Posttranscriptional regulation of cspE in Escherichia coli: involvement of the short 5'-untranslated region.

Escherichia coli K-12 contains nine paralogs of CspA, namely CspA-CspI. In spite of considerable sequence similarity among these genes, the individual members of this family show significant differences in their expression regulation. Among these nine members, cspA, B, G and I have been reported to be cold-induced. The unusually long 5'-untranslated region (5'-UTR) of these four and other cold-induced genes has often been associated with their inducibility. Sequence analysis of the cspE upstream region revealed two promoter-like motifs having high scores. We identified the promoter site and established that cspE has a much shorter 5'-UTR compared to other cold-induced genes. Our results showed that cspE is induced to about threefold at both the transcript and the protein level in response to cold-shock. Its transcript half-life increases significantly upon cold-shock. Furthermore, we demonstrated that RNase E, a key endonuclease responsible for mRNA degradation in E. coli, regulates cspE transcript stability, possibly through the assembly of a degradosome. In silico analysis of the cspE 5'-UTR revealed alternative secondary structures at 37 and 15 degrees C. A point mutation that was predicted to relax the secondary structure of the 5'-UTR at 15 degrees C showed considerable reduction in transcript stability, indicating that alternative transcript secondary structures might be the cause of the differential stability.