S1 ribosomal protein over-expression inhibits RNase E-dependent decay in Escherichia coli

It is commonly accepted that in bacteria transcription, translation and degradation of RNA are tightly coordinated processes; however, the molecular bases of this interconnection are poorly understood. S1 is the largest E. coli ribosomal protein; it is very abundant and weakly associated with the 30S ribosomal subunit. Both its over-expression and depletion impair bacterial growth. In a previous work we showed that S1 over-expression leads to a general increase in mRNA stability. To further characterize this phenomenon, we tested the role of 5'-UTR in S1-dependent stabilization. As a model transcript, we chose the cspE mRNA, which is sensitive to S1 stabilization. We showed by EMSA that S1 still binds a cspE RNA lacking the 5'-UTR (cspE-Del), albeit with lower affinity relative to the complete mRNA (cspE-wt), suggesting that for this mRNA different S1 binding sites may exist. In vivo, cspE-Del was less stable than cspE-wt RNA. Upon S1 induction, both the transcripts were stabilized; moreover, different RNA decay intermediates, deriving from cspE-Del degradation at the 5'-end, were detected, whereas no cspE-wt degradation products were present. In an rne thermosensitive mutant expressing cspE-Del, these decay intermediates were produced and stabilized, suggesting that RNase E may be involved in their degradation but not in their production. On the whole, our data suggest that S1 may interact both with the 5'-UTR and/or the 3'-UTR and prevent RNase E-dependent mRNA degradation but not the RNase E-independent endonucleolytic pathway operating on the leaderless cspE mRNA.