N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD

Department of Molecular Biology, Yokohama City University, School of Medicine, 3-9, Fuku-ura, Kanazawa-ku, Yokohama 236-0004, Japan.
Nucleic Acids Research (Impact Factor: 9.11). 09/2011; 40(3):1251-66. DOI: 10.1093/nar/gkr791
Source: PubMed


Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that detects and degrades mRNAs containing premature termination codons (PTCs). SMG-1-mediated Upf1 phosphorylation takes place in the decay inducing complex (DECID), which contains a ribosome, release factors, Upf1, SMG-1, an exon junction complex (EJC) and a PTC-mRNA. However, the significance and the consequence of Upf1 phosphorylation remain to be clarified. Here, we demonstrate that SMG-6 binds to a newly identified phosphorylation site in Upf1 at N-terminal threonine 28, whereas the SMG-5:SMG-7 complex binds to phosphorylated serine 1096 of Upf1. In addition, the binding of the SMG-5:SMG-7 complex to Upf1 resulted in the dissociation of the ribosome and release factors from the DECID complex. Importantly, the simultaneous binding of both the SMG-5:SMG-7 complex and SMG-6 to phospho-Upf1 are required for both NMD and Upf1 dissociation from mRNA. Thus, the SMG-1-mediated phosphorylation of Upf1 creates a binding platforms for the SMG-5:SMG-7 complex and for SMG-6, and triggers sequential remodeling of the mRNA surveillance complex for NMD induction and recycling of the ribosome, release factors and NMD factors.

Download full-text


Available from: Shigeo Ohno
  • Source
    • "Improper translation termination due to PTCs is thought to recruit UPF1 to stalled ribosomes, which leads to UPF1 phosphorylation (Kashima et al., 2006). Phosphorylated UPF1 facilitates the recruitment of the proteins SMG5, SMG7, and SMG6, which then promote mRNA degradation (Eberle et al., 2009; Okada-Katsuhata et al., 2012; Unterholzner and Izaurralde, 2004). Although UPF1, UPF2, and UPF3 homologs are present in all eukaryotes, homologs of SMG5 and SMG6 appear to be absent from plant genomes (Riehs et al., 2008). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs. NMD impairment in Arabidopsis is linked to constitutive immune response activation and enhanced antibacterial resistance, but the underlying mechanisms are unknown. Here we show that NMD contributes to innate immunity in Arabidopsis by controlling the turnover of numerous TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptor-encoding mRNAs. Autoimmunity resulting from NMD impairment depends on TNL signaling pathway components and can be triggered through deregulation of a single TNL gene, RPS6. Bacterial infection of plants causes host-programmed inhibition of NMD, leading to stabilization of NMD-regulated TNL transcripts. Conversely, constitutive NMD activity prevents TNL stabilization and impairs plant defense, demonstrating that host-regulated NMD contributes to disease resistance. Thus, NMD shapes plant innate immunity by controlling the threshold for activation of TNL resistance pathways.
    Full-text · Article · Sep 2014 · Cell Host & Microbe
  • Source
    • "The association between SURF and UPF2-UPF3-EJC would induce SMG1- mediated UPF1 phosphorylation (Kashima et al., 2006; Yamashita et al., 2009). Phosphorylated UPF1 recruits phopho-UPF1 recognizing protein complexes that can degrade PTC-mRNA (Glavan et al., 2006; Loh et al., 2013; Okada-Katsuhata et al., 2012). In addition, binding of UPF2 to the CH domain of UPF1 induces a large conformational change that removes the inhibition of the ATPase activity and activates the RNA-dependent 5 0 to 3 "
    [Show abstract] [Hide abstract]
    ABSTRACT: SMG1, a PI3K-related kinase, plays a critical role in nonsense-mediated mRNA decay (NMD) in mammals. SMG1-mediated phosphorylation of the UPF1 helicase is an essential step during NMD initiation. Both SMG1 and UPF1 are presumably activated by UPF2, but this regulation is incompletely understood. Here we reveal that SMG1C (a complex containing SMG1, SMG8, and SMG9) contributes to regulate NMD by recruiting UPF1 and UPF2 to distinct sites in the vicinity of the kinase domain. UPF2 binds SMG1 in an UPF1-independent manner in vivo, and the SMG1C-UPF2 structure shows UPF2 recognizes the FRB domain, a region that regulates the related mTOR kinase. The molecular architectures of several SMG1C-UPFs complexes, obtained by combining electron microscopy with in vivo and in vitro interaction analyses, competition experiments, and mutations, suggest that UPF2 can be transferred to UPF1 within SMG1C, inducing UPF2-dependent conformational changes required to activate UPF1 within an SMG1C-UPF1-UPF2 complex.
    Preview · Article · Jul 2014 · Structure
  • Source
    • "Hyperphosphorylation of UPF1 is prerequisite for destruction of PTC-bearing mRNAs. SMG1-induced phosphorylation of UPF1 functions to recruit the additional SMG factors, SMG6 and SMG5–SMG7 (Okada-Katsuhata et al., 2012), as well as pro-line-rich nuclear receptor co-regulatory protein 2 (PNRC2) (Cho et al., 2009). Recruitment of SMG6 to PTC-containing templates causes one or more endonucleolytic cleavages between the PTC and EJC. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Mammalian-cell messenger RNAs (mRNAs) are generated in the nucleus from precursor RNAs (pre-mRNAs, which often contain one or more introns) that are complexed with an array of incompletely inventoried proteins. During their biogenesis, pre-mRNAs and their derivative mRNAs are subject to extensive cis-modifications. These modifications promote the binding of distinct polypeptides that mediate a diverse array of functions needed for mRNA metabolism, including nuclear export, inspection by the nonsense-mediated mRNA decay (NMD) quality-control machinery, and synthesis of the encoded protein product. Ribonucleoprotein complex (RNP) remodeling through the loss and gain of protein constituents before and after pre-mRNA splicing, during mRNA export, and within the cytoplasm facilitates NMD, ensuring integrity of the transcriptome. Here we review the mRNP rearrangements that culminate in detection and elimination of faulty transcripts by mammalian-cell NMD.
    Full-text · Article · Jan 2014 · Moleculer Cells
Show more