1
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38742660 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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2
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Bhushan V, Nita-Lazar A. Recent Advancements in Subcellular Proteomics: Growing Impact of Organellar Protein Niches on the Understanding of Cell Biology. J Proteome Res 2024. [PMID: 38451675 DOI: 10.1021/acs.jproteome.3c00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The mammalian cell is a complex entity, with membrane-bound and membrane-less organelles playing vital roles in regulating cellular homeostasis. Organellar protein niches drive discrete biological processes and cell functions, thus maintaining cell equilibrium. Cellular processes such as signaling, growth, proliferation, motility, and programmed cell death require dynamic protein movements between cell compartments. Aberrant protein localization is associated with a wide range of diseases. Therefore, analyzing the subcellular proteome of the cell can provide a comprehensive overview of cellular biology. With recent advancements in mass spectrometry, imaging technology, computational tools, and deep machine learning algorithms, studies pertaining to subcellular protein localization and their dynamic distributions are gaining momentum. These studies reveal changing interaction networks because of "moonlighting proteins" and serve as a discovery tool for disease network mechanisms. Consequently, this review aims to provide a comprehensive repository for recent advancements in subcellular proteomics subcontexting methods, challenges, and future perspectives for method developers. In summary, subcellular proteomics is crucial to the understanding of the fundamental cellular mechanisms and the associated diseases.
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Affiliation(s)
- Vanya Bhushan
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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3
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Kotani N, Araki T, Miyagawa-Yamaguchi A, Amimoto T, Nakano M, Honke K. Proximity Labeling and Proteomics: Get to Know Neighbors. Methods Enzymol 2022; 679:131-162. [PMID: 36682860 DOI: 10.1016/bs.mie.2022.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein-protein interactions are essential in biological reactions and fundamental to cell-cell communication (e.g., the binding of secreted proteins, such as hormones, to cell membrane receptors) and the subsequent intracellular signal transduction cascade. Several studies have been extensively carried out on protein-protein interactions because they have the potential to resolve various problems in molecular biology. Biochemical methods, such as chemical cross-linking and immunoprecipitation, have long been used to analyze which proteins interact with each other. However, there are some problems, such as unphysiological states and non-specific binding, that require the development of more useful experimental methods. This chapter discusses the "proximity labeling (Proteomics)" analysis technique, which has been attracting attention in protein-protein interaction analysis in recent years and is used in many biological studies. "Membrane proximity labeling (proteomics)," which analyzes the interaction of cell membrane proteins, and "intracellular proximity labeling (proteomics)" will be explained in-depth.
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Affiliation(s)
- Norihiro Kotani
- Medical Research Center, Saitama Medical University, Saitama, Japan; Department of Biochemistry, Saitama Medical University, Saitama, Japan.
| | - Tomoyuki Araki
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
| | | | - Tomoko Amimoto
- Natural Science Center for Basic Research and Development, Hiroshima University, Higashi-Hiroshima, Japan
| | - Miyako Nakano
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Japan
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4
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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5
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Hirata T, Yang J, Tomida S, Tokoro Y, Kinoshita T, Fujita M, Kizuka Y. ER entry pathway and glycosylation of GPI-anchored proteins are determined by N-terminal signal sequence and C-terminal GPI-attachment sequence. J Biol Chem 2022; 298:102444. [PMID: 36055406 PMCID: PMC9520029 DOI: 10.1016/j.jbc.2022.102444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 11/15/2022] Open
Abstract
Newly synthesized proteins in the secretory pathway, including glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs), need to be correctly targeted and imported into the endoplasmic reticulum (ER) lumen. GPI-APs are synthesized in the cytosol as preproproteins, which contain an N-terminal signal sequence (SS), mature protein part, and C-terminal GPI-attachment sequence (GPI-AS), and translocated into the ER lumen where SS and GPI-AS are removed, generating mature GPI-APs. However, how various GPI-APs are translocated into the ER lumen in mammalian cells is unclear. Here, we investigated the ER entry pathways of GPI-APs using a panel of KO cells defective in each signal recognition particle–independent ER entry pathway—namely, Sec62, GET, or SND pathway. We found GPI-AP CD59 largely depends on the SND pathway for ER entry, whereas prion protein (Prion) and LY6K depend on both Sec62 and GET pathways. Using chimeric Prion and LY6K constructs in which the N-terminal SS or C-terminal GPI-AS was replaced with that of CD59, we revealed that the hydrophobicity of the SSs and GPI-ASs contributes to the dependence on Sec62 and GET pathways, respectively. Moreover, the ER entry route of chimeric Prion constructs with the C-terminal GPI-ASs replaced with that of CD59 was changed to the SND pathway. Simultaneously, their GPI structures and which oligosaccharyltransferase isoforms modify the constructs were altered without any amino acid change in the mature protein part. Taking these findings together, this study revealed N- and C-terminal sequences of GPI-APs determine the selective ER entry route, which in turn regulates subsequent maturation processes of GPI-APs.
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Affiliation(s)
- Tetsuya Hirata
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Jing Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Seita Tomida
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Graduate School of Natural Science and Technology, Gifu University, Gifu 501-1193, Japan
| | - Yuko Tokoro
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita 565-0871, Japan
| | - Morihisa Fujita
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan.
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6
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Proximity labeling methods for proteomic analysis of membrane proteins. J Proteomics 2022; 264:104620. [DOI: 10.1016/j.jprot.2022.104620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/19/2022]
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7
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Chen Y, Zhou W, Li X, Yang K, Liang Z, Zhang L, Zhang Y. Research Progress of Protein-Protein Interaction Based on Liquid Chromatography Mass Spectrometry ※. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a22010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Kimmel J, Kehrer J, Frischknecht F, Spielmann T. Proximity-dependent biotinylation approaches to study apicomplexan biology. Mol Microbiol 2021; 117:553-568. [PMID: 34587292 DOI: 10.1111/mmi.14815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
In the last 10 years, proximity-dependent biotinylation (PDB) techniques greatly expanded the ability to study protein environments in the living cell that range from specific protein complexes to entire compartments. This is achieved by using enzymes such as BirA* and APEX that are fused to proteins of interest and biotinylate proteins in their proximity. PDB techniques are now also increasingly used in apicomplexan parasites. In this review, we first give an overview of the main PDB approaches and how they compare with other techniques that address similar questions. PDB is particularly valuable to detect weak or transient protein associations under physiological conditions and to study cellular structures that are difficult to purify or have a poorly understood protein composition. We also highlight new developments such as novel smaller or faster-acting enzyme variants and conditional PDB approaches, providing improvements in both temporal and spatial resolution which may offer broader application possibilities useful in apicomplexan research. In the second part, we review work using PDB techniques in apicomplexan parasites and how this expanded our knowledge about these medically important parasites.
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Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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9
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Zapatero-Belinchón FJ, Carriquí-Madroñal B, Gerold G. Proximity labeling approaches to study protein complexes during virus infection. Adv Virus Res 2021; 109:63-104. [PMID: 33934830 DOI: 10.1016/bs.aivir.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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10
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Qin W, Cho KF, Cavanagh PE, Ting AY. Deciphering molecular interactions by proximity labeling. Nat Methods 2021; 18:133-143. [PMID: 33432242 PMCID: PMC10548357 DOI: 10.1038/s41592-020-01010-5] [Citation(s) in RCA: 219] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Many biological processes are executed and regulated through the molecular interactions of proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the endogenous interaction partners of specific protein 'baits', via genetic fusion to promiscuous enzymes that catalyze the generation of diffusible reactive species in living cells. Tagged molecules that interact with baits can then be enriched and identified by mass spectrometry or nucleic acid sequencing. Here we review the development of PL technologies and highlight studies that have applied PL to the discovery and analysis of molecular interactions. In particular, we focus on the use of PL for mapping protein-protein, protein-RNA and protein-DNA interactions in living cells and organisms.
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Affiliation(s)
- Wei Qin
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kelvin F Cho
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter E Cavanagh
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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11
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Pseudotyping Lentiviral Vectors: When the Clothes Make the Virus. Viruses 2020; 12:v12111311. [PMID: 33207797 PMCID: PMC7697029 DOI: 10.3390/v12111311] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
Delivering transgenes to human cells through transduction with viral vectors constitutes one of the most encouraging approaches in gene therapy. Lentivirus-derived vectors are among the most promising vectors for these approaches. When the genetic modification of the cell must be performed in vivo, efficient specific transduction of the cell targets of the therapy in the absence of off-targeting constitutes the Holy Grail of gene therapy. For viral therapy, this is largely determined by the characteristics of the surface proteins carried by the vector. In this regard, an important property of lentiviral vectors is the possibility of being pseudotyped by envelopes of other viruses, widening the panel of proteins with which they can be armed. Here, we discuss how this is achieved at the molecular level and what the properties and the potentialities of the different envelope proteins that can be used for pseudotyping these vectors are.
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12
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Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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13
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Samavarchi-Tehrani P, Samson R, Gingras AC. Proximity Dependent Biotinylation: Key Enzymes and Adaptation to Proteomics Approaches. Mol Cell Proteomics 2020; 19:757-773. [PMID: 32127388 PMCID: PMC7196579 DOI: 10.1074/mcp.r120.001941] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The study of protein subcellular distribution, their assembly into complexes and the set of proteins with which they interact with is essential to our understanding of fundamental biological processes. Complementary to traditional assays, proximity-dependent biotinylation (PDB) approaches coupled with mass spectrometry (such as BioID or APEX) have emerged as powerful techniques to study proximal protein interactions and the subcellular proteome in the context of living cells and organisms. Since their introduction in 2012, PDB approaches have been used in an increasing number of studies and the enzymes themselves have been subjected to intensive optimization. How these enzymes have been optimized and considerations for their use in proteomics experiments are important questions. Here, we review the structural diversity and mechanisms of the two main classes of PDB enzymes: the biotin protein ligases (BioID) and the peroxidases (APEX). We describe the engineering of these enzymes for PDB and review emerging applications, including the development of PDB for coincidence detection (split-PDB). Lastly, we briefly review enzyme selection and experimental design guidelines and reflect on the labeling chemistries and their implication for data interpretation.
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Affiliation(s)
| | - Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
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14
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Cheerathodi MR, Meckes DG. BioID Combined with Mass Spectrometry to Study Herpesvirus Protein-Protein Interaction Networks. Methods Mol Biol 2020; 2060:327-341. [PMID: 31617188 DOI: 10.1007/978-1-4939-9814-2_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Herpes viruses are important human pathogens that cause a wide range of diseases from skin lesions to malignancies. Protein interactions drive many cellular events and mediate a number of biochemical pathways leading to different physiological outcomes. Protein interactions between viral proteins and host proteins play significant roles in viral entry, replication and suppression of host-immune responses. Therefore, the study of virus-host interactions promises significant advancement in designing therapeutics to control infection and disease. Various approaches are employed in the field to study and identify protein interactions that combine affinity purification along with different detection methods. Advancements in protein purification and high-throughput detection methods have resulted in an unprecedented level of discovery. Here we detail the use of proximity dependent biotinylation (BioID) as a means of affinity purification coupled with the use of LC-MS/MS for the detection and identification of protein-protein interaction networks.
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Affiliation(s)
- Mujeeb R Cheerathodi
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
| | - David G Meckes
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA.
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15
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Abstract
To understand cellular processes at molecular levels, elucidation of protein-protein interactions occurring at a specific location in living cells is required. We have developed a proximity labeling method mediated by the enzyme-mediated activation of radical source (EMARS) reaction, which features a radical formation from labeling reagents by horseradish peroxidase (HRP) set on a molecule of interest (probed molecule). Proximal molecules are covalently labeled with a tag conjugated with the labeling reagent. Here we describe protocols for preparation of a labeling reagent, labeling of neighboring proteins of the probed molecule in living cells, and identification of the labeled proteins.
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Affiliation(s)
- Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Nankoku, Kochi, Japan.
- Center for Innovative and Translational Medicine, Kochi University Medical School, Nankoku, Kochi, Japan.
| | | | - Norihiro Kotani
- Department of Biochemistry, Saitama Medical University, Saitama, Japan
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16
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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17
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Che Y, Khavari PA. Research Techniques Made Simple: Emerging Methods to Elucidate Protein Interactions through Spatial Proximity. J Invest Dermatol 2017; 137:e197-e203. [PMID: 29169465 DOI: 10.1016/j.jid.2017.09.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 01/12/2023]
Abstract
Interactions between proteins are essential for fundamental cellular processes, and the diversity of such interactions enables the vast variety of functions essential for life. A persistent goal in biological research is to develop assays that can faithfully capture different types of protein interactions to allow their study. A major step forward in this direction came with a family of methods that delineates spatial proximity of proteins as an indirect measure of protein-protein interaction. A variety of enzyme- and DNA ligation-based methods measure protein co-localization in space, capturing novel interactions that were previously too transient or low affinity to be identified. Here we review some of the methods that have been successfully used to measure spatially proximal protein-protein interactions.
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Affiliation(s)
- Yonglu Che
- Program in Epithelial Biology, Stanford University, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University, Stanford, California, USA; Dermatology Service, VA Palo Alto Health Care System, Palo Alto, California, USA.
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Honke K. Biological functions of sulfoglycolipids and the EMARS method for identification of co-clustered molecules in the membrane microdomains. J Biochem 2017; 163:253-263. [DOI: 10.1093/jb/mvx078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/03/2017] [Indexed: 01/24/2023] Open
Affiliation(s)
- Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783–8505, Japan
- Center for Innovative and Translational Medicine, Kochi University Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783–8505, Japan
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Wang H, Han X, Kunz E, Hartnett ME. Thy-1 Regulates VEGF-Mediated Choroidal Endothelial Cell Activation and Migration: Implications in Neovascular Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2017; 57:5525-5534. [PMID: 27768790 PMCID: PMC5080948 DOI: 10.1167/iovs.16-19691] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Purpose This study addresses the hypothesis that age-related stresses upregulate Thy-1 in choroidal endothelial cells (CECs) and contribute to CEC activation and migration, processes important in choroidal neovascularization (CNV). Methods Measurements were made of Thy-1 protein (Western blot) in CECs and Thy-1 mRNA (real time quantitative PCR) in CECs treated with VEGF, CCL11, or PBS or in RPE/choroids from young or old donors or lasered or nonlasered mice. Immunolabeled Thy-1 in ocular sections was compared from young versus old human donor eyes or those with or without neovascular AMD or from lasered versus nonlasered mice. Choroidal endothelial cells transfected with Thy-1 or control siRNA or pretreated with Thy-1 blocking peptide or control were stimulated with VEGF or 7-ketocholesterol (7-KC). Choroidal endothelial cell migration, proliferation, cytoskeletal stress fibers, Rac1 activation, and phosphorylated VEGF receptor 2 (VEGFR2), integrin β3, and Src were measured. Statistics were performed using ANOVA. Results Thy-1 was expressed in retinal ganglion cells and in vascular endothelial-cadherin–labeled choroid and localized to human or mouse laser-induced CNV lesions. Thy-1 protein and mRNA were significantly increased in CECs treated with VEGF or CCL11 and in RPE/choroids from aged versus young donor eyes or from lasered mice versus nonlasered controls. Knockdown or inhibition of Thy-1 in CECs significantly reduced VEGF-induced CEC migration and proliferation, stress fiber formation and VEGFR2, Src, integrin β3 and Rac1 activation, and 7-KC–induced Rac1 and Src activation. Conclusions Thy-1 in CECs regulates VEGF-induced CEC activation and migration and links extracellular 7-KC to intracellular signaling. Future studies elucidating Thy-1 mechanisms in neovascular AMD are warranted.
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Affiliation(s)
- Haibo Wang
- The John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States
| | - Xiaokun Han
- The John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States 2Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Eric Kunz
- The John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States
| | - M Elizabeth Hartnett
- The John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28387482 DOI: 10.1002/wdev.272] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 02/05/2023]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins with biotin. The biotinylated endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we describe and compare current methods of proximity labeling as well as their applications. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. WIREs Dev Biol 2017, 6:e272. doi: 10.1002/wdev.272 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiao-Lin Chen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Boston, MA, USA
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Filling the Void: Proximity-Based Labeling of Proteins in Living Cells. Trends Cell Biol 2016; 26:804-817. [PMID: 27667171 DOI: 10.1016/j.tcb.2016.09.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022]
Abstract
There are inherent limitations with traditional methods to study protein behavior or to determine the constituency of proteins in discrete subcellular compartments. In response to these limitations, several methods have recently been developed that use proximity-dependent labeling. By fusing proteins to enzymes that generate reactive molecules, most commonly biotin, proximate proteins are covalently labeled to enable their isolation and identification. In this review we describe current methods for proximity-dependent labeling in living cells and discuss their applications and future use in the study of protein behavior.
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Rees JS, Li XW, Perrett S, Lilley KS, Jackson AP. Protein Neighbors and Proximity Proteomics. Mol Cell Proteomics 2015; 14:2848-56. [PMID: 26355100 PMCID: PMC4638030 DOI: 10.1074/mcp.r115.052902] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 12/31/2022] Open
Abstract
Within cells, proteins can co-assemble into functionally integrated and spatially restricted multicomponent complexes. Often, the affinities between individual proteins are relatively weak, and proteins within such clusters may interact only indirectly with many of their other protein neighbors. This makes proteomic characterization difficult using methods such as immunoprecipitation or cross-linking. Recently, several groups have described the use of enzyme-catalyzed proximity labeling reagents that covalently tag the neighbors of a targeted protein with a small molecule such as fluorescein or biotin. The modified proteins can then be isolated by standard pulldown methods and identified by mass spectrometry. Here we will describe the techniques as well as their similarities and differences. We discuss their applications both to study protein assemblies and to provide a new way for characterizing organelle proteomes. We stress the importance of proteomic quantitation and independent target validation in such experiments. Furthermore, we suggest that there are biophysical and cell-biological principles that dictate the appropriateness of enzyme-catalyzed proximity labeling methods to address particular biological questions of interest.
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Affiliation(s)
- Johanna S Rees
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW, the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Xue-Wen Li
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Sarah Perrett
- the ‖National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
| | - Kathryn S Lilley
- the §Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QR, and
| | - Antony P Jackson
- From the ‡Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom CB2 1QW,
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Each GPI-anchored protein species forms a specific lipid raft depending on its GPI attachment signal. Glycoconj J 2015; 32:531-40. [DOI: 10.1007/s10719-015-9595-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/15/2015] [Accepted: 04/23/2015] [Indexed: 10/23/2022]
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Miyagawa-Yamaguchi A, Kotani N, Honke K. Segregation of Lipid Rafts Revealed by the EMARS Method Using GPI-Anchored HRP Fusion Proteins. TRENDS GLYCOSCI GLYC 2014. [DOI: 10.4052/tigg.26.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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