NMD overview. NMD involves three distinct processes. In the first, NMD substrates are detected by the NMD machinery. In the case of 3′UTR EJC-mediated NMD, if translation terminates, for example, at a premature termination codon (PTC), more than ∼50–55-nt upstream of an exon–exon junction (depicted as “^”), then termination is detected as aberrant. This is because a proteinaceous exon-junction complex (EJC), situated ∼20–24-nt upstream of the exon–exon junction, lies too far downstream from the PTC to be removed by the terminating ribosome. At the EJC, UPF2, anchored by UPF3X (also called UPF3B), interacts with UPF1 and SMG1 at the site of termination. Alternatively, on substrates with unusually long 3′UTRs, a large amount of UPF1 can promiscuously bind to the 3′UTR. The second phase of NMD is the commitment phase, where UPF1 is phosphorylated by its associated kinase, SMG1. This occurs efficiently during a series of regulated events on 3′UTR EJC-mediated NMD and less efficiently on 3′UTR EJC-independent NMD substrates. UPF1 phosphorylation represents a commitment to NMD. During the third phase of NMD, that is, mRNA degradation, phosphorylated UPF1 recruits RNA degradation activities either directly, by recruiting the SMG6 endonuclease (solid line with arrow to the scissors, which represent SMG6 itself) and/or the SMG5–SMG7 heterodimer, which recruits (dotted lines with arrow to the scissors) decapping and deadenylation enzymes (scissors) that produce unstable RNAs that are targeted for further degradation by exonucleases (red pacmen). CBP, cap-binding protein(s); 5′ dot, 7-methylguanine 5′ cap; AUG, translation initiation codon; AA(A)n, 3′ poly(A) tail; P, phosphate.
