Control of mRNA decapping by positive and negative regulatory elements in the Dcp2 C-terminal domain

Abstract

Decapping commits an mRNA to complete degradation and promotes general 5 ′ to 3 ′ decay, nonsense-mediated decay (NMD), and transcript-specific degradation. In Saccharomyces cerevisiae, a single decapping enzyme composed of a regulatory subunit (Dcp1) and a catalytic subunit (Dcp2) targets thousands of distinct substrate mRNAs. However, the mechanisms controlling this enzyme's in vivo activity and substrate specificity remain elusive. Here, using a genetic approach, we show that the large C-terminal domain of Dcp2 includes a set of conserved negative and positive regulatory elements. A single negative element inhibits enzymatic activity and controls the downstream functions of several positive elements. The positive elements recruit the specific decapping activators Edc3, Pat1, and Upf1 to form distinct decapping complexes and control the enzyme's substrate specificity and final activation. Our results reveal unforeseen regulatory mechanisms that control decapping enzyme activity and function in vivo, and define roles for several decapping activators in the regulation of mRNA decapping.

The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface

“…Competition is nevertheless possible as the local concentrations of Xrn1, Pat1, and Dhh1 are very high in processing bodies and as the EVH1:PRS affinity will be enhanced by avidity effects that arise due to the presence of multiple PRS within the IDRs and due to additional interactions between the decapping factors and the decapping machinery. In line with that, it was recently shown that the in vivo activity of the S. cerevisiae Dcp1:Dcp2 decapping enzyme increases in a gradual manner upon a stepwise shortening of the C-terminal tail of Dcp2 (He and Jacobson 2015). Here, we show that the Dcp2 C-terminal tail contains a number of PRS that can interact in cis with the Dcp1 aromatic groove.…”

Nonsense-Mediated mRNA Decay: Degradation of Defective Transcripts Is Only Part of the Story

“…Maximal in vitro activation of Upf1’s ATPase and helicase activities requires both Upf2 and Upf3 (30). The CH domain of yeast Upf1 binds to the C-terminal region of Upf2 (78), the ribosomal protein Rps26 (153), and the decapping enzyme subunit Dcp2 (80, 82), and also self-associates (79), suggesting that it may play a role in sequential molecular interactions during execution of NMD. Metazoan Upf1 contains extra conserved extensions at both its N and C termini.…”

High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection

“…EDC3 (CFY25), PAT1 (SYY2674), LSM1 (SYY2680), and DHH1 (SYY2686) were described in He and Jacobson (2015a). A strain harboring a deletion of SCD6 (SSY2352) was constructed by gene replacement (Guthrie and Fink 1991) using a DNA fragment harboring the scd6::KanMX6 null allele.…”

“…These three proteins interact with each other, the ribosome, and multiple translation and mRNA decay factors (Kervestin and Jacobson 2012). Based on these molecular interactions, several potential functions have been proposed for the Upf factors, including remodeling terminating mRNPs (Franks et al 2010), releasing and recycling ribosomal subunits (Ghosh et al 2010), and recruiting mRNA decay factors (Okada-Katsuhata et al 2012;Nicholson et al 2014;He and Jacobson 2015a). However, the exact roles for the Upfs, and their modes of action in NMD, remain largely unknown.…”