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. 1998 Jan;4(1):38–46.

Effect of frameshift-inducing mutants of elongation factor 1alpha on programmed +1 frameshifting in yeast.

P J Farabaugh 1, A Vimaladithan 1
PMCID: PMC1369594  PMID: 9436906

Abstract

The translational apparatus very efficiently eliminates errors that would cause a spontaneous shift in frames. The probability of frameshifting can be increased dramatically by either cis or trans-acting factors. Programmed translational frameshift sites are cis-acting sequences that greatly increase the frequency of such errors, at least in part by causing a transient translational pause. Pausing during programmed +1 frameshifts occurs because of slow recognition of the codon following the last read in the normal frame. Frameshifting can also be elevated in strains carrying mutations in the homologous elongation factors EF-Tu in bacteria, and EF-1alpha in the yeast Saccharomyces cerevisiae. This phenotype implies that the factors contribute to frame maintenance. Because EF-Tu/EF-1alpha modulate the kinetics of decoding, it is possible that the frameshift suppressor forms of the factors transiently slow normal decoding, allowing spontaneous frameshifting to occur more efficiently, resulting in phenotypic suppression. We have used a set of frameshift reporter plasmids to test the effect of suppressor forms of EF-1alpha on constructs that differ widely in the efficiency with which they stimulate +1 shifting. When these results were compared to the effect of increased translational pausing, it was apparent that the mutations affecting EF-1alpha do not simply prolong the translational pause. Rather, they appear to generally increase the likelihood of frame errors, apparently by affecting the error correction mechanism of the ribosome.

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Selected References

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  1. Atkins J. F., Elseviers D., Gorini L. Low activity of -galactosidase in frameshift mutants of Escherichia coli. Proc Natl Acad Sci U S A. 1972 May;69(5):1192–1195. doi: 10.1073/pnas.69.5.1192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Atkins J. F., Weiss R. B., Thompson S., Gesteland R. F. Towards a genetic dissection of the basis of triplet decoding, and its natural subversion: programmed reading frame shifts and hops. Annu Rev Genet. 1991;25:201–228. doi: 10.1146/annurev.ge.25.120191.001221. [DOI] [PubMed] [Google Scholar]
  3. Belcourt M. F., Farabaugh P. J. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell. 1990 Jul 27;62(2):339–352. doi: 10.1016/0092-8674(90)90371-K. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berchtold H., Reshetnikova L., Reiser C. O., Schirmer N. K., Sprinzl M., Hilgenfeld R. Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature. 1993 Sep 9;365(6442):126–132. doi: 10.1038/365126a0. [DOI] [PubMed] [Google Scholar]
  5. Curran J. F., Yarus M. Reading frame selection and transfer RNA anticodon loop stacking. Science. 1987 Dec 11;238(4833):1545–1550. doi: 10.1126/science.3685992. [DOI] [PubMed] [Google Scholar]
  6. Dinman J. D., Kinzy T. G. Translational misreading: mutations in translation elongation factor 1alpha differentially affect programmed ribosomal frameshifting and drug sensitivity. RNA. 1997 Aug;3(8):870–881. [PMC free article] [PubMed] [Google Scholar]
  7. Farabaugh P. J. Programmed translational frameshifting. Annu Rev Genet. 1996;30:507–528. doi: 10.1146/annurev.genet.30.1.507. [DOI] [PubMed] [Google Scholar]
  8. Farabaugh P. J., Zhao H., Vimaladithan A. A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell. 1993 Jul 16;74(1):93–103. doi: 10.1016/0092-8674(93)90297-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gregory S. T., Lieberman K. R., Dahlberg A. E. Mutations in the peptidyl transferase region of E. coli 23S rRNA affecting translational accuracy. Nucleic Acids Res. 1994 Feb 11;22(3):279–284. doi: 10.1093/nar/22.3.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hughes D., Atkins J. F., Thompson S. Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough. EMBO J. 1987 Dec 20;6(13):4235–4239. doi: 10.1002/j.1460-2075.1987.tb02772.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hughes D., Thompson S., O'Connor M., Tuohy T., Nichols B. P., Atkins J. F. Genetic characterization of frameshift suppressors with new decoding properties. J Bacteriol. 1989 Feb;171(2):1028–1034. doi: 10.1128/jb.171.2.1028-1034.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kawakami K., Pande S., Faiola B., Moore D. P., Boeke J. D., Farabaugh P. J., Strathern J. N., Nakamura Y., Garfinkel D. J. A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics. 1993 Oct;135(2):309–320. doi: 10.1093/genetics/135.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kawakami K., Shafer B. K., Garfinkel D. J., Strathern J. N., Nakamura Y. Ty element-induced temperature-sensitive mutations of Saccharomyces cerevisiae. Genetics. 1992 Aug;131(4):821–832. doi: 10.1093/genetics/131.4.821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kjeldgaard M., Nissen P., Thirup S., Nyborg J. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure. 1993 Sep 15;1(1):35–50. doi: 10.1016/0969-2126(93)90007-4. [DOI] [PubMed] [Google Scholar]
  16. Kjeldgaard M., Nyborg J. Refined structure of elongation factor EF-Tu from Escherichia coli. J Mol Biol. 1992 Feb 5;223(3):721–742. doi: 10.1016/0022-2836(92)90986-t. [DOI] [PubMed] [Google Scholar]
  17. Kurland C. G. Translational accuracy and the fitness of bacteria. Annu Rev Genet. 1992;26:29–50. doi: 10.1146/annurev.ge.26.120192.000333. [DOI] [PubMed] [Google Scholar]
  18. Moine H., Dahlberg A. E. Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis. J Mol Biol. 1994 Oct 28;243(3):402–412. doi: 10.1006/jmbi.1994.1668. [DOI] [PubMed] [Google Scholar]
  19. Nissen P., Kjeldgaard M., Thirup S., Polekhina G., Reshetnikova L., Clark B. F., Nyborg J. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science. 1995 Dec 1;270(5241):1464–1472. doi: 10.1126/science.270.5241.1464. [DOI] [PubMed] [Google Scholar]
  20. O'Connor M., Dahlberg A. E. Mutations at U2555, a tRNA-protected base in 23S rRNA, affect translational fidelity. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):9214–9218. doi: 10.1073/pnas.90.19.9214. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Pande S., Vimaladithan A., Zhao H., Farabaugh P. J. Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol Cell Biol. 1995 Jan;15(1):298–304. doi: 10.1128/mcb.15.1.298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Powers T., Noller H. F. The 530 loop of 16S rRNA: a signal to EF-Tu? Trends Genet. 1994 Jan;10(1):27–31. doi: 10.1016/0168-9525(94)90016-7. [DOI] [PubMed] [Google Scholar]
  23. Sandbaken M. G., Culbertson M. R. Mutations in elongation factor EF-1 alpha affect the frequency of frameshifting and amino acid misincorporation in Saccharomyces cerevisiae. Genetics. 1988 Dec;120(4):923–934. doi: 10.1093/genetics/120.4.923. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Smith D., Yarus M. tRNA-tRNA interactions within cellular ribosomes. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4397–4401. doi: 10.1073/pnas.86.12.4397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Song J. M., Picologlou S., Grant C. M., Firoozan M., Tuite M. F., Liebman S. Elongation factor EF-1 alpha gene dosage alters translational fidelity in Saccharomyces cerevisiae. Mol Cell Biol. 1989 Oct;9(10):4571–4575. doi: 10.1128/mcb.9.10.4571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Thompson R. C. EFTu provides an internal kinetic standard for translational accuracy. Trends Biochem Sci. 1988 Mar;13(3):91–93. doi: 10.1016/0968-0004(88)90047-3. [DOI] [PubMed] [Google Scholar]
  27. Tuohy T. M., Thompson S., Gesteland R. F., Hughes D., Atkins J. F. The role of EF-Tu and other translation components in determining translocation step size. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):274–278. doi: 10.1016/0167-4781(90)90180-a. [DOI] [PubMed] [Google Scholar]
  28. Van Noort J. M., Kraal B., Bosch L. A second tRNA binding site on elongation factor Tu is induced while the factor is bound to the ribosome. Proc Natl Acad Sci U S A. 1985 May;82(10):3212–3216. doi: 10.1073/pnas.82.10.3212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Vijgenboom E., Bosch L. Translational frameshifts induced by mutant species of the polypeptide chain elongation factor Tu of Escherichia coli. J Biol Chem. 1989 Aug 5;264(22):13012–13017. [PubMed] [Google Scholar]
  30. Vimaladithan A., Farabaugh P. J. Special peptidyl-tRNA molecules can promote translational frameshifting without slippage. Mol Cell Biol. 1994 Dec;14(12):8107–8116. doi: 10.1128/mcb.14.12.8107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Weiss-Brummer B., Hüttenhofer A. The paromomycin resistance mutation (parr-454) in the 15 S rRNA gene of the yeast Saccharomyces cerevisiae is involved in ribosomal frameshifting. Mol Gen Genet. 1989 Jun;217(2-3):362–369. doi: 10.1007/BF02464905. [DOI] [PubMed] [Google Scholar]

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