Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that likely exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons. Translation of these aberrant mRNAs could, in some cases, lead to deleterious gain-of-function or dominant-negative activity of the resulting proteins. NMD was first described in 1979 in yeast, and in 1981 in human cells which suggests broad phylogenetic conservation and an important biological role. NMD was discovered when it was observed that cells often contain unexpectedly low concentrations of mRNAs that are transcribed from alleles carrying nonsense mutations. Nonsense mutations code for a premature stop codon which causes the protein to be shortened. The truncated protein may or may not be functional, depending on the importance of the residues that are not translated. In human genetics, NMD has the potential not only to limit the translation of abnormal proteins but also to occasionally cause detrimental effects in specific genetic mutations. NMD regulates numerous biological functions in a diverse range of cells, such as contributing to the synaptic plasticity of neurons which shapes adult behavior.
Pathway While many of the proteins involved in NMD are not conserved between species, in Saccharomyces cerevisiae (brewer's yeast), the pathway has three main factors: UPF1, UPF2, and UPF3 (UPF3A and UPF3B in humans), which make up the conserved core of the NMD pathway. All three of these factors are trans-acting elements called up-frameshift (UPF) proteins. In mammals, UPF2 and UPF3 are part of the exon–exon junction complex (EJC) that remains bound to mRNA after splicing, along with other proteins, including eIF4AIII, MLN51, and the Y14/MAGOH heterodimer, which also function in NMD. UPF1 phosphorylation is controlled by the proteins SMG1, SMG5, SMG6, and SMG7. The process of detecting aberrant transcripts occurs during translation of the mRNA. A popular model for the detection of aberrant transcripts in mammals suggests that during the first round of translation, the ribosome removes the exon–exon junction complexes (EJCs) that were bound to the mRNA during splicing. If any of these proteins remain bound to the mRNA after this first round of translation, NMD is activated. EJCs located downstream of a stop codon are not removed from the transcript because the ribosome is released before reaching them, so transcripts to which EJCs remain attached after translation are almost invariably the product of a nonsense mutation. Termination of translation leads to the assembly of a complex composed of UPF1, SMG1 and the release factors, eRF1 and eRF3, on the mRNA. If an EJC is left on the mRNA because the transcript contains a premature stop codon, then UPF1 comes into contact with UPF2 and UPF3, triggering the phosphorylation of UPF1. In vertebrates, the location of the last EJC relative to the termination codon usually determines whether the transcript will be subjected to NMD or not. If the termination codon is downstream of or within about 50 nucleotides of the final EJC then the transcript is translated normally. However, if the termination codon is further than about 50 nucleotides upstream of any EJCs, then the transcript is downregulated by NMD. The phosphorylated UPF1 then interacts with SMG5, SMG6, and SMG7, which promote the dephosphorylation of UPF1. SMG7 is thought to be the terminating effector in NMD, as it accumulates in P-bodies, which are cytoplasmic sites for mRNA decay. In both yeast and human cells, the major pathway for mRNA decay is initiated by the removal of the 5' cap followed by degradation by XRN1, an exoribonuclease enzyme. The other pathway by which mRNA is degraded is by deadenylation in the 3'-to-5' direction. In addition to the well-recognized role of NMD in removing aberrant transcripts, there are transcripts that contain introns within their 3' untranslated regions (UTRs). These messages are predicted to be NMD targets yet a few examples (e.g. activity-regulated cytoskeleton-associated protein, known as ARC) appear to have crucial biological functions, suggesting that NMD may have physiologically relevant roles.
Mechanism and regulation NMD is a cellular mechanism that degrades mRNAs containing premature termination codons (PTCs), which can arise from mutations in the genomic template. Comprehensive analyses of large-scale genetics and gene expression datasets have enabled the systematic identification of NMD and its efficiency.
EJC model: NMD is typically triggered when a PTC is located upstream of the last exon junction complex (EJC). If the PTC is downstream of the last EJC, NMD is often inefficient. Start-proximal effect: PTCs located near the start codon can evade NMD. This evasion is associated with the presence of downstream in-frame stop codons, which can allow the ribosome to bypass the PTC and continue translation. Exon length and distance to normal stop codon: Long exons and large distances between the PTC and the normal stop codon are associated with inefficient NMD. This suggests that the spatial configuration of the mRNA can influence the accessibility of NMD machinery. mRNA turnover rate: Transcripts with rapid turnover rates tend to attenuate the effects of NMD. This means that mRNAs that are quickly degraded by other mechanisms may not be efficiently targeted by NMD. RNA-binding protein motifs: Certain RNA-binding protein motifs near the PTC or within the 3′UTR can modulate NMD efficiency. These motifs can either enhance or inhibit the recognition of PTCs by NMD machinery, depending on their specific interactions with NMD factors. Generalized frameshift: As a response to poor nutritional conditions, the bulk of the yeast transcriptome undergoes −1 ribosomal frameshifts which leads to an accelerated co-translational mRNA decay. Under such conditions NMD-dependent degradation represents at least one-third of the total mRNA decay. Less optimal codons are a key factor for ribosomes to induce out-of-frame mRNA decay. This mechanism appears to be conserved from bacteria to humans.
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