Widespread 3′-end uridylation in eukaryotic RNA viruses

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Huo, Yayun ^a   Shen, Jianguo ^b   Wu, Huanian ^a   Zhang, Chao ^a   Guo, Lihua ^a   Yang, Jinguang ^a   Li, Weimin ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b Fujian Technology Center of Entry Exit Inspection and Quarantine Bureau   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL VIRUS; EUKARYOTE; MYCOVIRUS; PLANT VIRUS; RNA DEGRADATION; RNA VIRUS; SPECIES; VIRUS CELL INTERACTION; 3' UNTRANSLATED REGION; ANIMAL; FUNGUS; METABOLISM; PHYSIOLOGY; PLANT; VIROLOGY;

POLYURIDYLIC ACID; VIRUS RNA;

3' UNTRANSLATED REGIONS; ANIMALS; EUKARYOTA; FUNGI; PLANTS; POLY U; RNA VIRUSES; RNA, VIRAL;

EID: 84967012320     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep25454     Document Type: Article

References (56)

1. Edmonds, M. A. history of poly A sequences: from formation to factors to function. Prog. Nucleic Acid Res. Mol. Biol. 71, 285-389 (2002).
2. Slomovic, S., Portnoy, V., Liveanu, V., Schuster, G. RNA Polyadenylation in Prokaryotes and Organelles; Different Tails Tell Different Tales. Crit. Rev. Plant Sci. 25, 65-77 (2006).
3. Slomovic, S., Portnoy, V., Yehudai-Resheff, S., Bronshtein, E., Schuster, G. Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases. Biochim Biophys Acta 1779, 247-255 (2008).
4. Moore, M. J., Proudfoot, N. J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688-700 (2009).
5. Schuster, G., Stern, D. RNA polyadenylation and decay in mitochondria and chloroplasts. Prog. Mol. Biol. Transl. Sci. 85, 393-422 (2009).
6. Sikorski, P. J., et al. Distinct 18S rRNA precursors are targets of the exosome complex, the exoribonuclease RRP6L2 and the terminal nucleotidyltransferase TRL in Arabidopsis thaliana. Plant J. 83, 991-1004 (2015).
7. Norbury, C. J., Cytoplasmic R. N. A.: a case of the tail wagging the dog. Nat. Rev. Mol. Cell Biol. 14, 643-653 (2013).
8. Lee, M., Kim. B., Kim, V. N. Emerging roles of RNA modification: m(6)A and U-tail. Cell 158, 980-987 (2014).
9. Viegas, S. C., Silva, I. J., Apura, P., Matos, R. G., Arraiano, C. M. Surprises in the 3?-end: 'U' can decide too! FEBS J. 282, 3489-3499 (2015).
10. Trippe, R., Sandrock, B., Benecke, B. J. A highly specific terminal uridylyl transferase modifies the 3?-end of U6 small nuclear RNA. Nucleic Acids Res. 26, 3119-3126 (1998).
11. Morozov, I. Y., Caddick, M. X. Cytoplasmic mRNA 3 tagging in eukaryotes: does it spell the end? Biochem. Soc. Trans. 40, 810-814 (2012).
12. Lim, J., et al. Uridylation by TUT4 and TUT7 marks mRNA for degradation. Cell 159, 1365-1376 (2014).
13. Simpson, L., Aphasizhev, R., Gao, G., Kang, X. Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing. RNA 10, 159-170 (2004).
14. Heo, I., et al. Mono-uridylation of pre-MicroRNA as a key step in the biogenesis of group II let-7 MicroRNAs. Cell 151, 521-532 (2012).
15. Lund, E., Dahlberg, J. E. Cyclic 2,3-phosphates and nontemplated nucleotides at the 3 end of spliceosomal U6 small nuclear RNA's. Science 255, 327-330 (1992).
16. Mullen, T. E., Marzluff, W. F. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5? to 3 and 3 to 5? . Genes Dev. 22, 50-65 (2008).
17. Shen, B., Goodman, H. M. Uridine addition after microRNA directed cleavage. Science 306, 997 (2004).
18. Rissland, O. S., Norbury, C. J. Decapping is preceded by 3 uridylation in a novel pathway of bulk mRNA turnover. Nat. Struct. Mol. Biol. 16, 616-623 (2009).
19. Sement, F. M., et al. Uridylation prevents 3 trimming of oligoadenylated mRNAs. Nucleic Acids Res. 41, 7115-7127 (2013).
20. van Wolfswinkel, J. C., et al. CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell 139, 135-148 (2009).
21. Ibrahim, F., et al. Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc. Natl. Acad. Sci. USA 107, 3906-3911 (2010).
22. Kamminga, L. M., et al. Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J. 29, 3688-3700 (2010).
23. Ren, G., Chen, X., Yu, B. Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis. Curr. Biol. 22, 695-700 (2012).
24. Zhao, Y., et al. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr. Biol. 22, 689-694 (2012).
25. Lehrbach, N. J., et al. LIN-28 and the poly(U) polymerase PUP-2 regulate let-7 microRNA processing in Caenorhabditis elegans. Nat. Struct. Mol. Biol. 16, 1016-1020 (2009).
26. Heo, I., et al. Lin28 mediates the terminal uridylation of let-7 precursor microRNA. Mol. Cell 32, 276-284 (2008).
27. Hagan, J. P., Piskounova, E., Gregory, R. I. Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 16, 1021-1025 (2009).
28. Suzuki, H. I., Katsura, A., Miyazono, K. A role of uridylation pathway for blockade of let-7 microRNA biogenesis by Lin28B. Cancer Sci. 106, 1174-1181 (2015).
29. Ren, G., Chen, X., Yu, B. Small RNAs meet their targets: when methylation defends miRNAs from uridylation. RNA Biol. 11, 1099-1104 (2014).
30. King, A. M. Q., Adams, M. J., Carstens, E. B., Lefkowitz, E. J. Virus taxonomy: classification and nomenclature of viruses in the Ninth Report of the International Committee on Taxonomy of Viruses (Elsevier, 2012).
31. Dreher, T. W. Funcations of the 3?-untranslated regions of positive strand RNA viral genomes. Annu. Rev. Phytopathol. 37, 151-174 (1999).
32. Barr, J. N., Fearns, R. How RNA viruses maintain their genome integrity. J. Gen. Virol. 91, 1373-1387 (2010).
33. Li, W., et al. Presence of poly(A) and poly(A)-rich tails in a positive-strand RNA virus known to lack 3 poly(A) tails. Virology 454-455, 1-10 (2014).
34. He, M., Jiang, Z., Li, S., He, P. Presence of poly(A) tails at the 3?-termini of some mRNAs of a double-stranded RNA virus, southern rice black-streaked dwarf virus. Viruses 7, 1642-1650 (2015).
35. Jupin, I., Bouzoubaa, S., Richards, K., Jonard, G., Guilley, H. Multiplication of beet necrotic yellow vein virus RNA 3 lacking a 3 poly(A) tail is accompanied by reappearance of the poly(A) tail and a novel short U-rich tract preceding it. Virology 178, 281-284 (1990).
36. Raju, R., Hajjou, M., Hill, K. R., Botta, V., Botta, S. In vivo addition of poly(A) tail and AU-rich sequences to the 3 terminus of the Sindbis virus RNA genome: a novel 3?-end repair pathway. J. Virol. 73, 2410-2419 (1999).
37. van Ooij, M. J., et al. Polyadenylation of genomic RNA and initiation of antigenomic RNA in a positive-strand RNA virus are controlled by the same cis-element. Nucleic Acids Res. 34, 2953-2965 (2006).
38. van Leeuwen, H. C., Liefhebber, J. M., Spaan, W. J. Repair and polyadenylation of a naturally occurring hepatitis C virus 3 nontranslated region-shorter variant in selectable replicon cell lines. J. Virol. 80, 4336-4343 (2006).
39. Furnari, F. B., Adams, M. D., Pagano, J. S. Unconventional processing of the 3 termini of the Epstein-Barr Virus DNA polymerase messenger RNA. Proc. Natl. Acad. Sci. USA 90, 378-382 (1993).
40. Pfeffer, S., et al. Identification of virus-encoded microRNAs. Science 304, 734-736 (2004).
41. Rissland, O. S., Norbury, C. J. The Cid1 poly(U) polymerase. Biochimica et Biophysica Acta 1779, 286-294 (2008).
42. Creager, A. N., Scholthof, K. B., Citovsky, V., Scholthof, H. B. Tobacco mosaic virus. Pioneering research for a century. Plant Cell 11, 301-308 (1999).
43. Lisitsky, I., Klaff, P., Schuster, G. Addition of destabilizing poly (A)-rich sequences to endonuclease cleavage sites during the degradation of chloroplast mRNA. Proc. Natl. Acad. Sci. USA 93, 13398-13403 (1996).
44. Scott, D. D., Norbury, C. J. RNA decay via 3 uridylation. Biochim Biophys Acta 1829, 654-665 (2013).
45. Morozov, I. Y., Jones, M. G., Razak, A. A., Rigden, D. J., Caddick, M. X. CUCU modification of mRNA promotes decapping and transcript degradation in Aspergillus nidulans. Mol. Cell. Biol. 30, 460-469 (2010).
46. Dickson, A. M., Wilusz, J. Strategies for viral RNA stability: live long and prosper. Trends Genet. 27, 286-293 (2011).
47. Moon, S. L., Barnhart, M. D., Wilusz, J. Inhibition and avoidance of mRNA degradation by RNA viruses. Curr. Opin. Microbiol. 15, 500-505 (2012).
48. Sokoloski, K. J., Chaskey, E. L., Wilusz, J. Virus-mediated mRNA decay by hyperadenylation. Genome Biol. 10, 234 (2009).
49. Gaglia, M. M., Glaunsinger, B. A. Viruses and the cellular RNA decay machinery. Wiley Interdiscip Rev RNA 1, 47-59 (2010).
50. Garcia, D., Garcia, S., Voinnet, O. Nonsense-mediated decay serves as a general viral restriction mechanism in plants. Cell Host Microbe 16, 391-402 (2014).
51. Wu, J., et al. Viral-inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA. Elife 4, e05733 (2015).
52. Du, P., et al. Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog. 7, e1002176 (2011).
53. Zhou, L., et al. The 30-amino-acid deletion in the Nsp2 of highly pathogenic porcine reproductive and respiratory syndrome virus emerging in China is not related to its virulence. J. Virol. 83, 5156-5167 (2009).
54. Gao, Y., et al. Phylogenetic analysis of porcine epidemic diarrhea virus field strains prevailing recently in China. Arch. Virol. 158, 711-715 (2013).
55. Li, P., Zhang, H., Chen, X., Qiu, D., Guo, L. Molecular characterization of a novel hypovirus from the plant pathogenic fungus Fusarium graminearum. Virology 481, 151-160 (2015).
56. Lin, Y., Zhang, H., Zhao, C., Liu, S., Guo, L. The complete genome sequence of a novel mycovirus from Alternaria longipes strain HN28. Arch. Virol. 160, 577-580 (2015).