The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection

RNase E, a multifunctional endoribonuclease of Escherichia coli, attacks substrates at highly specific sites. By using synthetic oligoribonucleotides containing repeats of identical target sequences protected from cleavage by 2′-O-methylated nucleotide substitutions at specific positions, we investigated how RNase E identifies its cleavage sites. We found that the RNase E catalytic domain (i.e., N-Rne) binds selectively to 5′-monophosphate RNA termini but has an inherent mode of cleavage in the 3′ to 5′ direction. Target sequences made uncleavable by the introduction of 2′-O-methyl-modified nucleotides bind to RNase E and impede cleavages at normally susceptible sites located 5′ to, but not 3′ to, the protected target. Our results indicate that RNase E can identify cleavage sites by a 3′ to 5′ “scanning” mechanism and imply that anchoring of the enzyme to the 5′-monophosphorylated end of these substrates orients the enzyme for directional cleavages that occur in a processive or quasiprocessive mode. In contrast, we find that RNase G, which has extensive structural homology with and size similarity to N-Rne, and can functionally complement RNase E gene deletions when overexpressed, has a nondirectional and distributive mode of action.