Figure 2.

Mechanism of 5′-end-dependent degradation of triphosphorylated RNA in E. coli. In the principal pathway for 5′-end-dependent degradation, the γ and β phosphates of the triphosphorylated primary transcript are sequentially removed by an unidentified enzyme and by RppH, respectively, to generate first a diphosphorylated intermediate and then a monophosphorylated intermediate. The latter intermediate is vulnerable to rapid endonucleolytic cleavage by RNase E (scissors), whose 5′-end binding pocket can selectively accommodate a 5′ monophosphate but not a 5′ triphosphate or diphosphate. The resulting RNA fragments are then swiftly degraded (not shown). Although E. coli RppH prefers RNA substrates that are diphosphorylated, it can also convert triphosphates directly to monophosphates, albeit more slowly, releasing pyrophosphate as a by-product.