Proximity-Dependent Protein Biotinylation

This volume explores the cutting-edge of proximity-dependent protein biotinylation approaches, focusing on innovative biotin ligase (BioID) and peroxidase-based methods, like APEX. Spanning a diverse array of biological systems, including bacteria, zebrafish, plants, and mammals, this collection showcases methods that aid in the identification of protein interactions, localization, membrane topology, trafficking, and secretion dynamics. Additionally, the book features applications at the host/microbe interface and for the use of tissue-specific biotinylation for studying interorgan communication, as well as in silico validation methods. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, detailed lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and expert tips for troubleshooting and avoiding known pitfalls.

Authoritative and practical, Proximity-Dependent Protein Biotinylation: Methods and Protocols serves as an essential guide for researchers advancing the study of proxeome biology.

Cross-Species Proximity-Dependent Protein Biotinylation: A Standardized Approach for Mapping Proxeomes. - BioID in Bacteria: Selection of a Suitable Biotin Ligase for Proxeome Mapping. - Uncovering Transient Protein Interactions in the Yersinia enterocolitica Type III Secretion System Using MiniTurbo-Mediated Proximity Labeling. - Exploring Bacterial Surface Proteome Dynamics During Infection Using Proximity Labeling. - Identification of In Vivo Protein Networks Using MiniTurbo Proximity Labeling in Bacteria. - Unraveling N-Terminal Proteoform Interactomes via Multiplexed Recombineering in Salmonella. - Probing Pairwise Protein-Protein Interactions with the Bacterial POLAR Assay. - Detection and Quantification of Biotinylated Proteins for TurboID-Based Proximity Labeling Mass Spectrometry in Arabidopsis. - Detection and Quantification of Biotinylated Sites for TurboID-Based Proximity Labeling Mass Spectrometry in Arabidopsis. - Coupling Affinity Purification with Proximity Labeling in Arabidopsis: The APEAL Approach. - Characterization of the Protein Interactome of Membrane-Bound Transcription Factors Using TurboID-Based Proximity Labeling In Planta. - Identification of Cytosol-Facing Organelle Membrane-Proximal Proteins via Proximity-Dependent Biotinylation. - BioID2-Based Proximity Labeling in Adult Zebrafish. - On-Demand Proximity Labeling Using Light-Activated BioID. - Tissue-Specific Biotinylation for Interorgan Communication. - Spatiotemporally-Resolved Profiling of Protein Movement by TransitID. - An Integrated High-Throughput Proteocistromic Framework for Mapping the Interactome and Targetome of Human Transcription Factors. - Step-by-Step Application of Proximity-Dependent Biotinylation Tools for Identification of Astrocyte and Neuron Subproteomes In Vivo Across the Whole Brain. - Antibody-Mediated Protein A-APEX2 Labeling (AMAPEX) for Proximity Proteome Exploration. - A Ready-to-Use Data Analysis Pipeline for BioID Experiments Using Data-Dependent or Data-Independent Acquisition Mass Spectrometry.