A stop codon-dependent internal secondary translation initiation region in Escherichia coli rpoS

Sigma S (σ s ) encoded by rpoS is a stationary phase-specific σ subunit of the Escherichia coli RNA polymerase holoenzyme. In many E. coli strains, rpoS has an amber stop as codon 33 ( rpoSAm ), resulting in a 32-amino-acid-long peptide. Nevertheless, suppressor-free rpoSAm strains have functional σ S . This led us to hypothesize the presence of an intracistronic secondary translational initiation region (STIR) in the E. coli rpoS gene. Here, we demonstrate that the STIR is functional and is controlled by the upstream amber stop codon 33. Removal of the primary translational initiation region did not abolish translation from STIR, ruling out translational coupling. Importantly, the functional STIR conferred survival advantage. Taken together, our results reveal a hitherto unknown physiologically significant post-transcriptional process in E. coli rpoSAm strains.