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The signal recognition particle contacts uL23 and scans substrate translation inside the ribosomal tunnel

Nature Microbiology volume 2, Article number: 16265 (2017) Cite this article

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Abstract

The signal recognition particle (SRP) delivers ∼25% of all bacterial proteins to the membrane for cotranslational insertion. However, a comprehensive model on how the low-abundant SRP scans the vast number of translating ribosomes to identify the correct substrates is lacking. Here, we show that the C-terminal helix of the signal-sequence-binding domain of SRP penetrates into the ribosomal tunnel and contacts the intra-tunnel loop of ribosomal protein uL23. This allows SRP to obtain information about the translational status of the ribosome and possibly the character of the approaching nascent chain. Correct substrates reposition the C-terminal helix of SRP, which facilitates stable binding of the signal sequence by the M-domain of SRP. Thus, SRP already surveys translating ribosomes before the signal sequence is surface exposed. This early interaction probably enables the small number of SRP molecules to scan many ribosomes and to initiate efficient targeting of proper substrates.

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Figure 1: Localization of uL23 at the E. coli ribosome.
Figure 2: Ffh contacts both the globular domain and the intra-tunnel loop of uL23.
Figure 3: The intra-tunnel loop of uL23 contacts the M-domain of Ffh.
Figure 4: Length-dependent contact of the intra-tunnel loop of uL23 with nascent membrane proteins.
Figure 5: Nascent membrane protein displaces SRP from the intra-tunnel loop.
Figure 6: Model for the early recognition steps during co-translational protein targeting in E. coli.

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Acknowledgements

The authors thank G. Kramer (University Heidelberg) for providing the rplW deletion strain, T. Bornemann and W. Wintermeyer (MPI Biophysical Chemistry, Göttingen) for plasmid pCDF-L23 and purified MAP, PDF and TF, E. Bibi (Weizmann Institute, Israel) for plasmids pIY1043 and pIY1045, D. Vikström and G. von Heijne (University Stockholm) for plasmid pRha and the LepB construct, and C. Schaffitzel (University Bristol) for the FtsQ construct. The authors also thank B. Graf for the automated cell size measurement protocol. This work was supported by grants from the DFG (FOR967, FOR929, GRK2202 and KO2184/8) and by a ‘Fill-in-the-gap’ fellowship of the University Freiburg Medical School.

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  1. Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany

    Kärt Denks, Nadine Sliwinski, Veronika Erichsen, Bogdana Borodkina, Andrea Origi & Hans-Georg Koch

  2. Faculty of Biology, Albert-Ludwigs Universität Freiburg, Stefan Meier Strasse 17, 79104 Freiburg, Germany

    Kärt Denks & Andrea Origi

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  1. Kärt Denks
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K.D. carried out study design, experimental work, data analyses and writing of the manuscript. N.S., V.E., B.B. and A.O. performed experimental work and data analyses. H.-G.K. carried out study design and data analyses and contributed to writing the manuscript.

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Correspondence to Hans-Georg Koch.

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Supplementary Figures 1–7, Supplementary Notes and Discussion, Supplementary References. (PDF 4646 kb)

Supplementary Table 1

Oligonucleotide list. (XLS 37 kb)

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Denks, K., Sliwinski, N., Erichsen, V. et al. The signal recognition particle contacts uL23 and scans substrate translation inside the ribosomal tunnel. Nat Microbiol 2, 16265 (2017). https://doi.org/10.1038/nmicrobiol.2016.265

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