Takashi Nagata

The University of Tokyo | Todai · Institute for Solid State Physics

Chirality pervades multiple scientific domains-physics, chemistry, biology, and astronomy-and profoundly influences their foundational principles. Recently, the chirality-induced spin selectivity (CISS) phenomenon has captured significant attention in physical chemistry due to its potential applications and intriguing underlying physics. Despite it...

Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption,...

Channelrhodopsins are light-gated ion channels consisting of seven transmembrane helices and a retinal chromophore, which are used as popular optogenetic tools for modulating neuronal activity. Cation channelrhodopsins (CCRs), first recognized as the photoreceptors in the chlorophyte Chlamydomonas reinhardtii, have since been identified in diverse...

Microbial rhodopsins are a family of photoreactive membrane proteins that have seven transmembrane helices and a retinal chromophore. Among them, channelrhodopsins are light-induced ion channels making them popular tools for modulating neuronal activity in optogenetics. Cation channelrhodopsins (CCRs), first recognized as the main photoreceptors in...

Opsins are G protein-coupled receptors (GPCRs) that have evolved to detect light stimuli and initiate intracellular signaling cascades. Their role as signal transducers is critical to light perception across the animal kingdom. Opsins covalently bind to the chromophore 11-cis retinal, which isomerizes to the all-trans isomer upon photon absorption,...

Background Rhabdomeric photoreceptors of eyes in the terrestrial slug Limax are the typical invertebrate-type but unique in that three visual opsins (Gq-coupled rhodopsin, xenopsin, Opn5A) and one retinochrome, all belonging to different groups, are co-expressed. However, molecular properties including spectral sensitivity and G protein selectivity...

KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced...

Retinal G-protein-coupled receptor (RGR) plays a crucial role in the visual system of vertebrates as a retinal photoisomerase, which isomerizes all-trans-retinal to 11-cis-retinal to maintain the photosensitivity of visual rhodopsins. Despite the previous characterization of bovine RGR, little is known about the spectral properties of RGR from othe...

Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their impo...

Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium¹ and a terrestrial cyanobacterium². Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps³ from marine photoheterotrophs...

Optical control of G protein-coupled receptor (GPCR) signaling is a highly valuable approach for comprehensive understanding of GPCR-based physiologies and controlling them precisely. However, optogenetics for GPCR signaling is still developing and requires effective and versatile tools with performance evaluation from their molecular properties. H...

The KCR channelrhodopsins are recently-discovered light-gated ion channels with high K ⁺ selectivity, a property that has attracted broad attention among biologists– due to intense interest in creating novel inhibitory tools for optogenetics leveraging this K ⁺ selectivity, and due to the mystery of how this selectivity is achieved in the first pla...

Insect vision starts with light absorption by visual pigments based on opsins that drive Gq-type G protein-mediated phototransduction. Since Drosophila , the most studied insect in vision research, has only Gq-coupled opsins, the Gq-mediated phototransduction has been solely focused on insect vision for decades. However, genome projects on mosquito...

Energy transfer from light-harvesting ketocarotenoids to light-driven proton pumps xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium and a terrestrial cyanobacterium. Attempts to find carotenoids that bind and transfer energy to rhodopsin proton pumps from the abundant marine and freshwater photo...

Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domain...

Optogenetics for GPCR signaling is highly valuable but still requires effective and versatile tools with performance evaluation from molecular properties. Here we investigated performance of two animal opsins, mosquito Opn3 (MosOpn3) and lamprey parapinopsin (LamPP) in optical manipulation in vivo by using C. elegans . MosOpn3 introduced in a nocic...

ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsin...

The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional m...

In the pineal organ of zebrafish larvae, the bistable opsin parapinopsin alone generates color opponency between UV and visible light. Our previous study suggested that dark inactivation of the parapinopsin photoproduct, which activates G-proteins, is important for the regulation of the amount of the photoproduct. In turn, the photoproduct is respo...

Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halo...

ChRmine, a recently-discovered bacteriorhodopsin-like cation-conducting channelrhodopsin, exhibits puzzling properties (unusually-large photocurrents, exceptional red-shift in action spectrum, and extreme light-sensitivity) that have opened up new opportunities in optogenetics. ChRmine and its homologs function as light-gated ion channels, but by p...

Microbial rhodopsins are photoreceptive membrane proteins, which are used as molecular tools in optogenetics. Here, a machine learning (ML)-based experimental design method is introduced for screening rhodopsins that are likely to be red-shifted from representative rhodopsins in the same subfamily. Among 3,022 ion-pumping rhodopsins that were sugge...

Rhodopsins are widespread in microbes residing in diverse aquatic environments across the globe. Recently, a new unusual rhodopsin family, the heliorhodopsins (HeRs), was discovered, distributed among diverse bacteria, archaea, eukarya and even viruses. Here, using functional metagenomics on samples from Lake Ha’Hula and Ein Afek reserve, we found...

Animal opsin-based pigments are light-activated G-protein-coupled receptors (GPCRs), which drive signal transduction cascades via G-proteins. Thousands of animal opsins have been identified, and molecular phylogenetic and biochemical analyses have revealed the unexpected diversity in selectivity of G-protein activation and photochemical property. H...

Microbial rhodopsin is a large family of membrane proteins having seven transmembrane helices (TM1-7) with an all-trans retinal (ATR) chromophore that is covalently bound to Lys in the TM7. The Trp residue in the middle of TM3, which is homologous to W86 of bacteriorhodopsin (BR), is highly conserved among microbial rhodopsins with various light-dr...

Microbial rhodopsins are photoreceptive membrane proteins utilized as molecular tools in optogenetics. In this paper, a machine learning (ML)-based model was constructed to approximate the relationship between amino acid sequences and absorption wavelengths using ≈800 rhodopsins with known absorption wavelengths. This ML-based model was specificall...

Animals receive light from their environments using photosensitive proteins, opsins, for many purposes. Since opsins are diversified in some aspects including absorption and biochemical properties, it is essential to investigate properties of opsins for understanding characteristics and mechanisms of opsin-based photoreceptions. We previously inves...

Abstract Absorption spectra of opsin-based pigments are tuned from the UV to the red regions by interactions of the chromophore with surrounding amino acid residues. Both vertebrates and invertebrates possess long-wavelength-sensitive (LWS) opsins, which underlie color vision involving “red” sensing. The LWS opsins have independently evolved in eac...

Animals sense light using photosensitive proteins—rhodopsins—containing a chromophore—retinal—that intrinsically absorbs in the ultraviolet. Visible light-sensitivity depends primarily on protonation of the retinylidene Schiff base (SB), which requires a negatively-charged amino acid residue—counterion—for stabilization. Little is known about how t...

Jumping spiders have four pairs of eyes (ocelli) of which only the principal eyes (PEs) are used to detect features of objects. Photoreceptors in the retina of the PEs form four layers (PL1‐4) and terminate in the first optic ganglion (FOG). Here we focus on Hasarius adansoni because it has unique depth vision besides color vision and its FOG appea...

Significance Color discrimination in animals is considered to require opponent processing of signals from two or more opsins sensitive to different parts of the spectrum. We previously reported that lower vertebrate pineal organs, which discriminate between UV and visible light, employ a bistable opsin called parapinopsin that has two stable photoi...

Significance Complex photoreceptors have independently evolved in animals with radial and bilateral symmetry, but little is known about the proteins that transduce light information (opsins) in radially symmetrical animals. We use homology modeling and heterologous action spectroscopy to study the structure of an opsin (JellyOp) from the lens eye o...

Peropsin or retinal pigment epithelium-derived rhodopsin homolog, found in many animals, belongs to the opsin family. Most opsins bind to 11-cis-retinal as a chromophore and act as light-activated G protein-coupled receptors. Some peropsins, however, bind all-trans-retinal and isomerise it into 11-cis form by light, and peropsin has been suggested...

Most animals possess multiple opsins which sense light for visual and non-visual functions. Here, we show spectral characteristics of non-visual opsins, vertebrate Opn3s, which are widely distributed among vertebrates. We successfully expressed zebrafish Opn3 in mammalian cultured cells and measured its absorption spectrum spectroscopically. When i...

Spectra of monochromatic lights. From left to right, spectra of 410 nm, 430 nm, 470 nm, 510 nm, 540nm, 580 nm, 600 nm and 630 nm monochromatic lights are shown. (PDF)

Light-induced intracellular cAMP decreases in HEK293 cells expressing wild type vertebrate Opn3s. (A) pufferfish Opn3 (B) anole Opn3, (C) chicken Opn3, (D) mouse Opn3, (E) human Opn3, (F) Mock (cells not transfected with opsins). Blue arrowheads and black arrows indicate the timing of green light (500 nm) irradiations and forskolin treatments, resp...

Goodness of fit between experimentally obtained sensitivities and rhodopsin nomogram curves. Residual sum of squares as a function of λmax of various nomograms are shown as an indication of goodness of fit between experimentally obtained sensitivities and the estimated spectral sensitivity curves. (A) zebrafish Opn3-JiL3, (B) pufferfish Opn3-JiL3,...

Alignment of amino acid sequences of the third intracellular loops of opsin. Third intracellular loops of opsins (black plane letters) were replaced with that of Gs-coupled jellyfish opsin (red bold letter). The schematic drawing of chimeric mutants is also shown. (PDF)

Spectral changes of crude extract containing zebrafish Opn3 and chicken Opn3 during irradiation in alkaline condition. Difference spectra of crude extracts from the cultured cells expressing zebrafish Opn3 (A) and chicken Opn3 (B) at ~ pH 10. The difference absorption spectra were generated by subtracting values obtained before from after irradiati...

Estimation of the spectral sensitivities of various opsin-based pigments. The spectral sensitivity curves (red curves) of cells expressing mosquito Opn3-JiL3 mutant (A), spider Rh1-JiL3 (B), jellyfish opsin WT (C), and bovine rhodopsin-JiL3 mutant (D) with absorption spectra of the respective wild type pigments (blue curves). The spectral sensitivi...

Pineal organs of lower vertebrates contain several kinds of photosensitive molecules, opsins that are suggested to be involved in different light-regulated physiological functions. We previously reported that parapinopsin is an ultraviolet (UV)-sensitive opsin that underlies hyperpolarization of the pineal photoreceptor cells of lower vertebrates t...

Animal opsin-based pigments are light-activated G-protein-coupled receptors (GPCRs), which drive signal transduction cascades via G proteins. Thousands of animal opsins have been identified, and molecular phylogenetic and biochemical analyses have revealed that opsin-based pigments have basically diversified in selective activation of G proteins (G...

Many animals have developed systems for sensing environmental conditions during evolution. In sensory cells, receptor molecules are responsible for their sensing abilities. In light sensing, most animals capture light information via rhodopsin-like photoreceptive proteins known as opsin-based pigments. A body of evidence from comparisons of amino a...

Mammals contain 1 melanopsin (Opn4) gene that is expressed in a subset of retinal ganglion cells to serve as a photopigment involved in non-image-forming vision such as photoentrainment of circadian rhythms. In contrast, most nonmammalian vertebrates possess multiple melanopsins that are distributed in various types of retinal cells; however, their...

Absorption spectra of visual pigments are adaptively tuned to optimize informational capacity in most visual systems. Our recent investigation of the eyes of the jumping spider reveals an apparent exception: the absorption characteristics of a visual pigment cause defocusing of the image, reducing visual acuity generally in a part of the retina. Ho...

Most opsins selectively bind 11-cis retinal as a chromophore to form a photosensitive pigment, which underlies various physiological functions, such as vision and circadian photoentrainment. Recently, opsin 3 (Opn3), originally called encephalopsin or panopsin, and its homologs were identified in various tissues including brain, eye, and liver in b...

The principal eyes of jumping spiders have a unique retina with four tiered photoreceptor layers, on each of which light of different wavelengths is focused by a lens with appreciable chromatic aberration. We found that all photoreceptors in both the deepest and second-deepest layers contain a green-sensitive visual pigment, although green light is...

Peropsin, a member of the opsin family, has characteristics of two functionally distinct opsin-groups, that is, amino acid residues conserved among opsins for light-sensing and a retinal-photoisomerase-like molecular property. Although such a bilateral feature of peropsin seems to be important for understanding the diversity of the opsin family, pr...

Among terrestrial animals, only vertebrates and arthropods possess wavelength-discrimination ability, so-called "color vision". For color vision to exist, multiple opsins which encode visual pigments sensitive to different wavelengths of light are required. While the molecular evolution of opsins in vertebrates has been well investigated, that in a...