Letter

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation

  • Nature volume 553, pages 356360 (18 January 2018)
  • doi:10.1038/nature25174
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Abstract

In addition to acting as template for protein synthesis, messenger RNA (mRNA) often contains sensory sequence elements that regulate this process1,2. Here we report a new mechanism that limits the number of complete protein molecules that can be synthesized from a single mRNA molecule of the human AMD1 gene encoding adenosylmethionine decarboxylase 1 (AdoMetDC). A small proportion of ribosomes translating AMD1 mRNA stochastically read through the stop codon of the main coding region. These readthrough ribosomes then stall close to the next in-frame stop codon, eventually forming a ribosome queue, the length of which is proportional to the number of AdoMetDC molecules that were synthesized from the same AMD1 mRNA. Once the entire spacer region between the two stop codons is filled with queueing ribosomes, the queue impinges upon the main AMD1 coding region halting its translation. Phylogenetic analysis suggests that this mechanism is highly conserved in vertebrates and existed in their common ancestor. We propose that this mechanism is used to count and limit the number of protein molecules that can be synthesized from a single mRNA template. It could serve to safeguard from dysregulated translation that may occur owing to errors in transcription or mRNA damage.

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Acknowledgements

We are grateful to I. Jungreis and M. Kellis for allowing us to use CodAlignView and to P.R. Bhatt for technical advice on stable peptidyl–tRNA complex formation. We acknowledge financial support from Science Foundation Ireland ((12/IA/1335) to P.V.B., (13/IA/1853) to J.F.A. and (12/RC/2276) to D.B.P.); National Institute of Health (CA080946) and (GM065204) to V.N.G.; Health Research Board (PhD/2007/04) to I.T.; and Russian Science Foundation (16-14-10065) to D.E.A.

Author information

Author notes

    • Martina M. Yordanova
    •  & Gary Loughran

    These authors contributed equally to this work.

Affiliations

  1. School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland

    • Martina M. Yordanova
    • , Gary Loughran
    • , Alexander V. Zhdanov
    • , Marco Mariotti
    • , Stephen J. Kiniry
    • , Patrick B. F. O’Connor
    • , Dmitry E. Andreev
    • , Ioanna Tzani
    • , Paul Saffert
    • , Audrey M. Michel
    • , Dmitry B. Papkovsky
    • , John F. Atkins
    •  & Pavel V. Baranov
  2. Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA

    • Marco Mariotti
    •  & Vadim N. Gladyshev
  3. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia

    • Dmitry E. Andreev
  4. Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA

    • John F. Atkins

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Contributions

P.B.F.O. made the initial observation of unusual ribosome footprint density. M.M. and P.V.B. performed phylogenetic analysis. M.M.Y., G.L., A.V.Z., I.T., P.S. and D.E.A. designed and performed biochemical experiments. S.J.K. and A.M.M. analysed publicly available ribosome profiling data. P.V.B. proposed the model. M.M.Y. and P.V.B. drafted the manuscript. V.N.G., D.B.P. and J.F.A. contributed to interpretation of the experimental data and editing of the manuscript.

Competing interests

A.M.M., G.L. and P.V.B. are founders and shareholders of RiboMaps Ltd, a company providing ribosome profiling as a service. As the finding reported here stemmed from the analysis of ribosome profiling data, its publication may increase the attractiveness of this technology and indirectly benefit the company.

Corresponding author

Correspondence to Pavel V. Baranov.

Reviewer Information Nature thanks A. Geballe, P. Van Damme and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains the sequences of DNA primers used in this study, the Python code for identifying peaks of ribosome density in extended ORFs and a guide to the supplementary files.

  2. 2.

    Supplementary Figure 1

    Gel Source Data. Original source Images of the gels that have been used for making figures with weight markers. Cropped parts are indicated.

  3. 3.

    Supplementary Data 1

    Genomic alignment of tetrapods from UCSC Genome browser 100 species alignment. Codon alignment obtained with CodAlignView, positions of AMD1 stop and AMD1 tail stop are annotated (second row).

  4. 4.

    Supplementary Data 2

    Alignment of AMD1 coding region and surrounding areas from 146 vertebrate species. Synonymous and nonsynonymous substitutions are indicated by blue and red colours, respectively, and gaps are in grey. Ka/Ks ratio and sequence identity (see Methods) are shown at the bottom.

  5. 5.

    Life Sciences Reporting Summary

Text files

  1. 1.

    Supplementary Data 3

    Human transcripts with ribosome density profiles similar to AMD1. List of GENCODE transcripts containing peaks of ribosome density downstream and in-frame of protein coding regions. For each transcript information on the chromosome, coordinates, locus, GENCODE ID and the number of footprints are provided in comma delimited format.

  2. 2.

    Supplementary Data 4

    Vectors and plasmids. Sequences of vectors and plasmids used in this study in fasta format.

  3. 3.

    Supplementary Data 5

    Genomic sequences of AMD1 coding regions. Genomic sequence of AMD1 coding regions for 146 vertebrate species used in this study in fasta format. Genbank IDs for the source sequences are provided in the comment line for each sequence.

Excel files

  1. 1.

    Supplementary Data 6

    Ribosome profiling datasets used for GWIPS-viz global aggregate tracks. Datasets are listed on separate sheets for each genome, first column indicates the publication in which the datasets are described (first author name followed by the year, full reference can be found in GWIPS-viz), second column provides GEO or SRA IDs for each individual dataset from the corresponding study.

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