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Interrogating kinase-substrate relationships with proximity labeling and phosphorylation enrichment

ABSTRACT: Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase “ON” and kinase “OFF” conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification. TMT1: pAPEX-MAPK1 experiment in HEK293T cells TMT2: pAPEX-MAPK1 experiment in HCT116 cells TMT3: pAPEX-PKA experiment in HEK293T cells

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Tian Zhang

LAB HEAD: Steven Gygi

PROVIDER: PXD028150 | Pride | 2022-03-11

REPOSITORIES: Pride

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			Action	DRS
	TMT1_phos_1.mzIdentML	Mzid
	TMT1_phos_1.raw	Raw
	TMT1_phos_2.mzIdentML	Mzid
	TMT1_phos_2.raw	Raw
	TMT1_phos_3.mzIdentML	Mzid

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Interrogating kinase-substrate relationships with proximity labeling and phosphorylation enrichment

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