Upf1p control of nonsense mRNA translation is regulated by Nmd2p and Upf3p

Molecular and Cellular Biology

Volumn 20, Issue 13, 2000, Pages 4591-4603

  Maderazo, Alan B ^a   He, Feng ^a   Mangus, David A ^a   Jacobson, Allan ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSLATION TERMINATION FACTOR;

ALLELE; ARTICLE; CONTROLLED STUDY; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE REPRESSION; GENOTYPE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; RNA TRANSLATION; STOICHIOMETRY;

AMINO ACID TRANSPORT SYSTEMS; CODON, NONSENSE; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; MEMBRANE TRANSPORT PROTEINS; MUTATION; PROTEIN BIOSYNTHESIS; RNA CAPS; RNA HELICASES; RNA, MESSENGER; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE PROTEINS; SUPPRESSION, GENETIC; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC; YEASTS;

EID: 0034043404     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.20.13.4591-4603.2000     Document Type: Article

References (63)

1. Altamura, N., O. Groudinsky, G. Dujardin, and P. P. Slonimski. 1992. NAM7 nuclear gene encodes a novel member of a family of helicases with a Zn-ligand motif and is involved in mitochondrial functions in Saccharomyces cerevisiae. J. Mol. Biol. 224:575-587.
2. Applequist, S. E., M. Selg, C. Roman, and H. M. Jack. 1997. Cloning and characterization of HUPF1, a human homolog of the Saccharomyces cerevisiae nonsense mRNA-reducing UPF1 protein. Nucleic Acids Res. 25:814-821.
3. Atkin, A. L., L. R. Schenkman, M. Eastham, J. N. Dahlseid, M. J. Lelivelt, and M. R. Culbertson. 1997. Relationship between yeast polyribosomes and the Upf proteins required for nonsense mRNA decay. J. Biol. Chem. 272: 22163-22172.
4. Beelman, C. A., A. Stevens, G. Caponigro, T. E. LaGrandeur, L. Hatfield, and R. Parker. 1996. An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature 382:642-646.
5. Caponigro, G., and R. Parker. 1996. Mechanisms and control of mRNA turnover in Saccharomyces cerevisiae. Microbiol. Rev. 60:233-249.
6. Chin, K., and A. M. Pyle. 1995. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5′-splice site selection. RNA 1:391-406.
7. Cui, Y., K. W. Hagan, S. Zhang, and S. W. Peltz. 1995. Identification and characterization of genes that are required for the accelerated degradation of mRNAs containing a premature translational termination codon. Genes Dev. 9:423-436.
8. Cui, Y., J. D. Dinman, and S. W. Peltz. 1996. Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. EMBO J. 15:5726-5736.
9. Culbertson, M. R., K. M. Underbrink, and G. R. Fink. 1980. Frameshift suppression in Saccharomyces cerevisiae. II. Genetic properties of group II suppressors. Genetics 95:833-853.
10. Czaplinski, K., Y. Weng, K. W. Hagan, and S. W. Peltz. 1995. Purification and characterization of the Upf1p: a factor involved in mRNA turnover. RNA 1:610-623.
11. 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.
12. Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6-13.
13. 2). Eur. J. Biochem. 240:526-531.
14. Gottesman, S., R. Wickner, and M. R. Maurizi. 1997. Protein quality control: triage by chaperones and proteases. Genes Dev. 11:815-823.
15. Guthrie, C., and G. R. Fink (ed.). 1991. Methods in enzymology: molecular biology of Saccharomyces cerevisiae. Academic Press, Inc., New York, N.Y.
16. Gygi, S. P., Y. Rochon, B. R. Franza, and R. Aebersold. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720-1730.
17. Hagan, K. W., M. J. Ruiz-Echevarria, Y. Quan, and S. W. Peltz. 1995. Characterization of cis-acting sequences and decay intermediates involved in nonsense-mediated mRNA turnover. Mol. Cell. Biol. 15:809-823.
18. Harlow, E., and D. Lane. 1988. Antibodies: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
19. - mutant. Proc. Natl. Acad. Sci. USA 90:7034-7038.
20. He, F., and A. Jacobson. 1995. Identification of a novel component of the nonsense-mediated mRNA decay pathway using an interacting protein screen. Genes Dev. 9:437-454.
21. He, F., A. H. Brown, and A. Jacobson. 1996. Interaction between Nmd2p and Upf1p is required for activity but not for dominant-negative inhibition of the nonsense-mediated mRNA decay pathway in yeast. RNA 2:153-170.
22. 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.
23. Hereford, L. M., and M. Rosbash. 1977. Number and distribution of polyadenylated RNA sequences in yeast. Cell 10:453-462.
24. Herrick, D., R. Parker, and A. Jacobson. 1990. Identification and comparison of stable and unstable mRNAs in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 10:2269-2284.
25. Heyer, W. D., A. W. Johnson, U. Reinhart, and R. D. Kolodner. 1995. Regulation and intracellular localization of Saccharomyces cerevisiae strand exchange protein 1 (Sep1/Xrn1/Kem1), a multifunctional exonuclease. Mol. Cell. Biol. 15:2728-2736.
26. Hoffmann, W. 1985. Molecular characterization of the CAN1 locus in Saccharomyces cerevisiae. A transmembrane protein without N-terminal hydrophobic signal sequence. J. Biol. Chem. 260:11831-11837.
27. Hsu, C. L., and A. Stevens. 1993. Yeast cells lacking 5′→3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Mol. Cell. Biol. 13:4826-4835.
28. Hurt, D. J., S. S. Wang, Y. H. Lin, and A. K. Hopper. 1987. Cloning and characterization of LOS1, a Succharomyces cerevisiae gene that affects tRNA splicing. Mol. Cell. Biol. 3:1208-1216.
29. Jacobson, A., and S. W. Peltz. 1996. Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Annu. Rev. Biochem. 65: 693-739.
30. Jeon, C., and K. Agarwal. 1996. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc. Natl. Acad. Sci. USA 93:13677-13682.
31. Koonin, E. V. 1992. A new group of putative RNA helicases. Trends Biochem. Sci. 17:495-497.
32. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
33. LaGrandeur, T. E., and R. Parker. 1998. Isolation and characterization of Dcp1p, the yeast mRNA decapping enzyme, EMBO J. 17:1487-1496.
34. Lee, B. S., and M. R. Culbertson. 1995. Identification of an additional gene required for eukaryotic nonsense mRNA turnover. Proc. Natl. Acad. Sci. USA 92:10354-10358.
35. Leeds, P., S. W. Peltz, A. Jacobson, and M. R. Culbertson. 1991. The product of the yeast UPfI gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 5:2303-2314.
36. Leeds, P., J. M. Wood, B. S. Lee, and M. R. Culbertson. 1992. Gene products that promote mRNA turnover in Saccharomyces cerevisiae. Mol. Cell. Biol. 12:2165-2177.
37. Lelivelt, M. J., and M. R. Culbertson. 1999. Yeast Upf proteins required for RNA surveillance affect global expression of the yeast transcriptome. Mol. Cell. Biol. 10:6710-6719.
38. Mangus, D. A., and A. Jacobson. 1999. Linking turnover and translation: assessing the polyribosomal association of mRNA decay factors and degradative intermediates. Methods 17:28-37.
39. Maquat, L. E. 1995. When cells stop making sense: effects of nonsense codons on RNA metabolism in vertebrate cells. RNA 1:453-465.
40. Muhlrad, D., C. Decker, and R. Parker. 1994. Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5′-3′ digestion of the transcript. Genes Dev. 8:855-866.
41. Muhlrad, D., and R. Parker. 1994. Premature translational termination triggers mRNA decapping. Nature 370:578-581.
42. Muhlrad, D., and R. Parker. 1999. Recognition of yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping. Mol. Biol. Cell 10:3971-3978.
43. Opekarova, M., and J. Kubin. 1997. On the unidirectionality of arginine uptake in the yeast Saccharomyces cerevisiae. FEMS Microbiol. Lett. 152: 261-267.
44. 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.
45. Peltz, S. W., A. H. Brown, and A. Jacobson. 1993. mRNA destabilization triggered by premature translational termination depends on at least three cis-acting sequence elements and one trans-acting factor. Genes Dev. 7: 1737-1754.
46. Peltz, S. W., C. Trotta, F. He, A. Brown, J. Donahue, E. Welch, and A. Jacobson. 1993. Identification of the cis-acting sequences and trans-acting factors involved in nonsense-mediated mRNA decay, p. 1-10. In A. Brown, M. Tuite, and J. McCarthy (ed.), Protein synthesis and targeting in yeast. Springer-Verlag, Berlin, Germany.
47. Peltz, S. W., K. He, E. Welch, and A. Jacobson. 1994. Nonsense-mediated mRNA decay in yeast. Prog. Nucleic Acids Res. Mol. Biol. 47:271-298.
48. Perlick, H. A., S. M. Medghalchi, F. A. Spencer, R. J. Kendzior, Jr., and H. C. Dietz. 1996. Mammalian orthologues of a yeast regulator of nonsense-transcript stability. Proc. Natl. Acad. Sci. USA 93:10928-10932.
49. Pulak, R., and P. Anderson. 1993. mRNA surveillance by the Caenorhabditis elegans smg genes. Genes Dev. 7:1885-1897.
50. Rose, M. D., F. Winston, and P. Heiter. 1990. Methods in yeast genetics: a laboratory course manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
51. Ruiz-Echevarria, M. J., K. Czaplinski, and S. W. Peltz. 1996. Making sense of nonsense in yeast. Trends Biochem. Sci. 21:433-438.
52. Ruiz-Echevarria, M. J., J. M. Yasenchak, X. Han, J. D. Dinman, and S. W. Peltz. 1998. The Upf3 protein is a component of the surveillance complex that monitors both translation and mRNA turnover and affects viral propagation. Proc. Natl. Acad. Sci. USA 95:8721-8726.
53. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
54. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
55. Soni, R., J. P. Carmichael, and J. A. H. Murray. 1993. Parameters affecting lithium acetate-mediated transformation of Saccharomyces cerevisiae and development of a rapid and simple procedure. Curr. Genet. 24:455-459.
56. Waldron, C., and F. Lacroute. 1975. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast. J. Bacteriol. 122:855-865.
57. Welch, E. M., and A. Jacobson. 1999. An internal open reading frame triggers nonsense-mediated decay of the yeast SPT10 mRNA. EMBO J. 18: 6134-6145.
58. Weng, Y., K. Czaplinski, and S. W. Peltz. 1996. Identification and characterization of mutations in the UPFI gene that affect nonsense suppression and the formation of the Upf protein complex but not mRNA turnover. Mol. Cell. Biol. 16:5491-5506.
59. Weng, Y., K. Czaplinski, and S. W. Peltz. 1996. Genetic and biochemical characterization of mutations in the ATPase and helicase regions of the Upf1 protein. Mol. Cell. Biol. 16:5477-5490.
60. Weng, Y., K. Czaplinski, and S. W. Peltz. 1998. ATP is a cofactor of the Upf1p protein that modulates its translation termination and RNA binding activities. RNA 4:205-214.
61. While, T. J., N. Arnheim, and H. A. Erlich. 1989. The polymerase chain reaction. Trends Genet. 5:185-189.
62. Yarus, M. 1992. Proofreading. NTPases and translation: successful increase in specificity. Trends Biochem. Sci. 17:171-174.
63. Zuk, D., and A. Jacobson. 1998. A single amino acid substitution in yeast eIF-5A results in mRNA stabilization. EMBO J. 17:2914-2925.