Dataset Information

In-situ proximity labeling of proteins associated with specific circRNA and RNA G-quadruplex

ABSTRACT: We developed a method named TAPRIP (TurboID-Assisted Proximity labeling of targeted RNA Interacting Proteins.

ORGANISM(S): Homo Sapiens

SUBMITTER: Xiang Zhou

PROVIDER: PXD060240 | iProX | Mon Jan 27 00:00:00 GMT 2025

REPOSITORIES: iProX

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Publications

Proteomics Landscape of Host-Pathogen Interaction in Acinetobacter baumannii Infected Mouse Lung.

Li Xin X Liu Xiaofen X Horvatovich Peter P Hu Yingwei Y Zhang Jing J

Frontiers in genetics 20210507

Acinetobacter baumannii is an important pathogen of nosocomial infection worldwide, which can primarily cause pneumonia, bloodstream infection, and urinary tract infection. The increasing drug resistance rate of A. baumannii and the slow development of new antibacterial drugs brought great challenges for clinical treatment. Host immunity is crucial to the defense of A. baumannii infection, and understanding the mechanisms of immune response can facilitate the development of ...[more]

PMID: 34025711

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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.

Dataset Information

In-situ proximity labeling of proteins associated with specific circRNA and RNA G-quadruplex

Publications

Proteomics Landscape of Host-Pathogen Interaction in <i>Acinetobacter baumannii</i> Infected Mouse Lung.

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