Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon

Journal of Virology

Volumn 70, Issue 9, 1996, Pages 5884-5892

  Brown, Chris M ^a   Dinesh Kumar, S P ^a,b   Allen Miller, W ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b PLANT GENE EXPRESSION CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COAT PROTEIN;

ARTICLE; LUTEOVIRUS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTOPLAST; REPORTER GENE; SEQUENCE ANALYSIS; STOP CODON; VIRION;

EID: 0029793207     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.70.9.5884-5892.1996     Document Type: Article

References (69)

1. Ambion Inc. 1995. In vitro translation kits. Ambion, Austin. Tex.
2. Bahner, I., J. Lamb, M. A. Mayo, and R. T. Hay. 1990. Expression of the genome of potato leafroll virus: readthrough of the coat protein termination codon in vivo. J. Gen. Virol. 71:2251-2256.
3. Berry, M. J., L. Banu, J. W. Harney, and P. R. Larsen. 1993. Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. EMBO J. 12:3315-3322.
4. Berry, M. J., J. W. Harney, T. Ohama, and D. L. Hatfield. 1994. Selenocysteine insertion or termination: factors affecting UGA codon fate and complementary anticodon:codon mutations. Nucleic Acids Res. 22:3753-3759.
5. Bonetti, B., L. W. Fu, J. Moon, and D. M. Bedwell. 1995. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol. 251:334-345.
6. Boonham, N., C. M. Henry, and K. R. Wood. 1995. The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soilborne virus of cereals. J. Gen. Virol. 76:2025-2034.
7. Brault, V., and W. A. Miller. 1992. Translational frameshifting mediated by a viral sequence in plant cells. Proc. Natl. Acad. Sci. USA 89:2262-2266.
8. Brault, V., J. F. J. M. Van den Heuvel, M. Verbeek, G. V. Ziegler, A. Reutenauer, E. Herrbach, J. C. Garaud, H. Guilley, K. Richards, and G. Jonard. 1995. Aphid transmission of beet western yellows luteovirus requires the minor capsid read-through protein P74. EMBO J. 14:650-659.
9. Brown, C. M. 1995. Unpublished data.
10. Chay, C., U. B. Umasinge, S. P. Dinesh-Kumar, W. A. Miller, and S. L. Gray. 1996. Aphid transmission and systemic spread of barley yellow dwarf virus-PAV are mediated by the coat protein read-through domain and 17K protein, respectively. Virology 219:57-65.
11. Cheng, S. L., L. L. Domier, and C. J. D'Arcy. 1994. Detection of the read-through protein of barley yellow dwarf virus. Virology 202:1003-1006.
12. de Miranda, J., M. Stevens, E. de Bruyne, H. Smith, C. Bird, and R. Hull. 1995. Sequence comparison and classification of beet western yellows isolates. Ann. Appl. Biol. 127:113-124.
13. Demler, S. A., and G. A. de Zoeten. 1991. The nucleotide sequence and luteovirus-like nature of RNA 1 of an aphid non-transmissible strain of pea enation mosaic virus. J. Gen. Virol. 72:1819-1834.
14. Di, R., S. P. Dinesh-Kumar, and W. A. Miller. 1993. Translational frame-shifting by barley yellow dwarf virus RNA (PAV serotype) in Escherichia coli and in eukaryotic cell-free extracts. Mol. Plant-Microbe Interact. 6:444-452.
15. Dinesh-Kumar, S. P. 1993. Gene expression strategies of barley yellow dwarf virus. Ph.D. thesis. Iowa State University, Ames.
16. Dinesh-Kumar, S. P., V. Brault, and W. A. Miller. 1992. Precise mapping and in vitro translation of a trifunctional subgenomic RNA of barley yellow dwarf virus. Virology 187:711-722.
17. Dinesh-Kumar, S. P., and W. A. Miller. 1993. Control of start codon choice on a plant viral RNA encoding overlapping genes. Plant Cell 5:679-692.
18. Domier, L. L. 1995. Genome structure and function of barley yellow dwarf viruses, p. 181-202. in C. J. D'Arcy and P. A. Burnett (ed.), Barley yellow dwarf - 40 years of progress. APS Press, St. Paul, Minn.
19. Feng, Y. X., H. Yuan, A. Rein, and J. G. Levin. 1992. Bipartite signal for readthrough suppression in murine leukemia virus mRNA - an 8-nucleotide purine-rich sequence immediately downstream of the GAG termination codon followed by an RNA pseudoknot. J. Virol. 66:5127-5132.
20. Filichkin, S. A., R. M. Lister, P. F. Mcgrath, and M. J. Young. 1994. In vivo expression and mutational analysis of the barley yellow dwarf virus read-through gene. Virology 205:290-299.
21. Guilley, H., S. C. Wipf, K. Richards, H. Lecoq, and G. Jonard. 1994. Nucleotide sequence of cucurbit aphid-borne yellows luteovirus. Virology 202: 1012-1017.
22. Hampton, R., E. Ball, and S. De Boer. 1990. Serological methods for the detection and identification of viral and bacterial plant pathogens. APS Press, St. Paul, Minn.
23. Hatfield, D., and A. Diamond. 1993. UGA - a split personality in the universal genetic code. Trends Genet. 9:69-70.
24. Hatfield, D. L., J. G. Levin, A. Rein, and S. Oroszalan. 1992. Translational suppression in retroviral gene expression. Adv. Virus Res. 41:193-239.
25. Hatfield, D. L., D. W. E. Smith. B. J. Lee, P. J. Worland, and S. Oroszlan. 1990. Structure and function of suppressor transfer-RNAs in higher eukaryotes. Crit. Rev. Biochem. Mol. Biol. 25:71-96.
26. Jefferson, R. A. 1987. Assaying chimeric genes in plants: the GUS gene fusion system. Plant Mol. Biol. 5:387-405.
27. Jolly, C. A., and M. A. Mayo. 1994. Changes in the amino acid sequence of the coal protein readthrough domain of potato leafroll luteovirus affect the formation of an epitope and aphid transmission. Virology 201:182-185.
28. Kelly, L., W. L. Gerlach, and P. M. Waterhouse. 1994. Characterisation of the subgenomic RNAs of an australian isolate of barley yellow dwarf luteovirus. Virology 202:565-573.
29. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London) 227:680-685.
30. Landt, O., H. P. Grunert, and U. Hahn. 1990. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene 96:125-128.
31. Lei, C-H., R. M. Lister, J. K. Vincent, and M. N. Karanjkar. 1995. SGV serotype isolates of barley yellow dwarf virus differing in vectors and molecular relationships. Phytopathology 85:820-826.
32. Li, G. P., and C. M. Rice. 1989. Mutagenesis of the in-frame opal termination codon preceding nsP4 of Sindhis virus: studies of translational readthrough and its effect on virus replication. J. Virol. 63:1326-1337.
33. Li, G. P., and C. M. Rice. 1993. The signal for translational readthrough of a UGA codon in Sindbis virus RNA involves a single cytidine residue immediately downstream of the termination codon. J. Virol. 67:5062-5067.
34. Martin, R. R., and C. J. D'Arcy. 1995. Taxonomy of barley yellow dwarf viruses, p. 203-214. In C. J. D'Arcy and P. A. Burnett (ed.), Barley yellow dwarf - 40 years of progress APS Press, St. Paul, Minn.
35. Mayo, M. A., D. J. Robinson, C. A. Jolly, and L. Hyman. 1989. Nucleotide sequence of potato leafroll luteovirus RNA. J. Gen. Virol. 70:1037-1051.
36. Mayo, M. A., and V. Ziegler-Graf. 1996. Molecular biology of luteoviruses. Adv. Virus Res. 46:413-460.
37. McCaughan, K. K., C. M. Brown, M. E. Dalphin, M. J. Berry, and W. P. Tate. 1995. Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc. Natl. Acad. Sci. USA 92:5431-5435.
38. Miller, W. A., S. P. Dinesh-Kumar, and C. P. Paul. 1995. Luteovirus gene expression. Crit. Rev. Plant Sci. 14:179-211.
39. Miller, W. A., P. M. Waterhouse, and W. L. Gerlach. 1988. Sequence and organisation of barley yellow dwarf virus genomic RNA. Nucleic Acids Res. 16:6097-6111.
40. Mohan, B. R., S. P. Dinesh-Kumar, and W. A. Miller. 1995. Genes and cis-acting sequences involved in replication of barley yellow dwarf virus-PAV RNA. Virology 212:186-195.
41. Pelham, H. R. B. 1978. Leaky UAG termination codon in TMV RNA. Nature (London) 272:469-471.
42. Poole, E. S., C. M. Brown, and W. P. Tate. 1995. The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J. 14:151-158.
43. Promega Corp. 1992. Large scale RNA synthesis. Promega Notes 39:12-18.
44. Promega Corp. 1992. Wheat germ extract. Promega, Madison, Wis.
45. Rathjen, J. P., L. E. Karageorgos, N. Habili, P. M. Waterhouse, and R. H. Symons. 1994. Soybean dwarf luteovirus contains the third variant genome type in the luteovirus group. Virology 198:571-579.
46. Rizzo, T. M., and S. M. Gray. 1992. Localization of a surface domain of the capsid protein of barley yellow dwarf virus. Virology 186:300-302.
47. 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.
48. Shen, Q., J. L. Leonard, and P. E. Newburger. 1995. Structure and function of the selenium translation clement in the 3′-untranslated region of human cellular glutathione peroxidase mRNA. RNA 1:519-525.
49. Skuzeski, J. M., L. M. Nichols, and R. F. Gesteland. 1990. Analysis of leaky viral translation termination codons in vivo by transient expression of improved beta-glucuronidase vectors. Plant Mol. Biol. 15:65-79.
50. Skuzeski, J. M., L. M. Nichols, R. F. Gesteland, and J. F. Atkins. 1991. The signal for a leaky UAG stop codon in several plant viruses includes the 2 downstream codons. J. Mol. Biol. 218:365-373.
51. Stahl, G., L. Bidou, J. Rousset, and M. Cassan. 1995. Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. Nucleic Acids Res. 23:1557-1560.
52. Stansfield, I., K. M. Jones, V. V. Kushnirov, A. R. Dagkesamanskaya, A. I. Poznyakovski, S. V. Pauskin, C. R. Nierras, B. S. Cox, M. D. Ter-Avanesyan, and M. F. Tuile. 1995. The products of the SUP45 (cRF1) and SUP35 genes interact to mediate termination in Saccharomyces cerevisiae. EMBO J. 14: 4365-4373.
53. Stansfield, I., and M. F. Tuite. 1995. The end in sight: terminating translation in eukaryotes. Trends Biochem. Sci. 20:489-491.
54. Strauss, J. H., and E. G. Strauss. 1994. The alphaviruses: gene expression, replication, and evolution. Microbiol. Rev. 58:491-562.
55. Tacke, E., D. Prufer, F. Salamini, and W. Rohde. 1990. Characterization of a potato leafroll luteovirus subgenomic RNA: differential expression by internal translation initiation and UAG suppression. J. Gen. Virol. 7:2265-2272.
56. Tate, W. P., and C. M. Brown. 1992. Translational termination: "stop" for protein synthesis or "pause" for regulation of gene expression. Biochemistry 31:2443-2450.
57. Urban, C., and H. Beier. 1995. Cysteinc tRNAs of plant origin as novel UGA suppressors. Nucleic Acids Res. 23:4591-4597.
58. Valle, R. P. C., G. Drugeon, M. D. Devignesmorch, A. B. Legocki, and A. L. Haenni. 1992. Codon context effect in virus translational readthrough - a study in vitro of the determinants of TMV and Mo-MuLV amber suppression. FEBS Lett. 306:133-139.
59. Veidt, I., H. Lot, M. Leiser, D. Scheidecker, H. Guilley, K. Richards, and G. Jonard. 1988. Nucleotide sequence of beet western yellows virus RNA. Nucleic Acids Res. 16:9917-9932.
60. Vincent, J. R., R. M. Lister, and B. A. Larkins. 1991. Nucleotide sequence analysis and genomic organization of the NY-RPV isolate of barley yellow dwarf virus. J. Gen. Virol. 72:2347-2355.
61. Vincent, J. R., P. P. Ueng, R. M. Lister, and B. A. Larkins. 1990. Nucleotide sequences of coat protein genes for three isolates of barley yellow dwarf virus and their relationships to other luteovirus coat protein sequences. J. Gen. Virol. 71:2791-2799.
62. Wadsworth, G. J., M. G. Redinbaugh, and J. G. Scandalios. 1988. A procedure for the small-scale isolation of plant RNA suitable for RNA blot analysis. Anal. Biochem. 172:279-283.
63. Wang, J. Y., C. Chay, F. E. Gildow, and S. M. Gray. 1995. Readthrough protein associated with virions of barley yellow dwarf luteovirus and its potential role in regulating the efficiency of aphid transmission. Virology 206:954-962.
64. Wang, S., and W. A. Miller. 1995. A sequence located 4.5 to 5 kilobases from the 5′ end of the barley yellow dwarf virus (PAV) genome strongly stimulates translation of uncapped mRNA. J. Biol. Chem. 270:13446-13452.
65. Wills, N. M., R. F. Gesteland, and J. F. Atkins. 1994. Pseudoknot-dependent read-through of retroviral GAG termination codons: importance of sequences in the spacer and loop 2. EMBO J. 13:4137-4144.
66. Young, M. J., L. Kelly, P. J. Larkin, P. M. Waterhouse, and W. L. Gerlach. 1991. Infectious in vitro transcripts from a cloned cDNA of barley yellow dwarf virus. Virology 180:372-379.
67. Zaccomer, B., A. L. Haenni, and G. Macaya. 1995. The remarkable variety of plant RNA virus genomes. J. Gen. Virol. 76:231-247.
68. Zerfass, K., and H. Beier. 1992. Pseudouridine in the anticodon GPsiA of plant cytoplasmic transfer RNA (Tyr) is required for UAG and UAA suppression in the TMV-specific context. Nucleic Acids Res. 20:5911-5918.
69. Zhouravleva, G., L. Frovlova, X. Le Gaff, R. Le Guellec, S. Inge-Vechtomov, L. Kisselev, and M, Philippe. 1995. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and cRF3. EMBO J. 14:4065-4072.