4.6 Review

Proximity Labeling Techniques: A Multi-Omics Toolbox

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Developmental Biology

Proximity-dependent labeling methods for proteomic profiling in living cells: An update

Justin A. Bosch et al.

Summary: Proteome composition of organelles and subcellular regions can be analyzed using proximity labeling-based methods coupled with mass spectrometry (MS) to understand cellular organization and protein interactome networks. These methods utilize enzymes that generate reactive radicals to covalently tag neighboring proteins, allowing for systematic analysis of spatially restricted proteomes. By fusing enzymes to specific proteins or signal peptides targeting to particular subcellular regions, spatial expression can be achieved for studying protein-protein interactions or identifying components in discrete subcellular compartments.

WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Cell type-selective secretome profiling in vivo

Wei Wei et al.

Summary: This study introduced a proximity biotinylation strategy to label, detect, and enrich secreted polypeptides in a cell type-selective manner in mice, resulting in a proteomic atlas of secretomes from various cell types. The research confirmed known cell type-protein pairs, identified new secreted polypeptides distinguishing between cell types, and uncovered a dynamic nutrient-dependent reprogramming of hepatocyte secretome. The strategy enables dynamic and cell type-specific dissection of the plasma proteome and intercellular signaling mediators.

NATURE CHEMICAL BIOLOGY (2021)

Article Multidisciplinary Sciences

Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics

Mi Ke et al.

Summary: By developing more selective proximity labeling probes and combining them with label-free quantitative proteomics, the study enables exploration of cytosolic protein assemblies, such as phosphotyrosine-mediated protein complexes formed in response to minute-scale EGF stimulation. The authors demonstrate the application of this method in profiling the spatiotemporal interactome of the EGFR signaling component STS1.

NATURE COMMUNICATIONS (2021)

Article Cell Biology

PUPIL enables mapping and stamping of transient electrical connectivity in developing nervous systems

Shu Xie et al.

Summary: PUPIL is a genetically encoded system for mapping and labeling transient electrical synapses in the mouse brain, revealing spatial subcellular localizations and physiological functions of electrical synapses.

CELL REPORTS (2021)

Article Cell Biology

Time-resolved proteomics profiling of the ciliary Hedgehog response

Elena A. May et al.

Summary: The study utilized quantitative mass spectrometry and proximity labeling techniques to profile the time-dependent alterations of the ciliary proteome in response to Hedgehog signals, identifying new proteins involved in Hedgehog signaling and highlighting the important roles of PKA and Paladin.

JOURNAL OF CELL BIOLOGY (2021)

Review Biochemistry & Molecular Biology

RNA Proximity Labeling: A New Detection Tool for RNA-Protein Interactions

Ronja Weissinger et al.

Summary: The interaction between RNAs and proteins controls multiple cellular functions and specific knowledge is required to understand their interactions. Various techniques have been developed to study RNA-protein interactions including CLIP and RNA affinity purification. In vivo proximity labeling can be used to study RNA-protein interactions and analyze tagged molecules via mass spectrometry or RNA-Seq.

MOLECULES (2021)

Review Neurosciences

Tripartite synaptomics: Cell-surface proximity labeling in vivo

Tetsuya Takano et al.

Summary: Astrocytes play a critical role in the architecture and activity of neuronal circuits through forming a tripartite synapse with neurons. Dysfunction in tripartite synaptic connections is implicated in various psychiatric and neurodevelopmental disorders. Recent advancements in transcriptome profiling and proteomic approaches have provided new insights into the molecular mechanisms by which astrocytes control synaptogenesis in the brain.

NEUROSCIENCE RESEARCH (2021)

Article Multidisciplinary Sciences

Proteomics of protein trafficking by in vivo tissue-specific labeling

Ilia A. Droujinine et al.

Summary: This study developed a method based on protein labeling to study cell-specific secretomes and interorgan protein trafficking, demonstrated in Drosophila and mouse models, revealing a vast communication network of secreted proteins. It identified muscle-secreted proteins in Drosophila and serum proteins in mice, highlighting the potential of this approach for identifying cell-specific secretomes and mediators of interorgan communication in different model systems.

NATURE COMMUNICATIONS (2021)

Article Biology

In vivo proximity labeling identifies cardiomyocyte protein networks during zebrafish heart regeneration

Mira Pronobis et al.

Summary: Recent strategies utilizing BioID2 proximity labeling have allowed for the uncovering of specific protein networks within cardiomyocytes during innate heart regeneration in zebrafish, identifying key protein interactions and signaling pathways involved in tissue regeneration.
Article Multidisciplinary Sciences

Spatially resolved cell polarity proteomics of a human epiblast model

Sicong Wang et al.

Summary: Critical early steps in human embryonic development involve the polarization of the inner cell mass, followed by the formation of an expanded lumen called the epiblast cavity. Recent studies have shown that 3D human pluripotent stem cell-derived cyst structures can replicate these processes. Using APEX2-based proximity biotinylation and quantitative mass spectrometry, researchers identified previously unannotated proteins in apical and basolateral membrane territories of these cysts. Functional experiments confirmed the importance of apically enriched proteins in cyst morphogenesis, highlighting the role of AP-1 clathrin adaptor complex in expanding apical membrane domains during the formation of the lumen. This study demonstrates the effectiveness of proximity labeling in discovering novel regulators of epithelial morphogenesis in 3D stem cell-based models.

SCIENCE ADVANCES (2021)

Article Biology

Developing Nanodisc-ID for label-free characterizations of membrane proteins

Huan Bao

Summary: Nanodisc-ID utilizes nanodiscs and proximity labeling for the analysis of membrane protein-lipid and protein-protein interactions, demonstrating its versatility in characterizing a wide range of integral and peripheral membrane proteins.

COMMUNICATIONS BIOLOGY (2021)

Review Biochemistry & Molecular Biology

From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants

Sandra M. Kerbler et al.

Summary: AP-MS and PL-MS are two powerful techniques for studying protein-protein interactions, providing insights into the interactions between proteins in plant systems.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemical Research Methods

Proximity Proteomics Has Potential for Extracellular Vesicle Identification

Hisako Kaneda et al.

Summary: Extracellular vesicles (EVs) play vital roles in intercellular communication and can serve as biomarkers for diseases like cancer. Proximity-labeling method-based proteomic approach was used in this study to identify proteins in EVs, particularly focusing on CHL1 and SLC4A1 proteins as potential markers for cancer.

JOURNAL OF PROTEOME RESEARCH (2021)

Article Multidisciplinary Sciences

A proximity-dependent biotinylation map of a human cell

Christopher D. Go et al.

Summary: The study utilized BioID technology to construct a map of subcellular compartments in human cells, identifying the intracellular locations of numerous unique proteins and demonstrating the superior predictive ability of this technique compared to previous methods.

NATURE (2021)

Review Biochemistry & Molecular Biology

Strategies for monitoring cell-cell interactions

Tyler J. Bechtel et al.

Summary: Multicellular organisms rely on physical cell-cell interactions to regulate physiological processes. Understanding the complexity of these interactions has greatly improved insight into cell-cell engagement biology and led to opportunities for therapeutic development. Emerging approaches that combine chemistry and biology technologies effectively interrogate cell-cell interfaces with molecular-level detail.

NATURE CHEMICAL BIOLOGY (2021)

Article Multidisciplinary Sciences

Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum

V. Dumrongprechachan et al.

Summary: This study employed a genetically targeted APEX2-based proximity labeling approach to uncover proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain. The findings were validated using imaging, electron microscopy, and mass spectrometry, providing important insights for understanding the development and functional organization of neural circuits in the brain.

NATURE COMMUNICATIONS (2021)

Article Biochemical Research Methods

Identification of Endogenous Kinase Substrates by Proximity Labeling Combined with Kinase Perturbation and Phosphorylation Motifs

Tomoya Niinae et al.

Summary: Mass-spectrometry-based phosphoproteomics can identify over 10,000 phosphorylated sites in a single experiment, but understanding protein kinase-substrate relationships remains a challenge. This study presents a new method using a combination of techniques to identify endogenous substrates of kinases, successfully applied to CK2 and PKA. The approach extends our knowledge of physiological kinase-substrate networks and is particularly relevant for understanding cancer-related mutations affecting downstream signaling pathways.

MOLECULAR & CELLULAR PROTEOMICS (2021)

Review Biochemistry & Molecular Biology

Proximity labeling: an emerging tool for probing in planta molecular interactions

Xinxin Yang et al.

Summary: This article summarizes recent advances in the use of proximity labeling (PL) in plant biology, including the development and comparison of different PL enzymes, and the application of PL in deciphering various molecular interactions in different organisms with a focus on plant systems.

PLANT COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Identification of a Small Probe That Can Be Conjugated to Proteins by Proximity Labeling

Weiping Sun et al.

ACS CHEMICAL BIOLOGY (2020)

Review Biochemical Research Methods

Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches

Paymany Samavarchi-Tehrani et al.

MOLECULAR & CELLULAR PROTEOMICS (2020)

Article Multidisciplinary Sciences

Mechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics

Guoxia Liu et al.

NATURE (2020)

Article Biotechnology & Applied Microbiology

ChromID identifies the protein interactome at chromatin marks

Rodrigo Villasenor et al.

NATURE BIOTECHNOLOGY (2020)

Article Multidisciplinary Sciences

Split-TurboID enables contact-dependent proximity labeling in cells

Kelvin F. Cho et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation

Chulhwan Kwak et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells

Diu T. T. Nguyen et al.

NATURE COMMUNICATIONS (2020)

Review Genetics & Heredity

Proximity Labeling Techniques to Study Chromatin

Henning Ummethum et al.

FRONTIERS IN GENETICS (2020)

Article Chemistry, Multidisciplinary

Chromophore-Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells

Tao Ding et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Article Multidisciplinary Sciences

RNA-protein interaction mapping via MS2-or Cas13-based APEX targeting

Shuo Han et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

Records of RNA locations in living yeast revealed through covalent marks

Hugo C. Medina-Munoz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biochemistry & Molecular Biology

The evolving capabilities of enzyme-mediated proximity labeling

Ying Zhou et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2020)

Article Developmental Biology

DamID as a versatile tool for understanding gene regulation

Gabriel N. Aughey et al.

DEVELOPMENT (2019)

Article Chemistry, Multidisciplinary

Enzyme-Mediated Intercellular Proximity Labeling for Detecting Cell-Cell Interactions

Yun Ge et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Chemistry, Multidisciplinary

Expanding APEX2 Substrates for Proximity-Dependent Labeling of Nucleic Acids and Proteins in Living Cells

Ying Zhou et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Biochemistry & Molecular Biology

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

Furqan M. Fazal et al.

Article Biochemistry & Molecular Biology

Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling

Pengchong Wang et al.

NATURE CHEMICAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Directed Evolution of Split APEX2 Peroxidase

Yisu Han et al.

ACS CHEMICAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Mechanistic implications of enhanced editing by a HyperTRIBE RNA-binding protein

Weijin Xu et al.

Article Biochemical Research Methods

C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2

Xin D. Gao et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

RNA-protein interaction detection in living cells

Muthukumar Ramanathan et al.

NATURE METHODS (2018)

Article Biotechnology & Applied Microbiology

Efficient proximity labeling in living cells and organisms with TurboID

Tess C. Branon et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemical Research Methods

A proximity-tagging system to identify membrane protein-protein interactions

Qiang Liu et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

Daniel Benhalevy et al.

NATURE METHODS (2018)

Article Biochemistry & Molecular Biology

Split-BioID: a proximity biotinylation assay for dimerization-dependent protein interactions

Sofie De Munter et al.

FEBS LETTERS (2017)

Article Multidisciplinary Sciences

Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes

Isabel Myriam Schopp et al.

NATURE COMMUNICATIONS (2017)

Article Chemistry, Medicinal

Photoactivatable protein labeling by singlet oxygen mediated reactions

Tsz-Leung To et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2016)

Article Biochemistry & Molecular Biology

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

Aoife C. McMahon et al.

Article Chemistry, Multidisciplinary

Direct Proximity Tagging of Small Molecule Protein Targets Using an Engineered NEDD8 Ligase

Zachary B. Hill et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

Article Cell Biology

An improved smaller biotin ligase for BioID proximity labeling

Dae In Kim et al.

MOLECULAR BIOLOGY OF THE CELL (2016)

Article Biochemical Research Methods

Directed evolution of APEX2 for electron microscopy and proximity labeling

Stephanie S. Lam et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

New Insights into the DT40 B Cell Receptor Cluster Using a Proteomic Proximity Labeling Assay

Xue-Wen Li et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2014)

Article Biotechnology & Applied Microbiology

Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy

Jeffrey D. Martell et al.

NATURE BIOTECHNOLOGY (2012)

Article Biochemistry & Molecular Biology

Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe

Katrina J. Woolcock et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2011)

Article Biochemistry & Molecular Biology

DamID in C-elegans reveals longevity-associated targets of DAF-16/FoxO

Eugene Schuster et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Review Biochemical Research Methods

Organelle proteomics experimental designs and analysis

Laurent Gatto et al.

PROTEOMICS (2010)

Article Multidisciplinary Sciences

Biochemical visualization of cell surface molecular clustering in living cells

Norihiro Kotani et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemical Research Methods

Detection of in vivo protein-DNA interactions using DamID in mammalian cells

Maartje J. Vogel et al.

NATURE PROTOCOLS (2007)

Article Biochemistry & Molecular Biology

Targeted and proximity-dependent promiscuous protein biotinylation by a mutant Escherichia coli biotin protein ligase

JE Cronan

JOURNAL OF NUTRITIONAL BIOCHEMISTRY (2005)