DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription

TLDR

DsrA RNA regulates transcription and translation of the stress σ factor RpoS, with its first stem‑loop sequence complementary to the rpoS leader region. The study aims to determine whether DsrA pairing functions as an anti‑antisense RNA to stimulate RpoS translation. DsrA contains three stem‑loops; the third acts as a transcription terminator that can be replaced by a trp terminator, while the first stem‑loop pairs with rpoS mRNA to relieve antisense inhibition. Mutational analysis shows the first stem‑loop is essential for RpoS translation but not for anti‑H‑NS action, the second stem‑loop is critical for antisilencing, and the predicted DsrA–rpoS pairing is required for translation stimulation.

Abstract

DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress σ factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of rpoS messenger RNA, suggesting that pairing of DsrA with the rpoS message might be important for translational regulation. Mutations in the Rpos leader and compensating mutations in DsrA confirm that this predicted pairing is necessary for DsrA stimulation of RpoS translation. We propose that DsrA pairing stimulates RpoS translation by acting as an anti-antisense RNA, freeing the translation initiation region from the cis-acting antisense RNA and allowing increased translation.