Abstract
Only few small, regulatory RNAs encoded opposite another gene have been identified in bacteria. Here, we report the characterization of a locus where a small RNA (SymR) is encoded in cis to an SOS-induced gene whose product shows homology to the antitoxin MazE (SymE). Synthesis of the SymE protein is tightly repressed at multiple levels by the LexA repressor, the SymR RNA and the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of the toxin-antitoxin modules, and we show that the SymE protein represents evolution of a toxin from the AbrB fold, whose representatives are typically antitoxins. We suggest that SymE promotion of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions.
Highlights
In Escherichia coli, a combination of approaches based on sequence conservation, structural features and direct detection has led to the identification of approximately 80 small RNAs that do not encode tRNAs, rRNAs or proteins but rather are thought to be regulators (Storz and Gottesman, 2006)
In our cloning-based screen for E. coli small RNAs (sRNAs), we identified a 77 nucleotide RNA, denoted RyjC based on its genomic position, which is encoded opposite the 5′ end of the yjiW mRNA (Kawano et al, 2005)
We compared symE mRNA levels in wild-type MG1655 cells and the corresponding strain carrying the -10 promoter mutation at different times before and after cells were treated with the DNA damaging agent mitomycin C (Fig. 1B)
Summary
In Escherichia coli, a combination of approaches based on sequence conservation, structural features and direct detection has led to the identification of approximately 80 small RNAs (sRNAs) that do not encode tRNAs, rRNAs or proteins but rather are thought to be regulators (Storz and Gottesman, 2006). In contrast to the sRNAs encoded on the bacterial chromosome, most of the characterized plasmid sRNAs are encoded opposite the genes that they regulate and have perfect complementarity with their target mRNAs (Wagner et al, 2002) Many of these cis-encoded sRNAs modulate the synthesis of replication proteins and control the copy number of the plasmids. They act by blocking ribosome binding or by promoting the formation of an mRNA secondary structure that leads to transcription termination. The Sok RNA is very unstable and is quickly degraded when the R1 plasmid is lost from the cell Under these conditions, the more stable hok mRNA is translated, and the Hok protein kills the cells that no longer carry the plasmid
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