1
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Zouhir S, Abidi W, Krasteva PV. Large Complexes: Cloning Strategy, Production, and Purification. Methods Mol Biol 2024; 2715:395-413. [PMID: 37930542 DOI: 10.1007/978-1-0716-3445-5_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
With few exceptions-such as myxobacteria, filamentous cyanobacteria, and actinomycetes (Rokas, Annu Rev Genet 42:235-251, 2008)-bacteria are defined as unicellular prokaryotes or single, self-sufficient cells containing all the genetic material necessary for their physiology and reproduction, while maintaining none or a minimum of intracellular organelles for pathway compartmentalization. The latter is therefore primarily achieved through the assembly of macromolecular complexes that can secure spatiotemporal control of a plethora of physiological processes, such as precise midcell division, assembly of diverse motility organelles and chemotaxis sensory arrays, metabolic channeling of substrates and toxic intermediates, localized signal transduction via soluble intracellular second messengers or the secretion of signaling molecules, competition effectors, and extracellular matrix components (Cornejo et al., Curr Opin Cell Biol 26:132-138, 2014; de Lorenzo et al., FEMS Microbiol Rev 39:96-119, 2015; Krasteva and Sondermann, Nat Chem Biol 13:350-359, 2017; Abidi et al., FEMS Microbiol Rev 46(2):fuab051, 2022; Altinoglu et al., PLoS Genet 18:e1009991, 2022). Oftentimes, pathway-specific components are encoded by clusters of co-regulated genes (Lawrence, Annu Rev Microbiol 57:419-440, 2003), which not only allows for facilitated macrocomplex assembly and rapid physiological adaptation in cellulo but can also be harnessed for the recombinant coexpression and purification of intact multicomponent nanomachines for structure-function studies of medical or biotechnological relevance. Important examples are synthase-dependent exopolysaccharide secretion systems that provide key biofilm matrix components in a vast variety of free-living or pathogenic species and at the molecular level secure the physical conduit, protection, chemical modifications and energetics for the processive extrusion of hydrophilic biopolymers through the complex bacterial envelope (Abidi et al., FEMS Microbiol Rev 46(2):fuab051, 2022). Here, we present cloning, expression, and purification strategies for the structure-function studies of macromolecular assemblies involved in bacterial cellulose secretion (Bcs) (Krasteva et al. Nat Commun 8:2065, 2017; Abidi et al. Sci Adv 7:eabd8049, 2021) that can be adapted to a variety of multicomponent cytosolic or membrane-embedded assemblies.
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Affiliation(s)
- Samira Zouhir
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- 'Structural Biology of Biofilms' Group, European Institute of Chemistry and Biology (IECB), Pessac, France
- CNRS, LBPA, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Wiem Abidi
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France
- 'Structural Biology of Biofilms' Group, European Institute of Chemistry and Biology (IECB), Pessac, France
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Petya V Krasteva
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac, France.
- 'Structural Biology of Biofilms' Group, European Institute of Chemistry and Biology (IECB), Pessac, France.
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2
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Beyer T, Martins T, Srikaran JJ, Seda M, Peskett E, Klose F, Junger K, Beales PL, Ueffing M, Boldt K, Jenkins D. Affinity Purification of Intraflagellar Transport (IFT) Proteins in Mice Using Endogenous Streptavidin/FLAG Tags. Methods Mol Biol 2024; 2725:199-212. [PMID: 37856026 DOI: 10.1007/978-1-0716-3507-0_12] [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] [Indexed: 10/20/2023]
Abstract
Biological complexity is achieved through elaborate interactions between relatively few individual components. Affinity purification (AP) has allowed these networks of protein-protein interactions that regulate key biological processes to be interrogated systematically. In order to perform these studies at the required scale, easily transfectable immortalized cell lines have typically been used. Gene-editing now affords the systematic creation of isogenic mouse models carrying endogenous tags for affinity proteomics. This may allow protein-protein interactions to be characterized in the appropriate tissue for a particular biological process or disease phenotype under physiological conditions, and for interaction landscapes to be compared across tissues. Here we demonstrate application to intraflagellar transport (IFT) proteins, which are WD40-domain-containing proteins that are essential for the formation and function of all types of cilia. We describe a method to generate mice with an endogenous C-terminal streptavidin/FLAG tag, using Ift80 as an example, and demonstrate the successful implementation of AP in this model. This method can easily be adapted for N- and C-terminal tagging of many other proteins in vivo.
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Affiliation(s)
- Tina Beyer
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Tiago Martins
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Marian Seda
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emma Peskett
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Franziska Klose
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Katrin Junger
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philip L Beales
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Dagan Jenkins
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
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3
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Yim YY, Nestler EJ. Cell-Type-Specific Neuroproteomics of Synapses. Biomolecules 2023; 13:998. [PMID: 37371578 PMCID: PMC10296650 DOI: 10.3390/biom13060998] [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: 05/11/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders.
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Affiliation(s)
- Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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4
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Fic E, Cieślik A, Figiel M, Dziedzicka-Wasylewska M. Identification of mitogen-activated protein kinase phosphatase-1 (MKP-1) protein partners using tandem affinity purification and mass spectrometry. Pharmacol Rep 2023; 75:474-481. [PMID: 36964420 PMCID: PMC10060364 DOI: 10.1007/s43440-023-00471-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND According to the World Health Organization Report, depressive disorders affect about 10% of the population. The molecular mechanism of the pathogenesis of depression is still not well understood. The new findings point to phosphatases as potential targets for effective depression therapy. The aim of the present work was the development of a method that would enable the identification of mitogen-activated protein kinase phosphatase-1 (MKP-1) protein partners using a proteomic approach. METHODS The research was carried out using the PC12 cell line, often used as a model for neurobiological research. The use of the procedure for efficient purification of protein complexes-tandem affinity purification (TAP) will facilitate the identification of proteins interacting with MKP-1, a potential goal of effective antidepressant therapy. RESULTS Identified proteins belong to various groups: cytoskeletal, ribosomal, nucleic acid binding, chaperones, and enzymes and may potentially be involved in the molecular mechanism of depression. CONCLUSIONS The presented protocol for the purification of protein complexes is universal and can be successfully used in different mammalian cell lines. Proteins identified in the present work have been reported in the literature concerning studies on depressive disorders, which speaks in favour of their role in depression.
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Affiliation(s)
- Ewelina Fic
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland.
| | - Agata Cieślik
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Małgorzata Figiel
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
| | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Cracow, Poland
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5
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Kattan RE, Ayesh D, Wang W. Analysis of affinity purification-related proteomic data for studying protein-protein interaction networks in cells. Brief Bioinform 2023; 24:bbad010. [PMID: 36682002 PMCID: PMC10025443 DOI: 10.1093/bib/bbad010] [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: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 01/23/2023] Open
Abstract
During intracellular signal transduction, protein-protein interactions (PPIs) facilitate protein complex assembly to regulate protein localization and function, which are critical for numerous cellular events. Over the years, multiple techniques have been developed to characterize PPIs to elucidate roles and regulatory mechanisms of proteins. Among them, the mass spectrometry (MS)-based interactome analysis has been increasing in popularity due to its unbiased and informative manner towards understanding PPI networks. However, with MS instrumentation advancing and yielding more data than ever, the analysis of a large amount of PPI-associated proteomic data to reveal bona fide interacting proteins become challenging. Here, we review the methods and bioinformatic resources that are commonly used in analyzing large interactome-related proteomic data and propose a simple guideline for identifying novel interacting proteins for biological research.
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Affiliation(s)
- Rebecca Elizabeth Kattan
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Deena Ayesh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
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Hu JH, Liu Y, Hoffman DA. Identification of Kv4.2 protein complex and modifications by tandem affinity purification-mass spectrometry in primary neurons. Front Cell Neurosci 2022; 16:1070305. [PMID: 36568885 PMCID: PMC9788671 DOI: 10.3389/fncel.2022.1070305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Proteins usually form complexes to fulfill variable physiological functions. In neurons, communication relies on synapses where receptors, channels, and anchoring proteins form complexes to precisely control signal transduction, synaptic integration, and action potential firing. Although there are many published protocols to isolate protein complexes in cell lines, isolation in neurons has not been well established. Here we introduce a method that combines lentiviral protein expression with tandem affinity purification followed by mass-spectrometry (TAP-MS) to identify protein complexes in neurons. This protocol can also be used to identify post-translational modifications (PTMs) of synaptic proteins. We used the A-type voltage-gated K+ channel subunit Kv4.2 as the target protein. Kv4.2 is highly expressed in the hippocampus where it contributes to learning and memory through its regulation of neuronal excitability and synaptic plasticity. We tagged Kv4.2 with the calmodulin-binding-peptide (CBP) and streptavidin-binding-peptide (SBP) at its C-terminus and expressed it in neurons via lentivirus. Kv4.2 was purified by two-step TAP and samples were analyzed by MS. MS identified two prominently known Kv4.2 interacting proteins [dipeptidyl peptidase like (DPPs) and Kv channel-interacting proteins (KChIPs)] in addition to novel synaptic proteins including glutamate receptors, a calcium channel, and anchoring proteins. Co-immunoprecipitation and colocalization experiments validated the association of Kv4.2 with glutamate receptors. In addition to protein complex identification, we used TAP-MS to identify Kv4.2 phosphorylation sites. Several known and unknown phosphorylation sites were identified. These findings provide a novel path to identify protein-protein interactions and PTMs in neurons and shed light on mechanisms of neuronal signaling potentially involved in the pathology of neurological diseases.
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Bian W, Jiang H, Feng S, Chen J, Wang W, Li X. Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. STAR Protoc 2022; 3:101569. [PMID: 35874475 PMCID: PMC9304681 DOI: 10.1016/j.xpro.2022.101569] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Identification of protein interactors is fundamental to understanding their functions. Here, we describe a modified protocol for tandem affinity purification coupled with mass spectrometry (TAP/MS), which includes two-step purification. We detail the S-, 2×FLAG-, and Streptavidin-Binding Peptide (SBP)- tandem tags (SFB-tag) system for protein purification. This protocol can be used to identify protein interactors and establish a high-confidence protein-protein interaction network based on computational models. This is particularly useful for identifying bona fide interacting proteins for subsequent functional studies. For complete details on the use and execution of this protocol, please refer to Bian et al. (2021).
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Affiliation(s)
- Weixiang Bian
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Hua Jiang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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8
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Coker JA, Katis VL, Fairhead M, Schwenzer A, Clemmensen SB, Frandsen BU, de Jongh WA, Gileadi O, Burgess-Brown NA, Marsden BD, Midwood KS, Yue WW. FAS2FURIOUS: Moderate-Throughput Secreted Expression of Difficult Recombinant Proteins in Drosophila S2 Cells. Front Bioeng Biotechnol 2022; 10:871933. [PMID: 35600892 PMCID: PMC9117644 DOI: 10.3389/fbioe.2022.871933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Recombinant protein expression in eukaryotic insect cells is a powerful approach for producing challenging targets. However, due to incompatibility with standard baculoviral platforms and existing low-throughput methodology, the use of the Drosophila melanogaster “S2” cell line lags behind more common insect cell lines such as Sf9 or High-Five™. Due to the advantages of S2 cells, particularly for secreted and secretable proteins, the lack of a simple and parallelizable S2-based platform represents a bottleneck, particularly for biochemical and biophysical laboratories. Therefore, we developed FAS2FURIOUS, a simple and rapid S2 expression pipeline built upon an existing low-throughput commercial platform. FAS2FURIOUS is comparable in effort to simple E. coli systems and allows users to clone and test up to 46 constructs in just 2 weeks. Given the ability of S2 cells to express challenging targets, including receptor ectodomains, secreted glycoproteins, and viral antigens, FAS2FURIOUS represents an attractive orthogonal approach for protein expression in eukaryotic cells.
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Affiliation(s)
- Jesse A. Coker
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Vittorio L. Katis
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michael Fairhead
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anja Schwenzer
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | | | - Bent U. Frandsen
- ExpreSion Biotechnologies, SCION-DTU Science Park, Hørsholm, Denmark
| | | | - Opher Gileadi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola A. Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Brian D. Marsden
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Kim S. Midwood
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Wyatt W. Yue
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- *Correspondence: Wyatt W. Yue,
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9
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Li S, Wu S, Wang L, Li F, Jiang H, Bai F. Recent advances in predicting protein-protein interactions with the aid of artificial intelligence algorithms. Curr Opin Struct Biol 2022; 73:102344. [PMID: 35219216 DOI: 10.1016/j.sbi.2022.102344] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are essential in the regulation of biological functions and cell events, therefore understanding PPIs have become a key issue to understanding the molecular mechanism and investigating the design of drugs. Here we highlight the major developments in computational methods developed for predicting PPIs by using types of artificial intelligence algorithms. The first part introduces the source of experimental PPI data. The second part is devoted to the PPI prediction methods based on sequential information. The third part covers representative methods using structural information as the input feature. The last part is methods designed by combining different types of features. For each part, the state-of-the-art computational PPI prediction methods are reviewed in an inclusive view. Finally, we discuss the flaws existing in this area and future directions of next-generation algorithms.
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Affiliation(s)
- Shiwei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Sanan Wu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Fenglei Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Information Science and Technology, ShanghaiTech University, Shanghai, China.
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10
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Kulyyassov A, Ramankulov Y, Ogryzko V. Generation of Peptides for Highly Efficient Proximity Utilizing Site-Specific Biotinylation in Cells. Life (Basel) 2022; 12:life12020300. [PMID: 35207587 PMCID: PMC8875956 DOI: 10.3390/life12020300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022] Open
Abstract
Protein tags are peptide sequences genetically embedded into a recombinant protein for various purposes, such as affinity purification, Western blotting, and immunofluorescence. Another recent application of peptide tags is in vivo labeling and analysis of protein–protein interactions (PPI) by proteomics methods. One of the common workflows involves site-specific in vivo biotinylation of an AviTag-fused protein in the presence of the biotin ligase BirA. However, due to the rapid kinetics of labeling, this tag is not ideal for analysis of PPI. Here we describe the rationale, design, and protocol for the new biotin acceptor peptides BAP1070 and BAP1108 using modular assembling of biotin acceptor fragments, DNA sequencing, transient expression of proteins in cells, and Western blotting methods. These tags were used in the Proximity Utilizing Biotinylation (PUB) method, which is based on coexpression of BAP-X and BirA-Y in mammalian cells, where X or Y are candidate interacting proteins of interest. By changing the sequence of these peptides, a low level of background biotinylation is achieved, which occurs due to random collisions of proteins in cells. Over 100 plasmid constructs, containing genes of transcription factors, histones, gene repressors, and other nuclear proteins were obtained during implementation of projects related to this method.
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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;
- Correspondence: ; Tel.: +7-7172-707534
| | - Yerlan Ramankulov
- 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;
| | - Vasily Ogryzko
- UMR8126, Institut de Cancerologie Gustave Roussy, Universite Paris-Sud 11, CNRS, 94805 Villejuif, France;
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11
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Leissing F, Misch NV, Wang X, Werner L, Huang L, Conrath U, Beckers GJM. Purification of MAP-kinase protein complexes and identification of candidate components by XL-TAP-MS. PLANT PHYSIOLOGY 2021; 187:2381-2392. [PMID: 34609515 PMCID: PMC8644975 DOI: 10.1093/plphys/kiab446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
The purification of low-abundance protein complexes and detection of in vivo protein-protein interactions in complex biological samples remains a challenging task. Here, we devised crosslinking and tandem affinity purification coupled to mass spectrometry (XL-TAP-MS), a quantitative proteomics approach for analyzing tandem affinity-purified, crosslinked protein complexes from plant tissues. We exemplarily applied XL-TAP-MS to study the MKK2-Mitogen-activated protein kinase (MPK4) signaling module in Arabidopsis thaliana. A tandem affinity tag consisting of an in vivo-biotinylated protein domain flanked by two hexahistidine sequences was adopted to allow for the affinity-based isolation of formaldehyde-crosslinked protein complexes under fully denaturing conditions. Combined with 15N stable isotopic labeling and tandem MS we captured and identified a total of 107 MKK2-MPK4 module-interacting proteins. Consistent with the role of the MPK signaling module in plant immunity, many of the module-interacting proteins are involved in the biotic and abiotic stress response of Arabidopsis. Validation of binary protein-protein interactions by in planta split-luciferase assays and in vitro kinase assays disclosed several direct phosphorylation targets of MPK4. Together, the XL-TAP-MS approach purifies low abundance protein complexes from biological samples and discovers previously unknown protein-protein interactions.
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Affiliation(s)
- Franz Leissing
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Nicola V Misch
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Xiaorong Wang
- Department of Physiology & Biophysics, University of California, Irvine, California 92697, USA
| | - Linda Werner
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, California 92697, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Gerold J M Beckers
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
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12
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Calvo IA, Sharma S, Paulo JA, Gulka AO, Boeszoermenyi A, Zhang J, Lombana JM, Palmieri CM, Laviolette LA, Arthanari H, Iliopoulos O, Gygi SP, Motamedi M. The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability. iScience 2021; 24:103338. [PMID: 34805795 PMCID: PMC8590082 DOI: 10.1016/j.isci.2021.103338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/10/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
The target of Rapamycin complex1 (TORC1) senses and integrates several environmental signals, including amino acid (AA) availability, to regulate cell growth. Folliculin (FLCN) is a tumor suppressor (TS) protein in renal cell carcinoma, which paradoxically activates TORC1 in response to AA supplementation. Few tractable systems for modeling FLCN as a TS are available. Here, we characterize the FLCN-containing complex in Schizosaccharomyces pombe (called BFC) and show that BFC augments TORC1 repression and activation in response to AA starvation and supplementation, respectively. BFC co-immunoprecipitates V-ATPase, a TORC1 modulator, and regulates its activity in an AA-dependent manner. BFC genetic and proteomic networks identify the conserved peptide transmembrane transporter Ptr2 and the phosphoribosylformylglycinamidine synthase Ade3 as new AA-dependent regulators of TORC1. Overall, these data ascribe an additional repressive function to Folliculin in TORC1 regulation and reveal S. pombe as an excellent system for modeling the AA-dependent, FLCN-mediated repression of TORC1 in eukaryotes.
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Affiliation(s)
- Isabel A. Calvo
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Shalini Sharma
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander O.D. Gulka
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Andras Boeszoermenyi
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingyu Zhang
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Jose M. Lombana
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Christina M. Palmieri
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Laura A. Laviolette
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Othon Iliopoulos
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
- Division of Hematology-Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mo Motamedi
- Massachusetts General Hospital Center for Cancer Research and Department of Medicine Harvard Medical School, Charlestown, MA 02129, USA
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13
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Kerbler SM, Natale R, Fernie AR, Zhang Y. From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants. Int J Mol Sci 2021; 22:ijms22137101. [PMID: 34281155 PMCID: PMC8267905 DOI: 10.3390/ijms22137101] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 02/02/2023] Open
Abstract
The study of protein–protein interactions (PPIs) is fundamental in understanding the unique role of proteins within cells and their contribution to complex biological systems. While the toolkit to study PPIs has grown immensely in mammalian and unicellular eukaryote systems over recent years, application of these techniques in plants remains under-utilized. Affinity purification coupled to mass spectrometry (AP-MS) and proximity labeling coupled to mass spectrometry (PL-MS) are two powerful techniques that have significantly enhanced our understanding of PPIs. Relying on the specific binding properties of a protein to an immobilized ligand, AP is a fast, sensitive and targeted approach used to detect interactions between bait (protein of interest) and prey (interacting partners) under near-physiological conditions. Similarly, PL, which utilizes the close proximity of proteins to identify potential interacting partners, has the ability to detect transient or hydrophobic interactions under native conditions. Combined, these techniques have the potential to reveal an unprecedented spatial and temporal protein interaction network that better understands biological processes relevant to many fields of interest. In this review, we summarize the advantages and disadvantages of two increasingly common PPI determination techniques: AP-MS and PL-MS and discuss their important application to plant systems.
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Affiliation(s)
- Sandra M. Kerbler
- Theodor-Echtermeyer-Weg 1, Leibniz-Institut für Gemüse- und Zierpflanzenbau, 14979 Groβbeeren, Germany;
| | - Roberto Natale
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; (R.N.); (A.R.F.)
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence:
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14
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Mishra V. Affinity Tags for Protein Purification. Curr Protein Pept Sci 2021; 21:821-830. [PMID: 32504500 DOI: 10.2174/1389203721666200606220109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 11/22/2022]
Abstract
The affinity tags are unique proteins/peptides that are attached at the N- or C-terminus of the recombinant proteins. These tags help in protein purification. Additionally, some affinity tags also serve a dual purpose as solubility enhancers for challenging protein targets. By applying a combinatorial approach, carefully chosen affinity tags designed in tandem have proven to be very successful in the purification of single proteins or multi-protein complexes. In this mini-review, the key features of the most commonly used affinity tags are discussed. The affinity tags have been classified into two significant categories, epitope tags, and protein/domain tags. The epitope tags are generally small peptides with high affinity towards a chromatography resin. The protein/domain tags often perform double duty as solubility enhancers as well as aid in affinity purification. Finally, protease-based affinity tag removal strategies after purification are discussed.
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Affiliation(s)
- Vibhor Mishra
- Department of Biology, Indiana University, Bloomington, IN 47405, USA,Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA
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15
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Gabriel L, Srinivasan B, Kuś K, Mata JF, João Amorim M, Jansen LET, Athanasiadis A. Enrichment of Zα domains at cytoplasmic stress granules is due to their innate ability to bind to nucleic acids. J Cell Sci 2021; 134:268376. [PMID: 34037233 DOI: 10.1242/jcs.258446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/08/2021] [Indexed: 01/14/2023] Open
Abstract
Zα domains recognize the left-handed helical Z conformation of double-stranded nucleic acids. They are found in proteins involved in the nucleic acid sensory pathway of the vertebrate innate immune system and host evasion by viral pathogens. Previously, it has been demonstrated that ADAR1 (encoded by ADAR in humans) and DAI (also known as ZBP1) localize to cytoplasmic stress granules (SGs), and this localization is mediated by their Zα domains. To investigate the mechanism, we determined the interactions and localization pattern for the N-terminal region of human DAI (ZαβDAI), which harbours two Zα domains, and for a ZαβDAI mutant deficient in nucleic acid binding. Electrophoretic mobility shift assays demonstrated the ability of ZαβDAI to bind to hyperedited nucleic acids, which are enriched in SGs. Furthermore, using immunofluorescence and immunoprecipitation coupled with mass spectrometry, we identified several interacting partners of the ZαβDAI-RNA complex in vivo under conditions of arsenite-induced stress. These interactions are lost upon loss of nucleic acid-binding ability or upon RNase treatment. Thus, we posit that the mechanism for the translocation of Zα domain-containing proteins to SGs is mainly mediated by the nucleic acid-binding ability of their Zα domains. This article has an associated First Person interview with Bharath Srinivasan, joint first author of the paper.
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Affiliation(s)
- Luisa Gabriel
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Bharath Srinivasan
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Krzysztof Kuś
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - João F Mata
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Maria João Amorim
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Lars E T Jansen
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Alekos Athanasiadis
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
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16
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Mahmoudi Gomari M, Saraygord-Afshari N, Farsimadan M, Rostami N, Aghamiri S, Farajollahi MM. Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry. Biotechnol Adv 2020; 45:107653. [PMID: 33157154 DOI: 10.1016/j.biotechadv.2020.107653] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/16/2023]
Abstract
Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Shahin Aghamiri
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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17
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In Vivo Quantitative Estimation of DNA-Dependent Interaction of Sox2 and Oct4 Using BirA-Catalyzed Site-Specific Biotinylation. Biomolecules 2020; 10:biom10010142. [PMID: 31963153 PMCID: PMC7022529 DOI: 10.3390/biom10010142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/03/2020] [Accepted: 01/09/2020] [Indexed: 11/25/2022] Open
Abstract
Protein–protein interactions of core pluripotency transcription factors play an important role during cell reprogramming. Cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. Thus, methods that help to quantify protein–protein interactions may be useful for understanding the mechanisms of pluripotency at the molecular level. Here, a detailed protocol for the detection and quantitative analysis of in vivo protein–protein proximity of Sox2 and Oct4 using the proximity-utilizing biotinylation (PUB) method is described. The method is based on the coexpression of two proteins of interest fused to a biotin acceptor peptide (BAP)in one case and a biotin ligase enzyme (BirA) in the other. The proximity between the two proteins leads to more efficient biotinylation of the BAP, which can be either detected by Western blotting or quantified using proteomics approaches, such as a multiple reaction monitoring (MRM) analysis. Coexpression of the fusion proteins BAP-X and BirA-Y revealed strong biotinylation of the target proteins when X and Y were, alternatively, the pluripotency transcription factors Sox2 and Oct4, compared with the negative control where X or Y was green fluorescent protein (GFP), which strongly suggests that Sox2 and Oct4 come in close proximity to each other and interact.
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18
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DeCaprio J, Kohl TO. Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies. Cold Spring Harb Protoc 2019; 2019:2019/2/pdb.prot098657. [PMID: 30710027 DOI: 10.1101/pdb.prot098657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10-15) to attomole (10-18) range is required to be of exceptional purity. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP). In TAP, the cDNA of the target protein is engineered to contain at least two different epitope tags, and the target protein is extracted under nondenaturing conditions upon expression using an appropriate protein expression platform (CHO cells, HEK 293 cells, or yeast). The expressed protein is initially immunoprecipitated using an antibody against one epitope tag and is eluted in the presence of excess peptide by competition for antibody-binding sites, before being reimmunoprecipitated using an antibody that specifically recognizes the second epitope. These sequential immunoprecipitations significantly reduce the presence of associated nonspecific proteins. Numerous combinations of epitope tags have been applied for tandem affinity purification, and this protocol illustrates the use of tandem hemagglutinin (HA) and FLAG epitope tags. The first immunoprecipitation uses an anti-FLAG antibody followed by the elution in the presence of a competing FLAG peptide before the reimmunoprecipitation of the protein using an anti-HA antibody. Numerous high-quality antiepitope tag antibodies are commercially available from different antibody manufacturers.
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19
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Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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20
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Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
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Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
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21
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Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells. Biochem Biophys Rep 2018; 17:1-9. [PMID: 30450427 PMCID: PMC6226565 DOI: 10.1016/j.bbrep.2018.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/08/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022] Open
Abstract
Many biophysical techniques that are available to study the structure, function and dynamics of cellular constituents require modification of the target molecules. Site-specific labelling of a protein is of particular interest for fluorescence-based single-molecule measurements including single-molecule FRET or super-resolution microscopy. The labelling procedure should be highly specific but minimally invasive to preserve sensitive biomolecules. The modern molecular engineering toolkit provides elegant solutions to achieve the site-specific modification of a protein of interest often necessitating the incorporation of an unnatural amino acid to introduce a unique reactive moiety. The Amber suppression strategy allows the site-specific incorporation of unnatural amino acids into a protein of interest. Recently, this approach has been transferred to the mammalian expression system. Here, we demonstrate how the combination of unnatural amino acid incorporation paired with current bioorthogonal labelling strategies allow the site-specific engineering of fluorescent dyes into proteins produced in the cellular environment of a human cell. We describe in detail which parameters are important to ensure efficient incorporation of unnatural amino acids into a target protein in human expression systems. We furthermore outline purification and bioorthogonal labelling strategies that allow fast protein preparation and labelling of the modified protein. This way, the complete eukaryotic proteome becomes available for single-molecule fluorescence assays. Optimal conditions for incorporation of unnatural amino acids in mammalian cells. Fast small scale purification/labelling for unnatural amino acid-carrying proteins. Evaluation of biorthogonal labelling reactions for dye engineering into proteins.
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22
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Padkina MV, Sambuk EV. Prospects for the Application of Yeast Display in Biotechnology and Cell Biology (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818040105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Struk S, Braem L, Walton A, De Keyser A, Boyer FD, Persiau G, De Jaeger G, Gevaert K, Goormachtig S. Quantitative Tandem Affinity Purification, an Effective Tool to Investigate Protein Complex Composition in Plant Hormone Signaling: Strigolactones in the Spotlight. FRONTIERS IN PLANT SCIENCE 2018; 9:528. [PMID: 29755490 PMCID: PMC5932160 DOI: 10.3389/fpls.2018.00528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/04/2018] [Indexed: 05/13/2023]
Abstract
Phytohormones tightly regulate plant growth by integrating changing environmental and developmental cues. Although the key players have been identified in many plant hormonal pathways, the molecular mechanisms and mode of action of perception and signaling remain incompletely resolved. Characterization of protein partners of known signaling components provides insight into the formed protein complexes, but, unless quantification is involved, does not deliver much, if any, information about the dynamics of the induced or disrupted protein complexes. Therefore, in proteomics research, the discovery of what actually triggers, regulates or interrupts the composition of protein complexes is gaining importance. Here, tandem affinity purification coupled to mass spectrometry (TAP-MS) is combined with label-free quantification (LFQ) to a highly valuable tool to detect physiologically relevant, dynamic protein-protein interactions in Arabidopsis thaliana cell cultures. To demonstrate its potential, we focus on the signaling pathway of one of the most recently discovered phytohormones, strigolactones.
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Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lukas Braem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Alan Walton
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - François-Didier Boyer
- UMR 1318, Institut National de la Recherche Agronomique – Institut Jean-Pierre Bourgin, Versailles, France
- Institut de Chimie des Substances Naturelles – UPR 2301, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, Paris, France
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- *Correspondence: Sofie Goormachtig,
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Li S, Yang K, Liu L, Zhao B, Chen Y, Li X, Zhang L, Zhang Y. Surface sieving coordinated IMAC material for purification of His-tagged proteins. Anal Chim Acta 2018; 997:9-15. [DOI: 10.1016/j.aca.2017.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 10/18/2022]
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25
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García-León M, Iniesto E, Rubio V. Tandem Affinity Purification of Protein Complexes from Arabidopsis Cell Cultures. Methods Mol Biol 2018; 1794:297-309. [PMID: 29855967 DOI: 10.1007/978-1-4939-7871-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tandem affinity purification (TAP) coupled to mass spectrometry has become a powerful approach to identify protein-protein interactions from different biological systems, including plants, in a proteome-wide manner. By using two sequential affinity purification steps, TAP allows for isolation of high-purity TAP-tagged proteins of interest and their associated proteins. Here we describe optimized procedures to use the GSRhino TAP technology for protein complex isolation from Arabidopsis cell suspension cultures.
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Affiliation(s)
- Marta García-León
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Elisa Iniesto
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Vicente Rubio
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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26
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Guidelines to reach high-quality purified recombinant proteins. Appl Microbiol Biotechnol 2017; 102:81-92. [DOI: 10.1007/s00253-017-8623-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
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27
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Havugimana PC, Hu P, Emili A. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks. Expert Rev Proteomics 2017; 14:845-855. [PMID: 28918672 DOI: 10.1080/14789450.2017.1374179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OVERVIEW Elucidation of the networks of physical (functional) interactions present in cells and tissues is fundamental for understanding the molecular organization of biological systems, the mechanistic basis of essential and disease-related processes, and for functional annotation of previously uncharacterized proteins (via guilt-by-association or -correlation). After a decade in the field, we felt it timely to document our own experiences in the systematic analysis of protein interaction networks. Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of 'functional proteomics'. These include mass spectrometry-based methods to characterize macromolecular complexes on a global-scale and sophisticated data analysis tools - most notably machine learning - that allow for the generation of high-quality protein association maps. Expert commentary: Here, we recount some key lessons learned, with an emphasis on successful workflows, and challenges, arising from our own and other groups' ongoing efforts to generate, interpret and report proteome-scale interaction networks in increasingly diverse biological contexts.
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Affiliation(s)
- Pierre C Havugimana
- a Donnelly Centre for Cellular and Biomolecular Research , University of Toronto , Toronto , ON , Canada.,b Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada
| | - Pingzhao Hu
- c Department of Biochemistry and Medical Genetics , University of Manitoba , Winnipeg , MB , Canada
| | - Andrew Emili
- a Donnelly Centre for Cellular and Biomolecular Research , University of Toronto , Toronto , ON , Canada.,b Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada
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Kosobokova EN, Skrypnik KA, Kosorukov VS. Overview of Fusion Tags for Recombinant Proteins. BIOCHEMISTRY (MOSCOW) 2017; 81:187-200. [PMID: 27262188 DOI: 10.1134/s0006297916030019] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Virtually all recombinant proteins are now prepared using fusion domains also known as "tags". The use of tags helps to solve some serious problems: to simplify procedures of protein isolation, to increase expression and solubility of the desired protein, to simplify protein refolding and increase its efficiency, and to prevent proteolysis. In this review, advantages and disadvantages of such fusion tags are analyzed and data on both well-known and new tags are generalized. The authors own data are also presented.
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Affiliation(s)
- E N Kosobokova
- Blokhin Russian Cancer Research Center, Moscow, 115478, Russia.
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29
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Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Müller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G. An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client. Mol Cell Proteomics 2016; 15:1139-50. [PMID: 26933192 PMCID: PMC4813694 DOI: 10.1074/mcp.o115.055350] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tandem affinity purification–mass spectrometry (TAP-MS) is a popular strategy for the identification of protein–protein interactions, characterization of protein complexes, and entire networks. Its employment in cellular settings best fitting the relevant physiology is limited by convenient expression vector systems. We developed an easy-to-handle, inducible, dually selectable retroviral expression vector allowing dose- and time-dependent control of bait proteins bearing the efficient streptavidin-hemagglutinin (SH)-tag at their N- or C termini. Concomitant expression of a reporter fluorophore allows to monitor bait-expressing cells by flow cytometry or microscopy and enables high-throughput phenotypic assays. We used the system to successfully characterize the interactome of the neuroblastoma RAS viral oncogene homolog (NRAS) Gly12Asp (G12D) mutant and exploited the advantage of reporter fluorophore expression by tracking cytokine-independent cell growth using flow cytometry. Moreover, we tested the feasibility of studying cytotoxicity-mediating proteins with the vector system on the cell death-inducing mixed lineage kinase domain-like protein (MLKL) Ser358Asp (S358D) mutant. Interaction proteomics analysis of MLKL Ser358Asp (S358D) identified heat shock protein 90 (HSP90) as a high-confidence interacting protein. Further phenotypic characterization established MLKL as a novel HSP90 client. In summary, this novel inducible expression system enables SH-tag-based interaction studies in the cell line proficient for the respective phenotypic or signaling context and constitutes a valuable tool for experimental approaches requiring inducible or traceable protein expression.
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Affiliation(s)
- Johannes W Bigenzahn
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Astrid Fauster
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuele Rebsamen
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Richard K Kandasamy
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefania Scorzoni
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gregory I Vladimer
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Gstaiger
- §Department of Biology, Institute of Mol. Syst. Biol., ETH Zürich, Zürich, Switzerland
| | - Johannes Zuber
- ¶Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Keiryn L Bennett
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- From the ‡CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; ‖Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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30
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Goossens J, De Geyter N, Walton A, Eeckhout D, Mertens J, Pollier J, Fiallos-Jurado J, De Keyser A, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Goormachtig S, Goossens A. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:476-489. [PMID: 27377668 DOI: 10.1111/tpj.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 05/26/2023]
Abstract
Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most powerful techniques to isolate protein complexes and elucidate protein interaction networks. Here, we describe the development of a TAP-MS strategy for the model legume Medicago truncatula, which is widely studied for its ability to produce valuable natural products and to engage in endosymbiotic interactions. As biological material, transgenic hairy roots, generated through Agrobacterium rhizogenes-mediated transformation of M. truncatula seedlings, were used. As proof of concept, proteins involved in the cell cycle, transcript processing and jasmonate signalling were chosen as bait proteins, resulting in a list of putative interactors, many of which confirm the interologue concept of protein interactions, and which can contribute to biological information about the functioning of these bait proteins in planta. Subsequently, binary protein-protein interactions among baits and preys, and among preys were confirmed by a systematic yeast two-hybrid screen. Together, by establishing a M. truncatula TAP-MS platform, we extended the molecular toolbox of this model species.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Nathan De Geyter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jan Mertens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jennifer Fiallos-Jurado
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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Sudhir PR, Chen CH. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. Int J Mol Sci 2016; 17:432. [PMID: 27011181 PMCID: PMC4813282 DOI: 10.3390/ijms17030432] [Citation(s) in RCA: 2] [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: 10/08/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.
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Affiliation(s)
| | - Chung-Hsuan Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
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32
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A Novel Recombinant DNA System for High Efficiency Affinity Purification of Proteins in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2015; 6:573-8. [PMID: 26715090 DOI: 10.1534/g3.115.025106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Isolation of endogenous proteins from Saccharomyces cerevisiae has been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs) using homologous recombination of DNA fragments. Tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this, we have created a recombinant "CelTag" DNA construct from which PCR fragments can be created to easily tag C-termini of S. cerevisiae ORFs using selection for a nat1 marker. The tag has a C-terminal cellulose binding module to be used in the first affinity step. Microgranular cellulose is very inexpensive and has an effectively continuous ligand on its surface, allowing rapid, highly efficient purification with minimal background. Cellulose-bound proteins are released by specific cleavage of an included site for TEV protease, giving nearly pure product. The tag can be lifted from the recombinant DNA construct either with or without a 13x myc epitope tag between the target ORF and the TEV protease site. Binding of CelTag protein fusions to cellulose is stable to high salt, nonionic detergents, and 1 M urea, allowing stringent washing conditions to remove loosely associated components, as needed, before specific elution. It is anticipated that this reagent could allow isolation of protein complexes from large quantities of yeast extract, including soluble, membrane-bound, or nucleic acid-associated assemblies.
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33
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Stellato C, Porreca I, Cuomo D, Tarallo R, Nassa G, Ambrosino C. The “busy life” of unliganded estrogen receptors. Proteomics 2015; 16:288-300. [DOI: 10.1002/pmic.201500261] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/14/2015] [Accepted: 10/15/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Claudia Stellato
- Laboratory of Molecular Medicine and Genomics; Department of Medicine and Surgery; University of Salerno; Baronissi Salerno Italy
| | | | - Danila Cuomo
- Department of Science and Technology; University of Sannio; Benevento Italy
- Biogem scarl; Ariano Irpino (AV); Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics; Department of Medicine and Surgery; University of Salerno; Baronissi Salerno Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics; Department of Medicine and Surgery; University of Salerno; Baronissi Salerno Italy
| | - Concetta Ambrosino
- Department of Science and Technology; University of Sannio; Benevento Italy
- Biogem scarl; Ariano Irpino (AV); Italy
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34
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Characterization and application of a common epitope recognized by a broad-spectrum C4 monoclonal antibody against capsid proteins of plant potyviruses. Appl Microbiol Biotechnol 2015; 100:1853-1869. [PMID: 26541335 DOI: 10.1007/s00253-015-7116-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/14/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
A broad-spectrum monoclonal antibody (C4 MAb) against the capsid proteins (CPs) of plant potyviruses has been generated in previous studies. To clarify which epitope is recognized by this MAb, epitope mapping was performed via phage display library screening and amino acid substitution analysis. Subsequently, a 12-residue epitope in the core region of potyvirus CPs was identified and termed the C4 epitope (WxMMDGxxQxxY/F). This epitope contains tryptophan and tyrosine residues that are crucial for reacting with C4 MAb. The CP of Odontoglossum ringspot tobamovirus (ORSV) separately fused with the C4 epitope of Konjak mosaic potyvirus (KoMV), Zantedeschia mild mosaic potyvirus (ZaMMV), or Dasheen mosaic potyvirus (DsMV) was expressed in a bacterial system and purified. The results of indirect ELISA and Western blotting demonstrated that the C4 epitope of KoMV (Ko) fused to ORSV CP showed the strongest binding affinity to C4 MAb among the three viral epitope tags examined. The binding affinity between Ko tag (WTMMDGEEQIEY) and C4 MAb was determined. To examine the applicability of the Ko tag in planta, GFP and ORSV CP were transiently expressed in Nicotiana benthamiana, and both Ko-tagged proteins were specifically detected using C4 MAb. The Ko tag did not affect the silencing suppressor function of Tomato bushy stunt tombusvirus P19 in N. benthamiana. Furthermore, Ko-tagged EGFP could be successfully expressed, specifically detected and subsequently immunoprecipitated using C4 MAb in a mammalian cell system. Thus, the present study identified a common C4 epitope of potyviruses recognized by the broad-spectrum C4 and PTY 1 MAbs, and the results indicated that the newly designed Ko tag is suitable for application in bacterial, plant, and mammalian cell systems.
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35
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Stellato C, Nassa G, Tarallo R, Giurato G, Ravo M, Rizzo F, Marchese G, Alexandrova E, Cordella A, Baumann M, Nyman TA, Weisz A, Ambrosino C. Identification of cytoplasmic proteins interacting with unliganded estrogen receptor α and β in human breast cancer cells. Proteomics 2015; 15:1801-7. [PMID: 25604459 DOI: 10.1002/pmic.201400404] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/29/2014] [Accepted: 01/16/2015] [Indexed: 01/15/2023]
Abstract
Estrogen receptor subtypes (ERα and ERβ) are transcription factors sharing a similar structure but exerting opposite roles in breast cancer cells. Besides the well-characterized genomic actions of nuclear ERs upon ligand binding, specific actions of ligand-free ERs in the cytoplasm also affect cellular functions. The identification of cytoplasmic interaction partners of unliganded ERα and ERβ may help characterize the molecular basis of the extra-nuclear mechanism of action of these receptors, revealing novel mechanisms to explain their role in breast cancer response or resistance to endocrine therapy. To this aim, cytoplasmic extracts from human breast cancer MCF-7 cells stably expressing tandem affinity purification-tagged ERα and ERβ and maintained in estrogen-free medium were subject to affinity-purification and MS analysis, leading to the identification of 84 and 142 proteins associated with unliganded ERα and ERβ, respectively. Functional analyses of ER subtype-specific interactomes revealed significant differences in the molecular pathways targeted by each receptor in the cytoplasm. This work, reporting the first identification of the unliganded ERα and ERβ cytoplasmic interactomes in breast cancer cells, provides novel experimental evidence on the nongenomic effects of ERs in the absence of hormonal stimulus. All MS data have been deposited in the ProteomeXchange with identifier PXD001202 (http://proteomecentral.proteomexchange.org/dataset/PXD001202).
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Affiliation(s)
- Claudia Stellato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Maria Ravo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Giovanna Marchese
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | | | - Marc Baumann
- Protein Chemistry Unit, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Tuula A Nyman
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine and Surgery, University of Salerno, Baronissi, Salerno, Italy
| | - Concetta Ambrosino
- Department of Biological and Environmental Sciences, University of Sannio, Benevento, Italy
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LaCava J, Molloy KR, Taylor MS, Domanski M, Chait BT, Rout MP. Affinity proteomics to study endogenous protein complexes: pointers, pitfalls, preferences and perspectives. Biotechniques 2015; 58:103-19. [PMID: 25757543 PMCID: PMC4465938 DOI: 10.2144/000114262] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls.
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Affiliation(s)
- John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Institute for Systems Genetics, New York University School of Medicine, New York, NY
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Martin S. Taylor
- High Throughput Biology Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michal Domanski
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York
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37
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An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Nat Protoc 2014; 10:169-87. [DOI: 10.1038/nprot.2014.199] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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38
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Dual tagging as an approach to isolate endogenous chromatin remodeling complexes from Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:198-208. [PMID: 25486077 DOI: 10.1016/j.bbapap.2014.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 11/11/2014] [Accepted: 11/25/2014] [Indexed: 11/23/2022]
Abstract
Affinity isolation has been an essential technique for molecular studies of cellular assemblies, such as the switch/sucrose non-fermentable (SWI/SNF) family of ATP-dependent chromatin remodeling complexes. However, even biochemically pure isolates can contain heterogeneous mixtures of complexes and their components. In particular, purification strategies that rely on affinity tags fused to only one component of a complex may be susceptible to this phenomenon. This study demonstrates that fusing purification tags to two different proteins enables the isolation of intact complexes of remodels the structure of chromatin (RSC). A Protein A tag was fused to one of the RSC proteins and a Twin-Strep tag to another protein of the complex. By mass spectrometry, we demonstrate the enrichment of the RSC complexes. The complexes had an apparent Svedberg value of about 20S, as shown by glycerol gradient ultracentrifugation. Additionally, purified complexes were demonstrated to be functional. Electron microscopy and single-particle analyses revealed a conformational rearrangement of RSC upon interaction with acetylated histone H3 peptides. This purification method is useful to purify functionally active, structurally well-defined macromolecular assemblies.
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39
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Wood DW. New trends and affinity tag designs for recombinant protein purification. Curr Opin Struct Biol 2014; 26:54-61. [DOI: 10.1016/j.sbi.2014.04.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 01/14/2023]
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40
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Yang P, Lu Y, Li M, Zhang K, Li C, Chen H, Tao D, Zhang S, Ma Y. Identification of RNF114 as a novel positive regulatory protein for T cell activation. Immunobiology 2014; 219:432-9. [PMID: 24631332 DOI: 10.1016/j.imbio.2014.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 08/28/2013] [Accepted: 02/13/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Ping Yang
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China; Department of Biomedicine, Chengdu Medical College, Chengdu, PR China
| | - Yilu Lu
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Minhui Li
- Center of Science and Research, Chengdu Medical College, Chengdu, PR China
| | - Kun Zhang
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Chao Li
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Huijuan Chen
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Dachang Tao
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Sizhong Zhang
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China
| | - Yongxin Ma
- Department of Medical Genetics and Division of Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, PR China.
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41
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Several affinity tags commonly used in chromatographic purification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2013; 2013:581093. [PMID: 24490106 PMCID: PMC3893739 DOI: 10.1155/2013/581093] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/11/2013] [Accepted: 12/02/2013] [Indexed: 02/05/2023]
Abstract
Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP) tag, calmodulin-binding peptide (CBP), glutathione S-transferase (GST), maltose-binding protein (MBP), S-tag, HA tag, and c-Myc tag. In some cases, a large-size affinity tag, such as GST or MBP, can significantly impact on the structure and biological activity of the fusion partner protein. So it is usually necessary to excise the tag by protease. The most commonly used endopeptidases are enterokinase, factor Xa, thrombin, tobacco etch virus, and human rhinovirus 3C protease. The proteolysis features of these proteases are described in order to provide a general guidance on the proteolytic removal of the affinity tags.
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42
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Tian X, Zhu M, Li L, Wu C. Identifying protein-protein interaction in Drosophila adult heads by Tandem Affinity Purification (TAP). J Vis Exp 2013:50968. [PMID: 24335807 DOI: 10.3791/50968] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genetic screens conducted using Drosophila melanogaster (fruit fly) have made numerous milestone discoveries in the advance of biological sciences. However, the use of biochemical screens aimed at extending the knowledge gained from genetic analysis was explored only recently. Here we describe a method to purify the protein complex that associates with any protein of interest from adult fly heads. This method takes advantage of the Drosophila GAL4/UAS system to express a bait protein fused with a Tandem Affinity Purification (TAP) tag in fly neurons in vivo, and then implements two rounds of purification using a TAP procedure similar to the one originally established in yeast(1) to purify the interacting protein complex. At the end of this procedure, a mixture of multiple protein complexes is obtained whose molecular identities can be determined by mass spectrometry. Validation of the candidate proteins will benefit from the resource and ease of performing loss-of-function studies in flies. Similar approaches can be applied to other fly tissues. We believe that the combination of genetic manipulations and this proteomic approach in the fly model system holds tremendous potential for tackling fundamental problems in the field of neurobiology and beyond.
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Affiliation(s)
- Xiaolin Tian
- Neuroscience Center of Excellence, Louisiana State University Health Sciences Center
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Han Y, Garcia BA. Combining genomic and proteomic approaches for epigenetics research. Epigenomics 2013; 5:439-52. [PMID: 23895656 DOI: 10.2217/epi.13.37] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Epigenetics is the study of changes in gene expression or cellular phenotype that do not change the DNA sequence. In this review, current methods, both genomic and proteomic, associated with epigenetics research are discussed. Among them, chromatin immunoprecipitation (ChIP) followed by sequencing and other ChIP-based techniques are powerful techniques for genome-wide profiling of DNA-binding proteins, histone post-translational modifications or nucleosome positions. However, mass spectrometry-based proteomics is increasingly being used in functional biological studies and has proved to be an indispensable tool to characterize histone modifications, as well as DNA-protein and protein-protein interactions. With the development of genomic and proteomic approaches, combination of ChIP and mass spectrometry has the potential to expand our knowledge of epigenetics research to a higher level.
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Affiliation(s)
- Yumiao Han
- Epigenetics Program, Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, 1009C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA
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Abstract
Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future.
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Affiliation(s)
- Michelle E Kimple
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Allison L Brill
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Renee L Pasker
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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Kimple ME, Brill AL, Pasker RL. Overview of affinity tags for protein purification. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2013. [PMID: 24510596 DOI: 10.1002/0471140864.ps0909s73.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future.
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Affiliation(s)
- Michelle E Kimple
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Allison L Brill
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Renee L Pasker
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
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Dieppedale J, Gesbert G, Ramond E, Chhuon C, Dubail I, Dupuis M, Guerrera IC, Charbit A. Possible links between stress defense and the tricarboxylic acid (TCA) cycle in Francisella pathogenesis. Mol Cell Proteomics 2013; 12:2278-92. [PMID: 23669032 PMCID: PMC3734585 DOI: 10.1074/mcp.m112.024794] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 05/01/2013] [Indexed: 12/16/2022] Open
Abstract
Francisella tularensis is a highly infectious bacterium causing the zoonotic disease tularemia. In vivo, this facultative intracellular bacterium survives and replicates mainly in the cytoplasm of infected cells. We have recently identified a genetic locus, designated moxR that is important for stress resistance and intramacrophage survival of F. tularensis. In the present work, we used tandem affinity purification coupled to mass spectrometry to identify in vivo interacting partners of three proteins encoded by this locus: the MoxR-like ATPase (FTL_0200), and two proteins containing motifs predicted to be involved in protein-protein interactions, bearing von Willebrand A (FTL_0201) and tetratricopeptide (FTL_0205) motifs. The three proteins were designated here for simplification, MoxR, VWA1, and TPR1, respectively. MoxR interacted with 31 proteins, including various enzymes. VWA1 interacted with fewer proteins, but these included the E2 component of 2-oxoglutarate dehydrogenase and TPR1. The protein TPR1 interacted with one hundred proteins, including the E1 and E2 subunits of both oxoglutarate and pyruvate dehydrogenase enzyme complexes, and their common E3 subunit. Remarkably, chromosomal deletion of either moxR or tpr1 impaired pyruvate dehydrogenase and oxoglutarate dehydrogenase activities, supporting the hypothesis of a functional role for the interaction of MoxR and TPR1 with these complexes. Altogether, this work highlights possible links between stress resistance and metabolism in F. tularensis virulence.
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Affiliation(s)
- Jennifer Dieppedale
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Gael Gesbert
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Elodie Ramond
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Cerina Chhuon
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- ¶Plateau Protéome Necker, PPN, IFR94, Université Paris-Descartes, Faculté de Médecine René Descartes, Paris 75015 France
| | - Iharilalao Dubail
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Marion Dupuis
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
| | - Ida Chiara Guerrera
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- ¶Plateau Protéome Necker, PPN, IFR94, Université Paris-Descartes, Faculté de Médecine René Descartes, Paris 75015 France
| | - Alain Charbit
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche. 96 rue Didot 75993 Paris Cedex 14 – France
- §INSERM, U1002, Unité de Pathogénie des Infections Systémiques, Paris, France
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Gordon SM, Deng J, Tomann AB, Shah AS, Lu LJ, Davidson WS. Multi-dimensional co-separation analysis reveals protein-protein interactions defining plasma lipoprotein subspecies. Mol Cell Proteomics 2013; 12:3123-34. [PMID: 23882025 DOI: 10.1074/mcp.m113.028134] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The distribution of circulating lipoprotein particles affects the risk for cardiovascular disease (CVD) in humans. Lipoproteins are historically defined by their density, with low-density lipoproteins positively and high-density lipoproteins (HDLs) negatively associated with CVD risk in large populations. However, these broad definitions tend to obscure the remarkable heterogeneity within each class. Evidence indicates that each class is composed of physically (size, density, charge) and compositionally (protein and lipid) distinct subclasses exhibiting unique functionalities and differing effects on disease. HDLs in particular contain upward of 85 proteins of widely varying function that are differentially distributed across a broad range of particle diameters. We hypothesized that the plasma lipoproteins, particularly HDL, represent a continuum of phospholipid platforms that facilitate specific protein-protein interactions. To test this idea, we separated normal human plasma using three techniques that exploit different lipoprotein physicochemical properties (gel filtration chromatography, ionic exchange chromatography, and preparative isoelectric focusing). We then tracked the co-separation of 76 lipid-associated proteins via mass spectrometry and applied a summed correlation analysis to identify protein pairs that may co-reside on individual lipoproteins. The analysis produced 2701 pairing scores, with the top hits representing previously known protein-protein interactions as well as numerous unknown pairings. A network analysis revealed clusters of proteins with related functions, particularly lipid transport and complement regulation. The specific co-separation of protein pairs or clusters suggests the existence of stable lipoprotein subspecies that may carry out distinct functions. Further characterization of the composition and function of these subspecies may point to better targeted therapeutics aimed at CVD or other diseases.
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Affiliation(s)
- Scott M Gordon
- Center for Lipid and Arteriosclerosis Science, University of Cincinnati, 2120 East Galbraith Rd., Cincinnati, Ohio 45237-0507
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Wu SC, Wong SL. Structure-guided design of an engineered streptavidin with reusability to purify streptavidin-binding peptide tagged proteins or biotinylated proteins. PLoS One 2013; 8:e69530. [PMID: 23874971 PMCID: PMC3712923 DOI: 10.1371/journal.pone.0069530] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/13/2013] [Indexed: 12/13/2022] Open
Abstract
Development of a high-affinity streptavidin-binding peptide (SBP) tag allows the tagged recombinant proteins to be affinity purified using the streptavidin matrix without the need of biotinylation. The major limitation of this powerful technology is the requirement to use biotin to elute the SBP-tagged proteins from the streptavidin matrix. Tight biotin binding by streptavidin essentially allows the matrix to be used only once. To address this problem, differences in interactions of biotin and SBP with streptavidin were explored. Loop3-4 which serves as a mobile lid for the biotin binding pocket in streptavidin is in the closed state with biotin binding. In contrast, this loop is in the open state with SBP binding. Replacement of glycine-48 with a bulkier residue (threonine) in this loop selectively reduces the biotin binding affinity (Kd) from 4 × 10(-14) M to 4.45 × 10(-10) M without affecting the SBP binding affinity. Introduction of a second mutation (S27A) to the first mutein (G48T) results in the development of a novel engineered streptavidin SAVSBPM18 which could be recombinantly produced in the functional form from Bacillus subtilis via secretion. To form an intact binding pocket for tight binding of SBP, two diagonally oriented subunits in a tetrameric streptavidin are required. It is vital for SAVSBPM18 to be stably in the tetrameric state in solution. This was confirmed using an HPLC/Laser light scattering system. SAVSBPM18 retains high binding affinity to SBP but has reversible biotin binding capability. The SAVSBPM18 matrix can be applied to affinity purify SBP-tagged proteins or biotinylated molecules to homogeneity with high recovery in a reusable manner. A mild washing step is sufficient to regenerate the matrix which can be reused for multiple rounds. Other applications including development of automated protein purification systems, lab-on-a-chip micro-devices, reusable biosensors, bioreactors and microarrays, and strippable detection agents for various blots are possible.
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Affiliation(s)
- Sau-Ching Wu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Bottermann K, Reinartz M, Barsoum M, Kötter S, Gödecke A. Systematic Analysis Reveals Elongation Factor 2 and α-Enolase as Novel Interaction Partners of AKT2. PLoS One 2013; 8:e66045. [PMID: 23823123 PMCID: PMC3688836 DOI: 10.1371/journal.pone.0066045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/27/2013] [Indexed: 11/25/2022] Open
Abstract
AKT2 is one of the three isoforms of the protein kinase AKT being involved in the modulation of cellular metabolism. Since protein-protein interactions are one possibility to convey specificity in signal transduction, we performed AKT2-protein interaction analysis to elucidate their relevance for AKT2-dependent cellular functions. We identified heat shock protein 90 kDa (HSP90), Cdc37, heat shock protein 70 kDa (HSP70), 78 kDa glucose regulated protein (GRP78), tubulin, GAPDH, α-enolase and elongation factor 2 (EF2) as AKT2-interacting proteins by a combination of tandem affinity purification and mass spectrometry in HEK293T cells. Quantitative MS-analysis using stable isotope labeling by amino acids in cell culture (SILAC) revealed that only HSP90 and Cdc37 interact stably with AKT2, whereas the other proteins interact with low affinity with AKT2. The interactions of AKT2 with α-enolase and EF2 were further analyzed in order to uncover the functional relevance of these newly discovered binding partners. Despite the interaction of AKT2 and α-enolase, which was additionally validated by proximity ligation assay (PLA), no significant impact of AKT on α-enolase activity was detected in activity measurements. AKT stimulation via insulin and/or inhibition with the ATP-competitive inhibitor CCT128930 did not alter enzymatic activity of α-enolase. Interestingly, the direct interaction of AKT2 and EF2 was found to be dynamically regulated in embryonic rat cardiomyocytes. Treatment with the PI3-kinase inhibitor LY294002 before stimulation with several hormones stabilized the complex, whereas stimulation alone led to complex dissociation which was analyzed in situ with PLA. Taken together, these findings point to new aspects of AKT2-mediated signal transduction in protein synthesis and glucose metabolism.
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Affiliation(s)
- Katharina Bottermann
- Department of Cardiovascular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Michael Reinartz
- Department of Cardiovascular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marian Barsoum
- Department of Cardiovascular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Kötter
- Department of Cardiovascular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Axel Gödecke
- Department of Cardiovascular Physiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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Hirani N, Westenberg M, Gami MS, Davis P, Hope IA, Dolphin CT. A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones. BMC Biotechnol 2013; 13:1. [PMID: 23281894 PMCID: PMC3561212 DOI: 10.1186/1472-6750-13-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 12/07/2012] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recombineering is a genetic engineering tool that enables facile modification of large episomal clones, e.g. BACs, fosmids. We have previously adapted this technology to generate, directly from fosmid-based genomic clones, fusion gene reporter constructs designed to investigate gene expression patterns in C. elegans. In our adaptation a rpsL-tet(A) positive/negative-selection cassette (RT-cassette) is first inserted and then, under negative selection, seamlessly replaced with the desired sequence. We report here on the generation and application of a resource comprising two sets of constructs designed to facilitate this particular recombineering approach. RESULTS Two complementary sets of constructs were generated. The first contains different fluorescent protein reporter coding sequences and derivatives while the second set of constructs, based in the copy-number inducible vector pCC1Fos, provide a resource designed to simplify RT-cassette-based recombineering. These latter constructs are used in pairs the first member of which provides a template for PCR-amplification of an RT-cassette while the second provides, as an excised restriction fragment, the desired fluorescent protein reporter sequence. As the RT-cassette is flanked by approximately 200 bp from the ends of the reporter sequence the subsequent negative selection replacement step is highly efficient. Furthermore, use of a restriction fragment minimizes artefacts negating the need for final clone sequencing. Utilizing this resource we generated single-, double- and triple-tagged fosmid-based reporters to investigate expression patterns of three C. elegans genes located on a single genomic clone. CONCLUSIONS We describe the generation and application of a resource designed to facilitate counter-selection recombineering of fosmid-based C. elegans genomic clones. By choosing the appropriate pair of 'insertion' and 'replacement' constructs recombineered products, devoid of artefacts, are generated at high efficiency. Gene expression patterns for three genes located on the same genomic clone were investigated via a set of fosmid-based reporter constructs generated with the modified protocol.
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Affiliation(s)
- Nisha Hirani
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
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