Optogenetic switches for light-controlled gene expression in yeast

Abstract

Light is increasingly recognized as an efficient means of controlling diverse biological processes with high spatiotemporal resolution. Optogenetic switches are molecular devices for regulating light-controlled gene expression, protein localization, signal transduction and protein-protein interactions. Such molecular components have been mainly developed through the use of photoreceptors, which upon light stimulation undergo conformational changes passing to an active state. The current repertoires of optogenetic switches include red, blue and UV-B light photoreceptors and have been implemented in a broad spectrum of biological platforms. In this review, we revisit different optogenetic switches that have been used in diverse biological platforms, with emphasis on those used for light-controlled gene expression in the budding yeast Saccharomyces cerevisiae. The implementation of these switches overcomes the use of traditional chemical inducers, allowing precise control of gene expression at lower costs, without leaving chemical traces, and positively impacting the production of high-value metabolites and heterologous proteins. Additionally, we highlight the potential of utilizing this technology beyond laboratory strains, by optimizing it for use in yeasts tamed for industrial processes. Finally, we discuss how fungal photoreceptors could serve as a source of biological parts for the development of novel optogenetic switches with improved characteristics. Although optogenetic tools have had a strong impact on basic research, their use in applied sciences is still undervalued. Therefore, the invitation for the future is to utilize this technology in biotechnological and industrial settings.

A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae

“…Optogenetics take advantage of light‐sensitive genetically encoded proteins to actuate processes inside of the cell in a light‐dependent manner. Light is a powerful actuator as it is inexpensive, easily controlled in time and space, and S. cerevisiae contains no known native photoreceptors (Salinas, Rojas, Delgado, Agosin, & Larrondo, ). The ability to rapidly add and remove light from cell culture or spatially target specific cells makes it particularly advantageous for applications that require spatiotemporal precision such as dynamic stimulation or real‐time feedback control of cellular processes (Benzinger & Khammash, ; Castillo‐Hair, Igoshin, & Tabor, ; Harrigan, Madani, & El‐Samad, ; Lugagne & Dunlop, ; Milias‐Argeitis, Rullan, Aoki, Buchmann, & Khammash, ; Ng et al, ; Rullan, Benzinger, Schmidt, Milias‐Argeitis, & Khammash, ; Toettcher, Gong, Lim, & Weiner, ).…”

Light-responsive monobodies for dynamic control of customizable protein binding

“…The performance of our light-dependent OptoMB/SH2 binding pair is comparable to that of other optical dimerization systems previously used to control transcription, protein-protein interactions, or protein localization 60–62 . However, these previous systems have been developed by fusing proteins of interest to specific light-dependent interaction partners (such as PhyB/PIF3 or Cry2/CIB) evolved in photosensitive organisms.…”

Physical model of protein cluster positioning in growing bacteria

“…Alternatively, bursting could be controlled directly with a time course of induced gene expression. For chemical inducers, this can be accomplished in a microfluidics setting via regulated flow [25], but recent developments also allow arbitrary time courses of induction in bulk cultures using optogenetics [26]. Regarding duration of the expression bursts, our expectation is that for a detectable effect this duration should be shorter than the timescale to nucleate new clusters.…”