Article | Published:

Position-dependent termination and widespread obligatory frameshifting in Euplotes translation

Nature Structural & Molecular Biology 24, 61–68 (2017) | Download Citation

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Abstract

The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, and +1 frameshifting at AAA was the most frequent. The frameshifts showed unusual plasticity and rapid evolution, and had little influence on translation rates. The proximity of a stop codon to the 3′ mRNA end, rather than its occurrence or sequence context, appeared to designate termination. Thus, a 'stop codon' is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and probably requires additional factors.

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DDBJ/GenBank/EMBL

Proteomics Identifications Database

Sequence Read Archive

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Acknowledgements

Supported by NIH GM061603 and GM065402 to V.N.G. S.M.H. and P.V.B. are supported by the grants from Wellcome Trust (094423) and Science Foundation Ireland (12/IA/1335). Portions of this research were also supported by NIH GM103493 and the W.R. Wiley Environmental Molecular Science Laboratory (sponsored by DOE and located at Pacific Northwest National Laboratory). Pacific Northwest National Laboratory is operated by the Battelle Memorial Institute under the DOE contract DE-AC05-76RLO-1830. C.M. acknowledges the Italian PNRA and the COST action BM1102 for supporting a part of this work.

Author information

    • Alexei V Lobanov
    •  & Stephen M Heaphy

    These authors contributed equally to this work.

Affiliations

  1. Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Alexei V Lobanov
    • , Anton A Turanov
    • , Maxim V Gerashchenko
    •  & Vadim N Gladyshev

  2. School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.

    • Stephen M Heaphy
    • , John F Atkins
    •  & Pavel V Baranov

  3. School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.

    • Sandra Pucciarelli
    • , Raghul R Devaraj
    •  & Cristina Miceli

  4. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.

    • Fang Xie
    • , Vladislav A Petyuk
    •  & Richard D Smith

  5. Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.

    • Lawrence A Klobutcher

  6. Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, USA.

    • Dolph L Hatfield

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Contributions

A.V.L., S.M.H., P.V.B. and V.N.G. analyzed the data and wrote the paper with advice from D.L.H. and J.F.A.; A.A.T. and M.V.G. prepared samples for sequencing; S.P., R.R.D., C.M. and L.A.K. performed cell culture maintenance and growth, F.X., V.A.P. and R.D.S. conducted MS analysis. All authors discussed the results and implications and commented on the manuscript at all stages.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Pavel V Baranov or Vadim N Gladyshev.

Integrated supplementary information

Supplementary figures

  1. 1.

    Features of Euplotes genomes.

  2. 2.

    Features of the Euplotes transcriptome.

  3. 3.

    Termination at AAATAA and two mRNAs with long 3′ UTRs.

  4. 4.

    Metagene analysis of RNA-seq density surrounding frameshifting sites.

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–4, Supplementary Table 1 and Supplementary Notes 1–4

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DOI

https://doi.org/10.1038/nsmb.3330

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