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Single-cell characterization of bacterial optogenetic Cre recombinases

Hellen Huang,Fereshteh Jafarbeglou,M. Dunlop

Published 2025 in bioRxiv

ABSTRACT

Microbial optogenetic tools can regulate gene expression with high 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 systematically 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. Our results indicate that optogenetic recombinase performance can be reporter-dependent. Further, single-cell analysis revealed highly heterogeneous activity across cells. Although general trends match expectations for light-dependent recombination, we found substantial variation in the efficiency and timing of recombinase activity from cell to cell. These findings suggest critical criteria for selecting optogenetic recombinase systems and indicate areas for optimization to improve single-cell capabilities of bacterial optogenetic tools.

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