Skip to main content
PMC home page
Elsevier - PMC COVID-19 Collection logoLink to Elsevier - PMC COVID-19 Collection
. 2004 Apr 16;62(2):339–352. doi: 10.1016/0092-8674(90)90371-K

Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site

Michael F Belcourt ★,†, Philip J Farabaugh ‡
PMCID: PMC7133245  PMID: 2164889

Abstract

Ribosomal frameshifting regulates expression of the TYB gene of yeast Ty retrotransposons. We previously demonstrated that a 14 nucleotide sequence conserved between two families of Ty elements was necessary and sufficient to support ribosomal frameshifting. This work demonstrates that only 7 of these 14 nucleotides are needed for normal levels of frameshifting. Any change to the sequence CUU-AGG-C drastically reduces frameshifting; this suggests that two specific tRNAs, tRNALeuUAG and tRNAArgCCU, are involved in the event. Our tRNA overproduction data suggest that a leucyl-tRNA, probably tRNALeuUAG, an unusual leucine isoacceptor that recognizes all six leucine codons, slips from CUU-Leu onto UUA-Leu (in the +1 reading frame) during a translational pause at the AGG-Arg codon induced by the low availability of tRNAArgCCU, encoded by a single-copy essential gene. Frameshifting is also directional and reading frame specific. Interestingly, frameshifting is inhibited when the “slip” CUU codon is located three codons downstream, but not four or more codons downstream, of the translational initiation codon.

References

  1. Adams S.E., Mellor J., Gull K., Sim R.B., Tuite M.F., Kingsman S.M., Kingsman A.J. The functions and relationships of Ty-VLP proteins in yeast reflect those of mammalian retroviral proteins. Cell. 1987;49:111–119. doi: 10.1016/0092-8674(87)90761-6. [DOI] [PubMed] [Google Scholar]
  2. Aota S.I., Gojobori T., Ishibashi F., Maruyama T., Ikemura T. Codon usage tabulated from the GenBank genetic sequence data. Nucl. Acids Res. 1988;16:r315–r402. doi: 10.1093/nar/16.suppl.r315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Barrell B.G., Anderson S., Bankier A.T., DeBruijn M.H.L., Chen E., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.A., Sanger F., Schreier P.H., Smith A.J.H., Staden R., Young I.G. Vol. 77. 1980. Different pattern of codon recognition by mammalian mitochondrial tRNAs; pp. 3164–3166. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beremand M.N., Blumenthal T. Overlapping genes in RNA phage: a new protein implicated in lysis. Cell. 1979;18:257–266. doi: 10.1016/0092-8674(79)90045-x. [DOI] [PubMed] [Google Scholar]
  5. Boeke J.D., Garfinkel D.J., Styles C.A., Fink G.R. Ty elements transpose through an RNA intermediate. Cell. 1985;40:491–500. doi: 10.1016/0092-8674(85)90197-7. [DOI] [PubMed] [Google Scholar]
  6. Bonekamp F., Jensen K.F. The AGG codon is translated slowly in E. coli even at very low expression levels. Nucl. Acids Res. 1988;16:3013–3024. doi: 10.1093/nar/16.7.3013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bonekamp F., Dalboge H., Christensen T., Jensen K.F. Translation rates of individual codons are not correlated with tRNA abundances or with frequencies of utilization in Escherichia coli. J. Bacteriol. 1989;171:5812–5816. doi: 10.1128/jb.171.11.5812-5816.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bonitz S.G., Berlani R., Coruzzi G., Li M., Macino G., Nobrega F.G., Nobrega M.P., Thalenfeld B.E., Tzagoloff A. Vol. 77. 1980. Codon recognition rules in yeast mitochondria; pp. 3167–3170. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Bossi L. Context effects: translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J. Mol. Biol. 1983;164:73–87. doi: 10.1016/0022-2836(83)90088-8. [DOI] [PubMed] [Google Scholar]
  10. Bossi L., Roth J.R. The influence of codon context on genetic code translation. Nature. 1980;286:123–127. doi: 10.1038/286123a0. [DOI] [PubMed] [Google Scholar]
  11. Brierley I., Boursnell M.E.G., Binns M.M., Bilimoria B., Blok V.C., Brown T.D.K., Inglis S.C. An efficient ribosomal frame-shifting signal in the polymerase-encoding region of the coronavirus IBV. EMBO J. 1987;6:3779–3785. doi: 10.1002/j.1460-2075.1987.tb02713.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Brierley I., Digard P., Inglis S.C. Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot. Cell. 1989;57:537–547. doi: 10.1016/0092-8674(89)90124-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Burke D.T. Ph.D. thesis. Washington University; St. Louis, Missouri: 1988. Molecular genetics of yeast chromosomes. [Google Scholar]
  14. Cameron J.R., Loh E.Y., Davis R.W. Evidence for transposition of dispersed repetitive DNA families in yeast. Cell. 1979;16:739–751. doi: 10.1016/0092-8674(79)90090-4. [DOI] [PubMed] [Google Scholar]
  15. Carrier M.J., Buckingham R.H. An effect of codon context on the mistranslation of UGU codons in vitro. J. Mol. Biol. 1984;175:29–38. doi: 10.1016/0022-2836(84)90443-1. [DOI] [PubMed] [Google Scholar]
  16. Casadaban M.J., Martinez-Arias A., Shapira S.K., Chou J. β-Galactosidase gene fusions for analyzing gene expression in Escherichia coli and yeast. Meth. Enzymol. 1983;100:293–308. doi: 10.1016/0076-6879(83)00063-4. [DOI] [PubMed] [Google Scholar]
  17. Cigan A.M., Feng L., Donahue T.F. tRNAmeti functions in directing the scanning ribosome to the start site of translation. Science. 1988;242:93–97. doi: 10.1126/science.3051379. [DOI] [PubMed] [Google Scholar]
  18. Clare J., Farabaugh P.J. Vol. 82. 1985. Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression; pp. 2829–2833. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Clare J.J., Belcourt M., Farabaugh P.J. Vol. 85. 1988. Efficient translational frameshifting occurs within a conserved sequence of the overlap between the two genes of a yeast Ty1 transposon; pp. 6816–6820. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Craigen W.J., Caskey C.T. Expression of peptide chain release factor 2 requires high-efficiency frameshift. Nature. 1986;322:273–275. doi: 10.1038/322273a0. [DOI] [PubMed] [Google Scholar]
  21. Craigen W.J., Cook R.G., Tate W.P., Caskey C.T. Vol. 82. 1985. Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2; pp. 3616–3620. (Proc. Natl. Acad. Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Derbyshire K.M., Salvo J.J., Grindley N.D.F. A simple and efficient procedure for saturation mutagenesis using mixed oligodeoxynucleotides. Gene. 1986;46:145–152. doi: 10.1016/0378-1119(86)90398-7. [DOI] [PubMed] [Google Scholar]
  23. Donahue T.F., Farabaugh P.J., Fink G.R. The nucleotide sequence of the HIS4 region of yeast. Gene. 1982;18:47–59. doi: 10.1016/0378-1119(82)90055-5. [DOI] [PubMed] [Google Scholar]
  24. Dunn J.J., Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 1983;166:477–535. doi: 10.1016/s0022-2836(83)80282-4. [DOI] [PubMed] [Google Scholar]
  25. Emori Y., Shiba T., Kanaya S., Inouye S., Yuki S., Saigo K. The nucleotide sequences of copia and copia-related RNA in Drosophila virus-like particles. Nature. 1985;315:773–776. doi: 10.1038/315773a0. [DOI] [PubMed] [Google Scholar]
  26. Etcheverry T., Salvato M., Guthrie C. Recessive lethality of yeast strains carrying the SUP61 suppressor results from loss of a transfer RNA with a unique decoding function. J. Mol. Biol. 1982;158:599–618. doi: 10.1016/0022-2836(82)90251-0. [DOI] [PubMed] [Google Scholar]
  27. Farabaugh P., Liao X.-B., Belcourt M., Zhao H., Kapakos J., Clare J. Enhancer and silencerlike sites within the transcribed portion of a Ty2 transposable element of Saccharomyces cerevisiae. Mol. Cell. Biol. 1989;9:4824–4834. doi: 10.1128/mcb.9.11.4824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Fluck M.M., Salser W., Epstein R.H. The influence of the reading context upon the suppression of nonsense codons. Mol. Gen. Genet. 1977;151:137–149. doi: 10.1007/BF00338688. [DOI] [PubMed] [Google Scholar]
  29. Fox T.D., Weiss-Brummer B. Leaky +1 and −1 frame shift mutations at the same site in a yeast mitochondrial gene. Nature. 1980;288:60–63. doi: 10.1038/288060a0. [DOI] [PubMed] [Google Scholar]
  30. Gafner J., De Robertis E.M., Philippsen P. Deita sequences in the 5′ non-coding region of yeast tRNA genes. EMBO J. 1983;2:583–591. doi: 10.1002/j.1460-2075.1983.tb01467.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Garfinkel D.J., Boeke J.D., Fink G.R. Ty element transposition: reverse transcriptase and virus-like particles. Cell. 1985;42:507–517. doi: 10.1016/0092-8674(85)90108-4. [DOI] [PubMed] [Google Scholar]
  32. Guarente L., Yocum R., Gifford P. Vol. 79. 1982. A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site; pp. 7410–7414. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Heckman J.E., Sarnoff J., Alzner-DeWeerd B., Yin S., RajBhandary U.L. Vol. 77. 1980. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on six mitochondrial tRNAs; pp. 3159–3163. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Hemsley A., Arnheim N., Toney M.D., Cortopassi G., Galas D.J. A simple method for site directed mutagenesis using the polymerase chain reaction. Nucl. Acids Res. 1989;17:6545–6551. doi: 10.1093/nar/17.16.6545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. J. Mol. Biol. 1982;158:573–597. doi: 10.1016/0022-2836(82)90250-9. [DOI] [PubMed] [Google Scholar]
  36. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 1983;153:163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Jacks T., Varmus H.E. Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. Science. 1985;230:1237–1242. doi: 10.1126/science.2416054. [DOI] [PubMed] [Google Scholar]
  38. Jacks T., Madhani H.D., Masiarz F.R., Varmus H.E. Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region. Cell. 1988;55:447–458. doi: 10.1016/0092-8674(88)90031-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Jacks T., Power M.D., Masiarz F.R., Luciw P.A., Barr P.J., Varmus H.E. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature. 1988;331:280–283. doi: 10.1038/331280a0. [DOI] [PubMed] [Google Scholar]
  40. Jacks T., Townsley K., Varmus H.E., Majors J. Vol. 84. 1987. Two efficient ribosomal frameshifting events are required for synthesis of mouse mammary tumor virus gag-related polyproteins; pp. 4298–4302. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Kastelein R.A., Ramaut E., Fiers W., VanDuin J. Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene. Nature. 1982;295:35–41. doi: 10.1038/295035a0. [DOI] [PubMed] [Google Scholar]
  42. Liao X.-B., Clare J.J., Farabaugh P.J. Vol. 84. 1987. The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element; pp. 8520–8524. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Loeb D.D., Padgett R.W., Hardies S.C., Shehee W.R., Comer M.B., Edgell M.H., Hutchison C.A., III The sequence of a large L1Md element reveals a tandemly repeated 5′ end and several features found in retrotransposóns. Mol. Cell. Biol. 1986;6:168–182. doi: 10.1128/mcb.6.1.168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Mellor J., Fulton S.M., Dobson M.J., Wilson W., Kingsman S.M., Kingsman A.J. A retrovirus-like strategy for expression of a fusion protein encoded by yeast transposon Ty1. Nature. 1985;313:243–246. doi: 10.1038/313243a0. [DOI] [PubMed] [Google Scholar]
  45. Mellor J., Malim M.H., Gull K., Tuite M.F., McCready S.M., Dibbayawan T., Kingsman S.M., Kingsman A.J. Reverse transcriptase activity and Ty RNA are associated with virus-like particles in yeast. Nature. 1985;318:583–586. doi: 10.1038/318583a0. [DOI] [PubMed] [Google Scholar]
  46. Mierendorf R.C., Pfeffer D. Direct sequencing of denatured plasmid DNA. Meth. Enzymol. 1987;152:556–562. doi: 10.1016/0076-6879(87)52061-4. [DOI] [PubMed] [Google Scholar]
  47. Miller J.H., Albertini A.M. Effects of surrounding sequence on the suppression of nonsense codons. J. Mol. Biol. 1983;164:59–71. doi: 10.1016/0022-2836(83)90087-6. [DOI] [PubMed] [Google Scholar]
  48. Moore R., Dixon M., Smith R., Peters G., Dickson C. Complete nucleotide sequence of a milk-transmitted mouse mammary tumor virus: two frameshift suppression events are required for translation of gag and pol. J. Virol. 1987;61:480–490. doi: 10.1128/jvi.61.2.480-490.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Mount S.M., Rubin G.M. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol. Cell. Biol. 1985;5:1630–1638. doi: 10.1128/mcb.5.7.1630. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Murgola E.J., Pagel F.T., Hijazi K.A. Codon context effects in missense suppression. J. Mol. Biol. 1984;175:19–27. doi: 10.1016/0022-2836(84)90442-x. [DOI] [PubMed] [Google Scholar]
  51. Olson M.V., Montgomery D.L., Hopper A.K., Page G.S., Horodyski F., Hall B.D. Molecular characterization of the tyrosine tRNA genes in yeast. Nature. 1977;267:639–641. doi: 10.1038/267639a0. [DOI] [PubMed] [Google Scholar]
  52. Olson M.V., Page G.S., Sentenac A., Piper P.W., Worthington M., Weiss R.B., Hall B.D. Only one of two closely related yeast suppressor tRNA genes contains an intervening sequence. Nature. 1981;291:464–469. doi: 10.1038/291464a0. [DOI] [PubMed] [Google Scholar]
  53. RajBhandary U.L., Chang J.H., Stuart A., Faulkner B.D., Hoskinson R.M., Khorana H.G. Vol. 57. 1967. The primary structure of yeast phenylalanine transfer RNA; pp. 751–758. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Randerath E., Gupta R.C., Chia L.L.S.Y., Chang S.H., Randerath K. Yeast tRNALEUUAG. Purification, properties, and determination of the nucleotide sequence by radioactive derivative methodsEur. J. Biochem. 1979;93:79–94. doi: 10.1111/j.1432-1033.1979.tb12797.x. [DOI] [PubMed] [Google Scholar]
  55. Sanger F., Nicklen S., Coulson A.R. Vol. 74. 1977. DNA sequencing with chain-terminating inhibitors; pp. 5463–5467. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Scolnick E.M., Caskey C.T. Vol. 64. 1969. Peptide chain termination, V. The role of release factors in mRNA termination codon recognition; pp. 1235–1241. (Proc. Natl. Acad. Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Sherman F. Suppression in the yeast Saccharomyces cerevisiae. In: Strathern J.N., Jones E.W., Broach J.R., editors. The Molecular Biology of the Yeast Saccharomyces: Metabolism and Gene Expression. Cold Spring Harbor Laboratory; Cold Spring Harbor, New York: 1982. pp. 463–486. [Google Scholar]
  58. Sherman F., Fink G.R., Hicks J.B. Cold Spring Harbor Laboratory; Cold Spring Harbor, New York: 1986. Methods in Yeast Genetics; pp. 163–167. [Google Scholar]
  59. Shine J., Dalgarno L. Vol. 71. 1974. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites; pp. 1342–1346. (Proc. Natl. Acad. Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Sibler A.P., Dirheimer G., Martin R.P. Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs. J. Mol. Biol. 1986;194:131–138. doi: 10.1016/0014-5793(86)80064-3. [DOI] [PubMed] [Google Scholar]
  61. Spanjaard R.A., van Duin J. Vol. 85. 1988. Translation of the sequence AGG-AGG yields 50% ribosomal frameshift; pp. 7967–7971. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Thompson R.C., Dix D.B., Eccleston J.F. Single turn-over kinetic studies of guanosine triphosphate hydrolysis and peptide formation in the elongation factor Tu-dependent binding of aminoacyl-tRNA to Escherichia coli ribosomes. J. Biol. Chem. 1980;255:11088–11090. [PubMed] [Google Scholar]
  63. Valenzuela P., Venegas A., Weinberg F., Bishop R., Rutter W.J. Vol. 75. 1978. Structure of yeast phenylalanine-tRNA genes: an intervening DNA segment within the region coding for the tRNA; pp. 190–194. (Proc. Natl. Acad. Sci. USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Varmus H.E. Retroviruses. In: Shapiro J.A., editor. Mobile Genetic Elements. Academic Press; New York: 1983. pp. 411–503. [Google Scholar]
  65. Weiss R.B. Vol. 81. 1984. Molecular model of ribosome frameshifting; pp. 5797–5801. (Proc. Natl. Acad. Sci USA). [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Weiss R.B., Gallant J.A. Frameshift suppression in aminoacyl-tRNA limited cells. Genetics. 1986;112:727–739. doi: 10.1093/genetics/112.4.727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Weiss R.B., Dunn D.M., Atkins J.F., Gesteland R.F. Vol. 52. 1987. Slippery runs, shifty stops, backward steps, and forward hops: −2, −1, +1, +2, +5, and +6 ribosomal frameshifting; pp. 687–693. (Cold Spring Harbor Symp. Quant. Biol.). [DOI] [PubMed] [Google Scholar]
  68. Weiss R.B., Dunn D.M., Dahlberg A.E., Atkins J.F., Gesteland R.F. Reading-frame switch caused by basepair formation between the 3′ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 1988;7:1503–1507. doi: 10.1002/j.1460-2075.1988.tb02969.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Weiss R.B., Dunn D.M., Shuh M., Atkins J.F., Gesteland R.F. E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent. New Biologist. 1989;1:159–169. [PubMed] [Google Scholar]
  70. Weiss R., Lindsley D., Falahee B., Gallant J. On the mechanism of ribosomal frameshifting at hungry codons. J. Mol. Biol. 1988;203:403–410. doi: 10.1016/0022-2836(88)90008-3. [DOI] [PubMed] [Google Scholar]
  71. Weissenbach J., Dirheimer G., Falcoff R., Sanceau J., Falcoff E. Yeast tRNALeu (anticodon UAG) translates all six leucine codons in extracts from interferon treated cells. FEBS Lett. 1977;82:71–76. doi: 10.1016/0014-5793(77)80888-0. [DOI] [PubMed] [Google Scholar]
  72. Wilson W., Malim M.H., Mellor J., Kingsman A.J., Kingsman S.M. Expression strategies of the yeast retrotransposon Ty: a short sequence directs ribosomal frameshifting. Nucl. Acids Res. 1986;14:7001–7016. doi: 10.1093/nar/14.17.7001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  73. Wilson W., Braddock M., Adams S.E., Rathjen P.D., Kingsman S.M., Kingsman A.J. HIV expression strategies: ribosomal frameshifting is directed by a short sequence in both mammalian and yeast systems. Cell. 1988;55:1159–1169. doi: 10.1016/0092-8674(88)90260-7. [DOI] [PubMed] [Google Scholar]

Articles from Cell are provided here courtesy of Elsevier

RESOURCES