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Chakraborty A, Blatch GL, Edkins AL. Bimolecular Fluorescence Complementation Assay to Evaluate HSP90-Client Protein Interactions in Cells. Methods Mol Biol 2023; 2693:95-103. [PMID: 37540429 DOI: 10.1007/978-1-0716-3342-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Protein-protein interactions (PPI) in cells play a pivotal role in cellular function and dynamics. Cellular proteostasis is maintained by PPI networks between molecular chaperones, co-chaperones, and client proteins. Consequently, strategies to visualize and analyze PPI in cells are useful in understanding protein homeostasis regulation. The Bimolecular Fluorescence Complementation (BiFC) assay has emerged as a useful tool for studying PPI between proteins in live or fixed cells. BiFC is based on the detection of fluorescence generated when interacting protein pairs, produced as fusion proteins with either the N- or C-terminal fragment of a fluorescent protein, are in sufficient proximity to permit reconstitution of the split fluorophore. Here, we describe the application of the BiFC assay to a model of chaperone-client interactions using Hsp90 and the validated client protein CDK4. This assay allows for the distribution and spatiotemporal analysis of HSP90-CDK4 complexes in live or fixed cells and is amenable to studying the effects of inhibitors and mutations on chaperone-client protein networks.
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Affiliation(s)
- Abir Chakraborty
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Gregory L Blatch
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
- The Vice Chancellery, The University of Notre Dame Australia, Fremantle, WA, Australia
| | - Adrienne L Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa.
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2
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Glahn-Martínez B, Lucchesi G, Pradanas-González F, Manzano AI, Canales Á, Caminati G, Benito-Peña E, Moreno-Bondi MC. Biosensing Tacrolimus in Human Whole Blood by Using a Drug Receptor Fused to the Emerald Green Fluorescent Protein. Anal Chem 2022; 94:16337-16344. [DOI: 10.1021/acs.analchem.2c03122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Bettina Glahn-Martínez
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040Madrid, Spain
| | - Giacomo Lucchesi
- Department of Chemistry “Ugo Schiff” and CSGI, University of Florence, Via della Lastruccia 13, 50019Sesto Fiorentino, Italy
| | - Fernando Pradanas-González
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040Madrid, Spain
| | - Ana Isabel Manzano
- Department of Organic Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040Madrid, Spain
| | - Ángeles Canales
- Department of Organic Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040Madrid, Spain
| | - Gabriella Caminati
- Department of Chemistry “Ugo Schiff” and CSGI, University of Florence, Via della Lastruccia 13, 50019Sesto Fiorentino, Italy
| | - Elena Benito-Peña
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040Madrid, Spain
| | - María C. Moreno-Bondi
- Department of Analytical Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040Madrid, Spain
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3
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Torres-Garcia L, P Domingues JM, Brandi E, Haikal C, Mudannayake JM, Brás IC, Gerhardt E, Li W, Svanbergsson A, Outeiro TF, Gouras GK, Li JY. Monitoring the interactions between alpha-synuclein and Tau in vitro and in vivo using bimolecular fluorescence complementation. Sci Rep 2022; 12:2987. [PMID: 35194057 PMCID: PMC8863885 DOI: 10.1038/s41598-022-06846-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) and Alzheimer's disease (AD) are characterized by pathological accumulation and aggregation of different amyloidogenic proteins, α-synuclein (aSyn) in PD, and amyloid-β (Aβ) and Tau in AD. Strikingly, few PD and AD patients' brains exhibit pure pathology with most cases presenting mixed types of protein deposits in the brain. Bimolecular fluorescence complementation (BiFC) is a technique based on the complementation of two halves of a fluorescent protein, which allows direct visualization of protein-protein interactions. In the present study, we assessed the ability of aSyn and Tau to interact with each other. For in vitro evaluation, HEK293 and human neuroblastoma cells were used, while in vivo studies were performed by AAV6 injection in the substantia nigra pars compacta (SNpc) of mice and rats. We observed that the co-expression of aSyn and Tau led to the emergence of fluorescence, reflecting the interaction of the proteins in cell lines, as well as in mouse and rat SNpc. Thus, our data indicates that aSyn and Tau are able to interact with each other in a biologically relevant context, and that the BiFC assay is an effective tool for studying aSyn-Tau interactions in vitro and in different rodent models in vivo.
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Affiliation(s)
- Laura Torres-Garcia
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Joana M P Domingues
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
- Department of Clinical Neurosciences, University of Cambridge, The Clifford Albbutt Building, Cambridge, UK
| | - Edoardo Brandi
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Caroline Haikal
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Janitha M Mudannayake
- Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Inês C Brás
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Ellen Gerhardt
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
| | - Wen Li
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
- Institute of Health Sciences, China Medical University, Shenyang, China
| | - Alexander Svanbergsson
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, Göttingen, Germany
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
- Faculty of Medical Sciences, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Scientific Employee With an Honorary Contract at German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Gunnar K Gouras
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Jia-Yi Li
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Institute of Health Sciences, China Medical University, Shenyang, China.
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4
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mtIF3 is locally translated in axons and regulates mitochondrial translation for axonal growth. BMC Biol 2022; 20:12. [PMID: 34996455 PMCID: PMC8742369 DOI: 10.1186/s12915-021-01215-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Background The establishment and maintenance of functional neural connections relies on appropriate distribution and localization of mitochondria in neurites, as these organelles provide essential energy and metabolites. In particular, mitochondria are transported to axons and support local energy production to maintain energy-demanding neuronal processes including axon branching, growth, and regeneration. Additionally, local protein synthesis is required for structural and functional changes in axons, with nuclear-encoded mitochondrial mRNAs having been found localized in axons. However, it remains unclear whether these mRNAs are locally translated and whether the potential translated mitochondrial proteins are involved in the regulation of mitochondrial functions in axons. Here, we aim to further understand the purpose of such compartmentalization by focusing on the role of mitochondrial initiation factor 3 (mtIF3), whose nuclear-encoded transcripts have been shown to be present in axonal growth cones. Results We demonstrate that brain-derived neurotrophic factor (BDNF) induces local translation of mtIF3 mRNA in axonal growth cones. Subsequently, mtIF3 protein is translocated into axonal mitochondria and promotes mitochondrial translation as assessed by our newly developed bimolecular fluorescence complementation sensor for the assembly of mitochondrial ribosomes. We further show that BDNF-induced axonal growth requires mtIF3-dependent mitochondrial translation in distal axons. Conclusion We describe a previously unknown function of mitochondrial initiation factor 3 (mtIF3) in axonal protein synthesis and development. These findings provide insight into the way neurons adaptively control mitochondrial physiology and axonal development via local mtIF3 translation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01215-w.
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Sun Y, Wang Y, Chen K, Sun Y, Wang S. Rational engineering and synthetic applications of a high specificity BiFC probe derived from Springgreen-M. Analyst 2022; 147:4326-4336. [DOI: 10.1039/d2an01124g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high signal-to-noise (S/N) ratio BiFC assay was developed for efficient detection and flexible visualization of protein–protein interactions under physiological conditions in live cells.
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Affiliation(s)
- Yuao Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yao Wang
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Keyang Chen
- Yuanpei College, Peking University, Beijing 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing 100871, China
| | - Sheng Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute of Nanjing University, Changzhou 213164, China
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6
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Tang Z, Bernards MA, Wang A. Simultaneous Determination and Subcellular Localization of Protein-Protein Interactions in Plant Cells Using Bimolecular Fluorescence Complementation Assay. Methods Mol Biol 2022; 2400:75-85. [PMID: 34905192 DOI: 10.1007/978-1-0716-1835-6_8] [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: 06/14/2023]
Abstract
The bimolecular fluorescence complementation (BiFC) assay allows the visualization of protein-protein interactions in their native state within living systems. The BiFC assay is based on the in vivo complementation of nonfluorescent component parts of a fluorescent protein through the interaction or proximity target proteins, each fused to a different component of the fluorescent protein. Expansion of the BiFC toolkit with an increasing spectrum of fluorescence markers and catalog of Gateway-compatible vectors for high-throughput screening, has made BiFC an exceedingly powerful tool in discovering new protein interactions or providing backup evidence for known ones. Apart from the validation of protein-protein interactions, BiFC offers the additional benefit of providing information on the subcellular localization of protein interaction complexes. Subcellular localization to a specific subcellular compartment or organelle may be further validated by the coexpression of a fluorescence-labeled protein marker. Here we describe an efficient yet simple protocol for simultaneous determination and subcellular localization of protein-protein interactions in plant cells.
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Affiliation(s)
- Ziwei Tang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Mark A Bernards
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Aiming Wang
- Department of Biology, The University of Western Ontario, London, ON, Canada.
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Ho N, Yap WS, Xu J, Wu H, Koh JH, Goh WWB, George B, Chong SC, Taubert S, Thibault G. Stress sensor Ire1 deploys a divergent transcriptional program in response to lipid bilayer stress. J Cell Biol 2020; 219:e201909165. [PMID: 32349127 PMCID: PMC7337508 DOI: 10.1083/jcb.201909165] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/26/2020] [Accepted: 04/07/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane integrity at the endoplasmic reticulum (ER) is tightly regulated, and its disturbance is implicated in metabolic diseases. Using an engineered sensor that activates the unfolded protein response (UPR) exclusively when normal ER membrane lipid composition is compromised, we identified pathways beyond lipid metabolism that are necessary to maintain ER integrity in yeast and in C. elegans. To systematically validate yeast mutants that disrupt ER membrane homeostasis, we identified a lipid bilayer stress (LBS) sensor in the UPR transducer protein Ire1, located at the interface of the amphipathic and transmembrane helices. Furthermore, transcriptome and chromatin immunoprecipitation analyses pinpoint the UPR as a broad-spectrum compensatory response wherein LBS and proteotoxic stress deploy divergent transcriptional UPR programs. Together, these findings reveal the UPR program as the sum of two independent stress responses, an insight that could be exploited for future therapeutic intervention.
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Affiliation(s)
- Nurulain Ho
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Wei Sheng Yap
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jiaming Xu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Haoxi Wu
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jhee Hong Koh
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Wilson Wen Bin Goh
- Bio-Data Science and Education Research Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Bhawana George
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Shu Chen Chong
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
| | - Stefan Taubert
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Guillaume Thibault
- Lipid Regulation and Cell Stress Group, School of Biological Sciences, Nanyang Technological University, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore
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Baune MC, Lansing H, Fischer K, Meyer T, Charton L, Linka N, von Schaewen A. The Arabidopsis Plastidial Glucose-6-Phosphate Transporter GPT1 is Dually Targeted to Peroxisomes via the Endoplasmic Reticulum. THE PLANT CELL 2020; 32:1703-1726. [PMID: 32111666 PMCID: PMC7203913 DOI: 10.1105/tpc.19.00959] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 05/22/2023]
Abstract
Studies on Glucose-6-phosphate (G6P)/phosphate translocator isoforms GPT1 and GPT2 reported the viability of Arabidopsis (Arabidopsis thaliana) gpt2 mutants, whereas heterozygous gpt1 mutants exhibited a variety of defects during fertilization/seed set, indicating that GPT1 is essential for this process. Among other functions, GPT1 was shown to be important for pollen and embryo-sac development. Because our previous work on the irreversible part of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 may dually localize to plastids and peroxisomes. In reporter fusions, GPT2 localized to plastids, but GPT1 also localized to the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted two oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast (Saccharomyces cerevisiae) proteoliposomes revealed that GPT1 preferentially exchanges G6P for ribulose-5-phosphate (Ru5P). Complementation analyses of heterozygous +/gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas GPT1 without the transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Because OPPP activity in peroxisomes is essential for fertilization, and immunoblot analyses hinted at the presence of unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable in both plastids and peroxisomes. Together with its G6P-Ru5P exchange preference, GPT1 appears to play a role distinct from that of GPT2 due to dual targeting.
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Affiliation(s)
- Marie-Christin Baune
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Hannes Lansing
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Kerstin Fischer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Tanja Meyer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Lennart Charton
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicole Linka
- Biochemie der Pflanzen, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antje von Schaewen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
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Li P, Wang L, Di LJ. Applications of Protein Fragment Complementation Assays for Analyzing Biomolecular Interactions and Biochemical Networks in Living Cells. J Proteome Res 2019; 18:2987-2998. [PMID: 31274323 DOI: 10.1021/acs.jproteome.9b00154] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-protein interactions (PPIs) are indispensable for the dynamic assembly of multiprotein complexes that are central players of nearly all of the intracellular biological processes, such as signaling pathways, metabolic pathways, formation of intracellular organelles, establishment of cytoplasmic skeletons, etc. Numerous approaches have been invented to study PPIs both in vivo and in vitro, including the protein-fragment complementation assay (PCA), which is a widely applied technology to study PPIs and biomolecular interactions. PCA is a technology based on the expression of the bait and prey proteins in fusion with two complementary reporter protein fragments, respectively, that will reassemble when in close proximity. The reporter protein can be the enzymes or fluorescent proteins. Recovery of the enzymatic activity or fluorescent signal can be the indicator of PPI between the bait and prey proteins. Significant effort has been invested in developing many derivatives of PCA, along with various applications, in order to address specific questions. Therefore, a prompt review of these applications is important. In this review, we will categorize these applications according to the scenarios that the PCAs were applied and expect to provide a reference guideline for the future selection of PCA methods in solving a specific problem.
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Affiliation(s)
- Peipei Li
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| | - Li Wang
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China.,Metabolomics Core, Faculty of Health Sciences , University of Macau , Macau , SAR of China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences , University of Macau , Macau , SAR of China
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10
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Lybrand DB, Naiman M, Laumann JM, Boardman M, Petshow S, Hansen K, Scott G, Wehrli M. Destruction complex dynamics: Wnt/β-catenin signaling alters Axin-GSK3β interactions in vivo. Development 2019; 146:dev164145. [PMID: 31189665 PMCID: PMC6633605 DOI: 10.1242/dev.164145] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/05/2019] [Indexed: 01/20/2023]
Abstract
The central regulator of the Wnt/β-catenin pathway is the Axin/APC/GSK3β destruction complex (DC), which, under unstimulated conditions, targets cytoplasmic β-catenin for degradation. How Wnt activation inhibits the DC to permit β-catenin-dependent signaling remains controversial, in part because the DC and its regulation have never been observed in vivo Using bimolecular fluorescence complementation (BiFC) methods, we have now analyzed the activity of the DC under near-physiological conditions in Drosophila By focusing on well-established patterns of Wnt/Wg signaling in the developing Drosophila wing, we have defined the sequence of events by which activated Wnt receptors induce a conformational change within the DC, resulting in modified Axin-GSK3β interactions that prevent β-catenin degradation. Surprisingly, the nucleus is surrounded by active DCs, which principally control the degradation of β-catenin and thereby nuclear access. These DCs are inactivated and removed upon Wnt signal transduction. These results suggest a novel mechanistic model for dynamic Wnt signal transduction in vivo.
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Affiliation(s)
- Daniel B Lybrand
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
- Reed College, Portland, OR 97202, USA
| | - Misha Naiman
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
- Reed College, Portland, OR 97202, USA
| | - Jessie May Laumann
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Mitzi Boardman
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Samuel Petshow
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Kevin Hansen
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Gregory Scott
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
| | - Marcel Wehrli
- Dept. of Integrative Biosciences, School of Dentistry, Oregon Health and Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Portland, OR 97239, USA
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11
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Ito DW, Hannigan KI, Ghosh D, Xu B, Del Villar SG, Xiang YK, Dickson EJ, Navedo MF, Dixon RE. β-adrenergic-mediated dynamic augmentation of sarcolemmal Ca V 1.2 clustering and co-operativity in ventricular myocytes. J Physiol 2019; 597:2139-2162. [PMID: 30714156 PMCID: PMC6462464 DOI: 10.1113/jp277283] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/03/2019] [Indexed: 01/25/2023] Open
Abstract
Key points Prevailing dogma holds that activation of the β‐adrenergic receptor/cAMP/protein kinase A signalling pathway leads to enhanced L‐type CaV1.2 channel activity, resulting in increased Ca2+ influx into ventricular myocytes and a positive inotropic response. However, the full mechanistic and molecular details underlying this phenomenon are incompletely understood. CaV1.2 channel clusters decorate T‐tubule sarcolemmas of ventricular myocytes. Within clusters, nanometer proximity between channels permits Ca2+‐dependent co‐operative gating behaviour mediated by physical interactions between adjacent channel C‐terminal tails. We report that stimulation of cardiomyocytes with isoproterenol, evokes dynamic, protein kinase A‐dependent augmentation of CaV1.2 channel abundance along cardiomyocyte T‐tubules, resulting in the appearance of channel ‘super‐clusters’, and enhanced channel co‐operativity that amplifies Ca2+ influx. On the basis of these data, we suggest a new model in which a sub‐sarcolemmal pool of pre‐synthesized CaV1.2 channels resides in cardiomyocytes and can be mobilized to the membrane in times of high haemodynamic or metabolic demand, to tune excitation–contraction coupling.
Abstract Voltage‐dependent L‐type CaV1.2 channels play an indispensable role in cardiac excitation–contraction coupling. Activation of the β‐adrenergic receptor (βAR)/cAMP/protein kinase A (PKA) signalling pathway leads to enhanced CaV1.2 activity, resulting in increased Ca2+ influx into ventricular myocytes and a positive inotropic response. CaV1.2 channels exhibit a clustered distribution along the T‐tubule sarcolemma of ventricular myocytes where nanometer proximity between channels permits Ca2+‐dependent co‐operative gating behaviour mediated by dynamic, physical, allosteric interactions between adjacent channel C‐terminal tails. This amplifies Ca2+ influx and augments myocyte Ca2+ transient and contraction amplitudes. We investigated whether βAR signalling could alter CaV1.2 channel clustering to facilitate co‐operative channel interactions and elevate Ca2+ influx in ventricular myocytes. Bimolecular fluorescence complementation experiments reveal that the βAR agonist, isoproterenol (ISO), promotes enhanced CaV1.2–CaV1.2 physical interactions. Super‐resolution nanoscopy and dynamic channel tracking indicate that these interactions are expedited by enhanced spatial proximity between channels, resulting in the appearance of CaV1.2 ‘super‐clusters’ along the z‐lines of ISO‐stimulated cardiomyocytes. The mechanism that leads to super‐cluster formation involves rapid, dynamic augmentation of sarcolemmal CaV1.2 channel abundance after ISO application. Optical and electrophysiological single channel recordings confirm that these newly inserted channels are functional and contribute to overt co‐operative gating behaviour of CaV1.2 channels in ISO stimulated myocytes. The results of the present study reveal a new facet of βAR‐mediated regulation of CaV1.2 channels in the heart and support the novel concept that a pre‐synthesized pool of sub‐sarcolemmal CaV1.2 channel‐containing vesicles/endosomes resides in cardiomyocytes and can be mobilized to the sarcolemma to tune excitation–contraction coupling to meet metabolic and/or haemodynamic demands. Prevailing dogma holds that activation of the β‐adrenergic receptor/cAMP/protein kinase A signalling pathway leads to enhanced L‐type CaV1.2 channel activity, resulting in increased Ca2+ influx into ventricular myocytes and a positive inotropic response. However, the full mechanistic and molecular details underlying this phenomenon are incompletely understood. CaV1.2 channel clusters decorate T‐tubule sarcolemmas of ventricular myocytes. Within clusters, nanometer proximity between channels permits Ca2+‐dependent co‐operative gating behaviour mediated by physical interactions between adjacent channel C‐terminal tails. We report that stimulation of cardiomyocytes with isoproterenol, evokes dynamic, protein kinase A‐dependent augmentation of CaV1.2 channel abundance along cardiomyocyte T‐tubules, resulting in the appearance of channel ‘super‐clusters’, and enhanced channel co‐operativity that amplifies Ca2+ influx. On the basis of these data, we suggest a new model in which a sub‐sarcolemmal pool of pre‐synthesized CaV1.2 channels resides in cardiomyocytes and can be mobilized to the membrane in times of high haemodynamic or metabolic demand, to tune excitation–contraction coupling.
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Affiliation(s)
- Danica W Ito
- Department of Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
| | - Karen I Hannigan
- Department of Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
| | - Debapriya Ghosh
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Bing Xu
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Silvia G Del Villar
- Department of Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
| | - Yang K Xiang
- Department of Pharmacology, University of California Davis, Davis, CA, USA.,VA Northern California Health Care System, Mather, CA, USA
| | - Eamonn J Dickson
- Department of Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
| | - Manuel F Navedo
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Rose E Dixon
- Department of Physiology & Membrane Biology, University of California Davis, Davis, CA, USA
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12
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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13
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Choi M, Baek J, Han SB, Cho S. Facile analysis of protein-protein interactions in living cells by enriched visualization of the p-body. BMB Rep 2019. [PMID: 29898808 PMCID: PMC6235090 DOI: 10.5483/bmbrep.2018.51.10.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein-Protein Interactions (PPIs) play essential roles in diverse biological processes and their misregulations are associated with a wide range of diseases. Especially, the growing attention to PPIs as a new class of therapeutic target is increasing the need for an efficient method of cell-based PPI analysis. Thus, we newly developed a robust PPI assay (SeePPI) based on the co-translocation of interacting proteins to the discrete subcellular compartment ‘processing body’ (p-body) inside living cells, enabling a facile analysis of PPI by the enriched fluorescent signal. The feasibility and strength of SeePPI (Signal enhancement exclusively on P-body for Protein-protein Interaction) assay was firmly demonstrated with FKBP12/FRB interaction induced by rapamycin within seconds in real-time analysis of living cells, indicating its recapitulation of physiological PPI dynamics. In addition, we applied p53/MDM2 interaction and its dissociation by Nutlin-3 to SeePPI assay and further confirmed that SeePPI was quantitative and well reflected the endogenous PPI. Our SeePPI assay will provide another useful tool to achieve an efficient analysis of PPIs and their modulators in cells.
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Affiliation(s)
- Miri Choi
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116; College of Pharmacy, Chungbuk National University, Cheongju 28644, South Korea
| | - Jiyeon Baek
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116; College of Pharmacy, Chungbuk National University, Cheongju 28644, South Korea
| | - Sang-Bae Han
- College of Pharmacy, Chungbuk National University, Cheongju 28644, South Korea
| | - Sungchan Cho
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, South Korea; Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, South Korea
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14
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Greenwald EC, Mehta S, Zhang J. Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks. Chem Rev 2018; 118:11707-11794. [PMID: 30550275 PMCID: PMC7462118 DOI: 10.1021/acs.chemrev.8b00333] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cellular signaling networks are the foundation which determines the fate and function of cells as they respond to various cues and stimuli. The discovery of fluorescent proteins over 25 years ago enabled the development of a diverse array of genetically encodable fluorescent biosensors that are capable of measuring the spatiotemporal dynamics of signal transduction pathways in live cells. In an effort to encapsulate the breadth over which fluorescent biosensors have expanded, we endeavored to assemble a comprehensive list of published engineered biosensors, and we discuss many of the molecular designs utilized in their development. Then, we review how the high temporal and spatial resolution afforded by fluorescent biosensors has aided our understanding of the spatiotemporal regulation of signaling networks at the cellular and subcellular level. Finally, we highlight some emerging areas of research in both biosensor design and applications that are on the forefront of biosensor development.
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Affiliation(s)
- Eric C Greenwald
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Sohum Mehta
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
| | - Jin Zhang
- University of California , San Diego, 9500 Gilman Drive, BRFII , La Jolla , CA 92093-0702 , United States
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15
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Krastev DB, Pettitt SJ, Campbell J, Song F, Tanos BE, Stoynov SS, Ashworth A, Lord CJ. Coupling bimolecular PARylation biosensors with genetic screens to identify PARylation targets. Nat Commun 2018; 9:2016. [PMID: 29789535 PMCID: PMC5964205 DOI: 10.1038/s41467-018-04466-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/01/2018] [Indexed: 12/26/2022] Open
Abstract
Poly (ADP-ribose)ylation is a dynamic protein modification that regulates multiple cellular processes. Here, we describe a system for identifying and characterizing PARylation events that exploits the ability of a PBZ (PAR-binding zinc finger) protein domain to bind PAR with high-affinity. By linking PBZ domains to bimolecular fluorescent complementation biosensors, we developed fluorescent PAR biosensors that allow the detection of temporal and spatial PARylation events in live cells. Exploiting transposon-mediated recombination, we integrate the PAR biosensor en masse into thousands of protein coding genes in living cells. Using these PAR-biosensor "tagged" cells in a genetic screen we carry out a large-scale identification of PARylation targets. This identifies CTIF (CBP80/CBP20-dependent translation initiation factor) as a novel PARylation target of the tankyrase enzymes in the centrosomal region of cells, which plays a role in the distribution of the centrosomal satellites.
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Affiliation(s)
- Dragomir B Krastev
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Barbara E Tanos
- The Cancer Therapeutics Division, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Stoyno S Stoynov
- The Institute of Molecular Biology, Bulgarian Academy of Sciences, 1113, Sofia, Bulgaria
| | - Alan Ashworth
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
- UCSF Helen Diller Family Comprehensive Cancer Center, 1450 3rd Street, San Francisco, CA, 94158, USA.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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16
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Liu TY, Chou WC, Chen WY, Chu CY, Dai CY, Wu PY. Detection of membrane protein-protein interaction in planta based on dual-intein-coupled tripartite split-GFP association. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:426-438. [PMID: 29451720 DOI: 10.1111/tpj.13874] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/19/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Despite the great interest in identifying protein-protein interactions (PPIs) in biological systems, only a few attempts have been made at large-scale PPI screening in planta. Unlike biochemical assays, bimolecular fluorescence complementation allows visualization of transient and weak PPIs in vivo at subcellular resolution. However, when the non-fluorescent fragments are highly expressed, spontaneous and irreversible self-assembly of the split halves can easily generate false positives. The recently developed tripartite split-GFP system was shown to be a reliable PPI reporter in mammalian and yeast cells. In this study, we adapted this methodology, in combination with the β-estradiol-inducible expression cassette, for the detection of membrane PPIs in planta. Using a transient expression assay by agroinfiltration of Nicotiana benthamiana leaves, we demonstrate the utility of the tripartite split-GFP association in plant cells and affirm that the tripartite split-GFP system yields no spurious background signal even with abundant fusion proteins readily accessible to the compartments of interaction. By validating a few of the Arabidopsis PPIs, including the membrane PPIs implicated in phosphate homeostasis, we proved the fidelity of this assay for detection of PPIs in various cellular compartments in planta. Moreover, the technique combining the tripartite split-GFP association and dual-intein-mediated cleavage of polyprotein precursor is feasible in stably transformed Arabidopsis plants. Our results provide a proof-of-concept implementation of the tripartite split-GFP system as a potential tool for membrane PPI screens in planta.
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Affiliation(s)
- Tzu-Yin Liu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wen-Chun Chou
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Wei-Yuan Chen
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Ching-Yi Chu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Chen-Yi Dai
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Pei-Yu Wu
- Department of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
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17
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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18
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Bimolecular Fluorescence Complementation to Assay the Interactions of Ubiquitylation Enzymes in Living Yeast Cells. Methods Mol Biol 2018; 1449:223-41. [PMID: 27613039 DOI: 10.1007/978-1-4939-3756-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Ubiquitylation is a versatile posttranslational protein modification catalyzed through the concerted action of ubiquitin-conjugating enzymes (E2s) and ubiquitin ligases (E3s). These enzymes form transient complexes with each other and their modification substrates and determine the nature of the ubiquitin signals attached to their substrates. One challenge in the field of protein ubiquitylation is thus to identify the E2-E3 pairs that function in the cell. In this chapter, we describe the use of bimolecular fluorescence complementation to assay E2-E3 interactions in living cells, using budding yeast as a model organism.
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19
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Sasaki N, Takashima E, Nyunoya H. Altered Subcellular Localization of a Tobacco Membrane Raft-Associated Remorin Protein by Tobamovirus Infection and Transient Expression of Viral Replication and Movement Proteins. FRONTIERS IN PLANT SCIENCE 2018; 9:619. [PMID: 29868075 PMCID: PMC5962775 DOI: 10.3389/fpls.2018.00619] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 04/18/2018] [Indexed: 05/20/2023]
Abstract
Remorins are plant specific proteins found in plasma membrane microdomains (termed lipid or membrane rafts) and plasmodesmata. A potato remorin is reported to be involved in negatively regulating potexvirus movement and plasmodesmal permeability. In this study, we isolated cDNAs of tobacco remorins (NtREMs) and examined roles of an NtREM in infection by tomato mosaic virus (ToMV). Subcellular localization analysis using fluorescently tagged NtREM, ToMV, and viral replication and movement proteins (MPs) indicated that virus infection and transient expression of the viral proteins promoted the formation of NtREM aggregates by altering the subcellular distribution of NtREM, which was localized uniformly on the plasma membrane under normal conditions. NtREM aggregates were often observed associated closely with endoplasmic reticulum networks and bodies of the 126K replication and MPs. The bimolecular fluorescence complementation assay indicated that NtREM might interact directly with the MP on the plasma membrane and around plasmodesmata. In addition, transient overexpression of NtREM facilitated ToMV cell-to-cell movement. Based on these results, we discuss possible roles of the tobacco remorin in tobamovirus movement.
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Affiliation(s)
- Nobumitsu Sasaki
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Japan
- *Correspondence: Nobumitsu Sasaki,
| | - Eita Takashima
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Hiroshi Nyunoya
- Gene Research Center, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
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20
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Deng H, Kerppola TK. Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes. Methods Enzymol 2017; 589:429-455. [PMID: 28336073 DOI: 10.1016/bs.mie.2017.02.003] [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] [Indexed: 02/23/2023]
Abstract
We have developed a procedure that enables visualization of the genomic loci that are bound by complexes formed by a specific combination of chromatin-binding proteins. This procedure is based on imaging bimolecular fluorescence complementation (BiFC) complexes on Drosophila polytene chromosomes. BiFC complexes are formed by the facilitated association of two fluorescent protein fragments that are fused to proteins that interact with, or are in close proximity to, each other. The intensity of BiFC complex fluorescence at individual genomic loci is greatly enhanced by the parallel alignment of hundreds of chromatids within the polytene chromosomes. The loci that are bound by the complexes are mapped by comparing the locations of BiFC complex fluorescence with the stereotypical banding patterns of the chromosomes. We describe strategies for the design, expression, and validation of fusion proteins for the analysis of BiFC complex binding on polytene chromosomes. We detail protocols for the preparation of polytene chromosome spreads that have been optimized for the purpose of BiFC complex visualization. Finally, we provide guidance for the interpretation of results from studies of BiFC complex binding on polytene chromosomes and for comparison of the genomic loci that are bound by BiFC complexes with those that are bound by subunits of the corresponding endogenous complexes. The visualization of BiFC complex binding on polytene chromosomes provides a unique method to visualize multiprotein complex binding at specific loci, throughout the genome, in individual cells.
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Affiliation(s)
- Huai Deng
- University of Michigan, Ann Arbor, MI, United States
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21
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Mie M, Naoki T, Kobatake E. Development of a Split SNAP-CLIP Double Labeling System for Tracking Proteins Following Dissociation from Protein–Protein Complexes in Living Cells. Anal Chem 2016; 88:8166-71. [DOI: 10.1021/acs.analchem.6b01906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masayasu Mie
- Department of Life Science
and Technology, School of Life Science and Technology, Tokyo Institute of Technology. 4259 Nagatsuta, Midori-ku,
Yokohama 226-8502, Japan
| | - Tatsuhiko Naoki
- Department of Life Science
and Technology, School of Life Science and Technology, Tokyo Institute of Technology. 4259 Nagatsuta, Midori-ku,
Yokohama 226-8502, Japan
| | - Eiry Kobatake
- Department of Life Science
and Technology, School of Life Science and Technology, Tokyo Institute of Technology. 4259 Nagatsuta, Midori-ku,
Yokohama 226-8502, Japan
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22
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Sharma H, Anand B. Fluorescence bimolecular complementation enables facile detection of ribosome assembly defects in Escherichia coli. RNA Biol 2016; 13:872-82. [PMID: 27388791 DOI: 10.1080/15476286.2016.1207037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Assembly factors promote the otherwise non-spontaneous maturation of ribosome under physiological conditions inside the cell. Systematic identification and characterization of candidate assembly factors are fraught with bottlenecks due to lack of facile assay system to capture assembly defects. Here, we show that bimolecular fluorescence complementation (BiFC) allows detection of assembly defects that are induced by the loss of assembly factors. The fusion of N and C-terminal fragments of Venus fluorescent protein to the ribosomal proteins uS13 and uL5, respectively, in Escherichia coli facilitated the incorporation of the tagged uS13 and uL5 onto the respective ribosomal subunits. When the ribosomal subunits associated to form the 70S particle, the complementary fragments of Venus were brought into proximity and rendered the Venus fluorescent. Assembly defects that inhibit the subunits association were provoked by either the loss of the known assembly factors such as RsgA and SrmB or the presence of small molecule inhibitors of ribosome maturation such as Lamotrigine and several ribosome-targeting antibiotics and these showed abrogation of the fluorescence complementation. This suggests that BiFC can be employed as a surrogate measure to detect ribosome assembly defects proficiently by circumventing the otherwise cumbersome procedures. BiFC thus offers a facile platform not only for systematic screening to validate potential assembly factors but also to discover novel small molecule inhibitors of ribosome assembly toward mapping the complex assembly landscape of ribosome.
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Affiliation(s)
- Himanshu Sharma
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Assam , India
| | - Baskaran Anand
- a Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Assam , India
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23
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Kudla J, Bock R. Lighting the Way to Protein-Protein Interactions: Recommendations on Best Practices for Bimolecular Fluorescence Complementation Analyses. THE PLANT CELL 2016; 28:1002-8. [PMID: 27099259 PMCID: PMC4904677 DOI: 10.1105/tpc.16.00043] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/22/2016] [Accepted: 04/17/2016] [Indexed: 05/19/2023]
Abstract
Techniques to detect and verify interactions between proteins in vivo have become invaluable tools in functional genomic research. While many of the initially developed interaction assays (e.g., yeast two-hybrid system and split-ubiquitin assay) usually are conducted in heterologous systems, assays relying on bimolecular fluorescence complementation (BiFC; also referred to as split-YFP assays) are applicable to the analysis of protein-protein interactions in most native systems, including plant cells. Like all protein-protein interaction assays, BiFC can produce false positive and false negative results. The purpose of this commentary is to (1) highlight shortcomings of and potential pitfalls in BiFC assays, (2) provide guidelines for avoiding artifactual interactions, and (3) suggest suitable approaches to scrutinize potential interactions and validate them by independent methods.
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Affiliation(s)
- Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
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24
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Zhang Z, Xu Y, Xie Z, Li X, He ZH, Peng XX. Association–Dissociation of Glycolate Oxidase with Catalase in Rice: A Potential Switch to Modulate Intracellular H 2 O 2 Levels. MOLECULAR PLANT 2016; 9:737-748. [PMID: 26900141 DOI: 10.1016/j.molp.2016.02.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/17/2016] [Accepted: 02/08/2016] [Indexed: 05/20/2023]
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25
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To TL, Zhang Q, Shu X. Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions. Protein Sci 2016; 25:748-53. [PMID: 26690964 DOI: 10.1002/pro.2866] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 12/19/2022]
Abstract
A reversible green fluorogenic protein-fragment complementation assay was developed based on the crystal structure of UnaG, a recently discovered fluorescent protein. In living mammalian cells, the nonfluorescent fragments complemented and rapidly became fluorescent upon rapamycin-induced FKBP and Frb protein interaction, and lost fluorescence when the protein interaction was inhibited. This reversible fluorogenic reporter, named uPPI [UnaG-based protein-protein interaction (PPI) reporter], uses bilirubin (BR) as the chromophore and requires no exogenous cofactor. BR is an endogenous molecule in mammalian cells and is not fluorescent by itself. uPPI may have many potential applications in visualizing spatiotemporal dynamics of PPIs.
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Affiliation(s)
- Tsz-Leung To
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California
| | - Qiang Zhang
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, California.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, California
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26
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Hertel F, Mo GCH, Duwé S, Dedecker P, Zhang J. RefSOFI for Mapping Nanoscale Organization of Protein-Protein Interactions in Living Cells. Cell Rep 2015; 14:390-400. [PMID: 26748717 DOI: 10.1016/j.celrep.2015.12.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/04/2015] [Accepted: 12/06/2015] [Indexed: 11/27/2022] Open
Abstract
It has become increasingly clear that protein-protein interactions (PPIs) are compartmentalized in nanoscale domains that define the biochemical architecture of the cell. Despite tremendous advances in super-resolution imaging, strategies to observe PPIs at sufficient resolution to discern their organization are just emerging. Here we describe a strategy in which PPIs induce reconstitution of fluorescent proteins (FPs) that are capable of exhibiting single-molecule fluctuations suitable for stochastic optical fluctuation imaging (SOFI). Subsequently, spatial maps of these interactions can be resolved in super-resolution in living cells. Using this strategy, termed reconstituted fluorescence-based SOFI (refSOFI), we investigated the interaction between the endoplasmic reticulum (ER) Ca(2+) sensor STIM1 and the pore-forming channel subunit ORAI1, a crucial process in store-operated Ca(2+) entry (SOCE). Stimulating SOCE does not appear to change the size of existing STIM1/ORAI1 interaction puncta at the ER-plasma membrane junctions, but results in an apparent increase in the number of interaction puncta.
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Affiliation(s)
- Fabian Hertel
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gary C H Mo
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sam Duwé
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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27
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Nickerson A, Huang T, Lin LJ, Nan X. Photoactivated Localization Microscopy with Bimolecular Fluorescence Complementation (BiFC-PALM). J Vis Exp 2015:e53154. [PMID: 26779930 DOI: 10.3791/53154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions (PPIs) are key molecular events to biology. However, it remains a challenge to visualize PPIs with sufficient resolution and sensitivity in cells because the resolution of conventional light microscopy is diffraction-limited to ~250 nm. By combining bimolecular fluorescence complementation (BiFC) with photoactivated localization microscopy (PALM), PPIs can be visualized in cells with single molecule sensitivity and nanometer spatial resolution. BiFC is a commonly used technique for visualizing PPIs with fluorescence contrast, which involves splitting of a fluorescent protein into two non-fluorescent fragments. PALM is a recent superresolution microscopy technique for imaging biological samples at the nanometer and single molecule scales, which uses phototransformable fluorescent probes such as photoactivatable fluorescent proteins (PA-FPs). BiFC-PALM was demonstrated by splitting PAmCherry1, a PA-FP compatible with PALM, for its monomeric nature, good single molecule brightness, high contrast ratio, and utility for stoichiometry measurements. When split between amino acids 159 and 160, PAmCherry1 can be made into a BiFC probe that reconstitutes efficiently at 37 °C with high specificity to PPIs and low non-specific reconstitution. Ras-Raf interaction is used as an example to show how BiFC-PALM helps to probe interactions at the nanometer scale and with single molecule resolution. Their diffusion can also be tracked in live cells using single molecule tracking (smt-) PALM. In this protocol, factors to consider when designing the fusion proteins for BiFC-PALM are discussed, sample preparation, image acquisition, and data analysis steps are explained, and a few exemplary results are showcased. Providing high spatial resolution, specificity, and sensitivity, BiFC-PALM is a useful tool for studying PPIs in intact biological samples.
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Affiliation(s)
- Andrew Nickerson
- Department of Biomedical Engineering, Oregon Health and Science University; Knight Cancer Institute, Oregon Health and Science University; OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health and Science University; Knight Cancer Institute, Oregon Health and Science University; OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University
| | - Li-Jung Lin
- Department of Biomedical Engineering, Oregon Health and Science University; Knight Cancer Institute, Oregon Health and Science University; OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University
| | - Xioalin Nan
- Department of Biomedical Engineering, Oregon Health and Science University; Knight Cancer Institute, Oregon Health and Science University; OHSU Center for Spatial Systems Biomedicine, Oregon Health and Science University;
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28
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Offenborn JN, Waadt R, Kudla J. Visualization and translocation of ternary Calcineurin-A/Calcineurin-B/Calmodulin-2 protein complexes by dual-color trimolecular fluorescence complementation. THE NEW PHYTOLOGIST 2015; 208:269-79. [PMID: 25919910 DOI: 10.1111/nph.13439] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 06/04/2023]
Abstract
Fluorescence complementation (FC) techniques are expedient for analyzing bimolecular protein-protein interactions. Here we aimed to develop a method for visualization of ternary protein complexes using dual-color trimolecular fluorescence complementation (TriFC). Dual-color TriFC combines protein fragments of mCherry and mVenus, in which a scaffold protein is bilaterally fused to C-terminal fragments of both fluorescent proteins and combined with potential interacting proteins fused to an N-terminal fluorescent protein fragment. For efficient visual verification of ternary complex formation, TriFC was combined with a cytoplasm to plasma membrane translocation assay. Modular vector sets were designed which are fully compatible with previously reported bimolecular fluorescence complementation (BiFC) vectors. As a proof-of-principle, the ternary complex formation of the PP2B protein phosphatase Calcineurin-A/Calcineurin-B with Calmodulin-2 was investigated in transiently transformed Nicotiana benthamiana leaf epidermal cells. The results indicate a Calcineurin-B-induced interaction of Calmodulin-2 with Calcineurin-A. TriFC and the translocation of TriFC complexes provide a novel tool to investigate ternary complex formations with the simplicity of a BiFC approach. The robustness of FC applications and the opportunity to quantify fluorescence complementation render this assay suitable for a broad range of interaction analyses.
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Affiliation(s)
- Jan Niklas Offenborn
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Rainer Waadt
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, Münster, 48149, Germany
- Plant Developmental Biology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, Münster, 48149, Germany
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29
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Zhang XE, Cui Z, Wang D. Sensing of biomolecular interactions using fluorescence complementing systems in living cells. Biosens Bioelectron 2015; 76:243-50. [PMID: 26316254 DOI: 10.1016/j.bios.2015.07.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/09/2023]
Abstract
Sensing biomolecule interactions in living cells allows for a deeper understanding of the mechanisms governing biological processes, and has increasing significance for improvements in clinical diagnosis. It is now possible by using molecular biosensors. One method involving molecular biosensors is called molecular fluorescence complementation, usually referred to as BiFC (bimolecular fragment/fluorescence complementary/complementation) or TriFC (trimolecular fragment complementary/complementation). This complementation method is based on the principle that two non-fluorescent fragments of a fluorescent protein are brought into sufficient lyclose proximity, upon which they are reconstructed so that fluorescence is re-established. This process relies on the interaction between the two fusion partners, which normally are proteins. This method is simple, noninvasive, sensitive, and does not require specialized tools, hence being available to most standard laboratories. Here, we selectively describe three relevant examples, although many other molecular interactions have been shown to work with this method. Recent developments of this method include multicolor BiFC, which allows for simultaneous detection of multi-biomolecule interactions, RNA-protein interactions, far red and near infrared sensing systems for deep tissue imaging. Challenges in the utilization of this method are discussed. Given the current rate of technological advancements, we believe that fluorescence fragment complementing systems have the potential to be utilized across a wide range of areas, including in routine research and clinical diagnosis.
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Affiliation(s)
- Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zongqiang Cui
- State Key Laboratory of Virology and Center for Analytical Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, China
| | - Dianbing Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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30
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Cooper SE, Hodimont E, Green CM. A fluorescent bimolecular complementation screen reveals MAF1, RNF7 and SETD3 as PCNA-associated proteins in human cells. Cell Cycle 2015; 14:2509-19. [PMID: 26030842 PMCID: PMC4613188 DOI: 10.1080/15384101.2015.1053667] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The proliferating cell nuclear antigen (PCNA) is a conserved component of DNA replication factories, and interactions with PCNA mediate the recruitment of many essential DNA replication enzymes to these sites of DNA synthesis. A complete description of the structure and composition of these factories remains elusive, and a better knowledge of them will improve our understanding of how the maintenance of genome and epigenetic stability is achieved. To fully characterize the set of proteins that interact with PCNA we developed a bimolecular fluorescence complementation (BiFC) screen for PCNA-interactors in human cells. This 2-hybrid type screen for interactors from a human cDNA library is rapid and efficient. The fluorescent read-out for protein interaction enables facile selection of interacting clones, and we combined this with next generation sequencing to identify the cDNAs encoding the interacting proteins. This method was able to reproducibly identify previously characterized PCNA-interactors but importantly also identified RNF7, Maf1 and SetD3 as PCNA-interacting proteins. We validated these interactions by co-immunoprecipitation from human cell extracts and by interaction analyses using recombinant proteins. These results show that the BiFC screen is a valuable method for the identification of protein-protein interactions in living mammalian cells. This approach has potentially wide application as it is high throughput and readily automated. We suggest that, given this interaction with PCNA, Maf1, RNF7, and SetD3 are potentially involved in DNA replication, DNA repair, or associated processes.
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Affiliation(s)
- Simon E Cooper
- a Department of Zoology ; University of Cambridge ; Cambridge , UK
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31
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Takamura A, Hattori M, Yoshimura H, Ozawa T. Simultaneous time-lamination imaging of protein association using a split fluorescent timer protein. Anal Chem 2015; 87:3366-72. [PMID: 25679333 DOI: 10.1021/ac504583t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of temporal behaviors of protein association in living cells are crucially important for elucidating the fundamental roles and the mechanism of interactive coordination for cell activities. We developed a method for investigating the temporal alternation of a particular protein assembly using monomeric fluorescent proteins, fluorescent timers (FTs), of which the fluorescent color changes from blue to red over time. We identified a dissection site of the FTs, which allows complementation of the split FT fragments. The split fragments of each FT variant recovered their fluorescence and maintained inherent rates of the color changes upon the reassembly of the fragments in vitro. We applied this method to visualize the aggregation process of α-synuclein in living cells. The size of the aggregates with the temporal information was analyzed from ratio values of the blue and red fluorescence of the reconstituted FTs, from which the aggregation rates were evaluated. This method using the split FT fragments enables tracing and visualizing temporal alternations of various protein associations by single fluorescence measurements at a given time point.
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Affiliation(s)
- Ayari Takamura
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mitsuru Hattori
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- †Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan
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32
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Fujinaga K, Luo Z, Schaufele F, Peterlin BM. Visualization of positive transcription elongation factor b (P-TEFb) activation in living cells. J Biol Chem 2014; 290:1829-36. [PMID: 25492871 DOI: 10.1074/jbc.m114.605816] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Regulation of transcription elongation by positive transcription elongation factor b (P-TEFb) plays a central role in determining the state of cell activation, proliferation, and differentiation. In cells, P-TEFb exists in active and inactive forms. Its release from the inactive 7SK small nuclear ribonucleoprotein complex is a critical step for P-TEFb to activate transcription elongation. However, no good method exists to analyze this P-TEFb equilibrium in living cells. Only inaccurate and labor-intensive cell-free biochemical assays are currently available. In this study, we present the first experimental system to monitor P-TEFb activation in living cells. We created a bimolecular fluorescence complementation assay to detect interactions between P-TEFb and its substrate, the C-terminal domain of RNA polymerase II. When cells were treated with suberoylanilide hydroxamic acid, which releases P-TEFb from the 7SK small nuclear ribonucleoprotein, they turned green. Other known P-TEFb-releasing agents, including histone deacetylase inhibitors, bromodomain and extraterminal bromodomain inhibitors, and protein kinase C agonists, also scored positive in this assay. Finally, we identified 5'-azacytidine as a new P-TEFb-releasing agent. This release of P-TEFb correlated directly with activation of human HIV and HEXIM1 transcription. Thus, our visualization of P-TEFb activation by fluorescent complementation assay could be used to find new P-TEFb-releasing agents, compare different classes of agents, and assess their efficacy singly and/or in combination.
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Affiliation(s)
- Koh Fujinaga
- From the Departments of Medicine, Microbiology, and Immunology and
| | - Zeping Luo
- From the Departments of Medicine, Microbiology, and Immunology and
| | - Fred Schaufele
- the Diabetes and Endocrinology Research Center, University of California, San Francisco, California 94143-0703
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33
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Abstract
Survivin is a well-established target in experimental cancer therapy. The molecule is over-expressed in most human tumors, but hardly detectable in normal tissues. Multiple functions in different subcellular compartments have been assigned. It participates in the control of cell division, apoptosis, the cellular stress response, and also in the regulation of cell migration and metastasis. Survivin expression has been recognized as a biomarker: high expression indicates an unfavorable prognosis and resistance to chemotherapeutic agents and radiation treatment. Survivin is an unconventional drug target and several indirect approaches have been exploited to affect its function and the phenotype of survivin-expressing cells. Interference with the expression of the survivin gene, the utilization of its messenger RNA, the intracellular localization, the interaction with binding partners, the stability of the survivin protein, and the induction of survivin-specific immune responses have been taken into consideration. A direct strategy to inhibit survivin has been based on the identification of a specifically interacting peptide. This peptide can recognize survivin intracellularly and cause the degradation of the ligand–survivin complex. Technology is being developed that might allow the derivation of small molecular-weight, drug-like compounds that are functionally equivalent to the peptide ligand.
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Affiliation(s)
- Bernd Groner
- Georg Speyer Haus, Institute for Biomedical Research, Paul Ehrlich Str. 42, 60322, Frankfurt am Main, Germany,
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34
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Hoffmann C, Moes D, Dieterle M, Neumann K, Moreau F, Tavares Furtado A, Dumas D, Steinmetz A, Thomas C. Live cell imaging reveals actin-cytoskeleton-induced self-association of the actin-bundling protein WLIM1. J Cell Sci 2014; 127:583-98. [PMID: 24284066 DOI: 10.1242/jcs.134536] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crosslinking of actin filaments into bundles is essential for the assembly and stabilization of specific cytoskeletal structures. However, relatively little is known about the molecular mechanisms underlying actin bundle formation. The two LIM-domain-containing proteins define a novel and evolutionarily conserved family of actin-bundling proteins whose actin-binding and -crosslinking activities primarily rely on their LIM domains. Using TIRF microscopy, we describe real-time formation of actin bundles induced by tobacco NtWLIM1 in vitro. We show that NtWLIM1 binds to single filaments and subsequently promotes their interaction and zippering into tight bundles of mixed polarity. NtWLIM1-induced bundles grew by both elongation of internal filaments and addition of preformed fragments at their extremities. Importantly, these data are highly consistent with the modes of bundle formation and growth observed in transgenic Arabidopsis plants expressing a GFP-fused Arabidopsis AtWLIM1 protein. Using two complementary live cell imaging approaches, a close relationship between NtWLIM1 subcellular localization and self-association was established. Indeed, both BiFC and FLIM-FRET data revealed that, although unstable NtWLIM1 complexes can sporadically form in the cytosol, stable complexes concentrate along the actin cytoskeleton. Remarkably, disruption of the actin cytoskeleton significantly impaired self-association of NtWLIM1. In addition, biochemical analyses support the idea that F-actin facilitates the switch of purified recombinant NtWLIM1 from a monomeric to a di- or oligomeric state. On the basis of our data, we propose a model in which actin binding promotes the formation and stabilization of NtWLIM1 complexes, which in turn might drive the crosslinking of actin filaments.
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Affiliation(s)
- Céline Hoffmann
- Centre de Recherche Public-Santé, 84 Val Fleuri, L-1526 Luxembourg, Luxembourg
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35
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Sander IM, Chaney JL, Clark PL. Expanding Anfinsen's principle: contributions of synonymous codon selection to rational protein design. J Am Chem Soc 2014; 136:858-61. [PMID: 24392935 PMCID: PMC3959793 DOI: 10.1021/ja411302m] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
Anfinsen’s principle asserts
that all information required
to specify the structure of a protein is encoded in its amino acid
sequence. However, during protein synthesis by the ribosome, the N-terminus
of the nascent chain can begin to fold before the C-terminus is available.
We tested whether this cotranslational folding can alter the folded
structure of an encoded protein in vivo, versus the structure formed
when refolded in vitro. We designed a fluorescent protein consisting
of three half-domains, where the N- and C-terminal half-domains compete
with each other to interact with the central half-domain. The outcome
of this competition determines the fluorescence properties of the
resulting folded structure. Upon refolding after chemical denaturation,
this protein produced equimolar amounts of the N- and C-terminal folded
structures, respectively. In contrast, translation in Escherichia coli resulted in a 2-fold enhancement
in the formation of the N-terminal folded structure. Rare synonymous
codon substitutions at the 5′ end of the C-terminal half-domain
further increased selection for the N-terminal folded structure. These
results demonstrate that the rate at which a nascent protein emerges
from the ribosome can specify the folded structure of a protein.
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Affiliation(s)
- Ian M Sander
- Department of Chemistry & Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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36
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Fluorescent protein-based biosensors and their clinical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 113:313-48. [PMID: 23244794 DOI: 10.1016/b978-0-12-386932-6.00008-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Green fluorescent protein and its relatives have shed their light on a wide range of biological problems. To date, with a color palette consisting of fluorescent proteins with different spectra, researchers can "paint" living cells as they desire. Moreover, sophisticated biosensors engineered to contain single or multiple fluorescent proteins, including FRET-based biosensors, spatiotemporally unveil molecular mechanisms underlying physiological processes. Although such molecules have contributed considerably to basic research, their abilities to be used in applied life sciences have yet to be fully explored. Here, we review the molecular bases of fluorescent proteins and fluorescent protein-based biosensors and focus on approaches aimed at applying such proteins to the clinic.
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37
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Waadt R, Schlücking K, Schroeder JI, Kudla J. Protein fragment bimolecular fluorescence complementation analyses for the in vivo study of protein-protein interactions and cellular protein complex localizations. Methods Mol Biol 2014; 1062:629-58. [PMID: 24057390 PMCID: PMC4073779 DOI: 10.1007/978-1-62703-580-4_33] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The analyses of protein-protein interactions are crucial for understanding cellular processes including signal transduction, protein trafficking, and movement. Protein fragment complementation assays are based on the reconstitution of protein function when non-active protein fragments are brought together by interacting proteins that were genetically fused to these protein fragments. Bimolecular fluorescence complementation (BiFC) relies on the reconstitution of fluorescent proteins and enables both the analysis of protein-protein interactions and the visualization of protein complex formations in vivo. Transient expression of proteins is a convenient approach to study protein functions in planta or in other organisms and minimizes the need for time-consuming generation of stably expressing transgenic organisms. Here we describe protocols for BiFC analyses in Nicotiana benthamiana and Arabidopsis thaliana leaves transiently transformed by Agrobacterium infiltration. Further, we discuss different BiFC applications and provide examples for proper BiFC analyses in planta.
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Affiliation(s)
- Rainer Waadt
- University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive #0116, La Jolla, CA 92093-0116, USA
| | - Kathrin Schlücking
- Universität Münster, Molekulargenetik und Zellbiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany
| | - Julian I. Schroeder
- University of California San Diego, Division of Biological Sciences, Cell and Developmental Biology Section, 9500 Gilman Drive #0116, La Jolla, CA 92093-0116, USA
| | - Jörg Kudla
- Universität Münster, Molekulargenetik und Zellbiologie der Pflanzen, Institut für Biologie und Biotechnologie der Pflanzen, Schlossplatz 4, 48149 Münster, Germany
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38
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Cabantous S, Nguyen HB, Pedelacq JD, Koraïchi F, Chaudhary A, Ganguly K, Lockard MA, Favre G, Terwilliger TC, Waldo GS. A new protein-protein interaction sensor based on tripartite split-GFP association. Sci Rep 2013; 3:2854. [PMID: 24092409 PMCID: PMC3790201 DOI: 10.1038/srep02854] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/16/2013] [Indexed: 11/12/2022] Open
Abstract
Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.
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Affiliation(s)
- Stéphanie Cabantous
- INSERM UMR1037, Cancer Research Center of Toulouse, Université de Toulouse, Institut Claudius Regaud, F-31052 Toulouse, France
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39
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Chen Z, Zhong Y, Wang Y, Xu S, Liu Z, Baskakov IV, Monteiro MJ, Karbowski M, Shen Y, Fang S. Ubiquitination-induced fluorescence complementation (UiFC) for detection of K48 ubiquitin chains in vitro and in live cells. PLoS One 2013; 8:e73482. [PMID: 24039955 PMCID: PMC3764048 DOI: 10.1371/journal.pone.0073482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/21/2013] [Indexed: 12/17/2022] Open
Abstract
Proteins can be modified with eight homogenous ubiquitin chains linked by an isopeptide bond between the C-terminus of one ubiquitin and an amine from one of the seven lysines or the N-terminal methionine of the next ubiquitin. These topologically distinct ubiquitin chains signal for many essential cellular functions, such as protein degradation, cell cycle progression, DNA repair, and signal transduction. The lysine 48 (K48)-linked ubiquitin chain is one of the most abundant chains and a major proteasome-targeting signal in cells. Despite recent advancements in imaging linkage-specific polyubiquitin chains, no tool is available for imaging K48 chains in live cells. Here we report on a ubiquitination-induced fluorescence complementation (UiFC) assay for detecting K48 ubiquitin chains in vitro and in live cells. For this assay, two nonfluorescent fragments of a fluorescent protein were fused to the ubiquitin-interacting motifs (UIMs) of epsin1 protein. Upon simultaneous binding to a ubiquitin chain, the nonfluorescent fragments of the two fusion proteins are brought in close proximity to reconstitute fluorescence. When used in vitro, UiFC preferentially detected K48 ubiquitin chains with excellent signal-to-noise ratio. Time-lapse imaging revealed that UiFC is capable of monitoring increases in polyubiquitination induced by treatment with proteasome inhibitor, by agents that induce stress, and during mitophagy in live cells.
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Affiliation(s)
- Zhiliang Chen
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Physiology, Anhui Medical University, Hefei, China
| | - Yongwang Zhong
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Physiology, Anhui Medical University, Hefei, China
| | - Yang Wang
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Physiology, Anhui Medical University, Hefei, China
- School of Basic Medical Science and Biopharmaceutical Research Institute, Anhui Medical University, Hefei, China
| | - Shan Xu
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland, United States of America
| | - Zheng Liu
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Physiology, Anhui Medical University, Hefei, China
| | - Ilia V. Baskakov
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
| | - Mervyn J. Monteiro
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
| | - Mariusz Karbowski
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland, United States of America
- * E-mail: (SF); (YS); (MK)
| | - Yuxian Shen
- School of Basic Medical Science and Biopharmaceutical Research Institute, Anhui Medical University, Hefei, China
- * E-mail: (SF); (YS); (MK)
| | - Shengyun Fang
- Center for Biomedical Engineering and Technology, Anhui Medical University, Hefei, China
- Department of Physiology, Anhui Medical University, Hefei, China
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland, United States of America
- * E-mail: (SF); (YS); (MK)
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40
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Amyloid precursor proteins interact with the heterotrimeric G protein Go in the control of neuronal migration. J Neurosci 2013; 33:10165-81. [PMID: 23761911 DOI: 10.1523/jneurosci.1146-13.2013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Amyloid precursor protein (APP) belongs to a family of evolutionarily conserved transmembrane glycoproteins that has been proposed to regulate multiple aspects of cell motility in the nervous system. Although APP is best known as the source of β-amyloid fragments (Aβ) that accumulate in Alzheimer's disease, perturbations affecting normal APP signaling events may also contribute to disease progression. Previous in vitro studies showed that interactions between APP and the heterotrimeric G protein Goα-regulated Goα activity and Go-dependent apoptotic responses, independent of Aβ. However, evidence for authentic APP-Go interactions within the healthy nervous system has been lacking. To address this issue, we have used a combination of in vitro and in vivo strategies to show that endogenously expressed APP family proteins colocalize with Goα in both insect and mammalian nervous systems, including human brain. Using biochemical, pharmacological, and Bimolecular Fluorescence Complementation assays, we have shown that insect APP (APPL) directly interacts with Goα in cell culture and at synaptic terminals within the insect brain, and that this interaction is regulated by Goα activity. We have also adapted a well characterized assay of neuronal migration in the hawkmoth Manduca to show that perturbations affecting APPL and Goα signaling induce the same unique pattern of ectopic, inappropriate growth and migration, analogous to defective migration patterns seen in mice lacking all APP family proteins. These results support the model that APP and its orthologs regulate conserved aspects of neuronal migration and outgrowth in the nervous system by functioning as unconventional Goα-coupled receptors.
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41
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Kerppola TK. Design of fusion proteins for bimolecular fluorescence complementation (BiFC). Cold Spring Harb Protoc 2013; 2013:714-718. [PMID: 23906916 DOI: 10.1101/pdb.top076489] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. It is based on the facilitated association of two nonfluorescent fragments of a fluorescent protein fused to putative interaction partners. The intrinsic fluorescence of the active complex enables detection of protein interactions with high sensitivity, fine spatial resolution, and minimal perturbation of the cells. As discussed in more detail here, BiFC analysis requires careful consideration of the design and expression of the fusion proteins for the results to be interpretable.
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42
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Kodama Y, Hu CD. Bimolecular fluorescence complementation (BiFC): a 5-year update and future perspectives. Biotechniques 2013; 53:285-98. [PMID: 23148879 DOI: 10.2144/000113943] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 09/28/2012] [Indexed: 11/23/2022] Open
Abstract
Over the past decade, bimolecular fluorescence complementation (BiFC) has emerged as a key technique to visualize protein-protein interactions in a variety of model organisms. The BiFC assay is based on reconstitution of an intact fluorescent protein when two complementary non-fluorescent fragments are brought together by a pair of interacting proteins. While the originally reported BiFC method has enabled the study of many protein-protein interactions, increasing demands to visualize protein-protein interactions under various physiological conditions have not only prompted a series of recent BiFC technology improvements, but also stimulated interest in developing completely new approaches. Here we review current BiFC technology, focusing on the development and improvement of BiFC systems, the understanding of split sites in fluorescent proteins, and enhancements in the signal-to-noise ratio. In addition, we provide perspectives on possible future improvements of the technique.
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Affiliation(s)
- Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan.
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43
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Mie M, Naoki T, Uchida K, Kobatake E. Development of a split SNAP-tag protein complementation assay for visualization of protein-protein interactions in living cells. Analyst 2013; 137:4760-5. [PMID: 22910969 DOI: 10.1039/c2an35762c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A split SNAP-tag protein complementation assay was developed for visualization of protein-protein interactions in living cells. Split SNAP-tagμs, fragments of divided SNAP-tag between amino acid residues 91 and 92, were fused to proteins that can interact with each other. After incubation with a fluorescent SNAP-tag substrate, cells that expressed split SNAP-tag fusion proteins generated fluorescent signals when these proteins interacted. Moreover, by combination with the split CLIP-tag (SNAP-tag mutant), simultaneous labeling was achieved. This split SNAP-tag labeling method should be a useful tool for visualization of protein-protein interaction processes.
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Affiliation(s)
- Masayasu Mie
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
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Nissilä E, Ohsaki Y, Weber-Boyvat M, Perttilä J, Ikonen E, Olkkonen VM. ORP10, a cholesterol binding protein associated with microtubules, regulates apolipoprotein B-100 secretion. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1821:1472-84. [PMID: 22906437 DOI: 10.1016/j.bbalip.2012.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 07/31/2012] [Accepted: 08/03/2012] [Indexed: 12/30/2022]
Abstract
ORP10/OSBPL10 is a member of the oxysterol-binding protein family, and genetic variation in OSBPL10 is associated with dyslipidemias and peripheral artery disease. In this study we investigated the ligand binding properties of ORP10 in vitro as well as its localization and function in human HuH7 hepatocytes. The pleckstrin homology (PH) domain of ORP10 selectively interacts with phosphatidylinositol-4-phosphate, while the C-terminal ligand binding domain binds cholesterol and several acidic phospholipids. Full-length ORP10 decorates microtubules (MT), while the ORP10 N-terminal fragment (aa 1-318) localizes at Golgi membranes. Removal of the C-terminal aa 712-764 of ORP10 containing a predicted coiled-coil segment abolishes the MT association, but allows partial Golgi targeting. A PH domain-GFP fusion protein is distributed mainly in the cytosol and the plasma membrane, indicating that the Golgi affinity of ORP10 involves other determinants in addition to the PH domain. HuH7 cells expressing ORP10-specific shRNA display increased accumulation of apolipoprotein B-100 (apoB-100), but not of albumin, in culture medium, and contain reduced levels of intracellular apoB-100. Pulse-chase analysis of cellular [(35)S]apoB-100 demonstrates enhanced apoB-100 secretion by cells expressing ORP10-specific shRNA. The apoB-100 secretion phenotype is replicated in HepG2 cells transduced with the ORP10 shRNA lentiviruses. As a conclusion, the present study dissects the determinants of ORP10 association with MT and the Golgi complex and provides evidence for a specific role of this protein in β-lipoprotein secretion by human hepatocytes.
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Affiliation(s)
- Eija Nissilä
- Institute of Biomedicine, Anatomy, PO Box 63, FI-00014 University of Helsinki, Finland
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Berendzen KW, Böhmer M, Wallmeroth N, Peter S, Vesić M, Zhou Y, Tiesler FKE, Schleifenbaum F, Harter K. Screening for in planta protein-protein interactions combining bimolecular fluorescence complementation with flow cytometry. PLANT METHODS 2012; 8:25. [PMID: 22789293 PMCID: PMC3458939 DOI: 10.1186/1746-4811-8-25] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Accepted: 05/26/2012] [Indexed: 05/20/2023]
Abstract
Understanding protein and gene function requires identifying interaction partners using biochemical, molecular or genetic tools. In plants, searching for novel protein-protein interactions is limited to protein purification assays, heterologous in vivo systems such as the yeast-two-hybrid or mutant screens. Ideally one would be able to search for novel protein partners in living plant cells. We demonstrate that it is possible to screen for novel protein-protein interactions from a random library in protoplasted Arabidopsis plant cells and recover some of the interacting partners. Our screen is based on capturing the bi-molecular complementation of mYFP between an YN-bait fusion partner and a completely random prey YC-cDNA library with FACS. The candidate interactions were confirmed using in planta BiFC assays and in planta FRET-FLIM assays. From this work, we show that the well characterized protein Calcium Dependent Protein Kinase 3 (CPK3) interacts with APX3, HMGB5, ORP2A and a ricin B-related lectin domain containing protein At2g39050. This is one of the first randomin planta screens to be successfully employed.
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Affiliation(s)
- Kenneth Wayne Berendzen
- Universität Tübingen, ZMBP, Plant Physiology, Auf der Morgenstelle 1, D-72076, Tübingen, Germany
| | - Maik Böhmer
- University of California, San Diego, Division of Biological Sciences, Cell and Developmental Biology Section & Ctr for Mol. Genetics 0116, 9500 Gilman Drive #0116, La Jolla, CA, 92093-0116, USA
| | - Niklas Wallmeroth
- Universität Tübingen, ZMBP, Plant Physiology, Auf der Morgenstelle 1, D-72076, Tübingen, Germany
| | - Sébastien Peter
- Universität Tübingen, ZMBP, Biophysical Chemistry, Auf der Morgenstelle 18, D-72076, Tübingen, Germany
| | - Marko Vesić
- Universität Tübingen, ZMBP, Plant Physiology, Auf der Morgenstelle 1, D-72076, Tübingen, Germany
| | - Ying Zhou
- Universität Tübingen, ZMBP, Plant Physiology, Auf der Morgenstelle 1, D-72076, Tübingen, Germany
| | | | - Frank Schleifenbaum
- Universität Tübingen, ZMBP, Biophysical Chemistry, Auf der Morgenstelle 18, D-72076, Tübingen, Germany
| | - Klaus Harter
- Universität Tübingen, ZMBP, Plant Physiology, Auf der Morgenstelle 1, D-72076, Tübingen, Germany
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Imaging Protein Oligomerization in Neurodegeneration Using Bimolecular Fluorescence Complementation. Methods Enzymol 2012; 506:157-74. [DOI: 10.1016/b978-0-12-391856-7.00033-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Kilpatrick LE, Holliday ND. Dissecting the pharmacology of G protein-coupled receptor signaling complexes using bimolecular fluorescence complementation. Methods Mol Biol 2012; 897:109-38. [PMID: 22674163 DOI: 10.1007/978-1-61779-909-9_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The affinity of G protein-coupled receptors (GPCRs) for particular ligands is altered by allosteric regulation with other proteins, for example signaling partners such as G proteins or β-arrestins, or multimeric receptor complexes. Studying the ways in which such interactions modulate pharmacology requires techniques that report these events at the molecular level. Options include bimolecular fluorescence complementation (BiFC), an imaging-based method that can directly demonstrate protein-protein association in living cells. Commonly used fluorescent proteins are split into two nonfluorescent halves, which then tag the protein partners under investigation. Interaction between the partners brings the complementary fragments together, allowing refolding and regeneration of the fluorescent protein to indicate that association has occurred. BiFC is irreversible and is not a real-time technique, yet the simplicity of its fluorescent signal holds key advantages for quantification and cellular localization of the resultant complexes.This review introduces general experimental considerations for using the BiFC approach, and describes specific protocols to develop a BiFC assay for GPCR-β-arrestin association, quantified using high content imaging and analysis. A further application of BiFC is to identify a particular protein-protein complex, thereby allowing investigation of its functional properties. This is illustrated in a protocol to quantify ligand-induced internalization of GPCR dimers of precise composition.
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Affiliation(s)
- Laura E Kilpatrick
- Cell Signalling Research Group, School of Biomedical Sciences, University of Nottingham, The Medical School, Nottingham, UK
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Slavoff SA, Liu DS, Cohen JD, Ting AY. Imaging protein-protein interactions inside living cells via interaction-dependent fluorophore ligation. J Am Chem Soc 2011; 133:19769-76. [PMID: 22098454 DOI: 10.1021/ja206435e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report a new method, Interaction-Dependent PRobe Incorporation Mediated by Enzymes, or ID-PRIME, for imaging protein-protein interactions (PPIs) inside living cells. ID-PRIME utilizes a mutant of Escherichia coli lipoic acid ligase, LplA(W37V), which can catalyze the covalent ligation of a coumarin fluorophore onto a peptide recognition sequence called LAP1. The affinity between the ligase and LAP1 is tuned such that, when each is fused to a protein partner of interest, LplA(W37V) labels LAP1 with coumarin only when the protein partners to which they are fused bring them together. Coumarin labeling in the absence of such interaction is low or undetectable. Characterization of ID-PRIME in living mammalian cells shows that multiple protein-protein interactions can be imaged (FRB-FKBP, Fos-Jun, and neuroligin-PSD-95), with as little as 10 min of coumarin treatment. The signal intensity and detection sensitivity are similar to those of the widely used fluorescent protein complementation technique (BiFC) for PPI detection, without the disadvantage of irreversible complex trapping. ID-PRIME provides a powerful and complementary approach to existing methods for visualization of PPIs in living cells with spatial and temporal resolution.
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Affiliation(s)
- Sarah A Slavoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Haider AJ, Briggs D, Self TJ, Chilvers HL, Holliday ND, Kerr ID. Dimerization of ABCG2 analysed by bimolecular fluorescence complementation. PLoS One 2011; 6:e25818. [PMID: 21991363 PMCID: PMC3185054 DOI: 10.1371/journal.pone.0025818] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/11/2011] [Indexed: 12/18/2022] Open
Abstract
ABCG2 is one of three human ATP binding cassette transporters that are functionally capable of exporting a diverse range of substrates from cells. The physiological consequence of ABCG2 multidrug transport activity in leukaemia, and some solid tumours is the acquisition of cancer multidrug resistance. ABCG2 has a primary structure that infers that a minimal functional transporting unit would be a homodimer. Here we investigated the ability of a bimolecular fluorescence complementation approach to examine ABCG2 dimers, and to probe the role of individual amino acid substitutions in dimer formation. ABCG2 was tagged with fragments of venus fluorescent protein (vYFP), and this tagging did not perturb trafficking or function. Co-expression of two proteins bearing N-terminal and C-terminal fragments of YFP resulted in their association and detection of dimerization by fluorescence microscopy and flow cytometry. Point mutations in ABCG2 which may affect dimer formation were examined for alterations in the magnitude of fluorescence complementation signal. Bimolecular fluorescence complementation (BiFC) demonstrated specific ABCG2 dimer formation, but no changes in dimer formation, resulting from single amino acid substitutions, were detected by BiFC analysis.
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Affiliation(s)
- Ameena J. Haider
- School of Biomedical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Deborah Briggs
- School of Biomedical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Tim J. Self
- School of Biomedical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Hannah L. Chilvers
- School of Biomedical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nicholas D. Holliday
- School of Biomedical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ian D. Kerr
- School of Biomedical Sciences, University of Nottingham, Nottingham, United Kingdom
- * E-mail:
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Hernandez FP, Sandri-Goldin RM. Bimolecular Fluorescence Complementation analysis to reveal protein interactions in herpes virus infected cells. Methods 2011; 55:182-7. [PMID: 21820055 PMCID: PMC3208806 DOI: 10.1016/j.ymeth.2011.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 10/17/2022] Open
Abstract
Protein interactions are at the basis of all processes in living organisms. In particular, regulatory proteins do not act alone but participate in multifaceted sets of interactions that are organized into complex networks. In herpes simplex virus (HSV-1) infected cells, viral proteins interact with cellular proteins and with other viral proteins to form the protein complexes required for virus production, including transcription complexes, replication complexes and virion assembly complexes. While a number of methods have been developed to investigate protein-protein interactions such as coimmunoprecipitation, GST-binding assays and yeast 2-hybrid analyses, these approaches require removal of the proteins from the cellular environment and do not provide information on the spatial localization of the protein-protein interaction in living cells. The fluorescence based approach Bimolecular Fluorescence Complementation (BiFC) allows direct visualization of the subcellular localization of the protein complex in living cells. In BiFC, two halves of a fluorescent protein are fused to each of two interacting proteins of interest, resulting in nonfluorescent fusion proteins. Interaction of the protein partners tethers the fused fluorescent fragments in close proximity, which facilitates their association and restoration of fluorescence. Two limitations of BiFC are that there is a delay between the time that the interacting proteins associate and fluorescence complex formation and thus complex formation cannot be measured in real-time, and fluorescence complex formation is irreversible in vivo. Despite these limitations, BiFC is a powerful and sensitive approach that can be performed using standard molecular biology and cell culture protocols and a fluorescence microscope.
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Affiliation(s)
- Felicia P Hernandez
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, USA
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