Coordinate regulation of the expression of SdsR toxin and its downstream pphA gene by RyeA antitoxin in Escherichia coli

Abstract

In Escherichia coli , SdsR and RyeA, a unique pair of mutually cis -encoded small RNAs (sRNAs), act as toxin and antitoxin, respectively. SdsR and RyeA expression are reciprocally regulated; however, how each regulates the synthesis of the other remains unclear. Here, we characterized the biosynthesis of the two sRNAs during growth and investigated their coordinate regulation using sdsR and ryeA promoter mutant strains. We found that RyeA transcription occurred even upon entry of cells into the stationary phase, but its apparent expression was restricted to exponentially growing cells because of its degradation by SdsR. Likewise, the appearance of SdsR was delayed owing to its RyeA-mediated degradation. We also found that the sdsR promoter was primarily responsible for transcription of the downstream pphA gene encoding a phosphatase and that pphA mRNA was synthesized by transcriptional read-through over the sdsR terminator. Transcription from the σ 70 -dependent ryeA promoter inhibited transcription from the σ S -dependent sdsR promoter through transcriptional interference. This transcriptional inhibition also downregulated pphA expression, but RyeA itself did not downregulate pphA expression.

Overlapping genes in natural and engineered genomes

“…In prokaryotic genomes, ncRNAs are an increasingly identified feature 84 , with cis- encoded antisense RNA regulation being a major player in physiological responses 84 , 85 . Examples of these pairings have demonstrated tight-knit regulation of expression of the protein-coding gene such as in type I toxin/antitoxin systems 86 and in Mg 2+ tolerance and virulence 87 . Interestingly, examples of unusually long antisense RNA have also been found, which likely hold greater regulatory control functions (such as regulation of entire operons) and have acquired their own designation as ‘excludons’ 84 , 88 .…”

Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

“…In fact, 301 candidate structured RNAs overlapped one or more other candidate structured RNAs in the opposing orientation (Additional file 3 : Table S3). This may be a system in which one candidate structured RNA regulates the other, as is seen in the SdsR and RyeA toxin-antitoxin system [ 20 , 21 ]. HMP2_6893 and HMP2_905 appeared to be exclusive to Prevotella in HMP29 and were mostly found near UvrABC endonuclease subunit C ( uvrC ).…”

Nucleoid openness profiling links bacterial genome structure to phenotype

“…Therefore, it is possible that high transcription or highly compacted genomic regions negatively affect genome accessibility measured by POP-seq. To assess this possibility, we evaluated the global relationship between DNA compaction 11 , RNA expression 24 , and Tn5 accessibility (POP-seq). To enable direct comparison, the 3-dimensional matrix of DNA-DNA contacts from a HiC experiment 11 was flattened into a 1-dimensional array.…”

“…The B. subtilis SMC ChIP-seq was acquired from Wang et al (2017) 25 (GSE85612). The E. coli RNA-seq data was acquired from Choi et al (2019) 24 (SRR8242101 and SRR8242105). The B. subtilis RNA-seq data was acquired from SRR2984942-3 under accession number PRJNA304431.…”