Ribonuclease E is a 5′-end-dependent endonuclease

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Abstract
The selective degradation of messenger RNAs enables cells to regulate the levels of particular mRNAs in response to changes in the environment. Ribonuclease (RNase) E (ref. 1), a single-strand-specific endonuclease2,3,4 that is found in a multi-enzyme complex known as the ‘degradosome’5,6,7, initiates the degradation of many mRNAs in Escherichia coli3,8,9. Its relative lack of sequence specificity and the presence of many potential cleavage sites in mRNA substrates2,3 cannot explain why mRNA decay frequently proceeds in a net 5′-to-3′ direction9,10,11. I have prepared covalently closed circular derivatives of natural substrates, the rpsT mRNA encoding ribosomal protein S20 (ref. 2) and the 9S precursor to 5S ribosomal RNA1,12, and find that these derivatives are considerably more resistant to cleavage in vitro by RNase E than are linear molecules. Moreover, antisense oligo-deoxynucleotides complementary to the 5′ end of linear substrates significantly reduce the latter's susceptibility to attack by RNase E. Finally, natural substrates with terminal 5′-triphosphate groups are poorly cleaved by RNase E in vitro, whereas 5′ monophosphorylated substrates are strongly preferred (compare with ref. 13). These results show that RNase E has inherent vectorial properties, with its activity depending on the 5′ end of its substrates; this can account for the direction of mRNA decay in E. coli, the phenomenon of ‘all or none’ mRNA decay, and the stabilization provided by 5′ stem–loop structures14,15,16,17.