Eukaryotic mRNA Decapping Activation

Abstract

The 5'-terminal cap is a fundamental determinant of eukaryotic gene expression which facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation. Enzyme-directed hydrolysis of the cap (decapping) decisively affects mRNA expression and turnover, and is a heavily regulated event. Following the identification of the decapping holoenzyme (Dcp1/2) over two decades ago, numerous studies revealed the complexity of decapping regulation across species and cell types. A conserved set of Dcp1/2-associated proteins, implicated in decapping activation and molecular scaffolding, were identified through genetic and molecular interaction studies, and yet their exact mechanisms of action are only emerging. In this review, we discuss the prevailing models on the roles and assembly of decapping co-factors, with considerations of conservation across species and comparison across physiological contexts. We next discuss the functional convergences of decapping machineries with other RNA-protein complexes in cytoplasmic P bodies and compare current views on their impact on mRNA stability and translation. Lastly, we review the current models of decapping activation and highlight important gaps in our current understanding.

Keywords: Cup/Me31B/Tral complex; Dcp1/Dcp2; Edc1; Edc3; Edc4; P bodies; PatL1; mRNA decapping and decay.

FIGURE 1

Domain organization of the decapping holocomplex in various organisms. The decapping holocomplex is composed of Dcp2 and Dcp1. (A) Dcp2 is the catalytic subunit that contains the catalytic core composed of the Nudix hydrolase domain and Box A. The N- and C-terminal ends are regulatory domains mainly composed of intrinsically disordered regions which vary in length and sequence in different species. (B) Dcp1 is the main activator of Dcp2 and is characterized by a conserved EVH1 domain. Metazoan Dcp1 acquires an intrinsically disordered extension in the C-terminus and can form a trimer. Abbreviations: IDR = Intrinsically Disordered Region; IM = Inhibitory Motif; HLM = Helical Leucine-rich Motif; EVH1 = Enabled/Vasodilator-stimulated Phosphoprotein Homology 1.

FIGURE 2

Domain organization of various decapping activators. The archetypal domain organization of (A) Edc1, (B) Edc2, (C) Edc3, (D) Edc4, (E) Pby1, (F) PatL1, (G) 4E-T, (H) Lsm14 and (I) Ddx6 are illustrated. Depicted are the S. cerevisiae orthologs of Edc1, Edc2 and Pby1, and the H. sapiens orthologs of the other decapping activators. Conserved domains and motifs are highlighted, and species-specific features are discussed in the main text. Abbreviation: IDR = Intrinsically Disordered Region.

FIGURE 3

Summary of all reported interactions between decapping proteins in S. cerevisiae, S. pombe, D. melanogaster and H. sapiens. Due to space constraints, we only include evidence from experimentally validated interactions and indicate whether evidence for direct physical interaction has been reported.

FIGURE 4

Models of decapping activation in yeast and metazoans. (A) The current model of Dcp2 activation from S. pombe is depicted. Dcp1/2 predominantly exists in an autoinhibited state that self-assemble into LLPS condensates and maintained by the interaction between W49 and Y220. Edc3 binding to Dcp2 HLM likely reorganizes the C-terminal IDR, allowing the formation of an active site in which W49 and Y220 interact with the cap, and activating Dcp2 inside LLPS condensates. On its own, Edc1 may stabilize the opened/active conformation of Dcp2 or consolidate the formation of active site from a pre-catalytic conformation from outside of LLPS condensates. Edc1 can also stabilize the Edc3-alleviated conformation in LLPS condensates, contributing to full activation of Dcp2. (B) Hypothetical model of metazoan Dcp2 activation. It is currently unknown whether or not metazoan Dcp1/2 is regulated through autoinhibition. Since metazoan Edc4 promotes the interaction between metazoan Dcp1 and Dcp2, it may help to alleviate autoinhibition or promote the formation of active site on Dcp2. Other decapping activators might enable decapping by promoting phase separation and Dcp2 localization to LLPS condensates. Abbreviations: IDR = Intrinsically Disordered Region; HLM = Helical Leucine-rich Motif.