How to train your microbe: methods for dynamically characterizing gene networks

•Gene regulation is highly dynamic, but most experimental perturbations are static.•Engineering approaches are being used to characterize gene network dynamics.•Recent optogenetic methods and instrumentation allow more advanced dynamical studies.•The role of transcription factor pulsing in sporulation and other pathways could be revealed.

Gene networks regulate biological processes dynamically. However, researchers have largely relied upon static perturbations, such as growth media variations and gene knockouts, to elucidate gene network structure and function. Thus, much of the regulation on the path from DNA to phenotype remains poorly understood. Recent studies have utilized improved genetic tools, hardware, and computational control strategies to generate precise temporal perturbations outside and inside of live cells. These experiments have, in turn, provided new insights into the organizing principles of biology. Here, we introduce the major classes of dynamical perturbations that can be used to study gene networks, and discuss technologies available for creating them in a wide range of microbial pathways.