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

Dijk, Erwin van; Hir, Hervé Le; Séraphin, Bertrand

doi:10.1073/pnas.1635192100

Cited by 79 publications

(85 citation statements)

References 36 publications

(53 reference statements)

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“…The Dcs1 protein also includes an enzyme that can cleave the cap structure (27,28). We tested whether Dcs1 was required for generation of these 5′ Ps by examining their presence in dcs1Δ dcp2Δ xrn1Δ strains compared with dcp2Δ xrn1Δ.…”

Section: ′ P Ends Located In Intronsmentioning

confidence: 99%

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

Harigaya

Parker

2012

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

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The general pathways of eukaryotic mRNA decay occur via deadenylation followed by 3′ to 5′ degradation or decapping, although some endonuclease sites have been identified in metazoan mRNAs. To determine the role of endonucleases in mRNA degradation in Saccharomyces cerevisiae, we mapped 5′ monophosphate ends on mRNAs in wild-type and dcp2Δ xrn1Δ yeast cells, wherein mRNA endonuclease cleavage products are stabilized. This led to three important observations. First, only few mRNAs that undergo low-level endonucleolytic cleavage were observed, suggesting that endonucleases are not a major contributor to yeast mRNA decay. Second, independent of known decapping enzymes, we observed low levels of 5′ monophosphates on some mRNAs, suggesting that an unknown mechanism can generate 5′ exposed ends, although for all substrates tested, Dcp2 was the primary decapping enzyme. Finally, we identified debranched lariat intermediates from intron-containing genes, demonstrating a significant discard pathway for mRNAs during the second step of pre-mRNA splicing, which is a potential step to regulate gene expression.D egradation of mRNA plays a crucial role in the control and fidelity of gene expression. In eukaryotes, the general mRNA decay pathway initiates with shortening of the 3′ poly(A) tail, followed by 3′ to 5′ exonucleolytic degradation and/or removal of the 5′ 7-methylguanosine cap by the Dcp2 decapping enzyme allowing degradation by the Xrn1 5′ to 3′ exonuclease (1, 2).In some organisms, the decay of specific mRNAs can be initiated by endonucleolytic cleavage (3, 4). In plants, mRNA decay mediated by small interfering (si)RNAs and micro-RNAs (miRNAs) often occurs via endonucleolytic cleavage (5), leading to 5′ to 3′ decay by the Xrn1 homolog XRN4 (6, 7). Moreover, in mammalian cells miRNA dependent and independent endonuclease cleavage sites in mRNAs have been identified (8, 9). Endonucleolytic cleavage also initiates mRNA decay in quality control mechanisms, such as nonsense-mediated decay (NMD) in metazoans and no-go decay (NGD) in yeast (10-13). In both NGD and NMD pathways, the 3′ endonuclease cleavage product with a 5′ monophosphate end is rapidly degraded by Xrn1. Endonucleases can also function in cytoplasmic RNA processing events. For example, during the unfolded protein response (UPR), the IRE1 endonucleolytically cleaves XBP1 mRNA (a metazoan homolog of HAC1 in S. cerevisiae) to cause its unconventional splicing and production of the UPR-specific transcription factor encoded by the mRNA (14).In this work, we set out to determine the contribution of endonucleases to mRNA degradation in Saccharomyces cerevisiae and to determine whether any other processes contribute to 5′ to 3′ degradation of mRNAs. Although our analysis revealed few endonucleolytic cleavage events at appreciable levels, we identified debranched lariat intermediates arising from endogenous intron-containing genes that were subject to degradation by Xrn1. This observation identifies a discard pathway for natural pre-mRNA splicing substrates and ra...

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Section: ′ P Ends Located In Intronsmentioning

confidence: 99%

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

Harigaya

Parker

2012

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

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“…During deadenylation, the size of the poly(A) tail of the target mRNA is reduced to 10-15 residues (Muhlrad et al 1994). This event triggers the degradation of the mRNA body by various exonucleases (Muhlrad et al 1994) while the mRNA cap is catabolized by various decapping enzymes (Wang and Kiledjian 2001;LykkeAndersen 2002;van Dijk et al 2002van Dijk et al , 2003Wang et al 2002). Interestingly, the speed of the deadenylation process has been shown to vary widely between mRNAs and degradation of the poly(A) tail appears to be a rate-limiting step in the decay process (Muhlrad et al 1995).…”

Section: Introductionmentioning

confidence: 99%

Conservation of the deadenylase activity of proteins of the Caf1 family in human

Bianchin

Mauxion²,

Sentis³

et al. 2005

RNA

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The yeast Pop2 protein, belonging to the eukaryotic Caf1 family, is required for mRNA deadenylation in vivo. It also catalyzes poly(A) degradation in vitro, even though this property has been questioned. Caf1 proteins are related to RNase D, a feature supported by the recently published structure of Pop2. Yeast Pop2 contains, however, a divergent active site while its human homologs harbor consensus catalytic residues. Given these differences, we tested whether its deadenylase activity is conserved in the human homologs Caf1 and Pop2. Our data demonstrate that both human factors degrade poly(A) tails indicating their involvement in mRNA metabolism.

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“…These pathways need not be mutually exclusive and could occur simultaneously (14, 15), and an interplay between the two pathways could also exist. DcpS, which was originally characterized as the decapping enzyme in the 3Ј-5Ј pathway, is also able to hydrolyze the 5Ј-3Ј decapping product m 7 Gpp to release m 7 Gp (16,17). Furthermore, disruption of the yeast DcpS ortholog, Dcs1p, impeded the 5Ј-exonuclease activity (18), indicating that the Dcs1p decapping products might serve as signaling molecules for the 5Ј decay pathway.…”

mentioning

confidence: 99%

Mechanistic and Kinetic Analysis of the DcpS Scavenger Decapping Enzyme

Liu

Rajagopal²,

Patel³

et al. 2008

Journal of Biological Chemistry

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Decapping is an important process in the control of eukaryotic mRNA degradation. The control of mRNA degradation is a critical step in the posttranscriptional regulation of gene expression, and the steady state level of any mRNA species depends on both the rate of mRNA synthesis and its breakdown. In eukaryotic cells, cytoplasmic mRNA degradation proceeds predominantly through an initial removal of the polyadenylated tail (1, 2) followed by 5Ј to 3Ј or 3Ј to 5Ј decay (3, 4). In the 5Ј-3Ј decay pathway, the 5Ј cap structure is cleaved by the catalytic activity of the Dcp2 decapping enzyme to release the m 7 Gpp and monophosphorylated RNA (5-8). The resulting uncapped monophosphorylated RNA is digested by a 5Ј-3Ј exonuclease, XrnI (1, 9). In the 3Ј-5Ј pathway, subsequent to deadenylation, the capped RNA body is continuously degraded by an exosome complex (10, 11). The resulting capped oligonucleotide m 7 GpppN(pN) n (n Ͻ 9) is hydrolyzed by a second type of decapping enzyme, DcpS, to release the m 7 Gp and ppN(pN) n products (12, 13). These pathways need not be mutually exclusive and could occur simultaneously (14, 15), and an interplay between the two pathways could also exist. DcpS, which was originally characterized as the decapping enzyme in the 3Ј-5Ј pathway, is also able to hydrolyze the 5Ј-3Ј decapping product m 7 Gpp to release m 7 Gp (16,17). Furthermore, disruption of the yeast DcpS ortholog, Dcs1p, impeded the 5Ј-exonuclease activity (18), indicating that the Dcs1p decapping products might serve as signaling molecules for the 5Ј decay pathway.DcpS is a member of the histidine triad (HIT) 3 hydrolase family of proteins that contain a stretch of His-X-His-X-His-X residues, where X denotes hydrophobic amino acid residues. HIT proteins are dimeric nucleotide binding proteins that have hydrolase activities (19 -21). The central histidine residue is critical for the hydrolase activity, since it is thought to serve as the nucleophile attacking the phosphate most proximal to the methylated guanosine in m 7 GpppG (22) and is also critical for DcpS hydrolysis (13).Structural analysis of DcpS has revealed that it is a homodimer with a symmetric structure when in the ligand-free form (16, 23) or asymmetric homodimer in the ligand-bound form (16,24). Each DcpS monomer possesses a distinct N-terminal domain and a C-terminal domain containing the HIT motif linked by a hinge region. The N-terminal domain displays a domain-swapped form by exchanging an identical ␣-helix and two antiparallel ␤-strands with the second monomer. The DcpS homodimer contains two cap binding pockets, which serve as the active sites for cap hydrolysis. In the ligand-bound form, DcpS forms a closed conformation on one side and an open conformation on the other, with substrate bound at the C-terminal domain of each side (24). The structure suggests that the closed conformation constitutes the cap hydrolysis productive site, whereas the open site would be nonproductive. The N-terminal domains can both be in the open state, or one side can be in an...

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

Cited by 79 publications

References 36 publications

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

Conservation of the deadenylase activity of proteins of the Caf1 family in human

Mechanistic and Kinetic Analysis of the DcpS Scavenger Decapping Enzyme

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