Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors

Abstract

Nonsense-mediated decay is well known by the lucid definition of being a RNA surveillance mechanism that ensures the speedy degradation of mRNAs containing premature translation termination codons. However, as we review here, NMD is far from being a simple quality control mechanism; it also regulates the stability of many wild-type transcripts. We summarise the abundance of research that has characterised each of the NMD factors and present a unified model for the recognition of NMD substrates. The contentious issue of how and where NMD occurs is also discussed, particularly with regard to P-bodies and SMG6-driven endonucleolytic degradation. In recent years, the discovery of additional functions played by several of the NMD factors has further complicated the picture. Therefore, we also review the reported roles of UPF1, SMG1 and SMG6 in other cellular processes.

Fig. 1

Schematic model of efficient translation termination in the proper mRNP environment. The model postulates that normal translation termination involves an interaction between PABP and eRF3, which by a currently unknown mechanism promotes fast polypeptide release, disassembly of the ribosomal subunits and re-initiation of the ribosome at the start codon. The proper termination-stimulating mRNP environment is characterised by a protein complex involving PABP, eIF4G, the cap binding factor (eIF4E or CBP80/CBP20) and additional factors that bring the 5′ and the 3′ ends of the mRNA in close proximity and constrain the mRNP in a circular structure

Fig. 2

Model for aberrant translation termination, which leads to the assembly of a mRNA surveillance complex that marks the mRNA for subsequent degradation. When the stop codon is located in an mRNP environment where it fails to receive the PABP-mediated termination-stimulating signal, the ribosome stalls for a prolonged period of time at the stop codon, which allows binding of UPF1 to eRF3. The assembly of this SURF complex marks the mRNA for NMD. The model further postulates that this marking step is still reversible and that the mRNA is only irreversibly committed to NMD after UPF1 phosphorylation (licensing step). UPF2 and/or UPF3 are necessary for SMG1-mediated UPF1 phosphorylation. The presence of an EJC in the 3′ UTR serves as a strong enhancer of NMD (EJC-enhanced licensing), because UPF2 and/or UPF3 interaction with the SURF is greatly facilitated by virtue of their close proximity, whereas UPF2 and/or UPF3 recruitment take longer in the absence of an EJC (EJC-independent licensing), resulting in overall less efficient NMD. Following phosphorylation and possibly induced by ATP hydrolysis, UPF1 undergoes a conformational change that increases its affinity for RNA and is then ready for interaction with SMG5–7, which initiate mRNA degradation (see Fig. 3)

Fig. 3

Model for degradation of NMD substrates. The model posits that UPF1-bound mRNAs can be degraded by two different pathways, depending on whether the SMG5/SMG7 heterodimer or the endonuclease SMG6 binds to phosphorylated UPF1. Interaction of SMG5/SMG7 with phospho-UPF1 promotes deadenylation followed by decapping and exonucleolytic RNA decay from both ends (left branch). Interaction of SMG6 with phospho-UPF1 leads to a SMG6-mediated endonucleolytic cleavage near the aberrant termination site, followed by the exonucleolytic degradation of the two RNA fragments from the initial cleavage site