Rhodopsin, light-sensor of vision

Insights into the function and research status of membrane protein APJ

APJ, a membrane protein belonging to the G protein-coupled receptor (GPCR) family, was first discovered in 1993. It is activated by endogenous ligands such as Apelin and Elabela, coupling with various G proteins to trigger downstream signaling pathways. APJ is ubiquitously expressed in various organs and tissues, and plays pivotal roles in numerous physiological and pathological processes. This review provides a comprehensive overview of APJ's physiological functions, including its involvement in the cardiovascular system, metabolism, neuroendocrine stress responses, respiratory diseases, and appetite regulation. Furthermore, it discusses the potential of APJ as a biomarker for various tumors and its crucial role in tumor angiogenesis. Additionally, the review covers the development of small molecule antagonists targeting APJ and highlights the major challenges and future prospects in current APJ research. In conclusion, this review offers valuable insights into the multifaceted functions of APJ, its targeting antagonists, existing research challenges, and potential future directions, thereby contributing to further advancements in research and drug development in this field.

Beacon of Hope for Age-Related Retinopathy: Antioxidative Mechanisms and Pre-Clinical Trials of Quercetin Therapy

Age-related retinopathy is one of the leading causes of visual impairment and irreversible blindness, characterized by progressive neuronal and myelin loss. The damages caused by oxidation contributes to the hallmarks of aging and represents fundamental components in pathological pathways that are thought to drive multiple age-related retinopathies. Quercetin (Que), a natural polyphenol abundant in vegetables, herbs, and fruits, has been extensively studied for its long-term antioxidative effects mediated through diverse mechanisms. Additionally, Que and its derivatives exhibit a broad spectrum of pharmacological characteristics in the cellular responses of age-related retinopathy induced by oxidative stress, including anti-inflammatory, anti-neovascularization, regulatory, and neuroprotective effects in autophagy and apoptosis processes. This review mainly focuses on the antioxidative mechanisms and curative effects of Que treatment for various age-related retinopathies, such as retinitis pigmentosa, diabetic retinopathy, age-related macular degeneration, and glaucoma. Furthermore, we discuss emerging technologies and methods involving Que and its derivatives in the therapeutic strategies for age-related retinopathies, highlighting their promise for clinical translation.

Exploring the Molecular Intersection of Posterior Ocular Tuberculosis: Mycobacterium tuberculosis Proteins, Ocular Autoimmunity, and Immune Receptor Interactions

Purpose

The presentation of posterior ocular tuberculosis (TB) varies greatly along with the need for immunomodulatory therapy to control inflammation. In this study, we explore the potential mechanisms and pathways for autoimmune-related inflammation in ocular TB using molecular mimicry-based mathematical modeling.

Design

Computational protein analysis.

Methods

Twenty-three TB-related proteins, including ESAT-6 subgroup proteins, and 23 retinal ganglion cells, photoreceptor, and retinal pigment epithelium (RPE) cellular proteins were included in this study. The 3-dimensional structure and sequence of the TB AG proteins were compared to the above-mentioned retinal, photoreceptor, and RPE cellular proteins. All retinal proteins were obtained from the UniProt database. The sequence and 3-dimensional structure of TB-related proteins and retinal proteins were compared with the TM-align server. The interactions of proteins showing significant similarity (template modeling score above 0.5, root mean square deviation [RMSD] value below 5A°) with cytokines (interleukin [IL]6, IL10, IL12A, IL12B, TLR2, TLR3, and TLR4) were analyzed. Autoimmune and autoinflammation-related protein-receptor interaction of similar proteins was assessed using the CABS-dock web server.

Main Outcome Measures

Template modeling score, structural alignment accuracy using RMSD value, protein-cytokine interaction.

Results

We detected a high level of structural similarity between ESAT-6 (EsxA, EsxB) proteins and rhodopsin, HSPA1A, RPE-related BEST-1, ABCC-1, ABCC-4, ABCC-5, SLC47A1, SLC1A5, SLC38A7, SLC6A6, SLC5A6, LAT-1, and SLC16A1 proteins. When we evaluated the likelihood/potential to stimulate an immune response via a cytokine release, TLR-2 (most common), TLR-3, and TLR-4, which are highly susceptible to Mycobacterium tuberculosis ESAT-6 (ESXA and ESXB) proteins, showed a potential receptor-protein interaction with retinal proteins. Moreover, some eye-related proteins had the capacity to trigger the T-cell response by binding to cytokines such as IL-12, IL-10, and IL-6, which are all highly overexpressed in TB infections.

Conclusions

Our study demonstrates that TB proteins may have significant structural similarities with many eye-related proteins. These eye-related proteins are therefore immunological target sites and may be secondarily affected by any immune response toward TB.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Organic-solvent mediated self-assembly of protoporphyrin IX with human serum albumin

This study investigates the non-native interactions between the photosensitizer protoporphyrin IX (PPIX) and human serum albumin (HSA). Non-covalent binding between small molecules and proteins, is crucial for various applications in biomedicine, food processing, energy conversion, and sensing. The research focuses on the role of a series of organic solvents in facilitating the binding of water-insoluble PPIX to the protein. By using dialysis and centrifugation for sample preparation and combining experimental and computational methods for characterization, the study found that non-protic solvents such as THF and DMSO are more effective in forming the PPIX:HSA complex compared to protic solvents. Additionally, the temporary presence of these organic solvents during incubation does not cause significant and irreversible changes in the protein structure. Instead, THF and DMSO temporarily loosen the protein, increasing the distance between two tyrosine residues (Y138 and Y161) that are believed to coordinate the porphyrin at its binding site. This finding underscores the importance of selecting appropriate solvents to enhance the binding efficiency of small ligands to proteins.

Modulation of terahertz absorption by a single mutation of rhodopsin mimics

The collective vibration of many biomolecules such as the skeletal vibration, dipole rotation and conformational bending falls in the terahertz (THz) frequency domain. Terahertz time-domain spectroscopy (THz-TDS), which is very sensitive to the conformational changes, can be used to characterize the collective vibration of biomolecules. In this study, we investigated the low-frequency THz absorption spectra of two rhodopsin mimics using transmission THz-TDS. Using the normal model analysis (NMA) and molecular dynamics (MD), we successfully modelled the experimental THz absorption spectral curve. Furthermore, we attributed a unique collective motion pattern to each distinctive THz absorption frequency. By comparing the THz absorption spectra between without and with retinal, we show that the retinal binding can significantly alter the THz absorption spectra as well as the vibration modes. Furthermore, by comparing the THz absorption spectra between the two mutants, we observed that a single mutation can significantly change the influence of retinal binding on the THz absorption spectrum.

Monogenic Retinal Diseases Associated With Genes Encoding Phototransduction Proteins: A Review

Phototransduction, the process by which captured photons elicit electrical changes in retinal rod and cone cells, represents the first neuronal step in vision and involves interactions between several highly specialised proteins. Pathogenic variants in genes encoding many of these proteins can give rise to significant vision impairment, accounting for a substantial portion of inherited retinal disease. Such genes include RHO, OPN1LW, OPN1MW, GNAT1, GNAT2, GNB3, PDE6A, PDE6B, PDE6G, PDE6C, PDE6H, CNGA1, CNGB1, CNGA3, CNGB3, GRK1, SAG, ARR3, RGS9, RGS9BP, GUCY2D, GUCA1A and SLC24A1. Many of these conditions have distinct mechanisms and clinical features. They follow several modes of inheritance (including in one case digenic, or tri-allelic, inheritance). Some conditions also entail myopia. Rod and cone phototransduction will be outlined, followed by the discussion of diseases associated with these genes. Some phenotypic features will be highlighted as well as their prevalence in a large genotyped inherited retinal disease cohort.

Optoretinography reveals rapid rod photoreceptor movement upon photoisomerization

Rod photoreceptors are essential for vision under dim light conditions. The onset of rod-mediated vision is marked by the isomerization of rhodopsin. Here we demonstrate that human and rodent rods undergo a minute and rapid contraction of their outer segments immediately upon photoisomerization. The contraction is explained as an electro-mechanical manifestation of the rod early receptor potential generated in the disk membranes, which is challenging to access in electrophysiology. The bleach-strength dependence of the contraction was accounted by a voltage-dependent membrane tension model, developed earlier to explain a similar behavior in cones. The in vivo optical imaging of light-evoked electrical activity in rodent rods was facilitated by an ultrahigh-resolution point-scan optical coherence tomography (OCT) system coupled with unsupervised learning, while in humans, an adaptive optics line-scan OCT facilitated high-speed recordings in individual rods. The non-invasive in vivo optical imaging of rhodopsin activation will have a significant impact on diagnostics and treatment of retinal disease, especially given the vulnerability of rods in inherited and age-related macular degeneration.

Human Retinal Organoid Model of Ocular Toxoplasmosis

The health burden of ocular toxoplasmosis is substantial, and there is an unmet need for safe and curative anti-microbial drugs. One major barrier to research on new therapeutics is the lack of in vitro human-based models beyond two-dimensional cultured cells and tissue explants. We aimed to address this research gap by establishing a human retinal organoid model of ocular toxoplasmosis. Retinal organoids, generated from human induced pluripotent stem cells and grown to two stages of organization, were incubated with a suspension of live or heat-killed GT-1 strain T. gondii tachyzoites, or medium without tachyzoites. Both developing (1 month post-isolation) and matured (6 months post-isolation) organoids were susceptible to infection. Spread of live parasites from the margin to the entire organoid over 1 week was indicated by immunolabelling for T. gondii surface antigen 1. This progression was accompanied by changes in the levels of selected tachyzoite transcripts-SAG1, GRA6, and ROP16-and human cytokine transcripts-CCL2, CXCL8, CXCL10, and IL6-in infected versus control conditions. Our human retinal organoid model of ocular toxoplasmosis offers the opportunity for many future lines of study, including tachyzoite interactions with retinal cell populations and leukocyte subsets, parasite stage progression, and disease processes of different T. gondii strains, as well as drug testing.

An Extensive Survey of Vertebrate-specific, Nonvisual Opsins Identifies a Novel Subfamily, Q113-Bistable Opsin

A group of nonvisual opsins specific to vertebrates is essential to understand evolution of lateral eyes, one of the most prominent innovations in this lineage. Nevertheless, our knowledge of their evolutionary history remains limited. To develop an integrated view of their evolution, we surveyed these non-visual opsins (VA opsin, pinopsin, parapinopsin, parietopsin, and parapinopsin-like) in 451 vertebrate genomes. Through extensive manual curation, we completed a high-quality catalog. We could not find them in 202 mammals, supporting previous reports of their loss. VA opsins are highly conserved among nonmammals. In contrast, other opsin subfamilies experienced more dynamic molecular evolution with many secondary losses. In addition, we found a previously unreported opsin subfamily that we named Q113-Bistable (QB) opsin. We found its orthologs only in several lizards and the tuatara. Nevertheless, QB opsin pseudogenes were discovered in diverse taxa, including ray-finned fishes, indicating its ancient origin. QB opsin, parapinopsin, and parietopsin are extremely prone to be lost in the course of evolution, and loss events involving these opsins seem to occur concomitantly. Furthermore, we demonstrated the spectral properties of QB opsin as a UV-sensitive, bistable photo-pigment. This study provides the first integrated view of the entire evolutionary history of this group of opsins.

Temporal Transformation of the Rod Single-Photon Response in the Retinal Circuitry

Purpose

The temporal sensitivity of rod vision is higher than expected based on slow single-photon responses produced by phototransduction in rod outer segments. We sought to establish the retinal basis for the temporal speeding of rod responses and their dependence on phototransduction.

Methods

We made patch-clamp recordings of photocurrent and photovoltage from rods and rod bipolar cells (RBCs), and loose-patch and voltage-clamp recordings from ON α retinal ganglion cells, in three mouse strains: wild-type (WT), rhodopsin hemizygotes (Rh+/-), and GCAPs-/-.

Results

Single-photon responses from the three strains differed in the kinetics of their waveforms: Rh+/- were more rapid than WT and GCAPs-/- considerably slower. RBCs in all three strains decayed much faster than their respective rod current responses, and much of this transformation was the prior result of conversion of rod photocurrent to photovoltage. Light responses were further accelerated at the bipolar-cell synapse and in the inner plexiform layer, with the remarkable result that ganglion-cell EPSPs and spike output both nearly overlap in waveform from all three strains despite large differences in rod photocurrents. These kinetic alterations were mostly affected by linear filters at each step in integration, with some contribution also from nonlinear interactions especially apparent in the GCAPs-/- retina.

Conclusions

The retina extracts principally the initial phase of single-photon responses through a series of high-pass, largely linear filters at each integration stage. Much of this transformation occurs in the rods themselves, but important contributions are also made at the rod-to-RBC synapse and within the inner plexiform layer.

Defining proteoform-specific interactions for drug targeting in a native cell signalling environment

Understanding the dynamics of membrane protein-ligand interactions within a native lipid bilayer is a major goal for drug discovery. Typically, cell-based assays are used, however, they are often blind to the effects of protein modifications. In this study, using the archetypal G protein-coupled receptor rhodopsin, we found that the receptor and its effectors can be released directly from retina rod disc membranes using infrared irradiation in a mass spectrometer. Subsequent isolation and dissociation by infrared multiphoton dissociation enabled the sequencing of individual retina proteoforms. Specifically, we categorized distinct proteoforms of rhodopsin, localized labile palmitoylations, discovered a Gβγ proteoform that abolishes membrane association and defined lipid modifications on G proteins that influence their assembly. Given reports of undesirable side-effects involving vision, we characterized the off-target drug binding of two phosphodiesterase 5 inhibitors, vardenafil and sildenafil, to the retina rod phosphodiesterase 6 (PDE6). The results demonstrate differential off-target reactivity with PDE6 and an interaction preference for lipidated proteoforms of G proteins. In summary, this study highlights the opportunities for probing proteoform-ligand interactions within natural membrane environments.

Deletion of Transmembrane protein 184b leads to retina degeneration in mice

Transmembrane protein 184b (Tmem184b) has been implicated in axon degeneration and neuromuscular junction dysfunction. Notably, Tmem184b exhibits high expression levels in the retina; however, its specific function within this tissue remains poorly understood. To elucidate the role of Tmem184b in the mammalian visual system, we developed a Tmem184b knockout (KO) model for further investigation. Loss of Tmem184b led to significant decreases in both a and b wave amplitudes of scotopic electroretinogram (ERG) and reduced b wave amplitudes of photopic ERG, respectively, reflecting damage to both the photoreceptors and secondary neuronal cells of the retina. Histologic analyses showed a progressive retinal thinning accompanied by the significantly loss of retinal cells including cone, rod, bipolar, horizontal and retinal ganglion cells. The expression levels of photo-transduction-related proteins were down-regulated in KO retina. TUNEL (terminal deoxynucleotidyl transferase-mediated biotinylated Uridine-5'-triphosphate [UTP] nick end labelling) and glial fibrillary acidic protein (GFAP)-labelling results suggested the increased cell death and inflammation in the KO mice. RNA-sequencing analysis and GO enrichment analysis revealed that Tmem184b deletion resulted in down-regulated genes involved in various biological processes such as visual perception, response to hypoxia, regulation of transmembrane transporter activity. Taken together, our study revealed essential roles of Tmem184b in the mammalian retina and confirmed the underlying mechanisms including cell death, inflammation and hypoxia pathway in the absence of Tmem184b, providing a potential target for therapeutic and diagnostic development.

From resting potential to dynamics: advances in membrane voltage indicators and imaging techniques

The membrane potential is a critical aspect of cellular physiology, essential for maintaining homeostasis, facilitating signal transduction, and driving various cellular processes. While the resting membrane potential (RMP) represents a key physiological parameter, membrane potential fluctuations, such as depolarization and hyperpolarization, are equally vital in understanding dynamic cellular behavior. Traditional techniques, such as microelectrodes and patch-clamp methods, offer valuable insights but are invasive and less suited for high-throughput applications. Recent advances in voltage indicators, including fast and slow dyes, and novel imaging modalities such as second harmonic generation (SHG) and photoacoustic imaging, enable noninvasive, high-resolution measurement of both RMP and membrane potential dynamics. This review explores the mechanisms, development, and applications of these tools, emphasizing their transformative potential in neuroscience and cellular electrophysiology research.

The Role of Individual Residues in the N-Terminus of Arrestin-1 in Rhodopsin Binding

Sequences and three-dimensional structures of the four vertebrate arrestins are very similar, yet in sharp contrast to other subtypes, arrestin-1 demonstrates exquisite selectivity for the active phosphorylated form of its cognate receptor, rhodopsin. The N-terminus participates in receptor binding and serves as the anchor of the C-terminus, the release of which facilitates arrestin transition into a receptor-binding state. We tested the effects of substitutions of fourteen residues in the N-terminus of arrestin-1 on the binding to phosphorylated and unphosphorylated light-activated rhodopsin of wild-type protein and its enhanced mutant with C-terminal deletion that demonstrates higher binding to both functional forms of rhodopsin. Profound effects of mutations identified lysine-15 as the main phosphate sensor and phenylalanine-13 as the key anchor of the C-terminus. These residues are conserved in all arrestin subtypes. Substitutions of five other residues reduced arrestin-1 selectivity for phosphorylated rhodopsin, indicating that wild-type residues participate in fine-tuning of arrestin-1 binding. Differential effects of numerous substitutions in wild-type and an enhanced mutant arrestin-1 suggest that these two proteins bind rhodopsin differently.

In Vitro Models of Diabetes: Focus on Diabetic Retinopathy

Diabetic retinopathy is a major eye complication in patients with diabetes mellitus, and it is the leading cause of blindness and visual impairment in the world. Chronic hyperglycemia induces endothelial damage with consequent vascular lesions, resulting in global vasculitis, which affects the small vessels of the retina. These vascular lesions cause ischemic conditions in certain areas of the retina, with a consequent increase in the release of pro-angiogenic mediators. In addition to pharmacological interventions for controlling the blood glycaemic level, the main strategies for treating diabetic retinopathy are the intravitreal injections of drugs, surgical treatments, and vitrectomies. The complexity of diabetic retinopathy is due to its close interactions with different cell types (endothelial cells, astrocytes, and Müller cells). The evaluation of the efficacy of novel pharmacological strategies is mainly performed through in vivo models. However, the use of different animal species leads to heterogenic results and ethical concerns. For these reasons, the development of new and reliable in vitro models, such as cell co-cultures and eye organoids, represents an urgent need in this area of research. This review features an overview of the in vitro models used to date and highlights the advances in technology used to study this pathology.

Retigabine increases the conformational stability of the visual photoreceptor rhodopsin

Rhodopsin is the key photoreceptor protein that mediates vision in low-light conditions. Mutations in rhodopsin are the cause of retinal degenerative diseases such as retinitis pigmentosa. Some of these mutations cause a decreased stability of the receptor. It is, therefore, of interest to find new approaches that can help improving rhodopsin conformational stability. In this study, we have analyzed the effect of retigabine, an anticonvulsant formerly used to treat epilepsy, on rhodopsin thermal stability, regeneration capacity, and signal transduction by means of UV-visible and fluorescence spectroscopic techniques. We find that retigabine enhances the thermal stability of dark-state rhodopsin and improves chromophore regeneration without disrupting the photobleaching process. Furthermore, retigabine does not significantly affect transducin activation. These results provide novel insights into the potential therapeutic applications of retigabine in the treatment of retinitis pigmentosa caused by rhodopsin mutations that cause a decreased stability of the mutated receptors.

Blue light-driven cell cycle arrest in thyroid cancer via Retinal-OPN3 complex

BACKGROUND

Papillary thyroid carcinoma (PTC) is the most common type of thyroid malignancy, with a rising incidence. Traditional treatments, such as thyroidectomy and radiotherapy, often lead to significant side effects, including impaired thyroid function. Therefore, there is an urgent need for non-invasive therapeutic approaches. This study aims to explore the potential of photobiomodulation therapy (PBMT), a non-invasive treatment using specific wavelengths of light, in the management of PTC.

METHODS

We investigated the effects of blue light PBMT on PTC cells, focusing on the Retinal-OPSIN 3 (OPN3) complex's role in mediating cellular responses. Blue light exposure was applied to PTC cells, and subsequent changes in cellular proliferation, cell cycle progression, and protein expression were analyzed. Statistical tests, including one-way ANOVA and t-tests, were used to evaluate the significance of the findings.

RESULTS

Blue light exposure led to the dissociation of 11-cis-retinal from OPN3, resulting in the accumulation of all-trans retinal. This accumulation disrupted cellular proliferation pathways and induced G0/G1 cell cycle arrest in PTC cells. The Retinal-OPN3 complex was found to be a key mediator in these processes, demonstrating that thyroid cells can respond to specific light wavelengths and utilize their photoreceptive potential for therapeutic purposes.

CONCLUSIONS

Our findings suggest that PBMT, through the modulation of the Retinal-OPN3 complex, offers a promising non-invasive approach for treating PTC. This study highlights the therapeutic potential of light signal transduction in non-ocular tissues and opens new avenues for non-invasive cancer therapies.

Functional diversification process of opsin genes for teleost visual and pineal photoreceptions

Most vertebrates have a rhodopsin gene with a five-exon structure for visual photoreception. By contrast, teleost fishes have an intron-less rhodopsin gene for visual photoreception and an intron-containing rhodopsin (exo-rhodopsin) gene for pineal photoreception. Here, our analysis of non-teleost and teleost fishes in various lineages of the Actinopterygii reveals that retroduplication after branching of the Polypteriformes produced the intron-less rhodopsin gene for visual photoreception, which converted the parental intron-containing rhodopsin gene into a pineal opsin in the common ancestor of the Teleostei. Additional analysis of a pineal opsin, pinopsin, shows that the pinopsin gene functions as a green-sensitive opsin together with the intron-containing rhodopsin gene for pineal photoreception in tarpon as an evolutionary intermediate state but is missing in other teleost fishes, probably because of the redundancy with the intron-containing rhodopsin gene. We propose an evolutionary scenario where unique retroduplication caused a "domino effect" on the functional diversification of teleost visual and pineal opsin genes.

Light sensitivity in Beroidae ctenophores: Insights from laboratory studies and genomics

Light detection underlies a variety of animal behaviors, including those related to spatial orientation, feeding, avoidance of predators, and reproduction. Ctenophores are likely the oldest animal group in which light sensitivity based on opsins evolved, so they may still have the ancestral molecular mechanisms for photoreception. However, knowledge about ctenophore photosensitivity, associated morphological structures, molecular mechanisms involved, and behavioral reactions is limited and fragmented. We present the initial experiments on the responses of adult Beroe ovata to high-intensity light exposure with different spectra and photosensitivity in various parts of the animal's body. Ctenophores have shown a consistent behavioral response when their aboral organ is exposed to a household-grade laser in the violet spectrum. To investigate the genes responsible for the photosensitivity of Beroidae, we have analyzed transcriptome and genome-wide datasets. We identified three opsins in Beroe that are homologous to those found in Mnemiopsis leidyi (Lobata) and Pleurobrachia bachei (Cydippida). These opsins form clades Ctenopsin1, 2, and 3, respectively. Ctenopsin3 is significantly distinct from other ctenophore opsins and clustered outside the main animal opsin groups. The Ctenopsin1 and Ctenopsin2 groups are sister clusters within the canonical animal opsin tree. These two groups could have originated from gene duplication in the common ancestor of the species we studied and then developed independently in different lineages of Ctenophores. So far, there is no evidence of additional expansion of the opsin family in ctenophore evolution. The involvement of ctenophore opsins in photoreception is discussed by analyzing their protein structures.

Caspase-8 promotes NLRP3 inflammasome activation mediates eye development defects in zebrafish larvae exposed to perfulorooctane sulfonate (PFOS)

Epidemiological evidence showed that serum high perfluorooctane sulfonate (PFOS) levels are associated with multiple eye related diseases, but the potential underlying molecular mechanisms remain poorly understood. Zebrafish and photoreceptor cell (661w) models were used to investigate the molecular mechanism of PFOS induced eye development defects. Our results showed a novel molecular mechanism of PFOS-induced inflammation response-mediated photoreceptor cell death associated with eye development defects. Inhibition of Caspase-8 activation significantly decreased photoreceptor cell death in PFOS exposure. Mechanistically, Toll-like receptor 4 (TLR4) mediates activation of Caspase-8 promote activation of NLR family pyrin domain-containing 3 (NLRP3) inflammasome to elicit maturation of interleukin-1 beta (IL-1β) via Caspase-1 activation, facilitating photoreceptor cell inflammation damage in PFOS exposure. In addition, we also made a novel finding that Caspase-3 activation was increased via Caspase-8 activation and directly intensified cell death. Our results show the important role of Caspase-8 activation in PFOS induced eye development defects and highlight Caspase-8 mediated activation of the NLRP3 inflammation triggers activation of Caspase-1 and promote the maturation of IL-1β in retinal inflammatory injury.

Toxicity Evaluation and Transcriptome Analysis of Yellowstripe Goby (Mugilogobius chulae) in Response to 2,7-Dibromocarbazole Exposure during Early Development

Polyhalogenated carbazoles (PHCZs) are a class of nitrogen-containing heterocyclic compounds that are widely distributed throughout the marine environment and sediment. These compounds share structural and toxicity similarities with dioxins. However, our understanding of the toxicological effects of PHCZs on marine organisms and their underlying molecular mechanisms remains limited. In this study, we employed the marine model organism Mugilogobius chulae as the experimental subject and selected 2,7-dibromocarbazole (2,7-DBCZ), a compound known for its high toxicity and detection frequency, to conduct both an acute toxicity test and transcriptome analysis on M. chulae embryos. Our findings revealed that the 96 h median lethal concentration (LC50) of 2,7-DBCZ for M. chulae embryos was 174 μg/L, with a median effective concentration (EC50) resulting in pericardial edema deformity of 88.82 μg/L. Transcriptome analysis revealed significant impacts on various systems in M. chulae embryos following exposure to 2,7-DBCZ, including the sensory, cardiovascular, immune, and endocrine systems. Furthermore, this compound perturbed signaling pathways such as phototransduction, protein folding and processing, amino acid metabolism, lipid transport, and exogenous compound metabolism. Notably, transcript abundance of the CYP1A gene associated with the activation of the AhR signaling pathway, similar to dioxin-like compounds, was 18.18 times higher than that in the control group. This observation suggests that M. chulae embryos mount a stress response when exposed to PHCZs. In summary, this study contributes to our understanding of the toxicological implications of PHCZ in marine fish and offers a theoretical foundation for risk assessment and regulatory frameworks for PHCZs in the marine environment.

A Polarizable QM/MM Model That Combines the State-Averaged CASSCF and AMOEBA Force Field for Photoreactions in Proteins

This study presents the polarizable quantum mechanics/molecular mechanics (QM/MM) embedding of the state-averaged complete active space self-consistent field (SA-CASSCF) in the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field for the purpose of studying photoreactions in protein environments. We describe two extensions of our previous work that combine SA-CASSCF with AMOEBA water models, allowing it to be generalized to AMOEBA models for proteins and other macromolecules. First, we discuss how our QM/MM model accounts for the discrepancy between the direct and polarization electric fields that arises in the AMOEBA description of intramolecular polarization. A second improvement is the incorporation of link atom schemes to treat instances in which the QM/MM boundary goes through covalent bonds. A single-link atom scheme and double-link atom scheme are considered in this work, and we will discuss how electrostatic interaction, van der Waals interaction, and various kinds of valence terms are treated across the boundary. To test the accuracy of the link atom scheme, we will compare QM/MM with full QM calculations and study how the errors in ground state properties, excited state properties, and excitation energies change when tuning the parameters in the link atom scheme. We will also test the new SA-CASSCF/AMOEBA method on an elementary reaction step in NanoLuc, an artificial bioluminescence luciferase. We will show how the reaction mechanism is different when calculated in the gas phase, in polarizable continuum medium (PCM), versus in protein AMOEBA models.

Rhodopsin-based light-harvesting system for sustainable synthetic biology

Rhodopsins, a diverse class of light-sensitive proteins found in various life domains, have attracted considerable interest for their potential applications in sustainable synthetic biology. These proteins exhibit remarkable photochemical properties, undergoing conformational changes upon light absorption that drive a variety of biological processes. Exploiting rhodopsin's natural properties could pave the way for creating sustainable and energy-efficient technologies. Rhodopsin-based light-harvesting systems offer innovative solutions to a few key challenges in sustainable engineering, from bioproduction to renewable energy conversion. In this opinion article, we explore the recent advancements and future possibilities of employing rhodopsins for sustainable engineering, underscoring the transformative potential of these biomolecules.

Quality and applicability of cadaveric donor eyes for molecular biology research: An Indian experience

PURPOSE

Human ocular tissue banking plays an important part in the advancement of translational research for identifying the molecular processes involved in disease etiology and pathogenesis. Timely obtaining a good-quality ocular tissue from a cadaveric donor is exceedingly difficult, especially in remote areas, with a variable transportation time (within 12-24 h), raising concerns about RNA quality and its subsequent applications. Therefore, we assessed the utility of retinal tissues from cadaver donor and enucleated eyes based on the RNA quality and gene expression by real-time polymerase chain reaction (PCR).

SETTINGS AND DESIGN

Prospective study.

METHODS

Retina tissues were separated from the donor/enucleated eyes received in the eye bank within 24 h of death (n = 15) and within an hour from OR (n = 3), respectively, and stored immediately at -80 degree. RNA was isolated using trizol, and the quantity and quality were assessed using Qubit and agarose gel electrophoresis, respectively. QPCR was performed for measuring the expression of different retinal-specific genes. The cellular viability of the retina was assessed by establishing explant primary cell cultures.

STATISTICAL ANALYSIS

The data were calculated as an average of normalised Ct values ± standard error of the mean.

RESULTS

RNA obtained from cadaveric tissues despite being partially degraded showed a uniform strong gene expression of several retinal-specific genes such as PAX6, RHO, TUBB3, CRX , and ALDH1L1 . The primary cultures established from cadaveric tissues showed viable cells.

CONCLUSION

The cadaver donor tissues collected within 24 hours of death can be effectively utilized for gene expression profiling.

The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications

Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.

Arrestins: A Small Family of Multi-Functional Proteins

The first member of the arrestin family, visual arrestin-1, was discovered in the late 1970s. Later, the other three mammalian subtypes were identified and cloned. The first described function was regulation of G protein-coupled receptor (GPCR) signaling: arrestins bind active phosphorylated GPCRs, blocking their coupling to G proteins. It was later discovered that receptor-bound and free arrestins interact with numerous proteins, regulating GPCR trafficking and various signaling pathways, including those that determine cell fate. Arrestins have no enzymatic activity; they function by organizing multi-protein complexes and localizing their interaction partners to particular cellular compartments. Today we understand the molecular mechanism of arrestin interactions with GPCRs better than the mechanisms underlying other functions. However, even limited knowledge enabled the construction of signaling-biased arrestin mutants and extraction of biologically active monofunctional peptides from these multifunctional proteins. Manipulation of cellular signaling with arrestin-based tools has research and likely therapeutic potential: re-engineered proteins and their parts can produce effects that conventional small-molecule drugs cannot.

Enhancement-Mode Carbon Nanotube Optoelectronic Synaptic Transistors with Large and Controllable Threshold Voltage Modulation Window for Broadband Flexible Vision Systems

The development of large-scale integration of optoelectronic neuromorphic devices with ultralow power consumption and broadband responses is essential for high-performance bionics vision systems. In this work, we developed a strategy to construct large-scale (40 × 30) enhancement-mode carbon nanotube optoelectronic synaptic transistors with ultralow power consumption (33.9 aJ per pulse) and broadband responses (from 365 to 620 nm) using low-work function yttrium (Y)-gate electrodes and the mixture of eco-friendly photosensitive Ag2S quantum dots (QDs) and ionic liquids (ILs)-cross-linking-poly(4-vinylphenol) (PVP) (ILs-c-PVP) as the dielectric layers. Solution-processable carbon nanotube thin-film transistors (TFTs) showed enhancement-mode characteristics with the wide and controllable threshold voltage window (-1 V∼0 V) owing to use of the low-work-function Y-gate electrodes. It is noted that carbon nanotube optoelectronic synaptic transistors exhibited high on/off ratios (>106), small hysteresis and low operating voltage (≤2 V), and enhancement mode even under the illumination of ultraviolet (UV, 365 nm), blue (450 nm), and green (550 nm) to red (620 nm) pulse lights when introducing eco-friendly Ag2S QDs in dielectric layers, demonstrating that they have the strong fault-tolerant ability for the threshold voltage drifts caused by various manufacturing scenarios. Furthermore, some important bionic functions including a high paired pulse facilitation index (PPF index, up to 290%), learning and memory function with the long duration (200 s), and rapid recovery (2 s). Pavlov's dog experiment (retention time up to 20 min) and visual memory forgetting experiments (the duration of high current for 180 s) are also demonstrated. Significantly, the optoelectronic synaptic transistors can be used to simulate the adaptive process of vision in varying light conditions, and we demonstrated the dynamic transition of light adaptation to dark adaptation based on light-induced conditional behavior. This work undoubtedly provides valuable insights for the future development of artificial vision systems.

Non-canonical G protein signaling

The original paradigm of classical - also referred to as canonical - cellular signal transduction of heterotrimeric G proteins (G protein) is defined by a hierarchical, orthograde interaction of three players: the agonist-activated G protein-coupled receptor (GPCR), which activates the transducing G protein, that in turn regulates its intracellular effectors. This receptor-transducer-effector concept was extended by the identification of regulators and adapters such as the regulators of G protein signaling (RGS), receptor kinases like βARK, or GPCR-interacting arrestin adapters that are integrated into this canonical signaling process at different levels to enable fine-tuning. Finally, the identification of atypical signaling mechanisms of classical regulators, together with the discovery of novel modulators, added a new and fascinating dimension to the cellular G protein signal transduction. This heterogeneous group of accessory G protein modulators was coined "activators of G protein signaling" (AGS) proteins and plays distinct roles in canonical and non-canonical G protein signaling pathways. AGS proteins contribute to the control of essential cellular functions such as cell development and division, intracellular transport processes, secretion, autophagy or cell movements. As such, they are involved in numerous biological processes that are crucial for diseases, like diabetes mellitus, cancer, and stroke, which represent major health burdens. Although the identification of a large number of non-canonical G protein signaling pathways has broadened the spectrum of this cellular communication system, their underlying mechanisms, functions, and biological effects are poorly understood. In this review, we highlight and discuss atypical G protein-dependent signaling mechanisms with a focus on inhibitory G proteins (Gi) involved in canonical and non-canonical signal transduction, review recent developments and open questions, address the potential of new approaches for targeted pharmacological interventions.

Molecular Property, Manipulation, and Potential Use of Opn5 and Its Homologs

Animal opsin is a G-protein coupled receptor (GPCR) and binds retinal as a chromophore to form a photopigment. The Opsin 5 (Opn5) group within the animal opsin family comprises a diverse array of related proteins, such as Opn5m, a protein conserved across all vertebrate lineages including mammals, and other members like Opn5L1 and Opn5L2 found in non-mammalian vertebrate genomes, and Opn6 found in non-therian vertebrate genomes, along with Opn5 homologs present in invertebrates. Although these proteins collectively constitute a single clade within the molecular phylogenetic tree of animal opsins, they exhibit markedly distinct molecular characteristics in areas such as retinal binding properties, photoreaction, and G-protein coupling specificity. Based on their molecular features, they are believed to play a significant role in physiological functions. However, our understanding of their precise physiological functions and molecular characteristics is still developing and only partially realized. Furthermore, their unique molecular characteristics of Opn5-related proteins suggest a high potential for their use as optogenetic tools through more specialized manipulations. This review intends to encapsulate our current understanding of Opn5, discuss potential manipulations of its molecular attributes, and delve into its prospective utility in the burgeoning field of animal opsin optogenetics.

Computational drug development for membrane protein targets

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learning structure-based design and the evaluation of big data. Recent protein structure predictions based on machine learning tools have delivered surprisingly reliable results for water-soluble and membrane proteins but have limitations for development of drugs that target membrane proteins. Structural transitions of membrane proteins have a central role during transmembrane signaling and are often influenced by therapeutic compounds. Resolving the structural and functional basis of dynamic transmembrane signaling networks, especially within the native membrane or cellular environment, remains a central challenge for drug development. Tackling this challenge will require an interplay between experimental and computational tools, such as super-resolution optical microscopy for quantification of the molecular interactions of cellular signaling networks and their modulation by potential drugs, cryo-electron microscopy for determination of the structural transitions of proteins in native cell membranes and entire cells, and computational tools for data analysis and prediction of the structure and function of cellular signaling networks, as well as generation of promising drug candidates.

Osmotic stress studies of G-protein-coupled receptor rhodopsin activation

We summarize and critically review osmotic stress studies of the G-protein-coupled receptor rhodopsin. Although small amounts of structural water are present in these receptors, the effect of bulk water on their function remains uncertain. Studies of the influences of osmotic stress on the GPCR archetype rhodopsin have given insights into the functional role of water in receptor activation. Experimental work has discovered that osmolytes shift the metarhodopsin equilibrium after photoactivation, either to the active or inactive conformations according to their molar mass. At least 80 water molecules are found to enter rhodopsin in the transition to the photoreceptor active state. We infer that this movement of water is both necessary and sufficient for receptor activation. If the water influx is prevented, e.g., by large polymer osmolytes or by dehydration, then the receptor functional transition is back shifted. These findings imply a new paradigm in which rhodopsin becomes solvent swollen in the activation mechanism. Water thus acts as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.

Losing, preserving, and restoring vision from neurodegeneration in the eye

The retina is a part of the brain that sits at the back of the eye, looking out onto the world. The first neurons of the retina are the rod and cone photoreceptors, which convert changes in photon flux into electrical signals that are the basis of vision. Rods and cones are frequent targets of heritable neurodegenerative diseases that cause visual impairment, including blindness, in millions of people worldwide. This review summarizes the diverse genetic causes of inherited retinal degenerations (IRDs) and their convergence onto common pathogenic mechanisms of vision loss. Currently, there are few effective treatments for IRDs, but recent advances in disparate areas of biology and technology (e.g., genome editing, viral engineering, 3D organoids, optogenetics, semiconductor arrays) discussed here enable promising efforts to preserve and restore vision in IRD patients with implications for neurodegeneration in less approachable brain areas.

Similarities and Differences in Photochemistry of Type I and Type II Rhodopsins

The diversity of the retinal-containing proteins (rhodopsins) in nature is extremely large. Fundamental similarity of the structure and photochemical properties unites them into one family. However, there is still a debate about the origin of retinal-containing proteins: divergent or convergent evolution? In this review, based on the results of our own and literature data, a comparative analysis of the similarities and differences in the photoconversion of the rhodopsin of types I and II is carried out. The results of experimental studies of the forward and reverse photoreactions of the bacteriorhodopsin (type I) and visual rhodopsin (type II) rhodopsins in the femto- and picosecond time scale, photo-reversible reaction of the octopus rhodopsin (type II), photovoltaic reactions, as well as quantum chemical calculations of the forward photoreactions of bacteriorhodopsin and visual rhodopsin are presented. The issue of probable convergent evolution of type I and type II rhodopsins is discussed.

A comparative analysis of gene and protein expression in chronic and acute models of photoreceptor degeneration in adult zebrafish

Background: Adult zebrafish are capable of photoreceptor (PR) regeneration following acute phototoxic lesion (AL). We developed a chronic low light (CLL) exposure model that more accurately reflects chronic PR degeneration observed in many human retinal diseases. Methods: Here, we characterize the morphological and transcriptomic changes associated with acute and chronic models of PR degeneration at 8 time-points over a 28-day window using immunohistochemistry and 3'mRNA-seq. Results: We first observed a differential sensitivity of rod and cone PRs to CLL. Next, we found no evidence for Müller glia (MG) gliosis or regenerative cell-cycle re-entry in the CLL model, which is in contrast to the robust gliosis and proliferative response from resident MG in the AL model. Differential responses of microglia between the models was also observed. Transcriptomic comparisons between the models revealed gene-specific networks of PR regeneration and degeneration, including genes that are activated under conditions of chronic PR stress. Finally, we showed that CLL is at least partially reversible, allowing for rod and cone outer segment outgrowth and replacement of rod cell nuclei via an apparent upregulation of the existing rod neurogenesis mechanism. Discussion: Collectively, these data provide a direct comparison of the morphological and transcriptomic PR degeneration and regeneration models in zebrafish.

Molecular characterization of MAP9 in the photoreceptor sensory cilia as a modifier in canine RPGRIP1-associated cone-rod dystrophy

Photoreceptors possess a highly specialized primary cilium containing expanded ciliary membrane discs called the outer segment. The photoreceptor cilium is essential for the maintenance of the outer segment, and pathogenic variants in more than 50 cilia-related genes have been identified as causing non-syndromic inherited retinal diseases in patients. The retinitis pigmentosa GTPase regulator interacting protein 1 (RPGRIP1) is a structural protein localized to the photoreceptor cilium and biallelic RPGRIP1 variants have been associated with non-syndromic human inherited retinal diseases. In a canine cone-rod dystrophy model, a naturally occurring 44-bp exonic insertion in RPGRIP1 (RPGRIP1ins44/ins44) is the primary disease locus while an additional homozygous variant in MAP9 (microtubule associated protein 9) (MAP9aff/aff) acts as a modifier associated with early disease onset. MAP9 was originally identified as a microtubule-binding protein stabilizing microtubule structure during both mitosis and interphase in human cell lines. However, the roles of MAP9 in primary cilia, including photoreceptor neurosensory cilia, have not been well understood. Hence, we characterized the pathogenic phenotypes associated with homozygous MAP9 variant, and investigated the molecular function of MAP9 in primary cilia using the RPGRIP1-associated oligogenic canine cone-rod dystrophy model as well as cultured cells. Both functionally and structurally, the RPGRIP1ins44/ins44 MAP9aff/aff retina exhibited progressive cone photoreceptor degeneration starting earlier than the retina affected by RPGRIP1ins44/ins44 alone. Based on immunostaining of canine retinal sections and cultured cells, we found that MAP9 is prominently localized in the basal body of primary cilia and played an important role in maintaining the structure of ciliary microtubule axoneme. These findings suggest that the affected MAP9, together with mutant RPGRIP1, is deprived of critical roles in cilia organization and maintenance resulting in altered cilia structure and function giving rise to early onset and accelerated disease progression in the RPGRIP1ins44/ins44 MAP9aff/aff double homozygote cone-rod dystrophy canine model.

Ultrafast Transient Absorption Spectra and Kinetics of Rod and Cone Visual Pigments

Rods and cones are the photoreceptor cells containing the visual pigment proteins that initiate visual phototransduction following the absorption of a photon. Photon absorption induces the photochemical transformation of a visual pigment, which results in the sequential formation of distinct photo-intermediate species on the femtosecond to millisecond timescales, whereupon a visual electrical signal is generated and transmitted to the brain. Time-resolved spectroscopic studies of the rod and cone photo-intermediaries enable the detailed understanding of initial events in vision, namely the key differences that underlie the functionally distinct scotopic (rod) and photopic (cone) visual systems. In this paper, we review our recent ultrafast (picoseconds to milliseconds) transient absorption studies of rod and cone visual pigments with a detailed comparison of the transient molecular spectra and kinetics of their respective photo-intermediaries. Key results include the characterization of the porphyropsin (carp fish rhodopsin) and human green-cone opsin photobleaching sequences, which show significant spectral and kinetic differences when compared against that of bovine rhodopsin. These results altogether reveal a rather strong interplay between the visual pigment structure and its corresponding photobleaching sequence, and relevant outstanding questions that will be further investigated through a forthcoming study of the human blue-cone visual pigment are discussed.

Mammalian Fuel Cells Produce Electric Current

The increasing concern about climate change has led scientists around the world to develop clean energy technologies that may replace the traditional use of fossil fuels. A promising approach is the utilization of unicellular organisms as electron donors in bio-fuel cells. To date, this method has been limited to microorganisms such as bacteria, yeast, and microalgae. In this work, we show for the first time the concept of using mammalian cell cultures and organoids as electron donors in biofuel cells. We apply cyclic voltammetry to show that upon association of ARPE19 cells with the anode, they release reducing molecules to produce electricity. Furthermore, we apply 2D-fluorescence measurements and show that upon illumination, photosensitive stem cell-derived retinal organoids, which consist of rod photoreceptors and interneurons, secrete NADH and NADPH molecules that can donate electrons at the anode to produce photocurrent.

Smooth Things Come in Threes: A Diabatic Surrogate Model for Conical Intersection Optimization

The optimization of conical intersection structures is complicated by the nondifferentiability of the adiabatic potential energy surfaces. In this work, we build a pseudodiabatic surrogate model, based on Gaussian process regression, formed by three smooth and differentiable surfaces that can adequately reproduce the adiabatic surfaces. Using this model with the restricted variance optimization method results in a notable decrease of the overall computational effort required to obtain minimum energy crossing points.

Kinetics of cone specific G-protein signaling in avian photoreceptor cells

Cone photoreceptor cells of night-migratory songbirds seem to process the primary steps of two different senses, vision and magnetoreception. The molecular basis of phototransduction is a prototypical G protein-coupled receptor pathway starting with the photoexcitation of rhodopsin or cone opsin thereby activating a heterotrimeric G protein named transducin. This interaction is well understood in vertebrate rod cells, but parameter describing protein-protein interactions of cone specific proteins are rare and not available for migratory birds. European robin is a model organism for studying the orientation of birds in the earth magnetic field. Recent findings showed a link between the putative magnetoreceptor cryptochrome 4a and the cone specific G-protein of European robin. In the present work, we investigated the interaction of European robin cone specific G protein and cytoplasmic regions of long wavelength opsin. We identified the second loop in opsin connecting transmembrane regions three and four as a critical binding interface. Surface plasmon resonance studies using a synthetic peptide representing the second cytoplasmic loop and purified G protein α-subunit showed a high affinity interaction with a K _D value of 21 nM. Truncation of the G protein α-subunit at the C-terminus by six amino acids slightly decreased the affinity. Our results suggest that binding of the G protein to cryptochrome can compete with the interaction of G protein and non-photoexcited long wavelength opsin. Thus, the parallel presence of two different sensory pathways in bird cone photoreceptors is reasonable under dark-adapted conditions or during illumination with short wavelengths.

Bicarbonate boosts flash response amplitude to augment absolute sensitivity and extend dynamic range in murine retinal rods

Rod photoreceptors in the retina adjust their responsiveness and sensitivity so that they can continue to provide meaningful information over a wide range of light intensities. By stimulating membrane guanylate cyclases in the outer segment to synthesize cGMP at a faster rate in a Ca²⁺-dependent fashion, bicarbonate increases the circulating "dark" current and accelerates flash response kinetics in amphibian rods. Compared to amphibian rods, mammalian rods are smaller in size, operate at a higher temperature, and express visual cascade proteins with somewhat different biochemical properties. Here, we evaluated the role of bicarbonate in rods of cpfl3 mice. These mice are deficient in their expression of functional cone transducin, Gnat2, making cones very insensitive to light, so the rod response to light could be observed in isolation in electroretinogram recordings. Bicarbonate increased the dark current and absolute sensitivity and quickened flash response recovery in mouse rods to a greater extent than in amphibian rods. In addition, bicarbonate enabled mouse rods to respond over a range that extended to dimmer flashes. Larger flash responses may have resulted in part from a bicarbonate-induced elevation in intracellular pH. However, high pH alone had little effect on flash response recovery kinetics and even suppressed the accelerating effect of bicarbonate, consistent with a direct, modulatory action of bicarbonate on Ca²⁺- dependent, membrane guanylate cyclase activity.