Commentary and Perspective
Functional diversity and evolution in animal rhodopsins: Report for the session 11
2023 Volume 20 Issue Supplemental Article ID: e201019
Details
2023 Volume 20 Issue Supplemental Article ID: e201019
In the session of “Functional diversity and evolution in animal rhodopsins”, 5 speakers gave a talk about their recent studies.
Dr. Jonathan R. Church (The Hebrew University of Jerusalem, Israel) talked about “QM/MM study of photochemistry in jumping spider rhodopsin-1”. Bistable rhodopsins are often considered ideal candidates for applications such as optogenetics due to their ability to act as photoswitches. This ability stems from the thermal stability of their photoproducts, which need an additional photon to be reconverted to the reactant state. In this work the bistable rhodopsin found in jumping spider Hasarius adansoni, Jumping Spider Rhodopsin-1 (JSR1), was analyzed to observe how different retinal isomers interact with the protein environment. [1–4] The main aim was to gain insight into the specific chromophore-protein interactions of each isomer and their impact on the absorption maximum in JSR1. The absorption spectra were computed using sampled snapshots from hybrid QM/MM molecular dynamics trajectories and compared to their experimental counterparts. The chromophore-protein interactions were analyzed by visualizing the electrostatic potential of the protein and projecting it onto chromophore. The primary counterion of the chromophore, E194, is located approximately 6–7 Å from the protonated Schiff base, limiting its direct interactions. On the other hand, there is a tyrosine, Y126, located within hydrogen bonding distance of the Schiff base and this residue is found to play large role in the spectral tuning of this protein. Geometric differences between the isomers were also noted including a structural change in the polyene chain of the chromophore as well as changes in the nearby hydrogen bond network.[1] Non-adiabatic dynamics were also performed using the crystal structure containing the 9-cis isomer to study the photoisomerization reaction of this protein.
Dr. Keiichi Kojima (Okayama University, Japan) presented the data on the “Evolutionary adaptation of visual pigments in geckos for their photic environment” Vertebrates generally have a single type of rod for scotopic vision and multiple types of cones for photopic vision. Noteworthily, nocturnal geckos transmuted ancestral photoreceptor cells into rods containing not rhodopsin but cone pigments, and subsequently diurnal geckos retransmuted these rods into cones containing cone pigments. High sensitivity of scotopic vision is underlain by the rod’s low background noise, which originated from a much lower spontaneous activation rate of rhodopsin than of cone pigments. They analyzed how geckos changed the molecular properties of cone pigments to adjust to their activity rhythm during the photoreceptor transmutation process [5]. Nocturnal gecko cone pigments in rods decreased their spontaneous activation rates to mimic rhodopsin, whereas diurnal gecko cone pigments in cones recovered high rates similar to those of typical cone pigments. Their mutational analysis revealed that several amino acid residues around the chromophore retinal are responsible for the alterations of the spontaneous activation rates of nocturnal and diurnal gecko cone pigments. They concluded that the switch between diurnality and nocturnality in geckos was achieved by not only morphological transmutation of photoreceptors but also by adjustment of the spontaneous activation rates of visual pigments.
Dr. Takahiro Yamashita (Kyoto University, Japan) talked on “Creation of photocyclic vertebrate visual rhodopsin by single amino acid substitution” Vertebrate rhodopsin functions as a visual photoreceptive protein and produces a G protein-activating state upon photoreception. This active state is a metastable intermediate and cannot revert back to the original dark state by either photoreaction or thermal reaction. Thus, vertebrate rhodopsin is specialized for photoactivation and categorized as a mono-stable opsin. By contrast, many opsins, including mollusk and arthropod rhodopsins, form a stable active state upon photoreception and the active state can photo-convert back to the original dark state. These opsins show photoreversibility between the dark and active states and are categorized as bistable opsins. In addition, they recently identified a novel type of opsin, Opn5L1, whose activity is controlled by photocyclic reaction. This photocyclic reaction includes thermal recovery to the original dark state mediated by light-dependent adduct formation between the chromophore retinal and the cysteine residue at position 188. Sequence comparison shows that mono-stable opsins instead share a glycine residue at position 188. They showed that the G188C mutant of vertebrate rhodopsin photoconverts to the active state, which thermally recovers to the original dark state. In addition, light irradiation of the active state G188C mutant induces reversion to the original dark state. They successfully created photocyclic vertebrate rhodopsin by a single mutation and revealed that the residue at position 188 contributes to the diversification of photoreaction properties of opsins by its regulation of the recovery from the active state to the original dark state [6].
Dr. Ajith Karunarathne (Saint Louis University, USA) talked on “Engineered opsins for subcellular and in vivo optogenetic applications” Monostable opsins need a continuous retinal supply for sustained signaling, making theirs in vivo use challenging. However, spectral and signaling properties of bistable melanopsin and lamprey parapinopsin indicate compatibility for in vivo signaling control. They showed that ultra-low retinal concentrations (in cell culture medium from FBS) are sufficient for functionalizing these opsins, showcasing their potential to function in vivo and outside the retina. Enhancing its signaling bandwidth, they also demonstrate that melanopsin activates two major G protein pathways (Gq and Gi/o) with near-similar efficacies. Additionally, they establish the feasibility of engineering mutant melanopsins with exclusive G protein-selectivity. Using in silico QM/MM models of squid rhodopsin and human and mouse melanopsins and the Automatic Rhodopsin Modeling (ARM) protocol, they investigated single-residue blue-shift mutations and subsequently engineered several melanopsin mutants that are resistant to red light, however sensitive to blue and green lights. They further show the utility of these novel blue-shifted melanopsins in single cell and subcellular optogenetics. Similarly, their engineered novel color opsins offer features such as extended plasma membrane life and endomembrane exclusive signaling.
Dr. Mitsumasa Koyanagi (Osaka Metropolitan University, Japan) talked on “Diversity of animal opsins and molecular property-based optical control of GPCR signaling by bistable opsins” Most animal opsins bind to 11-cis retinal as a chromophore to form a photosensitive pigment. Upon light absorption, opsin-based pigments initiate cell signaling including changes of second messenger levels such as cAMP and Ca2+ through G protein-mediated signal transduction cascades. Thousands of opsins have been identified and they are diversified in spectral sensitivity and G-protein selectivity. They investigated various kinds of nonconventional animal opsins such as non-visual opsins and invertebrate visual opsins, to uncover the diversity of animal opsins [7]. Their findings revealed that most opsins excluding vertebrate visual opsins (rhodopsin and cone visual opsins) are bleach-resistant or bistable, that is, the light-activated state is stable and, in many cases, reverts to the original dark state by subsequent light absorption. They also found that some bistable opsins have characteristics suitable for optogenetic applications [8,9]. In particular, in the case of parapinopsin, a UVsensitive bistable opsin, the stable active state has an absorption maximum in the green region and largely distinct from that of the UV-sensitive inactive dark state. The large spectral difference between the inactive and active states allows selective illumination of active state, resulting in its complete recovery to the inactive state. With this property, the G protein activation by parapinopsin were up- and down-regulated upon UV and green light illumination, respectively in vitro [10]. They evaluated the performance of lamprey parapinopsin as an optogenetic tool for controlling cellular signal transduction in a color-dependent manner using C. elegans. They also examined optogenetic potentials of other bistable opsins having different molecular properties.
