Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent to sdiA

Here, we report the characterization of a set of small, regulatory RNAs (sRNAs) expressed from an Escherichia coli locus we have denoted sdsN located adjacent to the LuxR-homolog gene sdiA Two longer sRNAs, SdsN137 and SdsN178 are transcribed from two σ(S)-dependent promoters but share the same terminator. Low temperature, rich nitrogen sources and the Crl and NarP transcription factors differentially affect the levels of the SdsN transcripts. Whole genome expression analysis after pulse overexpression of SdsN137 and assays of lacZ fusions revealed that the SdsN137 directly represses the synthesis of the nitroreductase NfsA, which catalyzes the reduction of the nitrogroup (NO2) in nitroaromatic compounds and the flavohemoglobin HmpA, which has aerobic nitric oxide (NO) dioxygenase activity. Consistent with this regulation, SdsN137 confers resistance to nitrofurans. In addition, SdsN137 negatively regulates synthesis of NarP. Interestingly, SdsN178 is defective at regulating the above targets due to unusual binding to the Hfq protein, but cleavage leads to a shorter form, SdsN124, able to repress nfsA and hmpA.