SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)

In bacteria, SsrA RNA recognizes ribosomes stalled on defective messages an d acts as a tRNA and mRNA to mediate the addition of a short peptide tag to the C-terminus of the partially synthesized nascent polypeptide chain. The SsrA-tagged protein is then degraded by C-terminal-specific proteases. Smp B, a unique RNA-binding protein that is conserved throughout the bacterial kingdom, is shown here to be an essential component of the SsrA quality-con trol system. Deletion of the smpB gene in Escherichia coli results in the s ame phenotypes observed in ssrA-defective cells, including a variety of pha ge development defects and the failure to tag proteins translated from defe ctive mRNAs. Purified SmpB binds specifically and with high affinity to Ssr A RNA and is required for stable association of SsrA with ribosomes in vivo . Formation of an SmpB-SsrA complex appears to be critical in mediating Ssr A activity after aminoacylation with alanine but prior to the transpeptidat ion reaction that couples this alanine to the nascent chain. SsrA RNA is pr esent at wild-type levels in the smpB mutant arguing against a model of Ssr A action that involves direct competition for transcription factors.