A tale of two mRNA degradation pathways mediated by RNase E

Abstract

RNase E is an essential endoribonuclease with a preference for RNA substrates with 5'-monophosphate ends. Primary transcripts, which have 5' triphosphate ends, are thus protected from RNase E. Their conversion to 5'-monophosphate transcripts by RppH is a prerequisite for RNase E-mediated processing and degradation. 5'-monophosphate recognition involves binding to a subdomain in the catalytic core of RNase E known as the 5' sensor. There are, however, transcripts that can be attacked directly by RNase E in a 5'-end-independent pathway. Direct entry involves elements outside of the catalytic domain that are located in the carboxyl terminal half (CTH) of RNase E. Strains harbouring rne alleles that express variants of RNase E in which 5' sensing (rneR169Q) or direct entry (rneΔCTH) are inactivated, are viable. However, the rneR169Q/rneΔCTH and ΔrppH/rneΔCTH combinations are synthetic lethal suggesting that the essential function(s) of RNase E requires at least one of these pathways to be active. A striking result is the demonstration that mutations affecting Rho-dependent transcription termination can overcome synthetic lethality by a pathway that requires RNase H. It is hypothesized that R-loop formation and RNase H cleavage substitute for RNase E-dependent RNA processing and mRNA degradation.