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Hatab MH, Chen W, Abouelezz K, Elaroussi M, Badran A, Zoheir K, El-Komy E, Li S, Elokil A. Effects of exposing Japanese quail eggs to a low dose of gamma radiation and in ovo feeding by two sources of trace elements on embryonic development activities. Poult Sci 2024; 103:103364. [PMID: 38198914 PMCID: PMC10825557 DOI: 10.1016/j.psj.2023.103364] [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] [Received: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
The present study investigated the influence of exposing quail eggs to low-dose gamma radiation (GR) and in ovo feeding with 2 sources of a mixture of trace elements (Zn, Fe, and Cu), including sulfate (TES) and loaded with montmorillonite (TEM), on embryonic development activities and prehatch quality. A total of 960 eggs on the seventh day of incubation were randomly divided into 6 groups (160 eggs/group) with 4 replicate of 40 eggs in each. A 3 × 2 factorial arrangement experiment was performed and included 3 sources in ovo feeding with a mixture of trace elements (Zn, Fe, and Cu), including 0 mg/egg, 50 mg TES/egg, and 50 mg TEM/egg with egg irradiation using 0 and 0.2 Gy from GR. Eggs injected with 50 mg TEM/egg and exposed to 0.2 Gy from GR (TEM/GR) was significantly (P ≤ 0.05 and 0.01) higher in hatchability, hatch body weight, and relative organ weight (liver, gizzard, proventriculus, heart, and intestine). The obtained results indicated significant (P ≤ 0.05) decreased in the serum concentration of malondialdehyde (MDA) in TEM/GR group. There was significant (P ≤ 0.05) increased of catalase (CAT) activity and the concentrations of growth hormone (GH) and insulin-like growth factor-1 (IGF-1) in TEM/GR group; however; total antioxidant capacity (T-AOC) was significant (P ≤ 0.05) increased in CT/GR group. Serum concentrations of immunoglobulin M (IgM) (P ≤ 0.05) and tumor necrosis factor-alpha (TNF-α) were increased in the TEM/CR group; the concentration of transforming growth factor beta (TGF-β) significant (P ≤ 0.05) increased in the TEM/GR group; and interleukins (IL6 and IL10) showed no significant differences among the groups. Our results showed increase in thyroxine and myostatin concentrations with TES/CR and CT/GR of our study groups, respectively. The relative mRNA expression levels of the GH, IGF-1, and Fas cell surface death receptor (FAS) genes were significantly (P ≤ 0.05 and 0.01) upregulated in the liver tissue of the TEM/GR group compared with the other groups. In conclusion, TEM/GR was the best treatment for improving prehatch quality, increasing serum antioxidant enzyme activities, and promoting the expression of growth and immune genes in fertilized quail eggs.
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Affiliation(s)
- Mahmoud H Hatab
- Biological Application Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Wei Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agriculture Science and Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, Guangdong, China.
| | - Khaled Abouelezz
- Department of Poultry Production, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - Mahmoud Elaroussi
- Biological Application Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Aml Badran
- Poultry Breeding Department, Animal Production Research Institute, Agriculture Research center, Ministry of Agriculture, Dokki, Giza, Egypt
| | - Khairy Zoheir
- Cell biology department, Biotechnology Research Institute, National Research Centre, Dokki, Giza 12622, Egypt
| | - Esteftah El-Komy
- Animal Production Department, Agricultural and Biological Research Institute, National Research Centre, Dokki, Giza 12622, Egypt
| | - Shijun Li
- College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Abdelmotaleb Elokil
- State Key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agriculture Science and Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, Guangdong, China; College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Department of Animal Production, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
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2
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Yan Y, Bai Y, Zheng X, Cai Y. Production of hydroxytyrosol through whole-cell bioconversion from L-DOPA using engineered Escherichia coli. Enzyme Microb Technol 2023; 169:110280. [PMID: 37413913 DOI: 10.1016/j.enzmictec.2023.110280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/01/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023]
Abstract
Hydroxytyrosol (HT), a polyphenolic molecule of high value, is used in the nutraceutical, cosmetic, food, and livestock nutrition industries. As a natural product, HT is chemically manufactured or extracted from olives; nevertheless, the increasing demand mandates the exploration and development of alternative sources, such as heterologous production by recombinant bacteria. In order to achieve this purpose, we have molecularly modified Escherichia coli to carry two plasmids. For conversion of L-DOPA (Levodopa) into HT efficiently, it is necessary to enhance the expression of DODC (DOPA decarboxylase), ADH (alcohol dehydrogenases), MAO (Monoamine oxidase) and GDH (glucose dehydrogenases). The step that significantly affects the rate of ht biosynthesis is likely to be associated with the reaction facilitated by DODC enzymatic activity, as suggested by the result of in vitro catalytic experiment and HPLC. Then Pseudomonas putida, Sus scrofa, Homo sapiens and Levilactobacillus brevis DODC were taken into comparsion. The DODC from H. sapiens is superior to that of P. putida, S. scrofa or L. brevis for HT production. Seven promoters were introduced to increase the expression levels of catalase (CAT) to remove the byproduct H2O2 and optimized coexpression strains were obtained after screening. After the 10-hour operation, the optimized whole-cell biocatalyst produced HT at a maximum titer of 4.84 g/L with over 77.5% molar substrate conversion rate.
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Affiliation(s)
- Yi Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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3
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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4
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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5
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Kojima R, Uchiya K, Manshio H, Masuda K. Cell-free synthesis of functionally active HSPB5. Cell Stress Chaperones 2020; 25:287-301. [PMID: 31960264 PMCID: PMC7058722 DOI: 10.1007/s12192-020-01073-5] [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: 09/04/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 10/25/2022] Open
Abstract
Human αB-crystallin (HSPB5) is frequently modified post-translationally by UV radiation, oxidation, and age-associated processes, which complicates functional analyses of the protein using natural sources. Thus, determining the biological function of HSPB5 at the molecular structure level requires unmodified protein. Here, we employed an Escherichia coli cell-free protein synthesis system to prepare unmodified, functionally active human HSPB5. An S30 extract prepared from E. coli strain BL21 (DE3) was used for HSPB5 synthesis. The efficacy of protein synthesis was assessed by monitoring influencing factors, such as the concentrations of Mg2+ and other reaction mixture constituents, and by evaluating batch and/or dialysis synthesis systems. Chaperone-like activity of synthesized HSPB5 was assayed using alcohol dehydrogenase (ADH) under thermal stress. The amount of HSPB5 synthesized using the cell-free system depended significantly on the concentration of Mg2+ in the reaction mixture. Use of condensed S30 extract and increased levels of amino acids promoted HSPB5 production. Compared with the batch system, HSPB5 synthesis was markedly increased using the dialysis system. The construction vector played a critical role in regulating the efficacy of protein synthesis. HSPB5 synthesized using the cell-free system had a native molecular mass, as determined by mass spectrometry analysis. The co-presence of synthesized HSPB5 suppressed heat-associated denaturation of ADH. Human HSPB5 synthesized using the cell-free system thus retains functional activity as a molecular chaperone.
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Affiliation(s)
- Ryoji Kojima
- Laboratory of Analytical Pharmacology, Meijo University, Nagoya, 468-8503, Japan.
| | - Keiichi Uchiya
- Laboratory of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, 468-8503, Japan
| | - Hiroyuki Manshio
- Laboratory of Analytical Pharmacology, Meijo University, Nagoya, 468-8503, Japan
| | - Kastuyoshi Masuda
- Suntory Institute for Bioorganic Research, 1-1 Wakayamadai, Shimamoto, Osaka, 618-8503, Japan
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David G, Fogeron ML, Schledorn M, Montserret R, Haselmann U, Penzel S, Badillo A, Lecoq L, André P, Nassal M, Bartenschlager R, Meier BH, Böckmann A. Structural Studies of Self-Assembled Subviral Particles: Combining Cell-Free Expression with 110 kHz MAS NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:4787-4791. [PMID: 29457857 DOI: 10.1002/anie.201712091] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/25/2018] [Indexed: 01/08/2023]
Abstract
Viral membrane proteins are prime targets in combatting infection. Still, the determination of their structure remains a challenge, both with respect to sample preparation and the need for structural methods allowing for analysis in a native-like lipid environment. Cell-free protein synthesis and solid-state NMR spectroscopy are promising approaches in this context, the former with respect to its great potential in the native expression of complex proteins, and the latter for the analysis of membrane proteins in lipids. Herein, we show that milligram amounts of the small envelope protein of the duck hepatitis B virus (DHBV) can be produced by cell-free expression, and that the protein self-assembles into subviral particles. Proton-detected 2D NMR spectra recorded at a magic-angle-spinning frequency of 110 kHz on <500 μg protein show a number of isolated peaks with line widths comparable to those of model membrane proteins, paving the way for structural studies of this protein that is homologous to a potential drug target in HBV infection.
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Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | | | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis Germany, Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Susanne Penzel
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.,RD-Biotech, Recombinant Protein Unit, 3 rue Henri Baigue, 25000, Besançon, France
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Patrice André
- Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale Unité 1111, Centre National de la Recherche Scientifique Unités Mixte de Recherche, 5308, Lyon, France.,Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.,Université de Lyon, Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Michael Nassal
- University Hospital Freiburg, Internal Medicine II/Molecular Biology, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis Germany, Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
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7
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David G, Fogeron M, Schledorn M, Montserret R, Haselmann U, Penzel S, Badillo A, Lecoq L, André P, Nassal M, Bartenschlager R, Meier BH, Böckmann A. Strukturelle Untersuchung subviraler Partikel durch die Kombination von zellfreier Proteinherstellung mit 110 kHz MAS‐NMR‐Spektroskopie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Marie‐Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | | | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Uta Haselmann
- Department für Infektiologie Molekulare Virologie Universitätsklinikum Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Deutschland
- Abteilung Virus-assoziierte Karzinogenese Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 242 69120 Heidelberg Deutschland
| | - Susanne Penzel
- Lab. für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
- RD-Biotech Recombinant Protein Unit 3 rue Henri Baigue 25000 Besançon Frankreich
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Patrice André
- Centre International de Recherche en Infectiologie Institut National de la Santé et de la Recherche Médicale Unité 1111 Centre National de la Recherche Scientifique Unités Mixte de Recherche 5308 Lyon Frankreich
- Ecole Normale Supérieure de Lyon, Lyon, France Université Claude Bernard Lyon 1 Villeurbanne Frankreich
- Université de Lyon, Lyon, France Laboratoire de Virologie Hôpital de la Croix-Rousse Hospices Civils de Lyon Lyon Frankreich
| | - Michael Nassal
- Universitätsklinikum Freiburg Klinik für Innere Medizin II/ Molekulare Biologie Hugstetter Straße 55 79106 Freiburg Deutschland
| | - Ralf Bartenschlager
- Department für Infektiologie Molekulare Virologie Universitätsklinikum Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Deutschland
- Abteilung Virus-assoziierte Karzinogenese Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 242 69120 Heidelberg Deutschland
| | - Beat H. Meier
- Lab. für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
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8
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Matsuda T, Ito T, Takemoto C, Katsura K, Ikeda M, Wakiyama M, Kukimoto-Niino M, Yokoyama S, Kurosawa Y, Shirouzu M. Cell-free synthesis of functional antibody fragments to provide a structural basis for antibody-antigen interaction. PLoS One 2018; 13:e0193158. [PMID: 29462206 PMCID: PMC5819829 DOI: 10.1371/journal.pone.0193158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/05/2018] [Indexed: 11/19/2022] Open
Abstract
Growing numbers of therapeutic antibodies offer excellent treatment strategies for many diseases. Elucidation of the interaction between a potential therapeutic antibody and its target protein by structural analysis reveals the mechanism of action and offers useful information for developing rational antibody designs for improved affinity. Here, we developed a rapid, high-yield cell-free system using dialysis mode to synthesize antibody fragments for the structural analysis of antibody–antigen complexes. Optimal synthesis conditions of fragments (Fv and Fab) of the anti-EGFR antibody 059–152 were rapidly determined in a day by using a 30-μl-scale unit. The concentration of supplemented disulfide isomerase, DsbC, was critical to obtaining soluble antibody fragments. The optimal conditions were directly applicable to a 9-ml-scale reaction, with linear scalable yields of more than 1 mg/ml. Analyses of purified 059-152-Fv and Fab showed that the cell-free synthesized antibody fragments were disulfide-bridged, with antigen binding activity comparable to that of clinical antibodies. Examination of the crystal structure of cell-free synthesized 059-152-Fv in complex with the extracellular domain of human EGFR revealed that the epitope of 059-152-Fv broadly covers the EGF binding surface on domain III, including residues that formed critical hydrogen bonds with EGF (Asp355EGFR, Gln384EGFR, H409EGFR, and Lys465EGFR), so that the antibody inhibited EGFR activation. We further demonstrated the application of the cell-free system to site-specific integration of non-natural amino acids for antibody engineering, which would expand the availability of therapeutic antibodies based on structural information and rational design. This cell-free system could be an ideal antibody-fragment production platform for functional and structural analysis of potential therapeutic antibodies and for engineered antibody development.
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Affiliation(s)
- Takayoshi Matsuda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Takuhiro Ito
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Kazushige Katsura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Mariko Ikeda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Motoaki Wakiyama
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Mutsuko Kukimoto-Niino
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
| | - Yoshikazu Kurosawa
- Innovation Center for Advanced Medicine, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumiku, Yokohama, Japan
- * E-mail:
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9
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Katsura K, Matsuda T, Tomabechi Y, Yonemochi M, Hanada K, Ohsawa N, Sakamoto K, Takemoto C, Shirouzu M. A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis. J Biochem 2017; 162:357-369. [PMID: 28992119 PMCID: PMC7109869 DOI: 10.1093/jb/mvx039] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 05/21/2017] [Indexed: 01/30/2023] Open
Abstract
Cell-free protein synthesis is a useful method for preparing proteins for functional or structural analyses. However, batch-to-batch variability with regard to protein synthesis activity remains a problem for large-scale production of cell extract in the laboratory. To address this issue, we have developed a novel procedure for large-scale preparation of bacterial cell extract with high protein synthesis activity. The developed procedure comprises cell cultivation using a fermentor, harvesting and washing of cells by tangential flow filtration, cell disruption with high-pressure homogenizer and continuous diafiltration. By optimizing and combining these methods, ∼100 ml of the cell extract was prepared from 150 g of Escherichia coli cells. The protein synthesis activities, defined as the yield of protein per unit of absorbance at 260 nm of the cell extract, were shown to be reproducible, and the average activity of several batches was twice that obtained using a previously reported method. In addition, combinatorial use of the high-pressure homogenizer and diafiltration increased the scalability, indicating that the cell concentration at disruption varies from 0.04 to 1 g/ml. Furthermore, addition of Gam protein and examinations of the N-terminal sequence rendered the extract prepared here useful for rapid screening with linear DNA templates.
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Affiliation(s)
- Kazushige Katsura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayoshi Matsuda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuri Tomabechi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mayumi Yonemochi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazuharu Hanada
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation. Biochem J 2017; 474:3207-3226. [PMID: 28768733 PMCID: PMC5628404 DOI: 10.1042/bcj20161104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 12/02/2022]
Abstract
Really interesting new gene (RING)-finger protein 52 (RNF52), an E3 ubiquitin ligase, is found in eukaryotes from yeast to humans. Human RNF52 is known as breast cancer type 1 susceptibility protein (BRCA1)-associated protein 2 (BRAP or BRAP2). The central catalytic domain of BRAP comprises four subdomains: nucleotide-binding α/β plait (NBP), really interesting new gene (RING) zinc finger, ubiquitin-specific protease (UBP)-like zinc finger (ZfUBP), and coiled-coil (CC). This domain architecture is conserved in RNF52 orthologs; however, the domain's function in the ubiquitin system has not been delineated. In the present study, we discovered that the RNF52 domain, comprising NBP–RING–ZfUBP–CC, binds to ubiquitin chains (oligo-ubiquitin) but not to the ubiquitin monomers, and can utilize various ubiquitin chains for ubiquitylation and auto-ubiquitylation. The RNF52 domain preferentially bound to M1- and K63-linked di-ubiquitin chains, weakly to K27-linked chains, but not to K6-, K11-, or K48-linked chains. The binding preferences of the RNF52 domain for ubiquitin-linkage types corresponded to ubiquitin usage in the ubiquitylation reaction, except for K11-, K29-, and K33-linked chains. Additionally, the RNF52 domain directly ligated the intact M1-linked, tri-, and tetra-ubiquitin chains and recognized the structural alterations caused by the phosphomimetic mutation of these ubiquitin chains. Full-length BRAP had nearly the same specificity for the ubiquitin-chain types as the RNF52 domain alone. Mass spectrometry analysis of oligomeric ubiquitylation products, mediated by the RNF52 domain, revealed that the ubiquitin-linkage types and auto-ubiquitylation sites depend on the length of ubiquitin chains. Here, we propose a model for the oligomeric ubiquitylation process, controlled by the RNF52 domain, which is not a sequential assembly process involving monomers.
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