Control of RNase E-mediated RNA degradation by 5′-terminal base pairing in E. coil

Abstract

DESPITE the variety of messenger RNA half-lives in bacteria (0.5–30 min in Escherichia coli) and their importance in controlling gene expression, their molecular basis remains obscure. The life-time of an entire mRNA molecule can be determined by features near its 5′ end, but no 5′ exoribonuclease has been identified in any prokaryotic organism^1–6. A mutation that inactivates E. coli RNase E also increases the average lifetime of bulk E. coli mRNA and of many individual messages, suggesting that cleavage by this endonuclease may be the rate-determining step in the degradation of most mRNAs in E. coli^7–16. We have investigated the substrate preference of RNase E in E. coli by using variants of RNA I, a small untranslated RNA whose swift degradation in vivo is initiated by RNase E cleavage at an internal site. We report here that RNase E has an unprecedented substrate specificity for an endoribonuclease, as it preferentially cleaves RNAs that have several unpaired nucleotides at the 5′ end. The sensitivity of RNase E to 5′-terminal base pairing may explain how determinants near the 5′ end can control rates of mRNA decay in bacteria.