Caenorhabditis elegans SMG-2 Selectively Marks mRNAs Containing Premature Translation Termination Codons

REFERENCES

• Alonso, C. R. 2005. Nonsense-mediated RNA decay: a molecular system micromanaging individual gene activities and suppressing genomic noise. Bioessays 27:463–466.
   PubMedGoogle Scholar
• Amrani, N., R. Ganesan, S. Kervestin, D. A. Mangus, S. Ghosh, and A. Jacobson. 2004. A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature 432:112–118.
   PubMed Web of Science ®Google Scholar
• Anders, K. R., A. Grimson, and P. Anderson. 2003. SMG-5, required for C. elegans nonsense-mediated mRNA decay, associates with SMG-2 and protein phosphatase 2A. EMBO J. 22:641–650.
   PubMedGoogle Scholar
• Arciga-Reyes, L., L. Wootton, M. Kieffer, and B. Davies. 2006. UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J. 47:480–489.
   PubMedGoogle Scholar
• Aronoff, R., R. Baran, and J. Hodgkin. 2001. Molecular identification of smg-4, required for mRNA surveillance in C. elegans. Gene 268:153–164.
   PubMedGoogle Scholar
• Azzalin, C. M., and J. Lingner. 2006. The human RNA surveillance factor UPF1 is required for S phase progression and genome stability. Curr. Biol. 16:433–439.
   PubMedGoogle Scholar
• Barlow, D. J., M. S. Edwards, and J. M. Thornton. 1986. Continuous and discontinuous protein antigenic determinants. Nature 322:747–748.
   PubMed Web of Science ®Google Scholar
• Beelman, C. A., A. Stevens, G. Caponigro, T. E. LaGrandeur, L. Hatfield, D. M. Fortner, and R. Parker. 1996. An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature 382:642–646.
   PubMed Web of Science ®Google Scholar
• Behm-Ansmant, I., and E. Izaurralde. 2006. Quality control of gene expression: a stepwise assembly pathway for the surveillance complex that triggers nonsense-mediated mRNA decay. Genes Dev. 20:391–398.
   PubMed Web of Science ®Google Scholar
• Behm-Ansmant, I., D. Gatfield, J. Rehwinkel, V. Hilgers, and E. Izaurralde. 2007. A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J. 26:1591–1601.
   PubMed Web of Science ®Google Scholar
• Brenner, S. 1974. The genetics of Caenorhabditis elegans. Genetics 77:71–94.
   PubMed Web of Science ®Google Scholar
• Brumbaugh, K. M., D. M. Otterness, C. Geisen, V. Oliveira, J. Brognard, X. Li, F. Lejeune, R. S. Tibbetts, L. E. Maquat, and R. T. Abraham. 2004. The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. Mol. Cell 14:585–598.
   PubMed Web of Science ®Google Scholar
• Buhler, M., S. Steiner, F. Mohn, A. Paillusson, and O. Muhlemann. 2006. EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3′ UTR length. Nat. Struct. Mol. Biol. 13:462–464.
   PubMed Web of Science ®Google Scholar
• Cali, B. M., and P. Anderson. 1998. mRNA surveillance mitigates genetic dominance in Caenorhabditis elegans. Mol. Gen. Genet. 260:176–184.
   PubMedGoogle Scholar
• Cali, B. M., S. L. Kuchma, J. Latham, and P. Anderson. 1999. smg-7 is required for mRNA surveillance in Caenorhabditis elegans. Genetics 151:605–616.
   PubMed Web of Science ®Google Scholar
• Chiu, S. Y., G. Serin, O. Ohara, and L. E. Maquat. 2003. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG5 and SMG7 that functions in the dephosphorylation of Upf1. RNA 9:77–87.
   PubMedGoogle Scholar
• Conti, E., and E. Izaurralde. 2005. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17:316–325.
   PubMedGoogle Scholar
• Culbertson, M. R., and P. F. Leeds. 2003. Looking at mRNA decay pathways through the window of molecular evolution. Curr. Opin. Genet. Dev. 13:207–214.
   PubMedGoogle Scholar
• Czaplinski, K., M. J. Ruiz-Echevarria, S. V. Paushkin, X. Han, Y. Weng, H. A. Perlick, H. C. Dietz, M. D. Ter-Avanesyan, and S. W. Peltz. 1998. The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs. Genes Dev. 12:1665–1677.
   PubMedGoogle Scholar
• Denning, G., L. Jamieson, L. E. Maquat, E. A. Thompson, and A. P. Fields. 2001. Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein. J. Biol. Chem. 276:22709–22714.
   PubMed Web of Science ®Google Scholar
• Fasken, M. B., and A. H. Corbett. 2005. Process or perish: quality control in mRNA biogenesis. Nat. Struct. Mol. Biol. 12:482–488.
   PubMed Web of Science ®Google Scholar
• Fukuhara, N., J. Ebert, L. Unterholzner, D. Lindner, E. Izaurralde, and E. Conti. 2005. SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. Mol. Cell 17:537–547.
   PubMedGoogle Scholar
• Gatfield, D., L. Unterholzner, F. D. Ciccarelli, P. Bork, and E. Izaurralde. 2003. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J. 22:3960–3970.
   PubMed Web of Science ®Google Scholar
• Gehring, N. H., J. B. Kunz, G. Neu-Yilik, S. Breit, M. H. Viegas, M. W. Hentze, and A. E. Kulozik. 2005. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol. Cell 20:65–75.
   PubMed Web of Science ®Google Scholar
• Gehring, N. H., G. Neu-Yilik, T. Schell, M. W. Hentze, and A. E. Kulozik. 2003. Y14 and hUpf3b form an NMD-activating complex. Mol. Cell 11:939–949.
   PubMed Web of Science ®Google Scholar
• Grimson, A., S. O'Connor, C. L. Newman, and P. Anderson. 2004. SMG-1 is a phosphatidylinositol kinase-related protein kinase required for nonsense-mediated mRNA decay in Caenorhabditis elegans. Mol. Cell. Biol. 24:7483–7490.
   PubMed Web of Science ®Google Scholar
• Hall, G. W., and S. Thein. 1994. Nonsense codon mutations in the terminal exon of the beta-globin gene are not associated with a reduction in beta-mRNA accumulation: a mechanism for the phenotype of dominant beta-thalassemia. Blood 83:2031–2037.
   PubMed Web of Science ®Google Scholar
• Harlow, E., and D. Lane. 1999. Using antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
   Google Scholar
• He, F., A. H. Brown, and A. Jacobson. 1997. Upf1p, Nmd2p, and Upf3p are interacting components of the yeast nonsense-mediated mRNA decay pathway. Mol. Cell. Biol. 17:1580–1594.
   PubMed Web of Science ®Google Scholar
• Hosoda, N., Y. K. Kim, F. Lejeune, and L. E. Maquat. 2005. CBP80 promotes interaction of Upf1 with Upf2 during nonsense-mediated mRNA decay in mammalian cells. Nat. Struct. Mol. Biol. 12:893–901.
   PubMed Web of Science ®Google Scholar
• Kadlec, J., E. Izaurralde, and S. Cusack. 2004. The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3. Nat. Struct. Mol. Biol. 11:330–337.
   PubMed Web of Science ®Google Scholar
• Kashima, I., A. Yamashita, N. Izumi, N. Kataoka, R. Morishita, S. Hoshino, M. Ohno, G. Dreyfuss, and S. Ohno. 2006. Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay. Genes Dev. 20:355–367.
   PubMed Web of Science ®Google Scholar
• Kaygun, H., and W. F. Marzluff. 2005. Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1. Nat. Struct. Mol. Biol. 12:794–800.
   PubMed Web of Science ®Google Scholar
• Kim, V. N., N. Kataoka, and G. Dreyfuss. 2001. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293:1832–1836.
   PubMedGoogle Scholar
• Kim, Y. K., L. Furic, L. Desgroseillers, and L. E. Maquat. 2005. Mammalian Staufen1 recruits Upf1 to specific mRNA 3′UTRs so as to elicit mRNA decay. Cell 120:195–208.
   PubMed Web of Science ®Google Scholar
• Kobayashi, T., Y. Funakoshi, S. Hoshino, and T. Katada. 2004. The GTP-binding release factor eRF3 as a key mediator coupling translation termination to mRNA decay. J. Biol. Chem. 279:45693–45700.
   PubMedGoogle Scholar
• Kunz, J. B., G. Neu-Yilik, M. W. Hentze, A. E. Kulozik, and N. H. Gehring. 2006. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. RNA 12:1015–1022.
   PubMed Web of Science ®Google Scholar
• Le Hir, H., D. Gatfield, E. Izaurralde, and M. J. Moore. 2001. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 20:4987–4997.
   PubMed Web of Science ®Google Scholar
• Lejeune, F., and L. E. Maquat. 2005. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17:309–315.
   PubMed Web of Science ®Google Scholar
• Li, S., and M. F. Wilkinson. 1998. Nonsense surveillance in lymphocytes? Immunity 8:135–141.
   PubMedGoogle Scholar
• Longman, D., R. H. Plasterk, I. L. Johnstone, and J. F. Caceres. 2007. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev. 21:1075–1085.
   PubMed Web of Science ®Google Scholar
• Lykke-Andersen, J., M. D. Shu, and J. A. Steitz. 2000. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon. Cell 103:1121–1131.
   PubMed Web of Science ®Google Scholar
• Maryon, E. B., B. Saari, and P. Anderson. 1998. Muscle-specific functions of ryanodine receptor channels in Caenorhabditis elegans. J. Cell Sci. 111:2885–2895.
   PubMed Web of Science ®Google Scholar
• Medghalchi, S. M., P. A. Frischmeyer, J. T. Mendell, A. G. Kelly, A. M. Lawler, and H. C. Dietz. 2001. Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum. Mol. Genet. 10:99–105.
   PubMedGoogle Scholar
• Mello, C., and A. Fire. 1995. DNA transformation. Methods Cell Biol. 48:451–482.
   PubMed Web of Science ®Google Scholar
• Mendell, J. T., C. M. ap Rhys, and H. C. Dietz. 2002. Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science 298:419–422.
   PubMed Web of Science ®Google Scholar
• Mendell, J. T., S. M. Medghalchi, R. G. Lake, E. N. Noensie, and H. C. Dietz. 2000. Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes. Mol. Cell. Biol. 20:8944–8957.
   PubMedGoogle Scholar
• Metzstein, M. M., and M. A. Krasnow. 2006. Functions of the nonsense-mediated mRNA decay pathway in Drosophila development. PLoS Genet. 2:e180.
   PubMed Web of Science ®Google Scholar
• Mitrovich, Q. M., and P. Anderson. 2000. Unproductively spliced ribosomal protein mRNAs are natural targets of mRNA surveillance in C. elegans. Genes Dev. 14:2173–2184.
   PubMed Web of Science ®Google Scholar
• Morrison, M., K. S. Harris, and M. B. Roth. 1997. smg mutants affect the expression of alternatively spliced SR protein mRNAs in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 94:9782–9785.
   PubMedGoogle Scholar
• Muhlrad, D., and R. Parker. 1999. Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance. RNA 5:1299–1307.
   PubMed Web of Science ®Google Scholar
• Ohnishi, T., A. Yamashita, I. Kashima, T. Schell, K. R. Anders, A. Grimson, T. Hachiya, M. W. Hentze, P. Anderson, and S. Ohno. 2003. Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7. Mol. Cell 12:1187–1200.
   PubMed Web of Science ®Google Scholar
• Page, M. F., B. Carr, K. R. Anders, A. Grimson, and P. Anderson. 1999. SMG-2 is a phosphorylated protein required for mRNA surveillance in Caenorhabditis elegans and related to Upf1p of yeast. Mol. Cell. Biol. 19:5943–5951.
   PubMed Web of Science ®Google Scholar
• Pal, M., Y. Ishigaki, E. Nagy, and L. E. Maquat. 2001. Evidence that phosphorylation of human Upfl protein varies with intracellular location and is mediated by a wortmannin-sensitive and rapamycin-sensitive PI 3-kinase-related kinase signaling pathway. RNA 7:5–15.
   PubMedGoogle Scholar
• Pulak, R., and P. Anderson. 1993. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes Dev. 7:1885–1897.
   PubMedGoogle Scholar
• Rehwinkel, J., I. Letunic, J. Raes, P. Bork, and E. Izaurralde. 2005. Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets. RNA 11:1530–1544.
   PubMed Web of Science ®Google Scholar
• Serin, G., A. Gersappe, J. D. Black, R. Aronoff, and L. E. Maquat. 2001. Identification and characterization of human orthologues to Saccharomyces cerevisiae Upf2 protein and Upf3 protein (Caenorhabditis elegans SMG-4). Mol. Cell. Biol. 21:209–223.
   PubMedGoogle Scholar
• Shirley, R. L., A. S. Ford, M. R. Richards, M. Albertini, and M. R. Culbertson. 2002. Nuclear import of Upf3p is mediated by importin-alpha/-beta and export to the cytoplasm is required for a functional nonsense-mediated mRNA decay pathway in yeast. Genetics 161:1465–1482.
   PubMedGoogle Scholar
• Unterholzner, L., and E. Izaurralde. 2004. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol. Cell 16:587–596.
   PubMed Web of Science ®Google Scholar
• Wang, W., I. J. Cajigas, S. W. Peltz, M. F. Wilkinson, and C. I. Gonzalez. 2006. Role for Upf2p phosphorylation in Saccharomyces cerevisiae nonsense-mediated mRNA decay. Mol. Cell. Biol. 26:3390–3400.
   PubMedGoogle Scholar
• Weischenfeldt, J., J. Lykke-Andersen, and B. Porse. 2005. Messenger RNA surveillance: neutralizing natural nonsense. Curr. Biol. 15:R559–R562.
   PubMedGoogle Scholar
• Wittmann, J., E. M. Hol, and H. M. Jack. 2006. hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol. Cell. Biol. 26:1272–1287.
   PubMed Web of Science ®Google Scholar
• Yamashita, A., I. Kashima, and S. Ohno. 2005. The role of SMG-1 in nonsense-mediated mRNA decay. Biochim. Biophys. Acta 1754:305–315.
   PubMed Web of Science ®Google Scholar
• Yamashita, A., T. Ohnishi, I. Kashima, Y. Taya, and S. Ohno. 2001. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev. 15:2215–2228.
   PubMed Web of Science ®Google Scholar
• Yoine, M., T. Nishii, and K. Nakamura. 2006. Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth. Plant Cell Physiol. 47:572–580.
   PubMedGoogle Scholar
• Zhang, S., M. J. Ruiz-Echevarria, Y. Quan, and S. W. Peltz. 1995. Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay. Mol. Cell. Biol. 15:2231–2244.
   PubMedGoogle Scholar