Deadenylation-Dependent and -Independent Decay Pathways for α1-Tubulin mRNA in <i>Chlamydomonas reinhardtii</i>

Gera, Joseph; Baker, Ellen J.

doi:10.1128/mcb.18.3.1498

Cited by 23 publications

(18 citation statements)

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“…In Saccharomyces cerevisiae, Chlamydomonas reinhardtii (Gera and Baker, 1998), and possibly other eukaryotes (Lim and Maquat, 1992;Higgs and Colbert, 1994;Couttet et al, 1997), mRNA deadenylation leads to decapping of the mRNA, which is then followed by rapid 5Ј to 3Ј exonucleolytic degradation (Decker and Parker, 1993;Hsu and Stevens, 1993;Muhlrad et al, , 1995. Decapping is an important step in the turnover of yeast mRNAs, because it precedes the decay of the body of the transcript and is also a site of control, as individual mRNAs are decapped at different rates (Muhlrad et al, , 1995Caponigro and Parker, 1996).…”

Section: Introductionmentioning

confidence: 98%

Recognition of Yeast mRNAs as “Nonsense Containing” Leads to Both Inhibition of mRNA Translation and mRNA Degradation: Implications for the Control of mRNA Decapping

Muhlrad

Parker

1999

MBoC

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A critical step in the degradation of many eukaryotic mRNAs is a decapping reaction that exposes the transcript to 5' to 3' exonucleolytic degradation. The dual role of the cap structure as a target of mRNA degradation and as the site of assembly of translation initiation factors has led to the hypothesis that the rate of decapping would be specified by the status of the cap binding complex. This model makes the prediction that signals that promote mRNA decapping should also alter translation. To test this hypothesis, we examined the decapping triggered by premature termination codons to determine whether there is a down-regulation of translation when mRNAs were recognized as "nonsense containing." We constructed an mRNA containing a premature stop codon in which we could measure the levels of both the mRNA and the polypeptide encoded upstream of the premature stop codon. Using this system, we analyzed the effects of premature stop codons on the levels of protein being produced per mRNA. In addition, by using alterations either in cis or in trans that inactivate different steps in the recognition and degradation of nonsense-containing mRNAs, we demonstrated that the recognition of a nonsense codon led to a decrease in the translational efficiency of the mRNA. These observations argue that the signal from a premature termination codon impinges on the translation machinery and suggest that decapping is a consequence of the change in translational status of the mRNA.

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Section: Introductionmentioning

confidence: 98%

Recognition of Yeast mRNAs as “Nonsense Containing” Leads to Both Inhibition of mRNA Translation and mRNA Degradation: Implications for the Control of mRNA Decapping

Muhlrad

Parker

1999

MBoC

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“…Much less is known about mRNA turnover in other organisms. However, the decay pathways identified in yeast are likely to be conserved, because decay intermediates corresponding to these pathways have been identified in both plant and animal cells (9)(10)(11)(12). In addition, homologues to the yeast mRNA decay factors are also found in mammals (13)(14)(15)(16)(17).…”

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confidence: 99%

“…Taken together with studies on the effect of various mRNA structural modifications on mRNA decay in vitro (21,28) and immunodepletion experiments (29), these data have led to the suggestion that the exosome-dependent 3Ј-5Ј decay pathway is more important in mammalian cells. It is noteworthy, however, that specific intermediates of the 5Ј-3Ј pathways were detected in human cells (9)(10)(11)(12). Thus, the relative contribution of each pathway to in vivo mRNA degradation in human cells remains to be established.…”

mentioning

confidence: 99%

DcpS can act in the 5′–3′ mRNA decay pathway in addition to the 3′–5′ pathway

Dijk

Hir

Séraphin

2003

Proc. Natl. Acad. Sci. U.S.A.

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Eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3-5 mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5-3 pathway, the recently identified human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce m7GDP and 5-phosphorylated mRNA. We investigated mRNA decay in human cell extracts by using a new assay for decapping. We observed that 5-phosphorylated intermediates resulting from decapping appear after incubation of a substrate RNA in human cell extracts, indicating the presence of an active 5-3 mRNA decay pathway. Surprisingly, however, the cognate m7GDP product was not detected, whereas abundant amounts of m7GMP were generated. Additional experiments revealed that m7GDP is, unexpectedly, efficiently converted to m7GMP in extracts from various organisms. The factor necessary and sufficient for this reaction was identified as DcpS in both yeast and human. m7GMP is thus a general, pathway-independent, by-product of eukaryotic mRNA decay. m7GDP breakdown should prevent misincorporation of methylated nucleotides in nucleic acids and could generate a unique indicator allowing the cell to monitor mRNA decay. A major step of gene regulation occurs at the level of mRNA turnover (1-3), a process that has been extensively studied in the yeast Saccharomyces cerevisiae. In this organism, degradation of most wild-type mRNAs starts with the removal of the poly(A) tail (deadenylation) (1). A major pathway comprises subsequent hydrolysis of the cap structure by Dcp1͞Dcp2, followed by rapid 5Ј-3Ј exonucleolytic degradation by Xrn1 (5Ј-3Ј mRNA decay pathway) (4). In an alternative, minor, pathway, deadenylation is followed by exosome-dependent 3Ј-5Ј degradation of the mRNA body (3Ј-5Ј pathway) (5). In addition, two specialized surveillance pathways exist. On the one hand, mRNAs containing a premature stop codon are degraded by deadenylation-independent decapping and 5Ј-3Ј decay (nonsense-mediated mRNA decay, NMD) (6). On the other hand, mRNAs lacking a stop codon are degraded by exosomedependent 3Ј-5Ј exonucleolytic trimming (nonstop decay, NSD) (7,8). Much less is known about mRNA turnover in other organisms. However, the decay pathways identified in yeast are likely to be conserved, because decay intermediates corresponding to these pathways have been identified in both plant and animal cells (9-12). In addition, homologues to the yeast mRNA decay factors are also found in mammals (13-17).Eukaryotic mRNAs contain at their 5Ј end a cap structure containing a guanosine methylated at position 7, attached in an inverted manner (5Ј-5Ј) to the first mRNA nucleotide by a triphosphate linkage (18). This specific feature of eukaryotic mRNAs protects them from 5Ј-3Ј exonucleases and serves as a recognition site for factors involved in pre-mRNA splicing, RNA transport, and translation initiation (19). Degradation of eukaryotic mRNAs entails the specific removal of the mRNA cap (20). This process diff...

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“…For example, deadenylation can be the first step in mammalian mRNA turnover (42,47). Moreover, deadenylated decapped intermediates in turnover can be detected in mammals and in Chlamydomonas (12,18). In addition, several proteins functioning in mRNA decapping in yeast (Dcp1p, Dcp2p, Xrn1p, Pat1p [also known as Mrt1p], and Lsm1p) have homologs throughout the eukaryotic kingdom (4,15,37,38,46).…”

mentioning

confidence: 99%

mRNA Decapping in Yeast Requires Dissociation of the Cap Binding Protein, Eukaryotic Translation Initiation Factor 4E

Schwartz¹,

Parker

2000

Molecular and Cellular Biology

174

134

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A major pathway of eukaryotic mRNA turnover occurs by deadenylation-dependent decapping that exposes the transcript to 533 exonucleolytic degradation. A critical step in this pathway is decapping, since removal of the cap structure permits 533 exonucleolytic digestion. Based on alterations in mRNA decay rate from strains deficient in translation initiation, it has been proposed that the decapping rate is modulated by a competition between the cytoplasmic cap binding complex, which promotes translation initiation, and the decapping enzyme, Dcp1p. In order to test this model directly, we examined the functional interaction of Dcp1p and the cap binding protein, eukaryotic translation initiation factor 4E (eIF4E), in vitro. These experiments indicated that eIF4E is an inhibitor of Dcp1p in vitro due to its ability to bind the 5 cap structure. In addition, we demonstrate that in vivo a temperature-sensitive allele of eIF4E (cdc33-42) suppressed the decapping defect of a partial loss-of-function allele of DCP1. These results argue that dissociation of eIF4E from the cap structure is required before decapping. Interestingly, the temperature-sensitive allele of eIF4E does not suppress the decapping defect seen in strains lacking the decapping activators, Lsm1p and Pat1p. This indicates that these activators of decapping affect a step in mRNA turnover distinct from the competition between Dcp1 and eIF4E.The turnover of mRNAs is a significant aspect of the differential gene expression in the eukaryotic cell (for reviews, see references 5, 11, 23, and 36). It has become clear, at least in yeast, that mRNAs with different decay rates are largely degraded by a single general pathway of mRNA turnover. In this pathway, mRNAs are first deadenylated, which allows the transcript to become a substrate for a decapping reaction catalyzed by the decapping enzyme encoded by the DCP1 gene (6,14,22,(29)(30)(31). Once decapped, the mRNAs are then susceptible to 5Ј33Ј exonucleolytic degradation by the Xrn1p exoribonuclease (22,29,30). Several observations suggest a similar pathway of degradation is likely to exist in other eukaryotic cells. For example, deadenylation can be the first step in mammalian mRNA turnover (42,47). Moreover, deadenylated decapped intermediates in turnover can be detected in mammals and in Chlamydomonas (12, 18). In addition, several proteins functioning in mRNA decapping in yeast (Dcp1p, Dcp2p, Xrn1p, Pat1p [also known as Mrt1p], and Lsm1p) have homologs throughout the eukaryotic kingdom (4,15,37,38,46).In yeast, multiple lines of evidence suggest that the decapping of mRNAs is an important control point in the regulation of mRNA half-life. In the deadenylation-dependent decapping pathway of mRNA turnover, the basis for the differential decay rates of individual yeast mRNAs is that transcripts differ in their rates of deadenylation and decapping. Short-lived mRNAs decap rapidly, while longer-lived mRNAs decap more slowly (29,30). In addition, in the deadenylation-independent pathway of mRNA turnover, transcripts ...

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Deadenylation-Dependent and -Independent Decay Pathways for α1-Tubulin mRNA in Chlamydomonas reinhardtii

Cited by 23 publications

References 35 publications

Recognition of Yeast mRNAs as “Nonsense Containing” Leads to Both Inhibition of mRNA Translation and mRNA Degradation: Implications for the Control of mRNA Decapping

Recognition of Yeast mRNAs as “Nonsense Containing” Leads to Both Inhibition of mRNA Translation and mRNA Degradation: Implications for the Control of mRNA Decapping

DcpS can act in the 5′–3′ mRNA decay pathway in addition to the 3′–5′ pathway

mRNA Decapping in Yeast Requires Dissociation of the Cap Binding Protein, Eukaryotic Translation Initiation Factor 4E

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