Fluorescent reporter genes and the analysis of bacterial regulatory networks
Abstract
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.