Identification of RpoS Regulated Genes and their Functions in Escherichia Coli

Abstract

E. coli expresses an alternative sigma factor, RpoS, in response to starvation and environmental stresses. RpoS is a global regulator and it controls numerous genes, which aids in counteracting these stresses. The RpoS regulon is large but is not completely characterized. We have previously identified over one hundred RpoS-dependent fusions in a genetic screen based on the differential expression of an operon-lacZ fusion bank in rpoS mutant and wild type backgrounds. Forty-eight independent gene fusions were identified including several in well-characterized RpoS-regulated genes such as osmY, katE and otsA. Many of the fusions mapped to genes of unknown function or to genes that were not previously known to be under RpoS control. Based on the homology to other known bacterial genes, some of the RpoS regulated genes with unknown functions may be important for nutrient scavenging. To gain a better insight into the functions of these poorly characterized genes, we tested the ability of the fusion mutants to utilize various carbon sources and to utilize individual amino acids as carbon and nitrogen sources. The results indicate that most of the strains in rpos-backgrounds exhibited better growth in succinate and fumarate and in several amino acids than did the corresponding strains in wild-type backgrounds.