Evolving visual pigments: hints from the opsin-based proteins in a phylogenetically old "eyeless" invertebrate

Eyeless razor clam Sinonovacula constricta discriminates light spectra through opsins to guide Ca2+ and cAMP signaling pathways

Phototransduction is based on opsins that drive distinct types of Gα cascades. Although nonvisual photosensitivity has long been known in marine bivalves, the underlying molecular basis and phototransduction mechanism are poorly understood. Here, we introduced the eyeless razor clam Sinonovacula constricta as a model to clarify this issue. First, we showed that S. constricta was highly diverse in opsin family members, with a significant expansion in xenopsins. Second, the expression of putative S. constricta opsins was highly temporal-spatio specific, indicating their potential roles in S. constricta development and its peripheral photosensitivity. Third, by cloning four S. constricta opsins with relatively higher expression (Sc_opsin1, 5, 7, and 12), we found that they exhibited different expression levels in response to different light environments. Moreover, we demonstrated that these opsins (excluding Sc_opsin7) couple with Gαq and Gαi cascades to mediate the light-dependent Ca2+ (Sc_opsin1 and 5) and cAMP (Sc_opsin12) signaling pathways. The results indicated that Sc_opsin1 and 5 belonged to Gq-opsins, Sc_opsin12 belonged to Gi-opsins, while Sc_opsin7 might act as a photo-isomerase. Furthermore, we found that the phototransduction function of S. constricta Gq-opsins was dependent on the lysine at the seventh transmembrane domain, and greatly influenced by the external light spectra in a complementary way. Thus, a synergistic photosensitive system mediated by opsins might exist in S. constricta to rapidly respond to the transient or subtle changes of the external light environment. Collectively, our findings provide valuable insights into the evolution of opsins in marine bivalves and their potential functions in nonvisual photosensitivity.

Diurnal and circadian regulation of opsin-like transcripts in the eyeless cnidarian Hydra

Opsins play a key role in the ability to sense light both in image-forming vision and in non-visual photoreception (NVP). These modalities, in most animal phyla, share the photoreceptor protein: an opsin-based protein binding a light-sensitive chromophore by a lysine (Lys) residue. So far, visual and non-visual opsins have been discovered throughout the Metazoa phyla, including the photoresponsive Hydra, an eyeless cnidarian considered the evolutionary sister species to bilaterians. To verify whether light influences and modulates opsin gene expression in Hydra, we utilized four expression sequence tags, similar to two classic opsins (SW rhodopsin and SW blue-sensitive opsin) and two non-visual opsins (melanopsin and peropsin), in investigating the expression patterns during both diurnal and circadian time, by means of a quantitative RT-PCR. The expression levels of all four genes fluctuated along the light hours of diurnal cycle with respect to the darkness one and, in constant dark condition of the circadian cycle, they increased. The monophasic behavior in the L12:D12 cycle turned into a triphasic expression profile during the continuous darkness condition. Consequently, while the diurnal opsin-like expression revealed a close dependence on light hours, the highest transcript levels were found in darkness, leading us to novel hypothesis that in Hydra, an "internal" biological rhythm autonomously supplies the opsins expression during the circadian time. In conclusion, in Hydra, both diurnal and circadian rhythms apparently regulate the expression of the so-called visual and non-visual opsins, as already demonstrated in higher invertebrate and vertebrate species. Our data confirm that Hydra is a suitable model for studying ancestral precursor of both visual and NVP, providing useful hints on the evolution of visual and photosensory systems.

Blue light responses in Cancer borealis stomatogastric ganglion neurons

In many animals, the daily cycling of light is a key environmental cue, encoded in part by specialized light-sensitive neurons without visual functions. We serendipitously discovered innate light-responsiveness while imaging the extensively studied stomatogastric ganglion (STG) of the crab, Cancer borealis. The STG houses a motor circuit that controls the rhythmic contractions of the foregut, and the system has facilitated deep understanding of circuit function and neuromodulation. We illuminated the crab STG in vitro with different wavelengths and amplitudes of light and found a dose-dependent increase in neuronal activity upon exposure to blue light (λ460-500 nm). The response was elevated in the absence of neuromodulatory inputs to the STG. The pacemaker kernel that drives the network rhythm was responsive to light when synaptically isolated, and light shifted the threshold for slow wave and spike activity in the hyperpolarized direction, accounting for the increased activity patterns. Cryptochromes are evolutionarily conserved blue-light photoreceptors that are involved in circadian behaviors.¹ Their activation by light can lead to enhanced neuronal activity.² We identified cryptochrome sequences in the C. borealis transcriptome as potential mediators of this response and confirmed their expression in pyloric dilator (PD) neurons, which are part of the pacemaker kernel, by single-cell RNA-seq analysis.

Non-visual Opsins and Novel Photo-Detectors in the Vertebrate Inner Retina Mediate Light Responses Within the Blue Spectrum Region

In recent decades, a number of novel non-visual opsin photopigments belonging to the family of G protein- coupled receptors, likely involved in a number of non-image-forming processes, have been identified and characterized in cells of the inner retina of vertebrates. It is now known that the vertebrate retina is composed of visual photoreceptor cones and rods responsible for diurnal/color and nocturnal/black and white vision, and cells like the intrinsically photosensitive retinal ganglion cells (ipRGCs) and photosensitive horizontal cells in the inner retina, both detecting blue light and expressing the photopigment melanopsin (Opn4). Remarkably, these non-visual photopigments can continue to operate even in the absence of vision under retinal degeneration. Moreover, inner retinal neurons and Müller glial cells have been shown to express other photopigments such as the photoisomerase retinal G protein-coupled receptor (RGR), encephalopsin (Opn3), and neuropsin (Opn5), all able to detect blue/violet light and implicated in chromophore recycling, retinal clock synchronization, neuron-to-glia communication, and other activities. The discovery of these new photopigments in the inner retina of vertebrates is strong evidence of novel light-regulated activities. This review focuses on the features, localization, photocascade, and putative functions of these novel non-visual opsins in an attempt to shed light on their role in the inner retina of vertebrates and in the physiology of the whole organism.

Molecular evolution and expression of opsin genes in Hydra vulgaris

BACKGROUND

The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions.

RESULTS

We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades.

CONCLUSIONS

This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgaris opsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.

Light and the evolution of vision

It might seem a little ridiculous to cover the period over which vision evolved, perhaps 1.5 billion years, in only 3000 words. Yet, if we examine the photoreceptor molecules of the most basic eukaryote protists and even before that, in those of prokaryote bacteria and cyanobacteria, we see how similar they are to those of mammalian rod and cone photoreceptor opsins and the photoreceptive molecules of light sensitive ganglion cells. This shows us much with regard the development of vision once these proteins existed, but there is much more to discover about the evolution of even more primitive vision systems.

Extraocular spectral photosensitivity in the tentacles of Hydra vulgaris

Previous electrophysiological studies on the cnidarian Hydra vulgaris have shown that hydra have a highly developed and specific photoresponse despite their lack of any structure recognizable as a traditional photoreceptor. In an effort to identify the site of hydra's photoreceptors, we recorded extracellularly from single excised tentacles and from ablated hypostomes lacking tentacles in absolute darkness and during exposure to light of various wavelengths. During recording, after an initial period of absolute darkness, tentacles or hypostomes were exposed to light from 450nm to 600nm, red, and white light. Exposure to light caused a change in the pattern and frequency of impulses in the tentacles that varied with color. The number of large tentacle pulses (TPs) increased at 550 and 600nm relative to darkness, whereas the number of small tentacle pulses (STPs) tended to decrease in 500nm light. Impulse frequency was significantly different among the different wavelengths. In addition to bursts of tentacle contraction pulses, long trains of pulses were observed. A change in lighting caused a switch from bursting to trains or vice versa. In contrast to excised tentacles, no change in electrical activity was seen in ablated hypostomes at any of the wavelengths relative to each other or relative to darkness. These results indicate that isolated tentacles can distinguish among and respond to various colors across the visible spectrum and suggest that electromagnetic information is transmitted from the tentacles to the hypostome where it may be integrated by the hypostomal nervous system, ultimately contributing to hydra's photoreceptive behavior.

Nocturnal light environments influence color vision and signatures of selection on the OPN1SW opsin gene in nocturnal lemurs

Although loss of short-wavelength-sensitive (SWS) cones and dichromatic color vision in mammals has traditionally been linked to a nocturnal lifestyle, recent studies have identified variation in selective pressure for the maintenance of the OPN1SW opsin gene (and thus, potentially dichromacy) among nocturnal mammalian lineages. These studies hypothesize that purifying selection to retain SWS cones may be associated with a selective advantage for nocturnal color vision under certain ecological conditions. In this study, we explore the effect of nocturnal light environment on OPN1SW opsin gene evolution in a diverse sample of nocturnal lemurs (106 individuals, 19 species, and 5 genera). Using both phylogenetic and population genetic approaches, we test whether species from closed canopy rainforests, which are impoverished in short-wavelength light, have experienced relaxed selection compared with species from open canopy forests. We identify clear signatures of differential selection on OPN1SW by habitat type. Our results suggest that open canopy species generally experience strong purifying selection to maintain SWS cones. In contrast, closed canopy species experience weaker purifying selection or a relaxation of selection on OPN1SW. We also found evidence of nonfunctional OPN1SW genes in all Phaner species and in Cheirogaleus medius, implying at least three independent losses of SWS cones in cheirogaleids. Our results suggest that the evolution of color vision in nocturnal lemurs has been influenced by nocturnal light environment.

Origins of neurogenesis, a cnidarian view

New perspectives on the origin of neurogenesis emerged with the identification of genes encoding post-synaptic proteins as well as many "neurogenic" regulators as the NK, Six, Pax, bHLH proteins in the Demosponge genome, a species that might differentiate sensory cells but no neurons. However, poriferans seem to miss some key regulators of the neurogenic circuitry as the Hox/paraHox and Otx-like gene families. Moreover as a general feature, many gene families encoding evolutionarily-conserved signaling proteins and transcription factors were submitted to a wave of gene duplication in the last common eumetazoan ancestor, after Porifera divergence. In contrast gene duplications in the last common bilaterian ancestor, Urbilateria, are limited, except for the bHLH Atonal-class. Hence Cnidaria share with Bilateria a large number of genetic tools. The expression and functional analyses currently available suggest a neurogenic function for numerous orthologs in developing or adult cnidarians where neurogenesis takes place continuously. As an example, in the Hydra polyp, the Clytia medusa and the Acropora coral, the Gsx/cnox2/Anthox-2 ParaHox gene likely supports neurogenesis. Also neurons and nematocytes (mechanosensory cells) share in hydrozoans a common stem cell and several regulatory genes indicating that they can be considered as sister cells. Performed in anthozoan and medusozoan species, these studies should tell us more about the way(s) evolution hazards achieved the transition from epithelial to neuronal cell fate, and about the robustness of the genetic circuitry that allowed neuromuscular transmission to arise and be maintained across evolution.

On the origins of arrestin and rhodopsin

Background

G protein coupled receptors (GPCRs) are the most numerous proteins in mammalian genomes, and the most common targets of clinical drugs. However, their evolution remains enigmatic. GPCRs are intimately associated with trimeric G proteins, G protein receptor kinases, and arrestins. We conducted phylogenetic studies to reconstruct the history of arrestins. Those findings, in turn, led us to investigate the origin of the photosensory GPCR rhodopsin.

Results

We found that the arrestin clan is comprised of the Spo0M protein family in archaea and bacteria, and the arrestin and Vps26 families in eukaryotes. The previously known animal arrestins are members of the visual/beta subfamily, which branched from the founding "alpha" arrestins relatively recently. Curiously, we identified both the oldest visual/beta arrestin and opsin genes in Cnidaria (but not in sponges). The arrestin clan has 14 human members: 6 alphas, 4 visual/betas, and 4 Vps26 genes. Others recently showed that the 3D structure of mammalian Vps26 and the biochemical function of the yeast alpha arrestin PalF are similar to those of beta arrestins. We note that only alpha arrestins have PY motifs (known to bind WW domains) in their C-terminal tails, and only visual/betas have helix I in the Arrestin N domain.

Conclusion

We identified ciliary opsins in Cnidaria and propose this subfamily is ancestral to all previously known animal opsins. That finding is consistent with Darwin's theory that eyes evolved once, and lends some support to Parker's hypothesis that vision triggered the Cambrian explosion of life forms. Our arrestin findings have implications on the evolution of GPCR signaling, and on the biological roles of human alpha arrestins.

Immunohistochemical evidence for multiple photosystems in box jellyfish

Cubomedusae (box jellyfish) possess a remarkable visual system with 24 eyes distributed in four sensory structures termed rhopalia. Each rhopalium is equipped with six eyes: two pairs of pigment cup eyes and two unpaired lens eyes. Each eye type probably captures specific features of the visual environment. To investigate whether multiple types of photoreceptor cells are present in the rhopalium, and whether the different eye types possess different types of photoreceptors, we have used immunohistochemistry with a range of vertebrate opsin antibodies to label the photoreceptors, and electroretinograms (ERG) to determine their spectral sensitivity. All photoreceptor cells of the two lens eyes of the box jellyfish Tripedalia cystophora and Carybdea marsupialis displayed immunoreactivity for an antibody directed against the zebrafish ultraviolet (UV) opsin, but not against any of eight other rhodopsin or cone opsin antibodies tested. In neither of the two species were the pigment cup eyes immunoreactive for any of the opsin antibodies. ERG analysis of the Carybdea lower lens eyes demonstrated a single spectral sensitivity maximum at 485 nm suggesting the presence of a single opsin type. Our data demonstrate that the lens eyes of box jellyfish utilize a single opsin and are thus color-blind, and that there is probably a different photopigment in the pigment cup eyes. The results support our hypothesis that the lens eyes and the pigment cup eyes of box jellyfish are involved in different and specific visual tasks.

Nitric oxide signaling pathways at neural level in invertebrates: functional implications in cnidarians

Nitric oxide (NO) is a small molecule with unconventional properties. It is found in organisms throughout the phylogenetic scale, from fungi to mammals, in which it acts as an intercellular messenger of main physiological events, or even as an intracellular messenger in invertebrates. In both vertebrates and invertebrates, NO is involved in many processes, regulated in part by cyclic guanosine monophosphate (cGMP), and reacts with different oxygen molecular species. The presence of NO in the early-diverging metazoan phylum of Cnidaria, of which Hydra represents the first known species having a nervous system, supports a role of this molecule as an ancestral neural messenger with physiological roles that remain to be largely elucidated. Therefore, our novel findings on the presence of NO in Hydra are here integrated in such a comparative frame.