Mechanism, factors, and physiological role of nonsense-mediated mRNA decay

Abstract

Nonsense-mediated mRNA decay (NMD) is a translation-dependent, multistep process that degrades irregular or faulty messenger RNAs (mRNAs). NMD mainly targets mRNAs with a truncated open reading frame (ORF) due to premature termination codons (PTCs). In addition, NMD also regulates the expression of different types of endogenous mRNA substrates. A multitude of factors are involved in the tight regulation of the NMD mechanism. In this review, we focus on the molecular mechanism of mammalian NMD. Based on the published data, we discuss the involvement of translation termination in NMD initiation. Furthermore, we provide a detailed overview of the core NMD machinery, as well as several peripheral NMD factors, and discuss their function. Finally, we present an overview of diseases associated with NMD factor mutations and summarize the current state of treatment for genetic disorders caused by nonsense mutations.

Keywords: Exon junction complex; Genetic disease; NMD; Quality control; UPF1.

Fig. 1

Function of nonsense-mediated mRNA decay. Top A normal transcript consists of a 5′ cap, followed by a 5′ UTR, the ORF, a 3′ UTR, and a poly(A) tail. The ORF of a transcript with a normal termination codon is translated into a full length protein. Bottom A transcript carrying a premature termination codon (PTC) will host a shortened ORF as well as an elongated 3′ UTR. Instead of continuously translating the transcript into a truncated protein with possible deleterious function in the cell, the PTC-containing transcript will be degraded via NMD

Fig. 2

Model for degradation of PTC carrying transcripts. Step 1 Translation is initiated at the AUG start codon. The ribosome starts translation in the 5′ to 3′ direction. Step 2 When the translating ribosome stalls at a PTC, eRF1 and eRF3 interact with and bind to the ribosome. The physical distance between poly(A)-bound PABPC1 and the stalled ribosome is too large for efficient interaction and subsequent translation termination. Step 3 Since the interaction between PABPC1 and eRF3 is inefficient in this scenario, UPF1 is able to interact with eRF3 instead. Furthermore, the EJC serves as a binding platform for UPF3b and UPF2. Additionally, SMG1 is recruited to UPF1. SMG1 not only interacts with UPF1 and UPF2 but also phosphorylates UPF1. Step 4 Phosphorylated UPF1 recruits the SMG5/7 heterodimer as well as the endonuclease SMG6. The stalling ribosome has been removed from the transcript by this point. SMG6 cleaves the transcript in close proximity of the PTC, whereas SMG5/7 recruit the catalytic subunit of the CCR4-NOT deadenylase complex POP2. Step 5 The NMD factors are removed from the cleaved transcript and decapping and deadenylation commences. As a last step, the exonuclease XRN1 is recruited and degrades the transcript in 5′ to 3′ direction, and the exosome supposedly mediates 3′ to 5′ degradation

Fig. 3

Examples of NMD substrates. a Alternative splicing of a pre-mRNA can lead to PTC formation by, for example, exon-skipping. The PTC-containing transcript isoform is degraded in an EJC-dependent manner, whereas regularly spliced transcripts without a PTC will not be targeted by NMD. b An error during gene expression can lead to a nonsense mutation in the ORF of a transcript. If the PTC that arises due to this nonsense mutation is upstream of the last exon–exon junction, an EJC will be present downstream of the PTC and the transcript will be degraded via NMD. c Some long ncRNAs are known to harbor snoRNAs within their introns. The snoRNAs are released when the introns are spliced. snoRNA host genes do not encode a protein, but instead have only a short ORF with a PTC, which will lead to activation of NMD followed by subsequent degradation of the transcript. d Top Many transcripts with long 3′ UTRs are known targets of NMD. Middle Some mRNAs can host one or multiple uORFs, which will lead to EJC-mediated NMD, since the EJCs will not be displaced by a translating ribosome. Bottom Selenoprotein-encoding transcripts are a class of NMD targets that incorporate the unusual amino acid selenocysteine (Sec) at UGA codons. With low concentrations of Sec present, the UGA codon is decoded as a classical stop codon and, depending on its position, is treated as a PTC

Fig. 4

Overview of the core NMD factors UPF1, UPF2, UPF3b/a, the kinase SMG1, and the decay inducing factors SMG5, SMG6, and SMG7. The domain architecture for all factors, as well as the NMD-specific functions of important regions are depicted here (for details, see text). The most studied isoforms of NMD factors were chosen for representation and match, except for SMG1, those indicated in Table 2 (see footnote b for SMG1 discrepancy). UPF1 phosphorylation sites (SQ and TQ motifs) verified by various experimental approaches (ultradeep HeLa cell phosphoproteome [222], in vitro phophorylation assay with UPF1 peptides [106] or full length UPF1 [154] ) are indicated. The phosphosites connected to specific recruiting functions are highlighted specifically