A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus

Abstract

Molecular research on the evolution of extraocular photoreception has drawn attention to photosensitive animals lacking proper eye organs. Outside of vertebrates, little is known about this type of sensory system in any other deuterostome. In this study, we investigate such an extraocular photoreceptor cell (PRC) system in developmental stages of the sea urchin Paracentrotus lividus. We provide a general overview of the cell type families present at the mature rudiment stage using single-cell transcriptomics, while emphasizing the PRCs complexity. We show that three neuronal and one muscle-like PRC type families express retinal genes prior to metamorphosis. Two of the three neuronal PRC type families express a rhabdomeric opsin as well as an echinoderm-specific opsin (echinopsin), and their genetic wiring includes sea urchin orthologs of key retinal genes such as hlf, pp2ab56e, barh, otx, ac/sc, brn3, six1/2, pax6, six3, neuroD, irxA, isl and ato. Using qPCR, in situ hybridization, and immunohistochemical analysis, we found that the expressed retinal gene composition becomes more complex from mature rudiment to juvenile stage. The majority of retinal genes are expressed dominantly in the animals’ podia, and in addition to the genes already expressed in the mature rudiment, the juvenile podia express a ciliary opsin, another echinopsin, and two Go-opsins. The expression of a core of vertebrate retinal gene orthologs indicates that sea urchins have an evolutionarily conserved gene regulatory toolkit that controls photoreceptor specification and function, and that their podia are photosensory organs.

Molecular evidence of anteroposterior patterning in adult echinoderms

“…FezF and dbx were only expressed in a limited number of cells in the ambulacral ectoderm (Supplementary Fig.9a,b). Only pax6 was not expressed in the medial ambulacral ectoderm and was restricted to the podia epidermis, as previously reported in other echinoderm species 37,38 (Fig.3t). Thus, the outer ambulacral ectoderm appears to have a more posterior molecular identity, similar to that of the hemichordate collar or the vertebrate midbrain.…”

“…9a,b). Only pax6 was not expressed in the medial ambulacral ectoderm and was restricted to the podia epidermis, as previously reported in other echinoderm species 37,38 (Fig. 3t).…”

“…In crinoids, the expression of six3/6, otx , and pax6 has been reported in the ambulacral ectoderm 50 . In echinoids, AP patterning related genes have been extensively surveyed in Peronella japonica 24,30 and to a lesser extent in other species 25,37,38 . In both cases, most of the anterior patterning related genes studied show expression patterns compatible with our model.…”

A model of decentralized vision in the sea urchin Diadema africanum

“…Moreover, in a recent analysis of scRNA-seq data of early developmental stages of the sea urchin Paracentrotus lividus , different gene expression profiles were found for two sub-clusters of r-opsin-expressing PRCs. 35 Those findings might reflect different functions of the two PRC clusters located, respectively, at the tip and base of the tube feet that had been initially reported in the study by Ullrich-Lüter et al. 16 …”

A model of decentralized vision in the sea urchinDiadema africanum

“…As a consequence, the PRCs located on the tube feet disks display continuously changing spatial properties and cannot provide the basis for spatial vision, unlike the PRCs at the base of the tube feet. Moreover, in a recent analysis of scRNA-seq data of early developmental stages of the sea urchin Paracentrotus lividus , different gene expression profiles were found for two sub-clusters of r-opsin expressing PRCs (Paganos et al, 2022). Those findings might reflect different functions of the two PRC clusters located, respectively, at the tip and base of the tube feet that had been initially reported in (Ullrich-Lüter et al, 2011).…”