The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon.

Abstract

mRNA decay rates often increase when translation is terminated prematurely due to a frameshift or nonsense mutation. We have identified a yeast gene, UPF1, that codes for a trans-acting factor whose function is necessary for enhanced turnover of mRNAs containing a premature stop codon. In the absence of UPF1 function, frameshift or nonsense mutations in the HIS4 or LEU2 genes that normally cause rapid mRNA decay fail to have this effect. Instead, the mRNAs decay at rates similar to the corresponding wild-type mRNAs. The stabilization of frameshift or nonsense mRNAs observed in upfl-strains does not appear to result from enhanced readthrough of the termination signal. Loss of UPF1 function has no effect on the accumulation or stability of HIS4 + or LEU2 + mRNA, suggesting that the UPF1 product functions only in response to a premature termination signal. When we examined the accumulation and stability of other wild-type mRNAs in the presence or absence of UPF1, including MAT~I, STE3, ACT1, PGK1, PAB1, and URA3 mRNAs, only the URA3 transcript was affected. On the basis of these and other results, the UPF1 product appears to participate in a previously uncharacterized pathway leading to the degradation of a limited class of yeast transcripts. Nonsense mutations that generate a premature translational termination signal often reduce the steady-state accumulation of the corresponding mRNA (Brown 1989;Peltz et al. 1990). In a study of the yeast URA3 gene, it was shown that the extent of reduced mRNA accumulation depends on the position of the nonsense mutation (Losson and Lacroute 1979). Mutations near the 5' end of the transcript were shown to have a greater destabilizing effect than mutations near the 3' end. Furthermore, introduction of an amber tRNA suppressor restabilized ura3 nonsense mRNA, indicating that the turnover rate is determined in part by the relative efficiencies of termination versus readthrough of the stop codon. These studies suggested that the turnover rate of nonsense mRNA is probably related to some aspect of its translation rather than to a potential change in mRNA structure that might result from the presence of a nonsense mutation.Similar studies in higher eukaryotes have proven more difficult to interpret. In some cases, the introduction of a premature stop codon into a gene has been linked to 3Corresponding author. increased cytoplasmic turnover (Maquat et al. 1981;Barker and Beemon 1991). However, other studies suggest that nonsense mutations may cause changes in nuclear processing and/or transport, and these changes, rather than cytoplasmic mRNA degradation, may be primarily responsible for decreased steady-state mRNA levels (Humphries et al. 1984;Takeshita et al. 1984;Urlaub et al. 1989;Cheng et al. 1990).Here, we report the characterization of mutations in the yeast Saccharomyces cerevisiae that specifically stabilize mRNAs containing a premature translational termination signal. The mutations arose in a strain containing his4-38, a + 1 frameshift mutation near the 5' end of the HIS4 tr...

Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise

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A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability

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Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay

“…The nonsense-mediated mRNA decay (NMD) pathway is a cellular quality control mechanism that degrades aberrant mRNAs harboring premature termination codons (Losson & Lacroute, 1979;Gozalbo & Hohmann, 1990;Maquat, 1995;Caponigro & Parker, 1996;Jacobson & Peltz, 1996;Ruiz-Echevarria et al+, 1996;Weng et al+, 1997)+ This mRNA surveillance pathway functions in all eukaryotic systems examined and appears to have evolved to recognize premature termination events during the protein synthesis process (Pulak & Anderson, 1993;Weng et al+, 1996aWeng et al+, , 1996bWeng et al+, , 1998Czaplinski et al+, 1998Czaplinski et al+, , 1999+ Several genes required for NMD have been identified in the yeast Saccharomyces cerevisiae+ Mutations in the UPF1, UPF2, UPF3, MOF2/SUI1, MOF5, MOF8, and HRPI genes were shown to selectively stabilize mRNAs containing early nonsense mutations without affecting the decay rates of most wild-type mRNAs (Leeds et al+, 1991(Leeds et al+, , 1992Cui et al+, 1995Cui et al+, , 1999He & Jacobson, 1995;Lee & Culbertson, 1995;Gonzalez et al+, 2000)+ Subsequently, Upf1p, Upf2p, and Upf3p were shown to form a complex (He & Jacobson, 1995;Weng et al+, 1996b;He et al+, 1997)+ In other studies using Caenorhabditis elegans, Smg genes were identified whose products were shown to be involved in NMD and a subset of those are homologous to the yeast UPF genes (Pulak & Anderson, 1993;Cali & Anderson, 1998)+…”

“…The yeast UPF1 gene and its protein product have been the most extensively investigated factor in the NMD pathway (Altamura et al+, 1992;Koonin, 1992;Leeds et al+, 1992;Atkin et al+, 1995Atkin et al+, , 1997Czaplinski et al+, 1995Czaplinski et al+, , 1999Cui et al+, 1996;Weng et al+, 1996aWeng et al+, , 1996bWeng et al+, , 1998)+ The Upf1p contains a cysteine-and histidine-rich region near its amino terminus and all the motifs of the superfamily group I helicases+ The yeast Upf1p has been purified and demonstrated to have RNA-binding activity, RNA-dependent ATPase activity, and RNA helicase activity (Czaplinski et al+, 1995, Weng et al+, 1996a, 1996b)+ Disruption of the UPF1 gene results in stabilization of nonsense-containing mRNAs and suppression of certain nonsense alleles (Leeds et al+, 1991;Cui et al+, 1995;Czaplinski et al+, 1995;Weng et al+, 1996aWeng et al+, , 1996b)+ A set of mutations was isolated in the UPF1 gene that separated its mRNA decay function from its activity in modulating translation termination at a nonsense codon (Weng et al+, 1996a(Weng et al+, , 1996b)+ Consistent with the view that the Upf1p is involved in modulating translation termination, recent results have shown that it interacts with the translation termination release factors eRF1 and eRF3 (Czaplinski et al+, 1998(Czaplinski et al+, , 1999)+ These data suggest that the NMD and translation termination pathways are linked (reviewed in Czaplinski et al+, 1998Czaplinski et al+, , 1999)+ Based on these observations, a "surveillance complex" consisting of at least Upf1p, Upf2p, Upf3p, and the release factors has been suggested to modulate translation termination and NMD (Czaplinski et al+, 1998(Czaplinski et al+, , 1999)+ Homologs of the Upf1p have been identified in humans cells (the HUPF1/RENT gene; Perlick et al+, 1996, Applequist et al+, 1997 and in C. elegans (Page et al+, 1999;Jacobson & Peltz, 1996; WORMPEP: Y48G8A 3304+a)+ It is evident that the Upf1p plays a conserved role in NMD...…”