When a ribosome encounters a premature termination codon

BMB Reports

Volumn 46, Issue 1, 2013, Pages 9-16

  Hwang, Jungwook ^a   Kim, Yoon Ki ^b  

^a Hanyang University   (South Korea)

^b Korea University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ALTERNATIVE RNA SPLICING; ANIMAL; GENE SILENCING; GENETICS; HUMAN; METABOLISM; NONSENSE MEDIATED MRNA DECAY; RIBOSOME; SHORT SURVEY; STOP CODON;

ALTERNATIVE SPLICING; ANIMALS; CODON, NONSENSE; GENE SILENCING; HUMANS; NONSENSE MEDIATED MRNA DECAY; RIBOSOMES; RNA, MESSENGER;

EID: 84874706482     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.5483/BMBRep.2013.46.1.002     Document Type: Short Survey

References (77)

1. Kuzmiak, H. A. and Maquat, L. E. (2006) Applying nonsense-mediated mRNA decay research to the clinic: progress and challenges. Trends Mol. Med. 12, 306-316.
2. Stoilov, P., Meshorer, E., Gencheva, M., Glick, D., Soreq, H. and Stamm, S. (2002) Defects in pre-mRNA processing as causes of and predisposition to diseases. DNA Cell Biol. 21, 803-818.
3. Caceres, J. F. and Kornblihtt, A. R. (2002) Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet. 18, 186-193.
4. Schoenberg, D. R. and Maquat, L. E. (2009) Re-capping the message. Trends Biochem. Sci. 34, 435-442.
5. Behm-Ansmant, I., Kashima, I., Rehwinkel, J., Sauliere, J., Wittkopp, N. and Izaurralde, E. (2007) mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons. FEBS Letters 581, 2845-2853.
6. Chang, Y. F., Imam, J. S. and Wilkinson, M. F. (2007) The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76, 51-74.
7. Isken, O. and Maquat, L. E. (2007) Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev. 21, 1833-1856.
8. Tange, T. O., Nott, A. and Moore, M. J. (2004) The ever-increasing complexities of the exon junction complex. Curr. Opin. Cell. Biol. 16, 279-284.
9. Reed, R. (2003) Coupling transcription, splicing and mRNA export. Curr. Opin. Cell. Biol. 15, 326-331.
10. Giorgi, C. and Moore, M. J. (2007) The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin. Cell. Dev. Biol. 18, 186-193.
11. Le Hir, H. and Andersen, G. R. (2008) Structural insights into the exon junction complex. Curr. Opin. Struct. Biol. 18, 112-119.
12. Diem, M. D., Chan, C. C., Younis, I. and Dreyfuss, G. (2007) PYM binds the cytoplasmic exon-junction complex and ribosomes to enhance translation of spliced mRNAs. Nat. Struct. Mol. Biol. 14, 1173-1179.
13. Le Hir, H. and Seraphin, B. (2008) EJCs at the heart of translational control. Cell 133, 213-216.
14. Ma, X. M., Yoon, S. O., Richardson, C. J., Julich, K. and Blenis, J. (2008) SKAR links pre-mRNA splicing to mTOR/S6K1-mediated enhanced translation efficiency of spliced mRNAs. Cell 133, 303-313.
15. Singh, G., Kucukural, A., Cenik, C., Leszyk, J. D., Shaffer, S. A., Weng, Z. and Moore, M. J. (2012) The cellular ejc interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell 151, 750-764.
16. Sauliere, J., Murigneux, V., Wang, Z., Marquenet, E., Barbosa, I., Le Tonqueze, O., Audic, Y., Paillard, L., Roest Crollius, H. and Le Hir, H. (2012) CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex. Nat. Struct. Mol. Biol. 19, 1124-1131.
17. Silva, A. L. and Romão, L. (2009) The mammalian nonsense-mediated mRNA decay pathway: to decay or not to decay! Which players make the decision? FEBS letters 583, 499-505.
18. Nicholson, P., Yepiskoposyan, H., Metze, S., Zamudio Orozco, R., Kleinschmidt, N. and Mühlemann, O. (2010) Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors. Cell Mol. Life Sci. 67, 677-700.
19. Shyu, A. B., Wilkinson, M. F. and van Hoof, A. (2008) Messenger RNA regulation: to translate or to degrade. EMBO J. 27, 471-481.
20. Neu-Yilik, G. and Kulozik, A. E. (2008) NMD: multitasking between mRNA surveillance and modulation of gene expression. Adv. Genet. 62, 185-243.
21. Mühlemann, O., Eberle, A. B., Stalder, L. and Zamudio Orozco, R. (2008) Recognition and elimination of nonsense mRNA. Biochim. Biophys. Acta. 1779, 538-549.
22. McGlincy, N. J. and Smith, C. W. (2008) Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends. Biochem. Sci. 33, 385-393.
23. Linde, L. and Kerem, B. (2008) Introducing sense into nonsense in treatments of human genetic diseases. Trends Genet. 24, 552-563.
24. Lejeune, F. and Maquat, L. E. (2005) Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17, 309-315.
25. Isken, O. and Maquat, L. E. (2008) The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nat. Rev. Genet. 9, 699-712.
26. Chiu, S. Y., Lejeune, F., Ranganathan, A. C. and Maquat, L. E. (2004) The pioneer translation initiation complex is functionally distinct from but structurally overlaps with the steady-state translation initiation complex. Genes Dev. 18, 745-754.
27. Ishigaki, Y., Li, X., Serin, G. and Maquat, L. E. (2001) Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. Cell 106, 607-617.
28. Kim, K. M., Cho, H., Choi, K., Kim, J., Kim, B. W., Ko, Y. G., Jang, S. K. and Kim, Y. K. (2009) A new MIF4G domain-containing protein, CTIF, directs nuclear cap-binding protein CBP80/20-dependent translation. Genes Dev. 23, 2033-2045.
29. Hwang, J., Sato, H., Tang, Y., Matsuda, D. and Maquat, L. E. (2010) UPF1 association with the cap-binding protein, CBP80, promotes nonsense-mediated mRNA decay at two distinct steps. Mol. Cell 39, 396-409.
30. Gehring, N. H., Lamprinaki, S., Kulozik, A. E. and Hentze, M. W. (2009) Disassembly of exon junction complexes by PYM. Cell 137, 536-548.
31. Maquat, L. E. (2005) Nonsense-mediated mRNA decay in mammals. J. Cell Sci. 118, 1773-1776.
32. Kashima, I., Yamashita, A., Izumi, N., Kataoka, N., Morishita, R., Hoshino, S., Ohno, M., Dreyfuss, G. and Ohno, S. (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.
33. Yamashita, A., Izumi, N., Kashima, I., Ohnishi, T., Saari, B., Katsuhata, Y., Muramatsu, R., Morita, T., Iwamatsu, A., Hachiya, T., Kurata, R., Hirano, H., Anderson, P. and Ohno, S. (2009) SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. Genes Dev. 23, 1091-1105.
34. Cho, H., Kim, K. M. and Kim, Y. K. (2009) Human proline-rich nuclear receptor coregulatory protein 2 mediates an interaction between mRNA surveillance machinery and decapping complex. Mol. Cell 33, 75-86.
35. Fukuhara, N., Ebert, J., Unterholzner, L., Lindner, D., Izaurralde, E. and Conti, E. (2005) SMG7 is a 14-3-3-like adaptor in the nonsense-mediated mRNA decay pathway. Mol. Cell 17, 537-547.
36. Unterholzner, L. and Izaurralde, E. (2004) SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol. Cell 16, 587-596.
37. Cho, H., Kim, K. M., Han, S., Choe, J., Park, S. G., Choi, S. S. and Kim, Y. K. (2012) Staufen1-mediated mRNA decay functions in adipogenesis. Mol. Cell 46, 495-506.
38. Yepiskoposyan, H., Aeschimann, F., Nilsson, D., Okoniewski, M. and Mühlemann, O. (2011) Autoregulation of the nonsense-mediated mRNA decay pathway in human cells. RNA 17, 2108-2118.
39. Cho, H., Han, S., Choe, J., Park, S. G., Choi, S. S. and Kim, Y. K. (2012) SMG5-PNRC2 is functionally dominant compared with SMG5-SMG7 in mammalian nonsense-mediated mRNA decay. Nucleic Acids Res. DOI:10.1093/nar/gks1222.
40. Lee, H. C., Oh, N., Cho, H., Choe, J. and Kim, Y. K. (2010) Nonsense-mediated translational repression involves exon junction complex downstream of premature translation termination codon. FEBS Letters 584, 795-800.
41. You, K. T., Li, L. S., Kim, N. G., Kang, H. J., Koh, K. H., Chwae, Y. J., Kim, K. M., Kim, Y. K., Park, S. M., Jang, S. K. and Kim, H. (2007) Selective translational repression of truncated proteins from frameshift mutation-derived mRNAs in tumors. PLoS Biol. 5, e109.
42. Zhang, J., Sun, X., Qian, Y., LaDuca, J. P. and Maquat, L. E. (1998) At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol. Cell Biol. 18, 5272-5283.
43. Cheng, J., Belgrader, P., Zhou, X. and Maquat, L. E. (1994) Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance. Mol. Cell Biol. 14, 6317-6325.
44. Buhler, M., Steiner, S., Mohn, F., Paillusson, A. and Mühlemann, O. (2006) EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length. Nat. Struct. Mol. Biol. 13, 462-464.
45. Choe, J., Cho, H., Chi, S. G. and Kim, Y. K. (2011) Ago2/miRISC-mediated inhibition of CBP80/20-dependent translation and thereby abrogation of nonsense-mediated mRNA decay require the cap-associating activity of Ago2. FEBS Letters 585, 2682-2687.
46. Choe, J., Cho, H., Lee, H. C. and Kim, Y. K. (2010) microRNA/Argonaute 2 regulates nonsense-mediated messenger RNA decay. EMBO Rep. 11, 380-386.
47. Kebaara, B., Nazarenus, T., Taylor, R. and Atkin, A. L. (2003) Genetic background affects relative nonsense mRNA accumulation in wild-type and upf mutant yeast strains. Curr. Genet. 43, 171-177.
48. Jensen, L. R., Amende, M., Gurok, U., Moser, B., Gimmel, V., Tzschach, A., Janecke, A. R., Tariverdian, G., Chelly, J., Fryns, J. P., Van Esch, H., Kleefstra, T., Hamel, B., Moraine, C., Gecz, J., Turner, G., Reinhardt, R., Kalscheuer, V. M., Ropers, H. H. and Lenzner, S. (2005) Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am. J. Hum. Genet. 76, 227-236.
49. Bateman, J. F., Freddi, S., Nattrass, G. and Savarirayan, R. (2003) Tissue-specific RNA surveillance? Nonsense-mediated mRNA decay causes collagen X haploinsufficiency in Schmid metaphyseal chondrodysplasia cartilage. Hum. Mol. Genet. 12, 217-225.
50. Resta, N., Susca, F. C., Di Giacomo, M. C., Stella, A., Bukvic, N., Bagnulo, R., Simone, C. and Guanti, G. (2006) A homozygous frameshift mutation in the ESCO2 gene: evidence of intertissue and interindividual variation in Nmd efficiency. J. Cell Physiol. 209, 67-73.
51. Viegas, M. H., Gehring, N. H., Breit, S., Hentze, M. W. and Kulozik, A. E. (2007) The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway. Nucleic Acids Res. 35, 4542-4551.
52. Linde, L., Boelz, S., Neu-Yilik, G., Kulozik, A. E. and Kerem, B. (2007) The efficiency of nonsense-mediated mRNA decay is an inherent character and varies among different cells. Eur. J. Hum. Genet. 15, 1156-1162.
53. Kerr, T. P., Sewry, C. A., Robb, S. A. and Roberts, R. G. (2001) Long mutant dystrophins and variable phenotypes: evasion of nonsense-mediated decay? Hum. Genet. 109, 402-407.
54. Linde, L., Boelz, S., Nissim-Rafinia, M., Oren, Y. S., Wilschanski, M., Yaacov, Y., Virgilis, D., Neu-Yilik, G., Kulozik, A. E., Kerem, E. and Kerem, B. (2007) Nonsense-mediated mRNA decay affects nonsense transcript levels and governs response of cystic fibrosis patients to gentamicin. J. Clin. Invest. 117, 683-692.
55. Maquat, L. E. and Kinniburgh, A. J. (1985) A beta zero-thalassemic beta-globin RNA that is labile in bone marrow cells is relatively stable in HeLa cells. Nucleic Acids Res. 13, 2855-2867.
56. Maquat, L. E., Kinniburgh, A. J., Rachmilewitz, E. A. and Ross, J. (1981) Unstable beta-globin mRNA in mRNA-deficient beta o thalassemia. Cell 27, 543-553.
57. Zhang, J., Sun, X., Qian, Y. and Maquat, L. E. (1998) Intron function in the nonsense-mediated decay of beta-globin mRNA: indications that pre-mRNA splicing in the nucleus can influence mRNA translation in the cytoplasm. RNA 4, 801-815.
58. Kugler, W., Enssle, J., Hentze, M. W. and Kulozik, A. E. (1995) Nuclear degradation of nonsense mutated beta-globin mRNA: a post-transcriptional mechanism to protect heterozygotes from severe clinical manifestations of beta-thalassemia? Nucleic Acids Res. 23, 413-418.
59. Lim, S. K. and Maquat, L. E. (1992) Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini. EMBO J. 11, 3271-3278.
60. Lim, S. K., Sigmund, C. D., Gross, K. W. and Maquat, L. E. (1992) Nonsense codons in human beta-globin mRNA result in the production of mRNA degradation products. Mol. Cell Biol. 12, 1149-1161.
61. Silva, A. L., Ribeiro, P., Inacio, A., Liebhaber, S. A. and Romão, L. (2008) Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay. RNA 14, 563-576.
62. Muhlrad, D. and Parker, R. (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.
63. Chang, Y. F., Chan, W. K., Imam, J. S. and Wilkinson, M. F. (2007) Alternatively spliced T-cell receptor transcripts are up-regulated in response to disruption of either splicing elements or reading frame. J. Biol. Chem. 282, 29738-29747.
64. Mendell, J. T., ap Rhys, C. M. and Dietz, H. C. (2002) Separable roles for rent1/hUpf1 in altered splicing and decay of nonsense transcripts. Science 298, 419-422.
65. Wang, J., Chang, Y. F., Hamilton, J. I. and Wilkinson, M. F. (2002) Nonsense-associated altered splicing: a framedependent response distinct from nonsense-mediated decay. Mol. Cell 10, 951-957.
66. Wang, J., Hamilton, J. I., Carter, M. S., Li, S. and Wilkinson, M. F. (2002) Alternatively spliced TCR mRNA induced by disruption of reading frame. Science 297, 108-110.
67. Mohn, F., Buhler, M. and Mühlemann, O. (2005) Nonsenseassociated alternative splicing of T-cell receptor beta genes: no evidence for frame dependence. RNA 11, 147-156.
68. Buhler, M., Wilkinson, M. F. and Mühlemann, O. (2002) Intranuclear degradation of nonsense codon-containing mRNA. EMBO Rep. 3, 646-651.
69. Mühlemann, O., Mock-Casagrande, C. S., Wang, J., Li, S., Custodio, N., Carmo-Fonseca, M., Wilkinson, M. F. and Moore, M. J. (2001) Precursor RNAs harboring nonsense codons accumulate near the site of transcription. Mol. Cell 8, 33-43.
70. de Turris, V., Nicholson, P., Orozco, R. Z., Singer, R. H. and Mühlemann, O. (2011) Cotranscriptional effect of a premature termination codon revealed by live-cell imaging. RNA 17, 2094-2107.
71. Buhler, M., Mohn, F., Stalder, L. and Mühlemann, O. (2005) Transcriptional silencing of nonsense codon-containing immunoglobulin minigenes. Mol. Cell 18, 307-317.
72. Mendell, J. T., Sharifi, N. A., Meyers, J. L., Martinez-Murillo, F. and Dietz, H. C. (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073-1078.
73. Mitrovich, Q. M. and Anderson, P. (2005) mRNA surveillance of expressed pseudogenes in C. elegans. Curr. Biol. 15, 963-967.
74. He, F., Li, X., Spatrick, P., Casillo, R., Dong, S. and Jacobson, A. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast. Mol. Cell 12, 1439-1452.
75. Weischenfeldt, J., Damgaard, I., Bryder, D., Theilgaard-Monch, K., Thoren, L. A., Nielsen, F. C., Jacobsen, S. E., Nerlov, C. and Porse, B. T. (2008) NMD is essential for hematopoietic stem and progenitor cells and for eliminating by-products of programmed DNA rearrangements. Genes Dev. 22, 1381-1396.
76. Wittmann, J., Hol, E. M. and Jack, H. M. (2006) hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol. Cell Biol. 26, 1272-1287.
77. Guan, Q., Zheng, W., Tang, S., Liu, X., Zinkel, R. A., Tsui, K. W., Yandell, B. S. and Culbertson, M. R. (2006) Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast. PLoS Genet. 2, e203.