1
|
Li S, Ouyang X, Su B. ATP6AP1 was Phast-ID'ed as a long-sought GEF for Rheb. Cell Res 2024; 34:397-398. [PMID: 38744982 PMCID: PMC11143262 DOI: 10.1038/s41422-024-00967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Affiliation(s)
- Song Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinxing Ouyang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Chest Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology at Basic Medical College, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Gastroenterology and Center for Immune-Related Diseases Research at Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
2
|
Schreiber KJ, Kadijk E, Youn JY. Exploring Options for Proximity-Dependent Biotinylation Experiments: Comparative Analysis of Labeling Enzymes and Affinity Purification Resins. J Proteome Res 2024; 23:1531-1543. [PMID: 38507741 PMCID: PMC11002925 DOI: 10.1021/acs.jproteome.3c00908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Proximity-dependent biotinylation (PDB) techniques provide information about the molecular neighborhood of a protein of interest, yielding insights into its function and localization. Here, we assessed how different labeling enzymes and streptavidin resins influence PDB results. We compared the high-confidence interactors of the DNA/RNA-binding protein transactive response DNA-binding protein 43 kDa (TDP-43) identified using either miniTurbo (biotin ligase) or APEX2 (peroxidase) enzymes. We also evaluated two commercial affinity resins for purification of biotinylated proteins: conventional streptavidin sepharose versus a new trypsin-resistant streptavidin conjugated to magnetic resin, which significantly reduces the level of contamination by streptavidin peptides following on-bead trypsin digestion. Downstream analyses involved liquid chromatography coupled to mass spectrometry in data-dependent acquisition mode, database searching, and statistical analysis of high-confidence interactors using SAINTexpress. The APEX2-TDP-43 experiment identified more interactors than miniTurbo-TDP-43, although miniTurbo provided greater overlap with previously documented TDP-43 interactors. Purifications on sepharose resin yielded more interactors than magnetic resin in small-scale experiments using a range of magnetic resin volumes. We suggest that resin-specific background protein binding profiles and different lysate-to-resin ratios cumulatively affect the distributions of prey protein abundance in experimental and control samples, which impact statistical confidence scores. Overall, we highlight key experimental variables to consider for the empirical optimization of PDB experiments.
Collapse
Affiliation(s)
- Karl J. Schreiber
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Eileigh Kadijk
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ji-Young Youn
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
3
|
Cronan JE. Biotin protein ligase as you like it: Either extraordinarily specific or promiscuous protein biotinylation. Proteins 2024; 92:435-448. [PMID: 37997490 PMCID: PMC10932917 DOI: 10.1002/prot.26642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
Biotin (vitamin H or B7) is a coenzyme essential for all forms of life. Biotin has biological activity only when covalently attached to a few key metabolic enzyme proteins. Most organisms have only one attachment enzyme, biotin protein ligase (BPL), which attaches biotin to all target proteins. The sequences of these proteins and their substrate proteins are strongly conserved throughout biology. Structures of both the biotin ligase- and biotin-acceptor domains of mammals, plants, several bacterial species, and archaea have been determined. These, together with mutational analyses of ligases and their protein substrates, illustrate the exceptional specificity of this protein modification. For example, the Escherichia coli BPL biotinylates only one of the >4000 cellular proteins. Several bifunctional bacterial biotin ligases transcriptionally regulate biotin synthesis and/or transport in concert with biotinylation. The human BPL has been demonstrated to play an important role in that mutations in the BPL encoding gene cause one form of the disease, biotin-responsive multiple carboxylase deficiency. Promiscuous mutant versions of several BPL enzymes release biotinoyl-AMP, the active intermediate of the ligase reaction, to solvent. The released biotinoyl-AMP acts as a chemical biotinylation reagent that modifies lysine residues of neighboring proteins in vivo. This proximity-dependent biotinylation (called BioID) approach has been heavily utilized in cell biology.
Collapse
Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
| |
Collapse
|
4
|
Merino-Cacho L, Barroso-Gomila O, Hernández-Sánchez S, Ramirez J, Mayor U, Sutherland JD, Barrio R. Biotin-Based Strategies to Explore the World of Ubiquitin and Ubiquitin-Like Modifiers. Chembiochem 2024; 25:e202300746. [PMID: 38081789 DOI: 10.1002/cbic.202300746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/07/2023] [Indexed: 01/06/2024]
Abstract
A complex code of cellular signals is mediated by ubiquitin and ubiquitin-like (Ub/UbL) modifications on substrate proteins. The so-called Ubiquitin Code specifies protein fates, such as stability, subcellular localization, functional activation or suppression, and interactions. Hundreds of enzymes are involved in placing and removing Ub/UbL on thousands of substrates, while the consequences of modifications and the mechanisms of specificity are still poorly defined. Challenges include rapid and transient engagement of enzymes and Ub/UbL interactors, low stoichiometry of modified versus non-modified cellular substrates, and protease-mediated loss of Ub/UbL in lysates. To decipher this complexity and confront the challenges, many tools have been created to trap and identify substrates and interactors linked to Ub/UbL modification. This review focuses on an assortment of biotin-based tools developed for this purpose (for example BioUbLs, UbL-ID, BioE3, BioID), taking advantage of the strong affinity of biotin-streptavidin and the stringent lysis/washing approach allowed by it, paired with sensitive mass-spectrometry-based proteomic methods. Knowing how substrates change during development and disease, the consequences of substrate modification, and matching substrates to particular UbL-ligating enzymes will contribute new insights into how Ub/UbL signaling works and how it can be exploited for therapies.
Collapse
Affiliation(s)
- Laura Merino-Cacho
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Orhi Barroso-Gomila
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Sandra Hernández-Sánchez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48013, Spain
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| |
Collapse
|
5
|
Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
Collapse
Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| |
Collapse
|
6
|
Wang Y, Li W, Ye B, Bi X. Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells. Chem Asian J 2023; 18:e202300226. [PMID: 37089007 PMCID: PMC10946512 DOI: 10.1002/asia.202300226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.
Collapse
Affiliation(s)
- You‐Yu Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoria3086Australia
| | - Bang‐Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Xiao‐Bao Bi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| |
Collapse
|
7
|
Abstract
Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.
Collapse
Affiliation(s)
- Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Sumudu S Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Pei-Qiao Xie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| |
Collapse
|
8
|
Studying the ubiquitin code through biotin-based labelling methods. Semin Cell Dev Biol 2022; 132:109-119. [PMID: 35181195 DOI: 10.1016/j.semcdb.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
Collapse
|
9
|
Establishment of in vivo proximity labeling with biotin using TurboID in the filamentous fungus Sordaria macrospora. Sci Rep 2022; 12:17727. [PMID: 36272986 PMCID: PMC9588061 DOI: 10.1038/s41598-022-22545-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/17/2022] [Indexed: 01/18/2023] Open
Abstract
Proximity-dependent biotin identification (BioID) has emerged as a powerful methodology to identify proteins co-localizing with a given bait protein in vivo. The approach has been established in animal cells, plants and yeast but not yet in filamentous fungi. BioID relies on promiscuous biotin ligases fused to bait proteins to covalently label neighboring proteins with biotin. Biotinylated proteins are specifically enriched through biotin affinity capture from denatured cell lysates and subsequently identified and quantified with liquid chromatography-mass spectrometry (LC-MS). In contrast to many other affinity capture approaches for studying protein-protein interactions, BioID does not rely on physical protein-protein binding within native cell lysates. This feature allows the identification of protein proximities of weak or transient and dynamic nature. Here, we demonstrate the application of BioID for the fungal model organism Sordaria macrospora (Sm) using the example of the STRIPAK complex interactor 1 (SCI1) of the well-characterized striatin-interacting phosphatase and kinase (SmSTRIPAK) complex as proof of concept. For the establishment of BioID in S. macrospora, a codon-optimized TurboID biotin ligase was fused to SCI1. Biotin capture of the known SmSTRIPAK components PRO11, SmMOB3, PRO22 and SmPP2Ac1 demonstrates the successful BioID application in S. macrospora. BioID proximity labeling approaches will provide a powerful proteomics tool for fungal biologists.
Collapse
|
10
|
Geoghegan V, Mottram JC, Jones NG. Tag Thy Neighbour: Nanometre-Scale Insights Into Kinetoplastid Parasites With Proximity Dependent Biotinylation. Front Cell Infect Microbiol 2022; 12:894213. [PMID: 35601102 PMCID: PMC9120650 DOI: 10.3389/fcimb.2022.894213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Proximity labelling is a powerful and rapidly developing technology for exploring the interaction space and molecular environment of a protein of interest at the nanometre scale. In proximity labelling, a promiscuous biotinylating enzyme is genetically fused to the protein of interest, initiation of labelling then results in the biotinylating enzyme generating reactive biotin which covalently ‘tags’ nearby molecules. Importantly, this labelling takes place in vivo whilst the protein of interest continues to perform its normal functions in the cell. Due to its unique advantageous characteristics, proximity labelling is driving discoveries in an ever increasing range of organisms. Here, we highlight the applications of proximity labelling to the study of kinetoplastids, a group of eukaryotic protozoa that includes trypanosomes and Leishmania which can cause serious disease in humans and livestock. We first provide a general overview of the proximity labelling experimental workflow including key labelling enzymes used, proper experimental design with appropriate controls and robust statistical analysis to maximise the amount of reliable spatial information that is generated. We discuss studies employing proximity labelling in kinetoplastid parasites to illustrate how these key principles of experimental design are applied. Finally, we highlight emerging trends in the development of proximity labelling methodology.
Collapse
|
11
|
Sparn C, Dimou E, Meyer A, Saleppico R, Wegehingel S, Gerstner M, Klaus S, Ewers H, Nickel W. Glypican-1 drives unconventional secretion of Fibroblast Growth Factor 2. eLife 2022; 11:75545. [PMID: 35348113 PMCID: PMC8986318 DOI: 10.7554/elife.75545] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Fibroblast Growth Factor 2 (FGF2) is a tumor cell survival factor that is transported into the extracellular space by an unconventional secretory mechanism. Cell surface heparan sulfate proteoglycans are known to play an essential role in this process. Unexpectedly, we found that among the diverse sub-classes consisting of syndecans, perlecans, glypicans and others, Glypican-1 (GPC1) is the principle and rate-limiting factor that drives unconventional secretion of FGF2. By contrast, we demonstrate GPC1 to be dispensable for FGF2 signaling into cells. We provide first insights into the structural basis for GPC1-dependent FGF2 secretion, identifying disaccharides with N-linked sulfate groups to be enriched in the heparan sulfate chains of GPC1 to which FGF2 binds with high affinity. Our findings have broad implications for the role of GPC1 as a key molecule in tumor progression.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Helge Ewers
- Institut für Chemie und Biochemie, Freie Universität Berlin
| | | |
Collapse
|
12
|
Alwash M, Gariépy J. Labeling Cell Surface Receptors with Ligand.BirA* Bispecifics. ACS Pharmacol Transl Sci 2022; 5:62-69. [PMID: 36742360 PMCID: PMC9890520 DOI: 10.1021/acsptsci.1c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BirA*, a mutant form of the biotinylating enzyme BirA, can nonspecifically biotinylate ε-amino groups on lysines of proteins. Based on the promiscuous labeling nature of BirA*, plasmids expressing fusion constructs of BirA* to a given ligand have been used to transfect eukaryotic cells, leading to the biotinylation of intracellular proteins interacting or in close proximity to such Ligand.BirA* constructs. Mass spectrometry performed on the recovered biotinylated partners allows one to map intracellular protein interactors, a technique known as BioID. In contrast, the expression and purification of recombinant Ligand.BirA* constructs could serve as a powerful tool for labeling and detecting cell surface receptors. Here, we report the design and expression of recombinant Affibody.BirA* constructs, ZEGFR:1907.BirA* and ZHER2:243.BirA*, as protein bispecifics able to biotinylate their respective receptors EGFR and HER2 on the surface of MDA-MB-231 (EGFR+, EpCaM+, and CD44+) and SK-OV-3 (HER2++, EGFR+, EpCaM+, and CD44+) cancer cells. These Affibody.BirA* constructs retain both their BirA* enzymatic activity as well as their receptor-binding function. Importantly, MDA-MB-231 and SK-OV-3 cells biotinylated with Affibody.BirA* constructs did label their receptors EGFR and HER2 but did not biotinylate irrelevant antigens such as EpCaM or CD44 present on the surface of both cell lines. Ligand.BirA* bispecifics may represent a promising class of agents to identify unknown receptors on cell surfaces.
Collapse
Affiliation(s)
- Mays Alwash
- Sunnybrook
Research Institute, 2075
Bayview Avenue, Toronto, Ontario M4N 3M5, Canada,Department
of Pharmaceutical Sciences, University of
Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Jean Gariépy
- Sunnybrook
Research Institute, 2075
Bayview Avenue, Toronto, Ontario M4N 3M5, Canada,Department
of Pharmaceutical Sciences, University of
Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada,Department
of Medical Biophysics, University of Toronto, 101 College St Suite 15-701, Toronto, Ontario M5G 1L7, Canada,
| |
Collapse
|
13
|
Pfeiffer CT, Paulo JA, Gygi SP, Rockman HA. Proximity labeling for investigating protein-protein interactions. Methods Cell Biol 2022; 169:237-266. [PMID: 35623704 PMCID: PMC10782847 DOI: 10.1016/bs.mcb.2021.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The study of protein complexes and protein-protein interactions is of great importance due to their fundamental roles in cellular function. Proximity labeling, often coupled with mass spectrometry, has become a powerful and versatile tool for studying protein-protein interactions by enriching and identifying proteins in the vicinity of a specified protein-of-interest. Here, we describe and compare traditional approaches to investigate protein-protein interactions to current day state-of-the-art proximity labeling methods. We focus on the wide array of proximity labeling strategies and underscore studies using diverse model systems to address numerous biological questions. In addition, we highlight current advances in mass spectrometry-based technology that exhibit promise in improving the depth and breadth of the data acquired in proximity labeling experiments. In all, we show the diversity of proximity labeling strategies and emphasize the broad range of applications and biological inquiries that can be addressed using this technology.
Collapse
Affiliation(s)
- Conrad T Pfeiffer
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Howard A Rockman
- Department of Medicine, Duke University Medical Center, Durham, NC, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC, United States.
| |
Collapse
|
14
|
Kulyyassov A. Application of Skyline for Analysis of Protein-Protein Interactions In Vivo. Molecules 2021; 26:molecules26237170. [PMID: 34885753 PMCID: PMC8658920 DOI: 10.3390/molecules26237170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative and qualitative analyses of cell protein composition using liquid chromatography/tandem mass spectrometry are now standard techniques in biological and clinical research. However, the quantitative analysis of protein–protein interactions (PPIs) in cells is also important since these interactions are the bases of many processes, such as the cell cycle and signaling pathways. This paper describes the application of Skyline software for the identification and quantification of the biotinylated form of the biotin acceptor peptide (BAP) tag, which is a marker of in vivo PPIs. The tag was used in the Proximity Utilizing Biotinylation (PUB) method, which is based on the co-expression of BAP-X and BirA-Y in mammalian cells, where X or Y are interacting proteins of interest. A high level of biotinylation was detected in the model experiments where X and Y were pluripotency transcription factors Sox2 and Oct4, or heterochromatin protein HP1γ. MRM data processed by Skyline were normalized and recalculated. Ratios of biotinylation levels in experiment versus controls were 86 ± 6 (3 h biotinylation time) and 71 ± 5 (9 h biotinylation time) for BAP-Sox2 + BirA-Oct4 and 32 ± 3 (4 h biotinylation time) for BAP-HP1γ + BirA-HP1γ experiments. Skyline can also be applied for the analysis and identification of PPIs from shotgun proteomics data downloaded from publicly available datasets and repositories.
Collapse
Affiliation(s)
- Arman Kulyyassov
- Republican State Enterprise "National Center for Biotechnology" under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, 13/5, Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan
| |
Collapse
|
15
|
Wang LT, Proulx MÈ, Kim AD, Lelarge V, McCaffrey L. A proximity proteomics screen in three-dimensional spheroid cultures identifies novel regulators of lumen formation. Sci Rep 2021; 11:22807. [PMID: 34815476 PMCID: PMC8610992 DOI: 10.1038/s41598-021-02178-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
Apical-basal cell polarity and lumen formation are essential features of many epithelial tissues, which are disrupted in diseases like cancer. Here, we describe a proteomics-based screen to identify proteins involved in lumen formation in three-dimensional spheroid cultures. We established a suspension-based culture method suitable for generating polarized cysts in sufficient quantities for proteomic analysis. Using this approach, we identified several known and unknown proteins proximally associated with PAR6B, an apical protein involved in lumen formation. Functional analyses of candidates identified PARD3B (a homolog of PARD3), RALB, and HRNR as regulators of lumen formation. We also identified PTPN14 as a component of the Par-complex that is required for fidelity of apical-basal polarity. Cells transformed with KRASG12V exhibit lumen collapse/filling concomitant with disruption of the Par-complex and down-regulation of PTPN14. Enforced expression of PTPN14 maintained the lumen and restricted the transformed phenotype in KRASG12V-expressing cells. This represents an applicable approach to explore protein–protein interactions in three-dimensional culture and to identify proteins important for lumen maintenance in normal and oncogene-expressing cells.
Collapse
Affiliation(s)
- Li-Ting Wang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1, Canada
| | - Marie-Ève Proulx
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Anne D Kim
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1, Canada
| | - Virginie Lelarge
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Luke McCaffrey
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada. .,Division of Experimental Medicine, McGill University, Montreal, QC, H4A 3J1, Canada. .,Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada. .,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, H4A 3T2, Canada.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Lee L, Perez Oliva AB, Martinez-Balsalobre E, Churikov D, Peter J, Rahmouni D, Audoly G, Azzoni V, Audebert S, Camoin L, Mulero V, Cayuela ML, Kulathu Y, Geli V, Lachaud C. UFMylation of MRE11 is essential for telomere length maintenance and hematopoietic stem cell survival. SCIENCE ADVANCES 2021; 7:eabc7371. [PMID: 34559557 PMCID: PMC8462904 DOI: 10.1126/sciadv.abc7371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Ubiquitin-fold modifier 1 (UFM1) is involved in neural and erythroid development, yet its biological roles in these processes are unknown. Here, we generated zebrafish models deficient in Ufm1 and Ufl1 that exhibited telomere shortening associated with developmental delay, impaired hematopoiesis and premature aging. We further report that HeLa cells lacking UFL1 have instability of telomeres replicated by leading-strand synthesis. We uncover that MRE11 UFMylation is necessary for the recruitment of the phosphatase PP1-α leading to dephosphorylation of NBS1. In the absence of UFMylation, NBS1 remains phosphorylated, thereby reducing MRN recruitment to telomeres. The absence of MRN at telomeres favors the formation of the TRF2-Apollo/SNM1 complex consistent with the loss of leading telomeres. These results suggest that MRE11-UFMylation may serve as module to recruit PP1-α. Last, zebrafish expressing Mre11 that cannot be UFMylated phenocopy Ufm1-deficient zebrafish, demonstrating that UFMylation of MRE11 is a previously undescribed evolutionarily conserved mechanisms regulating telomere length.
Collapse
Affiliation(s)
- Lara Lee
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Ana Belen Perez Oliva
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Elena Martinez-Balsalobre
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Dmitri Churikov
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Joshua Peter
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Dalicya Rahmouni
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Gilles Audoly
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Violette Azzoni
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Stephane Audebert
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Victoriano Mulero
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
- Departamento de Biología Celular e Histología, Facultad de Biología, Universidad de Murcia, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Maria L. Cayuela
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Centro de Investigación Biomédica en Red de Enfermedades Raras, Murcia, Spain
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Vincent Geli
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Christophe Lachaud
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| |
Collapse
|
18
|
Using BioID to Characterize the RAS Interactome. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:271-280. [PMID: 33977483 DOI: 10.1007/978-1-0716-1190-6_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Identifying the proteins that associate with RAS oncoproteins has great potential, not only to elucidate how these mutant proteins are regulated and signal but also to identify potential therapeutic targets. Here we describe a detailed protocol to employ proximity labeling by the BioID methodology, which has the advantage of capturing weak or transient interactions, to identify in an unbiased manner those proteins within the immediate vicinity of oncogenic RAS proteins.
Collapse
|
19
|
Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
Collapse
Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Rajak MK, Bhatnagar S, Pandey S, Kumar S, Verma S, Patel AK, Sundd M. Leishmania major biotin protein ligase forms a unique cross-handshake dimer. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:510-521. [PMID: 33825711 DOI: 10.1107/s2059798321001418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022]
Abstract
Biotin protein ligase catalyses the post-translational modification of biotin carboxyl carrier protein (BCCP) domains, a modification that is crucial for the function of several carboxylases. It is a two-step process that results in the covalent attachment of biotin to the ϵ-amino group of a conserved lysine of the BCCP domain of a carboxylase in an ATP-dependent manner. In Leishmania, three mitochondrial enzymes, acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase and propionyl-CoA carboxylase, depend on biotinylation for activity. In view of the indispensable role of the biotinylating enzyme in the activation of these carboxylases, crystal structures of L. major biotin protein ligase complexed with biotin and with biotinyl-5'-AMP have been solved. L. major biotin protein ligase crystallizes as a unique dimer formed by cross-handshake interactions of the hinge region of the two monomers formed by partial unfolding of the C-terminal domain. Interestingly, the substrate (BCCP domain)-binding site of each monomer is occupied by its own C-terminal domain in the dimer structure. This was observed in all of the crystals that were obtained, suggesting a closed/inactive conformation of the enzyme. Size-exclusion chromatography studies carried out using high protein concentrations (0.5 mM) suggest the formation of a concentration-dependent dimer that exists in equilibrium with the monomer.
Collapse
Affiliation(s)
- Manoj Kumar Rajak
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Sonika Bhatnagar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Shubhant Pandey
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752 050, India
| | - Sunil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110 016, India
| | - Shalini Verma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110 016, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| |
Collapse
|
22
|
Seath CP, Trowbridge AD, Muir TW, MacMillan DWC. Reactive intermediates for interactome mapping. Chem Soc Rev 2021; 50:2911-2926. [PMID: 33458734 DOI: 10.1039/d0cs01366h] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interactions of biomolecules underpin all cellular processes, and the understanding of their dynamic interplay can lead to significant advances in the treatment of disease through the identification of novel therapeutic strategies. Protein-protein interactions (PPIs) in particular play a vital role within this arena, providing the basis for the majority of cellular signalling pathways. Despite their great importance, the elucidation of weak or transient PPIs that cannot be identified by immunoprecipitation remains a significant challenge, particularly in a disease relevant cellular environment. Recent approaches towards this goal have utilized the in situ generation of high energy intermediates that cross-link with neighboring proteins, providing a snapshot of the biomolecular makeup of the local area or microenvironment, termed the interactome. In this tutorial review, we discuss these reactive intermediates, how they are generated, and the impact they have had on the discovery of new biology. Broadly, we believe this strategy has the potential to significantly accelerate our understanding of PPIs and how they affect cellular physiology.
Collapse
Affiliation(s)
- Ciaran P Seath
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544, USA.
| | | | | | | |
Collapse
|
23
|
Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. THE PLANT CELL 2020; 32:3388-3407. [PMID: 32843435 PMCID: PMC7610282 DOI: 10.1105/tpc.20.00235] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/22/2020] [Accepted: 08/21/2020] [Indexed: 05/19/2023]
Abstract
Proximity labeling is a powerful approach for detecting protein-protein interactions. Most proximity labeling techniques use a promiscuous biotin ligase or a peroxidase fused to a protein of interest, enabling the covalent biotin labeling of proteins and subsequent capture and identification of interacting and neighboring proteins without the need for the protein complex to remain intact. To date, only a few studies have reported on the use of proximity labeling in plants. Here, we present the results of a systematic study applying a variety of biotin-based proximity labeling approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols that combine mass spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as a test case. We further benchmark the efficiency of various promiscuous biotin ligases in comparison with one-step affinity purification approaches. We identified both known and novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both nonbiotinylated and biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to suggest structural information of protein complexes.
Collapse
Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| |
Collapse
|
24
|
Baudouin HCM, Pfeiffer L, Ochsenreiter T. A comparison of three approaches for the discovery of novel tripartite attachment complex proteins in Trypanosoma brucei. PLoS Negl Trop Dis 2020; 14:e0008568. [PMID: 32936798 PMCID: PMC7521757 DOI: 10.1371/journal.pntd.0008568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/28/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Trypanosoma brucei is a single celled eukaryotic parasite and the causative agent of human African trypanosomiasis and nagana in cattle. Aside from its medical relevance, T. brucei has also been key to the discovery of several general biological principles including GPI-anchoring, RNA-editing and trans-splicing. The parasite contains a single mitochondrion with a singular genome. Recent studies have identified several molecular components of the mitochondrial genome segregation machinery (tripartite attachment complex, TAC), which connects the basal body of the flagellum to the mitochondrial DNA of T. brucei. The TAC component in closest proximity to the mitochondrial DNA is TAC102. Here we apply and compare three different approaches (proximity labelling, immunoprecipitation and yeast two-hybrid) to identify novel interactors of TAC102 and subsequently verify their localisation. Furthermore, we establish the direct interaction of TAC102 and p166 in the unilateral filaments of the TAC. Trypanosoma brucei belongs to a group of organisms that exist as human, animal and plant parasites. T. brucei (a human and animal parasite) has been developed as a model system to study basic biological as well as disease related questions in this group of organisms. We study how the parasite duplicates and divides its mitochondrial genome, an essential component of its energy generating machinery. The structure involved in dividing the mitochondrial genome into the daughter cells during cell division is called the tripartite attachment complex (TAC). The TAC is likely a unique structure not present in the host and thus might provide a new avenue for drug development. In this manuscript, we compare different techniques that allow the identification of novel components of this structure and verify the localisation of some of them. Furthermore, we also establish the interaction of two previously identified protein components.
Collapse
Affiliation(s)
- Hélène Clémentine Margareta Baudouin
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laura Pfeiffer
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | |
Collapse
|
25
|
Hannigan MM, Hoffman AM, Thompson JW, Zheng T, Nicchitta CV. Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. Mol Cell Proteomics 2020; 19:1826-1849. [PMID: 32788342 DOI: 10.1074/mcp.ra120.002228] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of numerous cellular components. Together, resident ER membrane proteins, cytoplasmic translation factors, and both integral membrane and cytosolic RNA-binding proteins operate in concert with membrane-associated ribosomes to facilitate ER-localized translation. Little is known, however, regarding the spatial organization of ER-localized translation. This question is of growing significance as it is now known that ER-bound ribosomes contribute to secretory, integral membrane, and cytosolic protein synthesis alike. To explore this question, we utilized quantitative proximity proteomics to identify neighboring protein networks for the candidate ribosome interactors SEC61β (subunit of the protein translocase), RPN1 (oligosaccharyltransferase subunit), SEC62 (translocation integral membrane protein), and LRRC59 (ribosome binding integral membrane protein). Biotin labeling time course studies of the four BioID reporters revealed distinct labeling patterns that intensified but only modestly diversified as a function of labeling time, suggesting that the ER membrane is organized into discrete protein interaction domains. Whereas SEC61β and RPN1 reporters identified translocon-associated networks, SEC62 and LRRC59 reporters revealed divergent protein interactomes. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, with the latter likely representing proximity to an ER luminal chaperone reflux pathway. In contrast, the LRRC59 interactome is highly enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins, uncovering a functional link between LRRC59 and mRNA translation regulation. Importantly, analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Moreover, [35S]-methionine incorporation assays revealed that siRNA silencing of LRRC59 expression reduced steady state translation levels on the ER by ca. 50%, and also impacted steady state translation levels in the cytosol compartment. Collectively, these data reveal a functional domain organization for the ER and identify a key role for LRRC59 in the organization and regulation of local translation.
Collapse
Affiliation(s)
- Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alyson M Hoffman
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - J Will Thompson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Duke Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA; Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.
| |
Collapse
|
26
|
Ummethum H, Hamperl S. Proximity Labeling Techniques to Study Chromatin. Front Genet 2020; 11:450. [PMID: 32477404 PMCID: PMC7235407 DOI: 10.3389/fgene.2020.00450] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Mammals contain over 200 different cell types, yet nearly all have the same genomic DNA sequence. It is a key question in biology how the genetic instructions in DNA are selectively interpreted by cells to specify various transcriptional programs and therefore cellular identity. The structural and functional organization of chromatin governs the transcriptional state of individual genes. To understand how genomic loci adopt different levels of gene expression, it is critical to characterize all local chromatin factors as well as long-range interactions in the 3D nuclear compartment. Much of our current knowledge regarding protein interactions in a chromatin context is based on affinity purification of chromatin components coupled to mass spectrometry (AP-MS). AP-MS has been invaluable to map strong protein-protein interactions in the nucleus. However, the interaction is detected after cell lysis and biochemical enrichment, allowing for loss or gain of false positive or negative interaction partners. Recently, proximity-dependent labeling methods have emerged as powerful tools for studying chromatin in its native context. These methods take advantage of engineered enzymes that are fused to a chromatin factor of interest and can directly label all factors in proximity. Subsequent pull-down assays followed by mass spectrometry or sequencing approaches provide a comprehensive snapshot of the proximal chromatin interactome. By combining this method with dCas9, this approach can also be extended to study chromatin at specific genomic loci. Here, we review and compare current proximity-labeling approaches available for studying chromatin, with a particular focus on new emerging technologies that can provide important insights into the transcriptional and chromatin interaction networks essential for cellular identity.
Collapse
Affiliation(s)
- Henning Ummethum
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
27
|
Kido K, Yamanaka S, Nakano S, Motani K, Shinohara S, Nozawa A, Kosako H, Ito S, Sawasaki T. AirID, a novel proximity biotinylation enzyme, for analysis of protein-protein interactions. eLife 2020; 9:54983. [PMID: 32391793 PMCID: PMC7302878 DOI: 10.7554/elife.54983] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/07/2020] [Indexed: 12/21/2022] Open
Abstract
Proximity biotinylation based on Escherichia coli BirA enzymes such as BioID (BirA*) and TurboID is a key technology for identifying proteins that interact with a target protein in a cell or organism. However, there have been some improvements in the enzymes that are used for that purpose. Here, we demonstrate a novel BirA enzyme, AirID (ancestral BirA for proximity-dependent biotin identification), which was designed de novo using an ancestral enzyme reconstruction algorithm and metagenome data. AirID-fusion proteins such as AirID-p53 or AirID-IκBα indicated biotinylation of MDM2 or RelA, respectively, in vitro and in cells, respectively. AirID-CRBN showed the pomalidomide-dependent biotinylation of IKZF1 and SALL4 in vitro. AirID-CRBN biotinylated the endogenous CUL4 and RBX1 in the CRL4CRBN complex based on the streptavidin pull-down assay. LC-MS/MS analysis of cells that were stably expressing AirID-IκBα showed top-level biotinylation of RelA proteins. These results indicate that AirID is a novel enzyme for analyzing protein–protein interactions. Proteins in a cell need to interact with each other to perform the many tasks required for organisms to thrive. A technique called proximity biotinylation helps scientists to pinpoint the identity of the proteins that partner together. It relies on attaching an enzyme (either BioID or TurboID) to a protein of interest; when a partner protein comes in close contact with this construct, the enzyme can attach a chemical tag called biotin to it. The tagged proteins can then be identified, revealing which molecules interact with the protein of interest. Although BioID and TurboID are useful tools, they have some limitations. Experiments using BioID take more than 16 hours to complete and require high levels of biotin to be added to the cells. TurboID is more active than BioID and is able to label proteins within ten minutes. However, under certain conditions, it is also more likely to be toxic for the cell, or to make mistakes and tag proteins that do not interact with the protein of interest. To address these issues, Kido et al. developed AirID, a new enzyme for proximity biotinylation. Experiments were then conducted to test how well AirID would perform, using proteins of interest whose partners were already known. These confirm that AirID was able to label partner proteins in human cells; compared with TurboID, it was also less likely to mistakenly tag non-partners or to kill the cells, even over long periods. The results by Kido et al. demonstrate that AirID is suitable for proximity biotinylation experiments in cells. Unlike BioID and TurboID, the enzyme may also have the potential to be used for long-lasting experiments in living organisms, since it is less toxic for cells over time.
Collapse
Affiliation(s)
- Kohki Kido
- Division of Cell-Free Life Science, Proteo-Science Center, Matsuyama, Japan
| | - Satoshi Yamanaka
- Division of Cell-Free Life Science, Proteo-Science Center, Matsuyama, Japan
| | - Shogo Nakano
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kou Motani
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Souta Shinohara
- Division of Cell-Free Life Science, Proteo-Science Center, Matsuyama, Japan
| | - Akira Nozawa
- Division of Cell-Free Life Science, Proteo-Science Center, Matsuyama, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Sohei Ito
- Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Matsuyama, Japan
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
May DG, Scott KL, Campos AR, Roux KJ. Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation. Cells 2020; 9:cells9051070. [PMID: 32344865 PMCID: PMC7290721 DOI: 10.3390/cells9051070] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/21/2022] Open
Abstract
BioID is a well-established method for identifying protein–protein interactions and has been utilized within live cells and several animal models. However, the conventional labeling period requires 15–18 h for robust biotinylation which may not be ideal for some applications. Recently, two new ligases termed TurboID and miniTurbo were developed using directed evolution of the BioID ligase and were able to produce robust biotinylation following a 10 min incubation with excess biotin. However, there is reported concern about inducibility of biotinylation, cellular toxicity, and ligase stability. To further investigate the practical applications of TurboID and ascertain strengths and weaknesses compared to BioID, we developed several stable cell lines expressing BioID and TurboID fusion proteins and analyzed them via immunoblot, immunofluorescence, and biotin-affinity purification-based proteomics. For TurboID we observed signs of protein instability, persistent biotinylation in the absence of exogenous biotin, and an increase in the practical labeling radius. However, TurboID enabled robust biotinylation in the endoplasmic reticulum lumen compared to BioID. Induction of biotinylation could be achieved by combining doxycycline-inducible expression with growth in biotin depleted culture media. These studies should help inform investigators utilizing BioID-based methods as to the appropriate ligase and experimental protocol for their particular needs.
Collapse
Affiliation(s)
- Danielle G. May
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD 57104, USA; (D.G.M.); (K.L.S.)
| | - Kelsey L. Scott
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD 57104, USA; (D.G.M.); (K.L.S.)
| | - Alexandre R. Campos
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA;
| | - Kyle J. Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, SD 57104, USA; (D.G.M.); (K.L.S.)
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105, USA
- Correspondence: ; Tel.: +1-605-312-6418
| |
Collapse
|
30
|
Pereira EJ, Burns JS, Lee CY, Marohl T, Calderon D, Wang L, Atkins KA, Wang CC, Janes KA. Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies. Sci Signal 2020; 13:13/627/eaba4200. [PMID: 32291314 DOI: 10.1126/scisignal.aba4200] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Breast and mammary epithelial cells experience different local environments during tissue development and tumorigenesis. Microenvironmental heterogeneity gives rise to distinct cell regulatory states whose identity and importance are just beginning to be appreciated. Cellular states diversify when clonal three-dimensional (3D) spheroids are cultured in basement membrane, and one such state is associated with stress tolerance and poor response to anticancer therapeutics. Here, we found that this state was jointly coordinated by the NRF2 and p53 pathways, which were costabilized by spontaneous oxidative stress within 3D cultures. Inhibition of NRF2 or p53 individually disrupted some of the transcripts defining the regulatory state but did not yield a notable phenotype in nontransformed breast epithelial cells. In contrast, combined perturbation prevented 3D growth in an oxidative stress-dependent manner. By integrating systems models of NRF2 and p53 signaling in a single oxidative stress network, we recapitulated these observations and made predictions about oxidative stress profiles during 3D growth. NRF2 and p53 signaling were similarly coordinated in normal breast epithelial tissue and hormone-negative ductal carcinoma in situ lesions but were uncoupled in triple-negative breast cancer (TNBC), a subtype in which p53 is usually mutated. Using the integrated model, we correlated the extent of this uncoupling in TNBC cell lines with the importance of NRF2 in the 3D growth of these cell lines and their predicted handling of oxidative stress. Our results point to an oxidative stress tolerance network that is important for single cells during glandular development and the early stages of breast cancer.
Collapse
Affiliation(s)
- Elizabeth J Pereira
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Joseph S Burns
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Christina Y Lee
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Taylor Marohl
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Delia Calderon
- Biology and Chemistry Programs, California State University Channel Islands, Camarillo, CA 93012, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Kristen A Atkins
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Chun-Chao Wang
- Institute of Molecular Medicine and Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
31
|
Wang J, Samanta R, Custer G, Look C, Matysiak S, Beckett D. Tuning Allostery through Integration of Disorder to Order with a Residue Network. Biochemistry 2020; 59:790-801. [PMID: 31899864 DOI: 10.1021/acs.biochem.9b01006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In allostery, a signal from one site in a protein is transmitted to a second site to alter its function. Due to its ubiquity in biology and the potential for its exploitation in drug and protein design, the molecular basis of allosteric communication continues to be the subject of intense research. Although allosterically coupled sites are frequently characterized by disorder, how communication between disordered segments occurs remains obscure. Allosteric activation of Escherichia coli BirA dimerization occurs via coupled distant disorder-to-order transitions. In this work, combined structural and computational studies reveal an extensive residue network in BirA. Substitution of several network residues yields large perturbations to allostery. Force distribution analysis reveals that disruptions to the disorder-to-order transitions through amino acid substitution are manifested in shifts in the energy experienced by network residues as well as alterations in packing of an α-helix that plays a critical role in allostery. The combined results reveal a highly distributed allosteric mechanism that is robust to sequence change.
Collapse
Affiliation(s)
- Jingheng Wang
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Riya Samanta
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Gregory Custer
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Christopher Look
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| |
Collapse
|
32
|
O'Loughlin T, Kendrick-Jones J, Buss F. Approaches to Identify and Characterise MYO6-Cargo Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1239:355-380. [PMID: 32451866 DOI: 10.1007/978-3-030-38062-5_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Given the prevalence and importance of the actin cytoskeleton and the host of associated myosin motors, it comes as no surprise to find that they are linked to a plethora of cellular functions and pathologies. Although our understanding of the biophysical properties of myosin motors has been aided by the high levels of conservation in their motor domains and the extensive work on myosin in skeletal muscle contraction, our understanding of how the nonmuscle myosins participate in such a wide variety of cellular processes is less clear. It is now well established that the highly variable myosin tails are responsible for targeting these myosins to distinct cellular sites for specific functions, and although a number of adaptor proteins have been identified, our current understanding of the cellular processes involved is rather limited. Furthermore, as more adaptor proteins, cargoes and complexes are identified, the importance of elucidating the regulatory mechanisms involved is essential. Ca2+, and now phosphorylation and ubiquitination, are emerging as important regulators of cargo binding, and it is likely that other post-translational modifications are also involved. In the case of myosin VI (MYO6), a number of immediate binding partners have been identified using traditional approaches such as yeast two-hybrid screens and affinity-based pull-downs. However, these methods have only been successful in identifying the cargo adaptors, but not the cargoes themselves, which may often comprise multi-protein complexes. Furthermore, motor-adaptor-cargo interactions are dynamic by nature and often weak, transient and highly regulated and therefore difficult to capture using traditional affinity-based methods. In this chapter we will discuss the various approaches including functional proteomics that have been used to uncover and characterise novel MYO6-associated proteins and complexes and how this work contributes to a fuller understanding of the targeting and function(s) of this unique myosin motor.
Collapse
Affiliation(s)
- Thomas O'Loughlin
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge, UK
| | | | - Folma Buss
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge, UK.
| |
Collapse
|
33
|
Santin YG. Uncovering the In Vivo Proxisome Using Proximity‐Tagging Methods. Bioessays 2019; 41:e1900131. [DOI: 10.1002/bies.201900131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/04/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Yoann G. Santin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université – CNRS UMR7255 31 Chemin Joseph Aiguier, CS70071, 13402 Marseille Cedex 09 France
| |
Collapse
|
34
|
Abstract
Proximity-dependent labeling methods for detecting candidate protein-protein interactions (PPIs) or mapping the protein constituency of subcellular domains have become increasingly utilized by the scientific community. One such method, BioID, allows for the identification of not only strong interactions but also weak and transient associations between a protein of interest (POI) or targeting motif and adjacent proteins. A promiscuous biotin ligase is fused to a POI or targeting motif, expressed in living cells, and induced to biotinylate proximal proteins during a defined labeling period by biotin supplementation. This generates a history of protein-protein associations that occurred with the POI or the protein constituency within a discrete subcellular domain during the labeling period. Biotinylated proteins are subsequently isolated, identified via mass spectrometry, and investigated as candidate interactors with the POI or as constituents within a subcellular domain. The BioID method has been utilized by numerous research groups and is continually being optimized, applied to new models, and modified for use in novel applications. Here we describe a protocol by which a BioID fusion protein can be validated and utilized for BioID pull-downs.
Collapse
Affiliation(s)
- Danielle G May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD, USA
| | - Kyle J Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA.
| |
Collapse
|
35
|
Li T, Zhang F, Qin P, Wang Y, Wang A, Zhao L, Xu B, Gao Q. Exploring a Tumor-Intrinsic PD-L1 Signal with Proximity-Dependent Biotin Identification in Lung Cancer Cells. Biochemistry 2019; 58:2293-2296. [PMID: 31021072 DOI: 10.1021/acs.biochem.9b00113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blocking the PD-L1/PD-1 interaction with an antibody produces a durable response in patients with diverse advanced cancers. However, it remains elusive on whether the engagement of PD-L1 to PD-1 leads to tumor-intrinsic signaling. In this study, we aim to explore novel protein substrates participating in transducing this tumor-intrinsic PD-L1 signaling. To this end, we performed a BioID (proximity-dependent biotin identification) assay, in which we fused PD-L1 to BirA* (a promiscuous mutant of bacterial biotin ligase BirA) and overexpressed it in the lung adenocarcinoma A549 cell line. Through streptavidin affinity capture and mass spectrometry analysis, we identified 57 candidate proteins including 18 PD-L1/PD-1-interaction-dependent neighbors. In addition to this, 9 out of 57 candidates were involved in the EGFR signaling pathway, which is known to play a critical role in tumorigenesis and multiple therapeutic resistances of lung cancer. This study will provide a new insight in understanding tumor-intrinsic PD-L1-signaling effectors of lung cancer.
Collapse
Affiliation(s)
- Tiepeng Li
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Fang Zhang
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Peng Qin
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Yao Wang
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Axiang Wang
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Lingdi Zhao
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Benling Xu
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| | - Quanli Gao
- Department of Immunotherapy , Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital , Zhengzhou , Henan 450008 , People's Republic of China
| |
Collapse
|
36
|
Satiaputra J, Sternicki LM, Hayes AJ, Pukala TL, Booker GW, Shearwin KE, Polyak SW. Native mass spectrometry identifies an alternative DNA-binding pathway for BirA from Staphylococcus aureus. Sci Rep 2019; 9:2767. [PMID: 30808984 PMCID: PMC6391492 DOI: 10.1038/s41598-019-39398-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022] Open
Abstract
An adequate supply of biotin is vital for the survival and pathogenesis of Staphylococcus aureus. The key protein responsible for maintaining biotin homeostasis in bacteria is the biotin retention protein A (BirA, also known as biotin protein ligase). BirA is a bi-functional protein that serves both as a ligase to catalyse the biotinylation of important metabolic enzymes, as well as a transcriptional repressor that regulates biotin biosynthesis, biotin transport and fatty acid elongation. The mechanism of BirA regulated transcription has been extensively characterized in Escherichia coli, but less so in other bacteria. Biotin-induced homodimerization of E. coli BirA (EcBirA) is a necessary prerequisite for stable DNA binding and transcriptional repression. Here, we employ a combination of native mass spectrometry, in vivo gene expression assays, site-directed mutagenesis and electrophoretic mobility shift assays to elucidate the DNA binding pathway for S. aureus BirA (SaBirA). We identify a mechanism that differs from that of EcBirA, wherein SaBirA is competent to bind DNA as a monomer both in the presence and absence of biotin and/or MgATP, allowing homodimerization on the DNA. Bioinformatic analysis demonstrated the SaBirA sequence used here is highly conserved amongst other S. aureus strains, implying this DNA-binding mechanism is widely employed.
Collapse
Affiliation(s)
- Jiulia Satiaputra
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.,Harry Perkins Institute of Medical Research, Shenton Park, Western Australia, 6008, Australia
| | - Louise M Sternicki
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Andrew J Hayes
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia.,Faculty of Health and Medical Sciences, Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Grant W Booker
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Keith E Shearwin
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Steven W Polyak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia. .,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5001, Australia.
| |
Collapse
|
37
|
Olson MG, Jorgenson LM, Widner RE, Rucks EA. Proximity Labeling of the Chlamydia trachomatis Inclusion Membrane. Methods Mol Biol 2019; 2042:245-278. [PMID: 31385281 DOI: 10.1007/978-1-4939-9694-0_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the study of intracellular bacteria that reside within a membrane-bound vacuole, there are many questions related to how prokaryotic or eukaryotic transmembrane or membrane-associated proteins are organized and function within the membranes of these pathogen-containing vacuoles. Yet this host-pathogen interaction interface has proven difficult to experimentally resolve. For example, one method to begin to understand protein function is to determine the protein-binding partners; however, examining protein-protein interactions of hydrophobic transmembrane proteins is not widely successful using standard immunoprecipitation or coimmunoprecipitation techniques. In these scenarios, the lysis conditions that maintain protein-protein interactions are not compatible with solubilizing hydrophobic membrane proteins. In this chapter, we outline two proximity labeling systems to circumvent these issues to study (1) eukaryotic proteins that localize to the membrane-bound inclusion formed by Chlamydia trachomatis using BioID, and (2) chlamydial proteins that are inserted into the inclusion membrane using APEX2. BioID is a promiscuous biotin ligase to tag proximal proteins with biotin. APEX2 is an ascorbate peroxidase that creates biotin-phenoxyl radicals to label proximal proteins with biotin or 3,3'-diaminobenzidine intermediates for examination of APEX2 labeling of subcellular structures using transmission electron microscopy. We present how these methods were originally conceptualized and developed, so that the user can understand the strengths and limitations of each proximity labeling system. We discuss important considerations regarding experimental design, which include careful consideration of background conditions and statistical analysis of mass spectrometry results. When applied in the appropriate context with adequate controls, these methods can be powerful tools toward understanding membrane interfaces between intracellular pathogens and their hosts.
Collapse
Affiliation(s)
- Macy G Olson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lisa M Jorgenson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ray E Widner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Elizabeth A Rucks
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
| |
Collapse
|
38
|
Abstract
BioID has become an increasingly utilized tool for identifying candidate protein-protein interactions (PPIs) in living cells. This method utilizes a promiscuous biotin ligase, called BioID, fused to a protein of interest that when expressed in cells can be induced to biotinylate interacting and proximate proteins over a period of hours, thus generating a history of protein associations. These biotinylated proteins are subsequently purified and identified via mass spectrometry. Compared to other conventional methods typically used to screen strong PPIs, BioID allows for the detection of weak and transient interactions within a relevant biological setting over a defined period of time. Here we briefly review the scientific progress enabled by the BioID technology, detail an updated protocol for applying the method to proteins in living cells, and offer insights for troubleshooting commonly encountered setbacks.
Collapse
Affiliation(s)
- Rhiannon M. Sears
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104,Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069
| | - Danielle G. May
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104
| | - Kyle J. Roux
- Enabling Technology Group, Sanford Research, Sioux Falls, SD 57104,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
| |
Collapse
|
39
|
Oostdyk LT, Shank L, Jividen K, Dworak N, Sherman NE, Paschal BM. Towards improving proximity labeling by the biotin ligase BirA. Methods 2018; 157:66-79. [PMID: 30419333 DOI: 10.1016/j.ymeth.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/26/2018] [Accepted: 11/06/2018] [Indexed: 11/15/2022] Open
Abstract
The discovery and validation of protein-protein interactions provides a knowledge base that is critical for defining protein networks and how they underpin the biology of the cell. Identification of protein interactions that are highly transient, or sensitive to biochemical disruption, can be very difficult. This challenge has been met by proximity labeling methods which generate reactive species that chemically modify neighboring proteins. The most widely used proximity labeling method is BioID, which features a mutant biotin ligase BirA(Arg118Gly), termed BirA*, fused to a protein of interest. Here, we explore how amino acid substitutions at Arg118 affect the biochemical properties of BirA. We found that relative to wild-type BirA, the Arg118Lys substitution both slightly reduced biotin affinity and increased the release of reactive biotinyl-5'-AMP. BioID using a BirA(Arg118Lys)-Lamin A fusion enabled identification of PCNA as a lamina-proximal protein in HEK293T cells, a finding that was validated by immunofluorescence microscopy. Our data expand on the concept that proximity labeling by BirA fused to proteins of interest can be modulated by amino acid substitutions that affect biotin affinity and the release of biotinyl-5'-AMP.
Collapse
Affiliation(s)
- Luke T Oostdyk
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, VA 22908, USA
| | - Leonard Shank
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Kasey Jividen
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Natalia Dworak
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA
| | - Nicholas E Sherman
- W.M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, VA 22908, USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, VA 22908, USA.
| |
Collapse
|
40
|
Jamilloux Y, Lagrange B, Di Micco A, Bourdonnay E, Provost A, Tallant R, Henry T, Martinon F. A proximity-dependent biotinylation (BioID) approach flags the p62/sequestosome-1 protein as a caspase-1 substrate. J Biol Chem 2018; 293:12563-12575. [PMID: 29929983 DOI: 10.1074/jbc.ra117.000435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 06/08/2018] [Indexed: 01/24/2023] Open
Abstract
The inflammasome is a major component of the innate immune system, and its main function is to activate caspase-1, a cysteine protease that promotes inflammation by inducing interleukin-1β (IL-1β) maturation and release into the extracellular milieu. To prevent uncontrolled inflammation, this complex is highly regulated. When it is assembled, the inflammasome is insoluble, which has long precluded the analysis of its interactions with other proteins. Here we used the proximity-dependent biotinylation assay (BioID) to identify proteins associated with caspase-1 during inflammasome activation. Using the BioID in a cell-free system in which the inflammasome had been activated, we found that a caspase-1-biotin ligase fusion protein selectively labeled 111 candidates, including the p62/sequestosome-1 protein (p62). Using co-immunoprecipitation experiments, we demonstrated that p62 interacts with caspase-1. This interaction promoted caspase-1-mediated cleavage of p62 at Asp-329. Mechanistic and functional analyses revealed that caspase-1-mediated cleavage of p62 leads to loss of its interaction with the autophagosomal protein microtubule-associated protein 1 light chain 3 β (LC3B). Strikingly, overexpression of a p62 N-terminal fragment generated upon caspase-1 cleavage decreased IL-1β release, whereas overexpression of p62's C-terminal portion enhanced IL-1β release, by regulating pro-IL1β levels. Overall, the overexpression of both fragments together decreased IL-1β release. Taken together, our results indicate that caspase-1-mediated p62 cleavage plays a complex role in balancing caspase-1-induced inflammation.
Collapse
Affiliation(s)
- Yvan Jamilloux
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Brice Lagrange
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Antonia Di Micco
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Emilie Bourdonnay
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Angélina Provost
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Rémy Tallant
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland.,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Thomas Henry
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland, .,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| | - Fabio Martinon
- From the Department of Biochemistry, University of Lausanne, 1066 Epalinges, Switzerland, .,the Centre International de Recherche en Infectiologie, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, 69007 Lyon, France, and.,the Department of Internal Medicine, Hopital de la Croix-Rousse, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69004 Lyon, France
| |
Collapse
|
41
|
Neuronal Proteomic Analysis of the Ubiquitinated Substrates of the Disease-Linked E3 Ligases Parkin and Ube3a. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3180413. [PMID: 29693004 PMCID: PMC5859835 DOI: 10.1155/2018/3180413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/15/2018] [Indexed: 01/09/2023]
Abstract
Both Parkin and UBE3A are E3 ubiquitin ligases whose mutations result in severe brain dysfunction. Several of their substrates have been identified using cell culture models in combination with proteasome inhibitors, but not in more physiological settings. We recently developed the bioUb strategy to isolate ubiquitinated proteins in flies and have now identified by mass spectrometry analysis the neuronal proteins differentially ubiquitinated by those ligases. This is an example of how flies can be used to provide biological material in order to reveal steady state substrates of disease causing genes. Collectively our results provide new leads to the possible physiological functions of the activity of those two disease causing E3 ligases. Particularly, in the case of Parkin the novelty of our data originates from the experimental setup, which is not overtly biased by acute mitochondrial depolarisation. In the case of UBE3A, it is the first time that a nonbiased screen for its neuronal substrates has been reported.
Collapse
|
42
|
Roux KJ, Kim DI, Burke B, May DG. BioID: A Screen for Protein-Protein Interactions. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2018; 91:19.23.1-19.23.15. [PMID: 29516480 PMCID: PMC6028010 DOI: 10.1002/cpps.51] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BioID is a unique method to screen for physiologically relevant protein interactions that occur in living cells. This technique harnesses a promiscuous biotin ligase to biotinylate proteins based on proximity. The ligase is fused to a protein of interest and expressed in cells, where it biotinylates proximal endogenous proteins. Because it is a rare protein modification in nature, biotinylation of these endogenous proteins by BioID fusion proteins enables their selective isolation and identification with standard biotin-affinity capture. Proteins identified by BioID are candidate interactors for the protein of interest. BioID can be applied to insoluble proteins, can identify weak and/or transient interactions, and is amenable to temporal regulation. Initially applied to mammalian cells, BioID has potential application in a variety of cell types from diverse species. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Kyle J Roux
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota
| | - Dae In Kim
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
| | - Brian Burke
- Institute of Medical Biology, Immunos, Singapore
| | - Danielle G May
- Children's Health Research Center, Sanford Research, North Sioux Falls, South Dakota
| |
Collapse
|
43
|
Cheah JS, Yamada S. A simple elution strategy for biotinylated proteins bound to streptavidin conjugated beads using excess biotin and heat. Biochem Biophys Res Commun 2017; 493:1522-1527. [PMID: 28986262 DOI: 10.1016/j.bbrc.2017.09.168] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 09/30/2017] [Indexed: 12/31/2022]
Abstract
Protein-protein interactions are the molecular basis of cell signaling. Recently, proximity based biotin identification (BioID) has emerged as an alternative approach to traditional co-immunoprecipitation. In this protocol, a mutant biotin ligase promiscuously labels proximal binding partners with biotin, and resulting biotinylated proteins are purified using streptavidin conjugated beads. This approach does not require preservation of protein complexes in vitro, making it an ideal approach to identify transient or weak protein complexes. However, due to the high affinity bond between streptavidin and biotin, elution of biotinylated proteins from streptavidin conjugated beads requires harsh denaturing conditions, which are often incompatible with downstream processing. To effectively release biotinylated proteins bound to streptavidin conjugated beads, we designed a series of experiments to determine optimal binding and elution conditions. Interestingly, the concentrations of SDS and IGEPAL-CA630 during the incubation with streptavidin conjugated beads were the key to effective elution of biotinylated proteins using excess biotin and heating. This protocol provides an alternative method to isolate biotinylated proteins from streptavidin conjugated beads that is suitable for further downstream analysis.
Collapse
Affiliation(s)
- Joleen S Cheah
- Biomedical Engineering Department, University of California, Davis, United States
| | - Soichiro Yamada
- Biomedical Engineering Department, University of California, Davis, United States.
| |
Collapse
|
44
|
Wang J, Custer G, Beckett D, Matysiak S. Long Distance Modulation of Disorder-to-Order Transitions in Protein Allostery. Biochemistry 2017; 56:4478-4488. [PMID: 28718281 DOI: 10.1021/acs.biochem.7b00496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the Escherichia coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP. The effector acts by promoting BirA dimerization, which is a prerequisite for sequence-specific binding to the biotin biosynthetic operon operator sequence. A 30 Å distance separates the effector binding and dimerization surfaces in BirA, and previous studies indicate that allostery is mediated, in part, by disorder-to-order transitions on the two coupled sites. In this work, combined experimental and computational methods have been applied to investigate the molecular basis of allosteric communication in BirA. Double-mutant cycle analysis coupled with thermodynamic measurements indicates functional coupling between residues in disordered loops on the two distant surfaces. All atom molecular dynamics simulations reveal that this coupling occurs through long distance reciprocal modulation of the structure and dynamics of disorder-to-order transitions on the two surfaces.
Collapse
Affiliation(s)
- Jingheng Wang
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gregory Custer
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Dorothy Beckett
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering and ‡Department of Chemistry & Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| |
Collapse
|
45
|
Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes. Nat Commun 2017; 8:15690. [PMID: 28585547 PMCID: PMC5467174 DOI: 10.1038/ncomms15690] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/19/2017] [Indexed: 02/06/2023] Open
Abstract
Understanding the function of the thousands of cellular proteins is a central question in molecular cell biology. As proteins are typically part of multiple dynamic and often overlapping macromolecular complexes exerting distinct functions, the identification of protein–protein interactions (PPI) and their assignment to specific complexes is a crucial but challenging task. We present a protein fragments complementation assay integrated with the proximity-dependent biotinylation technique BioID. Activated on the interaction of two proteins, split-BioID is a conditional proteomics approach that allows in a single and simple assay to both experimentally validate binary PPI and to unbiasedly identify additional interacting factors. Applying our method to the miRNA-mediated silencing pathway, we can probe the proteomes of two distinct functional complexes containing the Ago2 protein and uncover the protein GIGYF2 as a regulator of miRNA-mediated translation repression. Hence, we provide a novel tool to study dynamic spatiotemporally defined protein complexes in their native cellular environment. The BioID approaches takes advantage of the promiscuous biotinylation enzyme (BirA*) to identify proteins that closely interact. Here the authors improve the resolution of BioID using a protein fragment complementation approach that allows the assignment of protein-protein interactions to specific complexes within a common interactome.
Collapse
|
46
|
Cann ML, McDonald IM, East MP, Johnson GL, Graves LM. Measuring Kinase Activity-A Global Challenge. J Cell Biochem 2017; 118:3595-3606. [PMID: 28464261 DOI: 10.1002/jcb.26103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 12/22/2022]
Abstract
The kinase enzymes within a cell, known collectively as the kinome, play crucial roles in many signaling pathways, including survival, motility, differentiation, stress response, and many more. Aberrant signaling through kinase pathways is often linked to cancer, among other diseases. A major area of scientific research involves understanding the relationships between kinases, their targets, and how the kinome adapts to perturbations of the cellular system. This review will discuss many of the current and developing methods for studying kinase activity, and evaluate their applications, advantages, and disadvantages. J. Cell. Biochem. 118: 3595-3606, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Marissa L Cann
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Ian M McDonald
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Michael P East
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| | - Lee M Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Genetic Medicine Building, Campus Box #7365, 120 Mason Farm Rd., Chapel Hill, North Carolina, 27599
| |
Collapse
|
47
|
Wang J, Beckett D. A conserved regulatory mechanism in bifunctional biotin protein ligases. Protein Sci 2017; 26:1564-1573. [PMID: 28466579 DOI: 10.1002/pro.3182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 11/10/2022]
Abstract
Class II bifunctional biotin protein ligases (BirA), which catalyze post-translational biotinylation and repress transcription initiation, are broadly distributed in eubacteria and archaea. However, it is unclear if these proteins all share the same molecular mechanism of transcription regulation. In Escherichia coli the corepressor biotinoyl-5'-AMP (bio-5'-AMP), which is also the intermediate in biotin transfer, promotes operator binding and resulting transcription repression by enhancing BirA dimerization. Like E. coli BirA (EcBirA), Staphylococcus aureus, and Bacillus subtilis BirA (Sa and BsBirA) repress transcription in vivo in a biotin-dependent manner. In this work, sedimentation equilibrium measurements were performed to investigate the molecular basis of this biotin-responsive transcription regulation. The results reveal that, as observed for EcBirA, Sa, and BsBirA dimerization reactions are significantly enhanced by bio-5'-AMP binding. Thus, the molecular mechanism of the Biotin Regulatory System is conserved in the biotin repressors from these three organisms.
Collapse
Affiliation(s)
- Jingheng Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| | - Dorothy Beckett
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| |
Collapse
|
48
|
Bond TEH, Sorenson AE, Schaeffer PM. Functional characterisation of Burkholderia pseudomallei biotin protein ligase: A toolkit for anti-melioidosis drug development. Microbiol Res 2017; 199:40-48. [PMID: 28454708 DOI: 10.1016/j.micres.2017.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 01/17/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis. The bacterium is responsible for 20% of community-acquired sepsis cases and 40% of sepsis-related mortalities in northeast Thailand, and is intrinsically resistant to aminoglycosides, macrolides, rifamycins, cephalosporins, and nonureidopenicillins. There is no vaccine and its diagnosis is problematic. Biotin protein ligase (BirA) which is essential for fatty acid synthesis has been proposed as a drug target in bacteria. Very few bacterial BirA have been characterized, and a better understanding of these enzymes is necessary to further assess their value as drug targets. BirA within the Burkholderia genus have not yet been investigated. We present for the first time the cloning, expression, purification and functional characterisation of the putative Bp BirA and orthologous B. thailandensis (Bt) biotin carboxyl carrier protein (BCCP) substrate. A GFP-tagged Bp BirA was produced and applied for the development of a high-throughput (HT) assay based on our differential scanning fluorimetry of GFP-tagged proteins (DSF-GTP) principle as well as an electrophoretic mobility shift assay. Our biochemical data in combination with the new HT DSF-GTP and biotinylation activity assay could facilitate future drug screening efforts against this drug-resistant organism.
Collapse
Affiliation(s)
- Thomas E H Bond
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Alanna E Sorenson
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia
| | - Patrick M Schaeffer
- Comparative Genomics Centre, James Cook University, DB21, James Cook Drive, Townsville, QLD 4811, Australia.
| |
Collapse
|
49
|
Groves JA, Maduka AO, O'Meally RN, Cole RN, Zachara NE. Fatty acid synthase inhibits the O-GlcNAcase during oxidative stress. J Biol Chem 2017; 292:6493-6511. [PMID: 28232487 DOI: 10.1074/jbc.m116.760785] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/10/2017] [Indexed: 01/01/2023] Open
Abstract
The dynamic post-translational modification O-linked β-N-acetylglucosamine (O-GlcNAc) regulates thousands of nuclear, cytoplasmic, and mitochondrial proteins. Cellular stress, including oxidative stress, results in increased O-GlcNAcylation of numerous proteins, and this increase is thought to promote cell survival. The mechanisms by which the O-GlcNAc transferase (OGT) and the O-GlcNAcase (OGA), the enzymes that add and remove O-GlcNAc, respectively, are regulated during oxidative stress to alter O-GlcNAcylation are not fully characterized. Here, we demonstrate that oxidative stress leads to elevated O-GlcNAc levels in U2OS cells but has little impact on the activity of OGT. In contrast, the expression and activity of OGA are enhanced. We hypothesized that this seeming paradox could be explained by proteins that bind to and control the local activity or substrate targeting of OGA, thereby resulting in the observed stress-induced elevations of O-GlcNAc. To identify potential protein partners, we utilized BioID proximity biotinylation in combination with stable isotopic labeling of amino acids in cell culture (SILAC). This analysis revealed 90 OGA-interacting partners, many of which exhibited increased binding to OGA upon stress. The associations of OGA with fatty acid synthase (FAS), filamin-A, heat shock cognate 70-kDa protein, and OGT were confirmed by co-immunoprecipitation. The pool of OGA bound to FAS demonstrated a substantial (∼85%) reduction in specific activity, suggesting that FAS inhibits OGA. Consistent with this observation, FAS overexpression augmented stress-induced O-GlcNAcylation. Although the mechanism by which FAS sequesters OGA remains unknown, these data suggest that FAS fine-tunes the cell's response to stress and injury by remodeling cellular O-GlcNAcylation.
Collapse
Affiliation(s)
- Jennifer A Groves
- From the Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185
| | - Austin O Maduka
- From the Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185.,the Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, and
| | - Robert N O'Meally
- From the Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185.,the Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Robert N Cole
- From the Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185.,the Mass Spectrometry and Proteomics Facility, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Natasha E Zachara
- From the Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185,
| |
Collapse
|
50
|
Ramirez J, Elu N, Martinez A, Lectez B, Mayor U. In Vivo Strategies to Isolate and Characterize the Neuronal Ubiquitinated Proteome. NEUROMETHODS 2017. [DOI: 10.1007/978-1-4939-7119-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|