Curated Optogenetic Publication Database

Abstract: Inflammatory bowel disease demands spatiotemporally precise drug delivery, yet the variable gut redox environment limits stimuli-responsive nanocarriers. Here we report a living biohybrid platform in which optogenetically engineered Shewanella oneidensis MR-1 is electrostatically conjugated with azo-bond covalent organic frameworks (TA-COFs) loaded with anti-inflammatory drugs magnolol or 4-iodobenzoic acid. Under intestinal conditions and non-invasive red-light irradiation (660 nm), light-induced restoration of the metal-reducing pathway promotes extracellular electron transfer, thereby cleaving azo bonds in the COF. This triggers rapid structural disassembly and a 2.8-fold increase in drug release. Although wild-type Shewanella is thermally inactivated at 37 °C and cannot utilize abundant colonic acetate, expression of heat-shock genes (groES/thiF) and an acetate-to-TCA pathway (ato1/ato2/gltA) confers 37 °C tolerance and robust metabolism in the gut. In DSS-induced colitis mice, oral administration of the biohybrid significantly alleviates inflammation, restores epithelial barrier integrity, rebalances gut microbiota (enrichment of Akkermansia, Muribaculaceae, and Lachnospiraceae). This work presents a generalizable strategy for constructing electroactive living composites by integrating microbial electron generation with stimuli-responsive nanomaterials, offering a new paradigm for light-programmed smart therapeutics and programmable living materials in biomedical applications.

Abstract: Evolving dynamic, multi-state, and computational protein functionalities is challenging because it requires selection pressure on all the states of a protein of interest (POI) and the transitions between them. To create a continuous directed evolution paradigm for such properties, we genetically engineered budding yeast for optogenetic input to switch a POI "on" and "off," which, in turn, controls a Cdk1 cyclin that is essential for one cell-cycle stage but detrimental for another. The method, "optovolution," generates dynamic selection pressure on POI cycling at the timescale of tens of minutes. We used it to evolve 19 new variants of the LOV transcription factor El222, including in vivo green-light-responsive variants allowing LOV color-multiplexing. Evolving the PhyB-Pif3 optogenetic system, we discovered that loss of YOR1 makes supplementing phycocyanobilin (PCB) unnecessary. Finally, we demonstrated the generality of the method by evolving a non-light-responsive AND gate (PEST-rtTA). Optovolution makes difficult-to-engineer protein functionalities continuously evolvable.

Abstract: As an interdisciplinary frontier integrating optical technologies and genetic principles, optogenetics enables precise spatiotemporal control of gene expression and neuronal activity via light-sensitive molecular assemblies, thereby driving transformative advancements in biomedical fields. Red/far-red light optogenetic tools, by virtue of the advantages of long wavelengths, have emerged as powerful platforms for deep-tissue manipulations for both basic researches and clinical applications. Although a number of in-depth studies on various red/far-red light optogenetic tools and their biomedical applications have been published, there has not yet been a comprehensive review that systematically summarizes the advancements of diverse researches on this type of optogenetics. This article systematically delineates the technology of red/far-red light optogenetics, focusing on the molecular mechanisms and biomedical applications of two core photoreceptor protein families: phytochromes and channelrhodopsins. Phytochromes distributed in plants, bacteria and fungi undergo reversible red/far-red light-driven conformational conversion, initiating downstream signaling cascades that support various optogenetic technologies. Channelrhodopsins, originally microalgal blue-light-gated cation channels, are engineered into red-shifted variants, enabling rapid and non-invasive red/far-red light-controlled neuronal excitability manipulation at precise spatiotemporal resolution. The representative case studies of applications of phytochromes-based optogenetic tools in gene editing, transcriptional regulation, light-gated drug delivery and deep tissue imaging and diagnosis; as well as applications of red-shifted channelrhodopsins-based optogenetic tools in spatiotemporally precise neuromodulation are discussed in detail. Moreover, the main technical challenges in the utilization of red/far-red light optogenetic tools are analyzed. With continuous advancements of wavelength-optimized actuators and closed-loop control architectures, red/far-red light optogenetic techniques are poised to drive multidisciplinary convergence, offering unprecedented tools for decoding cellular dynamics and accelerating therapeutic discoveries.

Abstract: Microbial optogenetic tools can regulate gene expression with spatial and temporal precision, offering excellent potential for single-cell resolution studies. However, bacterial optogenetic systems have primarily been deployed for population-level experiments. It is not always clear how these tools perform in single cells, where stochastic effects can be substantial. In this study, we focus on optogenetic Cre recombinase and compare the performance of three variants (OptoCre-REDMAP, OptoCre-Vvd, and PA-Cre) for their population-level and single-cell activity. We quantify recombination efficiency, expression variability, and activation dynamics using reporters which produce changes in fluorescence or antibiotic resistance following light-induced Cre activity. We find that optogenetic recombinase performance can be reporter-dependent. Further, single-cell analysis reveals highly heterogeneous activity, with substantial variation in the efficiency and timing of recombinase activity from cell to cell. These findings suggest important criteria for selecting optogenetic recombinases and indicate areas for optimization to improve single-cell capabilities of bacterial optogenetic tools.

Abstract: Bis(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) plays a crucial role in bacterial signaling pathways, allowing bacterial cells to respond to various environmental stimuli. The prevalence of c-di-GMP and its potential applications underscore the necessity for developing tools and methods to regulate intracellular c-di-GMP levels. Optogenetic control of c-di-GMP dynamics is particularly attractive because it enables tunable and spatiotemporal regulation of c-di-GMP metabolism. The development of sensitive optogenetic control systems requires highly active, light-responsive c-di-GMP synthases. Here, we report an engineered, highly active photosensitive c-di-GMP synthase, BphS-13. This engineered c-di-GMP synthase was developed from a near-infrared (NIR) light-activable bacteriophytochrome c-di-GMP synthase, BphS, using a three-step directed evolution process that included error-prone PCR, in vitro homologous recombination, and site-directed mutagenesis. After two rounds of this directed evolution strategy, we generated a BphS variant with 13 mutations, referred to as BphS-13. The diguanylate cyclase (DGC) activity of BphS-13 was approximately 13 times higher than that of the original BphS, and it exhibited tightly regulated DGC activity in response to NIR light with minimal leakage in the dark. We then demonstrated the effectiveness of BphS-13 in controlling biofilm dynamics. Overall, this study highlights BphS-13 as a highly active and photosensitive tool for optogenetic applications in biotechnology and suggests its future potential application in mammalian systems for precise control of gene expression, particularly given the lack of native c-di-GMP signaling pathways in mammalian cells.

Abstract: Despite its central role in signaling, the influence of protein architecture on phytochrome structure and reactivity remains poorly understood. Here, we test how removal of the PHY domain reshapes the far-red-absorbing Pfr energy landscape and photochemical branching in the knotless phytochrome All2699g1g2.

Abstract: The light-mediated, specific, and precise control of cell functions enabled by optogenetics has become a versatile method for investigating and combatting cancer. An increasing set of optogenetic tools enables tightly controlled regulation of ion flux across biological membranes, gene expression, gene editing, and protein-protein interactions and is being used to interrogate hallmark traits of cancer at the cellular, subcellular, and organismic level. This enables, on the one hand, the identification of critical signaling circuits required for cancer development and progression in vitro and in animal models and can flag potential intervention points for pharmacologic interference. On the other hand, optogenetics can improve the level of control in cell-based therapeutics. The current article provides a review of optogenetic tools and approaches used in the cancer research field and their multiple applications for improving our understanding of signal transduction pathways, modulating immune functions in the tumor microenvironment, facilitating drug screening, or directly attacking cancer cells. Key advantages and achievements of optogenetics in the cancer research field and remaining barriers for clinical applications are discussed.

Abstract: Despite the therapeutic potential of engineered immune cell therapy against metastases, it faces challenges including cytokine-driven systemic toxicity, off-target biodistribution, and host rejection. Here, we develop red/far-red light-regulated individually encapsulated (RL/FRL-EnE) cells, integrating optogenetics with biomaterial encapsulation for precise immunomodulation. This system uses a phytochrome A-based photoswitch (ΔPhyA-PCB) that enables bidirectional control. RL (660 nanometers) triggers interferon-γ, interleukin-6, and anti-CD47 expression via ΔPhyA-PCB-far-red elongated hypocotyl 1 heterodimerization, while FRL (740 nanometers) rapidly reverses production, minimizing toxicity. Single-cell nanoencapsulation prevents intercellular cross-talk and immune clearance, enabling strict light-dependent regulation and extended tumor residence. In vivo, RL/FRL-EnE cells remodeled the tumor microenvironment, reducing immunosuppressive myeloid cells (1.3- to 1.7-fold), while enhancing dendritic cell (1.4-fold) and CD8+ T cell (2.8-fold) infiltration. Collectively, this work establishes a paradigm for closed-loop cellular immunotherapy, where light-regulated living therapeutics achieve on-demand immune reprogramming.

Abstract: Precise regulation of protein abundance is essential for understanding dynamic cellular processes and for advancing therapeutic development. However, existing approaches lack the spatiotemporal resolution required to these cellular processes. Recent advances in optogenetics have enabled the design of optogenetic targeted protein degradation systems (Opto-TPD) allowing reversible and non-invasive control of protein stability with high spatiotemporal precision. In this review, we systematically summarize the design principles of Opto-TPD tools, including those based on light-oxygen-voltage (LOV)-domain conformational systems, light-inducible dimerization systems, and light-controlled degradation tool expression systems. We further highlight their applications in probing protein function, modulating signaling pathways, and therapeutic translations. By comparing the mechanistic features, performance, and limitations of each platform, we aim to provide a comprehensive resource for guiding future tool optimization. Altogether, these Opto-TPD tools represent a powerful and versatile complement to existing protein manipulation technologies, expanding the toolbox for precise control of protein homeostasis in living systems.

Abstract: Cellular receptors serve as central hubs that translate external signals into intracellular programs governing cell fate, function and behavior. Achieving precise and reversible control over receptor activity has long been a major challenge in both fundamental biology and translational medicine. Optogenetic receptor engineering provides a transformative solution by integrating photosensitive domains into natural receptor frameworks. This strategy enables light-dependent modulation of signaling with high spatial and temporal precision while maintaining minimal disturbance to endogenous pathways. Unlike chemogenetic systems or classical photoreceptive ion channels, this approach preserves endogenous ligand specificity and avoids slow ligand diffusion/clearance-associated artifacts. Through such systems, researchers can dissect causal relationships in dynamic signaling events, finely manipulate neuromodulatory and immune circuits and program cellular activities involved in development and tissue regeneration. The approach also allows quantitative control of signaling intensity and duration, offering new opportunities for linking molecular design to physiological outcomes. By combining optogenetic principles with advances in materials science and bioelectronics, future designs may achieve improved optical fidelity, enhanced light penetration and better signal amplification within complex biological environments. Integration with AI-guided protein engineering may also accelerate the discovery of optimized photosensory-receptor pairings. Together, these developments point to an emerging field where light-responsive receptors function as programmable interfaces between photonic control and cellular computation. In summary, the engineering of optogenetic receptors establishes a conceptual and technological framework for reversible, accurate and tunable regulation of cellular communication. This review summarizes current progress, outlines key design principles and provides conceptual guidelines for advancing next-generation light-responsive receptors and their biomedical applications. However, key translational challenges-including immunogenicity of non-human photoreceptors, limited gene-delivery efficiency and long-term biosafety-remain to be addressed through nonviral delivery strategies, autologous cell engineering and de-immunized or humanized photoreceptor design.

Abstract: Microtubules are crucial regulators of plant development and are organized by a suite of microtubule-associated proteins (MAPs) that can rapidly remodel the array in response to various cues. This complexity has inspired countless studies into microtubule function from the subcellular to tissue scale, revealing an ever-increasing number of microtubule-dependent processes. Developing a comprehensive understanding of how local microtubule configuration, dynamicity, and remodeling drive developmental progression requires new approaches to capture and alter microtubule behavior. In this review, we will introduce the technological advancements we believe are poised to transform the study of microtubules in plant cells. In particular, we focus on (1) advanced imaging and analysis methods to quantify microtubule organization and behavior, and (2) novel tools to target specific microtubule populations in vivo. By showcasing innovative methodologies developed in non-plant systems, we hope to motivate their increased adoption and raise awareness of possible means of adapting them for studying microtubules in plants.

Abstract: Cellular signaling cascades rely on transfer of information from one protein to another or within a single protein. To facilitate signal integration, specific structural motifs evolved that allow signal processing and also enable modular downstream response integration, facilitating sophisticated regulatory mechanisms. On a structural level, especially coiled-coil helices are frequently observed as signaling motifs. In diguanylate cyclases (DGCs) featuring GGDEF domains, N-terminal coiled-coils frequently activate systems by rearrangements of the interdimer active site. The variety of sensory domains that modulate this structural equilibrium in response to different stimuli highlights the importance of DGCs in bacterial adaptation. One interesting example of sensor DGCs is blue light-activated light-oxygen-voltage (LOV)-GGDEF couples. Here, we describe molecular details of a two-stage mechanism that allows tight dark-state inhibition while enabling high enzymatic activities upon illumination, achieving fold changes exceeding 10,000-fold. Using an in vivo activity assay, we screened amino acid substitutions at the inhibitory interface and the sensor-effector linker region to identify variants that promote enzymatic activity in the dark. In combination with chimeras of LOV and GGDEF domains preventing inhibitory interface formation, we successfully stabilized elongated active-state conformations and confirmed the role of the inhibitory interface between sensor and effector in the tight dark-state inhibition. Interestingly, the initially generated chimeras are still light regulatable as long as the linker sequence is not stabilized in either inhibiting or stimulating coiled-coil register. Our results offer valuable insights for potential optogenetic applications but also demonstrate inherent challenges associated with Methylotenera sp. LOV-activated DGCs.

Abstract: The modification of key enzymes for chemical production plays a crucial role in enhancing the yield of targeted products. However, manipulating key nodes in specific signalling pathways remains constrained by traditional gene overexpression or knockout strategies. Discovering and designing optogenetic tools enable us to regulate enzymatic activity or gene expression at key nodes in a spatiotemporal manner, rather than relying solely on chemical induction throughout production processes. In this review, we discuss the recent applications of optogenetic tools in the regulation of microbial metabolites, plant sciences and disease therapies. We categorize optogenetic tools into five classes based on their distinct applications. First, light-induced gene expression schedules can balance the trade-off between chemical production and cell growth phases. Second, light-triggered liquid-liquid phase separation (LLPS) modules provide opportunities to co-localize and condense key enzymes for enhancing catalytic efficiency. Third, light-induced subcellular localized photoreceptors enable the relocation of protein of interest across various subcellular compartments, allowing for the investigation of their dynamic regulatory processes. Fourth, light-regulated enzymes can dynamically regulate production of cyclic nucleotides or investigate endogenous components similar with conditional depletion or recovery function of protein of interest. Fifth, light-gated ion channels and pumps can be utilized to investigate dynamic ion signalling cascades in both animals and plants, or to boost ATP accumulation for enhancing biomass or bioproduct yields in microorganisms. Overall, this review aims to provide a comprehensive overview of optogenetic strategies that have the potential to advance both basic research and bioindustry within the field of synthetic biology.

Abstract: Intracellular optogenetics represents a rapidly advancing biotechnology that enables precise, reversible control of protein activity, signaling dynamics, and cellular behaviours using genetically encoded, light-responsive systems. Originally pioneered in neuroscience through channelrhodopsins to manipulate neuronal excitability, the field has since expanded into diverse intracellular applications with broad implications for medicine, agriculture, and biomanufacturing. Key to these advances are photoreceptors such as cryptochrome 2 (CRY2), light-oxygen-voltage (LOV) domains, and phytochromes, which undergo conformational changes upon illumination to trigger conditional protein-protein interactions, localization shifts, or phase transitions. Recent engineering breakthroughs-including the creation of red-light responsive systems such as MagRed that exploit endogenous biliverdin-have enhanced tissue penetration, minimized phototoxicity, and expanded applicability to complex biological systems. This review provides an overarching synthesis of the molecular principles underlying intracellular optogenetic actuators, including the photophysical basis of light-induced conformational changes, oligomerization, and signaling control. We highlight strategies that employ domain fusions, rational mutagenesis, and synthetic circuits to extend their utility across biological and industrial contexts. We also critically assess current limitations, such as chromophore dependence, light delivery challenges, and safety considerations, so as to frame realistic paths towards translation. Looking ahead, future opportunities include multi-colour and multiplexed systems, integration with high-throughput omics and artificial intelligence, and development of non-invasive modalities suited for in vivo and industrial applications. Intracellular optogenetics is thus emerging as a versatile platform technology, with the potential to reshape how we interrogate biology and engineer cells for therapeutic, agricultural, and environmental solutions.

Abstract: The SpyTag/SpyCatcher system is a modular protein assembly tool. Its core mechanism is the formation of isopeptide bonds, which achieves protein assembly through covalent coupling. This system is characterized by mild reaction conditions, rapid connection and no need for additional reagents, and shows good application potential in fields such as enzyme engineering. Although the system has made progress in application, it still faces challenges such as industrial scale and clinical immunogenicity. This paper systematically reviews the principle of the SpyTag/SpyCatcher system and its development progress. It also analyzes the deficiencies of the system in industrial applications, focuses on elaborating its specific application examples in enzyme engineering, discusses existing challenges, and looks forward to future research directions. Overall, this review aims to provide references and new ideas for research in related fields.

Abstract: T-cell activation is a highly regulated process requiring both antigen recognition via the T-cell receptor (TCR) and co-stimulatory signaling, notably through the co-stimulatory receptor CD28. Here, we introduce an optogenetic platform for reversible and tunable full activation of human T cells that does not require genetic modification. We engineered opto-CD28-REACT, a recombinant protein comprising an anti-CD28 single-chain variable fragment, GFP, and phytochrome-interacting factor 6 (PIF6). This construct binds CD28 and thereby attaches PIF6 to CD28. Upon red light (630 nm) illumination, PIF6 binds to PhyB tetramer-coated beads, triggering CD28 signaling that can be attenuated by far-red light (780 nm) in 2 min. We show that opto-CD28-REACT synergizes with opto-CD3ϵ-REACT-a complementary optogenetic tool targeting the TCR complex-to induce light-dependent activation of both Jurkat cells and primary human T cells. Co-stimulation through both opto-REACT systems promotes ERK phosphorylation, upregulation of the activation markers CD69 and CD25, interleukin-2 (IL-2) secretion, and T-cell proliferation, reaching levels similar to conventional antibody-mediated stimulation. This strategy enables precise optical control over TCR and CD28 signaling in non-genetically modified T cells, offering a powerful approach for dissecting the regulatory dynamics of T-cell activation and advancing applications in synthetic immunology.

Abstract: Cellular immunotherapy has transformed cancer treatment by harnessing T cells to target malignant cells. However, its broader adoption is hindered by challenges such as efficacy loss, limited persistence, tumor heterogeneity, an immunosuppressive tumor microenvironment (TME), and safety concerns related to systemic adverse effects. Optogenetics, a technology that uses light-sensitive proteins to regulate cellular functions with high spatial and temporal accuracy, offers a potential solution to overcome these issues. By enabling targeted modulation of T cell receptor signaling, ion channels, transcriptional programming, and antigen recognition, optogenetics provides dynamic control over T cell activation, cytokine production, and cytotoxic responses. Moreover, optogenetic strategies can be applied to remodel the TME by selectively activating immune responses or inducing targeted immune cell depletion, thereby enhancing T cell infiltration and immune surveillance. However, practical hurdles such as limited tissue penetration of visible light and the need for cell- or tissue-specific gene delivery must be addressed for clinical translation. Emerging solutions, including upconversion nanoparticles, are being explored to improve light delivery to deeper tissues. Future integration of optogenetics with existing immunotherapies, such as checkpoint blockade and adoptive T cell therapies, could improve treatment specificity, minimize adverse effects, and provide real-time control over immune responses. By refining the precision and adaptability of immunotherapy, optogenetics promises to further enhance both the safety and efficacy of cancer immunotherapy.

Abstract: Over the past two decades, optogenetics has evolved from a conceptual framework into a powerful and versatile technology for controlling cellular processes with light. Rooted in the discovery and characterization of natural photoreceptors, the field has advanced through the development of genetically encoded, light-sensitive proteins that enable precise spatiotemporal control of ion flux, intracellular signaling, gene expression, and protein interactions. This review traces key milestones in the emergence of optogenetics and highlights the development of major optogenetic tools. From the perspective of genetic tool innovation, the focus is on how these tools have been engineered and optimized for novel or enhanced functions, altered spectral properties, improved light sensitivity, subcellular targeting, and beyond. Their broadening applications are also explored across neuroscience, cardiovascular biology, hematology, plant sciences, and other emerging fields. In addition, current trends such as all-optical approaches, multiplexed control, and clinical translation, particularly in vision restoration are discussed. Finally, ongoing challenges are addressed and outline future directions in optogenetic tool development and in vivo applications, positioning optogenetics as a transformative platform for basic research and therapeutic advancement.

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.

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.

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.

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.

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.

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.

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.