Letter | Published:

Global profiling of SRP interaction with nascent polypeptides

Nature volume 536, pages 219223 (11 August 2016) | Download Citation

Abstract

Signal recognition particle (SRP) is a universally conserved protein–RNA complex that mediates co-translational protein translocation and membrane insertion by targeting translating ribosomes to membrane translocons1. The existence of parallel co- and post-translational transport pathways2, however, raises the question of the cellular substrate pool of SRP and the molecular basis of substrate selection. Here we determine the binding sites of bacterial SRP within the nascent proteome of Escherichia coli at amino acid resolution, by sequencing messenger RNA footprints of ribosome–nascent-chain complexes associated with SRP. SRP, on the basis of its strong preference for hydrophobic transmembrane domains (TMDs), constitutes a compartment-specific targeting factor for nascent inner membrane proteins (IMPs) that efficiently excludes signal-sequence-containing precursors of periplasmic and outer membrane proteins. SRP associates with hydrophobic TMDs enriched in consecutive stretches of hydrophobic and bulky aromatic amino acids immediately on their emergence from the ribosomal exit tunnel. By contrast with current models, N-terminal TMDs are frequently skipped and TMDs internal to the polypeptide sequence are selectively recognized. Furthermore, SRP binds several TMDs in many multi-spanning membrane proteins, suggesting cycles of SRP-mediated membrane targeting. SRP-mediated targeting is not accompanied by a transient slowdown of translation and is not influenced by the ribosome-associated chaperone trigger factor (TF), which has a distinct substrate pool and acts at different stages during translation. Overall, our proteome-wide data set of SRP-binding sites reveals the underlying principles of pathway decisions for nascent chains in bacteria, with SRP acting as the dominant triaging factor, sufficient to separate IMPs from substrates of the SecA–SecB post-translational translocation and TF-assisted cytosolic protein folding pathways.

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Acknowledgements

We thank members of the Bukau laboratory for valuable contributions; C. Gläßer for support with data analysis; and H. Bernstein for providing plasmid pHQ4. Sequencing was done at the Genomics & Proteomics Core (DKFZ) facility. I.P. and R.C.W. acknowledge support from the Klaus Tschira Foundation. This work was supported by research grants from the Deutsche Forschungsgemeinschaft (SFB638 and FOR1805) to G.K. and B.B., a Human Frontier Science Program grant to B.B. and a grant from the Swedish Research Council to G.v.H.

Author information

Affiliations

  1. Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany

    • Daniela Schibich
    • , Felix Gloge
    • , Rebecca C. Wade
    • , Bernd Bukau
    •  & Günter Kramer
  2. German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany

    • Daniela Schibich
    • , Felix Gloge
    • , Bernd Bukau
    •  & Günter Kramer
  3. Heidelberg Institute for Theoretical Studies, (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, Heidelberg D-69118, Germany

    • Ina Pöhner
    •  & Rebecca C. Wade
  4. Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden

    • Patrik Björkholm
    •  & Gunnar von Heijne
  5. Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden

    • Patrik Björkholm
    •  & Gunnar von Heijne
  6. Department of Molecular Evolution, Cell, and Molecular Biology, Uppsala University, 752 36 Uppsala, Sweden

    • Patrik Björkholm
  7. Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg D-69120, Germany

    • Rebecca C. Wade

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Contributions

B.B. and G.K. conceived the study. D.S., B.B. and G.K. designed the experiments. D.S. and F.G. performed the experiments. D.S., I.P., R.C.W., P.B., G.vH., B.B. and G.K. analysed the data. B.B. and G.K. wrote the manuscript. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Bernd Bukau or Günter Kramer.

Data have been deposited in the Figshare database and are accessible from https://dx.doi.org/10.6084/m9.figshare.2058051.

Reviewer Information

Nature thanks N. Stern-Ginossar and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    This file contains additional details about the proteome-wide SeRP data of SRP-nascent chain interactions in E. coli. Read counts of the translatome and the SRP interactome are compared, substrate identification methods are highlighted, quality scores (pearson correlation coefficient) are listed, initial SRP binding sites are given, retargeting and skipping events are indicated and topology information is provided.

  2. 2.

    Supplementary Table 2

    This file contains an analysis of the properties of bound and skipped transmembrane domains (TMDs), and signal sequences.

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DOI

https://doi.org/10.1038/nature19070

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