Preferential Cleavage of Degradative Intermediates of rpsT mRNA by the Escherichia coli RNA Degradosome

RNase E, the principal RNase capable of initiating mRNA decay, preferentially attacks 5′-monophosphorylated over 5′-triphosphorylated substrates. Site-specific cleavage in vitro of the rpsT mRNA by RNase H directed by chimeric 2′-O-methyl oligonucleotides was employed to create truncated RNAs which are identical to authentic degradative intermediates. The rates of cleavage of two such intermediates by RNase E in the RNA degradosome are significantly faster (2.5- to 8-fold) than that of intact RNA. This verifies the preference of RNase E for degradative intermediates and can explain the frequent “all-or-none” behavior of mRNAs during the decay process.