Letter | Published:

Cotranslational signal-independent SRP preloading during membrane targeting

Nature volume 536, pages 224228 (11 August 2016) | Download Citation

Abstract

Ribosome-associated factors must properly decode the limited information available in nascent polypeptides to direct them to their correct cellular fate1. It is unclear how the low complexity information exposed by the nascent chain suffices for accurate recognition by the many factors competing for the limited surface near the ribosomal exit site2,3. Questions remain even for the well-studied cotranslational targeting cycle to the endoplasmic reticulum, involving recognition of linear hydrophobic signal sequences or transmembrane domains by the signal recognition particle (SRP)4,5. Notably, the SRP has low abundance relative to the large number of ribosome–nascent-chain complexes (RNCs), yet it accurately selects those destined for the endoplasmic reticulum6. Despite their overlapping specificities, the SRP and the cotranslationally acting Hsp70 display precise mutually exclusive selectivity in vivo for their cognate RNCs7,8. To understand cotranslational nascent chain recognition in vivo, here we investigate the cotranslational membrane-targeting cycle using ribosome profiling9 in yeast cells coupled with biochemical fractionation of ribosome populations. We show that the SRP preferentially binds secretory RNCs before their targeting signals are translated. Non-coding mRNA elements can promote this signal-independent pre-recruitment of SRP. Our study defines the complex kinetic interaction between elongation in the cytosol and determinants in the polypeptide and mRNA that modulate SRP–substrate selection and membrane targeting.

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Accessions

Primary accessions

Gene Expression Omnibus

Data deposits

Data are deposited in Gene Expression Omnibus (GEO) under accession number GSE74393.

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Acknowledgements

We thank P. Walter, J. S. Weissman and C. Jan for discussions; R. Andino and R. Hegde for critical reading of the manuscript. We thank S. Pechmann, K. M. Dalton, E. M. Sontag, P. T. Dolan and other members of the Frydman laboratory for advice on analysis. Sequencing was performed at the UCSF Center for Advanced Technology with assistance from E. Chow, J. Lund and A. Acevedo. J.W.C. is supported by an NIH NRSA award. This work was additionally supported by grants to J.F. from the NIH and HFSP.

Author information

Affiliations

  1. Department of Biology, Stanford University Stanford, California 94305, USA

    • Justin W. Chartron
    • , Katherine C. L. Hunt
    •  & Judith Frydman
  2. Department of Genetics, Stanford University Stanford, California 94305, USA

    • Judith Frydman

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Contributions

J.W.C. and J.F. designed the study. K.C.L.H. performed experiments with prt1-1. J.W.C. performed all other experiments and analysis. J.W.C. and J.F. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Judith Frydman.

Reviewer Information

Nature thanks R. Keenan and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    Supplementary Discussion

    This file contains a Supplementary Discussion and additional references.

Excel files

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    Supplementary Table 1

    This file contains gene annotations, enrichment scores, and sequencing counts derived from sequencing experiments. The first tab provides descriptions for the data presented in the second tab. The third and fourth tabs provide raw sequencing counts from the Ribo-seq and RNA-seq samples.

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https://doi.org/10.1038/nature19309

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