Topological features of integrin adhesion complexes revealed by multiplexed proximity biotinylation

Chastney, Megan; Lawless, Craig; Humphries, Jonathan D.; Warwood, Stacey; Jones, Max; Knight, David; Jørgensen, Claus

doi:10.1083/jcb.202003038

Cited by 62 publications

(62 citation statements)

References 103 publications

(154 reference statements)

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“…1 E and Table S1 ; Dong et al, 2016 ). A similar overlap of adhesion proteins was also observed in the paxillin and kindlin-2 BioID datasets reported by Chastney et al (2020 ; Fig. S1 L and Table S1 ).…”

Section: Resultssupporting

confidence: 82%

mTORC1 activity is supported by spatial association with focal adhesions

Byron

Wirth

Madsen

et al. 2021

Journal of Cell Biology

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The mammalian target of rapamycin complex 1 (mTORC1) integrates mitogenic and stress signals to control growth and metabolism. Activation of mTORC1 by amino acids and growth factors involves recruitment of the complex to the lysosomal membrane and is further supported by lysosome distribution to the cell periphery. Here, we show that translocation of lysosomes toward the cell periphery brings mTORC1 into proximity with focal adhesions (FAs). We demonstrate that FAs constitute discrete plasma membrane hubs mediating growth factor signaling and amino acid input into the cell. FAs, as well as the translocation of lysosome-bound mTORC1 to their vicinity, contribute to both peripheral and intracellular mTORC1 activity. Conversely, lysosomal distribution to the cell periphery is dispensable for the activation of mTORC1 constitutively targeted to FAs. This study advances our understanding of spatial mTORC1 regulation by demonstrating that the localization of mTORC1 to FAs is both necessary and sufficient for its activation by growth-promoting stimuli.

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Section: Resultssupporting

confidence: 82%

mTORC1 activity is supported by spatial association with focal adhesions

Byron

Wirth

Madsen

et al. 2021

Journal of Cell Biology

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“…The use of proximity labelling by BioID [ 44 ] and mass spectrometry to define ‘adhesomes' has built up a comprehensive picture of their core components. We collated data from recently reported adhesomes for five major adhesion complexes: tight junctions [ 45 ], adherens junctions [ 46 ], hemidesmosomes [ 47 ], desmosomes [ 48 ] and focal adhesions [ 49 , 50 ]. We included an interactome of the mammalian Hippo signalling pathway [ 51 ], which links cell adhesion to transcriptional responses.…”

Section: Ptps and Cell Adhesion Complexesmentioning

confidence: 99%

Protein tyrosine phosphatases in cell adhesion

Young

Biggins

Sharpe

2021

Biochemical Journal

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Adhesive structures between cells and with the surrounding matrix are essential for the development of multicellular organisms. In addition to providing mechanical integrity, they are key signalling centres providing feedback on the extracellular environment to the cell interior, and vice versa. During development, mitosis and repair, cell adhesions must undergo extensive remodelling. Post-translational modifications of proteins within these complexes serve as switches for activity. Tyrosine phosphorylation is an important modification in cell adhesion that is dynamically regulated by the protein tyrosine phosphatases (PTPs) and protein tyrosine kinases. Several PTPs are implicated in the assembly and maintenance of cell adhesions, however, their signalling functions remain poorly defined. The PTPs can act by directly dephosphorylating adhesive complex components or function as scaffolds. In this review, we will focus on human PTPs and discuss their individual roles in major adhesion complexes, as well as Hippo signalling. We have collated PTP interactome and cell adhesome datasets, which reveal extensive connections between PTPs and cell adhesions that are relatively unexplored. Finally, we reflect on the dysregulation of PTPs and cell adhesions in disease.

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“…This article outlines only a few basic bioinformatic tools to interrogate proximity interaction networks. Various plugins are available in Cytoscape to interrogate networks, and datasets can be further examined through comparisons with PPI databases (e.g., BioGRID, STRING), published adhesomes (Horton et al, 2015;Winograd-Katz, Fässler, Geiger, & Legate, 2014), and other proximity interaction studies (Chastney et al, 2020;Dong et al, 2016).…”

Section: Understanding Resultsmentioning

confidence: 99%

“…Since its development, BioID has become a popular method to screen for proximal interactors, on scales ranging from individual proteins and complexes to large-scale network mapping initiatives (Chastney et al, 2020;Dong et al, 2016;Gupta et al, 2015;Roux et al, 2012;Youn et al, 2018). BioID uses a promiscuous mutant biotin ligase (BirA R118G; BirA*) from E. coli, fused to a protein of interest, to label proximal proteins (Roux et al, 2012).…”

Section: Commentary Background Informationmentioning

confidence: 99%

“…Nevertheless, BioID has proven effective for examining proximal interactors of individual proteins and larger complexes that are typically difficult to study, such as cell-cell contacts, the centrosome, and IACs (Chastney et al, 2020;Dong et al, 2016;Gupta et al, 2015;Van Itallie et al, 2013). In larger-scale network mapping studies, multiplexed BioID has been used to reveal the spatial relationships between components of large complexes, and even between multiple organelles (Chastney et al, 2020;Go et al, 2019;Gupta et al, 2015;Youn et al, 2018). In such initiatives, careful analysis is required to interpret the data and to infer potential biological insight.…”

Section: Commentary Background Informationmentioning

confidence: 99%

See 1 more Smart Citation

Multiplexed Proximity Biotinylation Coupled to Mass Spectrometry for Defining Integrin Adhesion Complexes

2020

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BioID, a proximity biotinylation technique, offers a valuable approach to examine the interactions occurring within protein complexes that complements traditional protein biochemical methods. BioID has various advantages that are beneficial to the study of complexes, including an ability to detect insoluble and transient proteins. We have applied BioID to the study of integrin adhesion complexes (IACs), which are located at the junction between the plasma membrane and actin cytoskeleton. The use of multiple BioID baits enables a complex‐wide, spatial annotation of IACs, which in turn facilitates the detection of novel proximal interactors and provides insights into IAC architecture. This article describes the labeling and affinity purification of IAC‐proximal proteins and their analysis by label‐free quantitative mass spectrometry. The article also outlines steps to identify high‐confidence proximity interactors, and to interrogate the topology and functional relevance of proximity interaction networks through bioinformatic analyses. © 2020 The Authors. Basic Protocol 1: Proximity biotinylation of integrin adhesion complex components Basic Protocol 2: Mass spectrometry data processing by MaxQuant and detection of high‐confidence proximal interactors Basic Protocol 3: Bioinformatic analysis and data visualization

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Topological features of integrin adhesion complexes revealed by multiplexed proximity biotinylation

Cited by 62 publications

References 103 publications

mTORC1 activity is supported by spatial association with focal adhesions

mTORC1 activity is supported by spatial association with focal adhesions

Protein tyrosine phosphatases in cell adhesion

Multiplexed Proximity Biotinylation Coupled to Mass Spectrometry for Defining Integrin Adhesion Complexes

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