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Bi Y, An H, Chi Z, Xu Z, Deng Y, Ren Y, Wang R, Lu X, Guo J, Hu R, Virolle MJ, Xu D. The acetyltransferase SCO0988 controls positively specialized metabolism and morphological differentiation in the model strains Streptomyces coelicolor and Streptomyces lividans. Front Microbiol 2024; 15:1366336. [PMID: 39113837 PMCID: PMC11303876 DOI: 10.3389/fmicb.2024.1366336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Streptomycetes are well-known antibiotic producers possessing in their genomes numerous silent biosynthetic pathways that might direct the biosynthesis of novel bio-active specialized metabolites. It is thus of great interest to find ways to enhance the expression of these pathways to discover most needed novel antibiotics. In this study, we demonstrated that the over-expression of acetyltransferase SCO0988 up-regulated the production of specialized metabolites and accelerated sporulation of the weak antibiotic producer, Streptomyces lividans and that the deletion of this gene had opposite effects in the strong antibiotic producer, Streptomyces coelicolor. The comparative analysis of the acetylome of a S. lividans strain over-expressing sco0988 with that of the original strain revealed that SCO0988 acetylates a broad range of proteins of various pathways including BldKB/SCO5113, the extracellular solute-binding protein of an ABC-transporter involved in the up-take of a signal oligopeptide of the quorum sensing pathway. The up-take of this oligopeptide triggers the "bald cascade" that regulates positively specialized metabolism, aerial mycelium formation and sporulation in S. coelicolor. Interestingly, BldKB/SCO5113 was over-acetylated on four Lysine residues, including Lys425, upon SCO0988 over-expression. The bald phenotype of a bldKB mutant could be complemented by native bldKB but not by variant of bldKB in which the Lys425 was replaced by arginine, an amino acid that could not be acetylated or by glutamine, an amino acid that is expected to mimic acetylated lysine. Our study demonstrated that Lys425 was a critical residue for BldKB function but was inconclusive concerning the impact of acetylation of Lys425 on BldKB function.
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Affiliation(s)
- Yunwen Bi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Hao An
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Zhewei Chi
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Zhongheng Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Yuan Deng
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Yuxian Ren
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Rui Wang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Xinyi Lu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Jia Guo
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Ren Hu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
| | - Marie-Joelle Virolle
- Université Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, Gif-sur-Yvette, France
| | - Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, China
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2
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Kim SI, Kim S, Shim JM, Lee HJ, Chang SY, Park S, Min JY, Park WB, Oh MD, Kim S, Chung J. Neutralization of Zika virus by E protein domain III-Specific human monoclonal antibody. Biochem Biophys Res Commun 2021; 545:33-39. [PMID: 33535104 DOI: 10.1016/j.bbrc.2021.01.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Zika virus (ZIKV) infection in both infants and adults is associated with neurological complications including, but not limited to, microcephaly and Guillain-Barre syndrome. Antibody therapy can be effective against virus infection. We isolated ZIKV envelope domain III-specific neutralizing antibodies (nAbs) from two convalescent patients with ZIKV infection. One antibody, 2F-8, exhibited potent in vitro neutralizing activity against Asian and American strains of ZIKV. To prevent FcγR-mediated antibody-dependent enhancement, we prepared IgG1 with LALA variation. A single dose of 2F-8 in the context of IgG1 or IgG1-LALA prior to or post lethal ZIKV challenge conferred complete protection in mice.
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Affiliation(s)
- Sang Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Sujeong Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea; Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jung Min Shim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Gyeonggi-do, 13488, Republic of Korea
| | - Hyo Jung Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Gyeonggi-do, 13488, Republic of Korea.
| | - So Young Chang
- Respiratory Virus Laboratory, Institut Pasteur Korea, Gyeonggi-do, 13488, Republic of Korea.
| | - Seoryeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Ji-Young Min
- Respiratory Virus Laboratory, Institut Pasteur Korea, Gyeonggi-do, 13488, Republic of Korea.
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Gyeonggi-do, 13488, Republic of Korea.
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea; Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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3
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Li Y. A brief introduction of IgG-like bispecific antibody purification: Methods for removing product-related impurities. Protein Expr Purif 2019; 155:112-119. [DOI: 10.1016/j.pep.2018.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/30/2018] [Indexed: 01/04/2023]
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4
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Jin J, Park G, Park JB, Kim S, Kim H, Chung J. An anti-EGFR × cotinine bispecific antibody complexed with cotinine-conjugated duocarmycin inhibits growth of EGFR-positive cancer cells with KRAS mutations. Exp Mol Med 2018; 50:1-14. [PMID: 29795377 PMCID: PMC5967348 DOI: 10.1038/s12276-018-0096-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 03/10/2018] [Accepted: 03/16/2018] [Indexed: 11/30/2022] Open
Abstract
Antibody-drug conjugates (ADCs) can selectively deliver cytotoxic agents to tumor cells and are frequently more potent than naked antibodies. However, optimization of the conjugation process between antibodies and cytotoxic agents and characterization of ADCs are laborious and time-consuming processes. Here, we describe a novel ADC platform using a tetravalent bispecific antibody that simultaneously binds to the tumor-associated antigen and a hapten conjugated to a cytotoxic agent. We selected cotinine as the hapten because it is not present in biological systems and is inert and nontoxic. We prepared an anti-epidermal growth factor receptor (EGFR) × cotinine bispecific antibody and mixed it with an equimolar amount of cotinine-conjugated duocarmycin to form the ADC. This ADC showed significant in vitro and in vivo antitumor activity against EGFR-positive, cetuximab-refractory lung adenocarcinoma cells with KRAS mutations. A new method for producing antibody-drug conjugates (ADCs), pairing anti-cancer drugs with antibodies that deliver them specifically to cancer cells, may help to develop therapies for hard-to-treat cancers. ADCs show promise for treating several cancers, but are difficult to produce. Junho Chung at the Seoul National University College of Medicine in South Korea and co-workers tested a new way of forming the conjugates, using cotinine, a non-toxic molecule related to nicotine, as a link. They bound cotinine to the anti-cancer drug duocarmycin, then formulated an antibody with two binding sites, one for cotinine, one for tumor cells. Combining the drug−cotinine complex with the antibody resulted in a drug–cotinine-antibody ADC that delivered duocarmycin exclusively to cancer cells and inhibited tumor growth in mice. This simplified method may help develop treatments for other drug-resistant cancers.
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Affiliation(s)
- Junyeong Jin
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea
| | - Gunwoo Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea.,Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
| | - Jong Bae Park
- Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea.,Department of Cancer Biomedical Science, National Cancer Center, Graduate School of Cancer Science and Policy, 323 Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
| | - Soohyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea
| | - Hyori Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea.,Asan Institute for Life Sciences, Asan Medical Center, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea. .,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea. .,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 00380, Republic of Korea.
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5
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Jo DH, Kim JH, Yang W, Kim H, Chang S, Kim D, Chang M, Lee K, Chung J, Kim JH. Anti-complement component 5 antibody targeting MG4 domain inhibits choroidal neovascularization. Oncotarget 2018; 8:45506-45516. [PMID: 28477014 PMCID: PMC5542204 DOI: 10.18632/oncotarget.17221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/15/2017] [Indexed: 12/27/2022] Open
Abstract
Age-related macular degeneration (AMD) is one of the main causes of visual impairment in adults. Visual deterioration is more prominent in neovascular AMD with choroidal neovascularization (CNV). Clinical and postmortem studies suggested that complement system activation might induce CNV. In this study, we demonstrated that an anti-mouse complement component 5 (C5) antibody targeting MG4 domain of β chain effectively inhibited CNV which was induced by laser photocoagulation in mice. The targeted epitope of this anti-C5 antibody was different from that of currently utilized anti-C5 antibody (eculizumab) in the MG7 domain in which a single nucleotide polymorphism (R885H/C) results in poor response to eculizumab. Even with targeting MG4 domain, this anti-C5 antibody reduced production of C5a, monocyte chemoattractant protein-1 and vascular endothelial growth factor to prevent infiltration of F4/80-positive cells into CNV lesions and formation of CNV. Furthermore, anti-C5 antibody targeting MG4 domain induced no definite toxicity in normal retina. These results demonstrated that anti-C5 antibody targeting MG4 domain inhibited CNV in neovascular AMD.
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Affiliation(s)
- Dong Hyun Jo
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Biomedical Sciences and Protein Metabolism, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jin Hyoung Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Wonjun Yang
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyori Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Shinjae Chang
- Biotechnology Research Institute, Celltrion, Inc., Incheon, Republic of Korea
| | - Dongjo Kim
- Biotechnology Research Institute, Celltrion, Inc., Incheon, Republic of Korea
| | - Minseok Chang
- Biotechnology Research Institute, Celltrion, Inc., Incheon, Republic of Korea
| | - Kihwang Lee
- Department of Ophthalmology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Biomedical Sciences and Protein Metabolism, Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
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6
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18F-FDG PET and histopathologic findings in a patient with severe fever with thrombocytopenia syndrome. Ticks Tick Borne Dis 2018; 9:972-975. [PMID: 29615316 DOI: 10.1016/j.ttbdis.2018.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/09/2018] [Accepted: 03/27/2018] [Indexed: 11/22/2022]
Abstract
We report on a patient with severe fever with thrombocytopenia syndrome who fully recovered. Imaging with 2-deoxy-2-fluoro-glucose positron emission tomography showed hypermetabolism in regional lymph nodes and the spleen. Histopathological findings of affected lymph nodes showed subacute necrotizing lymphadenitis and the presence of virus-infected cells.
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7
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Brinkmann U, Kontermann RE. The making of bispecific antibodies. MAbs 2017; 9:182-212. [PMID: 28071970 PMCID: PMC5297537 DOI: 10.1080/19420862.2016.1268307] [Citation(s) in RCA: 605] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/18/2016] [Accepted: 11/29/2016] [Indexed: 12/12/2022] Open
Abstract
During the past two decades we have seen a phenomenal evolution of bispecific antibodies for therapeutic applications. The 'zoo' of bispecific antibodies is populated by many different species, comprising around 100 different formats, including small molecules composed solely of the antigen-binding sites of two antibodies, molecules with an IgG structure, and large complex molecules composed of different antigen-binding moieties often combined with dimerization modules. The application of sophisticated molecular design and genetic engineering has solved many of the technical problems associated with the formation of bispecific antibodies such as stability, solubility and other parameters that confer drug properties. These parameters may be summarized under the term 'developability'. In addition, different 'target product profiles', i.e., desired features of the bispecific antibody to be generated, mandates the need for access to a diverse panel of formats. These may vary in size, arrangement, valencies, flexibility and geometry of their binding modules, as well as in their distribution and pharmacokinetic properties. There is not 'one best format' for generating bispecific antibodies, and no single format is suitable for all, or even most of, the desired applications. Instead, the bispecific formats collectively serve as a valuable source of diversity that can be applied to the development of therapeutics for various indications. Here, a comprehensive overview of the different bispecific antibody formats is provided.
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Affiliation(s)
- Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Im Nonnenwald, Penzberg, Germany
| | - Roland E. Kontermann
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring, Stuttgart, Germany
- Stuttgart Research Center Systems Biology, University of Stuttgart, Nobelstraße, Stuttgart, Germany
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8
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Lee HK, Jin J, Kim SI, Kang MJ, Yi EC, Kim JE, Park JB, Kim H, Chung J. A point mutation in the heavy chain complementarity-determining region 3 (HCDR3) significantly enhances the specificity of an anti-ROS1 antibody. Biochem Biophys Res Commun 2017; 493:325-331. [PMID: 28888985 DOI: 10.1016/j.bbrc.2017.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 09/06/2017] [Indexed: 12/20/2022]
Abstract
The proto-oncogene tyrosine kinase ROS1 plays a key role in carcinogenesis through gene rearrangement to form a fusion protein with other genes, in which the C-terminal intracellular region of ROS1 participates. The possibility of wild type ROS1 overexpression through epigenetic regulation has been proposed. Here, we generated an antibody, 3B20, reactive to the N-terminal region of ROS1 to use it for the detection of wild type ROS1 in cancerous tissues. Using immunoblot and immunoprecipitation analyses, we found that 3B20 also reacted with heat shock proteins (Hsp)70s. Using homology searching, ROS1 and Hsp70s were found to share an identical amino acid sequence: DLGT. Using alanine mutagenesis of ROS1, the epitope was found to harbor this sequence. To modify the idiotope with the aim of selecting more specific antibodies, we introduced random mutations into the heavy chain complementarity-determining region 3 and successfully generated an antibody clone, 3B20-G1K, with a point mutation that only reacted with ROS1 in enzyme-linked immunosorbent assays, and in immunoblot and immunoprecipitation analysis. In immunohistochemical analysis using 3B20-G1K, ROS1 was found to be absent in normal lung tissues and was overexpressed in a case of lung adenocarcinoma.
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Affiliation(s)
- Hwa Kyoung Lee
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junyeong Jin
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min Jueng Kang
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Ji Eun Kim
- Department of Pathology, Seoul National University College of Medicine SMG-SNU Boramae Hospital, Seoul, Republic of Korea
| | - Jong Bae Park
- Department of Cancer Biomedical Science, National Cancer Center, Graduate School of Cancer Science and Policy, Goyang, Republic of Korea
| | - Hyori Kim
- Biomedical Research Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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9
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Han J, Lee JH, Park S, Yoon S, Yoon A, Hwang DB, Lee HK, Kim MS, Lee Y, Yang WJ, Youn HD, Kim H, Chung J. A phosphorylation pattern-recognizing antibody specifically reacts to RNA polymerase II bound to exons. Exp Mol Med 2016; 48:e271. [PMID: 27857068 PMCID: PMC5133369 DOI: 10.1038/emm.2016.101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 05/20/2016] [Accepted: 05/25/2016] [Indexed: 11/23/2022] Open
Abstract
The C-terminal domain of RNA polymerase II is an unusual series of repeated residues appended to the C-terminus of the largest subunit and serves as a flexible binding scaffold for numerous nuclear factors. The binding of these factors is determined by the phosphorylation patterns on the repeats in the domain. In this study, we generated a synthetic antibody library by replacing the third heavy chain complementarity-determining region of an anti-HER2 (human epidermal growth factor receptor 2) antibody (trastuzumab) with artificial sequences of 7–18 amino-acid residues. From this library, antibodies were selected that were specific to serine phosphopeptides that represent typical phosphorylation patterns on the functional unit (YSPTSPS)2 of the RNA polymerase II C-terminal domain (CTD). Antibody clones pCTD-1stS2 and pCTD-2ndS2 showed specificity for peptides with phosphoserine at the second residues of the first or second heptamer repeat, respectively. Additional clones specifically reacted to peptides with phosphoserine at the fifth serine of the first repeat (pCTD-1stS5), the seventh residue of the first repeat and fifth residue of the second repeat (pCTD-S7S5) or the seventh residue of either the first or second repeat (pCTD-S7). All of these antibody clones successfully reacted to RNA polymerase II in immunoblot analysis. Interestingly, pCTD-2ndS2 precipitated predominately RNA polymerase II from the exonic regions of genes in genome-wide chromatin immunoprecipitation sequencing analysis, which suggests that the phosphoserine at the second residue of the second repeat of the functional unit (YSPTSPS)2 is a mediator of exon definition.
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Affiliation(s)
- Jungwon Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hyuk Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunyoung Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soomin Yoon
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Aerin Yoon
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Do B Hwang
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hwa K Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min S Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yujean Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Won J Yang
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hong-Duk Youn
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyori Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Biomedical science, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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10
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Singh PK, Agrawal R, Kamboj DV, Singh L. Construction of Recombinant Single Chain Variable Fragment (ScFv) Antibody Against Superantigen for Immunodetection Using Antibody Phage Display Technology. Methods Mol Biol 2016; 1396:207-225. [PMID: 26676049 DOI: 10.1007/978-1-4939-3344-0_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Superantigens are a class of antigens that bind to the major histocompatibility complex class (MHC) II and T-cell receptor (TCR) and cause the nonspecific activation of T cells, resulting in a massive release of pro-inflammatory mediators. They are produced by the gram-positive organisms Staphylococcus aureus and Streptococcus pyogenes, and by a variety of other microbes such as viruses and mycoplasma, and cause toxic shock syndrome (TSS) and even death in some cases. The immunodetection of superantigens is difficult due to the polyclonal activation of T-cells leading to nonspecific antibody production. The production of recombinant monoclonal antibodies against superantigens can solve this problem and are far better than polyclonal antibodies in terms of detection. Here, we describe the construction of recombinant single chain variable fragments (ScFv) antibodies against superantigens with specific reference to SEB (staphylococcal enterotoxin B) using antibody phage display technology.
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Affiliation(s)
- Pawan Kumar Singh
- Department of Ophthalmology, Anatomy and Cell Biology, Wayne State University School of Medicine, 4717 St. Antoine, Detroit, MI, 48201, USA.
| | - Ranu Agrawal
- Biotechnology Division, Defense R&D Establishment, Jhansi Road, Gwalior, 474002, India
- Department of Chemistry, Chaudhary Charan Singh University, Meerut, 250004, India
| | - D V Kamboj
- Biotechnology Division, Defense R&D Establishment, Jhansi Road, Gwalior, 474002, India.
| | - Lokendra Singh
- Biotechnology Division, Defense R&D Establishment, Jhansi Road, Gwalior, 474002, India
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11
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Kim H, Yoon S, Chung J. In vitro and in vivo application of anti-cotinine antibody and cotinine-conjugated compounds. BMB Rep 2014; 47:130-4. [PMID: 24499668 PMCID: PMC4163880 DOI: 10.5483/bmbrep.2014.47.3.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 01/09/2014] [Accepted: 01/20/2014] [Indexed: 12/04/2022] Open
Abstract
The combination of a high-affinity antibody to a hapten, and hapten-conjugated compounds, can provide an alternative to the direct chemical cross-linking of the antibody and compounds. An optimal hapten for in vitro use is one that is absent in biological systems. For in vivo applications, additional characteristics such as pharmacological safety and physiological inertness would be beneficial. Additionally, methods for cross-linking the hapten to various chemical compounds should be available. Cotinine, a major metabolite of nicotine, is considered advantageous in these aspects. A high-affinity anti-cotinine recombinant antibody has recently become available, and can be converted into various formats, including a bispecific antibody. The bispecific anti-cotinine antibody was successfully applied to immunoblot, enzyme immunoassay, immunoaffinity purification, and pre-targeted in vivo radioimmunoimaging. The anti-cotinine IgG molecule could be complexed with aptamers to form a novel affinity unit, and extended the in vivo half-life of aptamers, opening up the possibility of applying the same strategy to therapeutic peptides and chemical compounds. [BMB Reports 2014; 47(3): 130-134]
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Affiliation(s)
- Hyori Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799; Cancer Research Institute, Seoul National University, Seoul 110-799, Korea
| | - Soomin Yoon
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 110-799; Cancer Research Institute, Seoul National University, Seoul 110-799, Korea
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An antibody reactive to the Gly63-Lys68 epitope of NT-proBNP exhibits O-glycosylation-independent binding. Exp Mol Med 2014; 46:e114. [PMID: 25236766 PMCID: PMC4183943 DOI: 10.1038/emm.2014.57] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 02/03/2023] Open
Abstract
The N-terminal fragment of prohormone brain natriuretic peptide (NT-proBNP) is a commonly used biomarker for the diagnosis of congestive heart failure, although its biological function is not well known. NT-proBNP exhibits heavy O-linked glycosylation, and it is quite difficult to develop an antibody that exhibits glycosylation-independent binding. We developed an antibody that binds to the recombinant NT-proBNP protein and its deglycosylated form with similar affinities in an enzyme immunoassay. The epitope was defined as Gly63–Lys68 based on mimetic peptide screening, site-directed mutagenesis and a competition assay with a peptide mimotope. The nearest O-glycosylation residues are Thr58 and Thr71; therefore, four amino acid residues intervene between the epitope and those residues in both directions. In conclusion, we report that an antibody reactive to Gly63–Lys68 of NT-proBNP exhibits O-glycosylation-independent binding.
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Cheng CM, Tzou SC, Zhuang YH, Huang CC, Kao CH, Liao KW, Cheng TC, Chuang CH, Hsieh YC, Tai MH, Cheng TL. Functional production of a soluble and secreted single-chain antibody by a bacterial secretion system. PLoS One 2014; 9:e97367. [PMID: 24824752 PMCID: PMC4019604 DOI: 10.1371/journal.pone.0097367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/17/2014] [Indexed: 12/17/2022] Open
Abstract
Single-chain variable fragments (scFvs) serve as an alternative to full-length monoclonal antibodies used in research and therapeutic and diagnostic applications. However, when recombinant scFvs are overexpressed in bacteria, they often form inclusion bodies and exhibit loss of function. To overcome this problem, we developed an scFv secretion system in which scFv was fused with osmotically inducible protein Y (osmY), a bacterial secretory carrier protein, for efficient protein secretion. Anti-EGFR scFv (αEGFR) was fused with osmY (N- and C-termini) and periplasmic leader sequence (pelB) to generate αEGFR-osmY, osmY-αEGFR, and pelB-αEGFR (control), respectively. In comparison with the control, both the osmY-fused αEGFR scFvs were soluble and secreted into the LB medium. Furthermore, the yield of soluble αEGFR-osmY was 20-fold higher, and the amount of secreted protein was 250-fold higher than that of osmY-αEGFR. In addition, the antigen-binding activity of both the osmY-fused αEGFRs was 2-fold higher than that of the refolded pelB-αEGFR from inclusion bodies. Similar results were observed with αTAG72-osmY and αHer2-osmY. These results suggest that the N-terminus of osmY fused with scFv produces a high yield of soluble, functional, and secreted scFv, and the osmY-based bacterial secretion system may be used for the large-scale industrial production of low-cost αEGFR protein.
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Affiliation(s)
- Chiu-Min Cheng
- Department of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Shey-Cherng Tzou
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan
| | - Ya-Han Zhuang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Chiao Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chien-Han Kao
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan
| | - Ta-Chun Cheng
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Hung Chuang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yuan-Chin Hsieh
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Hong Tai
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Tian-Lu Cheng
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- * E-mail:
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