Role of S1 ribosomal protein in the post-transcriptional regulation of Escherichia coli pnp gene

The exoribonuclease polynucleotide phosphorylase (PNPase, encoded by pnp) is a major player in bacterial RNA decay. PNPase expression is post-transcriptionally regulated at the level of mRNA stability. The primary transcript is very efficiently processed by the endonuclease RNase III at a unique site. This processed pnp mRNA is very unstable and is subject to PNPase autoregulation. We have shown in vitro that both PNPase and the ribosomal protein S1 bind the pnp-mRNA leader region. Footprinting experiments indicated an extensive overlap of PNPase and S1 binding sites and suggest a competition of the two proteins for the target RNA. A model based on these data maintains that competitive S1-PNPase binding to common sites on pnp-mRNA leader would modulate stability/decay of the pnp transcript. In agreement with the model, in vivo over-expression of S1 from a plasmid led to a strong increase of pnp mRNA abundance and stabilization. On the contrary, repression of the chromosomal rpsA (S1) gene (placed under the arabinose inducible promoter araBp) decreased the abundance of pnp mRNA.