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: Early detection of pollutants in water discharge is an integral part of environmental monitoring. Electroactive biofilm (EAB)-enabled, microbial fuel cell (MFC)-based biosensors facilitate self-powered online pollutant detection. However, as EABs are highly dynamic, naturally formed EABs as sensing and transducing elements limit the performance of MFC-based biosensors. Here, we report a fast-response and sensitive MFC-based biosensor enabled by enhancing Shewanella oneidensis biofilms on the electrode using an optogenetic approach. We incorporated a near-infrared (NIR) light-responsive synthetic bis(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) module into S. oneidensis to promote biofilm formation on the anode under NIR light. The biosensors with enhanced EABs exhibited a rapid and sensitive response to Cr(VI), reducing the sensing time from approximately 30 min to just 3 min. This improved sensing performance was maintained over three sensing cycles, even with fluctuating Cr(VI) concentrations. Based on the analyses of the electrode biofilms and extracellular polymeric substance matrices, different Cr(VI) response mechanisms for the normal and enhanced EABs were proposed; enhanced EAB's massive dispersal by Cr(VI) was the cause of the improved response of the biosensors. Such improved response still held in the natural water matrix. This proof-of-concept study provides valuable insights into controlling electrode biofilm dynamics for the rapid and robust early detection of pollutants using MFC-based biosensors.

Abstract: Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported to new host strains. Here, we developed and adapted a red-light-inducible transcription factor for Shewanella oneidensis. This regulatory circuit is based on the iLight optogenetic system, which controls gene expression using red light. A thermodynamic model and promoter engineering were used to adapt this system to achieve differential gene expression in light and dark conditions within a S. oneidensis host strain. We further improved the iLight optogenetic system by adding a repressor to invert the genetic circuit and activate gene expression under red light illumination. The inverted iLight genetic circuit was used to control extracellular electron transfer within S. oneidensis. The ability to use both red- and blue-light-induced optogenetic circuits simultaneously was also demonstrated. Our work expands the synthetic biology capabilities in S. oneidensis, which could facilitate future advances in applications with electrogenic bacteria.

Abstract: Electroactive bacterial biofilms can function as living biomaterials that merge the functionality of living cells with electronic components. However, the development of such advanced living electronics has been challenged by the inability to control the geometry of electroactive biofilms relative to solid-state electrodes. Here, we developed a lithographic strategy to pattern conductive biofilms of Shewanella oneidensis by controlling aggregation protein CdrAB expression with a blue light-induced genetic circuit. This controlled deposition enabled S. oneidensis biofilm patterning on transparent electrode surfaces, and electrochemical measurements allowed us to both demonstrate tunable conduction dependent on pattern size and quantify the intrinsic conductivity of the living biofilms. The intrinsic biofilm conductivity measurements enabled us to experimentally confirm predictions based on simulations of a recently proposed collision-exchange electron transport mechanism. Overall, we developed a facile technique for controlling electroactive biofilm formation on electrodes, with implications for both studying and harnessing bioelectronics.