Photoreceptor and optogenetics research

Random Mutagenesis for the Generation of Repertoire of Aureochrome-based Optogenetic Scaffolds

This study uses random mutagenesis to generate diverse aureochrome variants with altered photocycle kinetics and DNA-binding affinity, identifying key residues and creating a repertoire for optogenetic applications.

Screening channelrhodopsins using robotic intracellularelectrophysiology and single cell sequencing

The paper introduces a method combining robotic electrophysiology and single-cell sequencing to link opsin sequences to their functional properties, demonstrating its efficiency over manual methods.

Bridging Evolution and Design: Mapping the Diversity of LOV Photosensors

The paper maps the photodynamic diversity of LOV domains, revealing kinetic diversity and functional classes, and demonstrates computational design of new LOV photosensors.

Functional insights into the photoactive yellow protein family from homologs, multidomain proteins and inferred pyp operons

The paper identifies 984 PYP homologs and uses bioinformatics to find candidate proteins involved in PYP signal transduction, including histidine kinase and GGDEF/EAL proteins.

Chemical mechanism of allosteric and asymmetric dark reversion in a bacterial phytochrome uncovered by cryo-EM.

This paper uses cryo-EM to study dark reversion in PaBphP, revealing asymmetric reversion between protomers and structural mechanisms controlling the reaction.

Light-harvesting by antenna-containing xanthorhodopsin from an Antarctic cyanobacterium

The paper identifies widespread xanthorhodopsin genes in cyanobacteria and characterizes a unique variant from an Antarctic cyanobacterium that binds hydroxylated lutein, enhancing light-harvesting efficiency in extreme environments.

Topological adaptation of heliorhodopsins enables exogenous second-antenna acquisition in monoderm phototrophs

The paper identifies a conserved carotenoid-binding site in heliorhodopsins, revealing their role in light harvesting through exogenous xanthophyll recruitment due to inverted membrane topology.

Opsins are Phospholipid Scramblases in All Domains of Life

The paper shows bacterial opsins function as phospholipid scramblases, independent of retinal, and highlights shared functions across domains of life.

Spectral tuning and signaling of diverse and most red sensitive animal opsins in Mantis Shrimp eyes

The paper identifies and characterizes far-red-sensitive opsins in mantis shrimp eyes, revealing their spectral tuning mechanisms and photoreversibility.

Novel algal modular LOV domain proteins expand opto-biotechnological avenues for controlling of eukaryotic riboswitching, translational and proteolytic processes.

The paper identifies 13 novel algal LOV domain proteins with potential applications in opto-biotechnology for controlling translational, ribogenetic, and proteolytic processes.

Single-component optogenetic control enables human portrait formation in cells

The paper develops a single-component optogenetic system using DmCRY to control gene expression and generate human portrait images from cultured cells.

Stabilized ion selectivity corrects activation drift in kalium channelrhodopsins

The paper identifies a KCR1 variant, C29D, that maintains stable potassium selectivity and provides reliable optogenetic inhibition across species and conditions.

Cryo-EM Structures of Methanogenic Schizorhodopsins Reveal Divergent Strategies for Proton Transport and Thermal Adaptation

The paper reports cryo-EM structures of two methanogenic Schizorhodopsins, revealing distinct proton transport mechanisms and structural adaptations for thermal stability.

Apusomonad rhodopsins, a new family of ultraviolet to blue light absorbing rhodopsin channels

The paper identifies a new family of rhodopsin channels in apusomonads that absorb ultraviolet to blue light and function as anion-selective channels involved in photoavoidance.

Discovery of Light-Powered Organic Ion Transport by a Natural Protein

This study shows that microbial rhodopsins can transport organic anions, expanding their known substrate range and suggesting new optogenetic applications.

Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics

The paper identifies blue-shifted channelrhodopsins from ancyromonads that enable multiplex optogenetics by conducting chloride or cation currents with improved spectral properties.

Structural basis for color tuning and passive ion conductance in red-shifted pump-fold channelrhodopsin ChR024

This study presents cryo-EM structures of ChR024, revealing its color-tuning mechanism and transition from a proton pump to a light-gated channel.

Functional characterization of red-shifted rhodopsin channels from giant viruses explored by a machine-learning model for long-wavelength optogenetics

The paper uses a machine-learning model to predict red-shifted channelrhodopsin variants, identifying ChR024 with a maximum absorption wavelength of ~578 nm for optogenetics.

WAChRs are excitatory opsins sensitive to indoor lighting

The paper identifies WAChR, an excitatory opsin variant with high sensitivity to indoor light, through high-throughput electrophysiological screening of over 1,750 opsins.

Ectopic expression of two cone opsins in mouse RGCs results in opposite responses to light stimulation, likely due to differential G protein activation

This study shows that expressing short-wavelength cone opsin in RGCs causes hyperpolarization, opposite to mid-wavelength opsin's depolarization, due to different G-protein activation.

Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating

The paper shows carotenoids enhance rhodopsin light utilization by accelerating photocycles and light-harvesting in marine bacteria.

A key spectral tuning site of UV-sensitive vertebrate non-visual opsin Opn5

This study identifies Lys91 as the key residue determining UV sensitivity in vertebrate Opn5, showing its role in spectral tuning and retinal isomer binding.

Efficient incorporation of dendrites into a large-scale cortical model reveals their surprising role in sharpening optogenetic responses

The paper uses simulations to show dendrites sharpen optogenetic responses in cortex, improving spatial fidelity of stimulation.

An essential experimental control for functional connectivity mapping with optogenetics

The paper identifies leaky Chrimson expression as a source of false-positive signals in optogenetic functional connectivity experiments and proposes a control to mitigate this issue.

Computational analysis of optogenetic inhibition of CA1 neurons using a data-efficient and interpretable potassium and chloride conducting opsin model

This study develops a data-efficient and interpretable model of optogenetic inhibition using potassium and chloride opsins to analyze how parameters and physiological conditions affect seizure suppression in CA1 neurons.

Computational optimization of two-photon holographic stimulation sites in vivo

This paper introduces a computational method to reduce off-target stimulation in two-photon holographic optogenetics by optimizing stimulation sites using adaptive non-negative basis function regression.

Structural basis for no retinal binding in flotillin-associated rhodopsins

The paper presents cryo-EM structures of FArhodopsin and proteorhodopsin, showing no retinal binding despite conserved lysine and similar fold to retinal-binding rhodopsins, with mutations identified that prevent retinal binding.

Advanced deep-tissue imaging and manipulation enabled by biliverdin reductase knockout.

This paper develops NIR imaging and optogenetic tools using Blvra-/- knockout to enhance light-controlled transcription and in vivo glucose regulation.

Traits of Bathy Phytochromes and Application to Bacterial Optogenetics

The paper identifies traits of bathy phytochromes and develops a far-red light-activated optogenetic system called pFREDusk.

All-Optical Mapping Reveals Distributed Suppression of Cortical Sensory Responses After Optogenetic Silencing

The paper develops an all-optical system to inhibit cortical neurons and monitor responses, showing widespread suppression of sensory responses after optogenetic silencing.