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J Virol. 1996 September; 70(9): 5884–5892.
PMCID: PMC190606

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


Many viruses use stop codon readthrough as a strategy to produce extended coat or replicase proteins. The stop codon of the barley yellow dwarf virus (PAV serotype) coat protein gene is read through at a low rate. This produces an extended polypeptide which becomes part of the virion. We have analyzed the cis-acting sequences in the barley yellow dwarf virus PAV genome required for this programmed readthrough in vitro in wheat germ extracts and reticulocyte lysates and in vivo in oat protoplasts. Two regions 3' to the stop codon were required. Deletion of sections containing the first 5 of the 16 CCN NNN repeats located 3' of the stop codon greatly reduced readthrough in vitro and in vivo. Surprisingly, readthrough also required a second, more distal element that is located 697 to 758 bases 3' of the stop codon within the readthrough open reading frame. This element also functioned in vivo in oat protoplasts when placed more than 2 kb from the coat protein gene stop in the untranslated region following a GUS reporter gene. This is the first report of a long-range readthrough signal in viruses.

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Selected References

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  • Berry MJ, Banu L, Harney JW, Larsen PR. Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. EMBO J. 1993 Aug;12(8):3315–3322. [PubMed]
  • Berry MJ, Harney JW, Ohama T, Hatfield DL. Selenocysteine insertion or termination: factors affecting UGA codon fate and complementary anticodon:codon mutations. Nucleic Acids Res. 1994 Sep 11;22(18):3753–3759. [PMC free article] [PubMed]
  • Bonetti B, Fu L, Moon J, Bedwell DM. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol. 1995 Aug 18;251(3):334–345. [PubMed]
  • Boonham N, Henry CM, Wood KR. The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals. J Gen Virol. 1995 Aug;76(Pt 8):2025–2034. [PubMed]
  • Brault V, Miller WA. Translational frameshifting mediated by a viral sequence in plant cells. Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2262–2266. [PubMed]
  • Brault V, van den Heuvel JF, Verbeek M, Ziegler-Graff V, Reutenauer A, Herrbach E, Garaud JC, Guilley H, Richards K, Jonard G. Aphid transmission of beet western yellows luteovirus requires the minor capsid read-through protein P74. EMBO J. 1995 Feb 15;14(4):650–659. [PubMed]
  • Chay CA, Gunasinge UB, Dinesh-Kumar SP, Miller WA, Gray SM. Aphid transmission and systemic plant infection determinants of barley yellow dwarf luteovirus-PAV are contained in the coat protein readthrough domain and 17-kDa protein, respectively. Virology. 1996 May 1;219(1):57–65. [PubMed]
  • Cheng SL, Domier LL, D'Arcy CJ. Detection of the readthrough protein of barley yellow dwarf virus. Virology. 1994 Aug 1;202(2):1003–1006. [PubMed]
  • Demler SA, de Zoeten GA. The nucleotide sequence and luteovirus-like nature of RNA 1 of an aphid non-transmissible strain of pea enation mosaic virus. J Gen Virol. 1991 Aug;72(Pt 8):1819–1834. [PubMed]
  • Di R, Dinesh-Kumar SP, Miller WA. Translational frameshifting by barley yellow dwarf virus RNA (PAV serotype) in Escherichia coli and in eukaryotic cell-free extracts. Mol Plant Microbe Interact. 1993 Jul-Aug;6(4):444–452. [PubMed]
  • Dinesh-Kumar SP, Brault V, Miller WA. Precise mapping and in vitro translation of a trifunctional subgenomic RNA of barley yellow dwarf virus. Virology. 1992 Apr;187(2):711–722. [PubMed]
  • Dinesh-Kumar SP, Miller WA. Control of start codon choice on a plant viral RNA encoding overlapping genes. Plant Cell. 1993 Jun;5(6):679–692. [PubMed]
  • Feng YX, Yuan H, Rein A, Levin JG. 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. 1992 Aug;66(8):5127–5132. [PMC free article] [PubMed]
  • Filichkin SA, Lister RM, McGrath PF, Young MJ. In vivo expression and mutational analysis of the barley yellow dwarf virus readthrough gene. Virology. 1994 Nov 15;205(1):290–299. [PubMed]
  • Guilley H, Wipf-Scheibel C, Richards K, Lecoq H, Jonard G. Nucleotide sequence of cucurbit aphid-borne yellows luteovirus. Virology. 1994 Aug 1;202(2):1012–1017. [PubMed]
  • Hatfield D, Diamond A. UGA: a split personality in the universal genetic code. Trends Genet. 1993 Mar;9(3):69–70. [PubMed]
  • Hatfield DL, Levin JG, Rein A, Oroszlan S. Translational suppression in retroviral gene expression. Adv Virus Res. 1992;41:193–239. [PubMed]
  • Hatfield DL, Smith DW, Lee BJ, Worland PJ, Oroszlan S. Structure and function of suppressor tRNAs in higher eukaryotes. Crit Rev Biochem Mol Biol. 1990;25(2):71–96. [PubMed]
  • Jolly CA, Mayo MA. Changes in the amino acid sequence of the coat protein readthrough domain of potato leafroll luteovirus affect the formation of an epitope and aphid transmission. Virology. 1994 May 15;201(1):182–185. [PubMed]
  • Kelly L, Gerlach WL, Waterhouse PM. Characterisation of the subgenomic RNAs of an Australian isolate of barley yellow dwarf luteovirus. Virology. 1994 Aug 1;202(2):565–573. [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Landt O, Grunert HP, Hahn U. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene. 1990 Nov 30;96(1):125–128. [PubMed]
  • Li GP, Rice CM. Mutagenesis of the in-frame opal termination codon preceding nsP4 of Sindbis virus: studies of translational readthrough and its effect on virus replication. J Virol. 1989 Mar;63(3):1326–1337. [PMC free article] [PubMed]
  • Li G, Rice CM. 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. 1993 Aug;67(8):5062–5067. [PMC free article] [PubMed]
  • Mayo MA, Robinson DJ, Jolly CA, Hyman L. Nucleotide sequence of potato leafroll luteovirus RNA. J Gen Virol. 1989 May;70(Pt 5):1037–1051. [PubMed]
  • Mayo MA, Ziegler-Graff V. Molecular biology of luteoviruses. Adv Virus Res. 1996;46:413–460. [PubMed]
  • McCaughan KK, Brown CM, Dalphin ME, Berry MJ, Tate WP. Translational termination efficiency in mammals is influenced by the base following the stop codon. Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5431–5435. [PubMed]
  • Miller WA, Waterhouse PM, Gerlach WL. Sequence and organization of barley yellow dwarf virus genomic RNA. Nucleic Acids Res. 1988 Jul 11;16(13):6097–6111. [PMC free article] [PubMed]
  • Mohan BR, Dinesh-Kumar SP, Miller WA. Genes and cis-acting sequences involved in replication of barley yellow dwarf virus-PAV RNA. Virology. 1995 Sep 10;212(1):186–195. [PubMed]
  • Pelham HR. Leaky UAG termination codon in tobacco mosaic virus RNA. Nature. 1978 Mar 30;272(5652):469–471. [PubMed]
  • Poole ES, Brown CM, Tate WP. The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli. EMBO J. 1995 Jan 3;14(1):151–158. [PubMed]
  • Rizzo TM, Gray SM. Localization of a surface domain of the capsid protein of barley yellow dwarf virus. Virology. 1992 Jan;186(1):300–302. [PubMed]
  • Shen Q, Leonard JL, Newburger PE. Structure and function of the selenium translation element in the 3'-untranslated region of human cellular glutathione peroxidase mRNA. RNA. 1995 Jul;1(5):519–525. [PubMed]
  • Skuzeski JM, Nichols LM, Gesteland RF. Analysis of leaky viral translation termination codons in vivo by transient expression of improved beta-glucuronidase vectors. Plant Mol Biol. 1990 Jul;15(1):65–79. [PubMed]
  • Skuzeski JM, Nichols LM, Gesteland RF, Atkins JF. The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J Mol Biol. 1991 Mar 20;218(2):365–373. [PubMed]
  • Stahl G, Bidou L, Rousset JP, Cassan M. Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. Nucleic Acids Res. 1995 May 11;23(9):1557–1560. [PMC free article] [PubMed]
  • Stansfield I, Jones KM, Kushnirov VV, Dagkesamanskaya AR, Poznyakovski AI, Paushkin SV, Nierras CR, Cox BS, Ter-Avanesyan MD, Tuite MF. The products of the SUP45 (eRF1) and SUP35 genes interact to mediate translation termination in Saccharomyces cerevisiae. EMBO J. 1995 Sep 1;14(17):4365–4373. [PubMed]
  • Stansfield I, Jones KM, Tuite MF. The end in sight: terminating translation in eukaryotes. Trends Biochem Sci. 1995 Dec;20(12):489–491. [PubMed]
  • Strauss JH, Strauss EG. The alphaviruses: gene expression, replication, and evolution. Microbiol Rev. 1994 Sep;58(3):491–562. [PMC free article] [PubMed]
  • Tacke E, Prüfer D, Salamini F, Rohde W. Characterization of a potato leafroll luteovirus subgenomic RNA: differential expression by internal translation initiation and UAG suppression. J Gen Virol. 1990 Oct;71(Pt 10):2265–2272. [PubMed]
  • Tate WP, Brown CM. Translational termination: "stop" for protein synthesis or "pause" for regulation of gene expression. Biochemistry. 1992 Mar 10;31(9):2443–2450. [PubMed]
  • Urban C, Beier H. Cysteine tRNAs of plant origin as novel UGA suppressors. Nucleic Acids Res. 1995 Nov 25;23(22):4591–4597. [PMC free article] [PubMed]
  • Valle RP, Drugeon G, Devignes-Morch MD, Legocki AB, Haenni AL. Codon context effect in virus translational readthrough. A study in vitro of the determinants of TMV and Mo-MuLV amber suppression. FEBS Lett. 1992 Jul 20;306(2-3):133–139. [PubMed]
  • Veidt I, Lot H, Leiser M, Scheidecker D, Guilley H, Richards K, Jonard G. Nucleotide sequence of beet western yellows virus RNA. Nucleic Acids Res. 1988 Nov 11;16(21):9917–9932. [PMC free article] [PubMed]
  • Vincent JR, Lister RM, Larkins BA. Nucleotide sequence analysis and genomic organization of the NY-RPV isolate of barley yellow dwarf virus. J Gen Virol. 1991 Oct;72(Pt 10):2347–2355. [PubMed]
  • Vincent JR, Ueng PP, Lister RM, Larkins BA. 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. 1990 Dec;71(Pt 12):2791–2799. [PubMed]
  • Wadsworth GJ, Redinbaugh MG, Scandalios JG. A procedure for the small-scale isolation of plant RNA suitable for RNA blot analysis. Anal Biochem. 1988 Jul;172(1):279–283. [PubMed]
  • Wang JY, Chay C, Gildow FE, Gray SM. Readthrough protein associated with virions of barley yellow dwarf luteovirus and its potential role in regulating the efficiency of aphid transmission. Virology. 1995 Feb 1;206(2):954–962. [PubMed]
  • Wang S, Miller WA. 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. 1995 Jun 2;270(22):13446–13452. [PubMed]
  • Wills NM, Gesteland RF, Atkins JF. Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2. EMBO J. 1994 Sep 1;13(17):4137–4144. [PubMed]
  • Young MJ, Kelly L, Larkin PJ, Waterhouse PM, Gerlach WL. Infectious in vitro transcripts from a cloned cDNA of barley yellow dwarf virus. Virology. 1991 Jan;180(1):372–379. [PubMed]
  • Zaccomer B, Haenni AL, Macaya G. The remarkable variety of plant RNA virus genomes. J Gen Virol. 1995 Feb;76(Pt 2):231–247. [PubMed]
  • Zerfass K, Beier H. Pseudouridine in the anticodon G psi A of plant cytoplasmic tRNA(Tyr) is required for UAG and UAA suppression in the TMV-specific context. Nucleic Acids Res. 1992 Nov 25;20(22):5911–5918. [PMC free article] [PubMed]
  • Zhouravleva G, Frolova L, Le Goff X, Le Guellec R, Inge-Vechtomov S, Kisselev L, Philippe M. Termination of translation in eukaryotes is governed by two interacting polypeptide chain release factors, eRF1 and eRF3. EMBO J. 1995 Aug 15;14(16):4065–4072. [PubMed]

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