SMG-1 Is a Phosphatidylinositol Kinase-Related Protein Kinase Required for Nonsense-Mediated mRNA Decay in Caenorhabditis elegans

REFERENCES

• Adam, R. D. 2001. Biology of Giardia lamblia. Clin. Microbiol. Rev. 14:447–475.
   PubMed Web of Science ®Google Scholar
• Anders, K. R., Grimson A., and Anderson P.. 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
• Aronoff, R., Baran R., and Hodgkin J.. 2001. Molecular identification of smg-4, required for mRNA surveillance in C. elegans. Gene 268:153–164.
   PubMedGoogle Scholar
• Bar-Peled, M., and Raikhel N. V.. 1996. A method for isolation and purification of specific antibodies to a protein fused to the GST. Anal. Biochem. 241:140–142.
   PubMedGoogle Scholar
• Blumenthal, T. 1995. Trans-splicing and polycistronic transcription in Caenorhabditis elegans. Trends Genet. 11:132–136.
   PubMedGoogle Scholar
• Bosotti, R., Isacchi A., and Sonnhammer E. L. L.. 2000. FAT: a novel domain in PIK-related kinases. Trends Biochem. Sci. 25:225–227.
   PubMed Web of Science ®Google Scholar
• Brenner, S. 1974. The genetics of Caenorhabditis elegans. Genetics 77:71–94.
   PubMed Web of Science ®Google Scholar
• Brown, E. J., Beal P. A., Keith C. T., Chen J., Shin T. B., and Schreiber S. L.. 1995. Control of p70 S6 kinase by kinase activity of FRAP in vivo. Nature 377:441–446.
   PubMed Web of Science ®Google Scholar
• Cali, B. M., and Anderson P.. 1998. mRNA surveillance mitigates genetic dominance in Caenorhabditis elegans. Mol. Gen. Genet. 260:176–184.
   PubMedGoogle Scholar
• Cali, B. M., Kuchma S. L., Latham J., and Anderson P.. 1999. smg-7 is required for mRNA surveillance in Caenorhabditis elegans. Genetics 151:605–616.
   PubMed Web of Science ®Google Scholar
• Carter, M. S., Doskow J., Morris P., Li S., Nhim R. P., Sandstedt S., and Wilkinson M. F.. 1995. A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro. J. Biol. Chem. 270:28995–29003.
   PubMed Web of Science ®Google Scholar
• Chen, C. Y., and Shyu A. B.. 2003. Rapid deadenylation triggered by a nonsense codon precedes decay of the RNA body in a mammalian cytoplasmic nonsense-mediated decay pathway. Mol. Cell. Biol. 23:4805–4813.
   PubMedGoogle Scholar
• Chiu, S. Y., Serin G., Ohara O., and Maquat L. E.. 2003. Characterization of human Smg5/7a: a protein with similarities to Caenorhabditis elegans SMG-5 and SMG-7 that functions in the dephosphorylation of Upf1. RNA 9:77–87.
   PubMedGoogle Scholar
• Clissold, P. M., and Ponting C. P.. 2000. PIN domains in nonsense-mediated mRNA decay and RNAi. Curr. Biol. 10:R888–R890.
   PubMedGoogle Scholar
• Crittenden, S. L., and Kimble J.. 1999. Confocal methods for Caenorhabditis elegans. Methods Mol. Biol. 122:141–151.
   PubMedGoogle Scholar
• Culbertson, M. R., and Leeds P. F.. 2003. Looking at mRNA decay pathways through the window of molecular evolution. Curr. Opin. Genet. Dev. 13:207–214.
   PubMedGoogle Scholar
• Czaplinski, K., Ruiz-Echevarria M. J., Paushkin S. V., Han X., Weng Y., Perlick H. A., Ter-Avanesyan M. D., and Peltz S. W.. 1998. The surveillance complex interacts with the translation release factors to enhance termination and degrade aberrant mRNAs. Genes Dev. 12:1665–1677.
   PubMedGoogle Scholar
• Davis, L. I., and Blobel G.. 1986. Identification and characterization of a nuclear pore complex protein. Cell 45:699–709.
   PubMedGoogle Scholar
• Denning, G., Jamieson L., Maquat L. E., Thompson E. A., and Fields A. P.. 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
• De Pinto, B., Lippolis R., Castaldo R., and Altamura N.. 2004. Overexpression of Upf1p compensates for mitochondrial splicing deficiency independently of its role in mRNA surveillance. Mol. Microbiol. 51:1129–1142.
   PubMedGoogle Scholar
• Di Como, C. J., and Arndt K. T.. 1996. Nutrients, via the Tor proteins, stimulate the association of Tap42 with type 2A phosphatases. Genes Dev. 10:1904–1916.
   PubMed Web of Science ®Google Scholar
• Dolferus, R., Van Den Bossche D., and Jacobs M.. 1990. Sequence analysis of two null-mutant alleles of the single Arabidopsis Adh locus. Mol. Gen. Genet. 224:297–302.
   PubMedGoogle Scholar
• Dunckley, T., and Parker R.. 1999. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J. 18:5411–5422.
   PubMed Web of Science ®Google Scholar
• Gatfield, D., Unterholzner L., Ciccarelli F. D., Bork P., and Izaurralde E.. 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., Neu-Yilik G., Schell T., Hentze M. W., and Kulozik A. E.. 2003. Y14 and hUpf3b form an NMD-activating complex. Mol. Cell 11:939–949.
   PubMed Web of Science ®Google Scholar
• Gonzalez, C. I., Ruiz-Echevarria M. J., Vasudevan S., Henry M. F., and Peltz S. W.. 2000. The yeast hnRNP-like protein Hrp1/Nab4 marks a transcript for nonsense-mediated mRNA decay. Mol. Cell 5:489–499.
   PubMed Web of Science ®Google Scholar
• Gonzalez, C. I., Bhattacharya A., Wang W., and Peltz S. W.. 2001. Nonsense-mediated mRNA decay in Saccharomyces cerevisiae. Gene 274:15–25.
   PubMed Web of Science ®Google Scholar
• Hall, G. W., and Thein S.. 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
• He, F., Peltz S. W., Donahue J. L., Rosbash M., and Jacobson A.. 1993. Stabilization and ribosome association of unspliced pre-mRNAs in a yeast upf1- mutant. Proc. Natl. Acad. Sci. USA 90:7034–7038.
   PubMed Web of Science ®Google Scholar
• He, F., and Jacobson A.. 1995. Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen. Genes Dev. 9:437–454.
   PubMedGoogle Scholar
• He, F., Brown A. H., and Jacobson A.. 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
• Hodgkin, J., Papp A., Pulak R., Ambros V., and Anderson P.. 1989. A new kind of informational suppression in the nematode Caenorhabditis elegans. Genetics 123:301–313.
   PubMed Web of Science ®Google Scholar
• Hoekstra, M. F. 1997. Responses to DNA damage and regulation of cell cycle checkpoints by the ATM protein kinase family. Curr. Opin. Genet. Dev. 7:170–175.
   PubMedGoogle Scholar
• Hunter, T. 1995. When is a lipid kinase not a lipid kinase? When it is a protein kinase. Cell 83:1–4.
   PubMed Web of Science ®Google Scholar
• Jiang, Y., and Broach J. R.. 1999. Tor proteins and protein phosphatase 2A reciprocally regulate Tap42 in controlling cell growth in yeast. EMBO J. 18:2782–2792.
   PubMed Web of Science ®Google Scholar
• Kim, V. N., Kataoka N., and Dreyfuss G.. 2001. Role of the nonsense-mediated decay factor hUpf3 in the splicing-dependent exon-exon junction complex. Science 293:1832–1836.
   PubMedGoogle Scholar
• Le Hir, H., Izaurralde E., Maquat L. E., and Moore M. J.. 2000. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 19:6860–6869.
   PubMed Web of Science ®Google Scholar
• Lejeune, F., Li X., and Maquat L. E.. 2003. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol. Cell 12:675–687.
   PubMed Web of Science ®Google Scholar
• Lewis, B. P., Green R. E., and Brenner S. E.. 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc. Natl. Acad. Sci. USA 100:189–192.
   PubMed Web of Science ®Google Scholar
• Lykke-Andersen, J., Shu M. D., and Steitz J. A.. 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
• Lykke-Andersen, J., Shu M. D., and Steitz J. A.. 2001. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 293:1836–1839.
   PubMed Web of Science ®Google Scholar
• Lykke-Andersen, J. 2002. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 22:8114–8121.
   PubMed Web of Science ®Google Scholar
• Maquat, L. E. 2004. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat. Rev. Mol. Cell. Biol. 5:89–99.
   PubMed Web of Science ®Google Scholar
• Mello, C., and Fire A.. 1995. DNA transformation. Methods Cell Biol. 48:451–482.
   PubMed Web of Science ®Google Scholar
• Mendell, J. T., Medghalchi S. M., Lake R. G., Noensie E. N., and Dietz H. C.. 2000. Novel Upf2p orthologues suggest a functional link between translation initiation and nonsense surveillance complexes. Mol. Cell. Biol. 20:8944–8957.
   PubMedGoogle Scholar
• Mendell, J. T., ap Rhys C. M. J., and Dietz H. C.. 2002. Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science 298:419–422.
   PubMed Web of Science ®Google Scholar
• Mitchell, P., and Tollervey D.. 2003. An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′-5′ degradation. Mol. Cell 11:1405–1413.
   PubMed Web of Science ®Google Scholar
• Mitrovich, Q. M., and Anderson P.. 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
• Ohnishi, T., Yamashita A., Kashima I., Schell T., Anders K. R., Grimson A., Hachiya T., Hentze M. W., Anderson P., and Ohno S.. 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., Carr B., Anders K. R., Grimson A., Anderson P.. 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., Ishigaki Y., Nagy E., and Maquat L. E.. 2001. Evidence that phosphorylation of human Upf1 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
• Praitis, V., Casey E., Collar D., and Austin J.. 2001. Creation of low-copy integrated transgenic lines in Caenorhabditis elegans. Genetics 157:1217–1226.
   PubMed Web of Science ®Google Scholar
• Pulak, R., and Anderson P.. 1993. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes Dev. 7:1885–1897.
   PubMedGoogle Scholar
• Ruiz-Echevarria, M. J., Gonzalez C. I., and Peltz S. W.. 1998. Identifying the right stop: determining how the surveillance complex recognizes and degrades an aberrant mRNA. EMBO J. 17:575–589.
   PubMedGoogle Scholar
• Saitou, N., and Nei M.. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425.
   PubMed Web of Science ®Google Scholar
• Schu, P. V., Takegawa K., Fry M. J., Stack J. H., Waterfield M. D., and Emr S. D.. 1993. Phosphatidylinositol 3-kinase encoded by yeast VPS34 gene essential for protein sorting. Science 260:88–91.
   PubMed Web of Science ®Google Scholar
• Serin, G., Gersappe A., Black J. D., Aronoff R., and Maquat L. E.. 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
• Sheth, U., and Parker R.. 2003. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300:805–808.
   PubMed Web of Science ®Google Scholar
• Shirley, R. L., Lelivelt M. J., Schenkman L. R., Dahlseid J. N., and Culbertson M. R.. 1998. A factor required for nonsense-mediated mRNA decay in yeast is exported from the nucleus to the cytoplasm by a nuclear export signal sequence. J. Cell Sci. 111:3129–3143.
   PubMedGoogle Scholar
• Strimmer, K., and Von Haeseler A.. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964–969.
   Web of Science ®Google Scholar
• Sun, X., Perlick H. A., Dietz H. C., and Maquat L. E.. 1998. A mutated human homologue to yeast Upf1 protein has a dominant-negative effect on the decay of nonsense-containing mRNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 95:10009–10014.
   PubMedGoogle Scholar
• Takahashi, S., Araki Y., Sakuno T., and Katada T.. 2003. Interaction between Ski7p and Upf1p is required for nonsense-mediated 3′-to-5′ mRNA decay in yeast. EMBO J. 22:3951–3959.
   PubMedGoogle Scholar
• Taylor, S. S., Knighton D. R., Zheng J., Sowadski J. M., Gibbs C. S., and Zoller M. J.. 1993. A template for the protein kinase family. Trends Biochem. Sci. 18:84–89.
   PubMed Web of Science ®Google Scholar
• Thompson, J. D., Higgins D. G., and Gibson T. J.. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673–4680.
   PubMed Web of Science ®Google Scholar
• Wagner, E., and Lykke-Andersen J.. 2002. mRNA surveillance: the perfect persist. J. Cell Sci. 115:3033–3038.
   PubMed Web of Science ®Google Scholar
• Weng, Y., Czaplinski K., and Peltz S. W.. 1996. Genetic and biochemical characterization of mutations in the ATPase and helicase regions of the Upf1 protein. Mol. Cell. Biol. 16:5477–5490.
   PubMed Web of Science ®Google Scholar
• Wickens, M., and Goldstrohm A.. 2003. Molecular biology: a place to die, a place to sleep. Science 300:753–755.
   PubMedGoogle Scholar
• Williams, J. A., Langeland J. A., Thalley B. S., Skeath J. B., and Carroll S. B.. 1995. Expression of foreign proteins in E. coli using plasmid vectors and purification of specific polyclonal antibodies, p. 15–58. In Glover D. M. and Hames B. D. (ed.), DNA cloning 2: expression systems. A practical approach. Oxford University Press, Oxford, England.
   Google Scholar
• Wilusz, C. J., Wang W., and Peltz S. W.. 2001. Curbing the nonsense: the activation and regulation of mRNA surveillance. Genes Dev. 15:2781–2785.
   PubMedGoogle Scholar
• Yamashita, A., Ohnishi T., Kashima I., Taya Y., and Ohno S.. 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