Versatile dual reporter gene systems for investigating stop codon readthrough in plants

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Lao, Nga T ^a   Maloney, Alan P ^a   Atkins, John F ^b,c   Kavanagh, Tony A ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTATHIONE TRANSFERASE; N ACETYLNEURAMINIC ACID; TRYPTOPHAN; TYROSINE; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; PLANT DNA; VIRUS DNA;

AMINO ACID ANALYSIS; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENE CASSETTE; GENE EXPRESSION; HISTOCHEMISTRY; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; REPORTER GENE; STOP CODON; GENETIC PROCEDURES; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; RIBOSOME; SEQUENCE HOMOLOGY; TOBACCO MOSAIC VIRUS; VIROLOGY; VIRUS GENE;

TOBACCO MOSAIC VIRUS;

ARABIDOPSIS; BASE SEQUENCE; CODON, TERMINATOR; DNA, PLANT; DNA, VIRAL; GENES, PLANT; GENES, REPORTER; GENES, VIRAL; GENETIC TECHNIQUES; GLUTATHIONE TRANSFERASE; GREEN FLUORESCENT PROTEINS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; RIBOSOMES; RNA, MESSENGER; SEQUENCE HOMOLOGY, NUCLEIC ACID; TOBACCO MOSAIC VIRUS;

EID: 70350540673     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007354     Document Type: Article

References (45)

1. Zhouravleva G, Frolova L, Le Goff X, Le Guellec R, Inge-Vechtomov S, et al. (1995) Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO J 14: 4065-4072.
2. Stansfield I, Tuite MF (1994) Polypeptide chain termination in Saccharomyces cerevisiae. Curr Genet 25: 385-395.
3. Tate WP, Poole ES, Dalphin ME, Major LL, Crawford DJ, et al. (1996) The translational stop signal: codon with a context, or extended factor recognition element? Biochimie 78: 945-952.
4. Namy O, Rousset JP (2009) Specification of standard amino acids by stop codons. In: Atkins JF, Gesteland RF, eds. Recoding: Expansion of decoding rules enriches gene expression. New York: Springer Publishers.
5. Wills NM, Gesteland RF, Atkins JF (1991) Evidence that a downstream pseudoknot is required for translational readthrough of the Moloney muribe leukemia virus gag stop codon. Proc Natl Acad Sci USA 88: 6991-6995.
6. Feng YX, Yuan H, Rein A, Levin JG (1992) Bipartite signal for read-through suppression in murine leukemia virus mRNA: an eight-nucleotide purine-rich sequence immediately downstream of the gag termination codon followed by an RNA pseudoknot. J Virol 66: 5127-5132.
7. Brown CM, Dinesh-Kumar SP, Miller WA (1996) Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon. J Virol 70: 5884-5892.
8. Salas-Marco J, Bedwell DM (2004) GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Mol Cell Biol 24: 7769-7778.
9. Fabret C, Cosnier B, Lekomtsev S, Gillet S, Hatin I, et al. (2008) A novel mutant of the Sup35 protein of Saccharomyces cerevisiae defective in translation termination and in GTPase activity still supports cell viability. BMC Mol Biol 9: 22.
10. Hirosawa-Takamori M, Ossipov D, Novoselov SV, Turanov AA, Zhang Y, et al. (2009) A novel stem loop control-element dependent UGA read-through system without selenocysteine incorporation in Drosophila. FASEB J 23: 107-113.
11. Bedwell DM, Kaenjak A, Benos DJ, Bebok Z, Bubien JK, et al. (1997) Suppression of a CFTR premature stop codon in a bronchial epithelial cell line. Nat Med 3: 1280-1284.
12. von der Haar T, Tuite MF (2006) Regulated translational bypass of stop codons in yeast. Trends in Microbiol 15: 78-86.
13. Steneberg P, Englund C, Kronhamn J, Weaver TA, Samakovlis C (1998) Translational readthrough in the hdc mRNA generates a novel branching inhibitor in the Drosophila trachea. Genes Dev 12: 956-967.
14. Steneberg P, Samakovlis C (2001) A novel stop codon readthrough mechanism produces functional Headcase protein in Drosophila trachea. EMBO Rep 2: 593-597.
15. Robinson DN, Cooley L (1997) Examination of the function of two kelch proteins generated by stop codon suppression. Development 124: 1405-1417.
16. Bergstrom DE, Merli CA, Cygan JA, Shelby R, Blackman RK (1995) Regulatory autonomy and molecular characterization of the Drosophila out at first gene. Genetics 139: 1331-1346.
17. Lin MF, Carlson JW, Crosby MA, Mathews BB, Yu C, et al. (2007) Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res 17: 1823-1836.
18. Liu Q, Xue Q (2004) Computational identification and sequence analysis of stop codon readthrough genes in Oryza sativa. Biosystems 77: 33-39.
19. Ohtsubo H, Kumekawa N, Ohtsubo E (1999) RIRE2, a novel gypsy-type retrotransposon from rice. Genes Genet Syst 74: 83-91.
20. Dreher TW, Miller WA (2006) Translational control in positive strand RNA plant viruses. Virology 344: 185-197.
21. Brault V, van den Heuvel JF, Verbeek M, Ziegler-Graff V, Reutenauer A, et al. (1995) Aphid transmission of beet western yellows luteovirus requires the minor capsid read-through protein P74. EMBO J 14: 650-659.
22. Pelham HR (1978) Leaky UAG termination codon in tobacco mosaic virus RNA. Nature 272: 469-471.
23. Ishikawa M, Meshi T, Motoyoshi F, Takamatsu N, Okada Y (1986) In vitro mutagenesis of the putative replicase genes of tobacco mosaic virus. Nucleic Acids Res 14: 8291-8305.
24. Ishikawa M, Meshi T, Ohno T, Okada Y (1991) Specific cessation of minus-strand RNA accumulation at an early stage of tobacco mosaic virus infection. J Virol 65: 861-868.
25. Lewandowski DJ, Dawson WO (2000) Functions of the 126- and 183-kDa proteins of tobacco mosaic virus. Virology 271: 90-98.
26. Skuzeski JM, Nichols LM, Gesteland RF (1990) Analysis of leaky viral translation termination codons in vivo by transient expression of improved β-glucuronidase vectors. Plant Mol Biol 15: 65-79.
27. Stahl G, Bidou L, Rousset JP, Cassan M (1995) Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. Nucleic Acids Res 23: 1557-1560.
28. Skuzeski JM, Nichols LM, Gesteland RF, Atkins JF (1991) The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J Mol Biol 218: 365-373.
29. Tyr is required for UAG and UAA suppression in the TMV-specific context. Nucleic Acids Res 20: 5911-5918.
30. Beier H, Barciszewska M, Krupp G, Mitnacht R, Gross HJ (1984) UAG readthrough during TMV RNA translation: isolation and sequence of two tRNAs with suppressor activity from tobacco plants. EMBO J 3: 351-356.
31. Gln isoacceptors and their genes. Plant Mol Biol 38: 689-697.
32. Beier H, Grimm M (2001) Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Nucleic Acids Res 29: 4767-4782.
33. Grentzmann G, Ingram JA, Kelly PJ, Gesteland RF, Atkins JF (1998) A dual-luciferase reporter system for studying recoding signals. RNA 4: 479-486.
34. Cardno TS, Poole ES, Mathew SF, Graves R, Tate WP (2009) A homogeneous cell-based bicistronic fluorescence assay for high-throughput identification of drugs that perturb viral gene recoding and read-through of nonsense stop codons. RNA 15: 1614-1621.
35. Kirby J, Kavanagh TA (2002) NAN fusions: a synthetic sialidase reporter gene as a sensitive and versatile partner for GUS. Plant J 32: 391-400.
36. Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: β-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6: 3901-3907.
37. Smith DB, Johnson KS (1988) Single-step purification of polypeptides as fusions with glutathione-S-transferase. Gene 67: 31-40.
38. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC (1994) Green fluorescent protein as a marker for gene expression. Science 263: 802-805.
39. Marillonnet S, Giritch A, Gils M, Kandzia R, Klimyuk V, et al. (2004) In planta engineering of viral RNA replicons: efficient assembly by recombination of DNA modules delivered by Agrobacterium. Proc Natl Acad Sci USA 101: 6852-6857.
40. Cazzonelli CI, McCallum EJ, Lee R, Botella JR (2005) Characterization of a strong, constitutive mung bean (Vigna radiata L.) promoter with a complex mode of regulation in planta. Transgenic Res 14: 941-967.
41. Schmidt TG, Skerra A (2007) The Strep-tag system for one-step purification and high-affinity detection or capturing of proteins. Nat Protoc 2: 1528-1535.
42. Herr AJ, Wills NM, Nelson CC, Gesteland RF, Atkins JF (2004) Factors that influence selection of coding resumption sites in translational bypassing: minimal conventional peptidyl-tRNA:mRNA pairing can suffice. J Biol Chem 279: 11081-11087.
43. Valle RP, Morch MD, Haenni AL (1987) Novel amber suppressor tRNAs of mammalian origin. EMBO J 6: 3049-3055.
44. Urban C, Zerfass K, Fingerhut C, Beier H (1996) UGA suppression by tRNACmCATrp occurs in diverse virus RNAs due to a limited influence of the codon context. Nucleic Acids Res 24: 3424-3430.
45. Clough SG, Bent AF (1998) "Floral dip": a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743.