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

Max Planck Institute for Developmental Biology, Tübingen, Germany.
The EMBO Journal (Impact Factor: 10.43). 11/2011; 31(2):279-90. DOI: 10.1038/emboj.2011.408
Source: PubMed


The Dcp1:Dcp2 decapping complex catalyses the removal of the mRNA 5' 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.

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Available from: Remco Sprangers, Apr 05, 2014
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    • "Edc3 binds to various HLM motifs with affinities within the low micromolar to millimolar range[49]. The valency of the HLM motifs in Pdc1 is increased through oligomerization via a central coiled-coil domain[49,75]. These examples illustrate how multivalent interaction modules and oligomerization domains can cooperate to initiate phase separation in the context of different types of membrane-less organelles. "
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    • "In turn, Edc3 and Lsm14 directly bind and activate the decapping complex, DCP1-DCP2 (Fromm et al., 2012; Nissan et al., 2010; Tritschler et al., 2008). DDX6 also uses the same Edc3/Lsm14- binding surface to interact with Pat1 (Sharif et al., 2013), another modulator of mRNA stability and translation (Marnef and Standart , 2010). "
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    ABSTRACT: The DEAD-box protein DDX6 is a central component of translational repression mechanisms in maternal mRNA storage in oocytes and microRNA-mediated silencing in somatic cells. DDX6 interacts with the CCR4-NOT complex and functions in concert with several post-transcriptional regulators, including Edc3, Pat1, and 4E-T. We show that the conserved CUP-homology domain (CHD) of human 4E-T interacts directly with DDX6 in both the presence and absence of the central MIF4G domain of CNOT1. The 2.1-Å resolution structure of the corresponding ternary complex reveals how 4E-T CHD wraps around the RecA2 domain of DDX6 and contacts CNOT1. Although 4E-T CHD lacks recognizable sequence similarity with Edc3 or Pat1, it shares the same DDX6-binding surface. In contrast to 4E-T, however, the Edc3 and Pat1 FDF motifs dissociate from DDX6 upon CNOT1 MIF4G binding in vitro. The results underscore the presence of a complex network of simultaneous and/or mutually exclusive interactions in DDX6-mediated repression.
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    • "In this pathway, shortening of the poly(A) tail to oligo(A) length triggers decapping by Dcp1/Dcp2 holoenzyme and subsequent 5 ′ – 3 ′ degradation of the body of the message by the exonuclease Xrn1 (Chen and Shyu 2011; Parker 2012; Schoenberg and Maquat 2012). Several factors facilitate decapping and they include Dhh1, the Lsm1-7-Pat1 complex, Edc1, Edc2, Edc3 (Kshirsagar and Parker 2004; Nissan et al. 2010; Borja et al. 2011; Fromm et al. 2012; Sweet et al. 2012; Arribas-Layton et al. 2013) and in metazoans Edc4 (Chang et al. 2014). The Lsm1-7-Pat1 complex is made up of the Pat1 protein, which is implicated in translational repression (Coller and Parker 2005; Marnef and Standart 2010), and the seven Sm-like proteins, Lsm1 through Lsm7 (Bouveret et al. 2000; Tharun 2009a; Tharun et al. 2000; Totaro et al. 2011). "
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