Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach

Abstract: Bacteria develop a number of devices for sens-ing, responding, and adapting to different environmental conditions. Understanding within a genomic perspective how the transcriptional machinery of bacteria is modulat-ed, as a response to changing conditions, is a major chal-lenge for biologists. Knowledge of which genes are turned on or turned off under specific conditions is essential for our understanding of cell behavior. In this study we de-scribe how the information pertaining to gene expression and associated growth conditions (even with very little knowledge of the associated regulatory mechanisms) is gathered from the literature and incorporated into Regulon-DB, a database on transcriptional regulation and operon organization in E. coli. The link between growth condi-tions, signal transduction, and transcriptional regulation is modeled in the database in a simple format that high-lights biological relevant information. As far as we know, there is no other database that explicitly clarifies the effect of environmental conditions on gene transcription. We dis-cuss how this knowledge constitutes a benchmark that will impact future research aimed at integration of regulatory responses in the cell; for instance, analysis of microarrays, predicting culture behavior in biotechnological processes, and comprehension of dynamics of regulatory networks. This integrated knowledge will contribute to the future goal of modeling the behavior of E. coli as an entire cell. The RegulonDB database can be accessed on the web at th