Aberrant termination triggers nonsense-mediated mRNA decay

Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655-0122, USA.
Biochemical Society Transactions (Impact Factor: 3.19). 03/2006; 34(Pt 1):39-42. DOI: 10.1042/BST20060039
Source: PubMed


NMD (nonsense-mediated mRNA decay) is a cellular quality-control mechanism in which an otherwise stable mRNA is destabilized by the presence of a premature termination codon. We have defined the set of endogenous NMD substrates, demonstrated that they are available for NMD at every round of translation, and showed that premature termination and normal termination are not equivalent biochemical events. Premature termination is aberrant, and its NMD-stimulating defects can be reversed by the presence of tethered poly(A)-binding protein (Pab1p) or tethered eRF3 (eukaryotic release factor 3) (Sup35p). Thus NMD appears to be triggered by a ribosome's failure to terminate adjacent to a properly configured 3'-UTR (untranslated region), an event that may promote binding of the UPF/NMD factors to stimulate mRNA decapping.

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    • "Several models have been proposed to explain how these components of the NMD machinery recognize a PTC and recruit RNA degradation proteins (25–39). Most models revolve around the notion that RNA decay is triggered when a stop codon is followed by a second signal that defines the stop codon as premature (3,11). In the ‘faux 3′-UTR’ model, translation termination at a normal stop codon is proposed to be fundamentally different from translation termination at a PTC; mRNA decay is activated by the aberrant nature of premature termination (27). "
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    ABSTRACT: One third of inherited genetic diseases are caused by mRNAs harboring premature termination codons as a result of nonsense mutations. These aberrant mRNAs are degraded by the Nonsense-Mediated mRNA Decay (NMD) pathway. A central component of the NMD pathway is Upf1, an RNA-dependent ATPase and helicase. Upf1 is a known phosphorylated protein, but only portions of this large protein have been examined for phosphorylation sites and the functional relevance of its phosphorylation has not been elucidated in Saccharomyces cerevisiae. Using tandem mass spectrometry analyses, we report the identification of 11 putative phosphorylated sites in S. cerevisiae Upf1. Five of these phosphorylated residues are located within the ATPase and helicase domains and are conserved in higher eukaryotes, suggesting a biological significance for their phosphorylation. Indeed, functional analysis demonstrated that a small carboxy-terminal motif harboring at least three phosphorylated amino acids is important for three Upf1 functions: ATPase activity, NMD activity and the ability to promote translation termination efficiency. We provide evidence that two tyrosines within this phospho-motif (Y-738 and Y-742) act redundantly to promote ATP hydrolysis, NMD efficiency and translation termination fidelity.
    Full-text · Article · Nov 2013 · Nucleic Acids Research
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    • "NMD is coupled to translation termination. NMD trans factors identify a stop codon as a PTC and initiates rapid degradation of the transcript if its translation termination is inefficient owing to the presence of NMD cis elements in the 3′UTR (13). For efficient termination, the eukaryotic release factor 3 (eRF3) component of the terminating ribosome has to bind to the poly(A) tail-binding protein (PABP). "
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    ABSTRACT: Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control system that recognizes and degrades transcripts containing NMD cis elements in their 3'untranslated region (UTR). In yeasts, unusually long 3'UTRs act as NMD cis elements, whereas in vertebrates, NMD is induced by introns located >50 nt downstream from the stop codon. In vertebrates, splicing leads to deposition of exon junction complex (EJC) onto the mRNA, and then 3'UTR-bound EJCs trigger NMD. It is proposed that this intron-based NMD is vertebrate specific, and it evolved to eliminate the misproducts of alternative splicing. Here, we provide evidence that similar EJC-mediated intron-based NMD functions in plants, suggesting that this type of NMD is evolutionary conserved. We demonstrate that in plants, like in vertebrates, introns located >50 nt from the stop induces NMD. We show that orthologs of all core EJC components are essential for intron-based plant NMD and that plant Partner of Y14 and mago (PYM) also acts as EJC disassembly factor. Moreover, we found that complex autoregulatory circuits control the activity of plant NMD. We demonstrate that expression of suppressor with morphogenic effect on genitalia (SMG)7, which is essential for long 3'UTR- and intron-based NMD, is regulated by both types of NMD, whereas expression of Barentsz EJC component is downregulated by intron-based NMD.
    Full-text · Article · May 2013 · Nucleic Acids Research
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    • "The nonsense-mediated mRNA decay (NMD) pathway is a specialized pathway that contributes to the recognition and rapid degradation of mRNA with premature termination codons, thus preventing the production of non-functional, potentially harmful, truncated proteins. NMD influences the expression of a number of human genetic diseases by affecting the expression of genes carrying nonsense mutations (reviewed in Culbertson and Leeds, 2003; Amrani et al., 2006; Nicholson et al., 2009) Three core trans-acting factors are required for NMD in all eukaryotes. These are the upframeshift proteins Upf1p, Upf2p and Upf3p. "
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    ABSTRACT: The eukaryotic nonsense-mediated mRNA decay pathway (NMD) is a specialized pathway that contributes to the recognition and rapid degradation of mRNA with premature termination codons. In addition to mRNAs containing premature termination codons, NMD degrades non-nonsense-containing, natural mRNAs. Approximately 5-10% of the total Saccharomyces cerevisiae transcriptome is affected when NMD is inactivated. The regulation of natural mRNAs by NMD has physiological consequences. However, the physiological outcomes associated with the degradation of specific natural mRNAs by NMD are not fully understood. Here, we examined the physiological consequences resulting from the NMD-mediated regulation of an mRNA involved in copper homeostasis, in an attempt to understand why nmd mutant strains are more tolerant of toxic copper levels than wild-type yeast strains. We found that wild-type (UPF1) and upf1Δ mutants accumulate similar amounts of total copper when grown in medium containing elevated levels of copper; however, the copper levels in the cytoplasm of wild-type yeast cells were higher than in the upf1Δ mutant. Copper tolerance by the upf1Δ mutant is dependent on the presence of CTR2. Deletion of CTR2 resulted in similar cytoplasmic copper levels in wild-type and upf1Δ mutant strains, regardless of the environmental copper levels. This suggests that CTR2 plays a role in regulating the level of copper in the cytoplasm. We also found that the upf1Δ mutant contained elevated copper levels in the vacuole relative to wild-type yeast cells, after both strains were exposed to elevated copper levels
    Full-text · Article · May 2013 · Yeast
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