It has been proposed that the 7-methylguanosine cap and poly(A) tail of mRNAs have important functions in translation and transcript stability. To directly test these roles of the cap and poly(A) tail, we have constructed plasmids with a ribozyme within the coding region or 39 UTR of reporter genes. We show that the unadenylated 59 cleavage product is translated and is rapidly degraded by the cytoplasmic exosome. This exosome-mediated decay is independent of the nonstop mRNA decay pathway, and, thus, reveals an additional substrate for exosome-mediated decay that may have physiological equivalents. The rapid decay of this transcript in the cytoplasm indicates that this unadenylated cleavage product is rapidly exported from the nucleus. We also show that this cleavage product is not subject to rapid decapping; thus, the lack of a poly(A) tail does not always trigger rapid decapping of the transcript. We show that the 39 cleavage product is rapidly degraded by Xrn1p in the cytoplasm. We cannot detect any protein from this 39 cleavage product, which supports previous data concluding that the 59 cap is required for translation. The reporter genes we have utilized in these studies should be generally useful tools in studying the importance of the poly(A) tail and 59 cap of a transcript for export, translation, mRNA decay, and other aspects of mRNA metabolism in vivo

SUMMARY Histone mRNAs are rapidly degraded when DNA replication is inhibited during S-phase with degradation initiating with oligouridylation of the stemloop at the 3′ end. We developed a customized RNA-Seq strategy to identify the 3′ termini of degradation intermediates of histone mRNAs. Using this strategy, we identified two types of oligouridylated degradation intermediates: RNAs ending at different sites of the 3′ side of the stemloop that resulted from initial degradation by 3′hExo and intermediates near the stop codon and within the coding region. Sequencing of polyribosomal histone mRNAs revealed that degradation initiates and proceeds 3′ to 5′ on translating mRNA and many intermediates are capped. Knockdown of the exosome-associated exonuclease Pml/Scl-100, but not the Dis3L2 exonuclease, slows histone mRNA degradation, consistent with 3′ to 5′ degradation by the exosome containing PM/Scl-100. Knockdown of No-go decay factors also slowed histone mRNA degradation, suggesting a role in removing ribosomes from partially degraded mRNAs.

Nonstop mRNA decay, a specific mRNA surveillance pathway, rapidly degrades transcripts that lack inframe stop codons. The cytoplasmic exosome, a complex of 39-59 exoribonucleases involved in RNA degradation and processing events, degrades nonstop transcripts. To further understand how nonstop mRNAs are recognized and degraded, we performed a genomewide screen for nonessential genes that are required for nonstop mRNA decay. We identified 16 genes that affect the expression of two different nonstop reporters. Most of these genes affected the stability of a nonstop mRNA reporter. Additionally, three mutations that affected nonstop gene expression without stabilizing nonstop mRNA levels implicated the proteasome. This finding not only suggested that the proteasome may degrade proteins encoded by nonstop mRNAs, but also supported previous observations that rapid decay of nonstop mRNAs cannot fully explain the lack of the encoded proteins. Further, we show that the proteasome and Ski7p affected expression of nonstop reporter genes independently of each other. In addition, our results implicate inositol 1,3,4,5, 6-pentakisphosphate as an inhibitor of nonstop mRNA decay.

Eukaryotic mRNAs harboring premature translation termination codons are recognized and rapidly degraded by the nonsense-mediated mRNA decay (NMD) pathway. The mechanism for discriminating between mRNAs that terminate translation prematurely and those subject to termination at natural stop codons remains unclear. Studies in multiple organisms indicate that proximity of the termination codon to the 3' poly(A) tail and the poly(A) RNA-binding protein, PAB1, constitute the critical determinant in NMD substrate recognition. We demonstrate that mRNA in yeast lacking a poly(A) tail can be destabilized by introduction of a premature termination codon and, importantly, that this mRNA is a substrate of the NMD machinery. We further show that, in cells lacking Pab1p, mRNA substrate recognition and destabilization by NMD are intact. These results establish that neither the poly(A) tail nor PAB1 is required in yeast for discrimination of nonsense-codon-containing mRNA from normal by NMD.

The functions of the eRF3 protein in translation termination and prion propagation are easily separated. The N-terminal domain of eRF3 is required for prion propagation (7,8). Point mutations in, or deletion of, the N-terminal domain disrupt the prion propagation function of yeast eRF3, and the N-terminal domain by itself is sufficient for prion propagation (3,7,9). The translation termination function of eRF3 requires the well conserved C-terminal domain. Deletion of the C-terminal domain is lethal, presumably because of defects in translation termination, and point mutations in the C-terminal domain reduce translation termination efficiency (9). Thus, the prion property of eRF3 is a property of the N-terminal domain, whereas the C-terminal domain is required for translation termination.The ability of eRF3 to exist in [PSI ϩ ] and [psi Ϫ ] states has been conserved during evolution and is present in the eRF3 proteins of several species and genera of yeast (10)(11)(12)(13)(14) ] induces phenotypic variation by suppressing premature stop codons, it has been reported that in seven cases the effect of [PSI ϩ ] was similar to the effect of upf1⌬, which also suppresses premature stop codons (see below) (16). However, it was also reported that in four other cases the effect of [PSI ϩ ] was not mimicked by upf1⌬, suggesting that there may be additional mechanisms by which [PSI ϩ ] affects phenotypes (16).Two lines of evidence suggest that [PSI ϩ ] affects translation termination not only at premature stop codons, but also at wild-type stop codons naturally found at the 3Ј end of coding regions. First, the frequency of extra stop codons just 3Ј of the normal stop codon of yeast genes is higher than expected, suggesting that read-through of the normal stop codons occurs at a frequency that is a significant factor over evolutionary time (19). Second, Namy et al. (20) identified eight genes that had a poor stop codon context. In an artificial reporter gene, translation termination at these stop codon contexts was affected by [PSI ϩ ]. Thus, [PSI ϩ ] might affect phenotypic variation by promoting read-through of normal stop codons (16)(17)(18)20).In addition to PSI directly affecting translation termination of premature and͞or normal stop codons, there may be indirect effects on mRNA stability because translation termination and mRNA stability are intimately linked (16). Two aspects of this link are nonsense-mediated mRNA decay and nonstop mRNA decay. Nonsense-mediated mRNA decay is the process of rapidly degrading mRNAs that contain a premature stop codon (reviewed in ref. 21). It is thought that nonsense-containing mRNAs are recognized as a consequence of premature translation termination. Because [PSI ϩ ] affects the efficiency of translation termination, it may also affect nonsense-mediated mRNA decay. Nonstop mRNA decay is the process of degrading mRNAs that do not contain stop codons (22,23). Nonstop mRNAs are