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Matovina M, Tomašić Paić A, Tomić S, Brkić H, Horvat L, Barbarić L, Filić V, Pinterić M, Jurić S, Kussayeva A. Identification of SH2 Domain-Containing Protein 3C as a Novel, Putative Interactor of Dipeptidyl Peptidase 3. Int J Mol Sci 2023; 24:14178. [PMID: 37762480 PMCID: PMC10532290 DOI: 10.3390/ijms241814178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent exopeptidase with broad specificity for four to eight amino acid residue substrates. It has a role in the regulation of oxidative stress response NRF2-KEAP1 pathway through the interaction with KEAP1. We have conducted stable isotope labeling by amino acids in a cell culture coupled to mass spectrometry (SILAC-MS) interactome analysis of TRex HEK293T cells using DPP3 as bait and identified SH2 Domain-Containing Protein 3C (SH2D3C) as prey. SH2D3C is one of three members of a family of proteins that contain both the SH2 domain and a domain similar to guanine nucleotide exchange factor domains of Ras family GTPases (Ras GEF-like domain), named novel SH2-containing proteins (NSP). NSPs, including SH2D3C (NSP3), are adaptor proteins involved in the regulation of adhesion, migration, tissue organization, and immune response. We have shown that SH2D3C binds to DPP3 through its C-terminal Ras GEF-like domain, detected the colocalization of the proteins in living cells, and confirmed direct interaction in the cytosol and membrane ruffles. Computational analysis also confirmed the binding of the C-terminal domain of SH2D3C to DPP3, but the exact model could not be discerned. This is the first indication that DPP3 and SH2D3C are interacting partners, and further studies to elucidate the physiological significance of this interaction are on the way.
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Affiliation(s)
- Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Hrvoje Brkić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia;
| | - Lucija Horvat
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.H.); (V.F.)
| | - Lea Barbarić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Vedrana Filić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.H.); (V.F.)
| | - Marija Pinterić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Snježana Jurić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Akmaral Kussayeva
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
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2
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Putt KS, Du Y, Fu H, Zhang ZY. High-throughput screening strategies for space-based radiation countermeasure discovery. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:88-104. [PMID: 36336374 DOI: 10.1016/j.lssr.2022.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
As humanity begins to venture further into space, approaches to better protect astronauts from the hazards found in space need to be developed. One particular hazard of concern is the complex radiation that is ever present in deep space. Currently, it is unlikely enough spacecraft shielding could be launched that would provide adequate protection to astronauts during long-duration missions such as a journey to Mars and back. In an effort to identify other means of protection, prophylactic radioprotective drugs have been proposed as a potential means to reduce the biological damage caused by this radiation. Unfortunately, few radioprotectors have been approved by the FDA for usage and for those that have been developed, they protect normal cells/tissues from acute, high levels of radiation exposure such as that from oncology radiation treatments. To date, essentially no radioprotectors have been developed that specifically counteract the effects of chronic low-dose rate space radiation. This review highlights how high-throughput screening (HTS) methodologies could be implemented to identify such a radioprotective agent. Several potential target, pathway, and phenotypic assays are discussed along with potential challenges towards screening for radioprotectors. Utilizing HTS strategies such as the ones proposed here have the potential to identify new chemical scaffolds that can be developed into efficacious radioprotectors that are specifically designed to protect astronauts during deep space journeys. The overarching goal of this review is to elicit broader interest in applying drug discovery techniques, specifically HTS towards the identification of radiation countermeasures designed to be efficacious towards the biological insults likely to be encountered by astronauts on long duration voyages.
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Affiliation(s)
- Karson S Putt
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Zhong-Yin Zhang
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette IN 47907 USA.
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3
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Yadala R, Ratnikava M, Lermontova I. Bimolecular Fluorescence Complementation to Test for Protein-Protein Interactions and to Uncover Regulatory Mechanisms During Gametogenesis. Methods Mol Biol 2022; 2484:107-120. [PMID: 35461448 DOI: 10.1007/978-1-0716-2253-7_9] [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
Bimolecular fluorescence complementation (BiFC) assay is one of the sensitive techniques that allows to investigate direct protein-protein interactions (PPI) in vivo and visualize the subcellular localization of interacting proteins. It is based on splitting of a fluorescent protein into two nonfluorescent parts accordingly fused to two putative interacting partners. If interaction between studied proteins is possible, nonfluorescent parts come to close proximity resulting in reconstitution of the functional fluorescent protein and giving fluorescence under certain wavelength. BiFC analysis implies transient or stable expression of the proteins of interest and can be used as a method to test or validate the direct PPI in various biological pathways, including the regulation of gametogenesis, which is the main focus of this book. In our protocol we give detailed information for beginners about three main steps of BiFC analysis of centromeric protein interactions. These steps include (1) generation of appropriate expression clones with the help of Gateway cloning technology, (2) infiltration of Nicotiana benthamiana plants by Agrobacteria containing generated constructs, and (3) microscopic analysis of plants under fluorescence microscope. Also, we discuss appropriate negative controls that can be used for evaluation as well as recommendable vector systems, possible artifacts and measures to avoid artifactual interactions for BiFC assay.
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Affiliation(s)
- Ramakrishna Yadala
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Maryia Ratnikava
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
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4
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Montavon TC, Baldaccini M, Lefèvre M, Girardi E, Chane-Woon-Ming B, Messmer M, Hammann P, Chicher J, Pfeffer S. Human DICER helicase domain recruits PKR and modulates its antiviral activity. PLoS Pathog 2021; 17:e1009549. [PMID: 33984068 PMCID: PMC8118307 DOI: 10.1371/journal.ppat.1009549] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/08/2021] [Indexed: 11/18/2022] Open
Abstract
The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with alphaviruses such as the Sindbis virus and Semliki forest virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.
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Affiliation(s)
- Thomas C Montavon
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Morgane Baldaccini
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Mathieu Lefèvre
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Erika Girardi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Mélanie Messmer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Philippe Hammann
- Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg-Esplanade, Strasbourg, France
| | - Johana Chicher
- Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg-Esplanade, Strasbourg, France
| | - Sébastien Pfeffer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
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5
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Jia Y, Bleicher F, Reboulet J, Merabet S. Bimolecular Fluorescence Complementation (BiFC) and Multiplexed Imaging of Protein-Protein Interactions in Human Living Cells. Methods Mol Biol 2021; 2350:173-190. [PMID: 34331286 DOI: 10.1007/978-1-0716-1593-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Deciphering protein-protein interactions (PPIs) in vivo is crucial to understand protein function. Bimolecular fluorescence complementation (BiFC) makes applicable the analysis of PPIs in many different native contexts, including human live cells. It relies on the property of monomeric fluorescent proteins to be reconstituted from two separate subfragments upon spatial proximity. Candidate partners fused to such complementary subfragments can form a fluorescent protein complex upon interaction, allowing visualization of weak and transient PPIs. It can also be applied for investigation of distinct PPIs at the same time using a multicolor setup. In this chapter, we provide a detailed protocol for analyzing PPIs by doing BiFC in cultured cells. Proof-of-principle experiments rely on the complementation property between the N-terminal fragment of mVenus (designated VN173) and the C-terminal fragment of mCerulean (designated CC155) and the partnership between HOXA7 and PBX1 proteins. This protocol is compatible with any other fluorescent complementation pair fragments and any type of candidate interacting proteins.
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Affiliation(s)
- Yunlong Jia
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Françoise Bleicher
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Jonathan Reboulet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon Cedex 07, France.
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6
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Portillo F, Vázquez J, Pajares MA. Protein-protein interactions involving enzymes of the mammalian methionine and homocysteine metabolism. Biochimie 2020; 173:33-47. [DOI: 10.1016/j.biochi.2020.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
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Moustaqil M, Gambin Y, Sierecki E. Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy. Int J Mol Sci 2020; 21:E2301. [PMID: 32225120 PMCID: PMC7178067 DOI: 10.3390/ijms21072301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
In the post-genome era, pathologies become associated with specific gene expression profiles and defined molecular lesions can be identified. The traditional therapeutic strategy is to block the identified aberrant biochemical activity. However, an attractive alternative could aim at antagonizing key transcriptional events underlying the pathogenesis, thereby blocking the consequences of a disorder, irrespective of the original biochemical nature. This approach, called transcription therapy, is now rendered possible by major advances in biophysical technologies. In the last two decades, techniques have evolved to become key components of drug discovery platforms, within pharmaceutical companies as well as academic laboratories. This review outlines the current biophysical strategies for transcription manipulation and provides examples of successful applications. It also provides insights into the future development of biophysical methods in drug discovery and personalized medicine.
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Affiliation(s)
- Mehdi Moustaqil
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, UNSW Sydney, NSW 2052, Australia;
| | | | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, UNSW Sydney, NSW 2052, Australia;
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8
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Li P, Meng Y, Wang Y, Li J, Lam M, Wang L, Di LJ. Nuclear localization of Desmoplakin and its involvement in telomere maintenance. Int J Biol Sci 2019; 15:2350-2362. [PMID: 31595153 PMCID: PMC6775319 DOI: 10.7150/ijbs.34450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/28/2019] [Indexed: 12/21/2022] Open
Abstract
The interaction between genomic DNA and protein fundamentally determines the activity and the function of DNA elements. Capturing the protein complex and identifying the proteins associated with a specific DNA locus is difficult. Herein, we employed CRISPR, the well-known gene-targeting tool in combination with the proximity-dependent labeling tool BioID to capture a specific genome locus associated proteins and to uncover the novel functions of these proteins. By applying this research tool on telomeres, we identified DSP, out of many others, as a convincing telomere binding protein validated by both biochemical and cell-biological approaches. We also provide evidence to demonstrate that the C-terminal domain of DSP is required for its binding to telomere after translocating to the nucleus mediated by NLS sequence of DSP. In addition, we found that the telomere binding of DSP is telomere length dependent as hTERT inhibition or knockdown caused a decrease of telomere length and diminished DSP binding to the telomere. Knockdown of TRF2 also negatively influenced DSP binding to the telomere. Functionally, loss of DSP resulted in the shortened telomere DNA and induced the DNA damage response and cell apoptosis. In conclusion, our studies identified DSP as a novel potential telomere binding protein and highlighted its role in protecting against telomere DNA damage and resultant cell apoptosis.
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Affiliation(s)
- Peipei Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Yuan Meng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Yuan 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
| | - Jingjing Li
- 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
| | - Manting Lam
- Metabolomics Core, 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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9
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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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Knock-down of AHCY and depletion of adenosine induces DNA damage and cell cycle arrest. Sci Rep 2018; 8:14012. [PMID: 30228286 PMCID: PMC6143609 DOI: 10.1038/s41598-018-32356-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/03/2018] [Indexed: 01/09/2023] Open
Abstract
Recently, functional connections between S-adenosylhomocysteine hydrolase (AHCY) activity and cancer have been reported. As the properties of AHCY include the hydrolysis of S-adenosylhomocysteine and maintenance of the cellular methylation potential, the connection between AHCY and cancer is not obvious. The mechanisms by which AHCY influences the cell cycle or cell proliferation have not yet been confirmed. To elucidate AHCY-driven cancer-specific mechanisms, we pursued a multi-omics approach to investigate the effect of AHCY-knockdown on hepatocellular carcinoma cells. Here, we show that reduced AHCY activity causes adenosine depletion with activation of the DNA damage response (DDR), leading to cell cycle arrest, a decreased proliferation rate and DNA damage. The underlying mechanism behind these effects might be applicable to cancer types that have either significant levels of endogenous AHCY and/or are dependent on high concentrations of adenosine in their microenvironments. Thus, adenosine monitoring might be used as a preventive measure in liver disease, whereas induced adenosine depletion might be the desired approach for provoking the DDR in diagnosed cancer, thus opening new avenues for targeted therapy. Additionally, including AHCY in mutational screens as a potential risk factor may be a beneficial preventive measure.
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11
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Bimolecular Fluorescence Complementation to Visualize Protein-Protein Interactions in Human Cells Based on Gateway Cloning Technology. Methods Mol Biol 2018. [PMID: 29855963 DOI: 10.1007/978-1-4939-7871-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Bimolecular fluorescence complementation (BiFC) is a powerful and sensitive tool to discover new protein-protein interactions (PPIs). It enables visualization and localization of protein-protein interactions (PPIs) in living cells. The idea behind BiFC is to split a fluorescent protein, for example yellow fluorescent protein (YFP), into two parts that are unable to emit fluorescent signal on their own. Therefore, in order to regain fluorescence the split protein fragments must establish close proximity. This is accomplished by fusing the split fragments to proteins that are postulated to interact, and expressing them in living cells. Subsequently, detection of fluorescence indicates interaction of given proteins. Since complementation is practically irreversible it can capture weak and transient interactions. Using suitable vectors for human protein expression, thus avoiding viral cell transfection, we introduced Gateway-based cloning features to the BiFC system, thereby enabling time efficient vector construction in order to maximize the full potential of the BiFC approach to investigate many protein-protein interactions in a high-throughput fashion. This protocol explains steps in a typical protein-protein interaction survey, from the vector selection, cell transfection, and visualization of the fluorescent signal.
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12
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Grbeša I, Kalo A, Belužić R, Kovačević L, Lepur A, Rokić F, Hochberg H, Kanter I, Simunović V, Muńoz-Torres PM, Shav-Tal Y, Vugrek O. Mutations in S-adenosylhomocysteine hydrolase (AHCY) affect its nucleocytoplasmic distribution and capability to interact with S-adenosylhomocysteine hydrolase-like 1 protein. Eur J Cell Biol 2017. [PMID: 28647132 DOI: 10.1016/j.ejcb.2017.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
S-adenosylhomocysteine hydrolase (AHCY) is thought to be located at the sites of ongoing AdoMet-dependent methylation, presumably in the cell nucleus. Endogenous AHCY is located both in cytoplasm and the nucleus. Little is known regarding mechanisms that drive its subcellular distribution, and even less is known on how mutations causing AHCY deficiency affect its intracellular dynamics. Using fluorescence microscopy and GFP-tagged AHCY constructs we show significant differences in the intensity ratio between nuclei and cytoplasm for mutant proteins when compared with wild type AHCY. Interestingly, nuclear export of AHCY is not affected by leptomycin B. Systematic deletions showed that AHCY has two regions, located at both sides of the protein, that contribute to its nuclear localization, implying the interaction with various proteins. In order to evaluate protein interactions in vivo we engaged in bimolecular fluorescence complementation (BiFC) based studies. We investigated previously assumed interaction with AHCY-like-1 protein (AHCYL1), a paralog of AHCY. Indeed, significant interaction between both proteins exists. Additionally, silencing AHCYL1 leads to moderate inhibition of nuclear export of endogenous AHCY.
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Affiliation(s)
- Ivana Grbeša
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Alon Kalo
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Robert Belužić
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Lucija Kovačević
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Adriana Lepur
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Filip Rokić
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Hodaya Hochberg
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Itamar Kanter
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Vesna Simunović
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Pau Marc Muńoz-Torres
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Oliver Vugrek
- Laboratory for Advanced Genomics, Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
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13
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Li P, Li J, Wang L, Di LJ. Proximity Labeling of Interacting Proteins: Application of BioID as a Discovery Tool. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Peipei Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Jingjing Li
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li Wang
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
- Metabolomics Core; Faculty of Health Sciences; University of Macau; Macau SAR of China
| | - Li-Jun Di
- Cancer Center; Faculty of Health Sciences; University of Macau; Macau SAR of China
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14
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Afolayan AJ, Alexander M, Holme RL, Michalkiewicz T, Rana U, Teng RJ, Zemanovic S, Sahoo D, Pritchard KA, Konduri GG. Domain Mapping of Heat Shock Protein 70 Reveals That Glutamic Acid 446 and Arginine 447 Are Critical for Regulating Superoxide Dismutase 2 Function. J Biol Chem 2016; 292:2369-2378. [PMID: 28028182 DOI: 10.1074/jbc.m116.756122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/19/2016] [Indexed: 12/15/2022] Open
Abstract
Stress-inducible heat shock protein 70 (hsp70) interacts with superoxide dismutase 2 (SOD2) in the cytosol after synthesis to transfer the enzyme to the mitochondria for subsequent activation. However, the structural basis for this interaction remains to be defined. To map the SOD2-binding site in hsp70, mutants of hsp70 were made and tested for their ability to bind SOD2. These studies showed that SOD2 binds in the amino acid 393-537 region of the chaperone. To map the hsp70-binding site in SOD2, we used a series of pulldown assays and showed that hsp70 binds to the amino-terminal domain of SOD2. To better define the binding site, we used a series of decoy peptides derived from the primary amino acid sequence in the SOD2-binding site in hsp70. This study shows that SOD2 specifically binds to hsp70 at 445GERAMT450 Small peptides containing GERAMT inhibited the transfer of SOD2 to the mitochondria and decreased SOD2 activity in vitro and in vivo To determine the amino acid residues in hsp70 that are critical for SOD2 interactions, we substituted each amino acid residue for alanine or more conservative residues, glutamine or asparagine, in the GERAMT-binding site. Substitutions of E446A/Q and R447A/Q inhibited the ability of the GERAMT peptide to bind SOD2 and preserved SOD2 function more than other substitutions. Together, these findings indicate that the GERAMT sequence is critical for hsp70-mediated regulation of SOD2 and that Glu446 and Arg447 cooperate with other amino acid residues in the GERAMT-binding site for proper chaperone-dependent regulation of SOD2 antioxidant function.
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Affiliation(s)
- Adeleye J Afolayan
- From the Department of Pediatrics, Cardiovascular Research Center, .,Children's Research Institute
| | - Maxwell Alexander
- From the Department of Pediatrics, Cardiovascular Research Center.,Children's Research Institute
| | - Rebecca L Holme
- Children's Research Institute.,Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Teresa Michalkiewicz
- From the Department of Pediatrics, Cardiovascular Research Center.,Children's Research Institute
| | - Ujala Rana
- From the Department of Pediatrics, Cardiovascular Research Center.,Children's Research Institute
| | - Ru-Jeng Teng
- From the Department of Pediatrics, Cardiovascular Research Center.,Children's Research Institute
| | - Sara Zemanovic
- From the Department of Pediatrics, Cardiovascular Research Center.,Children's Research Institute
| | - Daisy Sahoo
- Children's Research Institute.,Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Kirkwood A Pritchard
- Children's Research Institute.,Department of Surgery, Division of Pediatric Surgery, and
| | - Girija G Konduri
- From the Department of Pediatrics, Cardiovascular Research Center.,Children's Research Institute
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