The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex

Abstract

The Dcp1:Dcp2 decapping complex catalyses the removal of the mRNA 5 0 cap structure. Activator proteins, including Edc3 (enhancer of decapping 3), modulate its activity. Here, we solved the structure of the yeast Edc3 LSm domain in complex with a short helical leucine-rich motif (HLM) from Dcp2. The motif interacts with the monomeric Edc3 LSm domain in an unprecedented manner and recognizes a noncanonical binding surface. Based on the structure, we identified additional HLMs in the disordered C-terminal extension of Dcp2 that can interact with Edc3. Moreover, the LSm domain of the Edc3-related protein Scd6 competes with Edc3 for the interaction with these HLMs. We show that both Edc3 and Scd6 stimulate decapping in vitro, presumably by preventing the Dcp1:Dcp2 complex from adopting an inactive conformation. In addition, we show that the C-terminal HLMs in Dcp2 are necessary for the localization of the Dcp1:Dcp2 decapping complex to P-bodies in vivo. Unexpectedly, in contrast to yeast, in metazoans the HLM is found in Dcp1, suggesting that details underlying the regulation of mRNA decapping changed throughout evolution.

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

“…We therefore termed this previously unannotated ORF in S. pombe Edc1 (see below). Edc1 lacks structural domains; however, in addition to the conserved region that we identified above, it displays a highly positive N-terminal region and a conserved HLM-like region (Fromm et al 2012(Fromm et al , 2014 in the C terminus that could interact with the Edc3 LSm domain. This feature highlights the complexity and redundancy of the interaction network between mRNA decapping factors.…”

“…In addition, in Saccharomyces cerevisiae the two intrinsically disordered decapping enhancers Edc1 and Edc2, which show limited sequence conservation with human PNRC2, have been identified (Dunckley et al 2001;Lai et al 2012). Importantly, for Edc3 (Harigaya et al 2010;Nissan et al 2010;Fromm et al 2012), Pat1 (Nissan et al 2010), Edc1 and Edc2 Steiger et al 2003;Borja et al 2011), and PNRC2 (Lai et al 2012), the activation of the decapping activity has been shown in in vitro, indicating that these proteins directly regulate catalytic activity.…”

“…Due to the central nature of the mRNA decapping reaction, the activity of the Dcp1:Dcp2 decapping complex needs to be tightly regulated and multiple factors have been identified that influence turnover rates. These factors include Edc3 (enhancer of decapping 3) (Kshirsagar and Parker 2004) that binds to a conserved region in the C-terminal disordered region of Dcp2 (Harigaya et al 2010;Fromm et al 2012), the Lsm1-7:Pat1 complex (Bouveret et al 2000;Tharun et al 2000) and the RNA DEAD box helicase Dhh1 (Coller et al 2001;Fischer and Weis 2002). In addition, in Saccharomyces cerevisiae the two intrinsically disordered decapping enhancers Edc1 and Edc2, which show limited sequence conservation with human PNRC2, have been identified (Dunckley et al 2001;Lai et al 2012).…”

RGG motif proteins: Modulators of mRNA functional states

“…1 This suggests three different models for how RGG motif proteins might be interacting with eIF4G and its implication on global cellular translation (Fig. 1) 47 Interestingly, the Lsm domain of Scd6 is responsible for the interaction with Dcp2, 45 whereas RGG motif domain interacts with eIF4G. 1 There are two non-mutually exclusive possibilities for how Scd6 might stimulate decapping.…”

Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex

“…Efficient decapping by Dcp2 requires the essential activator Dcp1 and in metazoans the scaffolding protein Edc4 (Fenger-Gron et al 2005;She et al 2006;Eulalio et al 2007;Chang et al 2014). Coactivator proteins that further activate decapping and may target the decapping complex to specific RNA decay pathways have also recently been characterized, including the enhancer of decapping proteins (Edc1-3) and PNRC2 (Borja et al 2010;Fromm et al 2011;Lai et al 2012). The Dcp1/2 decapping complex functions as part of a highly evolved network of protein-protein interactions that regulates cap hydrolysis and the degradation of mRNA.…”