Chapter 8 Retinal-binding protein: Function in a chromophore exchange system in the squid visual cell

Deep Diversity: Extensive Variation in the Components of Complex Visual Systems across Animals

Understanding the molecular underpinnings of the evolution of complex (multi-part) systems is a fundamental topic in biology. One unanswered question is to what the extent do similar or different genes and regulatory interactions underlie similar complex systems across species? Animal eyes and phototransduction (light detection) are outstanding systems to investigate this question because some of the genetics underlying these traits are well characterized in model organisms. However, comparative studies using non-model organisms are also necessary to understand the diversity and evolution of these traits. Here, we compare the characteristics of photoreceptor cells, opsins, and phototransduction cascades in diverse taxa, with a particular focus on cnidarians. In contrast to the common theme of deep homology, whereby similar traits develop mainly using homologous genes, comparisons of visual systems, especially in non-model organisms, are beginning to highlight a "deep diversity" of underlying components, illustrating how variation can underlie similar complex systems across taxa. Although using candidate genes from model organisms across diversity was a good starting point to understand the evolution of complex systems, unbiased genome-wide comparisons and subsequent functional validation will be necessary to uncover unique genes that comprise the complex systems of non-model groups to better understand biodiversity and its evolution.

The rhodopsin-retinochrome system for retinal re-isomerization predates the origin of cephalopod eyes

Background

The process of photoreception in most animals depends on the light induced isomerization of the chromophore retinal, bound to rhodopsin. To re-use retinal, the all-trans-retinal form needs to be re-isomerized to 11-cis-retinal, which can be achieved in different ways. In vertebrates, this mostly includes a stepwise enzymatic process called the visual cycle. The best studied re-isomerization system in protostomes is the rhodopsin-retinochrome system of cephalopods, which consists of rhodopsin, the photoisomerase retinochrome and the protein RALBP functioning as shuttle for retinal. In this study we investigate the expression of the rhodopsin-retinochrome system and functional components of the vertebrate visual cycle in a polyplacophoran mollusk, Leptochiton asellus, and examine the phylogenetic distribution of the individual components in other protostome animals.

Results

Tree-based orthology assignments revealed that orthologs of the cephalopod retinochrome and RALBP are present in mollusks outside of cephalopods. By mining our dataset for vertebrate visual cycle components, we also found orthologs of the retinoid binding protein RLBP1, in polyplacophoran mollusks, cephalopods and a phoronid. In situ hybridization and antibody staining revealed that L. asellus retinochrome is co-expressed in the larval chiton photoreceptor cells (PRCs) with the visual rhodopsin, RALBP and RLBP1. In addition, multiple retinal dehydrogenases are expressed in the PRCs, which might also contribute to the rhodopsin-retinochrome system.

Conclusions

We conclude that the rhodopsin-retinochrome system is a common feature of mollusk PRCs and predates the origin of cephalopod eyes. Our results show that this system has to be extended by adding further components, which surprisingly, are shared with vertebrates.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01939-x.

Large scale expression and purification of mouse melanopsin-L in the baculovirus expression system

Melanopsin is the mammalian photopigment that primarily mediates non-visual photoregulated physiology. So far, this photopigment is poorly characterized with respect to structure and function. Here, we report large-scale production and purification of the intact long isoform of mouse melanopsin (melanopsin-L) using the baculovirus/insect cell expression system. Exploiting the baculoviral GP67 signal peptide, we obtained expression levels that varied between 10-30pmol/10(6)cells, equivalent to 2-5mg/L. This could be further enhanced using DMSO as a chemical chaperone. LC-MS analysis confirmed that full-length melanopsin-L was expressed and demonstrated that the majority of the expressed protein was N-glycosylated at Asn(30) and Asn(34). Other posttranslational modifications were not yet detected. Purification was achieved exploiting a C-terminal deca-histag, realizing a purification factor of several hundred-fold. The final recovery of purified melanopsin-L averaged 2.5% of the starting material. This was mainly due to low extraction yields, probably since most of the protein was present as the apoprotein. The spectral data we obtained agree with an absorbance maximum in the 460-500nm wavelength region and a significant red-shift upon illumination. This is the first report on expression and purification of full length melanopsin-L at a scale that can easily be further amplified.

Evolution and the origin of the visual retinoid cycle in vertebrates

Absorption of a photon by visual pigments induces isomerization of 11-cis-retinaldehyde (RAL) chromophore to all-trans-RAL. Since the opsins lacking 11-cis-RAL lose light sensitivity, sustained vision requires continuous regeneration of 11-cis-RAL via the process called 'visual cycle'. Protostomes and vertebrates use essentially different machinery of visual pigment regeneration, and the origin and early evolution of the vertebrate visual cycle is an unsolved mystery. Here we compare visual retinoid cycles between different photoreceptors of vertebrates, including rods, cones and non-visual photoreceptors, as well as between vertebrates and invertebrates. The visual cycle systems in ascidians, the closest living relatives of vertebrates, show an intermediate state between vertebrates and non-chordate invertebrates. The ascidian larva may use retinochrome-like opsin as the major isomerase. The entire process of the visual cycle can occur inside the photoreceptor cells with distinct subcellular compartmentalization, although the visual cycle components are also present in surrounding non-photoreceptor cells. The adult ascidian probably uses RPE65 isomerase, and trans-to-cis isomerization may occur in distinct cellular compartments, which is similar to the vertebrate situation. The complete transition to the sophisticated retinoid cycle of vertebrates may have required acquisition of new genes, such as interphotoreceptor retinoid-binding protein, and functional evolution of the visual cycle genes.

Origin of the vertebrate visual cycle

In vertebrates, the absorption of light by rhodopsin leads to the isomerization of 11-cis-retinal chromophore to its all-trans form. In the visual cycle, all-trans retinal is converted back to 11-cis retinal. Mammalian visual cycle takes place in photoreceptor cells and retinal pigment epithelial (RPE) cells, while that of cephalopods is completed within a photoreceptor cell. To identify visual cycle system in the primitive chordate ascidians, we studied the localization of the ascidian visual cycle genes and proteins by in situ hybridization and whole-mount immunohistochemistry, respectively. We identified four genes encoding putative visual cycle proteins, homologs of retinal G protein-coupled receptor (Ci-opsin3), cellular retinaldehyde-binding protein (Ci-CRALBP), beta-carotene 15,15'monooxygenase (Ci-BCO) and RPE-specific 65 kDa protein (Ci-RPE65) in the ascidian, Ciona intestinalis. In contrast to Ci-BCO, which is predominantly localized in ocellus photoreceptor cells of the larva, Ci-RPE65 is not significantly expressed in the ocellus and brain vesicle of the larva. Ci-RPE65 is expressed in the neural complex, a photoreceptor organ of the adult ascidian, at a level comparable with that of Ci-opsin3 and Ci-CRALBP. Proteins of Ci-opsin3, Ci-CRALBP and Ci-BCO are localized in photoreceptor cells. These results suggest that the larval visual cycle uses Ci-opsin3 as a photoisomerase, while the visual cycle of the adult photoreceptors is RPE65-dependent. The colocalization of visual cycle proteins in the photoreceptor cells suggest that ascidian visual cycle takes place in a photoreceptor cell as seen in the cephalopod visual cycle.

Immunohistochemical localization of Papilio RBP in the eye of butterflies

We recently identified a novel retinoid binding protein, Papilio RBP, in the soluble fraction of the eye homogenate of the butterfly Papilio xuthus, and demonstrated that the protein is involved in the visual cycle. We now have localized the protein in the Papilio eye by light and electron microscopic immunohistochemistry using a monospecific antiserum produced against artificially expressed Papilio RBP. We found strong immunoreactivity in the primary as well as secondary pigment cells and in the tracheal cells. The pigment cells have long been regarded as an important site of the visual cycle, and this view is further supported by the present result. Interestingly, the cytoplasm and nuclei of these cells were equally labeled, indicating that the protein exists in both the cytoplasm and the nucleus. We conducted a survey for the existence of the Papilio RBP-like proteins in other insects including several species of butterflies, dragonflies, cicadas, grasshoppers and honeybees. Anti-Papilio RBP immunoreactivity was confirmed in the proteins isolated only from butterflies belonging to the superfamily Papilionoidea and not from other species. In all insects tested, however, fluorescing proteins were clearly detected, suggesting that these insects also have similar retinol-binding proteins.

Origin of the vertebrate visual cycle: II. Visual cycle proteins are localized in whole brain including photoreceptor cells of a primitive chordate

The visual cycle system in a primitive chordate, ascidian Ciona intestinalis, was studied by whole-mount in situ hybridization and by whole-mount immunohistochemistry. Three visual cycle proteins, Ciona homologue of RGR (Ci-opsin3), CRALBP (Ci-CRALBP), and BCO/RPE65 (Ci-BCO/RPE65) were widely distributed in the brain vesicle and visceral ganglion. To identify the visual cycle system in a primitive chordate, we compared the localization of photoreceptor-specific proteins (visual pigment and arrestin) and visual cycle proteins (Ci-opsin3 and Ci-CRALBP). The ascidian visual cycle is composed of two cellular compartments, the photoreceptors and the brain vesicle, but some photoreceptor cells also contain visual cycle proteins.

A novel retinol-binding protein in the retina of the swallowtail butterfly, Papilio xuthus

Retinoid-binding proteins are indispensable for visual cycles in both vertebrate and invertebrate retinas. These proteins stabilize and transport hydrophobic retinoids in the hydrophilic environment of plasma and cytoplasm, and allow regeneration of visual pigments. Here, we identified a novel retinol-binding protein in the eye of a butterfly, Papilio xuthus. The protein that we term Papilio retinol-binding protein (Papilio RBP) is a major component of retinal soluble proteins and exclusively binds 3-hydroxyretinol, and emits fluorescence peaking at 480 nm under ultraviolet (UV) illumination. The primary structure, deduced from the nucleotide sequence of the cDNA, shows no similarity to any other lipophilic ligand-binding proteins. The molecular mass and isoelectric point of the protein estimated from the amino-acid sequence are 26.4 kDa and 4.92, respectively. The absence of any signal sequence for secretion in the N-terminus suggests that the protein exists in the cytoplasmic matrix. All-trans 3-hydroxyretinol is the major ligand of the Papilio RBP in dark-adapted eyes. Light illumination of the eyes increases the 11-cis isomer of the ligand and induces redistribution of the Papilio RBP from the proximal to the distal part of the photoreceptor layer. These results suggest that the Papilio RBP is involved in visual pigment turnover.

Identification and immunolocalization of actin cytoskeletal components in light- and dark-adapted octopus retinas

Photoreceptors in the octopus retina are of the rhabdomeric type, with rhabdomeres arising from the plasma membrane on opposite sides of the cylindrical outer segment. Each rhabdomere microvillus has an actin filament core, but other actin-binding proteins have not been identified. We used immunoblotting techniques to identify actin-binding proteins in octopus retinal extracts and immunofluorescence microscopy to localize the same proteins in fixed tissue. Antibodies directed against alpha-actinin and vinculin recognized single protein bands on immunoblots of octopus retinal extract with molecular weights comparable to the same proteins in other tissues. Anti-filamin identified two closely spaced bands similar in molecular weight to filamin in other species. Antibodies to the larger of the Drosophila ninaC gene products, p174, identified two bands lower in molecular weight than p174. Anti-villin localized a band that was significantly less in molecular weight than villin found in other cells. Epifluorescence and confocal microscopy were used to map the location of the same actin-binding proteins in dark- and light-adapted octopus photoreceptors and other retinal cells. Antibodies to most of the actin-binding proteins showed heavy staining of the photoreceptor proximal/supportive cell region accompanied by rhabdom membrane and rhabdom tip staining, although subtle differences were detected with individual antibodies. In dark-adapted retinas anti-alpha-actinin stained the photoreceptor proximal/supportive cell region where an extensive junctional complex joins these two cell types, but in the light, immunoreactivity extended above the junctional complex into the rhabdom bases. Most antibodies densely stained the rhabdom tips but anti-villin exhibited a striated pattern of localization at the tips. We believe that the actin-binding proteins identified in the octopus retina may play a significant role in the formation of new rhabdomere microvilli in the dark. We speculate that these proteins and actin remain associated with an avillar membrane that connects opposing sets of rhabdomeres in light-adapted retinas. Association of these cytoskeletal proteins with the avillar membrane would constitute a pool of proteins that could be recruited for rapid microvillus formation from the previously avillar region.

Retinoid cycling proteins redistribute in light-/dark-adapted octopus retinas

In cephalopods, the complex rhodopsin-retinochrome system serves to regenerate metarhodopsin and metaretinochrome after illumination. In the dark, a soluble protein, retinal-binding protein (RALBP), shuttles 11-cis retinal released from metaretinochrome located in the photoreceptor inner segments to metarhodopsin present in the rhabdoms. While in the rhabdoms, RALBP delivers 11-cis retinal to regenerate rhodopsin and in turn binds the all-trans isomer released by metarhodopsin. RALBP then returns all-trans retinal to the inner segments to restore retinochrome. The conventional interpretation of retinoid cycling is contradicted by immunocytochemical studies showing that, in addition to rhodopsin, retinochrome is present in the rhabdomal compartment, making possible the direct exchange of chromophores between the metapigments with the potential exclusion of RALBP. By using immunofluorescence and laser scanning confocal microscopy, we have precisely located opsin, aporetinochrome, and RALBP in light-/dark-adapted octopus retinas. We found differences in the distribution of all three proteins throughout the retina. Most significantly, comparison of cross sections though light- and dark-adapted rhabdoms showed a dramatic shift in position of the proteins. In the dark, opsin and retinochrome colocalized at the base of the rhabdomal microvilli. In the light, opsin redistributed along the length of the microvillar membranes, and retinochrome retreated to a location that is perhaps extracellular. RALBP was present in the core cytoplasm of the photoreceptor outer segments in the dark, and RALBP moved to the periphery in the light. Because of the colocalization of opsin and retinochrome in the dark, we believe that the two metapigments participate directly in chromophore exchange. RALBP may serve to transport additional chromophore from the inner segments to the rhabdoms and may not be immediately involved in the exchange process.

Amino acid sequence surrounding the retinal-binding site in retinochrome of the squid, Todarodes pacificus

Squid (Todarodes pacificus) retinochrome was reduced to N-retinyl protein with borane dimethylamine and cleaved by CNBr. The retinyl peptide was then isolated by chromatography while being monitored for absorbances at 215 and 330 nm, and the N-terminal amino acid sequence was determined to be Ser-Lys-Thr-Gly-X-Ala-Leu-Phe-Pro. This sequence was the same that we had observed at the 7th transmembrane domain of retinochrome whose structure was reported previously. During Edman degradation of the retinyl peptide, the yield of the PTH-lysine at the second cycle was lower than those of the other PTH-amino acids, proving that the lysine residue forms a Schiff's base with retinal (Lys-275 in retinochrome). The amino acid sequence surrounding the retinal-binding lysine in retinochrome greatly differed from those in a variety of known visual pigments. This fact would be associated with the difference in the photoisomerization of chromophore between retinochrome and rhodopsin. The protein structure of retinochrome is also compared with that of rhodopsin in Todarodes.

Distribution of three retinal proteins in developing octopus photoreceptors

The expression of proteins unique to plasma membrane domains of developing photoreceptors is used as a marker for retinal differentiation in vertebrates. Invertebrate photoreceptors are also compartmentalized, but little information is available on the development of these compartments or the expression of retinal proteins specific to these cellular regions. Using routine electron microscopy techniques, we have made observations on the formation of photoreceptor organelles, including myeloid bodies and rhabdomeres, in embryonic octopus eyes from an early stage in development through hatching. Immunocytochemical experiments on the embryos demonstrate a timed expression of three retinal proteins during development, and the early separation of the octopus photoreceptor plasma membrane into distinct domains. Using polyclonal antibodies for opsin, retinochrome and retinal binding protein we have shown that opsin appears first and is confined to the distal end of the photoreceptor that will eventually differentiate into rhabdomeres. This membrane domain is separated from the proximal/inner segment plasma membrane by a septate junction. Retinochrome is expressed later when the myeloid bodies appear in the inner segments, and retinal binding protein is apparently not synthesized until sometime after hatching. These results suggest that, in the cephalopod retina, protein components of the retinoid cycling apparatus appear in a specific developmental sequence during the differentiation of this tissue.

Interphotoreceptor retinoid-binding protein (IRBP). Molecular biology and physiological role in the visual cycle of rhodopsin

The regeneration of visual pigment in rod photoreceptors of the vertebrate retina requires an exchange of retinoids between the neural retina and the retina pigment epithelium (RPE). It has been hypothesized that interphotoreceptor retinoid-binding protein (IRBP) functions as a two-way carrier of retinoid through the aqueous compartment (interphotoreceptor matrix) that separates the RPE and the photoreceptors. The first part of this review summarizes the cellular and molecular biology of IRBP. Work on the IRBP gene indicates that the protein contains a four-fold repeat structure that may be involved in binding multiple retinoid and fatty acid ligands. These repeats and other aspects of the gene structure indicate that the gene has had an active and complex evolutionary history. IRBP mRNA is detected only in retinal photoreceptors and in the pineal gland; expression is thus restricted to the two photosensitive tissues of vertebrate organisms. In the second part of this review, we consider the results obtained in experiments that have examined the activity of IRBP in the process of visual pigment regeneration. We also consider the results obtained on the bleaching and regeneration of rhodopsin in the acutely detached retina, as well as in experiments testing the ability of IRBP to protect its retinoid ligand from isomerization and oxidation. Taken together, the findings provide evidence that, in vivo, IRBP facilitates both the delivery of all-trans retinol to the RPE and the transfer of 11-cis retinal from the RPE to bleached rod photoreceptors, and thereby directly supports the regeneration of rhodopsin in the visual cycle.