Transcription of an antisense RNA of a gadE mRNA is regulated by GadE, the central activator of the acid resistance system in Escherichia coli

Abstract

6H57, a 69-nucleotide-long small RNA, was isolated in shotgun cloning using an RNA sample derived from early stationary-phase cells. The 6H57 gene is located in a 798-bp intergenic region between two acid resistance-related genes, hdeD and gadE, and is encoded on the strand opposite these flanking genes. In this study, we carried out stringent Northern blotting to determine target mRNAs of 6H57. A band approximately 1300 nucleotides in length was detected using a probe containing a partial sequence of 6H57 and was confirmed to be the gadE mRNA T3, which has a 566-nucleotide-long 5' untranslated region. These results show that 6H57 is an antisense RNA of gadE mRNA T3 and can base pair with a -380 to -312 region of the translation initiation site of gadE. We analyzed the transcription of 6H57 and showed that 6H57 transcription is dependent on GadE in the early stationary phase. Furthermore, 6H57 is induced in the exponential growth phase by an acid stimulus of pH 5.5. A 189-bp DNA fragment containing the upstream region of the 6H57 gene showed clear promoter activities in these culture conditions. These results suggest that 6H57 plays several roles in acid resistance, and we renamed it acid resistance-related small RNA.