The control of mRNA decapping and P-body formation

Abstract

mRNA decapping is a critical step in eukaryotic cytoplasmic mRNA turnover. Cytoplasmic mRNA decapping is catalyzed by Dcp2 in conjunction with its coactivator Dcp1 and is stimulated by decapping enhancer proteins. mRNAs associated with the decapping machinery can assemble into cytoplasmic mRNP granules called processing bodies (PBs). Evidence suggests that PB-associated mRNPs are translationally repressed and can be degraded or stored for subsequent translation. However, whether mRNP assembly into a PB is important for translational repression, decapping, or decay has remained controversial. Here, we discuss the regulation of decapping machinery recruitment to specific mRNPs and how their assembly into PBs is governed by the relative rates of translational repression, mRNP multimerization, and mRNA decay.

Figure 1. Multiple protein factors promote mRNA decapping

(A) Interactions between the decapping enzyme Dcp2 and factors that stimulate decapping, Dcp1, Edc3, Dhh1 (Rck/P54, Me31B, CGH-1, Xp54), metazoan-specific Hedls and yeast-specific Edc1/2. Direct interactions between the decapping factors and between Dcp2 and mRNA are indicated by solid lines and brackets. The interaction between Edc1/2 and Dcp1/2 has been shown indirectly, through activation of decapping in vitro and is represented by dashed lines. Putative PB assembly domains are shown in red. Specific protein domains are indicated. (Q/N): Putative glutamine/asparagine-rich region of Hedls. The catalytic Nudix domain of Dcp2 is indicated in yellow. The indicated interactions are based on observations described in: (a): (Fenger-Gron et al., 2005; Xu et al., 2006; Yu et al., 2005), (b): (Deshmukh et al., 2008; She et al., 2006; She et al., 2008), (c): (Decker et al., 2007; Tritschler et al., 2007), (d): (Tritschler et al., 2007; Fenger-Gron et al., 2005), (e): (Decker et al., 2007; Tritschler et al., 2007), (f): (Decker et al., 2007; Tritschler et al., 2007), (g): (Dunckley et al., 2001; Schwartz et al. 2000), and (h): (Deshmukh et al., 2008; She et al., 2006; She et al., 2008). (B) mRNA decapping activation is thought to occur in two distinct steps. First, the cap-binding complex (eIF4F) must be removed from the mRNA, a process that renders the mRNA translationally inactive. This process is stimulated, at least in yeast, by Dhh1 and the Lsm-Pat1 complex. The core decapping complex, including Dcp2, Dcp1 and possibly in metazoans Hedls, can then access and remove the mRNA cap through a process that can be stimulated by Edc1–3. The decapped mRNA is then degraded by Xrn1.

Figure 2. The kinetic model for PB formation

Model illustrating the hypothesis that the extent of PB formation is directly proportional to the cytoplasmic levels of repressed mRNPs and depends on competing rates of translational repression, PB factor recruitment, mRNP multimerization and mRNA decay. Before mRNAs can assemble into PBs, they must be translationally repressed. Translational silencing factors then promote the formation of a PB “monomer” by recruiting decapping factors and/or other PB assembly components. If mRNA decay enzymes are not limiting and thus mRNA decay is rapid, mRNAs may be degraded prior to PB assembly. However, if decay enzymes are limiting, the repressed mRNAs assemble into PBs where they can be degraded, or released back into the translational pool.

Figure 3. Model for the assembly step in PB formation

(A) Yeast Edc3 and Lsm4 contain Yjef-N and Q/N-rich domains, respectively (indicated by red tails), which are protein-protein interaction domains important for the assembly of mRNPs into the PB (Decker et al., 2007; Reijns et al., 2008). Edc3 and Lsm4 are part of separate complexes, the decapping complex and the Lsm-Pat1 complex, respectively. These complexes might promote the assembly of their associated mRNPs into PBs through homomeric interactions as indicated by arrows. (B) In human cells, Hedls and GW182 contain putative Q/N-rich prion-like domains (indicated by red tails), which might promote PB formation in cooperation with, or independently of, Edc3 or Lsm4. It is possible that the assembly of PBs containing a heterogeneous pool of mRNPs requires that a subset of PB mRNPs recruit multiple assembly complexes, which serve as scaffolds for assembly with mRNPs containing single assembly complexes as indicated by arrows. Alternatively, assembly domains may form heterologous interactions (e.g. between Hedls and GW182) to assemble heterogeneous PBs (see text for details).