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Giancola JB, Grimm JB, Jun JV, Petri YD, Lavis LD, Raines RT. Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye. ACS Chem Biol 2024; 19:908-915. [PMID: 38525961 PMCID: PMC11186736 DOI: 10.1021/acschembio.3c00713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.
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Affiliation(s)
- JoLynn B. Giancola
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147, United States
| | - Joomyung V. Jun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn VA 20147, United States
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Qi M, Yu H, Bredow M, Chicowski AS, Fields LD, Whitham SA. Insights into Phakopsora pachyrhizi Effector-Effector Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:227-231. [PMID: 37831963 DOI: 10.1094/mpmi-08-23-0120-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
The multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, wherein some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions among Phakopsora pachyrhizi effector candidates (PpECs). P. pachyrhizi haustorial transcriptome analysis identified a collection of predicted PpECs. Among these, PpEC23 was found to interact with PpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast two-hybrid screen to explore protein-protein interactions between PpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly, PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRPs), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain within PpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature of PpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions among P. pachyrhizi effector-effector interactions. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Haiyue Yu
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, 100193, Beijing, China
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Letícia Dias Fields
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Steven A Whitham
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
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Zhang Y, Chen M, Liu T, Qin K, Fernie AR. Investigating the dynamics of protein-protein interactions in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:965-983. [PMID: 36919339 DOI: 10.1111/tpj.16182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 05/27/2023]
Abstract
Both stable and transient protein interactions play an important role in the complex assemblies required for the proper functioning of living cells. Several methods have been developed to monitor protein-protein interactions in plants. However, the detection of dynamic protein complexes is very challenging, with few technologies available for this purpose. Here, we developed a new platform using the plant UBIQUITIN promoter to drive transgene expression and thereby to detect protein interactions in planta. Typically, to decide which side of the protein to link the tags, the subcellular localization of the protein fused either N-terminal or C-terminal mCitrine was firstly confirmed by using eight different specific mCherry markers. Following stable or transient protein expression in plants, the protein interaction network was detected by affinity purification mass spectrometry. These interactions were subsequently confirmed by bimolecular fluorescence complementation (BiFC), bioluminescence resonance energy transfer and co-immunoprecipitation assays. The dynamics of these interactions were monitored by Förster resonance energy transfer (FRET) and split-nano luciferase, whilst the ternary protein complex association was monitored by BiFC-FRET. Using the canonical glycolytic metabolon as an example, the interaction between these enzymes was characterized under conditions that mimic physiologically relevant energy statuses.
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Affiliation(s)
- Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Moxian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Tieyuan Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Kezhen Qin
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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Vora DS, Kalakoti Y, Sundar D. Computational Methods and Deep Learning for Elucidating Protein Interaction Networks. Methods Mol Biol 2023; 2553:285-323. [PMID: 36227550 DOI: 10.1007/978-1-0716-2617-7_15] [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: 06/16/2023]
Abstract
Protein interactions play a critical role in all biological processes, but experimental identification of protein interactions is a time- and resource-intensive process. The advances in next-generation sequencing and multi-omics technologies have greatly benefited large-scale predictions of protein interactions using machine learning methods. A wide range of tools have been developed to predict protein-protein, protein-nucleic acid, and protein-drug interactions. Here, we discuss the applications, methods, and challenges faced when employing the various prediction methods. We also briefly describe ways to overcome the challenges and prospective future developments in the field of protein interaction biology.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Yogesh Kalakoti
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
- School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.
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Yu J, Huang C, Wang Z, Kaushik RS, Sheng Z, Li F, Wang D. Development and characterization of an inducible assay system to measure Zika virus capsid interactions. J Med Virol 2022; 94:5392-5400. [PMID: 35822280 PMCID: PMC9474601 DOI: 10.1002/jmv.27991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 12/15/2022]
Abstract
The global spread of the mosquito-borne Zika virus (ZIKV) infection and its complications including Guillain-Barré syndrome and fetus microcephaly in 2015 have made ZIKV as a significant public health threat. The capsid protein plays crucial roles in ZIKV replication and thus represents an attractive therapeutic target. However, inhibitors of ZIKV capsid assembly have not been rigorously identified due to the lack of a target-based screening system. In this study, we developed a novel ZIKV capsid interaction method based on a split-luciferase complementation assay, which can be used to measure and quantify ZIKV capsid-capsid (C-C) interaction by the restored luciferase signal when capsid proteins interact with each other. Furthermore, a Tet-on inducible stable cell line was generated to screen inhibitors of capsid dimerization. By using of this system, peptides (Pep.15-24 in the N-terminal region of ZIKV capsid protein and Pep.44-58 in the α2 helix of ZIKV capsid protein) were identified to inhibit ZIKV C-C interaction. Overall, this study developed a novel inducible assay system to measure ZIKV capsid interaction and identify ZIKV capsid multimerization inhibitors, which will be applied for future discovery of ZIKV assembly inhibitors.
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Affiliation(s)
- Jieshi Yu
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Chen Huang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Zhao Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007
| | - Radhey S. Kaushik
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546, USA
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Yang YP, Lee ACL, Lin LT, Chen YW, Huang PI, Ma HI, Chen YC, Lo WL, Lan YT, Fang WL, Wang CY, Liu YY, Hsu PK, Lin WC, Li CP, Chen MT, Chien CS, Wang ML. Strategic Decoy Peptides Interfere with MSI1/AGO2 Interaction to Elicit Tumor Suppression Effects. Cancers (Basel) 2022; 14:cancers14030505. [PMID: 35158774 PMCID: PMC8833744 DOI: 10.3390/cancers14030505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Peptide drugs that can specifically target undesirable protein–protein interactions that lead to oncogenic developments have emerged as the next era of future medicine for cancers. To combat GBM tumor progression, our study offers an alternative therapeutic strategy via targeting the protein–protein interaction between MSI1 and AGO2 with synthetic peptides identified from the C-terminus of MSI1 in peptide arrays. Our present data revealed for the first time that peptidic disruption to the MSI1/AGO2 complex known for promoting cancer stemness and progression could lead to encouraging therapeutic efficacy at both in vitro and in vivo levels. The significantly suppressed tumor growth and prolonged survival rates in PDX tumor models by decoy peptides evidently provided a new rationale for stratifying patients with MSI1/AGO2-targeted therapeutics. Abstract Peptide drugs that target protein–protein interactions have attracted mounting research efforts towards clinical developments over the past decades. Increasing reports have indicated that expression of Musashi 1 (MSI1) is tightly correlated to high grade of cancers as well as enrichment of cancer stem cells. Treatment failure in malignant tumors glioblastoma multiform (GBM) had also been correlated to CSC-regulating properties of MSI1. It is thus imperative to develop new therapeutics that could effectively improve current regimens used in clinics. MSI1 and AGO2 are two emerging oncogenic molecules that both contribute to GBM tumorigenesis through mRNA regulation of targets involved in apoptosis and cell cycle. In this study, we designed peptide arrays covering the C-terminus of MSI1 and identified two peptides (Pep#11 and Pep#26) that could specifically interfere with the binding with AGO2. Our Biacore analyses ascertained binding between the identified peptides and AGO2. Recombinant reporter system Gaussian luciferase and fluorescent bioconjugate techniques were employed to determine biological functions and pharmacokinetic characteristics of these two peptides. Our data suggested that Pep#11 and Pep#26 could function as decoy peptides by mimicking the interaction function of MSI1 with its binding partner AGO2 in vitro and in vivo. Further experiments using GMB animal models corroborated the ability of Pep#11 and Pep#26 in disrupting MSI1/AGO2 interaction and consequently anti-tumorigenicity and prolonged survival rates. These striking therapeutic efficacies orchestrated by the synthetic peptides were attributed to the decoy function to C-terminal MSI1, especially in malignant brain tumors and glioblastoma.
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Affiliation(s)
- Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-P.Y.); (A.C.-L.L.); (Y.-C.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Institute of Food Safety and Health Risk Assessment, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Andy Chi-Lung Lee
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-P.Y.); (A.C.-L.L.); (Y.-C.C.)
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Liang-Ting Lin
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China;
| | - Yi-Wei Chen
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Department of Neurosurgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Oncology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Pin-I Huang
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Department of Neurosurgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Oncology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Hsin-I Ma
- Department of Neurological Surgery, Tri-Service General Hospital and National Defense Medical Center, Taipei 114, Taiwan;
| | - Yi-Chen Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-P.Y.); (A.C.-L.L.); (Y.-C.C.)
| | - Wen-Liang Lo
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Division of Oral and Maxillofacial Surgery, Department of Stomatology, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Yuan-Tzu Lan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Wen-Liang Fang
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Chien-Ying Wang
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Division of Trauma, Department of Emergency Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Critical Care Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Physical Education and Health, University of Taipei, Taipei 111, Taiwan
| | - Yung-Yang Liu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Chest Department, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Po-Kuei Hsu
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Department of Surgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan;
| | - Chung-Pin Li
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Department of Medical Education, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Ming-Teh Chen
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Department of Neurosurgery, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Department of Medical Education, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Chian-Shiu Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-P.Y.); (A.C.-L.L.); (Y.-C.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Correspondence: (C.-S.C.); (M.-L.W.); Tel.: +886-2-5568-1156 (M.-L.W.); Fax: +886-2-2875-7435 (M.-L.W.)
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 112, Taiwan; (Y.-P.Y.); (A.C.-L.L.); (Y.-C.C.)
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (Y.-W.C.); (P.-I.H.); (W.-L.L.); (Y.-T.L.); (W.-L.F.); (C.-Y.W.); (Y.-Y.L.); (P.-K.H.); (C.-P.L.); (M.-T.C.)
- Institute of Food Safety and Health Risk Assessment, College of Pharmaceutical Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Correspondence: (C.-S.C.); (M.-L.W.); Tel.: +886-2-5568-1156 (M.-L.W.); Fax: +886-2-2875-7435 (M.-L.W.)
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Targeted knockout of the gene OsHOL1 removes methyl iodide emissions from rice plants. Sci Rep 2021; 11:17010. [PMID: 34426588 PMCID: PMC8382704 DOI: 10.1038/s41598-021-95198-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/21/2021] [Indexed: 11/25/2022] Open
Abstract
Iodine deficiency represents a public health problem worldwide. To increase the amount of iodine in the diet, biofortification strategies of plants have been tried. They rely on the exogenous administration of iodine to increase its absorption and accumulation. However, iodine is not stable in plants and can be volatilized as methyl iodide through the action of specific methyltransferases encoded by the HARMLESS TO OZONE LAYER (HOL) genes. The release of methyl iodide in the atmosphere represents a threat for the environment due to its ozone depletion potential. Rice paddies are among the strongest producers of methyl iodide. Thus, the agronomic approach of iodine biofortification is not appropriate for this crop, leading to further increases of iodine emissions. In this work, we used the genome editing CRISPR/Cas9 technology to knockout the rice HOL genes and investigate their function. OsHOL1 resulted a major player in methyl iodide production, since its knockout abolished the process. Moreover, its overexpression reinforced it. Conversely, knockout of OsHOL2 did not produce effects. Our experiments helped elucidating the function of the rice HOL genes, providing tools to develop new rice varieties with reduced iodine emissions and thus more suitable for biofortification programs without further impacting on the environment.
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Deprey K, Batistatou N, Kritzer JA. A critical analysis of methods used to investigate the cellular uptake and subcellular localization of RNA therapeutics. Nucleic Acids Res 2020; 48:7623-7639. [PMID: 32644123 PMCID: PMC7430645 DOI: 10.1093/nar/gkaa576] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 12/21/2022] Open
Abstract
RNA therapeutics are a promising strategy to treat genetic diseases caused by the overexpression or aberrant splicing of a specific protein. The field has seen major strides in the clinical efficacy of this class of molecules, largely due to chemical modifications and delivery strategies that improve nuclease resistance and enhance cell penetration. However, a major obstacle in the development of RNA therapeutics continues to be the imprecise, difficult, and often problematic nature of most methods used to measure cell penetration. Here, we review these methods and clearly distinguish between those that measure total cellular uptake of RNA therapeutics, which includes both productive and non-productive uptake, and those that measure cytosolic/nuclear penetration, which represents only productive uptake. We critically analyze the benefits and drawbacks of each method. Finally, we use key examples to illustrate how, despite rigorous experimentation and proper controls, our understanding of the mechanism of gymnotic uptake of RNA therapeutics remains limited by the methods commonly used to analyze RNA delivery.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Nefeli Batistatou
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA 02155, USA
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Hosseini ES, Nikkhah M, Hamidieh AA, Fearnhead HO, Concordet JP, Hosseinkhani S. The Lumiptosome, an engineered luminescent form of the apoptosome can report cell death by using the same Apaf-1 dependent pathway. J Cell Sci 2020; 133:133/10/jcs242636. [DOI: 10.1242/jcs.242636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/28/2020] [Indexed: 01/09/2023] Open
Abstract
ABSTRACT
Detection of the apoptosis signature becomes central in understanding cell death modes. We present here a whole-cell biosensor that detects Apaf-1 association and apoptosome formation using a split-luciferase complementary assay. Fusion of N-terminal (Nluc) and C-terminal (Cluc)-fragments of firefly luciferase to the N-terminus of human Apaf-1 was performed in HEK293 cells by using CRISPR-Cas9 technology. This resulted in a luminescent form of the apoptosome that we named ‘Lumiptosome’. During Apaf-1 gene editing, a high number of knock-in events were observed without selection, suggesting that the Apaf-1 locus is important for the integration of exogenous transgenes. Since activation of caspase-9 is directly dependent on the apoptosome formation, measured reconstitution of luciferase activity should result from the cooperative association of Nluc-Apaf-1 and Cluc-Apaf-1. Time-response measurements also confirmed that formation of the apoptosome occurs prior to activation of caspase-3. Additionally, overexpression of the Bcl2 apoptosis regulator in transgenic and normal HEK293 cells confirmed that formation of the Lumiptosome depends on release of cytochrome c. Thus, HEK293 cells that stably express the Lumiptosome can be utilized to screen pro- and anti-apoptotic drugs, and to examine Apaf-1-dependent cellular pathways.
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Affiliation(s)
- Elaheh Sadat Hosseini
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Nanobiotechnology, Pharmacology and Therapeutics, School of Medicine, NUI, Galway, Ireland
- Department of Nanobiotechnology, Museum National d'Histoire Naturelle, Laboratoire Structure et Instabilité des Génomes - INSERM U1154 - CNRS 7196; Laboratoire de Biophysique, Sorbonne Universités, Paris, F-75231, France
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Ali Hamidieh
- Pediatric Cell Therapy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Howard O. Fearnhead
- Department of Nanobiotechnology, Pharmacology and Therapeutics, School of Medicine, NUI, Galway, Ireland
| | - Jean-Paul Concordet
- Department of Nanobiotechnology, Museum National d'Histoire Naturelle, Laboratoire Structure et Instabilité des Génomes - INSERM U1154 - CNRS 7196; Laboratoire de Biophysique, Sorbonne Universités, Paris, F-75231, France
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
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10
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Deprey K, Kritzer JA. Quantitative measurement of cytosolic penetration using the chloroalkane penetration assay. Methods Enzymol 2020; 641:277-309. [PMID: 32713526 PMCID: PMC7872221 DOI: 10.1016/bs.mie.2020.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A major barrier for drug development is ensuring molecules can access intracellular targets. This is especially true for biomolecules, which are notoriously difficult to deliver to the cytosol. Many current methods for measuring the internalization of therapeutic biomolecules are largely indirect and qualitative, and they do not offer information about subcellular localization. We recently reported a new assay, called the ChloroAlkane Penetration Assay (CAPA), that addresses some of the drawbacks of existing methods. CAPA is high-throughput, quantitative, and compartment-specific, and can be used to monitor cytosolic penetration over time and under a variety of culture conditions. We have used CAPA to investigate the cytosolic localization of peptides, proteins, and oligonucleotides. In this chapter, we discuss the materials, protocols, and troubleshooting necessary to perform CAPA and appropriately analyze the data. We end with a discussion about the applications and limitations of CAPA, and we speculate on the potential of the assay and its variations.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, Medford, MA, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, MA, United States.
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11
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Khowsathit J, Bazzoli A, Cheng H, Karanicolas J. Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation. ACS CENTRAL SCIENCE 2020; 6:390-403. [PMID: 32232139 PMCID: PMC7099597 DOI: 10.1021/acscentsci.9b01065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 05/08/2023]
Abstract
Therapeutic monoclonal antibodies have transformed medicine, especially with regards to treating cancers and disorders of the immune system. More than 50 antibody-derived drugs have already reached the clinic, the majority of which target cytokines or cell-surface receptors. Unfortunately, many of these targets have pleiotropic functions: they serve multiple different roles, and often not all of these roles are disease-related. This can be problematic because antibodies act throughout the body, and systemic neutralization of such targets can lead to safety concerns. To address this, we have developed a strategy whereby an antibody's ability to recognize its antigen is modulated by a second layer of control, relying on addition of an exogenous small molecule. In previous studies, we began to explore this idea by introducing a deactivating tryptophan-to-glycine mutation in the domain-domain interface of a single-chain variable fragment (scFv), and then restoring activity by adding back indole to fit the designed cavity. Here, we now describe a novel computational strategy for enumerating larger cavities that can be formed by simultaneously introducing multiple adjacent large-to-small mutations; we then carry out a complementary virtual screen to identify druglike compounds to match each candidate cavity. We first demonstrate the utility of this strategy in a fluorescein-binding single-chain variable fragment (scFv) and experimentally characterize a triple mutant with reduced antigen-binding (Rip-3) that can be rescued using a complementary ligand (Stitch-3). Because our design is built upon conserved residues in the antibody framework, we then show that the same mutation/ligand pair can also be used to modulate antigen-binding in an scFv build from a completely unrelated framework. This set of residues is present in many therapeutic antibodies as well, suggesting that this mutation/ligand pair may serve as a general starting point for introducing ligand-dependence into many clinically relevant antibodies.
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Affiliation(s)
- Jittasak Khowsathit
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Andrea Bazzoli
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
| | - Hong Cheng
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
| | - John Karanicolas
- Program
in Molecular Therapeutics, Fox Chase Cancer
Center, Philadelphia, Pennsylvania 19111, United States
- Department of Molecular
Biosciences and Center for Computational Biology, University
of Kansas, Lawrence, Kansas 66045, United
States
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12
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Deprey K, Becker L, Kritzer J, Plückthun A. Trapped! A Critical Evaluation of Methods for Measuring Total Cellular Uptake versus Cytosolic Localization. Bioconjug Chem 2019; 30:1006-1027. [PMID: 30882208 PMCID: PMC6527423 DOI: 10.1021/acs.bioconjchem.9b00112] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biomolecules have many properties that make them promising for intracellular therapeutic applications, but delivery remains a key challenge because large biomolecules cannot easily enter the cytosol. Furthermore, quantification of total intracellular versus cytosolic concentrations remains demanding, and the determination of delivery efficiency is thus not straightforward. In this review, we discuss strategies for delivering biomolecules into the cytosol and briefly summarize the mechanisms of uptake for these systems. We then describe commonly used methods to measure total cellular uptake and, more selectively, cytosolic localization, and discuss the major advantages and drawbacks of each method. We critically evaluate methods of measuring "cell penetration" that do not adequately distinguish total cellular uptake and cytosolic localization, which often lead to inaccurate interpretations of a molecule's cytosolic localization. Finally, we summarize the properties and components of each method, including the main caveats of each, to allow for informed decisions about method selection for specific applications. When applied correctly and interpreted carefully, methods for quantifying cytosolic localization offer valuable insight into the bioactivity of biomolecules and potentially the prospects for their eventual development into therapeutics.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Lukas Becker
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Joshua Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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13
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Identification of Compounds Targeting Hepatitis B Virus Core Protein Dimerization through a Split Luciferase Complementation Assay. Antimicrob Agents Chemother 2018; 62:AAC.01302-18. [PMID: 30224531 DOI: 10.1128/aac.01302-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/06/2018] [Indexed: 02/07/2023] Open
Abstract
The capsid of the hepatitis B virus is an attractive antiviral target for developing therapies against chronic hepatitis B infection. Currently available core protein allosteric modulators (CpAMs) mainly affect one of the two major types of protein-protein interactions involved in the process of capsid assembly, namely, the interaction between the core dimers. Compounds targeting the interaction between two core monomers have not been rigorously screened due to the lack of screening models. We report here a cell-based assay in which the formation of core dimers is indicated by split luciferase complementation (SLC). Making use of this model, 2 compounds, Arbidol (umifenovir) and 20-deoxyingenol, were identified from a library containing 672 compounds as core dimerization regulators. Arbidol and 20-deoxyingenol inhibit the hepatitis B virus (HBV) DNA replication in vitro by decreasing and increasing the formation of core dimer and capsid, respectively. Our results provided a proof of concept for the cell model to be used to screen new agents targeting the step of core dimer and capsid formation.
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14
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Park J, Lim CJ, Shen M, Park HJ, Cha JY, Iniesto E, Rubio V, Mengiste T, Zhu JK, Bressan RA, Lee SY, Lee BH, Jin JB, Pardo JM, Kim WY, Yun DJ. Epigenetic switch from repressive to permissive chromatin in response to cold stress. Proc Natl Acad Sci U S A 2018; 115:E5400-E5409. [PMID: 29784800 PMCID: PMC6003311 DOI: 10.1073/pnas.1721241115] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Switching from repressed to active status in chromatin regulation is part of the critical responses that plants deploy to survive in an ever-changing environment. We previously reported that HOS15, a WD40-repeat protein, is involved in histone deacetylation and cold tolerance in Arabidopsis However, it remained unknown how HOS15 regulates cold responsive genes to affect cold tolerance. Here, we show that HOS15 interacts with histone deacetylase 2C (HD2C) and both proteins together associate with the promoters of cold-responsive COR genes, COR15A and COR47 Cold induced HD2C degradation is mediated by the CULLIN4 (CUL4)-based E3 ubiquitin ligase complex in which HOS15 acts as a substrate receptor. Interference with the association of HD2C and the COR gene promoters by HOS15 correlates with increased acetylation levels of histone H3. HOS15 also interacts with CBF transcription factors to modulate cold-induced binding to the COR gene promoters. Our results here demonstrate that cold induces HOS15-mediated chromatin modifications by degrading HD2C. This switches the chromatin structure status and facilitates recruitment of CBFs to the COR gene promoters. This is an apparent requirement to acquire cold tolerance.
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Affiliation(s)
- Junghoon Park
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Chae Jin Lim
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Mingzhe Shen
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Hee Jin Park
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea
- Institute of Glocal Disease Control, Konkuk University, 05029 Seoul, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Elisa Iniesto
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Vicente Rubio
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Cientificas, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907
| | - Ray A Bressan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Byeong-Ha Lee
- Department of Life Science, Sogang University, 04107 Seoul, South Korea
| | - Jing Bo Jin
- Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China
| | - Jose M Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Cientificas, 41092 Seville, Spain
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 plus Program), Plant Molecular Biology and Biotechnology Research Center, Institute of Agriculture and Life Science, Gyeongsang National University, 52828 Jinju, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, 05029 Seoul, South Korea;
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15
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Abstract
Proteins rarely act alone as their functions tend to be regulated in vivo. Therefore, protein-protein interaction analyses provide key clues for understanding the complex biological processes in the living cell. Several techniques have been developed to elucidate the conformation of large protein complexes, dynamic protein complex rearrangement and transient protein interactions. Yeast two-hybrid system is a well-established method to analyze binary protein interactions. Here we describe a basic yeast three-hybrid method, which represents an additional refinement of the classical yeast two-hybrid system for analyzing further complex interactions among three proteins.
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16
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Nealon JO, Philomina LS, McGuffin LJ. Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. Int J Mol Sci 2017; 18:E2623. [PMID: 29206185 PMCID: PMC5751226 DOI: 10.3390/ijms18122623] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 11/17/2022] Open
Abstract
The elucidation of protein-protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development.
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Affiliation(s)
- John Oliver Nealon
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK.
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17
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Zhang Y, Beard KFM, Swart C, Bergmann S, Krahnert I, Nikoloski Z, Graf A, Ratcliffe RG, Sweetlove LJ, Fernie AR, Obata T. Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle. Nat Commun 2017; 8:15212. [PMID: 28508886 PMCID: PMC5440813 DOI: 10.1038/ncomms15212] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 03/09/2017] [Indexed: 11/29/2022] Open
Abstract
Protein complexes of sequential metabolic enzymes, often termed metabolons, may permit direct channelling of metabolites between the enzymes, providing increased control over metabolic pathway fluxes. Experimental evidence supporting their existence in vivo remains fragmentary. In the present study, we test binary interactions of the proteins constituting the plant tricarboxylic acid (TCA) cycle. We integrate (semi-)quantitative results from affinity purification-mass spectrometry, split-luciferase and yeast-two-hybrid assays to generate a single reliability score for assessing protein–protein interactions. By this approach, we identify 158 interactions including those between catalytic subunits of sequential enzymes and between subunits of enzymes mediating non-adjacent reactions. We reveal channelling of citrate and fumarate in isolated potato mitochondria by isotope dilution experiments. These results provide evidence for a functional TCA cycle metabolon in plants, which we discuss in the context of contemporary understanding of this pathway in other kingdoms. A metabolon is a complex of sequential metabolic enzymes that channels substrates directly between enzymes, thus optimizing metabolic flux. Here Zhang et al. provide protein interaction and isotope dilution data that support the existence of a metabolon that channels both citrate and fumarate in the plant TCA cycle.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Corné Swart
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Susan Bergmann
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ina Krahnert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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18
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Fontenot EB, Ditusa SF, Kato N, Olivier DM, Dale R, Lin WY, Chiou TJ, Macnaughtan MA, Smith AP. Increased phosphate transport of Arabidopsis thaliana Pht1;1 by site-directed mutagenesis of tyrosine 312 may be attributed to the disruption of homomeric interactions. PLANT, CELL & ENVIRONMENT 2015; 38:2012-22. [PMID: 25754174 DOI: 10.1111/pce.12522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/06/2015] [Accepted: 02/14/2015] [Indexed: 05/20/2023]
Abstract
Members of the Pht1 family of plant phosphate (Pi) transporters play vital roles in Pi acquisition from soil and in planta Pi translocation to maintain optimal growth and development. The study of the specificities and biochemical properties of Pht1 transporters will contribute to improving the current understanding of plant phosphorus homeostasis and use-efficiency. In this study, we show through split in vivo interaction methods and in vitro analysis of microsomal root tissues that Arabidopsis thaliana Pht1;1 and Pht1;4 form homomeric and heteromeric complexes. Transient and heterologous expression of the Pht1;1 variants, Pht1;1(Y312D), Pht1;1(Y312A) and Pht1;1(Y312F), was used to analyse the role of a putative Pi binding residue (Tyr 312) in Pht1;1 transporter oligomerization and function. The homomeric interaction among Pht1;1 proteins was disrupted by mutation of Tyr 312 to Asp, but not to Ala or Phe. In addition, the Pht1;1(Y312D) variant conferred enhanced Pi transport when expressed in yeast cells. In contrast, mutation of Tyr 312 to Ala or Phe did not affect Pht1;1 transport kinetics. Our study demonstrates that modifications to the Pht1;1 higher-order structure affects Pi transport, suggesting that oligomerization may serve as a regulatory mechanism for modulating Pi uptake.
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Affiliation(s)
- Elena B Fontenot
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Sandra Feuer Ditusa
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Danielle M Olivier
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Renee Dale
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Wei-Yi Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan, China
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan, China
| | - Megan A Macnaughtan
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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19
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Lund CH, Bromley JR, Stenbæk A, Rasmussen RE, Scheller HV, Sakuragi Y. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:85-97. [PMID: 25326916 PMCID: PMC4265154 DOI: 10.1093/jxb/eru401] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.
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Affiliation(s)
- Christian H Lund
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
| | - Jennifer R Bromley
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne Stenbæk
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
| | - Randi E Rasmussen
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
| | - Henrik V Scheller
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yumiko Sakuragi
- University of Copenhagen, Department of Plant Biology and Biotechnology, Frederiksberg, DK-1871, Denmark
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20
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Fujikawa Y, Nakanishi T, Kawakami H, Yamasaki K, Sato MH, Tsuji H, Matsuoka M, Kato N. Split luciferase complementation assay to detect regulated protein-protein interactions in rice protoplasts in a large-scale format. RICE (NEW YORK, N.Y.) 2014; 7:11. [PMID: 24987490 PMCID: PMC4077619 DOI: 10.1186/s12284-014-0011-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 05/27/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND The rice interactome, in which a network of protein-protein interactions has been elucidated in rice, is a useful resource to identify functional modules of rice signal transduction pathways. Protein-protein interactions occur in cells in two ways, constitutive and regulative. While a yeast-based high-throughput method has been widely used to identify the constitutive interactions, a method to detect the regulated interactions is rarely developed for a large-scale analysis. RESULTS A split luciferase complementation assay was applied to detect the regulated interactions in rice. A transformation method of rice protoplasts in a 96-well plate was first established for a large-scale analysis. In addition, an antibody that specifically recognizes a carboxyl-terminal fragment of Renilla luciferase was newly developed. A pair of antibodies that recognize amino- and carboxyl- terminal fragments of Renilla luciferase, respectively, was then used to monitor quality and quantity of interacting recombinant-proteins accumulated in the cells. For a proof-of-concept, the method was applied to detect the gibberellin-dependent interaction between GIBBERELLIN INSENSITIVE DWARF1 and SLENDER RICE 1. CONCLUSIONS A method to detect regulated protein-protein interactions was developed towards establishment of the rice interactome.
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Affiliation(s)
- Yukichi Fujikawa
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Hiroshima, Japan
| | - Takahiro Nakanishi
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Hiroshima, Japan
| | - Hiroko Kawakami
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Hiroshima, Japan
| | - Kanako Yamasaki
- Faculty of Human Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Masa H Sato
- Faculty of Human Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Hiroyuki Tsuji
- Department of Plant Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Nara, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya Aichi 464-8601, Japan
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, 226 Life Sciences Building, Baton Rouge 70803, LA, USA
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21
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Singh DK, Calviño M, Brauer EK, Fernandez-Pozo N, Strickler S, Yalamanchili R, Suzuki H, Aoki K, Shibata D, Stratmann JW, Popescu GV, Mueller LA, Popescu SC. The tomato kinome and the tomato kinase library ORFeome: novel resources for the study of kinases and signal transduction in tomato and solanaceae species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:7-17. [PMID: 24047240 DOI: 10.1094/mpmi-08-13-0218-ta] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein kinase-driven phosphorylation constitutes the core of cellular signaling. Kinase components of signal transduction pathways are often targeted for inactivation by pathogens. The study of kinases and immune signal transduction in the model crop tomato (Solanum lycopersicum) would benefit from the availability of community-wide resources for large scale and systems-level experimentation. Here, we defined the tomato kinome and performed a comprehensive comparative analysis of the tomato kinome and 15 other plant species. We constructed a tomato kinase library (TOKN 1.0) of over 300 full-length open reading frames (ORF) cloned into a recombination-based vector. We developed a high-throughput pipeline to isolate and transform tomato protoplasts. A subset of the TOKN 1.0 library kinases were expressed in planta, were purified, and were used to generate a functional tomato protein microarray. All resources created were utilized to test known and novel associations between tomato kinases and Pseudomonas syringae DC3000 effectors in a large-scale format. Bsk7 was identified as a component of the plant immune response and a candidate effector target. These resources will enable comprehensive investigations of signaling pathways and host-pathogen interactions in tomato and other Solanaceae spp.
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Ramkumar KM, Sekar TV, Foygel K, Elango B, Paulmurugan R. Reporter protein complementation imaging assay to screen and study Nrf2 activators in cells and living animals. Anal Chem 2013; 85:7542-9. [PMID: 23826874 PMCID: PMC3759980 DOI: 10.1021/ac401569j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
NF-E2-related factor-2 (Nrf2) activators promote cellular defense mechanism and facilitate disease prevention associated with oxidative stress. In the present study, Nrf2 activators were identified using cell-based luciferase enzyme fragment complementation (EFC) assay, and the mechanism of Nrf2 activation was studied by molecular imaging. Among the various Nrf2 activators tested, pterostilbene (PTS) showed effective Nrf2 activation, as seen by luminometric screening, and validation in a high throughput-intact cell-imaging platform. Further, PTS increased the expression of Nrf2 downstream target genes, which was confirmed using luciferase reporter driven by ARE-NQO1 and ARE-GST1 promoters. Daily administration of PTS disturbed Nrf2/Keap1 interaction and reduced complemented luciferase signals in HEK293TNKS mouse tumor xenografts. This study reveals the potentials of Nrf2 activators as chemosensitizing agents' for therapeutic intervention in cancer treatment. Hence, the validated assay can be used to evaluate the identified activators preclinically in small animal models by noninvasive molecular imaging approach.
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Affiliation(s)
| | - Thillai Veerapazham Sekar
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, Stanford University School of Medicine, Stanford, California, USA
| | - Kira Foygel
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Department of Radiology, Stanford University School of Medicine, Stanford, California, USA
- Corresponding Author: Ramasamy Paulmurugan, Ph.D. Department of Radiology, Stanford University School of Medicine 1501, South California Avenue, #2217 Palo Alto, CA 94304 Phone: 650-725-6097; Fax: 650-721-6921
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Novel split-luciferase-based genetically encoded biosensors for noninvasive visualization of Rho GTPases. PLoS One 2013; 8:e62230. [PMID: 23614039 PMCID: PMC3627919 DOI: 10.1371/journal.pone.0062230] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/19/2013] [Indexed: 02/05/2023] Open
Abstract
Rho family GTPases are critical regulators of many important cellular processes and the dysregulation of their activities is implicated in a variety of human diseases including oncogenesis and propagation of malignancy. The traditional methods, such as “pull-down” or two-hybrid procedures, are poorly suited to dynamically evaluate the activity of Rho GTPases, especially in living mammalian cells. To provide a novel alternative approach to analyzing Rho GTPase-associated signaling pathways in vivo, we developed a series of bioluminescent biosensors based on the genetically engineered firefly luciferase. These split-luciferase-based biosensors enable non-invasive visualization and quantification of the activity of Rho GTPases in living subjects. The strategy is to reasonably split the gene of firefly luciferase protein into two inactive fragments and then respectively fuse the two fragments to Rho GTPase and the GTPase-binding domain (GBD) of the specific effector. Upon Rho GTPase interacting with the binding domain in a GTP-dependent manner, these two luciferase fragments are brought into close proximity, leading to luciferase reconstitution and photon production in the presence of the substrate. Using these bimolecular luminescence complementation (BiLC) biosensors, we successfully visualized and quantified the activities of the three best characterized Rho GTPases by measuring the luminescence in living cells. We also experimentally investigated the sensitivity of these Rho GTPase biosensors to upstream regulatory proteins and extracellular ligands without lysing cells and doing labor-intensive works. By virtue of the unique functional characteristics of bioluminescence imaging, the BiLC-based biosensors provide an enormous potential for in vivo imaging of Rho GTPase signaling pathways and high-throughput screening of therapeutic drugs targeted to Rho GTPases and (or) upstream molecules in the near future.
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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25
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Keem JO, Lee IH, Kim SY, Jung Y, Chung BH. Splitting and self-assembling of far-red fluorescent protein with an engineered beta strand peptide: application for alpha-synuclein imaging in mammalian cells. Biomaterials 2011; 32:9051-8. [PMID: 21880361 DOI: 10.1016/j.biomaterials.2011.08.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/10/2011] [Indexed: 12/30/2022]
Abstract
We introduce the strategic development of self-assembling peptide/protein fragments based on the far-red fluorescent protein mPlum. The first beta strand (mPlum 1, 18 amino acids) of mPlum was engineered to spontaneously bind with the rest of the protein (mPlum 2-11, next 10 beta strands) and to form a native chromophore. The target beta strand mPlum 1 was separated from mPlum 2-11 and linked via a flexible peptide linker, resulting in fluorescently inactive circularly permuted mPlum protein (CpmPlum). In vitro evolution of this CpmPlum to a fluorescently active form and the subsequent splitting of the engineered mPlum 1 peptide afforded self-assembling mPlum fragments. Recombinantly expressed and synthetically prepared beta strand peptides were successfully assembled with the remaining mPlum protein in vitro and in cells. This developed pair of peptide/protein fragments was effectively used for peptide tag detection of alpha-synuclein in mammalian cells. Sequential expression of self-assembling mPlum fragments offered an entirely genetically encoded sensing system of naturally unfolded alpha-synuclein.
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Affiliation(s)
- Joo Oak Keem
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon, Republic of Korea
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26
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The orexin OX(1) receptor exists predominantly as a homodimer in the basal state: potential regulation of receptor organization by both agonist and antagonist ligands. Biochem J 2011; 439:171-83. [PMID: 21770891 DOI: 10.1042/bj20110230] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It is unclear what proportion of a G-protein-coupled receptor is present in cells as dimers or oligomers. Saturation bioluminescence resonance energy transfer studies demonstrated the orexin OX(1) receptor to be present in such complexes. Forms of this receptor containing a minimal epitope tag, with the C-terminus linked to yellow fluorescent protein or modified at the N-terminus to incorporate a SNAP tag, migrated in SDS/PAGE gels as monomers, indicating a lack of covalent interactions. Solubilization with dodecylmaltoside, followed by Blue native-PAGE, indicated that the receptor constructs migrated predominantly as anticipated for dimeric species with evidence for further, higher-order, complexes, and this was true over a wide range of expression levels. Addition of SDS prior to separation by Blue native-PAGE resulted in much of the previously dimeric, and all of the higher-order, complexes being dissociated and now migrating at the size predicted for monomeric species. Expression of forms of the OX(1) receptor capable of generating enzyme complementation confirmed that solubilization itself did not result in interaction artefacts. Addition of the endogenous agonist orexin A enhanced the proportion of higher-order OX(1) receptor complexes, whereas selective OX(1) antagonists increased the proportion the OX(1) receptor migrating in Blue native-PAGE as a monomer. The antagonist effects were produced in a concentration-dependent manner, consistent with the affinity of the ligands for the receptor. Homogeneous time-resolved fluorescence resonance energy transfer studies using Tag-Lite™ reagents on cells expressing the SNAP-tagged OX(1) receptor identified cell-surface OX(1) homomers. Predominantly at low receptor expression levels, orexin A increased such fluorescence resonance energy transfer signals, also consistent with ligand-induced reorganization of the homomeric complex.
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Kato N, Bai H. Expression, localization and interaction of SNARE proteins in Arabidopsis are selectively altered by the dark. PLANT SIGNALING & BEHAVIOR 2010; 5:1470-2. [PMID: 21051940 PMCID: PMC3115258 DOI: 10.4161/psb.5.11.13480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 08/31/2010] [Indexed: 05/08/2023]
Abstract
A method to detect binary interactions among SNAREs, membrane proteins mediating vesicle fusion, in Arabidopsis cells was established. In this method, a pair of recombinant SNAREs is first expressed within Arabidopsis protoplasts at levels similar to their endogenous proteins in 96-well plates. Changes of the interaction are then detected by luminescence. Here, we report that the interaction of SYP122 and VAMP721, a SNARE pair mediating exocytosis, is enhanced when Arabidopsis protoplasts are incubated in the dark. Microscopic observation of plants expressing GFP-SYP122 by the syp122 promoter suggests SYP122 is expressed in the root tip when the seedlings are grown in the dark but not in the light. In the identical dark-grown condition, the subcellular localization of SYP111/KNOLLE, specifically expressed in dividing cells, is altered. Together with our previous report, we hypothesize that expression, localization, and interaction of SNAREs are selectively altered by light conditions to regulate cargo transports in Arabidopsis.
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Affiliation(s)
- Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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