Structural basis for the multiple roles Edc3 plays in mRNA degradation

Abstract

The Dcp1:Dcp2 decapping complex catalyzes the removal of the protecting 5’ cap structure from mRNA. Adaptor proteins, including Edc3 (enhancer of decapping 3), modulate this decapping process through multiple mechanisms. First, the Edc3 protein enhances the activity of the Dcp2 enzyme directly. Secondly, Edc3 is involved in the formation of cellular processing bodies. Finally, Edc3 is important for the deadenylation independent degradation of the Rps28b mRNA. In the latter case, cellular Rps28b protein levels are regulated through a unique auto-regulatory pathway, where Rps28b that is not in complex with the ribosome binds to a specific stem-loop in the 3’-UTR of its own messenger-RNA. To understand how the Edc3 protein is able to preform these multiple functions, we solved the structure of the yeast Edc3 LSm domain in complex with a short helical leucine-rich motif (HLM) from Dcp2. Based on that structure, we identified additional HLMs in the disordered C-terminal extension of Dcp2 that can interact with Edc3. We show that these multiple HLMs in Dcp2, together with the dimeric nature of Edc3, can lead to the formation of a network of intermolecular interaction. Our experiments thus provide initial insights into one of the mechanisms that underlie processing body formation. Finally, we solved the structure of the Edc3 LSm domain in complex with the Rps28b protein. These data display how the dimeric Edc3 protein is able to bring the Rps28b mRNA and the Dcp1:Dcp2 decapping complex together, thereby targeting the mRNA for degradation. In summary, we show that the Edc3 LSm domain is a plastic platform for multiple protein:protein interactions that are important for the regulation of mRNA degradation