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Selective integrin endocytosis is driven by interactions between the integrin α-chain and AP2

Nature Structural & Molecular Biology volume 23, pages 172–179 (2016)Cite this article

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An Erratum to this article was published on 06 February 2017

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Abstract

Integrins are heterodimeric cell-surface adhesion molecules comprising one of 18 possible α-chains and one of eight possible β-chains. They control a range of cell functions in a matrix- and ligand-specific manner. Integrins can be internalized by clathrin-mediated endocytosis (CME) through β subunit–based motifs found in all integrin heterodimers. However, whether specific integrin heterodimers can be selectively endocytosed was unknown. Here, we found that a subset of α subunits contain an evolutionarily conserved and functional YxxΦ motif directing integrins to selective internalization by the most abundant endocytic clathrin adaptor, AP2. We determined the structure of the human integrin α4-tail motif in complex with the AP2 C-μ2 subunit and confirmed the interaction by isothermal titration calorimetry. Mutagenesis of the motif impaired selective heterodimer endocytosis and attenuated integrin-mediated cell migration. We propose that integrins evolved to enable selective integrin-receptor turnover in response to changing matrix conditions.

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Figure 1: Evolutionarily conserved Yxxφ motif defines a subset of integrin α-chains.
Figure 2: Structural analysis of the integrin α4–AP2 C-μ2 complex.
Figure 3: Yxxφ motif controls integrin recruitment to CCPs.
Figure 4: Yxxφ motif regulates integrin α2 and α4 endocytosis.
Figure 5: Introduction of the Yxxφ motif induces endocytosis of integrin αV.
Figure 6: Yxxφ mutagenesis impairs cell migration mediated by α2 and α4 integrin.

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  • 08 December 2016

    In the version of this article initially published, the x-axis of the bottom left graph in Figure 4d was incorrectly labeled as showing time in minutes; in actuality, the data in the graph align with the conditions indicated for the blot images above. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

M. Humphries (University of Manchester), R. Horwitz (University of Virginia), A. Helenius (Swiss Federal Institute of Technology (ETH)), M. Davidson (Florida State University), M. Robinson (University of Cambridge Institute for Medical Research (CIMR)) and S. Johansson (Uppsala University) are acknowledged for plasmids and cells, and S. Miller (CIMR) is acknowledged for assistance with ITC. We thank J. Siivonen, and P. Laasola for excellent technical assistance, H. Baghirov for help with the image analysis and M. Laasola for graphics generation; Turku Centre for Biotechnology Imaging Core facility and M. Saari for help with imaging; and H. Hamidi for scientific writing and editing of the manuscript. We gratefully acknowledge the following funding sources: N.D.F., FinPharma Doctoral Program, Instrumentarium Foundation, Orion Research Foundation, Liv och Halsa Foundation, Finsk-Norska Medicinska Stiftelsen and the Magnus Ehrnrooth Foundation; and J.I., Academy of Finland CoE, European Research Council Consolidator Grant, the Sigrid Juselius Foundation, the Finnish Heart Foundation and the Finnish Cancer Organizations. D.J.O., A.G.W. and T.W. are funded by Wellcome Trust fellowship 090909 (D.J.O.).

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Authors and Affiliations

  1. Turku Centre for Biotechnology, University of Turku, Turku, Finland

    Nicola De Franceschi, Antti Arjonen, Jeroen Pouwels & Johanna Ivaska

  2. Institut Gustave Roussy, Villejuif, France

    Nadia Elkhatib & Guillaume Montagnac

  3. Institut National de la Santé et de la Recherche Médicale (INSERM), U1170, Villejuif, France

    Nadia Elkhatib & Guillaume Montagnac

  4. Department of Biosciences, Åbo Akademi University, Turku, Finland

    Konstantin Denessiouk

  5. Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK

    Antoni G Wrobel, Thomas A Wilson & David J Owen

  6. Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland

    Johanna Ivaska

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Contributions

J.I. supervised the cell-biological part of the study, carried out experiments, analyzed the data and wrote the manuscript with the contribution of N.D.F., G.M. and D.J.O. A.G.W., T.A.W. and D.J.O. carried out the ITC and crystallography. N.D.F. conceived the study and designed, carried out and analyzed most of the experiments with crucial help from A.A., N.E. and J.P. N.D.F. and K.D. carried out the evolutionary studies.

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Correspondence to Johanna Ivaska.

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Integrated supplementary information

Supplementary Figure 1 Evolutionary and splicing analysis of Yxxφ-motif distribution.

a: Comparison of the distribution of the Yxxφ motif across integrin α-subunits in Homo Sapiens and Clupeocephala. b: Alignment of membrane proximal and cytoplasmic region of splice variants of α3, α6 and α7 integrins from Homo Sapiens. Uniprot accession codes are indicated; the Yxxφ motif is highlighted in red. c: Residue variation across 6 mammals in membrane-proximal and cytoplasmic region of ITAD, ITAE, ITAM, ITAX (organisms: Homo Sapiens, Mus Musculus, Canis Familiaris, Equus Caballus, Sus Scrofa, Bos Taurus). Values on the Y-axis indicate the number of substitution for each residue. d: Residue variation across 10 organisms in membrane-proximal and cytoplasmic region of ITA2 and ITA4 (Homo Sapiens, Mus Musculus, Canis Familiaris, Equus Caballus, Sus Scrofa, Bos Taurus, Gallus Gallus, Xenopus Tropicalis, Anolis Carolinensis and Danio Rerio). Asterisks indicate substitutions that are compatible with the Yxxφ motif.

Supplementary Figure 2 Characterization of C-μ2 interaction with α-integrins.

a: Purification of recombinant C-μ2. Enrichment of AP2µ in subsequent purification steps is shown, along with immunoblot with AP2μ Ab. b: Sequences of the peptides used in this study. c: Pulldown assay with recombinant C-μ2and integrin biotinylated peptides. Equal amount of AP2μ and equimolar peptide concentrations were added to each sample. Neg. CTRL= beads alone. Tenfold excess of soluble, unlabelled α2 peptide was pre-incubated with AP2μ CT. d: Representative isothermal titration calorimetry of integrin α2 peptide binding to C-μ2 (magenta). No detectable binding was seen for integrin α5 peptide (black). e: Proximity Ligation assay between endogenous AP2 and endogenous α5 integrin.

Supplementary Figure 3 Controls and additional information.

Related to Figures 2 and 3. a: Modelling of a tyrosine-phosphorylated integrin α4 peptide (yellow backbone) in the C-μ2 binding pocket. The phosphate head group of pY1009 (red) would not fit in the binding pocket. b: Co-endocytosis of AP2μ and endogenous α2-integrin in MDA-MB-231 cells expressing AP2μ-mCherry labelled with α2-integrin antibody (MCA2025) during live cell imaging. TIRF plane is shown. Dynamics of AP2μ-RFP and endogenous α2-integrin co-endocytosis was measured with live cell TIRFM over a 100 sec period. Fluorescence intensities of a single AP2μ positive pit were plotted over time. c: Sequence of the membrane-proximal and cytoplasmic domains of GFP-tagged integrin constructs used in this study. d: Surface α2 integrin levels detected by antibody labeling and fluorescence-activated cell sorting (FACS) analysis on HeLa cells. Solid red: Control IgG. Black line: GFP α2 WT cells stained with anti-α2 antibody; blue line: GFP α2 AxxA stained with anti-α2 antibody. GFP-positive cells were gated. e: Surface α4 integrin levels detected by antibody labeling and fluorescence-activated cell sorting (FACS) analysis on HeLa cells. Solid red: Control IgG. Black line: GFP α4 WT stained with anti-α4 antibody; blue line: GFP α4 AxxA stained with anti-α4 antibody. GFP-positive cells were gated.

Supplementary Figure 4 Subcellular localization of α2-GFP WT or AxxA mutant.

Co-localization analysis of α2-GFP WT or AxxA mutant in HEK293 cells labelled with the ER-TrackerTM or overexpressing different Rab GTPases as indicated. Yellow boxes indicate the regions of interest (ROI) enlarged in the black and white images. Arrows point to areas of overlapping signal. Images are single planes from confocal stacks acquired with 63x magnification.

Supplementary Figure 5 Controls and additional information.

Related to Figures 4 and 5. a: Western blot analysis of AP2μ, α2-integrin and tubulin levels in AP2μ and control siRNA transfected HeLa cells. b: AP2μ or control silenced HeLa cells stained for endogenous AP2 α-adaptin (white) and dapi (blue). c: Biotin-based endocytosis assays in HEK293 cells transfected with GFP-tagged α2-integrin WT or AxxM mutant. Biotin signal was normalized against total α2 amount measured from the GFP blot. Time point: 15 minutes (mean±SEM; n=3; *, p<0.05 (unpaired Student’s t test; 2-tails distribution)). d: Biotin-based endocytosis assays in HEK293 cells expressing either GFP-tagged α4-integrin WT or AxxA mutant in the presence or absence of primaquine treatment. Biotin signal was normalized against total α4 amount measured from the GFP blot. Time point: 15 minutes. Bars indicate mean±s.e.m.; n=4 (n=biological replicates, each one being an independent cell culture); *, p<0.05 (unpaired Student’s t test; 2-tails distribution). e: Antibody-based endocytosis assay using PLA to detect the active or inactive α2β1 heterodimers in AP2μ silenced background. Endocytosis of α2 was allowed for 15 min after which cells were fixed, permeabilized and counterstained with active and inactive epitope recognizing anti-β1 antibodies (clones 12G10 and 4B4, respectively). The endocytosed PLA signal was normalized against total cell surface α2β1 levels (α2+4B4 for inactive and α2+12G10 for active heterodimers). Bars indicate mean±s.e.m.; n=2 (n=biological replicates, each one being an independent cell culture. In total, 120–144 cells were analyzed for each condition); ***, p<0.0001 (Mann Whitney test; 2-tails distribution). f: Biotin-based endocytosis assays in HEK293 cells expressing GFP-tagged α5-integrin WT or AxxxA mutant. Endocytosis was allowed for 10 min and biotin signal was normalized against total α5 amount measured from the GFP blot. n=3 (n=biological replicates, each one being an independent cell culture). g: Western blot analysis of AP2μ, α2-integrin and tubulin levels in HEK293 stably expressing AP2μ-myc WT or F174A/D176S mutant. h: Western blot analysis of AP2μ, α2-integrin and tubulin levels in HEK293 stably expressing AP2μ-myc WT or F174A/D176S mutant and transfected with control or AP2μ siRNA. i: Surface α2 integrin levels detected by antibody labeling and fluorescence-activated cell sorting (FACS) analysis on GD25b1A cells. Solid red: α2 Ab staining of non-transfected cells. Red line: α2-GFP WT-gated cells; blue line: α2-GFP AxxA-gated cells. j: Surface α4 integrin levels detected by antibody labeling and fluorescence-activated cell sorting (FACS) analysis on GD25b1A cells. Solid red: α4 Ab staining of non-transfected cells. Red line: α4-GFP WT-gated cells; blue line: α4-GFP AxxA-gated cells. k: Retraction fibers in HEK293 cells plated on collagen I and expressing either α2-GFP WT or AxxA mutant.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 (PDF 1407 kb)

Supplementary Data Set 1

Uncropped blots (PDF 197 kb)

AP2μ–integrin α2 coendocytosis event

Single ROI of AP2μ positive clathrin pit is shown (2μm square). MDA-MB-231 cells were transfected with AP2μ-mCherry and endogenous α2-integrin was labelled using antibody (MCA2025). TIRF images were captured in 1s intervals. Movie is shown 20FPS. (AVI 121 kb)

Localization and dynamics of α2-GFP WT

Single plane of a HEK 293 cell plated on collagen I-coated glass-bottom dish. Localization and dynamics of α2-GFP WT-positive vesicles are shown. (AVI 997 kb)

Localization and dynamics of α2-GFP AxxA

Single plane of a HEK 293 cell plated on collagen I-coated glass-bottom dish. Membrane localization and dynamics of α2-GFP AxxA at lamellipodium are shown. (AVI 1654 kb)

HEK 293 cell expressing α2-GFP WT spreading on collagen I

Bottom plane of a HEK 293 cell expressing α2-GFP WT spreading on Collagen I. α2-GFPpositive vesicles and dynamic tubular compartments are visible. (AVI 5234 kb)

HEK 293 cell expressing α2-GFP AxxA spreading on collagen I

Bottom plane of a HEK 293 cell expressing α2-GFP AxxA spreading on Collagen I. Plasma membrane localization of α2-GFP is shown. (AVI 2963 kb)

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De Franceschi, N., Arjonen, A., Elkhatib, N. et al. Selective integrin endocytosis is driven by interactions between the integrin α-chain and AP2. Nat Struct Mol Biol 23, 172–179 (2016). https://doi.org/10.1038/nsmb.3161

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