Curated Optogenetic Publication Database

Abstract: Optogenetics which involves the use of light to control cell functions on a genetic level has found utility in studying cell physiology, biomaterials and metabolic engineering. S. cerevisiae is an industrially relevant model organism that is used in many applications, but due to the large number of genes required and issues relating to cross-activation between different colours, optogenetics for different wavelengths of light have not been multiplexed in S. cerevisiae. In this paper, we develop a compact red light responsive optogenetic system for S. cerevisiae that requires only a single gene and no exogenous cofactors. Through engineering modular protein domains, we reduce the cross-activation of our system by blue light. We integrate our red light optogenetic system with EL222 blue light optogenetics to establish dual channel optogenetics in S. cerevisiae and demonstrate its utility for engineering biology through the light-based control of flavonoid luteolin synthesis and flocculation for ease of product extraction. We also demonstrate our system's potential for the development of living materials by producing dual-coloured optogenetic patterns using S. cerevisiae. This work expands optogenetic applications in S. cerevisiae from single-light to multi-light systems, introducing the potential to multiplex different colours of light for dynamic, orthogonal control of separate cell processes.

Abstract: Bacterial motility is related to many cellular activities, such as cell migration, aggregation, and biofilm formations. The ability to control motility and direct the bacteria to certain location could be used to guide the bacteria in applications such as seeking for and killing pathogen, forming various population-level patterns, and delivering of drugs and vaccines. Currently, bacteria motility is mainly controlled by chemotaxis (prescribed chemical stimuli), which needs physical contact with the chemical inducer. This lacks the flexibility for pattern formation as it has limited spatial control. To overcome the limitations, we developed blue light-regulated synthetic genetic circuit to control bacterial directional motility, by taking the advantage that light stimulus can be delivered to cells in different patterns with precise spatial control. The circuit developed enables programmed Escherichia coli cells to increase directional motility and move away from the blue light, i.e., that negative phototaxis is utilized. This further allows the control of the cells to form aggregation with different patterns. Further, we showed that the circuit can be used to separate two different strains. The demonstrated ability of blue light-controllable gene circuits to regulate a CheZ expression could give researchers more means to control bacterial motility and pattern formation.

Abstract: To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. Here, we built two dual-input hybrid promoters, each retaining the function of the ligand-inducible promoter while being enhanced with a blue-light-switchable tuning knob. Using the new promoters, we show that both ligand and light inputs can be synchronously modulated to achieve desired amplitude or independently regulated to generate desired frequency at a specific amplitude. We exploit the versatile programmability and orthogonality of the two promoters to build the first reprogrammable logic gene circuit capable of reconfiguring into logic OR and N-IMPLY logic on the fly in both space and time without the need to modify the circuit. Overall, we demonstrate concentration- and time-based combinatorial regulation in live bacterial cells with potential applications in biotechnology and synthetic biology.