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PMID: 1461724 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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 research ·Vol. 20 ·No. 22 ·1992-11-25 ·Pages 5911-8

Zerfass K, Beier H

Abstract

We have previously isolated and sequenced Nicotiana cytoplasmic tRNA(Tyr) with G psi A anticodon which promotes readthrough over the leaky UAG termination codon at the end of the 126 K cistron of tobacco mosaic virus RNA and we have demonstrated that tRNA(Tyr) with Q psi A anticodon is no UAG suppressor. Here we show that the nucleotide in the middle of the anticodon (i.e., psi 35) also contributes to the suppressor efficiency displayed by cytoplasmic tRNA(Tyr). A tRNA(Tyr) with GUA anticodon was synthesized in vitro using T7 RNA polymerase transcription. This tRNA(Tyr) was unable to suppress the UAG codon, indicating that nucleotide modifications in the anticodon of tRNA(Tyr) have either stimulating (i.e., psi 35) or inhibitory (i.e., Q34) effects on suppressor activity. Furthermore, we have shown that the UAA but not the UGA stop codon is also efficiently recognized by tobacco tRNA(G psi ATyr), if placed in the TMV context. Hence this is the first naturally occurring tRNA for which UAA suppressor activity has been demonstrated. In order to study the influence of neighbouring nucleotides on the readthrough capacity of tRNA(Tyr), we have established a system, in which part of the sequence around the leaky UAG codon of TMV RNA was inserted into a zein pseudogene which naturally harbours an UAG codon in the middle of the gene. The construct was cloned into the vector pSP65 and in vitro transcripts, generated by SP6 RNA polymerase, were translated in a wheat germ extract depleted of endogenous mRNAs and tRNAs. A number of mutations in the codons flanking the UAG were introduced by site-directed mutagenesis. It was found that changes at specific positions of the two downstream codons completely abolished the readthrough over the UAG by Nicotiana tRNA(Tyr), indicating that this tRNA needs a very specific codon context for its suppressor activity.

MeSH Terms
Anticodon Base Sequence Cloning, Molecular Codon DNA Molecular Sequence Data Molecular Structure Mutagenesis, Site-Directed Plants, Toxic Protein Biosynthesis Pseudouridine/genetics RNA, Transfer, Tyr/chemistry,genetics Tobacco/genetics Tobacco Mosaic Virus/genetics Transcription, Genetic/physiology Zea mays/genetics,microbiology Zein/genetics
Chemicals
Anticodon Codon RNA, Transfer, Tyr Pseudouridine DNA Zein
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Zerfass K
Institut für Biochemie, Bayerische Julius-Maximilians-Universität, Würzburg, Germany.
Beier H
References (64)
64 references, click to expand
  1. On the physical basis for ambiguity in genetic coding interactions.
    Proc Natl Acad Sci U S A. 1978 Feb;75(2):610-4 PMID: 273223
  2. Conformational properties of polyformycin: a polyribonucleotide with individual residues in the syn conformation.
    Proc Natl Acad Sci U S A. 1968 Dec;61(4):1494-501 PMID: 4303481
  3. Ribonuclease P: an enzyme with an essential RNA component.
    Proc Natl Acad Sci U S A. 1978 Aug;75(8):3717-21 PMID: 358197
  4. Leaky UAG termination codon in tobacco mosaic virus RNA.
    Nature. 1978 Mar 30;272(5652):469-71 PMID: 634374
  5. The effect of tobacco mosaic virus infection on host and virus-specific protein synthesis in protoplasts.
    Virology. 1978 Apr;85(2):494-503 PMID: 664212
  6. Further studies on the translation products of tobacco rattle virus RNA in vitro.
    Virology. 1977 Apr;77(2):722-32 PMID: 855189
  7. Rabbit liver tRNA1Val:I. Primary structure and unusual codon recognition.
    Nucleic Acids Res. 1977 Jun;4(6):1999-2008 PMID: 896481
  8. In vitro and in vivo translation of the ribonucleic acids of a cowpea strain of tobacco mosaic virus.
    Virology. 1976 Jun;71(2):498-517 PMID: 936472
  9. Complementary base pairing and the origin of substitution mutations.
    Nature. 1976 Sep 23;263(5575):285-9 PMID: 958482
  10. Base pairing and fidelity in codon-anticodon interaction.
    Nature. 1976 Sep 23;263(5575):289-93 PMID: 958483
  11. Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine.
    Biochemistry. 1975 Sep 23;14(19):4198-208 PMID: 1101947
  12. Protein synthesis in tobacco protoplasts infected with tobacco mosaic virus.
    Virology. 1975 Mar;64(1):10-22 PMID: 1114703
  13. Quantitative film detection of 3H and 14C in polyacrylamide gels by fluorography.
    Eur J Biochem. 1975 Aug 15;56(2):335-41 PMID: 1175627
  14. The leaky UGA termination codon of tobacco rattle virus RNA is suppressed by tobacco chloroplast and cytoplasmic tRNAs(Trp) with CmCA anticodon.
    EMBO J. 1992 Nov;11(11):4167-73 PMID: 1396598
  15. Nucleotide sequence of the genomic RNA of pepper mild mottle virus, a resistance-breaking tobamovirus in pepper.
    J Gen Virol. 1991 Dec;72 ( Pt 12):2875-84 PMID: 1765765
  16. The complete nucleotide sequence of cucumber green mottle mosaic virus (SH strain) genomic RNA.
    J Gen Virol. 1991 Jul;72 ( Pt 7):1487-95 PMID: 1856687
  17. Amber codon suppression: the in vivo and in vitro analysis of two C-hordein genes from barley.
    Plant Mol Biol. 1991 Dec;17(6):1217-31 PMID: 1932695
  18. 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):365-73 PMID: 2010914
  19. Rapid and simple purification of T7 RNA polymerase.
    Nucleic Acids Res. 1991 Apr 25;19(8):1948 PMID: 2030975
  20. Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res. 1991 Apr 25;19 Suppl:2127-71 PMID: 2041802
  21. Analysis of the stop codon context in plant nuclear genes.
    FEBS Lett. 1990 Oct 1;271(1-2):144-6 PMID: 2226798
  22. The complete nucleotide sequence of the genomic RNA of the tobamovirus tobacco mild green mosaic virus.
    Virology. 1990 Aug;177(2):553-8 PMID: 2371769
  23. The design and catalytic properties of a simplified ribonuclease P RNA.
    Science. 1989 Jun 30;244(4912):1569-71 PMID: 2472671
  24. Synthesis of small RNAs using T7 RNA polymerase.
    Methods Enzymol. 1989;180:51-62 PMID: 2482430
  25. All human tRNATyr genes contain introns as a prerequisite for pseudouridine biosynthesis in the anticodon.
    Nucleic Acids Res. 1988 Mar 25;16(5):1951-66 PMID: 3357766
  26. Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA.
    Nucleic Acids Res. 1988 Jul 11;16(13):6157-73 PMID: 3399388
  27. Natural UAG suppressor glutamine tRNA is elevated in mouse cells infected with Moloney murine leukemia virus.
    Proc Natl Acad Sci U S A. 1987 May;84(9):2668-72 PMID: 3472229
  28. Cleavage of structural proteins during the assembly of the head of bacteriophage T4.
    Nature. 1970 Aug 15;227(5259):680-5 PMID: 5432063
  29. Codon--anticodon pairing: the wobble hypothesis.
    J Mol Biol. 1966 Aug;19(2):548-55 PMID: 5969078
  30. Nucleotide sequence of Moloney murine leukaemia virus.
    Nature. 1981 Oct 15-21;293(5833):543-8 PMID: 6169994
  31. Effects of surrounding sequence on the suppression of nonsense codons.
    J Mol Biol. 1983 Feb 15;164(1):59-71 PMID: 6188840
  32. Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses.
    Nucleic Acids Res. 1984 Sep 25;12(18):7269-82 PMID: 6207485
  33. The yeast tRNATyr gene intron is essential for correct modification of its tRNA product.
    Nature. 1983 Apr 21;302(5910):681-7 PMID: 6339954
  34. Nucleotide sequence of the tobacco mosaic virus (tomato strain) genome and comparison with the common strain genome.
    J Biochem. 1984 Dec;96(6):1915-23 PMID: 6549393
  35. Striking similarities in amino acid sequence among nonstructural proteins encoded by RNA viruses that have dissimilar genomic organization.
    Proc Natl Acad Sci U S A. 1984 Jul;81(14):4358-62 PMID: 6611550
  36. Nucleotide sequence of tobacco mosaic virus RNA.
    Proc Natl Acad Sci U S A. 1982 Oct;79(19):5818-22 PMID: 6964389
  37. Polypeptides induced by tobacco rattle virus during multiplication in tobacco protoplasts.
    Intervirology. 1982;17(4):240-6 PMID: 7129824
  38. In vivo and in vitro translation of the RNAs of four tobamoviruses.
    Intervirology. 1980;14(5-6):292-9 PMID: 7251334
  39. UAG readthrough during TMV RNA translation: isolation and sequence of two tRNAs with suppressor activity from tobacco plants.
    EMBO J. 1984 Feb;3(2):351-6 PMID: 16453503
  40. The molecular basis for the differential translation of TMV RNA in tobacco protoplasts and wheat germ extracts.
    EMBO J. 1984 May;3(5):1091-6 PMID: 16453524
  41. Dramatic events in ciliate evolution: alteration of UAA and UAG termination codons to glutamine codons due to anticodon mutations in two Tetrahymena tRNAs.
    EMBO J. 1986 Jun;5(6):1307-11 PMID: 16453685
  42. 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):1326-37 PMID: 2521676
  43. Suppression of UAA and UGA termination codons in mutant murine leukemia viruses.
    J Virol. 1989 Jun;63(6):2870-3 PMID: 2542597
  44. Sequence of a 21 kd zein gene from maize containing an in-frame stop codon.
    Nucleic Acids Res. 1989 Mar 25;17(6):2354 PMID: 2704623
  45. Nucleotide sequence of potato leafroll luteovirus RNA.
    J Gen Virol. 1989 May;70 ( Pt 5):1037-51 PMID: 2732710
  46. Properties of a transfer RNA lacking modified nucleosides.
    J Biol Chem. 1988 Sep 25;263(27):13692-9 PMID: 2843531
  47. Partial suppression of an ochre mutation in Saccharomyces cerevisiae by multicopy plasmids containing a normal yeast tRNAGln gene.
    J Mol Biol. 1985 May 5;183(1):31-42 PMID: 2989539
  48. Tetrahymena thermophila glutamine tRNA and its gene that corresponds to UAA termination codon.
    Proc Natl Acad Sci U S A. 1985 Jul;82(14):4758-62 PMID: 2991890
  49. The nucleotide sequence of a HMW glutenin subunit gene located on chromosome 1A of wheat (Triticum aestivum L.).
    Nucleic Acids Res. 1985 Oct 11;13(19):6817-32 PMID: 2997729
  50. Structure of wheat gamma-gliadin genes.
    Gene. 1986;43(3):221-9 PMID: 3017812
  51. Pseudouridine modification in the tRNA(Tyr) anticodon is dependent on the presence, but independent of the size and sequence, of the intron in eucaryotic tRNA(Tyr) genes.
    Mol Cell Biol. 1988 Aug;8(8):3332-7 PMID: 3145410
  52. The context effect does not require a fourth base pair.
    Science. 1986 Jan 24;231(4736):393-5 PMID: 3510456
  53. Dideoxy sequencing method using denatured plasmid templates.
    Anal Biochem. 1986 Feb 1;152(2):232-8 PMID: 3516005
  54. Specific substitution into the anticodon loop of yeast tyrosine transfer RNA.
    Biochemistry. 1986 Sep 23;25(19):5825-30 PMID: 3535890
  55. A gene for the major cytoplasmic tRNATyr from Nicotiana rustica contains a 13 nucleotides long intron.
    Nucleic Acids Res. 1986 Nov 11;14(21):8691 PMID: 3641192
  56. The complete nucleotide sequence of tobacco rattle virus RNA-1.
    J Gen Virol. 1987 Oct;68 ( Pt 10):2563-75 PMID: 3668507
  57. A cell-free plant extract for accurate pre-tRNA processing, splicing and modification.
    EMBO J. 1987 Sep;6(9):2811-8 PMID: 3678205
  58. In vitro mutagenesis of the putative replicase genes of tobacco mosaic virus.
    Nucleic Acids Res. 1986 Nov 11;14(21):8291-305 PMID: 3786131
  59. Nucleotide sequence and genome organization of carnation mottle virus RNA.
    Nucleic Acids Res. 1985 Sep 25;13(18):6663-77 PMID: 3840587
  60. Rapid and efficient site-specific mutagenesis without phenotypic selection.
    Proc Natl Acad Sci U S A. 1985 Jan;82(2):488-92 PMID: 3881765
  61. Murine leukemia virus protease is encoded by the gag-pol gene and is synthesized through suppression of an amber termination codon.
    Proc Natl Acad Sci U S A. 1985 Mar;82(6):1618-22 PMID: 3885215
  62. 15N-labeled Escherichia coli tRNAfMet, tRNAGlu, tRNATyr, and tRNAPhe. Double resonance and two-dimensional NMR of N1-labeled pseudouridine.
    J Biol Chem. 1985 Aug 15;260(17):9734-41 PMID: 3894360
  63. High-resolution structure of a DNA helix containing mismatched base pairs.
    Nature. 1985 Jun 13-19;315(6020):604-6 PMID: 4010774
  64. "Two out of three": an alternative method for codon reading.
    Proc Natl Acad Sci U S A. 1978 Apr;75(4):1759-62 PMID: 273907
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/20.22.5911
Published
1992-11-25
Pages
5911-8
Language
English
Region
England
NLM ID
0411011
PMCID
PMC334454
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/20.22.5911 PMC Full Text View journal details
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