Curated Optogenetic Publication Database

Search precisely and efficiently by using the advantage of the hand-assigned publication tags that allow you to search for papers involving a specific trait, e.g. a particular optogenetic switch or a host organism.

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Showing 51 - 75 of 1884 results
51.

Optogenetic actin network assembly on lipid bilayer uncovers the network density-dependent functions of actin-binding proteins.

blue iLID in vitro MDCK Control of cytoskeleton / cell motility / cell shape
Nat Commun, 26 Aug 2025 DOI: 10.1038/s41467-025-62653-6 Link to full text
Abstract: The actin cytoskeleton forms a meshwork that drives cellular deformation. Network properties, determined by density and actin-binding proteins, are crucial, yet how density governs protein penetration and dynamics remains unclear. Here, we report an in vitro optogenetic system, named OptoVCA, enabling Arp2/3 complex-mediated actin assembly on lipid membranes. By tuning illumination power, duration, and pattern, OptoVCA flexibly manipulates the density, thickness, and shape of the actin network. Taking these advantages, we examine how network density affects two actin-binding proteins: myosin and ADF/cofilin. We find that even modest increases in density strictly inhibit myosin filament penetration by steric hindrance. Penetrated myosin filaments generate directional actin flow in networks with density gradients. In contrast, ADF/cofilin accesses networks regardless of density, yet network disassembly is markedly reduced by increased density. Thus, OptoVCA reveals that network density differentially regulates actin-binding protein penetration and activity. These findings advance understanding of cell mechanics through precise, light-based manipulation of cytoskeletal structure.
52.

Investigating morphogen and patterning dynamics with optogenetic control of morphogen production.

blue VVD mESCs Endogenous gene expression Developmental processes
Dev Cell, 22 Aug 2025 DOI: 10.1016/j.devcel.2025.07.019 Link to full text
Abstract: Morphogen gradients provide the patterning cues that instruct cell fate decisions during development. Here, we establish an optogenetic system for the precise spatiotemporal control in vitro of Sonic hedgehog (Shh) morphogen production. Using a tunable light-inducible gene expression system, we generate long-range Shh gradients that pattern mouse neural progenitors into spatially distinct domains, mimicking neural tube development. We investigate how biochemical features of Shh and Shh-interacting proteins affect patterning length scales. By measuring clearance rates, we determine that Shh has an extracellular half-life below 1.5 h, substantially shorter than downstream gene expression dynamics, indicating gradients are continually renewed during patterning. We provide evidence that progenitor identity acquisition and maintenance depend on both Shh concentration and exposure duration. Together, this approach provides a quantitative framework for investigating morphogen patterning, enabling reproducible control of morphogen dynamics to dissect the interplay between biochemical cues, gradient formation biophysics, and transcriptional programs underlying developmental patterning.
53.

Endogenous OptoRhoGEFs reveal biophysical principles of epithelial tissue furrowing.

blue CRY2/CIB1 iLID D. melanogaster in vivo Signaling cascade control Developmental processes
Nat Commun, 18 Aug 2025 DOI: 10.1038/s41467-025-62483-6 Link to full text
Abstract: During development, epithelia function as malleable sheets that undergo extensive remodeling to shape developing embryos. Optogenetic control of Rho signaling provides an avenue to investigate mechanisms of epithelial morphogenesis, but transgenic optogenetic tools can be limited by variability in expression levels and deleterious effects of transgenic overexpression on development. Here, we use CRISPR/Cas9 to tag Drosophila RhoGEF2 and Cysts/Dp114RhoGEF with components of the iLID/SspB optogenetic heterodimer, permitting light-dependent control over endogenous protein activities. Using quantitative optogenetic perturbations, we uncover a dose-dependence of tissue furrow depth and bending behavior on RhoGEF recruitment, revealing mechanisms by which developing embryos can shape tissues into particular morphologies. We show that at the onset of gastrulation, furrows formed by cell lateral contraction are oriented and size-constrained by basal actomyosin. Our findings demonstrate the use of quantitative, 3D-patterned perturbations of cell contractility to precisely shape tissue structures and interrogate developmental mechanics.
54.

Multimodal Key Anti-Oncolytic Therapeutics Are Effective In Cancer Treatment?

blue cyan near-infrared red Cryptochromes Fluorescent proteins LOV domains Phytochromes Review
Int J Nanomedicine, 16 Aug 2025 DOI: 10.2147/ijn.s531849 Link to full text
Abstract: Oncolytic virus (OVs) therapy has emerged as a promising modality in cancer immunotherapy, attracting growing attention for its multifaceted mechanisms of tumor elimination. However, its efficacy as a monotherapy remains constrained by physiological barriers, limited delivery routes, and suboptimal immune activation. Phototherapy, an innovative and rapidly advancing cancer treatment technology, can mitigate these limitations when used in conjunction with OVs, enhancing viral delivery, amplifying tumor destruction, and boosting antitumor immune responses. This review provides the first comprehensive analysis of synergistic integration of OVs with both photodynamic therapy (PDT) and photothermal therapy (PTT). It also explores their applications in optical imaging-guided diagnosis and optogenetically controlled delivery. Furthermore, it discusses emerging strategies involving biomimetic virus or viroid-based vectors in conjunction with phototherapy, and delves into the immunomodulatory mechanisms of this combinatorial approach. While promising in preclinical models, these combined strategies are still largely in early-stage research. Challenges such as limited light penetration, delivery efficiency, and safety concerns remain to be addressed for clinical translation. Consequently, the integration of OV therapy and phototherapy represents a compelling strategy in cancer treatment, offering significant promise for advancing precision oncology and next-generation immunotherapies.
55.

OptoBarrier: An Optogenetic Platform for Modulating Endothelial Barriers In Vitro.

blue CRY2/CRY2 HUVEC Signaling cascade control Control of cell-cell / cell-material interactions
ACS Biomater Sci Eng, 14 Aug 2025 DOI: 10.1021/acsbiomaterials.5c00708 Link to full text
Abstract: Organ-on-a-chip platforms have emerged as promising human tissue models for drug screening and mechanistic studies, offering alternatives to traditional animal models. Integration of vascular structures into these platforms is pivotal for creating physiologically faithful models of individual organs and studying interorgan crosstalk. However, most vascular structures grown in vitro do not account for organ-specific endothelial permeability or its modulation in response to disease. Here, we present optoBarrier, an optogenetic organ-on-a-chip platform designed to modulate endothelial barrier permeability through light stimulation. By optically activating RhoA signaling in engineered optogenetic endothelial cells, we demonstrate the formation of stress fibers, disruption of vascular endothelial cadherin (VE-cadherin) and increased barrier permeability. We further show that permeability is tunable in a reversible and dose-dependent manner in response to light. We therefore propose that optoBarrier offers a user-defined, controlled and simple method to manipulate endothelial permeability for in vitro studies of human vasculature.
56.

A rapid and efficient red-light-activated Cre recombinase system for genome engineering in mammalian cells and transgenic mice.

red PhyA/FHY1 BHK-21 Hana3A HEK293T HeLa hMSCs mouse in vivo Neuro-2a Nucleic acid editing
Nucleic Acids Res, 11 Aug 2025 DOI: 10.1093/nar/gkaf758 Link to full text
Abstract: The Cre-loxP recombination system enables precise genome engineering; however, existing photoactivatable Cre tools suffer from several limitations, including low DNA recombination efficiency, background activation, slow activation kinetics, and poor tissue penetration. Here, we present REDMAPCre, a red-light-controlled split-Cre system based on the ΔPhyA/FHY1 interaction. REDMAPCre enables rapid activation (1-s illumination) and achieves an 85-fold increase in reporter expression over background levels. We demonstrate its efficient regulation of DNA recombination in mammalian cells and mice, as well as its compatibility with other inducible recombinase systems for Boolean logic-gated DNA recombination. Using a single-vector adeno-associated virus delivery system, we successfully induced REDMAPCre-mediated DNA recombination in mice. Furthermore, we generated a REDMAPCre transgenic mouse line and validated its efficient, light-dependent recombination across multiple organs. To explore its functional applications, REDMAPCre transgenic mice were crossed with isogenic Cre-dependent reporter mice, enabling optogenetic induction of insulin resistance and hepatic lipid accumulation via Cre-dependent overexpression of ubiquitin-like with PHD and RING finger domains 1 (UHRF1), as well as targeted cell ablation through diphtheria toxin fragment A expression. Collectively, REDMAPCre provides a powerful tool for achieving remote control of recombination and facilitating functional genetic studies in living systems.
57.

Decoding NF-κB: nucleocytoplasmic shuttling dynamics, synthetic modulation and post-therapeutic behavior in cancer.

blue Cryptochromes LOV domains Review
Mol Biol Rep, 7 Aug 2025 DOI: 10.1007/s11033-025-10917-1 Link to full text
Abstract: Nuclear factor kappa B (NF-κB) has been extensively investigated for approximately four decades. Throughout this timeframe, significant progress has been accomplished in determining the structure, function, and regulation of NF-κB; however, some nuanced complexities of this fundamental signaling pathway remain underexplored. A notable gap exists in the spatiotemporal regulation and molecular dynamics of NF-κB nucleocytoplasmic shuttling, which significantly impacts the complex function and behavior, yet lacks comprehensive characterization. The nucleocytoplasmic shuttling process is also related to resistance mechanisms that evolved following the application of NF-κB or proteasomal inhibitors. Furthermore, the NF-κB complex has a stochastic variability in its trafficking that contributes to heterogeneous cellular responses at the single-cell level and lacks a well-defined druggable pocket, making its complete suppression in cancer cells challenging and uncertain. Engineering synthetic gene circuits and utilizing optogenetic tools can pave the way for precise control of the NF-κB complex, enabling advanced investigations into NF-κB regulation and post-therapeutic behavior implicated in cancer resistance. This approach also permits tumor microenvironment (TME)-immune modulation by synthetic gene circuits that reactivate immune cells within the TME. In this review, we discussed the structure and function of NF-κB, the molecular dynamics of NF-κB nucleocytoplasmic shuttling based on established findings, NF-κB engineering via synthetic biology tools, and critically deciphered the post-therapeutic behavior of NF-κB in cancer, supported by potential therapeutic targets to abrogate resistance.
58.

Optogenetic enzymes: A deep dive into design and impact.

blue cyan near-infrared red BLUF domains Cryptochromes Fluorescent proteins LOV domains Phytochromes Review
Curr Opin Struct Biol, 5 Aug 2025 DOI: 10.1016/j.sbi.2025.103126 Link to full text
Abstract: Optogenetically regulated enzymes offer unprecedented spatiotemporal control over protein activity, intermolecular interactions, and intracellular signaling. Many design strategies have been developed for their fabrication based on the principles of intrinsic allostery, oligomerization or 'split' status, intracellular compartmentalization, and steric hindrance. In addition to employing photosensory domains as part of the traditional optogenetic toolset, the specificity of effector domains has also been leveraged for endogenous applications. Here, we discuss the dynamics of light activation while providing a bird's eye view of the crafting approaches, targets, and impact of optogenetic enzymes in orchestrating cellular functions, as well as the bottlenecks and an outlook into the future.
59.

Activation of NF-κB Signaling by Optogenetic Clustering of IKKα and β.

blue CRY2/CRY2 CRY2olig HEK293T Signaling cascade control Endogenous gene expression Organelle manipulation
Adv Biol (Weinh), 29 Jul 2025 DOI: 10.1002/adbi.202400384 Link to full text
Abstract: Molecular optogenetics allows the control of molecular signaling pathways in response to light. This enables the analysis of the kinetics of signal activation and propagation in a spatially and temporally resolved manner. A key strategy for such control is the light-inducible clustering of signaling molecules, which leads to their activation and subsequent downstream signaling. In this work, an optogenetic approach is developed for inducing graded clustering of different proteins that are fused to eGFP, a widely used protein tag. To this aim, an eGFP-specific nanobody is fused to Cryptochrome 2 variants engineered for different orders of cluster formation. This is exemplified by clustering eGFP-IKKα and eGFP-IKKβ, thereby achieving potent and reversible activation of NF-κB signaling. It is demonstrated that this approach can activate downstream signaling via the endogenous NF-κB pathway and is thereby capable of activating both an NF-κB-responsive reporter construct as well as endogenous NF-κB-responsive target genes as analyzed by RNA sequencing. The generic design of this system is likely transferable to other signaling pathways to analyze the kinetics of signal activation and propagation.
60.

Chemogenetic and optogenetic strategies for spatiotemporal control of split-enzyme-based calcium recording.

blue AsLOV2 CRY2/CIB1 HEK293 HEK293T Signaling cascade control
bioRxiv, 26 Jul 2025 DOI: 10.1101/2025.07.22.665990 Link to full text
Abstract: Methods for monitoring physiological changes in cellular Ca2+ levels have been in high demand for their utility in monitoring neuronal signaling. Recently, we introduced SCANR (Split-Tobacco Etch Virus (TEV) protease Calcium-regulated Neuron Recorder), which reports on Ca2+ changes in cells through the binding of calmodulin and M13 to reconstitute an active TEV protease. First-generation SCANR marked all of the Ca2+ spikes that occur throughout the lifetime of the cell, but it did not have a mechanism for controlling the time window in which recording of physiological changes in Ca2+ occurred. Here, we explore both chemical and light-based strategies for controlling the time and place in which Ca2+ recording occurs. We describe the adaptation of six popular chemo- and opto-genetics methods for controlling protein activity and subcellular localization to the SCANR system. We report two successful strategies, one that leverages the LOV-Jα optogenetics system for sterically controlling protein interactions and another that employs chemogenetic manipulation of subcellular protein distribution using the FKBP/FRB rapamycin binding pair.
61.

Using LEXY and LINuS Optogenetics Tools and Automated Image Analysis to Quantify Nucleocytoplasmic Transport Dynamics in Live Cells.

blue AsLOV2 NIH/3T3
J Vis Exp, 22 Jul 2025 DOI: 10.3791/68585 Link to full text
Abstract: Nucleocytoplasmic transport (NCT) is essential for maintaining cellular homeostasis, and its disruption is involved in various diseases, including neurodegenerative disorders and amyotrophic lateral sclerosis. This underscores the need to develop tools to monitor and quantify NCT. Amongst these tools, the fast and reversible optogenetics probes, LEXY (light-inducible nuclear export system) and LINuS (light-inducible nuclear localization signal), allow the measurement of NCT dynamics in live cells. The original publications describe manual segmentation and quantification of the fluorescent probe signal in the nucleus and cytosol upon transfection of LEXY and LINuS constructs in live-cell imaging. However, both transfection and manual segmentation limit the number of cells that can be analyzed and are subject to imprecision due to potential user-dependent errors. While the high speed and reversibility provided by optogenetics should, in principle, allow for high sensitivity in detecting changes in NCT dynamics, it depends on the acquisition parameters and analysis of a sufficient number of cells. We have therefore established lentiviral vectors expressing LEXY and LINuS to create stable cell lines, tested live imaging markers and control conditions, and implemented a semi-automated image analysis pipeline that allows for the analysis of hundreds of cells. This analysis method uses the open-access software FIJI, is accessible to beginners in bioinformatics, and does not require advanced computer setups. Here we provide a step-by-step protocol to set up LEXY as an example of these optogenetic tools to monitor nuclear export, from preparation of the samples to live-cell imaging acquisition and automated analysis, while demonstrating how to adapt the protocol for other conditions, controls, or models in any lab. All plasmids and cell lines used in this protocol will be made available to the scientific community, therefore further increasing the accessibility of the method.
62.

Ras-mediated dynamic and biphasic regulation of cell migration.

blue iLID D. discoideum Signaling cascade control Control of cytoskeleton / cell motility / cell shape
Proc Natl Acad Sci U S A, 22 Jul 2025 DOI: 10.1073/pnas.2503847122 Link to full text
Abstract: Ras has traditionally been regarded as a positive regulator and therapeutic target due to its role in cell proliferation, but recent findings indicate a more nuanced role in cell migration, where suppressed Ras activity can unexpectedly promote migration. To clarify this complexity, we systematically modulate Ras activity using various RasGEF and RasGAP proteins and assess their effects on migration dynamics. Leveraging optogenetics, we assess the immediate, nontranscriptional effects of Ras signaling on migration. Local RasGEF recruitment to the plasma membrane induces protrusions and new fronts to effectively guide migration, even in the absence of GPCR/G-protein signaling, whereas global recruitment causes immediate cell spreading halting cell migration. Local RasGAP recruitment suppresses protrusions, generates new backs, and repels cells, whereas global relocation either eliminates all protrusions to inhibit migration or preserves a single protrusion to maintain polarity. Consistent local and global increases or decreases in signal transduction and cytoskeletal activities accompany these morphological changes. Additionally, we performed cortical tension measurements and found that Ras activity is regulated by guanine nucleotide exchange factors generally increase cortical tension while Ras activity is regulated by GTPase-activating proteins decrease it. Our results reveal a biphasic relationship between Ras activity and cellular dynamics, reinforcing our previous findings that optimal Ras activity and cortical tension are critical for efficient migration.
63.

Optogenetic Clustering of Human IRE1 Reveals Differential Regulation of Transcription and mRNA Splice Isoform Abundance by the UPR.

blue CRY2clust U-2 OS Flp-In T-REx Signaling cascade control
bioRxiv, 21 Jul 2025 DOI: 10.1101/2025.07.16.665212 Link to full text
Abstract: Inositol-requiring enzyme 1 (IRE1) is one of three known sensor proteins that respond to homeostatic perturbations in the metazoan endoplasmic reticulum. The three sensors collectively initiate an intertwined signaling network called the Unfolded Protein Response (UPR). Although IRE1 plays pivotal roles in human health and development, understanding its specific contributions to the UPR remains a challenge due to signaling crosstalk from the other two stress sensors. To overcome this problem, we engineered a light-activatable version of IRE1 and probed the transcriptomic effects of IRE1 activity in isolation from the other branches of the UPR. We demonstrate that 1) oligomerization alone is sufficient to activate IRE1 in human cells, 2) IRE1's transcriptional response evolves substantially under prolonged activation, and 3) the UPR induces major changes in mRNA splice isoform abundance in an IRE1-independent manner. Our data reveal previously unknown targets of IRE1 transcriptional regulation and direct degradation. Additionally, the tools developed here will be broadly applicable for precise dissection of signaling networks in diverse cell types, tissues, and organisms.
64.

A versatile anti-CRISPR platform for opto- and chemogenetic control of CRISPR-Cas9 and Cas12 across a wide range of orthologs.

blue AsLOV2 HCT116 HEK293T HeLa Nucleic acid editing
Nucleic Acids Res, 19 Jul 2025 DOI: 10.1093/nar/gkaf752 Link to full text
Abstract: CRISPR-Cas technologies have revolutionized life sciences by enabling programmable genome editing across diverse organisms. Achieving dynamic and precise control over CRISPR-Cas activity with exogenous triggers, such as light or chemical ligands, remains an important need. Existing tools for CRISPR-Cas control are often limited to specific Cas orthologs or selected applications, restricting their versatility. Anti-CRISPR (Acr) proteins are natural inhibitors of CRISPR-Cas systems and provide a flexible regulatory layer but are constitutively active in their native forms. In this study, we built on our previously reported concept for optogenetic CRISPR-Cas control with engineered, light-switchable anti-CRISPR proteins and expanded it from ortholog-specific Acrs towards AcrIIA5 and AcrVA1, broad-spectrum inhibitors of CRISPR-Cas9 and CRISPR-Cas12a, respectively. We then conceived and implemented a novel, chemogenetic anti-CRISPR platform based on engineered, circularly permuted ligand receptor domains, that together respond to six clinically relevant drugs. The resulting toolbox achieves both optogenetic and chemogenetic control of genome editing in human cells with a wide range of CRISPR-Cas effectors, including type II-A and II-C CRISPR-Cas9s, and CRISPR-Cas12a. In sum, this work establishes a versatile platform for the multidimensional control of CRISPR-Cas systems, with immediate applications in basic research and biotechnology, and with the potential for therapeutic use in the future.
65.

Opto-CRISPR: new prospects for gene editing and regulation.

blue cyan green red Cryptochromes Fluorescent proteins LOV domains Phytochromes Review
Trends Biotechnol, 17 Jul 2025 DOI: 10.1016/j.tibtech.2025.06.018 Link to full text
Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) technology represents a landmark advance in the field of gene editing. However, conventional CRISPR/Cas systems are limited by inadequate temporal and spatial control. In recent years, the development of optically controlled CRISPR (Opto-CRISPR) technology has offered a novel solution to this issue. As a combination of optogenetics and the CRISPR technology, the Opto-CRISPR technology enables dynamic space-time-specific gene editing and regulation in cells and organisms. In this review, we concisely introduce the basic principles of Opto-CRISPR, summarize its operational mechanisms, and discuss its applications and recent advances across various research fields. In addition, this review analyzes the limitations of Opto-CRISPR, aiming to provide a reference for the development of this emerging field.
66.

De novo designed protein guiding targeted protein degradation.

blue EL222 Magnets E. coli Transgene expression
Nat Commun, 17 Jul 2025 DOI: 10.1038/s41467-025-62050-z Link to full text
Abstract: Targeted protein degradation is a powerful tool for biological research, cell therapy, and synthetic biology. However, conventional methods often depend on pre-fused degrons or chemical degraders, limiting their wider applications. Here we develop a guided protein labeling and degradation system (GPlad) in Escherichia coli, using de novo designed guide proteins and arginine kinase (McsB) for precise degradation of various proteins, including fluorescent proteins, metabolic enzymes, and human proteins. We expand GPlad into versatile tools such as antiGPlad, OptoGPlad, and GPTAC, enabling reversible inhibition, optogenetic regulation, and biological chimerization. The combination of GPlad and antiGPlad allows for programmable circuit construction, including ON/OFF switches, signal amplifiers, and oscillators. OptoGPlad-mediated degradation of MutH accelerates E. coli evolution under protocatechuic acid stress, reducing the required generations from 220 to 100. GPTAC-mediated degradation of AroE enhanced the titer of 3-dehydroshikimic acid to 92.6 g/L, a 23.8% improvement over the conventional CRISPR interference method. We provide a tunable, plug-and-play strategy for straightforward protein degradation without the need for pre-fusion, with substantial implications for synthetic biology and metabolic engineering.
67.

Advances in optogenetically engineered bacteria in disease diagnosis and therapy.

blue green red UV violet BLUF domains Cryptochromes LOV domains Phytochromes UV receptors Review
Biotechnol Adv, 15 Jul 2025 DOI: 10.1016/j.biotechadv.2025.108645 Link to full text
Abstract: Optogenetic bacterial technology is a cutting-edge approach that combines optogenetics and microbiology, offering a transformative strategy for disease diagnosis and therapy. This synergistic merger transcends the limitations of traditional diagnostic and therapeutic methodologies in a highly controllable, accurate and non-invasive manner. In this review, we introduce the optogenetic systems developed for microbial engineering and summarize fundamental in vitro design principles underlying light-responsive signal transduction in bacteria, as well as the optogenetic regulation of bacterial behaviors. We address multidisciplinary solutions to the challenges in the in vivo applications of light-controlled bacteria, such as limited light excitation, suboptimal delivery and targeting, and difficulties in signal tracking and management. Furthermore, we comprehensively highlight the recent progress in photo-responsive bacteria for disease diagnosis and therapy, and discuss how to accelerate translational applications.
68.

Deep-tissue high-sensitivity multimodal imaging and optogenetic manipulation enabled by biliverdin reductase knockout.

red DrBphP iLight HeLa mouse in vivo primary mouse cortical neurons primary mouse endothelial cells primary mouse fibroblasts Transgene expression
Nat Commun, 14 Jul 2025 DOI: 10.1038/s41467-025-61532-4 Link to full text
Abstract: Performance of near-infrared probes and optogenetic tools derived from bacterial phytochromes is limited by availability of their biliverdin chromophore. To address this, we use a biliverdin reductase-A knock-out mouse model (Blvra-/-), which elevates endogenous biliverdin levels. We show that Blvra⁻/⁻ significantly enhances function of bacterial phytochrome-based systems. Light-controlled transcription using iLight optogenetic tool improves ~25-fold in Blvra-/- cells, compared to wild-type controls, and achieves ~100-fold activation in neurons. Light-induced insulin production in Blvra-/- mice reduces blood glucose by ~60% in diabetes model. To overcome depth limitations in imaging, we employ 3D photoacoustic, ultrasound, and two-photon fluorescence microscopy. This enables simultaneous photoacoustic imaging of DrBphP in neurons and super-resolution ultrasound localization microscopy of brain vasculature at depths of ~7 mm through intact scalp and skull. Two-photon microscopy achieves cellular resolution of miRFP720-expressing neurons at ~2.2 mm depth. Overall, Blvra-/- model represents powerful platform for improving efficacy of biliverdin-dependent tools for deep-tissue imaging and optogenetic manipulation.
69.

Optogenetics-enabled discovery of integrated stress response modulators.

blue CRY2olig H4 Signaling cascade control Cell death
Cell, 11 Jul 2025 DOI: 10.1016/j.cell.2025.06.024 Link to full text
Abstract: The integrated stress response (ISR) is a conserved stress response that maintains homeostasis in eukaryotic cells. Modulating the ISR holds therapeutic potential for diseases including viral infection, cancer, and neurodegeneration, but few known compounds can do so without toxicity. Here, we present an optogenetic platform for the discovery of compounds that selectively modulate the ISR. Optogenetic clustering of PKR induces ISR-mediated cell death, enabling the high-throughput screening of 370,830 compounds. We identify compounds that potentiate cell death without cytotoxicity across diverse cell types and stressors. Mechanistic studies reveal that these compounds upregulate activating transcription factor 4 (ATF4), sensitizing cells to stress and apoptosis, and identify GCN2 as a molecular target. Additionally, these compounds exhibit antiviral activity, and one compound reduced viral titers in a mouse model of herpesvirus infection. Structure-activity and toxicology studies highlight opportunities to optimize therapeutic efficacy. This work demonstrates an optogenetic approach to drug discovery and introduces ISR potentiators with therapeutic potential.
70.

Traits of Bathy Phytochromes and Application to Bacterial Optogenetics.

red Phytochromes Background
ACS Synth Biol, 11 Jul 2025 DOI: 10.1021/acssynbio.5c00337 Link to full text
Abstract: Phytochromes are photoreceptors sensitive to red and far-red light, found in a wide variety of organisms, including plants, fungi, and bacteria. Bacteriophytochromes (BphPs) can be switched between a red light-sensitive Pr state and a far-red light-sensitive Pfr state by illumination. In so-called prototypical BphPs, the Pr state functions as the thermally favored resting state, whereas Pfr is more stable in bathy BphPs. The prototypical DrBphP from Deinococcus radiodurans has been shown to be compatible with different output module types. Even though red light-regulated optogenetic tools are available, like the pREDusk system based on the DrBphP photosensory module, far-red light-modulated variants are still rare. Here, we study the underlying contributors to bathy over prototypical BphP behavior by way of various chimeric constructs between pREDusk and representative bathy BphPs. We pinpoint shared traits of the otherwise heterogeneous subgroup of bathy BphPs and highlight the importance of the sensor-effector linker in light modulation of histidine kinase activity. Informed by these data, we introduce the far-red light-activated system "pFREDusk", based on a histidine kinase activity governed by a bathy photosensory module. With this tool, we expand the optogenetic toolbox into wavelengths of increased sample and tissue penetration.
71.

Capturing α-synuclein aggregation interactors using UltraID-LIPA.

blue Cryptochromes Review
Trends Neurosci, 10 Jul 2025 DOI: 10.1016/j.tins.2025.07.002 Link to full text
Abstract: Teixeira et al. present UltraID-light-inducible protein aggregation (UltraID-LIPA), a technique that combines optogenetic induction of α-synuclein aggregation with proximity-based proteomics. This system enables high-resolution capture of early aggregation events in live cells and implicates known and novel endolysosomal proteins, offering a robust framework for dissecting early pathogenic mechanisms in synucleinopathies and guiding future innovations.
72.

Optogenetic and chemical genetic tools for rapid repositioning of vimentin intermediate filaments.

blue iLID U-2 OS Control of cytoskeleton / cell motility / cell shape
J Cell Biol, 8 Jul 2025 DOI: 10.1083/jcb.202504004 Link to full text
Abstract: Intermediate filaments (IFs) are a key component of the cytoskeleton, essential for regulating cell mechanics, maintaining nuclear integrity, organelle positioning, and modulating cell signaling. Current insights into IF function primarily come from studies using long-term perturbations, such as protein depletion or mutation. Here, we present tools that allow rapid manipulation of vimentin IFs in the whole cytoplasm or within specific subcellular regions by inducibly coupling them to microtubule motors, either pharmacologically or using light. Rapid perinuclear clustering of vimentin had no major immediate effects on the actin or microtubule organization, cell spreading, or focal adhesion number, but it reduced cell stiffness. Mitochondria and endoplasmic reticulum (ER) sheets were reorganized due to vimentin clustering, whereas lysosomes were only briefly displaced and rapidly regained their normal distribution. Keratin moved along with vimentin in some cell lines but remained intact in others. Our tools help to study the immediate and local effects of vimentin perturbation and identify direct links of vimentin to other cellular structures.
73.

Dynamin-like Proteins Combine Mechano-constriction and Membrane Remodeling to Enable Two-Step Mitochondrial Fission via a "Snap-through" Instability.

blue iLID Cos-7 Organelle manipulation
J Am Chem Soc, 8 Jul 2025 DOI: 10.1021/jacs.5c06352 Link to full text
Abstract: Mitochondrial fission is controlled by dynamin-like proteins, the dysregulation of which is correlated with diverse diseases. Fission dynamin-like proteins are GTP hydrolysis-driven mechanoenzymes that self-oligomerize into helical structures that constrict membranes to achieve fission while also remodeling membranes by inducing negative Gaussian curvature, which is essential for the completion of fission. Despite advances in optical and electron imaging technologies, the underlying mechanics of mitochondrial fission remain unclear due to the multiple times involved in the dynamics of mechanoenzyme activity, oligomer disassembly, and membrane remodeling. Here, we examine how multiscale phenomena in dynamin Drp1 synergistically influence membrane fission using a mechanical model calibrated with small-angle X-ray scattering structural data and informed by a machine learning analysis of the Drp1 sequence, and tested the concept using optogenetic mechanostimulation of mitochondria in live cells. We find that free dynamin-like proteins can trigger a "snap-through instability" that enforces a shape transition from an oligomer-confined cylindrical membrane to a drastically narrower catenoid-shaped neck within the spontaneous hemi-fission regime, in a manner that depends critically on the length of the confined tube. These results indicate how the combination of assembly and paradoxically disassembly of dynamin-like proteins can lead to diverse pathways to scission.
74.

Shaping viral immunotherapy towards cancer-targeted immunological cell death.

blue red Cryptochromes LOV domains Phytochromes Review
Front Oncol, 8 Jul 2025 DOI: 10.3389/fonc.2025.1540397 Link to full text
Abstract: Oncolytic viruses (OVs) have the ability to efficiently enter, replicate within, and destroy cancer cells. This capacity to selectively target cancer cells while inducing long-term anti-tumor immune responses, makes OVs a promising tool for next-generation cancer therapy. Immunogenic cell death (ICD) induced by OVs initiates the cancer-immunity cycle (CIC) and plays a critical role in activating and reshaping anti-cancer immunity. Genetic engineering, including arming OVs with cancer cell-specific binders and immunostimulatory molecules, further enhances immune responses at various stages of the CIC, improving the specificity and safety of virotherapy.The aim of this study is to update current knowledge in immunotherapy using OVs and to highlight the remarkable plasticity of viruses in shaping the tumor immune microenvironment, which may facilitate anti-cancer treatment through various approaches.
75.

Optogenetic storage and release of protein and mRNA in live cells and animals.

blue LOVTRAP PixD/PixE HeLa mouse in vivo NIH/3T3 rat hippocampal neurons Signaling cascade control Organelle manipulation
Nat Commun, 7 Jul 2025 DOI: 10.1038/s41467-025-61322-y Link to full text
Abstract: Cells compartmentalize biomolecules in membraneless structures called biomolecular condensates. While their roles in regulating cellular processes are increasingly understood, tools for their synthetic manipulation remain limited. Here, we introduce RELISR (Reversible Light-Induced Store and Release), an optogenetic condensate system that enables reversible storage and release of proteins or mRNAs. RELISR integrates multivalent scaffolds, optogenetic switches, and cargo-binding domains to trap cargo in the dark and release it upon blue-light exposure. We demonstrate its utility in primary neurons and show that light-triggered release of signaling proteins can modulate fibroblast morphology. Furthermore, light-induced release of cargo mRNA results in protein translation both in vitro and in live mice. RELISR thus provides a versatile platform for spatiotemporal control of protein activity and mRNA translation in complex biological systems, with broad potential for research and therapeutic applications.
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