Transmembrane PhoxID: photoproximity labelling across the plasma membrane in vivo
Abstract
Transmembrane proteins perform essential roles in cellular transport, signalling, and communication. The function and dynamics of these proteins are precisely regulated by interactions on both sides of the plasma membrane; thus, mapping the composition of these interactomes is a fundamental challenge in molecular biology. Proximity labelling methods are powerful tools for this purpose; however, existing approaches that rely on membrane-impermeable reactive species generally focus on either the extracellular or the intracellular region of transmembrane proteins. Here, we capitalise on the membrane permeability of singlet oxygen to carry out simultaneous proximity labelling of both the extra- and intracellular sides of transmembrane proteins using an extracellularly anchored photosensitiser. We apply this method, termed transmembrane PhoxID (tmPhoxID), to several receptors (GRID2, GABAAR, and GRM1) in the living mouse brain and successfully determine their specific membrane-proximal intracellular interactomes. Notably, network analysis of the identified proteins reveals that this method can characterise the native components of transsynaptic nanocolumns formed at parallel fibre-Purkinje cell synapses. Furthermore, our study reveals a previously uncharacterised GABAAR-CAMKV interaction in mice and human brains. Our results provide a proof of concept for transmembrane and transcellular proximity labelling, establishing a powerful platform for analysing the interactomes of transmembrane proteins.
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BibTeX
@article{valor2026transmembrane,
title = {{Transmembrane PhoxID: photoproximity labelling across the plasma membrane in vivo}},
author = {Fátima Yuri Tanimura Valor and Mikiko Takato and Ayane Araki and Seiji Sakamoto and Tomonori Tamura and Itaru Hamachi},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-78135-2},
url = {https://www.nature.com/articles/s41467-026-78135-2},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Transmembrane PhoxID: photoproximity labelling across the plasma membrane in vivo
AU - Fátima Yuri Tanimura Valor
AU - Mikiko Takato
AU - Ayane Araki
AU - Seiji Sakamoto
AU - Tomonori Tamura
AU - Itaru Hamachi
PY - 2026
DA - 2026/10/05
JO - Nature Communications
DO - 10.1038/s41467-026-78135-2
UR - https://www.nature.com/articles/s41467-026-78135-2
AB - Transmembrane proteins perform essential roles in cellular transport, signalling, and communication. The function and dynamics of these proteins are precisely regulated by interactions on both sides of the plasma membrane; thus, mapping the composition of these interactomes is a fundamental challenge in molecular biology. Proximity labelling methods are powerful tools for this purpose; however, existing approaches that rely on membrane-impermeable reactive species generally focus on either the extracellular or the intracellular region of transmembrane proteins. Here, we capitalise on the membrane permeability of singlet oxygen to carry out simultaneous proximity labelling of both the extra- and intracellular sides of transmembrane proteins using an extracellularly anchored photosensitiser. We apply this method, termed transmembrane PhoxID (tmPhoxID), to several receptors (GRID2, GABAAR, and GRM1) in the living mouse brain and successfully determine their specific membrane-proximal intracellular interactomes. Notably, network analysis of the identified proteins reveals that this method can characterise the native components of transsynaptic nanocolumns formed at parallel fibre-Purkinje cell synapses. Furthermore, our study reveals a previously uncharacterised GABAAR-CAMKV interaction in mice and human brains. Our results provide a proof of concept for transmembrane and transcellular proximity labelling, establishing a powerful platform for analysing the interactomes of transmembrane proteins.
SN - 2041-1723
ER -