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Structural basis for membrane targeting of the BBSome by ARL6

Nature Structural & Molecular Biology volume 21, pages 1035–1041 (2014)Cite this article

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Abstract

The BBSome is a coat-like ciliary trafficking complex composed of proteins mutated in Bardet-Biedl syndrome (BBS). A critical step in BBSome-mediated sorting is recruitment of the BBSome to membranes by the GTP-bound Arf-like GTPase ARL6. We have determined crystal structures of Chlamydomonas reinhardtii ARL6–GDP, ARL6–GTP and the ARL6–GTP–BBS1 complex. The structures demonstrate how ARL6–GTP binds the BBS1 β-propeller at blades 1 and 7 and explain why GTP- but not GDP-bound ARL6 can recruit the BBSome to membranes. Single point mutations in the ARL6-GTP-BBS1 interface abolish the interaction of ARL6 with the BBSome and prevent the import of BBSomes into cilia. Furthermore, we show that BBS1 with the M390R mutation, responsible for 30% of all reported BBS disease cases, fails to interact with ARL6–GTP, thus providing a molecular rationale for patient pathologies.

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Figure 1: Structure of the Chlamydomonas reinhardtii ARL6ΔN–GTP–BBS1N complex.
Figure 2: Structural basis of the ARL6-BBS1 interaction.
Figure 3: Disruption of the ARL6-BBS1 interface prevents recruitment of the BBSome to cilia.
Figure 4: Nucleotide-dependent conformational changes in CrARL6.
Figure 5: HsBBS1 M390R disease mutant does not bind HsARL6–GTP.
Figure 6: Structural comparison of membrane recruitment of coating complexes by Arf, Sar and Arf-like proteins.

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Acknowledgements

We thank the staff at Swiss Light Source for guidance with X-ray diffraction data collection, the biochemistry core facility and the crystallization facility of the Max Planck Institute of Biochemistry (MPI-B, Munich) for access to crystallization screening and the Bavarian NMR Center for NMR measurement time. We also thank I.B. Schaefer (MPI-B) for DNA encoding BBS subunits, S. Wachter (MPI-B) for assistance with GTPase assays and M. Taschner (MPI-B) for expert advice on protein production from insect cells and for carefully reading the manuscript. This work was funded by an Emmy Noether grant (Deutsche Forschungsgemeinschaft; LO1627/1-1), by the European Research Council (grant 310343) and by the European Molecular Biology Organization Young Investigator program. A.R.N. was supported by the Fayez Sarofim Fellowship of the Damon Runyon Cancer Research Foundation (DRG 2160-13). This work was supported by a grant to M.V.N. from the NIH/National Institute of General Medical Sciences (R01GM089933).

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Authors and Affiliations

  1. Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany

    André Mourão & Esben Lorentzen

  2. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA

    Andrew R Nager & Maxence V Nachury

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  1. André Mourão
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Contributions

A.M. carried out the protein biochemistry and structural biology under the supervision of E.L.; A.R.N. carried out the pulldown experiments of native BBSome with wild-type and mutant ARL6 and the cell biology experiments under the supervision of M.V.N.; A.M. and E.L. designed the experiments and wrote the paper with input from A.R.N. and M.V.N.

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Correspondence to Esben Lorentzen.

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Integrated supplementary information

Supplementary Figure 1 Purification and Kd determination for ARL6ΔN–BBS1N complexes.

Binding experiments of HsARL6Q73LΔN to (a) HsBBS1N, (b) HsBBS1NE234K, (c) HsBBS1NM390R and (d) CrBBS1N. Left panel shows size exclusion chromatography profiles, the central panel the corresponding SDS gel and the right panel the ITC titration experiments. Stable ARL6ΔN-BBS1N complexes are observed in all cases except for the HsBBS1NM390R protein. The HsBBS1NM390R variant was soluble and eluted as a broad peak with a maximal A280 absorption at ~9.5-10.0ml (void volume where aggregated proteins elute is 7.5ml on the S200 column). Reported Kd values are the average of 3 independent experiments.

Supplementary Figure 2 Comparison of ARL6 structures and electron density for CrARL6–GTP–CrBBS1N and GDP or GTP nucleotides.

(a) Structural comparison of ARL6ΔN–GTP from different organisms, Chlamydomonas reinhardtii (green), Homo sapiens (cyan) and Trypanosoma brucei (pink) shows structural similarities between the three proteins. (b) The structures of CrARL6ΔN–GTP (orange) and CrARL6ΔN–GTP (green) from the BBS1N complex superimpose with an RMSD of 0.4Å. (c) Structures of CrARL6ΔN–GDP and Arf1–GDP (PDB code: 1HUR) superposed show a similar conformation of the interswitch region. The N-terminal amphipathic helix rests on the G-domain of Arf1. (d) Structures of CrARL6ΔN–GTP and Arf1–GTP (PDB code: 2KSQ 32) superposed show a similar conformation of the interswitch region. The N-terminal amphipathic helix is expelled from the G-domain of Arf1 and available for membrane association. (e) Structure of the CrARL6ΔN–GTP–CrBBS1N complex in transparent surface representation with the polypeptides also displayed as cartoon and the GTP molecule as sticks. CrARL6ΔN–GTP and BBS1N have been pull apart by 10Å in silico to allow visualization of the small but complementary interaction interface of 600Å2 (calculated using PISA server; Krissinel, E. & Henrick, K, J. Mol. Biol. 372, 774–797, 2007).). (f) Experimental electron density map at 1σ obtained by the MR-SAD protocol in Phaser using four molecules of CrARL6ΔN–GTP found by MR and 35 Hg sites. The final model for CrARL6 (yellow) and CrBBS1 (magenta) are displayed as Cα traces. Difference maps (Fo-Fc, 3σ) calculated using model phase before the addition of nucleotides to the model is shown in green for (g) GTP in CrARL6ΔN–GTP–CrBBS1N (h) GTP in CrARL6ΔN–GTP and (i) GDP in CrARL6ΔN–GDP. All structure figures were made using PYMOL (www.pymol.org) and electron density maps were obtained from Coot 51.

Supplementary Figure 3 Structure-based multiple sequence alignment.

Multiple sequence alignment of (a) BBS1 and (b) ARL6 proteins from Chlamydomonas reinhardtii, Homo sapiens, Danio rerio, Xenopus tropicalis and Caenorhabditis elegans using the Clustal omega server (http://www.clustal.org/omega/). Secondary structure elements derived from the CrARL6ΔN–GTP–CrBBS1N complex structure are shown above the sequences. Conservative substitutions are shown in red font and and identical residues in white font on a red background. Interacting residues between ARL6 and BBS1 are shown with a blue asterisk (hydrophobic) or a red asterisk (hydrophilic). The alignments were generated using the ESPript server (http://espript.ibcp.fr/).

Supplementary Figure 4 SEC and GTP binding by BBS1 and ARL6 point mutants.

(a) (left) SEC elution profile of structure-based HsBBS1N point-mutations and (right) the corresponding SDS gel. (b) (left) SEC elution profile of structure-based HsARL6ΔN point-mutations and (right) the corresponding SDS gel. All HsBBS1N and HsARL6ΔN mutants elute as symmetric peaks at the same elution volume as the WT proteins and are thus folded. Superpositioning of 1D-1H-NMR spectra of (c) WT, (d) R77A, (e) L100E and (f) R108A HsARL6ΔN without nucleotide (blue) and titrated with a 1.2 excess of GTP (red). The regions of the spectra that corresponds to amide and the methyl groups are shown in the green and purple boxes, respectively. The spectra demonstrate that the mutants are folded and chemical shift perturbations (highlighted by arrows) indicate that ARL6 mutants bind GTP.

Supplementary Figure 5 GTPase assay for CrARL6ΔN and CrARL6ΔN–CrBBS1N.

(a)The GTPase activity was measured in a phosphate release assay using the EnzCheck Phosphate kit (Invitrogen). 1mM GTP was incubated with buffer (neg. control) or with 50μM of CrARL6ΔN or CrARL6ΔN-CrBBS1N and the release of inorganic phosphate was followed over the course of 20min. The experiment shows that CrBBS1N does not enhance the GTPase activity of CrArL6ΔN. In the positive control, the conversion of 100μM inorganic phosphate was followed. Curves for CrARL6ΔN and CrARL6ΔN-CrBBS1N are the average of 3 independent experiments.

Supplementary Figure 6 BBS1 disease-mutation pulldowns with GST-HsARL6.

WB using anti-His antibody for a GST pull-down experiments of GST-HsARL6 Q73L with His-tagged HsBBS1N, HsBBS1E234K or HsBBS1M390R shows that ARL6 interacts with wild-type and the E234K mutant, but not with the M390R BBS1N mutant protein (even though the His-HsBBS1NM390R was added in large excess).

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Supplementary Data Set 1

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Mourão, A., Nager, A., Nachury, M. et al. Structural basis for membrane targeting of the BBSome by ARL6. Nat Struct Mol Biol 21, 1035–1041 (2014). https://doi.org/10.1038/nsmb.2920

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