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Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development

ABSTRACT: This entry contains 45 raw files from proteomic experiments involving TurboID-based proximity labeling (TurboID-PL, 9 samples with 2 injection replicates each, totaling 18 raw files) and HA-tagged affinity purification mass spectrometry (HA-AP, 9 samples with 3 injection replicates each, totaling 27 raw files). Arabidopsis tissues were used for both TurboID-PL and HA-AP. The ERECTA-TurboID (E) sample group served as the experimental group, with Lit6B-TurboID (L) and er-105 mutant (m) serving as negative controls. All samples were digested with trypsin, and LC-MS/MS analysis was performed by Dr. Marcotte lab to identify ERECTA-associated protein complexes.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702)

SUBMITTER: Keiko Torii

PROVIDER: MSV000096929 | MassIVE | Fri Jan 24 07:44:00 GMT 2025

SECONDARY ACCESSION(S): PXD060161

REPOSITORIES: MassIVE

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Project description:Classical methods of investigating protein-protein interactions (PPIs) are generally performed in non-living systems, yet in recent years new technologies utilizing proximity labeling (PL) have given researchers the tools to explore proximal PPIs in living systems. PL has distinct advantages over traditional protein interactome studies, such as the ability to identify weak and transient interactions in vitro and in vivo. Most PL studies are performed on targets within or on the cell membrane. We have adapted the original PL method to investigate PPIs within the extracellular compartment, using both BioID2 and TurboID, that we term extracellular PL (ePL). To demonstrate the utility of this modified technique, we investigate the interactome of the widely expressed matrisome protein Tissue inhibitors of metalloproteinases 2 (TIMP2). Tissue inhibitors of metalloproteinases (TIMPs) are a family of multi-functional proteins that were initially defined by their ability to inhibit the enzymatic activity of metalloproteinases (MPs), the major mediators of extracellular matrix (ECM) breakdown and turnover. TIMP2 exhibits a broad expression profile and is often abundant in both normal and diseased tissues. Understanding the functional transformation of matrisome regulators, like TIMP2, during the evolution of tissue microenvironments associated with disease progression is essential for the development of ECM targeted therapeutics. Using carboxyl- and amino-terminal fusion proteins of TIMP2 with BioID2 and TurboID, we describe the TIMP2 proximal interactome. We also illustrate how the TIMP2 interactome changes in the presence of different stimuli, in different cell types, in unique culture conditions (2D vs 3D), and with different reaction kinetics (BioID2 vs. TurboID); demonstrating the power of this technique versus classical PPI methods. We propose that the screening of matrisome targets in disease models using ePL will reveal new therapeutic targets for further comprehensive studies.

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Comparative Proteomic Profiling of Receptor Kinase Signaling Reveals Key Trafficking Components Enforcing Plant Stomatal Development

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