1
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Naveed M, Wen S, Chan MWH, Wang F, Aslam S, Yin X, Xu B, Ullah A. Expression of BSN314 lysozyme genes in Escherichia coli BL21: a study to demonstrate microbicidal and disintegarting potential of the cloned lysozyme. Braz J Microbiol 2024; 55:215-233. [PMID: 38146050 PMCID: PMC10920529 DOI: 10.1007/s42770-023-01219-4] [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: 09/09/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023] Open
Abstract
This study is an extension of our previous studies in which the lysozyme was isolated and purified from Bacillus subtilis BSN314 (Naveed et al., 2022; Naveed et al., 2023). In this study, the lysozyme genes were cloned into the E. coli BL21. For the expression of lysozyme in E. coli BL21, two target genes, Lyz-1 and Lyz-2, were ligated into the modified vector pET28a to generate pET28a-Lyz1 and pET28a-Lyz2, respectively. To increase the production rate of the enzyme, 0.5-mM concentration of IPTG was added to the culture media and incubated at 37 °C and 220 rpm for 24 h. Lyz1 was identified as N-acetylmuramoyl-L-alanine amidase and Lyz2 as D-alanyl-D-alanine carboxypeptidase. They were purified by multi-step methodology (ammonium sulfate, precipitation, dialysis, and ultrafiltration), and antimicrobial activity was determined. For Lyz1, the lowest MIC/MBC (0.25 μg/mL; with highest ZOI = 22 mm) were recorded against Micrococcus luteus, whereas the highest MIC/MBC with lowest ZOI were measured against Salmonella typhimurium (2.50 μg /mL; with ZOI = 10 mm). As compared with Aspergillus oryzae (MIC/MFC; 3.00 μg/mL), a higher concentration of lysozyme was required to control the growth of Saccharomyces cerevisiae (MIC/MFC; 50 μg/mL). Atomic force microscopy (AFM) was used to analyze the disintegrating effect of Lyz1 on the cells of selected Gram-positive bacteria, Gram-negative bacteria, and yeast. The AFM results showed that, as compared to Gram-negative bacteria, a lower concentration of lysozyme (Lyz1) was required to disintegrate the cell of Gram-positive bacteria.
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Affiliation(s)
- Muhammad Naveed
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Sai Wen
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Malik Wajid Hussain Chan
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China.
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China.
| | - Fenghuan Wang
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China.
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China.
| | - Sadar Aslam
- Department of Zoology, University of Baltistan, Skardu, Pakistan
| | - Xian Yin
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Baocai Xu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, Beijing, 100048, China
- Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, Beijing, 100048, China
| | - Asad Ullah
- Food and Marine Resources Research Center, Pakistan Council of Scientific and Industrial Research Laboratories Complex, Karachi, 75280, Pakistan
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2
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Peleg Y, Vincentelli R, Collins BM, Chen KE, Livingstone EK, Weeratunga S, Leneva N, Guo Q, Remans K, Perez K, Bjerga GEK, Larsen Ø, Vaněk O, Skořepa O, Jacquemin S, Poterszman A, Kjær S, Christodoulou E, Albeck S, Dym O, Ainbinder E, Unger T, Schuetz A, Matthes S, Bader M, de Marco A, Storici P, Semrau MS, Stolt-Bergner P, Aigner C, Suppmann S, Goldenzweig A, Fleishman SJ. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J Mol Biol 2021; 433:166964. [PMID: 33781758 DOI: 10.1016/j.jmb.2021.166964] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
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Affiliation(s)
- Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kai-En Chen
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Emma K Livingstone
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Saroja Weeratunga
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Kathryn Perez
- European Molecular Biology Laboratory (EMBL), Protein Expression and Purification Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gro E K Bjerga
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Øivind Larsen
- NORCE Norwegian Research Centre, Postboks 22 Nygårdstangen, 5038 Bergen, Norway
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Ondřej Skořepa
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840 Prague, Czech Republic
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, France
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Evangelos Christodoulou
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shira Albeck
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anja Schuetz
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Susann Matthes
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany
| | - Michael Bader
- Max-Delbrück Center for Molecular Medicine (MDC), Robert-Rössle-Straße 10, 13125 Berlin-Buch, Germany; University of Lübeck, Institute for Biology, Ratzeburger Allee 160, 23562 Lübeck, Germany; Charité University Medicine, Charitéplatz 1, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Paola Storici
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Marta S Semrau
- Elettra Sincrotrone Trieste - SS 14 - km 163, 5 in Area Science Park, 34149 Basovizza, Trieste, Italy
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Christian Aigner
- Vienna Biocenter Core Facilities GmbH, Dr. Bohr-gasse 3, 1030 Vienna, Austria
| | - Sabine Suppmann
- Max-Planck Institute of Biochemistry, Biochemistry Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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3
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Rovito D, Belorusova AY, Chalhoub S, Rerra AI, Guiot E, Molin A, Linglart A, Rochel N, Laverny G, Metzger D. Cytosolic sequestration of the vitamin D receptor as a therapeutic option for vitamin D-induced hypercalcemia. Nat Commun 2020; 11:6249. [PMID: 33288743 PMCID: PMC7721737 DOI: 10.1038/s41467-020-20069-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022] Open
Abstract
The bioactive vitamin D3, 1α,25(OH)2D3, plays a central role in calcium homeostasis by controlling the activity of the vitamin D receptor (VDR) in various tissues. Hypercalcemia secondary to high circulating levels of vitamin D3 leads to hypercalciuria, nephrocalcinosis and renal dysfunctions. Current therapeutic strategies aim at limiting calcium intake, absorption and resorption, or 1α,25(OH)2D3 synthesis, but are poorly efficient. In this study, we identify WBP4 as a new VDR interactant, and demonstrate that it controls VDR subcellular localization. Moreover, we show that the vitamin D analogue ZK168281 enhances the interaction between VDR and WBP4 in the cytosol, and normalizes the expression of VDR target genes and serum calcium levels in 1α,25(OH)2D3-intoxicated mice. As ZK168281 also blunts 1α,25(OH)2D3-induced VDR signaling in fibroblasts of a patient with impaired vitamin D degradation, this VDR antagonist represents a promising therapeutic option for 1α,25(OH)2D3-induced hypercalcemia. Current therapeutic strategies for vitamin D-induced hypercalcemia are poorly efficient. Here the authors identify a new interaction between the vitamin D receptor (VDR) and WBP4 controlling the subcellular localization of VDR and show that ZK168281, a VDR antagonist, enhances the interaction between VDR and WBP4 blunting VDR signalling and normalizing calcium levels in vitamin D-intoxicated mice.
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Affiliation(s)
- Daniela Rovito
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Anna Y Belorusova
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sandra Chalhoub
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Anna-Isavella Rerra
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Elvire Guiot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Arnaud Molin
- Université de Normandie, UNICAEN, CHU de Caen Normandie, Service de Génétique, EA 7450 BIOTARGEN, Caen, France.,Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism (OSCAR), Paris, France
| | - Agnès Linglart
- Reference Center for Rare Diseases of Calcium and Phosphorus Metabolism (OSCAR), Paris, France.,Université de Paris Saclay, AP-HP, Hôpital Bicêtre, DMU SEA, INSERM, U1185, Le Kremlin Bicêtre, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gilles Laverny
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
| | - Daniel Metzger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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4
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Woo SG, Kim SK, Oh BR, Lee SG, Lee DH. Genetically Encoded Biosensor-Based Screening for Directed Bacteriophage T4 Lysozyme Evolution. Int J Mol Sci 2020; 21:ijms21228668. [PMID: 33212940 PMCID: PMC7698408 DOI: 10.3390/ijms21228668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Lysozyme is widely used as a model protein in studies of structure–function relationships. Recently, lysozyme has gained attention for use in accelerating the degradation of secondary sludge, which mainly consists of bacteria. However, a high-throughput screening system for lysozyme engineering has not been reported. Here, we present a lysozyme screening system using a genetically encoded biosensor. We first cloned bacteriophage T4 lysozyme (T4L) into a plasmid under control of the araBAD promoter. The plasmid was expressed in Escherichia coli with no toxic effects on growth. Next, we observed that increased soluble T4L expression decreased the fluorescence produced by the genetic enzyme screening system. To investigate T4L evolution based on this finding, we generated a T4L random mutation library, which was screened using the genetic enzyme screening system. Finally, we identified two T4L variants showing 1.4-fold enhanced lytic activity compared to native T4L. To our knowledge, this is the first report describing the use of a genetically encoded biosensor to investigate bacteriophage T4L evolution. Our approach can be used to investigate the evolution of other lysozymes, which will expand the applications of lysozyme.
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Affiliation(s)
- Seung-Gyun Woo
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
| | - Baek-Rock Oh
- Microbial Biotechnology Research Center, Jeonbuk Branch Institute, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Korea;
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: (S.-G.L.); (D.-H.L.); Tel.: +82-42-860-4373 (S.-G.L.); +82-42-879-8225 (D.-H.L.)
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (S.-G.W.); (S.K.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: (S.-G.L.); (D.-H.L.); Tel.: +82-42-860-4373 (S.-G.L.); +82-42-879-8225 (D.-H.L.)
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5
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The Benefits of Cotranslational Assembly: A Structural Perspective. Trends Cell Biol 2019; 29:791-803. [DOI: 10.1016/j.tcb.2019.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 12/20/2022]
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6
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High-throughput stability screening for detergent-solubilized membrane proteins. Sci Rep 2019; 9:10379. [PMID: 31316088 PMCID: PMC6637136 DOI: 10.1038/s41598-019-46686-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
Protein stability in detergent or membrane-like environments is the bottleneck for structural studies on integral membrane proteins (IMP). Irrespective of the method to study the structure of an IMP, detergent solubilization from the membrane is usually the first step in the workflow. Here, we establish a simple, high-throughput screening method to identify optimal detergent conditions for membrane protein stabilization. We apply differential scanning fluorimetry in combination with scattering upon thermal denaturation to study the unfolding of integral membrane proteins. Nine different prokaryotic and eukaryotic membrane proteins were used as test cases to benchmark our detergent screening method. Our results show that it is possible to measure the stability and solubility of IMPs by diluting them from their initial solubilization condition into different detergents. We were able to identify groups of detergents with characteristic stabilization and destabilization effects for selected targets. We further show that fos-choline and PEG family detergents may lead to membrane protein destabilization and unfolding. Finally, we determined thenmodynamic parameters that are important indicators of IMP stability. The described protocol allows the identification of conditions that are suitable for downstream handling of membrane proteins during purification.
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7
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Efficient and robust preparation of tyrosine phosphorylated intrinsically disordered proteins. Biotechniques 2019; 67:16-22. [PMID: 31092000 DOI: 10.2144/btn-2019-0033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are subject to post-translational modifications. This allows the same polypeptide to be involved in different interaction networks with different consequences, ranging from regulatory signalling networks to the formation of membrane-less organelles. We report a robust method for co-expression of modification enzyme and SUMO-tagged IDPs with a subsequent purification procedure that allows for the production of modified IDP. The robustness of our protocol is demonstrated using a challenging system: RNA polymerase II C-terminal domain (CTD); that is, a low-complexity repetitive region with multiple phosphorylation sites. In vitro phosphorylation approaches fail to yield multiple-site phosphorylated CTD, whereas our in vivo protocol allows the rapid production of near homogeneous phosphorylated CTD at a low cost. These samples can be used in functional and structural studies.
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8
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Qin Y, Tan C, Lin J, Qin Q, He J, Wu Q, Cai Y, Chen Z, Dai J. EcoExpress-Highly Efficient Construction and Expression of Multicomponent Protein Complexes in Escherichia coli. ACS Synth Biol 2016; 5:1239-1246. [PMID: 27345099 DOI: 10.1021/acssynbio.5b00291] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacterium Escherichia coli remains the leading host for protein expression in large quantity for the purpose of crystallization or other biochemical studies. However, expression of multicomponent protein complexes remains a challenge, and is often laborious and time-consuming. Here we developed a method named EcoExpress, which allows efficient construction of plasmids to express individual protein with user-defined epitope-tag, followed by one-pot assembly of a single vector to express the entire protein complex for copurification. A versatile set of vectors was designed to provide various choices to control the expression of a protein with different promoters, and to accept different number of components for coexpression. Using EcoExpress, we demonstrated that each subunit within a protein complex could be expressed individually or simultaneously, and the entire complex could be copurified. In addition, to overcome the decreased assembly efficiency with the increasing number of components, a novel oligonucleotides blocking method was designed and tested. EcoExpress provides the scientific community with a toolbox to rapidly investigate the function of protein complexes.
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Affiliation(s)
- Yiran Qin
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chang Tan
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiwei Lin
- Wuxi Qinglan Biotechnology Inc., Yixing, Jiangsu 214200, China
| | - Qin Qin
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianghaiyang He
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qingyu Wu
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yizhi Cai
- School
of Biological Sciences, The King’s Buildings, University of Edinburgh, EH9 3BF Edinburgh, United Kingdom
| | - Zhucheng Chen
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Junbiao Dai
- MOE
Key Laboratory of Bioinformatics, MOE Key Laboratory of Industrial
Biocatalysis and Center for Synthetic and Systems Biology, School
of Life Sciences, Tsinghua University, Beijing 100084, China
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9
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Construction of a compatible Gateway-based co-expression vector set for expressing multiprotein complexes in E. coli. Anal Biochem 2016; 512:110-113. [DOI: 10.1016/j.ab.2016.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/17/2016] [Accepted: 08/20/2016] [Indexed: 02/06/2023]
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10
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Celie PHN, Parret AHA, Perrakis A. Recombinant cloning strategies for protein expression. Curr Opin Struct Biol 2016; 38:145-54. [DOI: 10.1016/j.sbi.2016.06.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/10/2016] [Indexed: 11/30/2022]
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11
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Takai K, Hisamatsu K. SfiNX: a method for assembly of protein coding sequences with high success rates. Biotechnol Lett 2016; 38:773-8. [DOI: 10.1007/s10529-016-2042-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 01/06/2016] [Indexed: 01/18/2023]
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12
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Baser B, van den Heuvel J. Assembling Multi-subunit Complexes Using Mammalian Expression. ADVANCED TECHNOLOGIES FOR PROTEIN COMPLEX PRODUCTION AND CHARACTERIZATION 2016; 896:225-38. [DOI: 10.1007/978-3-319-27216-0_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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13
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ACEMBL Tool-Kits for High-Throughput Multigene Delivery and Expression in Prokaryotic and Eukaryotic Hosts. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 896:27-42. [DOI: 10.1007/978-3-319-27216-0_3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Kumar S, Jain KK, Bhardwaj KN, Chakraborty S, Kuhad RC. Multiple Genes in a Single Host: Cost-Effective Production of Bacterial Laccase (cotA), Pectate Lyase (pel), and Endoxylanase (xyl) by Simultaneous Expression and Cloning in Single Vector in E. coli. PLoS One 2015; 10:e0144379. [PMID: 26642207 PMCID: PMC4671577 DOI: 10.1371/journal.pone.0144379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/17/2015] [Indexed: 11/18/2022] Open
Abstract
This study attempted to reduce the enzyme production cost for exploiting lignocellulosic materials by expression of multiple genes in a single host. Genes for bacterial laccase (CotA), pectate lyase (Pel) and endoxylanase (Xyl), which hold significance in lignocellulose degradation, were cloned in pETDuet-1 vector containing two independent cloning sites (MCS). CotA and xyl genes were cloned in MCS1 and MCS 2, respectively. Pel gene was cloned by inserting complete cassette (T7 promoter, ribosome binding site, pel gene, His tag and complete gene ORF) preceded by cotA open reading frame in the MCS1. IPTG induction of CPXpDuet-1 construct in E. coli BL21(DE3) resulted in expression of all three heterologous proteins of ~65 kDa (CotA), ~45 kDa (Pel) and ~25 kDa (Xyl), confirmed by SDS-PAGE and western blotting. Significant portions of the enzymes were also found in culture supernatant (~16, ~720 and ~370 IU/ml activities of CotA, Pel and Xyl, respectively). Culture media optimization resulted in 2, 3 and 7 fold increased secretion of recombinant CotA, Pel and Xyl, respectively. Bioreactor level optimization of the recombinant cocktail expression resulted in production of 19 g/L dry cell biomass at OD600nm 74 from 1 L induced culture after 15 h of cultivation, from which 9, 627 and 1090 IU/ml secretory enzyme activities of CotA, Xyl and Pel were obtained, respectively. The cocktail was also found to increase the saccharification of orange peel in comparison to the xylanase alone. Thus, simultaneous expression as well as extra cellular secretion of these enzymes as cocktail can reduce the enzyme production cost which increases their applicability specially for exploiting lignocellulosic materials for their conversion to value added products like alcohol and animal feed.
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Affiliation(s)
- Sandeep Kumar
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South campus, Benito Juarez Road, New Delhi, 110021, India
| | - Kavish Kumar Jain
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South campus, Benito Juarez Road, New Delhi, 110021, India
| | - Kailash N. Bhardwaj
- Uttarakhand State Council of Science and Technology [UCOST], Vigyan Dham, Post Office- Jhajra, Dehradun, Uttarakhand, 248007, India
| | - Subhojit Chakraborty
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South campus, Benito Juarez Road, New Delhi, 110021, India
| | - Ramesh Chander Kuhad
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South campus, Benito Juarez Road, New Delhi, 110021, India
- Central University of Haryana, Jant-Pali Village, Mahendergarh District, Pali, Haryana, 123029, India
- * E-mail:
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15
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Raasakka A, Myllykoski M, Laulumaa S, Lehtimäki M, Härtlein M, Moulin M, Kursula I, Kursula P. Determinants of ligand binding and catalytic activity in the myelin enzyme 2',3'-cyclic nucleotide 3'-phosphodiesterase. Sci Rep 2015; 5:16520. [PMID: 26563764 PMCID: PMC4643303 DOI: 10.1038/srep16520] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022] Open
Abstract
2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an enzyme highly abundant in the central nervous system myelin of terrestrial vertebrates. The catalytic domain of CNPase belongs to the 2H phosphoesterase superfamily and catalyzes the hydrolysis of nucleoside 2',3'-cyclic monophosphates to nucleoside 2'-monophosphates. The detailed reaction mechanism and the essential catalytic amino acids involved have been described earlier, but the roles of many amino acids in the vicinity of the active site have remained unknown. Here, several CNPase catalytic domain mutants were studied using enzyme kinetics assays, thermal stability experiments, and X-ray crystallography. Additionally, the crystal structure of a perdeuterated CNPase catalytic domain was refined at atomic resolution to obtain a detailed view of the active site and the catalytic mechanism. The results specify determinants of ligand binding and novel essential residues required for CNPase catalysis. For example, the aromatic side chains of Phe235 and Tyr168 are crucial for substrate binding, and Arg307 may affect active site electrostatics and regulate loop dynamics. The β5-α7 loop, unique for CNPase in the 2H phosphoesterase family, appears to have various functions in the CNPase reaction mechanism, from coordinating the nucleophilic water molecule to providing a binding pocket for the product and being involved in product release.
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Affiliation(s)
- Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Helmholtz Centre for Infection Research at German Electron Synchrotron (DESY), Hamburg, Germany
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Helmholtz Centre for Infection Research at German Electron Synchrotron (DESY), Hamburg, Germany
- European Spallation Source (ESS), Lund, Sweden
| | - Mari Lehtimäki
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | | | - Inari Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Helmholtz Centre for Infection Research at German Electron Synchrotron (DESY), Hamburg, Germany
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Helmholtz Centre for Infection Research at German Electron Synchrotron (DESY), Hamburg, Germany
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16
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Laulumaa S, Blakeley MP, Raasakka A, Moulin M, Härtlein M, Kursula P. Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2. Acta Crystallogr F Struct Biol Commun 2015; 71:1391-5. [PMID: 26527266 PMCID: PMC4631588 DOI: 10.1107/s2053230x15017902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 09/24/2015] [Indexed: 11/11/2022] Open
Abstract
The molecular details of the formation of the myelin sheath, a multilayered membrane in the nervous system, are to a large extent unknown. P2 is a peripheral membrane protein from peripheral nervous system myelin, which is believed to play a role in this process. X-ray crystallographic studies and complementary experiments have provided information on the structure-function relationships in P2. In this study, a fully deuterated sample of human P2 was produced. Crystals that were large enough for neutron diffraction were grown by a ten-month procedure of feeding, and neutron diffraction data were collected to a resolution of 2.4 Å from a crystal of 0.09 mm(3) in volume. The neutron crystal structure will allow the positions of H atoms in P2 and its fatty-acid ligand to be visualized, as well as shedding light on the fine details of the hydrogen-bonding networks within the P2 ligand-binding cavity.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- European Spallation Source, Lund, Sweden
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Arne Raasakka
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Härtlein
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, PO Box 5400, 90014 Oulu, Finland
- Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
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17
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de Marco A. Recombinant antibody production evolves into multiple options aimed at yielding reagents suitable for application-specific needs. Microb Cell Fact 2015; 14:125. [PMID: 26330219 PMCID: PMC4557595 DOI: 10.1186/s12934-015-0320-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 08/20/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Antibodies have been a pillar of basic research, while their relevance in clinical diagnostics and therapy is constantly growing. Consequently, the production of both conventional and fragment antibodies constantly faces more demanding challenges for the improvement of their quantity and quality. The answer to such an increasing need has been the development of a wide array of formats and alternative production platforms. This review offers a critical comparison and evaluation of the different options to help the researchers interested in expressing recombinant antibodies in their choice. RESULTS Rather than the compilation of an exhaustive list of the recent publications in the field, this review intendeds to analyze the development of the most innovative or fast-growing strategies. These have been illustrated with some significant examples and, when possible, compared with the existing alternatives. Space has also been given to those solutions that might represent interesting opportunities or that investigate critical aspects of the production optimization but for which the available data as yet do not allow for a definitive judgment. CONCLUSIONS The take-home message is that there is a clear process of progressive diversification concerning the antibody expression platforms and an effort to yield directly application-adapted immune-reagents rather than generic naked antibodies that need further in vitro modification steps before becoming usable.
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Affiliation(s)
- Ario de Marco
- Department of Biomedical Sciences and Engineering, University of Nova Gorica, Glavni Trg 9, 5261, Vipava, Slovenia.
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18
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Goyal M, Chaudhuri TK. GroEL–GroES assisted folding of multiple recombinant proteins simultaneously over-expressed in Escherichia coli. Int J Biochem Cell Biol 2015; 64:277-86. [DOI: 10.1016/j.biocel.2015.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/17/2015] [Accepted: 04/28/2015] [Indexed: 11/16/2022]
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19
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Bird LE, Rada H, Verma A, Gasper R, Birch J, Jennions M, Lӧwe J, Moraes I, Owens RJ. Green fluorescent protein-based expression screening of membrane proteins in Escherichia coli. J Vis Exp 2015:e52357. [PMID: 25590335 PMCID: PMC4354503 DOI: 10.3791/52357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The production of recombinant membrane proteins for structural and functional studies remains technically challenging due to low levels of expression and the inherent instability of many membrane proteins once solubilized in detergents. A protocol is described that combines ligation independent cloning of membrane proteins as GFP fusions with expression in Escherichia coli detected by GFP fluorescence. This enables the construction and expression screening of multiple membrane protein/variants to identify candidates suitable for further investment of time and effort. The GFP reporter is used in a primary screen of expression by visualizing GFP fluorescence following SDS polyacrylamide gel electrophoresis (SDS-PAGE). Membrane proteins that show both a high expression level with minimum degradation as indicated by the absence of free GFP, are selected for a secondary screen. These constructs are scaled and a total membrane fraction prepared and solubilized in four different detergents. Following ultracentrifugation to remove detergent-insoluble material, lysates are analyzed by fluorescence detection size exclusion chromatography (FSEC). Monitoring the size exclusion profile by GFP fluorescence provides information about the mono-dispersity and integrity of the membrane proteins in different detergents. Protein: detergent combinations that elute with a symmetrical peak with little or no free GFP and minimum aggregation are candidates for subsequent purification. Using the above methodology, the heterologous expression in E. coli of SED (shape, elongation, division, and sporulation) proteins from 47 different species of bacteria was analyzed. These proteins typically have ten transmembrane domains and are essential for cell division. The results show that the production of the SEDs orthologues in E. coli was highly variable with respect to the expression levels and integrity of the GFP fusion proteins. The experiment identified a subset for further investigation.
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Affiliation(s)
- Louise E Bird
- Oxford Protein Production Facility, Research Complex at Harwell
| | - Heather Rada
- Oxford Protein Production Facility, Research Complex at Harwell
| | - Anil Verma
- Oxford Protein Production Facility, Research Complex at Harwell
| | - Raphael Gasper
- Protein Crystallography Group, Ruhr University; MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus
| | - James Birch
- Membrane Protein Laboratory, Diamond Light Source
| | | | - Jan Lӧwe
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus
| | | | - Raymond J Owens
- Oxford Protein Production Facility, Research Complex at Harwell;
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20
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Characterization and production of protein complexes by co-expression in Escherichia coli. Methods Mol Biol 2015; 1261:63-89. [PMID: 25502194 DOI: 10.1007/978-1-4939-2230-7_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functional units within cells are often macromolecular complexes rather than single species. Production of these complexes as assembled homogenous samples is a prerequisite for their biophysical and structural characterization and hence an understanding of their function in molecular terms. Co-expression in Escherichia coli has been used routinely to decipher the subunit composition, assembly, and production of whole protein complexes. Such complexes can then be used to reconstitute protein/nucleic acid complexes in vitro. In this chapter we present protocols for the widely utilized ACEMBL and pET-MCN/pET-MCP vector series which enable the rapid and automated co-expression of protein complexes in Escherichia coli.
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21
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Application of In-Fusion™ cloning for the parallel construction of E. coli expression vectors. Methods Mol Biol 2014; 1116:209-34. [PMID: 24395367 DOI: 10.1007/978-1-62703-764-8_15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In-Fusion™ cloning is a flexible DNA ligase-independent cloning technology that has wide-ranging uses in molecular biology. In this chapter we describe the protocols used in the OPPF-UK to design and construct expression vectors using In-Fusion™. Our method for small scale expression screening in Escherichia coli of constructs generated by In-Fusion™ is also outlined.
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22
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Long Q, Liu X, Yang Y, Li L, Harvey L, McNeil B, Bai Z. The development and application of high throughput cultivation technology in bioprocess development. J Biotechnol 2014; 192 Pt B:323-38. [PMID: 24698846 DOI: 10.1016/j.jbiotec.2014.03.028] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/18/2014] [Accepted: 03/24/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on recent progress in the technology of high throughput (HTP) cultivation and its increasing application in quality by design (QbD) -driven bioprocess development. Several practical HTP strategies aimed at shortening process development (PD) timelines from DNA to large scale processes involving commercially available HTP technology platforms, including microtiter plate (MTP) culture, micro-scale bioreactors, and in parallel fermentation systems, etc., are critically reviewed in detail. This discussion focuses upon the relative strengths and weaknesses or limitations of each of these platforms in this context. Emerging prototypes of micro-bioreactors reported recently, such as milliliter (mL) scale stirred tank bioreactors, and microfludics integrated micro-scale bioreactors, and their potential for practical application in QbD-driven HTP process development are also critically appraised. The overall aim of such technology is to rapidly gain process insights, and since the analytical technology deployed in HTP systems is critically important to the achievement of this aim, this rapidly developing area is discussed. Finally, general future trends are critically reviewed.
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Affiliation(s)
- Quan Long
- Jiangnan University, Jiangsu, Wuxi, 214122, PR China
| | - Xiuxia Liu
- Jiangnan University, Jiangsu, Wuxi, 214122, PR China
| | - Yankun Yang
- Jiangnan University, Jiangsu, Wuxi, 214122, PR China
| | - Lu Li
- Jiangnan University, Jiangsu, Wuxi, 214122, PR China
| | | | | | - Zhonghu Bai
- Jiangnan University, Jiangsu, Wuxi, 214122, PR China.
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23
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Vincentelli R, Romier C. Expression in Escherichia coli: becoming faster and more complex. Curr Opin Struct Biol 2013; 23:326-34. [PMID: 23422067 DOI: 10.1016/j.sbi.2013.01.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/11/2013] [Accepted: 01/18/2013] [Indexed: 12/23/2022]
Abstract
Escherichia coli is the major expression host for the production of homogeneous protein samples for structural studies. The introduction of high-throughput technologies in the last decade has further revitalized E. coli expression, with rapid assessment of different expression strategies and successful production of an ever-increasing number of proteins. In addition, miniaturization of biophysical characterizations should soon help choosing expression strategies based on quantitative and qualitative observations. Since many proteins form larger assemblies in vivo, dedicated co-expression systems for E. coli are now addressing the reconstitution of protein complexes. Yet, co-expression approaches show an increasing experimental combinatorial intricacy when considering larger complexes. The current combination of high-throughput and co-expression technologies paves the way, however, for tackling larger and more complex macromolecular assemblies.
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Affiliation(s)
- Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 CNRS, Université Aix-Marseille, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
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24
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Lamppa JW, Tanyos SA, Griswold KE. Engineering Escherichia coli for soluble expression and single step purification of active human lysozyme. J Biotechnol 2012; 164:1-8. [PMID: 23220215 DOI: 10.1016/j.jbiotec.2012.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/07/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
Abstract
Genetically engineered variants of human lysozyme represent promising leads in the battle against drug-resistant bacterial pathogens, but early stage development and testing of novel lysozyme variants is constrained by the lack of a robust, scalable and facile expression system. While wild type human lysozyme is reportedly produced at 50–80 kg per hectare of land in recombinant rice, this plant-based system is not readily scaled down to bench top production, and it is therefore not suitable for development and characterization of novel lysozyme variants. Here, we describe a novel and efficient expression system capable of producing folded, soluble and functional human lysozyme in Escherichia coli cells. To achieve this goal, we simultaneously co-express multiple protein folding chaperones as well as harness the lysozyme inhibitory protein, Ivy. Our strategy exploits E. coli's ease of culture, short doubling time, and facile genetics to yield upwards of 30 mg/l of soluble lysozyme in a bioreactor system, a 3000-fold improvement over prior efforts in E. coli. Additionally, molecular interactions between lysozyme and a his-tagged Ivy allows for one-step purification by IMAC, yielding as much as 21 mg/l of purified enzyme. We anticipate that our expression and purification platform will facilitate further development of engineered lysozymes having utility in disease treatment and other practical applications.
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Affiliation(s)
- John W Lamppa
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
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25
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Liu M, Yu H. Cocktail production of an endo-β-xylanase and a β-glucosidase from Trichoderma reesei QM 9414 in Escherichia coli. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Available methods for assembling expression cassettes for synthetic biology. Appl Microbiol Biotechnol 2012; 93:1853-63. [PMID: 22311648 DOI: 10.1007/s00253-012-3920-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/19/2012] [Accepted: 01/20/2012] [Indexed: 12/11/2022]
Abstract
Studies in the structural biology of the multicomponent protein complex, metabolic engineering, and synthetic biology frequently rely on the efficient over-expression of these subunits or enzymes in the same cell. As a first step, constructing the multiple expression cassettes will be a complicated and time-consuming job if the classic and conventional digestion and ligation based cloning method is used. Some more efficient methods have been developed, including (1) the employment of a multiple compatible plasmid expression system, (2) the rare-cutter-based design of vectors, (3) in vitro recombination (sequence and ligation independent cloning, the isothermally enzymatic assembly of DNA molecules in a single reaction), and (4) in vivo recombination using recombination-efficient yeast (in vivo assembly of overlapping fragments, reiterative recombination for the chromosome integration of foreign expression cassettes). In this review, we systematically introduce these available methods.
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27
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28
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Bieniossek C, Imasaki T, Takagi Y, Berger I. MultiBac: expanding the research toolbox for multiprotein complexes. Trends Biochem Sci 2011; 37:49-57. [PMID: 22154230 PMCID: PMC7127121 DOI: 10.1016/j.tibs.2011.10.005] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/19/2011] [Accepted: 10/24/2011] [Indexed: 12/12/2022]
Abstract
Protein complexes composed of many subunits carry out most essential processes in cells and, therefore, have become the focus of intense research. However, deciphering the structure and function of these multiprotein assemblies imposes the challenging task of producing them in sufficient quality and quantity. To overcome this bottleneck, powerful recombinant expression technologies are being developed. In this review, we describe the use of one of these technologies, MultiBac, a baculovirus expression vector system that is particularly tailored for the production of eukaryotic multiprotein complexes. Among other applications, MultiBac has been used to produce many important proteins and their complexes for their structural characterization, revealing fundamental cellular mechanisms.
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Affiliation(s)
- Christoph Bieniossek
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
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29
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Berger I, Blanco AG, Boelens R, Cavarelli J, Coll M, Folkers GE, Nie Y, Pogenberg V, Schultz P, Wilmanns M, Moras D, Poterszman A. Structural insights into transcription complexes. J Struct Biol 2011; 175:135-46. [DOI: 10.1016/j.jsb.2011.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/09/2011] [Accepted: 04/27/2011] [Indexed: 01/24/2023]
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30
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Vijayachandran LS, Viola C, Garzoni F, Trowitzsch S, Bieniossek C, Chaillet M, Schaffitzel C, Busso D, Romier C, Poterszman A, Richmond TJ, Berger I. Robots, pipelines, polyproteins: enabling multiprotein expression in prokaryotic and eukaryotic cells. J Struct Biol 2011; 175:198-208. [PMID: 21419851 PMCID: PMC7128143 DOI: 10.1016/j.jsb.2011.03.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/11/2011] [Accepted: 03/11/2011] [Indexed: 11/17/2022]
Abstract
Multiprotein complexes catalyze vital biological functions in the cell. A paramount objective of the SPINE2 project was to address the structural molecular biology of these multiprotein complexes, by enlisting and developing enabling technologies for their study. An emerging key prerequisite for studying complex biological specimens is their recombinant overproduction. Novel reagents and streamlined protocols for rapidly assembling co-expression constructs for this purpose have been designed and validated. The high-throughput pipeline implemented at IGBMC Strasbourg and the ACEMBL platform at the EMBL Grenoble utilize recombinant overexpression systems for heterologous expression of proteins and their complexes. Extension of the ACEMBL platform technology to include eukaryotic hosts such as insect and mammalian cells has been achieved. Efficient production of large multicomponent protein complexes for structural studies using the baculovirus/insect cell system can be hampered by a stoichiometric imbalance of the subunits produced. A polyprotein strategy has been developed to overcome this bottleneck and has been successfully implemented in our MultiBac baculovirus expression system for producing multiprotein complexes.
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Affiliation(s)
- Lakshmi Sumitra Vijayachandran
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Cristina Viola
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Frederic Garzoni
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Simon Trowitzsch
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Christoph Bieniossek
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Maxime Chaillet
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Christiane Schaffitzel
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Didier Busso
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France
- Inserm, U964, Illkirch F-67400, France
- CNRS, UMR7104, Illkirch 67400, France
- Université de Strasbourg, Strasbourg F-67000, France
| | - Christophe Romier
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France
- Inserm, U964, Illkirch F-67400, France
- CNRS, UMR7104, Illkirch 67400, France
- Université de Strasbourg, Strasbourg F-67000, France
| | - Arnaud Poterszman
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France
- Inserm, U964, Illkirch F-67400, France
- CNRS, UMR7104, Illkirch 67400, France
- Université de Strasbourg, Strasbourg F-67000, France
| | - Timothy J. Richmond
- Institute for Molecular Biology and Biophysics IMB, Swiss Federal Institute of Technology ETH Hönggerberg, Schafmattstrasse 20, CH 8093 Zürich, Switzerland
| | - Imre Berger
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, and Unit of Virus Host Cell Interactions UVHCI, UJF-CNRS-EMBL Unite Mixte International UMI 3265, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
- Corresponding author. Address: European Molecular Biology Laboratory (EMBL Grenoble), BP 181, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France. Fax: +33 (0)476207199.
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