The Branched Nature of the Nonsense-Mediated mRNA Decay Pathway

Abstract

Nonsense-mediated mRNA decay (NMD) is a conserved translation-coupled quality control mechanism in all eukaryotes that regulates the expression of a significant fraction of both the aberrant and normal transcriptomes. In vertebrates, NMD has become an essential process owing to expansion of the diversity of NMD-regulated transcripts, particularly during various developmental processes. Surprisingly, however, some core NMD factors that are essential for NMD in simpler organisms appear to be dispensable for vertebrate NMD. At the same time, numerous NMD enhancers and suppressors have been identified in multicellular organisms including vertebrates. Collectively, the available data suggest that vertebrate NMD is a complex, branched pathway wherein individual branches regulate specific mRNA subsets to fulfill distinct physiological functions.

Keywords: 3′-UTR; UPF proteins; exon-junction complex; mRNA decay; nonsense codons; premature termination codons.

Figure 1.. Two Models of How UPF1 Differentiates Aberrant Translation Termination.

The first model suggests that, compared with short 3′-UTRs (A), long 3′-UTRs (B) provide a greater opportunity for UPF1 binding and accumulation on RNAs, which promotes premature termination and NMD. The second model suggests that, on short 3′-UTRs (A), PABP– eRF3 is a more dominant interaction (thicker arrow) than UPF1–eRF3 (thinner arrow), leading to normal termination, whereas long 3′-UTRs (B) favor UPF1–eRF3 (thicker arrow) over PABP–eRF3 (thinner arrow) interaction, leading to premature termination and NMD. The grey shape to the left of the ribosome shows a truncated portion of mRNA coding sequence, and the grey line to the right of the ribosome is the 3′-UTR. Shapes representing protein factors are labeled. Abbreviations: NMD, nonsense-mediated decay; UTR, untranslated region.

Figure 2.. Mechanism of UPF1 Activation in the Two Major NMD Branches.

(A) On mRNAs without downstream exon–exon junctions, UPF1, together with eRF1 and eRF3, interacts with SMG1 to form the SURF complex [146]. The SMG1 regulatory SMG8–SMG9 heterodimer and the scaffold protein DHX34 aid in SURF complex assembly, subsequent UPF1 phosphorylation, and interaction between the SURF complex and UPF2–UPF3, leading to formation of the decay-inducing (DECID) complex and UPF1 phosphorylation (right) [147,148]. Ribosome, eRFs, SMG1 and its regulators may dissociate from the RNA at this stage, and hence are shown by more transparent shapes. (B) The exon-junction complex (EJC), a key NMD enhancer in vertebrates, when present in 3′-UTRs can recruit UPF2/UPF3B to 3′-UTR (left) and facilitate formation of the UPF complex, and hence DECID complex formation (right), leading to UPF1 phosphorylation and NMD activation. Shapes representing various protein factors are labeled. Yellow circle, phosphate. Abbreviations: NMD, nonsense-mediated decay; SURF complex, SMG1–UPF1–eRF1–eRF3; UTR, untranslated region.

Figure 3.. Loss of Complete Dependence on UPF2/3 and Gain of Enhancers of UPF Function Leads to Specific NMD Branches.

(A) The EJC-dependent NMD branch. An EJC downstream of a terminated ribosome can lead to UPF1 activation at a termination event via EJC–UPF3B–UPF2–UPF1 interaction. SR proteins can enhance this EJC-dependent NMD by boosting EJC deposition/RNA binding. (B) The UPF3B-independent NMD branch. Interaction between RNPS1-containing EJC and UPF2 can cause EJC-dependent and UPF3B-independent NMD. (C) The UPF2-independent branch. UPF3B can directly interact with UPF1 and elicit NMD. CASC3-containing EJCs may contribute to this branch. (D) SRSF1 bound to the 3′-UTR can enhance NMD activation in an EJC-independent manner by interacting directly with UPF1. Abbreviations: EJC, exon-junction complex; NMD, nonsense-mediated decay; UTR, untranslated region.

Figure 4.. Two Main Routes for mRNA Degradation after UPF1 Activation.

(A) SMG5–SMG7 heterodimer recruited to phosphorylated UPF1 can interact with CNOT8 protein (also known as POP2) in the CCR4–NOT complex. The CCR4–NOT complex initiates mRNA degradation by deadenylating the poly(A) tails. (B) The SMG6 endonuclease recruited to phosphorylated UPF1 acts in SMG5/SMG7-dependent manner to cleave mRNA in the vicinity of PTCs. The action of SMG6 could further be enhanced by the presence of downstream NMD enhancer EJC. After cleavage of mRNAs, 5′ and 3′ fragments are degraded by exosomes and exonuclease XRN1 respectively. Green arrow, initiation codon; red stop-sign, stop codon. Abbreviations: EJC, exon-junction complex; NMD, nonsense-mediated decay; PTC, premature termination codon; UTR, untranslated region.

Figure 5.. A Schematic Summarizing the Flux of NMD Targets through Possible NMD Branches.

Individual branches/routes are labeled above each shaded region. The branch requiring only the UPF proteins may constitute the ‘core’ NMD branch that is maintained in most eukaryotes and remains active in vertebrates. Thick arrows indicate major NMD routes in mammals. UPF3A can serve as an NMD activator (thin arrow) or as a repressor (inhibitory line) of UPF3B function. SRSF1 may activate UPF1 independently of the EJC, but this constitutes only an optional nucleation point for the NMD pathway (indicated by dotted lines). Abbreviations: EJC, exon-junction complex; NMD, nonsense-mediated decay; UTR, untranslated region.

Figure I.. Gene Features That Cause NMD Susceptibility.

Light-shaded thinner rectangles are untranslated regions, and dark-shaded thicker rectangles represent coding regions. Introns are shown as a black line, green arrows denote start codons, and red stop-signs indicate stop codons.