Function and biogenesis of the SdsR-RyeA sRNA pair, a novel type of toxin-antitoxin in Escherichia coli

Abstract

Most noncoding small RNAs (sRNAs) are known to base pair with target mRNAs and regulate mRNA stability or translation to trigger various changes in the cell metabolism. Among them, RyeA and SdsR is a sRNA pair sharing same intergenic region (IGR) in the opposite strand with reciprocal expressions. The SdsR sRNA is emerged during the stationary phase and represses multiple target mRNAs. However, it was not known whether the growth-phase-dependent regulation of SdsR is important for cell growth. Here, it was found that ectopically expressed SdsR during the exponential phase led to a significant and Hfq-dependent cell death with accompanying cell filamentation. It was alleviated by overexpression of RyeA, suggesting that SdsR/RyeA is a novel type of toxin-antitoxin (T/A) system where both the toxin and the antitoxin are sRNAs. Through the RNA-seq and the seed region analysis for the SdsR-driven cell death, the SdsR-driven cell death was found to be mainly caused by the SdsR-mediated repression of yhcB encoding an inner membrane protein. Next, following the 3’-end of sdsR, pphA, encoding Ser/Thr phosphatase, exists of which the promoter appears upstream of sdsR. It is not known how RyeA and SdsR synthesis are regulated each other in phase and how this regulation affect pphA expression. To study this, the primary transcripts and the mutual regulation of RyeA and SdsR were examined. Also, RNA-seq with ryeA and sdsR mutant strains at exponential and stationary phase was performed and the change of mRNA levels were analyzed. It was found that RyeA and SdsR degrade each other, and pphA are co-transcribed from the sdsR promoter Transcription of both SdsR and pphA are inhibited by transcriptional interference (TI) of RyeA. Therefore, this study summarized the functional discovery of toxin-antitoxin of SdsR-RyeA sRNA pair and the mechanism of transcriptional biosynthesis of these and adjacent mRNA.