Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks

The understanding of the regulatory networks controlling the adaptation of bacteria to changes in their environment is critically dependent on the ability to monitor the dynamics of gene expression. Here, we review the use of fluorescent reporter genes for dynamically quantifying promoter activity and other quantities characterizing gene expression. We discuss critical physical and biological parameters in the design, development, and use of fluorescent reporter strains. Moreover, we review measurement models that have been proposed to interpret primary fluorescence data and inference methods for estimating gene expression profiles from these data. As an illustration of the use of fluorescent reporter strains for analyzing bacterial regulatory networks, we consider two applications in the model bacterium Escherichia coli in some detail: the joint control of gene expression by global physiological effects and specific regulatory interactions, and the importance of protein stability for the inference and analysis of transcriptional regulatory networks. We conclude by discussing some current trends in the use of fluorescent reporter genes.