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Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins

Nature Cell Biology volume 21, pages 1219–1233 (2019)Cite this article

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Abstract

Protein trafficking requires coat complexes that couple recognition of sorting motifs in transmembrane cargoes with biogenesis of transport carriers. The mechanisms of cargo transport through the endosomal network are poorly understood. Here, we identify a sorting motif for endosomal recycling of cargoes, including the cation-independent mannose-6-phosphate receptor and semaphorin 4C, by the membrane tubulating BAR domain-containing sorting nexins SNX5 and SNX6. Crystal structures establish that this motif folds into a β-hairpin, which binds a site in the SNX5/SNX6 phox homology domains. Over sixty cargoes share this motif and require SNX5/SNX6 for their recycling. These include cargoes involved in neuronal migration and a Drosophila snx6 mutant displays defects in axonal guidance. These studies identify a sorting motif and provide molecular insight into an evolutionary conserved coat complex, the ‘Endosomal SNX–BAR sorting complex for promoting exit 1’ (ESCPE-1), which couples sorting motif recognition to the BAR-domain-mediated biogenesis of cargo-enriched tubulo-vesicular transport carriers.

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Fig. 1: Mapping the interaction between SNX5 and CI-MPR.
Fig. 2: Crystal structure of the SNX5–CI-MPR complex.
Fig. 3: The interaction between SNX5 and the CI-MPR β-hairpin structure is required for CI-MPR retrograde trafficking.
Fig. 4: Interaction between CI-MPR and the hydrophobic groove of the SNX5 PX domain is required for CI-MPR retrograde trafficking.
Fig. 5: CI-MPR retrograde trafficking requires functional SNX5 heterodimers and co-incidence detection of multiple membrane features.
Fig. 6: Mechanism of SEMA4C and IGF1R cargo binding to SNX5.
Fig. 7: Interaction between the IGF1R cytosolic tail and the SNX5 PX-domain hydrophobic groove is required for the endosome-to-plasma membrane recycling of the receptor.
Fig. 8: Identification of a ФxΩxФ consensus motif for SNX5-mediated cargo recruitment.

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Data availability

The coordinates and structure factors for the SNX5 PX domain in complex with the CI-MPR sorting signal have been deposited at the PDB with accession codes 6N5X (form 1) and 6N5Y (form 2). The coordinates and structure factors for the SNX5 PX domain in complex with the SEMA4C sorting signal have been deposited at the PDB with the accession code 6N5Z. Supplementary Table 3 contains all of the raw data from the proteomic analysis shown in Fig. 7b,f. All of the other relevant raw data related to this study are available from the corresponding authors on request. The mass spectrometry data have been deposited in ProteomeXchange with the primary accession code PXD014927. The source data for Fig. 8a,d have been provided as Supplementary Table 3. All other data supporting the findings of this study are available from the corresponding author on reasonable request.

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Acknowledgements

This work was supported by the MRC (grant nos MR/L007363/1 and MR/P018807/1), the Wellcome Trust (grant no. 104568/Z/14/2), the Lister Institute of Preventive Medicine to P.J.C. and the Wellcome Trust PhD Studentship for the Dynamic Cell Biology programme (grant no. 083474) to B.S. B.M.C. is supported by an NHMRC Senior Research Fellowship (grant no. APP1136021) and the NHMRC (grant no. APP1099114), the Australian Research Council (grant no. DP160101743) and the Bright Focus Foundation (grant no. A2018627S). G.J.B. is supported by the National Institutes of Health (grant no. R35 NS097340). We thank the University of Queensland Remote Operation Crystallisation and X-ray facility and the staff for their support with the crystallization experiments, the staff of the Australian Synchrotron for assistance with X-ray diffraction data collection and the University of Bristol Wolfson Bioimaging Facility.

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Author notes

  1. The authors contributed equally: Boris Simonetti, Blessy Paul.

  2. These authors jointly supervised this work: Brett M. Collins, Peter J. Cullen.

Authors and Affiliations

  1. School of Biochemistry, University of Bristol, Bristol, UK

    Boris Simonetti & Peter J. Cullen

  2. Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia

    Blessy Paul, Saroja Weeratunga & Brett M. Collins

  3. Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA

    Karina Chaudhari, Madhavi Gorla & Greg J. Bashaw

  4. Center for Biological Systems Analysis (ZBSA), Faculty of Biology, Albert Ludwigs Universitaet Freiburg, Freiburg, Germany

    Florian Steinberg

  5. Proteomic Facility, School of Biochemistry, University of Bristol, Bristol, UK

    Kate J. Heesom

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Contributions

Initial conceptualization: B.S., F.S., B.M.C. and P.J.C. Evolution of conceptualization: B.S., B.P., S.W., F.S., G.J.B., B.M.C. and P.J.C. Formal analysis: K.J.H. Investigation: B.S., B.P., K.C., S.W., M.G., F.S. and K.J.H. Writing of the original draft: B.S., B.M.C. and P.J.C. Writing, review and editing: all authors. Funding acquisition: F.S., G.J.B., B.M.C. and P.J.C. Supervision: F.S., G.J.B., B.M.C. and P.J.C.

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Correspondence to Brett M. Collins or Peter J. Cullen.

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Integrated supplementary information

Supplementary Figure 1 Structures and electron density of the CI-MPR:SNX5 complex and comparison with the SNX5:IncE complex.

(A) For comparison the SNX5–IncE structure1 is shown in ribbon diagram (left panel), with a close-up of the bound IncE peptide in stick representation (right panel). (B) Comparison between the structures of SNX PX domain from the SNX5-IncE complex1, SNX32-IncE complex2 (PDB ID 6E8R2), SNX5–CI-MPR complex and the previously reported apo-SNX5 PX domain3 crystal structure (PDB ID 3HPB3).

Supplementary Figure 2 Comparison between the interactome and the surface proteome of SNX5 and SNX5(F136D).

(A) Schematics of the TMT-labelling based proteomics and the approach used to filter and analyse the datasets. Raw proteomic data is provided in Supplementary Table 3. (B) Gene names of the proteins whose relative enrichment was statistically different in the SNX5(F136D) interactome compared to the SNX5 interactome. Analysis of comparative interactome of wild-type SNX5 vs SNX5(F136D) mutant across n = 3 independent experiments using One-sample t-test and Benjamini–Hochberg FDR. The unprocessed original proteomic datasets and the corresponding analysis are provided in Supplementary Table 3. (C) Schematics of surface biotinylation coupled to the TMT-labelling based proteomics and the approach used to filter and analyse the datasets. (D) Gene names of the proteins whose relative enrichment was statistically decreased in the SNX5(F136D) surface proteome compared to that of SNX5 wild-type. Analysis was performed across n = 3 independent experiments using One-sample t-test and Benjamini–Hochberg FDR. The unprocessed original proteomic datasets and the corresponding analysis are provided in Supplementary Table 3.

Supplementary Figure 3 Unprocessed original scans of immunoblots.

Unprocessed images of all gels and blots.

Supplementary information

Supplementary Information

Supplementary Figures 1–3, Supplementary Table titles/legends and Supplementary References.

Reporting Summary

Supplementary Table 1

Binding parameters from ITC experiments.

Supplementary Table 2

Summary of crystallographic structure determination statistics.

Supplementary Table 3

Unprocessed original proteomics and analysis.

Supplementary Table 4

Statistics source data.

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Simonetti, B., Paul, B., Chaudhari, K. et al. Molecular identification of a BAR domain-containing coat complex for endosomal recycling of transmembrane proteins. Nat Cell Biol 21, 1219–1233 (2019). https://doi.org/10.1038/s41556-019-0393-3

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