Translational readthrough in tobacco necrosis virus-D

Virology

Volumn 450-451, Issue , 2014, Pages 258-265

  Newburn, Laura R ^a   Nicholson, Beth L ^a   Yosefi, Michael ^a   Cimino, Peter A ^a   White, K Andrew ^a  

^a YORK UNIVERSITY   (Canada)

Author keywords

Cap independent translation; Carmovirus; Frameshifting; Necrovirus; Plant virus; Readthrough; Recoding; RNA structure; RNA virus; Tombusviridae

Indexed keywords

3' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; GENETIC CODE; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; RNA SEQUENCE; RNA STRUCTURE; RNA TRANSLATION; STRUCTURE ACTIVITY RELATION; TOBACCO NECROSIS VIRUS D; TOMBUSVIRUS; VIRUS GENOME;

CAP-INDEPENDENT TRANSLATION; CARMOVIRUS; FRAMESHIFTING; NECROVIRUS; PLANT VIRUS; READTHROUGH; RECODING; RNA STRUCTURE; RNA VIRUS; TOMBUSVIRIDAE;

BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PLANT DISEASES; PROTEIN BIOSYNTHESIS; RNA, VIRAL; TOBACCO; TOMBUSVIRIDAE; VIRAL PROTEINS;

EID: 84891892908     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2013.12.006     Document Type: Article

References (27)

1. Barry J.K., Miller W.A. A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA. Proc. Nat. Acad. Sci. U.S.A 2002, 99:11133-11138.
2. Beier H., Grimm M. Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Nucleic Acids Res. 2001, 29:4767-4782.
3. Brown C.M., Dinesh-Kumar S.P., Miller W.A. Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon. J. Virol. 1996, 70:5884-5892.
4. Cimino P.A., Nicholson B.L., Wu B., Xu W., White K.A. Multifaceted regulation of translational readthrough by RNA replication elements in a tombusvirus. PLoS Pathog. 2011, 7(12):e1002423.
5. Coutts R.H.A., Ridgen J.E., Slabas A.R., Lomonossoff G.P., Wise P.J. The complete nucleotide sequence of tobacco necrosis virus strain D. J. Gen. Virol. 1991, 72:1521-1529.
6. Fang L., Coutts R.H. Investigations on the tobacco necrosis virus D p60 replicase protein. PLoS One 2013, 8(11):e80912.
7. Feng Y.X., Levin J.G., Hatfield D.L., Schaefer T.S., Gorelick R.J., Rein A. Suppression of UAA and UGA termination codons in mutant murine leukemia viruses. J. Virol. 1989, 63:2870-2873.
8. Fernández-Miragall O., Hernández C. An internal ribosome entry site directs translation of the 3'-gene from Pelargonium flower break virus genomic RNA: implications for infectivity. PLoS One 2011, 6(7):e22617.
9. Firth A.E., Brierley I. Non-canonical translation in RNA viruses. J. Gen. Virol. 2012, 93:1385-1409.
10. Firth A., Wills N.M., Gesteland R.F., Atkins J.F. Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element. Nucleic Acids Res. 2011, 39:6679-6691.
11. Jiwan S.D., Wu B., White K.A. Subgenomic mRNA transcription in tobacco necrosis virus. Virology 2011, 418:1-11.
12. Koh D.C., Wong S.M., Liu D.X. Synergism of the 3'-untranslated region and an internal ribosome entry site differentially enhances the translation of a plant virus coat protein. J. Biol. Chem 2003, 278:20565-20573.
13. Lin Z., Gilbert R.J., Brierley I. Spacer-length dependence of programmed -1 or -2 ribosomal frameshifting on a U6A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting. Nucleic Acids Res. 2012, 40:8674-8689.
14. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 1999, 288:911-940.
15. Molnár A., Havelda Z., Dalmay T., Szutorisz H., Burgyán J. Complete nucleotide sequence of tobacco necrosis virus strain DH and genes required for RNA replication and virus movement. J. Gen. Virol. 1997, 78:1235-1239.
16. Offei S.K., Coffin R.S., Coutts R.H.A. The tobacco necrosis virus p7a protein is a nucleic acid-binding protein. J. Gen. Virol. 1995, 76:1493-1496.
17. Offei S.K., Coutts R.H.A. Location of the 5' termini of Tobacco necrosis virus strain D subgenomic mRNAs. J. Phytopathol. 1996, 144:13-17.
18. Paul C.P., Barry J.K., Dinesh-Kumar S.P., Brault V., Miller W.A. A sequence required for -1 ribosomal frameshifting located four kilobases downstream of the frameshift site. J. Mol. Biol. 2001, 310:987-999.
19. Rubino L., Burgyan J., Russo M. Molecular cloning and complete nucleotide sequence of carnation Italian ringspot tombusvirus genomic and defective interfering RNAs. Arch. Virol. 1995, 140:2027-2039.
20. Shen R., Miller W.A. The 3' untranslated region of Tobacco necrosis virus RNA contains a Barley yellow dwarf virus-like cap-independent translation element. J. Virol. 2004, 78:4655-4664.
21. Shen R., Miller W.A. Structures required for poly(A) tail-independent translation overlap with, but are distinct from, cap-independent translation and RNA replication signals at the 3' end of Tobacco necrosis virus RNA. Virology 2007, 358:448-458.
22. Sit T.L., Lommel S.A. Tombusviridae. Encyclopedia of Life Sciences (ELS) 2010, John Wiley & Sons, Ltd, Chichester. 10.1002/9780470015902.a0000756.pub2.
23. Skuzeski J.M., Nichols L.M., Gesteland R.F., Atkins J.F. The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J. Mol. Biol. 1991, 218:365-373.
24. Tajima Y., Iwakawa H.O., Kaido M., Mise K., Okuno T. A long-distance RNA-RNA interaction plays an important role in programmed -1 ribosomal frameshifting in the translation of p88 replicase protein of Red clover necrotic mosaic virus. Virology 2011, 417:169-178.
25. White K.A., Morris T.J. Nonhomologous RNA recombination in tombusviruses: generation and evolution of defective interfering RNAs by stepwise deletions. J. Virol. 1994, 68:14-24.
26. Wu B., White K.A. A primary determinant of cap-independent translation is located in the 3'-proxminal region of the tomato bushy stunt virus genome. J. Virol. 1999, 73:8982-8988.
27. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.