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Quality Control of Gene Expression: a Stepwise Assembly Pathway for the Surveillance Complex That Triggers Nonsense-Mediated Mrna Decay

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Quality Control of Gene Expression: a Stepwise Assembly Pathway for the Surveillance Complex That Triggers Nonsense-Mediated Mrna Decay Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press PERSPECTIVE Quality control of gene expression: a stepwise assembly pathway for the surveillance complex that triggers nonsense-mediated mRNA decay Isabelle Behm-Ansmant1 and Elisa Izaurralde1,2,3 1European Molecular Biology Laboratory, D-69117 Heidelberg, Germany; 2Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany Eukaryotic cells have evolved elaborate mRNA quality metabolism. A deeper understanding of the mechanism control (surveillance) mechanisms to ensure that only underlying this pathway is therefore of critical impor- fully processed and error-free mRNAs are translated. tance. These quality control mechanisms operate in both the nucleus and the cytoplasm. For instance, in the nucleus, improperly processed mRNAs are degraded before they NMD effectors forming a conserved protein are transported to the cytoplasm (for review, see Fasken interaction network and Corbett 2005). In the cytoplasm, surveillance path- ways assess the translatability of the mRNA and degrade The RNA helicase UPF1 is a key effector of the NMD any that have no translation termination codons (non- pathway. Deletion or silencing of the UPF1 gene results stop-mediated mRNA decay, NSD) or nonsense codons in the stabilization of PTC-containing mRNAs in all or- (nonsense-mediated mRNA decay, NMD), thereby pre- ganisms in which the NMD pathway has been investi- venting the accumulation of potentially toxic aberrant gated (for review, see Conti and Izaurralde 2005; Lejeune proteins (for review, see Conti and Izaurralde 2005; and Maquat 2005). UPF1 activity is regulated by phos- Fasken and Corbett 2005; Lejeune and Maquat 2005). phorylation in multicellular organisms, and this requires NMD is one of the best characterized mRNA surveil- interaction with two other conserved NMD effectors lance pathways. Its importance as a protective surveil- (UPF2, UPF3) and four additional proteins that, in con- lance mechanism is underscored by the fact that ∼30% of trast to UPF1–3, have no orthologs in yeast, namely, inherited genetic disorders are caused by nonsense mu- SMG1, SMG5, SMG6, and SMG7 (Pulak and Anderson tations or frameshifts, which generate nonsense codons 1993; Cali et al. 1999; Page et al. 1999). SMG1 is a phos- (for review, see Frischmeyer and Dietz 1999; Holbrook et phoinositide-3-kinase-related protein kinase required for al. 2004). Transcripts derived from the mutant alleles are UPF1 phosphorylation (Page et al. 1999; Denning et al. degraded by NMD, leading in general to a recessive mode 2001; Pal et al. 2001; Yamashita et al. 2001; Grimson et of inheritance. al. 2004). SMG5, SMG6, and SMG7 can recognize phos- NMD not only rids the cell of mRNAs containing pre- phorylated UPF1 and are thought to trigger its dephos- mature translation termination codons (PTCs or non- phorylation by recruiting protein phosphatase 2A (PP2A) sense codons) as a result of mutations or errors in tran- (Anders et al. 2003; Chiu et al. 2003; Ohnishi et al. 2003). scription or mRNA processing, but also regulates the The transient or stable interactions between NMD ef- expression of naturally occurring transcripts that repre- fectors lead to the formation of the so-called surveillance sent ∼10% of the transcriptome in yeast, Drosophila, and complex that assembles on mRNAs on which a prema- human cells (Lelivelt and Culbertson 1999; He et al. ture translation termination event occurs. The surveil- 2003; Mendell et al. 2004; Rehwinkel et al. 2005). In this lance complex, in turn, recruits RNA degradation en- way, NMD plays a role in biological processes as diverse zymes and ultimately triggers the decay of the mRNA as telomere maintenance, transcription, cell prolifera- that served as platform for its own assembly (for review, tion, cell cycle, cellular transport and organization, and see Conti and Izaurralde 2005; Lejeune and Maquat 2005). The role of the surveillance complex is therefore to couple a premature translation termination event to mRNA degradation. In agreement with this, NMD fac- 3Corresponding author. tors have genetic, functional, and/or physical interac- E-MAIL [email protected]; FAX 49-6221-387-306. Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/ tions with both translation factors and mRNA decay en- gad.1407606. zymes. GENES & DEVELOPMENT 20:391–398 © 2006 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/06; www.genesdev.org 391 Downloaded from genesdev.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Behm-Ansmant and Izaurralde In this regard, the association of yeast UPF1, UPF2, (EJC) for NMD in these organisms (for review, see and UPF3 with the eukaryotic translation termination Lejeune and Maquat 2005). Indeed, the positions of factors eRF1 and eRF3 provides a link between NMD and exon–exon boundaries are communicated to translating translation termination (Czaplinski et al. 1998; Kobaya- ribosomes by the EJC, a multiprotein assembly deposited shi et al. 2004). Moreover, multiple links between NMD by the spliceosome 20–24 nt upstream of exon–exon factors and mRNA decay enzymes have been described junctions (Le Hir et al. 2000). Consistent with this, the in different organisms. These include the interaction of EJC components Y14, MAGOH, eIF4AIII, Barentsz, and yeast UPF1 with the DCP1–DCP2 decapping complex, RNPS1, function in NMD (Lykke-Andersen et al. 2001; and the localization of human SMG7 to P-bodies, dis- Fribourg et al. 2003; Gehring et al. 2003, 2005; Ferraiuolo crete cytoplasmic foci where mRNA degradation en- et al. 2004; Palacios et al. 2004; Shibuya et al. 2004). zymes localize (for review; see Baker and Parker 2004; These proteins interact with mammalian UPF3, which is Conti and Izaurralde 2005). also loaded onto mRNAs during splicing and represents a genuine EJC component (Kim et al. 2001; Le Hir et al. 2001). The mechanism of NMD: an overview As mentioned above, in Drosophila as well as in yeast, In all eukaryotes a premature translation termination PTC recognition occurs independently of exon–exon event leads to the assembly of the surveillance complex, junctions, and although orthologs of mammalian EJC yet the mechanisms by which a stop codon is defined as proteins (i.e., Y14, MAGOH, eIF4AIII, Barentsz, and premature and the targeted mRNA is degraded differ RNPS1) are conserved in Drosophila, they are not essen- across species. In mammals, PTC recognition relies on tial for NMD (Gatfield et al. 2003), suggesting that EJC splicing: Stop codons are defined as premature if they are components have been co-opted by the NMD machinery located ∼50 nucleotides (nt) or more upstream of an ex- after the divergence of vertebrates and invertebrates. on–exon junction. In contrast, PTC recognition occurs None of these proteins has orthologs in S. cerevisiae. independently of exon–exon boundaries in both Dro- sophila and Saccharomyces cerevisiae (for review, see A trimeric UPF1:UPF2:UPF3 complex forms Conti and Izaurralde 2005; Lejeune and Maquat 2005). the conserved core of the NMD machinery Degradation of the targeted mRNA involves many of the enzymes in the general pathway for mRNA turnover Based on several lines of evidence, a model for NMD in including the decapping DCP1–DCP2 complex, the 5Ј- mammals has emerged in which UPF3 is loaded onto to-3Ј exonuclease XRN1, deadenylases, and the 3Ј-to-5Ј mRNAs during splicing, while UPF2 is thought to join exonucleases of the exosome (for review, see Baker and the complex in the cytoplasm after export. During the Parker 2004). In yeast and human cells, the major decay first round of translation, UPF2, UPF3, and the addi- pathway for NMD substrates is initiated by removal of tional EJC components are displaced by the ribosomes as the cap structure by the DCP1–DCP2 decapping com- they traverse the mRNA. If translating ribosomes were plex. Following decapping, the body of the transcript is to encounter a stop codon upstream of an EJC, this exposed to 5Ј-to-3Ј degradation by XRN1 (Cao and Parker would lead to the incomplete removal of UPF2 and UPF3 2003; Chen and Shyu 2003; Lejeune et al. 2003; Mitchell proteins from downstream mRNA sequences and to the and Tollervey 2003; Couttet and Grange 2004). An alter- recruitment of UPF1, probably via interactions with the native pathway, which also contributes to the decay of eRF1–eRF3 complex (see below). The recruitment of PTC-containing mRNAs, relies on the accelerated dead- UPF1 creates an opportunity for the assembly of the sur- enylation and 3Ј-to-5Ј degradation by the exosome (Cao veillance complex consisting of UPF1, UPF2, and UPF3, and Parker 2003; Chen and Shyu 2003; Lejeune et al. which triggers UPF1 phosphorylation and ultimately tar- 2003; Mitchell and Tollervey 2003). In Drosophila, deg- gets the mRNA for rapid degradation. radation of nonsense transcripts is initiated by endonu- A key step in this model is the formation of the tri- cleolytic cleavage near the PTC (Gatfield and Izaurralde meric UPF1:UPF2:UPF3 complex, which represents the 2004). The resulting 5Ј decay intermediate is degraded by conserved core of the NMD machinery and is thought to the exosome, while the 3Ј fragment is degraded by XRN1 assemble in all organisms independently of the mecha- (Gatfield and Izaurralde 2004). Thus, in this case, the nism by which PTCs are defined (for review, see Conti mRNA fragments are degraded from the newly generated and Izaurralde 2005; Lejeune and Maquat 2005). Forma- ends without being decapped or deadenylated, suggesting tion of the trimeric complex is supported by genetic, that, in contrast to yeast and mammals, the decapping biochemical, and structural evidence. UPF2 interacts di- enzymes and deadenylases may not interact with NMD rectly with UPF3 (Lykke-Andersen et al. 2000; Serin et effectors in Drosophila. al. 2001; Kadlec et al. 2004 and references therein). This As a consequence of the differences in the mecha- interaction has been visualized at the atomic level nisms of PTC recognition and mRNA decay described (Kadlec et al.
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