Normal and Aberrantly Capped mRNA Decapping

Messenger RNAs transcribed by RNA polymerase II are modified at their 5'-end by the cotranscriptional addition of a 7-methylguanosine (m(7)G) cap. The cap is an important modulator of gene expression and the mechanism and components involved in its removal have been extensively studied. At least two decapping enzymes, Dcp2 and Nudt16, and an array of decapping regulatory proteins remove the m(7)G cap from an mRNA exposing the 5'-end to exonucleolytic decay. In contrast, relatively less is known about the decay of mRNAs that may be aberrantly capped. The recent demonstration that the Saccharomyces cerevisiae Rai1 protein selectively hydrolyzes aberrantly capped mRNAs provides new insights into the modulation of mRNA that lack a canonical m(7)G cap 5'-end. Whether an mRNA is uncapped or capped but missing the N7 methyl moiety, Rai1 hydrolyzes its 5'-end to generate an mRNA with a 5' monophosphate. Interestingly, Rai1 heterodimerizes with the Rat1 5'-3' exoribonuclease, which subsequently degrades the 5'-end monophosphorylated mRNA. Importantly, Rat1 stimulates the 5'-end hydrolysis activities of Rai1 to generate a 5'-end unprotected mRNA substrate for Rat1 and, in turn, Rai1 stimulates the activity of Rat1. The Rai1-Rat1 heterodimer functions as a molecular motor to detect and degrade mRNAs with aberrant caps and defines a novel quality control mechanism that ensures mRNA 5'-end integrity. The increase in aberrantly capped mRNA population following nutritional stress in S. cerevisiae demonstrates the presence of aberrantly capped mRNAs in cells and further reinforces the functional significance of the Rai1 in ensuring mRNA 5'-end integrity.