Graded impact of obstacle size on scanning by RNase E

In countless bacterial species, the lifetimes of most mRNAs are controlled by the regulatory endonuclease RNase E, which preferentially degrades RNAs bearing a 5′ monophosphate and locates cleavage sites within them by scanning linearly from the 5′ terminus along single-stranded regions. Consequently, its rate of cleavage at distal sites is governed by any obstacles that it may encounter along the way, such as bound proteins or ribosomes or base pairing that is coaxial with the path traversed by this enzyme. Here, we report that the protection afforded by such obstacles is dependent on the size and persistence of the structural discontinuities they create, whereas the molecular composition of obstacles to scanning is of comparatively little consequence. Over a broad range of sizes, incrementally larger discontinuities are incrementally more protective, with corresponding effects on mRNA stability. The graded impact of such obstacles suggests possible explanations for why their effect on scanning is not an all-or-none phenomenon dependent simply on whether the size of the resulting discontinuity exceeds the step length of RNase E.