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SnapShot: Nonsense-Mediated mRNA DecaySébastien Durand and Jens Lykke-AndersenDivision of Biology, University of California San Diego, La Jolla, CA 92093, USA

324.e1 Cell 145, April 15, 2011 ©2011 Elsevier Inc. DOI 10.1016/j.cell.2011.03.038

The nonsense-mediated mRNA decay (NMD) pathway serves an important function in mRNA quality control by ridding the cell of aberrant mRNAs that encode truncated proteins due to premature translation termination codons (PTCs). PTC-containing mRNAs arise from errors in transcription or pre-mRNA processing or from mutation or recombination events within protein-coding genes. They are also produced from alternative pre-mRNA splicing events. In addition, a subset of normally expressed mRNAs are downregulated by the NMD pathway (reviewed in Chang et al., 2007; Lejeune and Maquat, 2005). This SnapShot summarizes current insights into the mechanism by which the NMD pathway identifies and degrades target mRNAs, highlighting similarities and differences between the pathway in the budding yeast Saccharomyces cerevisiae and human cells.

Translation Termination/Substrate RecognitionThe mechanism by which the NMD machinery discriminates target mRNAs from other cellular mRNAs has been intensely studied but remains enigmatic. The key step is the translation termination event. Evidence suggests that the composition of the mRNP downstream of the terminating ribosome plays a critical role in determining whether the mRNP is targeted for NMD or is allowed to continue translation (reviewed in Amrani et al., 2006; Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009). In budding yeast and human cells, as well as in cells of the fly Drosophila melanogaster, cytoplasmic poly(A)-binding protein (PABPC) antagonizes NMD when the poly(A) tail is close to the termination codon, thereby placing PABPC in proximity to the termination event. However, mRNP components other than PABPC must also affect NMD substrate recognition because PABPC is not required for the discrimination between normal mRNAs and NMD substrates in budding yeast. Moreover, some mRNAs that contain long 3′UTRs, placing the poly(A) tail distal to the termination codon, are resistant to NMD in human cells (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009).

In vertebrates, an exon junction complex (EJC), loaded on mRNAs upstream of exon-exon junctions as a consequence of pre-mRNA splicing, stimulates NMD when posi-tioned downstream of the translation termination event. It is currently unclear whether the EJC stimulates NMD through substrate recognition or at a downstream step in the pathway. The EJC is likely an evolutionary adaptation in the NMD pathway, as no EJC has been observed in budding yeast, and the EJC does not appear to be important for NMD in the fission yeast Schizosaccharomyces pombe or in the worm Caenorhabditis elegans (reviewed in Lejeune and Maquat, 2005; Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009). Another level at which mammalian and budding yeast NMD substrate recognition may differ is in regards to how long translating mRNPs remain sensi-tive to NMD. According to the pioneer round of translation model for NMD, mRNAs are, in mammalian cells but not in budding yeast, only sensitive to NMD before the nuclear cap-binding complex (CBC) has been replaced with the cap-binding translation initiation factor eIF4E (reviewed in Maquat et al., 2010).

NMD mRNP AssemblyTargeting of an mRNA for NMD is initiated by the assembly of an NMD mRNP. The most central component of the NMD pathway is the superfamily 1 helicase Upf1 (reviewed in Amrani et al., 2006; Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009). Upf1 forms an interaction with translation release factors eRF3 and eRF1, in what is thought to be an early event in the formation of an NMD mRNP. In mammalian cells, a phosphoinositide 3-kinase (PI3K)-like kinase, Smg1, which phosphorylates Upf1 at multiple [S/T]Q motifs, has also been observed in complex with Upf1 and eRFs 1 and 3, in what has been named the SURF complex. Smg1 is conserved between metazoans. In budding yeast, phosphorylated Upf1, but no Smg1 ortholog, has been observed. Two other central and conserved components of the NMD pathway are Upf2 and Upf3. These form a complex with one another and with Upf1. In metazoans, Upf2 and Upf3 stimulate Smg1-mediated phosphorylation of Upf1. In mammals, the EJC interacts with the Upf2-Upf3 complex and also stimulates Upf1 phosphorylation, which likely contributes to the mechanism by which the EJC stimulates mammalian NMD (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009).

Phosphorylated Upf1 subsequently serves as a recruitment platform for Smg5, Smg6, and Smg7 proteins (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009). These proteins contain 14-3-3-like domains, which, as shown in the case of Smg7, promote direct interaction with phosphorylated residues in Upf1. In addi-tion, human Smg6 directly interacts with the EJC (Kashima et al., 2010). Evidence suggests that Smg5–7 proteins serve as a link between phosphorylated Upf1 and cellular mRNA decay machineries. Smg6 possesses a PIN domain with intrinsic endonuclease activity, and Smg7 can promote cellular decapping and 5′-to-3′ exonuclease activities. An additional protein in human cells, PNRC2, interacts with phospho-Upf1 and components of the decapping complex (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009). In addition to recruiting Smg5–7 and PNRC2 proteins, phosphorylated Upf1 has also been reported to repress translation initiation on mammalian NMD mRNPs via an interaction with translation initiation factor eIF3 (Isken et al., 2008). The importance of Upf1 phosphorylation in budding yeast is unclear, but a presumed budding yeast ortholog of Smg7 called Ebs1p stimulates, but is not critical for, NMD (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009).

NMD mRNP Disassembly and DecayThe degradation of the NMD mRNP can be initiated by alternative mechanisms. In human and D. melanogaster cells, a major event appears to be endonucleolytic cleavage near the PTC by Smg6. However, evidence for initiation of mRNA decay by decapping and deadenylation has also been reported in human cells. In budding yeast, the major mRNA decay-initiating event appears to be decapping, although deadenylation is also stimulated. After the mRNA decay-initiating event, degradation of the NMD substrate is completed by the 5′-to-3′ exonuclease Xrn1 and/or the 3′-to-5′ exonuclease, the exosome (reviewed in Chang et al., 2007; Lejeune and Maquat, 2005; Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009).

In human cells, the completion of 5′-to-3′ exonucleolytic decay by Xrn1 following endonucleolytic cleavage by Smg6 requires Upf1 ATPase-dependent disassembly of the NMD mRNP (Franks et al., 2010). It is unclear at which step during the NMD pathway that ATP hydrolysis by Upf1 takes place. However, the Upf1 ATPase is stimulated by the Upf2-Upf3 complex, suggesting that a transition taking place in the NMD mRNP regulates the timing of mRNP disassembly and decay. In budding yeast, the Upf1 ATPase likely acts in a similar manner, as in the absence of Upf1 ATPase activity, both human and budding yeast NMD mRNPs, like many other mRNPs stalled during mRNA decay, accumulate in cytoplasmic mRNP granules called P bodies (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009). Another event that occurs late in the NMD pathway in metazoans is the dephosphorylation of Upf1. Upf1 dephosphorylation is impaired in the absence of Smg5–7 proteins and of Upf1 ATPase activity, suggesting that Smg5–7 stimu-late Upf1 dephosphorylation sometime after the remodeling of the mRNP by the Upf1 ATPase (reviewed in Nicholson et al., 2010; Rebbapragada and Lykke-Andersen, 2009).

Future QuestionsSeveral questions remain in understanding the mechanism of the NMD pathway. For example, it remains unclear exactly how a premature termination event leads to the formation of an NMD mRNP and why this does not occur during normal termination. Early ideas implicated differences in recruitment of Upf proteins, but a more recent study suggests that differences in activation of Upf1 downstream of recruitment may contribute to substrate differentiation (Hogg and Goff, 2010). It also remains to be determined how Upf1 phosphorylation, dephosphorylation, and ATPase activity are coordinated on the NMD mRNP to ensure an ordered sequence of mRNP remodeling events and initiation of mRNA decay prior to mRNP disassembly. Also, what determines which of the alternative mRNA decay initiating events is activated in different organisms and under different conditions? Finally, is NMD a regulated process? The observation that human NMD target mRNAs show differences in their reliance of individual NMD factors (reviewed in Chang et al., 2007) leaves open the possibility that subsets of NMD substrates could be coregulated under various conditions. Answering these questions should not only provide more detailed insights into the NMD pathway, but should also help our understanding of mechanisms of mRNA decay in general.

Acknowledgments

We thank Dr. Suzanne Lee for helpful comments. Work on NMD in the J.L.-A. lab is supported by a grant from the National Science Foundation (MCB-0946464).

SnapShot: Nonsense-Mediated mRNA DecaySébastien Durand and Jens Lykke-AndersenDivision of Biology, University of California San Diego, La Jolla, CA 92093, USA

324.e2 Cell 145, April 15, 2011 ©2011 Elsevier Inc. DOI 10.1016/j.cell.2011.03.038

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Franks, T.M., Singh, G., and Lykke-Andersen, J. (2010). Upf1 ATPase-dependent mRNP disassembly is required for completion of nonsense- mediated mRNA decay. Cell 143, 938–950.

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