Control of mRNA decapping by autoinhibition

Abstract

Abstract5′ mediated cytoplasmic RNA decay is a conserved cellular process in eukaryotes. While the functions of the structured core domains in this pathway are well-studied, the role of abundant intrinsically disordered regions (IDRs) is lacking. Here we reconstitute the Dcp1:Dcp2 complex containing a portion of the disordered C-terminus and show its activity is autoinhibited by linear interaction motifs. Enhancers of decapping (Edc) 1 and 3 cooperate to activate decapping by different mechanisms: Edc3 alleviates autoinhibition by binding IDRs and destabilizing an inactive form of the enzyme, whereas Edc1 stabilizes the transition state for catalysis. Both activators are required to fully stimulate an autoinhibited Dcp1:Dcp2 as Edc1 alone cannot overcome the decrease in activity attributed to the C-terminal extension. Our data provide a mechanistic framework for combinatorial control of decapping by protein cofactors, a principle that is likely conserved in multiple 5′ mRNA decay pathways.

mRNA decapping: finding the right structures

“…Another consequence of the binding of the Edc3 LSm domain to Dcp2 could also be its contribution to the release of the self-inhibitory effect exerted by Dcp2 sequences located downstream of the Edc3 binding site in S. cerevisiae and S. pombe proteins [22,23]. Other proteins known to bind to the Dcp2 C-terminal extension (i.e.…”

Pat1 activates late steps in mRNA decay by multiple mechanisms

“…While we could not purify full length Dcp2, a C-terminally extended Dcp2 containing up to 261 additional amino acids recapitulates the regulatory elements in the full-length C-terminal extension (Fig. 4A) (16, 17). The C-terminal domain of budding yeast Pat1 was crystallized with a helical leucine rich motif (HLM) of Dcp2, suggesting a mechanism by which Pat1 could promote decapping (41).…”

“…The Dcp1/Dcp2 holoenzyme is a conserved NUDIX hydrolase that cleaves the 5’ m 7 G cap and is targeted to specific mRNAs by cofactors (1, 8–13). These cofactors regulate the activity of Dcp1/Dcp2 by either binding the catalytic core of the enzyme or helical leucine motifs (HLMs) in the disordered C-terminus of Dcp2, which contains additional cis- regulatory elements that inhibit decapping (14–17). Thus, a dense network of protein interactions has evolved to coordinate decapping of specific mRNA targets (18).…”

“…Here, we determine how Pat1 interacts with and activates both the Lsm1-7 complex and Dcp1/Dcp2 from the fission yeast S.pombe (Sp) using recombinant purified proteins, which recapitulate the regulation of decapping observed in budding yeast (16, 17). We show that Pat1 promotes RNA binding of the Lsm1-7 complex using two short linear motifs from its middle domain that make physical interactions with the Lsm1-7 ring and enhance its interaction with RNA.…”

Biomolecular condensates amplify mRNA decapping by coupling protein interactions with conformational changes in Dcp1/Dcp2

“…The localization and regulation imparted by disordered regions in the decapping complex is mediated through conserved short-linear interaction motifs (Fromm et al, 2014;Jonas and Izaurralde, 2013;Xing et al, 2018). Recently, positive and negative regulatory motifs in the disordered C-terminus of Dcp2 were identified in yeast Dcp2 that affect catalytic activity in vitro and in vivo (He and Jacobson, 2015;Paquette et al, 2018). These results established a model where Dcp2 is autoinhibited and coactivators alleviate autoinhibition to increase RNA binding and catalysis (Lobel et al, 2019;Paquette et al, 2018).…”