Activation of the mRNA Decay-Associated DEAD-Box ATPase Dhh1 Requires Deadenylation and Decapping Factors

The DEAD-box ATPase Dhh1 (DDX6 in humans) is a general activator of 5’-3’ mRNA decay that acts between the deadenylation and decapping steps of the pathway, although the exact mechanism of its action remains unclear. Dhh1 has been shown to interact with the MIF4G domain of the central scaffold protein of the Ccr4-Not deadenylase complex, Not1, as well as the decapping activator Edc3. Although structures have been published of Dhh1 in complex with Not1 ^MIF4G or an Edc3 peptide, the impact of these interactions on the catalytic cycle of Dhh1 are unknown. Here, we show Edc3 enhances ATP and RNA binding by Dhh1, whereas Not1 ^MIF4G promotes the catalytic step of ATP hydrolysis. Additionally, the modulation of Dhh1 activity by Edc3 requires a more extensive set of interaction motifs and interfaces than was previously recognized. While the effect of either Not1 ^MIF4G or Edc3 on the ATPase activity of Dhh1 is modest, together both proteins increase Dhh1 activity over 200-fold, consistent with a role of Dhh1 in bridging 3’ deadenylation and 5’ decapping in the 5’-3’ mRNA decay pathway. These results suggest that Dhh1 coordinates deadenylation with decapping through changes in its ATP-coupled RNA binding affinity during its catalytic cycle.