base counterion. Since E113 was identified as the counterion in bovine rhodopsin, there has been growing evidence that the counterion has multiple functions besides proton stabilization. Here, we first introduce generally accepted findings as well as some controversial theories about the identity of the Schiff base counterion in the dark and in intermediate states and then review multiple functions of the counterion in vertebrate visual pigments. Special focus is placed on the recently demonstrated role in photoisomerization efficiency. Finally, differences in the position of the counterion between vertebrate visual pigments and other opsins and its relevance to the molecular evolution of opsins are discussed.

6-s-cis Conformation and polar binding pocket of the retinal chromophore in the photoactivated state of rhodopsin

The visual pigment rhodopsin is unique among the G protein-coupled receptors in having an 11-cis retinal chromophore covalently bound to the protein through a protonated Schiff base linkage. The chromophore locks the visual receptor in an inactive conformation through specific steric and electrostatic interactions. This efficient inverse agonist is rapidly converted to an agonist, the unprotonated Schiff base of all-trans retinal, upon light activation. Here, we use magic angle spinning NMR spectroscopy to obtain the (13)C chemical shifts (C5-C20) of the all-trans retinylidene chromophore and the (15)N chemical shift of the Schiff base nitrogen in the active metarhodopsin II intermediate. The retinal chemical shifts are sensitive to the conformation of the chromophore and its molecular interactions within the protein-binding site. Comparison of the retinal chemical shifts in metarhodopsin II with those of retinal model compounds reveals that the Schiff base environment is polar. In particular, the (13)C15 and (15)Nepsilon chemical shifts indicate that the C horizontal lineN bond is highly polarized in a manner that would facilitate Schiff base hydrolysis. We show that a strong perturbation of the retinal (13)C12 chemical shift observed in rhodopsin is reduced in wild-type metarhodopsin II and in the E181Q mutant of rhodopsin. On the basis of the T(1) relaxation time of the retinal (13)C18 methyl group and the conjugated retinal (13)C5 and (13)C8 chemical shifts, we have determined that the conformation of the retinal C6-C7 single bond connecting the beta-ionone ring and the retinylidene chain is 6-s-cis in both the inactive and the active states of rhodopsin. These results are discussed within the general framework of ligand-activated G protein-coupled receptors.

Evolution of opsins and phototransduction

Opsins are the universal photoreceptor molecules of all visual systems in the animal kingdom. They can change their conformation from a resting state to a signalling state upon light absorption, which activates the G protein, thereby resulting in a signalling cascade that produces physiological responses. This process of capturing a photon and transforming it into a physiological response is known as phototransduction. Recent cloning techniques have revealed the rich and diverse nature of these molecules, found in organisms ranging from jellyfish to humans, functioning in visual and non-visual phototransduction systems and photoisomerases. Here we describe the diversity of these proteins and their role in phototransduction. Then we explore the molecular properties of opsins, by analysing site-directed mutants, strategically designed by phylogenetic comparison. This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules. In particular, we will discuss the evolution of the counterion, the reduction of agonist binding to the receptor, and the molecular properties that characterize rod opsins apart from cone opsins. We will show how the advances in molecular biology and biophysics have given us insights into how evolution works at the molecular level.