σ E Regulates and Is Regulated by a Small RNA in Escherichia coli

RybB is a small, Hfq-binding noncoding RNA originally identified in a screen of conserved intergenic regions inEscherichia coli . Fusions of therybB promoter tolacZ were used to screen plasmid genomic libraries and genomic transposon mutants for regulators ofrybB expression. A number of plasmids, including some carryingrybB , negatively regulated the fusion. An insertion in therep helicase and one upstream ofdnaK decreased expression of the fusion. Multicopy suppressors of these insertions led to identification of two plasmids that stimulated the fusion. One contained the gene for the response regulator OmpR; the second containedmipA , encoding a murein hydrolase. The involvement of MipA and OmpR in cell surface synthesis suggested that therybB promoter might be dependent on σE . The sequence upstream of the +1 ofrybB contains a consensus σE promoter. The activity ofrybB -lacZ was increased in cells lacking the RseA anti-sigma factor and when σE was overproduced from a heterologous promoter. The activity ofrybB -lacZ and the detection of RybB were totally abolished in anrpoE -null strain. In vitro, σE efficiently transcribes from this promoter. Both arybB mutation and anhfq mutation significantly increased expression of bothrybB -lacZ andrpoE -lacZ fusions, consistent with negative regulation of the σE response by RybB and other small RNAs. Based on the plasmid screens, NsrR, a repressor sensitive to nitric oxide, was also found to negatively regulate σE -dependent promoters in an RseA-independent fashion.