Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species

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Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway that ensures the rapid degradation of mRNAs containing premature translation termination codons (PTCs), thereby preventing the synthesis of truncated and potentially harmful proteins. In addition, this pathway regulates the expression of ∼10% of the transcriptome and is essential in mice. Although NMD is conserved in eukaryotes, recent studies in several organisms have revealed that different mechanisms have evolved to discriminate natural from premature stop codons and to degrade the targeted mRNAs. With the elucidation of the first crystal structures of components of the NMD machinery, the way is paved towards a molecular understanding of the protein interaction network underlying this process.

Introduction

Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved mRNA surveillance pathway that detects and eliminates mRNAs harboring premature translation termination codons (PTCs) in eukaryotes [1, 2] (see review by Lejeune and Maquat in this issue). Recently, it has become clear that the NMD pathway not only degrades aberrant mRNAs containing PTCs as a result of mutations or errors during transcription or RNA processing, but is also implicated in regulating the expression of wild-type transcripts [3] (see review by Lejeune and Maquat in this issue). Indeed, gene expression profiling of yeast, Drosophila or human cells defective in NMD has revealed that NMD regulates the expression of ∼10–20% of the transcriptome [4•, 5••, 6].

Two critical steps in the NMD pathway have attracted much attention in recent years: the mechanism by which premature stop codons are recognized and discriminated from natural stops (PTC definition), and the mechanism by which PTC-containing mRNAs are targeted for fast degradation. PTC definition is a translation-dependent step involving cross-talk between the ribosome stalled at a stop codon and a downstream cis-acting signal on the mRNA. This cross-talk leads to the recruitment of trans-acting NMD factors, the assembly of the surveillance complex and ultimately the degradation of the mRNA. Despite conservation of the NMD pathway, the nature of the cis-acting signals and the decay pathway of targeted mRNAs vary across species (Figure 1, see below). In this review, we discuss these mechanistic variations and the molecular insights to which recent structural studies have contributed by visualizing some of the interactions that lead to PTC definition and decay of targeted transcripts.

Section snippets

The conserved core of the surveillance complex consists of UPF1, UPF2 and UPF3

The key players in the NMD pathway were initially identified in genetic screens in Saccharomyces cerevisiae and Caenorhabditis elegans [7, 8, 9, 10]. These screens led to the identification of three yeast (UPF13) and seven C. elegans (smg-1–7) genes that play an essential role in NMD. The UPF1, UPF2 and UPF3 proteins (known as SMG-2, SMG-3 and SMG-4 in C. elegans) are core components of the surveillance complex whose basic function is conserved in eukaryotes [7, 8, 9, 10, 11, 12, 13]. Deletion

Phosphorylation/dephosphorylation cycles of UPF1 in multicellular organisms

In metazoans, UPF1 has N- and C-terminal extensions with multiple serine residues that are targets for phosphorylation [11, 21]. Regulation of the phosphorylation state of UPF1 involves four additional proteins (SMG1,5,6,7) that were identified as essential NMD factors in C. elegans [21, 22, 23, 24, 25, 26, 27•, 28•, 29]. With the exception of SMG7, these proteins are conserved in metazoa [13, 29].

Phosphorylation of UPF1 is catalyzed by SMG1, a phosphoinositide-3-kinase-related protein kinase [

PTC definition in mammals: the exon junction complex

In mammals, recognition of premature stop codons results from the cross-talk between terminating ribosomes and a downstream EJC comprising UPF3 and UPF2 [1, 2] (see review by Lejeune and Maquat in this issue). According to the current model, if translating ribosomes encounter a stop codon upstream of an EJC, UPF1 is recruited by translation release factors and interacts with the UPF2 and UPF3 proteins bound to the downstream EJC. This event would create an opportunity for the assembly of an

PTC definition in yeast and Drosophila occurs independently of exon boundaries

As mentioned above, although several components of the human EJC are conserved in Drosophila and are involved in post-transcriptional mRNA metabolism, they do not play a role in PTC definition or NMD [13]. Indeed, in both Drosophila and S. cerevisiae, PTC definition occurs independently of exon–exon boundaries [1, 2, 13] (see review by Lejeune and Maquat in this issue). This is consistent with the observation that PTC-containing mRNAs transcribed from intronless genes are subjected to NMD in

Degradation of PTC-containing mRNAs: XRN1, the Ski complex and the exosome

Independent of the mechanism by which PTCs are defined, once the mRNA is recognized as being aberrant, its degradation is mediated by the enzymes that are involved in general mRNA decay. In eukaryotic cells, general mRNA degradation is initiated by shortening of the poly(A)-tail by deadenylases [51]. Following this first rate-limiting step, mRNAs can be degraded via one of two pathways. In one pathway, deadenylation triggers decapping, and this exposes the mRNA body for digestion by the major

From PTC recognition to mRNA degradation in metazoa

What is the molecular mechanism that leads from the recognition of a PTC and assembly of the surveillance complex to the recruitment of mRNA decay enzymes? A hint on how the decay enzymes are recruited to NMD targets in mammals comes from studies on the cellular localization and function of the SMG5–7 proteins [59]. When overexpressed, SMG7 accumulates in cytoplasmic foci corresponding to endogenous P-bodies. Overexpression of SMG7 also causes the accumulation of SMG5 or UPF1 in P-bodies, and

Conclusions and perspectives

NMD factors have been identified by genetic screens in S. cerevisiae or C. elegans and more recently by biochemical approaches in human cells. Although there are certainly more factors to be discovered, the complexity of the protein interaction network involved in NMD is already emerging (Figure 5). Moreover, investigations of the NMD pathway across species suggest that the complexity of the network increases from simpler organisms such as S. cerevisiae to humans by the introduction of

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

We apologize to colleagues whose original work we could not cite due to limitations of space. We are grateful to members of our groups for their comments on the manuscript and to Petra Riedinger for helping with the schematic drawings. Both authors are supported by the European Molecular Biology Organization (EMBO) and the Human Frontier Science Program Organization (HFSPO).

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