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Hashemzaei M, Ghoshoon MB, Jamshidi M, Moradbeygi F, Hashemzehi A. A Review on Romiplostim Mechanism of Action and the Expressive Approach in E. coli. Recent Pat Biotechnol 2024; 18:95-109. [PMID: 38282441 DOI: 10.2174/1872208317666230503094451] [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: 11/01/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 01/30/2024]
Abstract
Immune thrombocytopenic purpura (ITP) is an autoimmune disorder determined by immune-mediated platelet demolition and reduction of platelet production. Romiplostim is a new thrombopoiesis motivating peptibody that binds and stimulates the human thrombopoietin receptor the patent of which was registered in 2008. It is used to treat thrombocytopenia in patients with chronic immune thrombocytopenic purpura. Romiplostim is a 60 kDa peptibody designed to inhibit cross-reacting immune responses. It consists of four high-affinity TPO-receptor binding domains for the Mpl receptor and one human IgG1 Fc domain. Escherichia coli is a good host for the fabrication of recombinant proteins such as romiplostim. The expression of a gene intended in E. coli is dependent on many factors such as a protein's inherent ability to fold, mRNA's secondary structure, its solubility, its toxicity preferential codon use, and its need for post-translational modification (PTM). This review focuses on the structure, function, mechanism of action, and expressive approach to romiplostim in E. coli.
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Affiliation(s)
- Masoud Hashemzaei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mehrnaz Jamshidi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Moradbeygi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Hashemzehi
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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2
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Lima GC, Chura-Chambi RM, Morganti L, Silva VJ, Cabral-Piccin MP, Rocha V, Medina TS, Ramos RN, Luz D. Recombinant human TIM-3 ectodomain expressed in bacteria and recovered from inclusion bodies as a stable and active molecule. Front Bioeng Biotechnol 2023; 11:1227212. [PMID: 37588136 PMCID: PMC10426796 DOI: 10.3389/fbioe.2023.1227212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/12/2023] [Indexed: 08/18/2023] Open
Abstract
Introduction: Microbial systems, such as Escherichia coli, as host recombinant expression is the most versatile and the cheapest system for protein production, however, several obstacles still remain, such as recovery of soluble and functional proteins from inclusion bodies, elimination of lipopolysaccharides (LPS) contamination, incomplete synthesis, degradation by proteases, and the lack of post-translational modifications, which becomes even more complex when comes to membrane proteins, because they are difficult not only to produce but also to keep in solution in its active state. T-cell Immunoglobulin and Mucin domain 3 (TIM-3) is a type I transmembrane protein that is predominantly expressed on the surface of T lymphocytes, natural killer (NK) cells, dendritic cells, and macrophages, playing a role as a negative immune checkpoint receptor. TIM-3 comprises a single ectodomain for interaction with immune system soluble and cellular components, a transmembrane domain, and a cytoplasmic tail, responsible for the binding of signaling and scaffolding molecules. TIM-3 pathway holds potential as a therapeutic target for immunotherapy against tumors, autoimmunity, chronic virus infections, and various malignancies, however, many aspects of the biology of this receptor are still incompletely understood, especially regarding its ligands. Methods: Here we overcome, for the first time, the challenge of the production of active immune checkpoint protein recovered from bacterial cytoplasmic inclusion bodies, being able to obtain an active, and non-glycosylated TIM-3 ectodomain (TIM-3-ECD), which can be used as a tool to better understand the interactions and roles of this immune checkpoint. The TIM-3 refolding was obtained by the association of high pressure and alkaline pH. Results: The purified TIM-3-ECD showed the correct secondary structure and was recognized from anti-TIM-3 structural-dependent antibodies likewise commercial TIM-3-ECD was produced by a mammal cells system. Furthermore, immunofluorescence showed the ability of TIM-3-ECD to bind to the surface of lung cancer A549 cells and to provide an additional boost for the expression of the lymphocyte activation marker CD69 in anti-CD3/CD28 activated human PBMC. Discussion: Taken together these results validated a methodology able to obtain active checkpoint proteins from bacterial inclusion bodies, which will be helpful to further investigate the interactions of this and others not yet explored immune checkpoints.
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Affiliation(s)
- G. C. Lima
- Laboratory of Bacteriology, Butantan Institute, São Paulo, Brazil
| | | | - L. Morganti
- Biotechnology Center, Institute of Energy and Nuclear Research—CNEN/SP, São Paulo, Brazil
| | - V. J. Silva
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Department of Hematology and Cell Therapy, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - M. P. Cabral-Piccin
- International Research Center, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - V. Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Department of Hematology and Cell Therapy, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- D’OR Institute of Research and Education, São Paulo, Brazil
| | - T. S. Medina
- International Research Center, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - R. N. Ramos
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology, Department of Hematology and Cell Therapy, Clinical Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- D’OR Institute of Research and Education, São Paulo, Brazil
| | - D. Luz
- Laboratory of Bacteriology, Butantan Institute, São Paulo, Brazil
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3
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Pouresmaeil M, Azizi-Dargahlou S. Factors involved in heterologous expression of proteins in E. coli host. Arch Microbiol 2023; 205:212. [PMID: 37120438 PMCID: PMC10148705 DOI: 10.1007/s00203-023-03541-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or prokaryotic heterologous hosts. By increasing the omics data especially related to different heterologous hosts as well as the presence of new amenable genetic engineering tools, we can artificially engineer heterologous hosts to produce recombinant proteins in sufficient quantities. Numerous recombinant proteins have been produced and applied in various industries, and the global recombinant proteins market size is expected to be cast to reach USD 2.4 billion by 2027. Therefore, identifying the weakness and strengths of heterologous hosts is critical to optimize the large-scale biosynthesis of recombinant proteins. E. coli is one of the popular hosts to produce recombinant proteins. Scientists reported some bottlenecks in this host, and due to the increasing demand for the production of recombinant proteins, there is an urgent need to improve this host. In this review, we first provide general information about the E. coli host and compare it with other hosts. In the next step, we describe the factors involved in the expression of the recombinant proteins in E. coli. Successful expression of recombinant proteins in E. coli requires a complete elucidation of these factors. Here, the characteristics of each factor will be fully described, and this information can help to improve the heterologous expression of recombinant proteins in E. coli.
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Affiliation(s)
- Mahin Pouresmaeil
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran.
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4
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Production of α-Synuclein Fibrillar-Specific scFv from Inclusion Bodies. Methods Mol Biol 2023; 2617:239-248. [PMID: 36656529 DOI: 10.1007/978-1-0716-2930-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recombinant antibody fragments such as Fab, scFvs, and diabodies against α-syn have become a viable alternative to the conventional full-length antibodies in immunotherapeutic approaches due to their benefits which include smaller size, higher stability, specificity, and affinity. However, the majority of recombinant antibody fragments typically express as inclusion bodies (IBs) in E. coli, which makes their purification incredibly difficult. Here, we describe a method involving a mild solubilizing protocol followed by slow on-column refolding to purify active single-chain variable fragment (scFv-pF) antibody that can recognize the pathogenic α-syn fibrils.
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Li R, Song H, Chen Q, Sun H, Chang Y, Luo H. Effect of SpyTag/SpyCatcher cyclization on reactivation of covalently immobilized biocatalysts. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Kamel S, Schollmeyer J, Kurreck A, Neubauer P. Optimization of Inclusion Body Formation and Purification in Multi-well Plates. Methods Mol Biol 2023; 2617:121-138. [PMID: 36656520 DOI: 10.1007/978-1-0716-2930-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Heterologous expression has long been used for the efficient production of proteins and enzymes as it offers significant advantages over purification of proteins from their native organisms. When first established, great efforts have been made to heterologously express proteins with high yields in the soluble fraction, hence, avoiding protein aggregation. In recent decades, however, it has been shown that the formation of aggregates (inclusion bodies; IBs) can be beneficial. To recover active protein, however, proteins should have been refolded from IBs after purification. The discovery that IBs themselves can also be active has revolutionized the entire protein production field. Therefore, several approaches have been described to generate catalytically active IBs during heterologous expression. Since several extrinsic and intrinsic factors such as protein structure and toxicity, pH and temperature of expression, and the used media might influence the formation of IBs, it is time and material consuming to use shake flask to examine and optimize different expression conditions. However, by using multi-well plates, it is possible to rapidly develop an efficient protocol for the expression of catalytically active IBs in a rational approach. The presented protocol was used for the heterologous expression of a 5'-adenosine monophosphate phosphorylase which forms catalytically active aggregates during expression in E. coli.
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Affiliation(s)
- Sarah Kamel
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany
| | - Julia Schollmeyer
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany
- BioNukleo GmbH, Berlin, Germany
| | | | - Peter Neubauer
- Technische Universität Berlin, Institute of Biotechnology, Chair of Bioprocess Engineering, Berlin, Germany.
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7
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Kachhawaha K, Singh S, Joshi K, Nain P, Singh SK. Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications. Prep Biochem Biotechnol 2022; 53:728-752. [PMID: 36534636 DOI: 10.1080/10826068.2022.2155835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.
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Affiliation(s)
- Kajal Kachhawaha
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Santanu Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Khyati Joshi
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Priyanka Nain
- Department of Chemical and Bimolecular Engineering, University of Delaware, Newark, DE, USA
| | - Sumit K Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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8
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Buscajoni L, Martinetz MC, Berkemeyer M, Brocard C. Refolding in the modern biopharmaceutical industry. Biotechnol Adv 2022; 61:108050. [PMID: 36252795 DOI: 10.1016/j.biotechadv.2022.108050] [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: 06/07/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2022]
Abstract
Inclusion bodies (IBs) often emerge upon overexpression of recombinant proteins in E. coli. From IBs, refolding is necessary to generate the native protein that can be further purified to obtain pure and active biologicals. This work focusses on refolding as a significant process step during biopharmaceutical manufacturing with an industrial perspective. A theoretical and historical background on protein refolding gives the reader a starting point for further insights into industrial process development. Quality requirements on IBs as starting material for refolding are discussed and further economic and ecological aspects are considered with regards to buffer systems and refolding conditions. A process development roadmap shows the development of a refolding process starting from first exploratory screening rounds to scale-up and implementation in manufacturing plant. Different aspects, with a direct influence on yield, such as the selection of chemicals including pH, ionic strength, additives, etc., and other often neglected aspects, important during scale-up, such as mixing, and gas-fluid interaction, are highlighted with the use of a quality by design (QbD) approach. The benefits of simulation sciences (process simulation and computer fluid dynamics) and process analytical technology (PAT) for seamless process development are emphasized. The work concludes with an outlook on future applications of refolding and highlights open research inquiries.
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Affiliation(s)
- Luisa Buscajoni
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Michael C Martinetz
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Matthias Berkemeyer
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
| | - Cécile Brocard
- Boehringer-Ingelheim RCV GmbH & Co KG, Biopharma Austria, Process Science Downstream Development, Dr. Boehringer-Gasse 5- 11, 1120 Vienna, Austria.
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9
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Single-Step Protocol for Isolating the Recombinant Extracellular Domain of the Luteinizing Hormone Receptor from the Ovis aries Testis. Curr Issues Mol Biol 2022; 44:5718-5727. [DOI: 10.3390/cimb44110387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/24/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
The luteinizing hormone receptor (LHR) is a glycoprotein member of the G protein-coupled receptors superfamily. It participates in corpus luteum formation and ovulation in females and acts in testosterone synthesis and spermatogenesis in males. In this study, we extracted RNA from sheep testicles and synthetized the cDNA to amplify the gene lhr-bed. This gene consists of 762 bp and encodes 273 amino acids of the extracellular domain of LHR. The lhr-bed was cloned into pJET1.2/blunt, then subcloned into pCOLD II, and finally, transformed in E. coli BL21 (DE3) cells. Because the induced rLHR-Bed protein was found in the insoluble fraction, we followed a modified purification protocol involving induction at 25 °C, subjection to denaturing conditions, and on-column refolding to increase solubility. We confirmed rLHR-Bed expression by means of Western blot and mass spectrometry analysis. It is currently known that the structure stem-loop 5′UTR on pCOLD II vector is stable at 15 °C. We predicted and obtained RNAfold stability at 25 °C. We successfully obtained the recombinant LHR extracellular domain, with protein yields of 0.2 mg/L, and purity levels of approximately 90%, by means of a single chromatographic purification step. The method described here may be used to obtain large quantities of rLHR-Bed in the future.
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Qafary M, Rashno F, Khajeh K, Khaledi M, Moosavi-Movahedi AA. Insulin fibrillation: Strategies for inhibition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:49-62. [DOI: 10.1016/j.pbiomolbio.2022.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 04/07/2023]
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11
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Gani K, Chirmade T, Ughade S, Thulasiram H, Bhambure R. Understanding unfolding and refolding of the antibody fragment (Fab) III: Mapping covalent and non-covalent interactions during in-vitro refolding of light chain, heavy chain, and Fab. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Shinoda S, Itakura A, Sasano H, Miyake R, Kawabata H, Asano Y. Rational Design of the Soluble Variant of l-Pipecolic Acid Hydroxylase using the α-Helix Rule and the Hydropathy Contradiction Rule. ACS OMEGA 2022; 7:29508-29516. [PMID: 36033675 PMCID: PMC9404520 DOI: 10.1021/acsomega.2c04247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The production of recombinant proteins in Escherichia coli is an important application of biotechnology. 2-Oxoglutarate-dependent l-pipecolic acid hydroxylase derived from Xenorhabdus doucetiae (XdPH) is an excellent biocatalyst that catalyzes the hydroxylation of l-pipecolic acid to produce cis-5-hydroxy-l-pipecolic acid. However, the enzyme tends to form aggregates in the E. coli expression system. Our group established two rules, namely, the "α-helix rule" and the "hydropathy contradiction rule," to select residues to be altered for improving the heterologous recombinant production of proteins, by analyzing their primary structure. We rationally designed XdPH variants that are expressed in highly soluble and active forms in the E. coli expression system using these hotspot prediction methods, and the L142R variant showed a remarkably high soluble expression level compared to the wild-type XdPH. Further mutations were introduced into the L142R gene by site-directed mutagenesis. Moreover, the I28P/L142R and C76Y/L142R double variants displayed improved soluble expression levels compared to the single variants. These variants were also more thermostable than the wild-type XdPH. To analyze the effect of the alteration on one of the hotspots, L142 was replaced with various hydrophilic and positively charged residues. The remarkable increase in soluble protein expression caused by the alterations suggests that the decrease in the hydrophobicity of the protein surface and the enhancement of the interaction between nearby residues are important factors determining the solubility of the protein. Overall, this study demonstrated the effectiveness of our protocol in identifying aggregation hotspots for recombinant protein production and in basic biochemical research.
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Affiliation(s)
- Suguru Shinoda
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu-shi, Toyama 939-0398, Japan
| | - Aoi Itakura
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu-shi, Toyama 939-0398, Japan
| | - Haruka Sasano
- Science
& Innovation Center, Mitsubishi Chemical
Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama-shi, Kanagawa 227-8502, Japan
| | - Ryoma Miyake
- Science
& Innovation Center, Mitsubishi Chemical
Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama-shi, Kanagawa 227-8502, Japan
| | - Hiroshi Kawabata
- Science
& Innovation Center, Mitsubishi Chemical
Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama-shi, Kanagawa 227-8502, Japan
- API
Corporation, 13-4 Uchikanda
1-chome, Chiyoda-ku, Tokyo 101-0047, Japan
| | - Yasuhisa Asano
- Biotechnology
Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu-shi, Toyama 939-0398, Japan
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Rolf J, Ngo ACR, Tischler D, Lütz S, Rosenthal K. Cell-free protein synthesis for the screening of novel azoreductases and their preferred electron donor. Chembiochem 2022; 23:e202200121. [PMID: 35593146 PMCID: PMC9401864 DOI: 10.1002/cbic.202200121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/19/2022] [Indexed: 11/26/2022]
Abstract
Azoreductases are potent biocatalysts for the cleavage of azo bonds. Various gene sequences coding for potential azoreductases are available in databases, but many of their gene products are still uncharacterized. To avoid the laborious heterologous expression in a host organism, we developed a screening approach involving cell‐free protein synthesis (CFPS) combined with a colorimetric activity assay, which allows the parallel screening of putative azoreductases in a short time. First, we evaluated different CFPS systems and optimized the synthesis conditions of a model azoreductase. With the findings obtained, 10 azoreductases, half of them undescribed so far, were screened for their ability to degrade the azo dye methyl red. All novel enzymes catalyzed the degradation of methyl red and can therefore be referred to as azoreductases. In addition, all enzymes degraded the more complex and bulkier azo dye Brilliant Black and four of them also showed the ability to reduce p‐benzoquinone. NADH was the preferred electron donor for the most enzymes, although the synthetic nicotinamide co‐substrate analogue 1‐benzyl‐1,4‐dihydronicotinamide (BNAH) was also accepted by all active azoreductases. This screening approach allows accelerated identification of potential biocatalysts for various applications.
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Affiliation(s)
- Jascha Rolf
- TU Dortmund University: Technische Universitat Dortmund, Biochemical & Chemical Engineering, Emil-Figge-Str. 66, 44227, Dortmund, GERMANY
| | - Anna Christina Reyes Ngo
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Microbial Biotechnology, Faculty of Biology and Biotechnology, GERMANY
| | - Dirk Tischler
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Microbial Biotechnology, Faculty of Biology and Biotechnology, GERMANY
| | - Stephan Lütz
- TU Dortmund University: Technische Universitat Dortmund, Department of Biochemical and Chemical Engineering, Chair for Bioprocess Engineering, GERMANY
| | - Katrin Rosenthal
- TU Dortmund university, Bioprocessengineering, Emil-Figge-Str. 66, 44227, Dortmund, GERMANY
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Barguilla I, Unzueta U, Carratalá JV, Cano-Garrido O, Villaverde A, Hernández A, Ferrer-Miralles N. Toxicity Profiling of Bacterial Inclusion Bodies in Human Caco-2 Cells. Front Bioeng Biotechnol 2022; 10:842256. [PMID: 35573225 PMCID: PMC9099286 DOI: 10.3389/fbioe.2022.842256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Bacterial inclusion bodies (IBs) are discrete macromolecular complexes that appear in recombinant prokaryotic cells under stress conditions. These structures are often discarded for biotechnological uses given the difficulty in recovering proteins of interest from them in a soluble form. However, recent approaches have revealed the potential of these protein clusters as biomaterials to promote cell growth and as protein depots for the release of recombinant proteins for biotechnological and biomedical applications. Although these kinds of natural supramolecular complexes have attracted great interest, no comprehensive study of their toxicity in cell cultures has been carried out. In this study, caco-2 cells were exposed to natural IBs, soluble protein-only nanoparticles (NPs), and non-assembled versions of the same protein for comparative purposes. Cytotoxicity, oxidative stress, and genotoxicity were analyzed for all these protein formats. Natural IBs and soluble protein formats demonstrated their safety in eukaryotic cells. No cytotoxicity, genotoxicity, or oxidative stress was detected in caco-2 cells exposed to the protein samples in any of the experimental conditions evaluated, which covered protein concentrations used in previous biological activity assays. These conditions evaluated the activity of protein samples obtained from three prokaryotic hosts [Escherichia coli and the endotoxin-free expression systems Lactococcus lactis and ClearColi® BL21 (DE3)]. Our results demonstrate that natural IBs and soluble protein nanoparticles are non-toxic materials for eukaryotic cells and that this may represent an interesting alternative to the classical unassembled format of recombinant proteins for certain applications in biotechnology and biomedicine.
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Affiliation(s)
- Irene Barguilla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Networking Center for Biomedical Research in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Carlos III Institute of Health, Madrid, Spain
| | - Jose Vicente Carratalá
- Networking Center for Biomedical Research in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Carlos III Institute of Health, Madrid, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Olivia Cano-Garrido
- Networking Center for Biomedical Research in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Carlos III Institute of Health, Madrid, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Antonio Villaverde
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Networking Center for Biomedical Research in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Carlos III Institute of Health, Madrid, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alba Hernández
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Carlos III Institute of Health, Madrid, Spain
- *Correspondence: Neus Ferrer-Miralles, ; Alba Hernández,
| | - Neus Ferrer-Miralles
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Networking Center for Biomedical Research in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Carlos III Institute of Health, Madrid, Spain
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- *Correspondence: Neus Ferrer-Miralles, ; Alba Hernández,
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Györkei Á, Daruka L, Balogh D, Őszi E, Magyar Z, Szappanos B, Fekete G, Fuxreiter M, Horváth P, Pál C, Kintses B, Papp B. Proteome-wide landscape of solubility limits in a bacterial cell. Sci Rep 2022; 12:6547. [PMID: 35449391 PMCID: PMC9023497 DOI: 10.1038/s41598-022-10427-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are prone to aggregate when expressed above their solubility limits. Aggregation may occur rapidly, potentially as early as proteins emerge from the ribosome, or slowly, following synthesis. However, in vivo data on aggregation rates are scarce. Here, we classified the Escherichia coli proteome into rapidly and slowly aggregating proteins using an in vivo image-based screen coupled with machine learning. We find that the majority (70%) of cytosolic proteins that become insoluble upon overexpression have relatively low rates of aggregation and are unlikely to aggregate co-translationally. Remarkably, such proteins exhibit higher folding rates compared to rapidly aggregating proteins, potentially implying that they aggregate after reaching their folded states. Furthermore, we find that a substantial fraction (~ 35%) of the proteome remain soluble at concentrations much higher than those found naturally, indicating a large margin of safety to tolerate gene expression changes. We show that high disorder content and low surface stickiness are major determinants of high solubility and are favored in abundant bacterial proteins. Overall, our study provides a global view of aggregation rates and hence solubility limits of proteins in a bacterial cell.
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Affiliation(s)
- Ádám Györkei
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Lejla Daruka
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Dávid Balogh
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erika Őszi
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zoltán Magyar
- Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Balázs Szappanos
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gergely Fekete
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Mónika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- Laboratory of Protein Dynamics, University of Debrecen, Debrecen, Hungary
| | - Péter Horváth
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute of Life Science-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Csaba Pál
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
| | - Bálint Kintses
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
- HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary.
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary.
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.
- Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
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16
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Xie X, Wu P, Huang X, Bai W, Li B, Shi N. Retro-protein XXA is a remarkable solubilizing fusion tag for inclusion bodies. Microb Cell Fact 2022; 21:51. [PMID: 35366873 PMCID: PMC8977028 DOI: 10.1186/s12934-022-01776-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background Producing large amounts of soluble proteins from bacteria remains a challenge, despite the help of current various solubilizing fusion tags. Thus, developing novel tags is necessary. Antifreeze protein (AFP) has excellent solubility and hydrophilicity, but there are no current reports on its use as a solubilizing fusion tag. Additionally, there is no precedent for using retro-proteins (reverse sequence) as solubilizing fusion tags. Therefore, we selected the antifreeze protein AXX and obtained its retro-protein XXA by synthesizing the XXA gene for the development of a new solubilizing fusion tag. Results XXA exhibits better stability and ease of expression than AXX; hence, we focused the development of the solubilizing fusion tag on XXA. XXA fused with the tested inclusion bodies, significantly increasing the soluble expression compared with commonly used solubilizing fusion tags such as GST, Trx, Sumo, MBP, and NusA. The tested proteins became soluble after fusion with the XXA tag, and they could be purified. They maintained a soluble form after XXA tag removal. Finally, we used enzymatic digestion reaction and western blot experiments to verify that bdNEDP1 and NbALFA, which were soluble expressed by fusion with XXA, were active. Conclusion We developed the novel solubilizing fusion tag XXA, which could more effectively facilitate the soluble expression of inclusion bodies compared with current commonly used tags. XXA could function at both low and high temperatures, and its moderate molecular weight has a limited impact on the output. These properties make XXA an ideal fusion tag for future research and industrial production. Moreover, for the first time, we highlighted the broad potential of antifreeze protein as a solubilizing fusion tag, bringing retro-protein into practical application. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01776-7.
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17
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Song H, Wang Y, Dong W, Chen Q, Sun H, Peng H, Li R, Chang Y, Luo H. Effect of SpyTag/SpyCatcher cyclization on stability and refolding of green fluorescent protein. Biotechnol Lett 2022; 44:613-621. [PMID: 35359178 DOI: 10.1007/s10529-022-03246-x] [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: 12/01/2021] [Accepted: 03/15/2022] [Indexed: 11/26/2022]
Abstract
To study the effect of SpyTag/SpyCatcher cyclization on stability and refolding of protein, we constructed a cyclized green fluorescent protein (SRGFP) and its derivative to act as a linear structure control (L-SRGFP). SRGFP and L-SRGFP showed similar fluorescence characteristics to the wild-type GFP, while compared with GFP and L-SRGFP, the thermal stability and denaturation resistance of SRGFP were improved. The refolding efficiencies of these three denatured proteins were investigated under different pH, temperature and initial protein concentration conditions, and it was found that SRGFP was superior to GFP and L-SRGFP in terms of refolding yield and refolding speed. In the pH range of 8.0-8.5, SRGFP could basically recover all fluorescence, while GFP and L-SRGFP recovered only about 87.52% and 88.58%. When refolded at a high temperature (37 °C), SRGFP still recovered 85.27% of the fluorescence, whereas GFP and L-SRGFP recovered only around 69.43% and 68.45%. At a high initial protein concentration (5 mg/mL), the refolding yield of SRGFP was about 15% higher than that of both GFP and L-SRGFP. These results suggest that the introduction of SpyRing structure (head-to-tail cyclization via SpyTag and SpyCatcher) improved the protein's stability and facilitated the refolding of denatured protein.
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Affiliation(s)
- Haiyan Song
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Yue Wang
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Wenge Dong
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qiwei Chen
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hongxu Sun
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hui Peng
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Ren Li
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China
| | - Yanhong Chang
- Department of Environmental Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, Beijing, 100083, China.
| | - Hui Luo
- Department of Biological Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Muronetz VI, Kudryavtseva SS, Leisi EV, Kurochkina LP, Barinova KV, Schmalhausen EV. Regulation by Different Types of Chaperones of Amyloid Transformation of Proteins Involved in the Development of Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23052747. [PMID: 35269889 PMCID: PMC8910861 DOI: 10.3390/ijms23052747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 02/06/2023] Open
Abstract
The review highlights various aspects of the influence of chaperones on amyloid proteins associated with the development of neurodegenerative diseases and includes studies conducted in our laboratory. Different sections of the article are devoted to the role of chaperones in the pathological transformation of alpha-synuclein and the prion protein. Information about the interaction of the chaperonins GroE and TRiC as well as polymer-based artificial chaperones with amyloidogenic proteins is summarized. Particular attention is paid to the effect of blocking chaperones by misfolded and amyloidogenic proteins. It was noted that the accumulation of functionally inactive chaperones blocked by misfolded proteins might cause the formation of amyloid aggregates and prevent the disassembly of fibrillar structures. Moreover, the blocking of chaperones by various forms of amyloid proteins might lead to pathological changes in the vital activity of cells due to the impaired folding of newly synthesized proteins and their subsequent processing. The final section of the article discusses both the little data on the role of gut microbiota in the propagation of synucleinopathies and prion diseases and the possible involvement of the bacterial chaperone GroE in these processes.
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Affiliation(s)
- Vladimir I. Muronetz
- Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.P.K.); (K.V.B.); (E.V.S.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence:
| | - Sofia S. Kudryavtseva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Evgeniia V. Leisi
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Lidia P. Kurochkina
- Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.P.K.); (K.V.B.); (E.V.S.)
| | - Kseniya V. Barinova
- Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.P.K.); (K.V.B.); (E.V.S.)
| | - Elena V. Schmalhausen
- Belozersky Institute of Physico Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.P.K.); (K.V.B.); (E.V.S.)
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19
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Kokotidou C, Tsitouroudi F, Nistikakis G, Vasila M, Papanikolopoulou K, Kretsovali A, Mitraki A. Adenovirus Fibers as Ultra-Stable Vehicles for Intracellular Nanoparticle and Protein Delivery. Biomolecules 2022; 12:biom12020308. [PMID: 35204809 PMCID: PMC8869412 DOI: 10.3390/biom12020308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 11/16/2022] Open
Abstract
Protein-based carriers are promising vehicles for the intracellular delivery of therapeutics. In this study, we designed and studied adenovirus protein fiber constructs with potential applications as carriers for the delivery of protein and nanoparticle cargoes. We used as a basic structural framework the fibrous shaft segment of the adenovirus fiber protein comprising of residues 61–392, connected to the fibritin foldon trimerization motif at the C-terminal end. A fourteen-amino-acid biotinylation sequence was inserted immediately after the N-terminal, His-tagged end of the construct in order to enable the attachment of a biotin moiety in vivo. We report herein that this His-tag biotinylated construct folds into thermally and protease-stable fibrous nanorods that can be internalized into cells and are not cytotoxic. Moreover, they can bind to proteins and nanoparticles through the biotin–streptavidin interaction and mediate their delivery to cells. We demonstrate that streptavidin-conjugated gold nanoparticles can be transported into NIH3T3 fibroblast and HeLa cancer cell lines. Furthermore, two streptavidin-conjugated model proteins, alkaline phosphatase and horseradish peroxidase can be delivered into the cell cytoplasm in their enzymatically active form. This work is aimed at establishing the proof-of-principle for the rational engineering of diverse functionalities onto the initial protein structural framework and the use of adenovirus fiber-based proteins as nanorods for the delivery of nanoparticles and model proteins. These constructs could constitute a stepping stone for the development of multifunctional and modular fibrous nanorod platforms that can be tailored to applications at the sequence level.
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Affiliation(s)
- Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Crete, Greece; (C.K.); (G.N.); (M.V.); (K.P.)
- Institute of Electronic Structure and Laser (IESL), FORTH, 70013 Heraklion, Crete, Greece;
| | - Fani Tsitouroudi
- Institute of Electronic Structure and Laser (IESL), FORTH, 70013 Heraklion, Crete, Greece;
| | - Georgios Nistikakis
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Crete, Greece; (C.K.); (G.N.); (M.V.); (K.P.)
- Institute of Electronic Structure and Laser (IESL), FORTH, 70013 Heraklion, Crete, Greece;
| | - Marita Vasila
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Crete, Greece; (C.K.); (G.N.); (M.V.); (K.P.)
| | - Katerina Papanikolopoulou
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Crete, Greece; (C.K.); (G.N.); (M.V.); (K.P.)
| | - Androniki Kretsovali
- Institute of Molecular Biology and Biotechnology (IMBB), FORTH, 70013 Heraklion, Crete, Greece;
| | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, 70013 Heraklion, Crete, Greece; (C.K.); (G.N.); (M.V.); (K.P.)
- Institute of Electronic Structure and Laser (IESL), FORTH, 70013 Heraklion, Crete, Greece;
- Correspondence:
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20
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Gilodi M, Lisi S, F. Dudás E, Fantini M, Puglisi R, Louka A, Marcatili P, Cattaneo A, Pastore A. Selection and Modelling of a New Single-Domain Intrabody Against TDP-43. Front Mol Biosci 2022; 8:773234. [PMID: 35237655 PMCID: PMC8884700 DOI: 10.3389/fmolb.2021.773234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder associated to deteriorating motor and cognitive functions, and short survival. The disease is caused by neuronal death which results in progressive muscle wasting and weakness, ultimately leading to lethal respiratory failure. The misbehaviour of a specific protein, TDP-43, which aggregates and becomes toxic in ALS patient’s neurons, is supposed to be one of the causes. TDP-43 is a DNA/RNA-binding protein involved in several functions related to nucleic acid metabolism. Sequestration of TDP-43 aggregates is a possible therapeutic strategy that could alleviate or block pathology. Here, we describe the selection and characterization of a new intracellular antibody (intrabody) against TDP-43 from a llama nanobody library. The structure of the selected intrabody was predicted in silico and the model was used to suggest mutations that enabled to improve its expression yield, facilitating its experimental validation. We showed how coupling experimental methodologies with in silico design may allow us to obtain an antibody able to recognize the RNA binding regions of TDP-43. Our findings illustrate a strategy for the mitigation of TDP-43 proteinopathy in ALS and provide a potential new tool for diagnostics.
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Affiliation(s)
- Martina Gilodi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Erika F. Dudás
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Rita Puglisi
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Alexandra Louka
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
| | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
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21
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Caballero AB, Gamez P, Sabate R, Espargaró A. Anti-Amyloid Drug Screening Methods Using Bacterial Inclusion Bodies. Methods Mol Biol 2022; 2538:165-188. [PMID: 35951300 DOI: 10.1007/978-1-0716-2529-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Amyloid aggregation is linked to a number of human disorders that range from non-neurological illnesses such as type 2 diabetes to neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. The formation of insoluble protein aggregates with amyloid conformation inside bacteria, namely, in bacterial inclusion bodies, offers the possibility to use bacteria as simple models to study amyloid aggregation processes and potential effects of both anti-amyloid drugs and/or pro-aggregative compounds. This chapter describes fast, simple, inexpensive, highly reproducible, and tunable in vitro and in cellulo methods that use bacterial inclusion bodies as preliminary screening tools for anti-amyloid drugs.
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Affiliation(s)
- Ana B Caballero
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
| | - Patrick Gamez
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona, Catalonia, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain.
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain.
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22
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Ortega C, Oppezzo P, Correa A. Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production. Methods Mol Biol 2022; 2406:35-64. [PMID: 35089549 DOI: 10.1007/978-1-0716-1859-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Despite the importance of recombinant protein production in the academy and industrial fields, many issues concerning the expression of soluble and homogeneous products are still unsolved. Several strategies were developed to overcome these obstacles; however, at present, there is no magic bullet that can be applied for all cases. Indeed, several key expression parameters need to be evaluated for each protein. Among the different hosts for protein expression, Escherichia coli is by far the most widely used. In this chapter, we review many of the different tools employed to circumvent protein insolubility problems.
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Affiliation(s)
- Claudia Ortega
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pablo Oppezzo
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Agustín Correa
- Recombinant Protein Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
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23
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Abstract
Recombinant protein expression in E. coli often induces the expressed protein to accumulate in insoluble aggregates, named inclusion bodies (IBs), that represent easy to isolate, highly pure protein reservoirs. IBs can be solubilized by denaturing agents but this procedure requires, for complex globular proteins, a refolding step that can be challenging. However, the lack of cooperatively folded tertiary structure in intrinsically disordered proteins (IDP) makes them ideal candidates for this purification strategy. Given the wide abundance of IDPs, their relevance in many disease areas and the numerous IDP-associated biological functions, the interest in this class of proteins has increased substantially over the last decade. Here we present a broad and versatile method for the production and isolation of IDPs from inclusion bodies under denaturant conditions that overcomes the challenges associated with the propensity of these sequences to precipitate from solution and becoming proteolytically degraded.
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Gil-Garcia M, Ventura S. Coiled-Coil Based Inclusion Bodies and Their Potential Applications. Front Bioeng Biotechnol 2021; 9:734068. [PMID: 34485264 PMCID: PMC8415879 DOI: 10.3389/fbioe.2021.734068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 02/01/2023] Open
Abstract
The production of recombinant proteins using microbial cell factories is frequently associated with the formation of inclusion bodies (IBs). These proteinaceous entities can be sometimes a reservoir of stable and active protein, might display good biocompatibility, and are produced efficiently and cost-effectively. Thus, these submicrometric particles are increasingly exploited as functional biomaterials for biotechnological and biomedical purposes. The fusion of aggregation-prone sequences to the target protein is a successful strategy to sequester soluble recombinant polypeptides into IBs. Traditionally, the use of these IB-tags results in the formation of amyloid-like scaffolds where the protein of interest is trapped. This amyloid conformation might compromise the protein's activity and be potentially cytotoxic. One promising alternative to overcome these limitations exploits the coiled-coil fold, composed of two or more α-helices and widely used by nature to create supramolecular assemblies. In this review, we summarize the state-of-the-art of functional IBs technology, focusing on the coiled-coil-assembly strategy, describing its advantages and applications, delving into future developments and necessary improvements in the field.
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Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Gil-Garcia M, Ventura S. Multifunctional antibody-conjugated coiled-coil protein nanoparticles for selective cell targeting. Acta Biomater 2021; 131:472-482. [PMID: 34192568 DOI: 10.1016/j.actbio.2021.06.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 12/22/2022]
Abstract
Nanostructures decorated with antibodies (Abs) are applied in bioimaging and therapeutics. However, most covalent conjugation strategies affect Abs functionality. In this study, we aimed to create protein-based nanoparticles to which intact Abs can be attached through tight, specific, and noncovalent interactions. Initially considered waste products, bacterial inclusion bodies (IBs) have been used in biotechnology and biomedicine. However, the amyloid-like nature of IBs limits their functionality and raises safety concerns. To bypass these obstacles, we have recently developed highly functional α-helix-rich IBs exploiting the natural self-assembly capacity of coiled-coil domains. We used this approach to create spherical, submicrometric, biocompatible and fluorescent protein nanoparticles capable of capturing Abs with high affinity. We showed that these IBs can be exploited for Ab-directed cell targeting. Simultaneous decoration of the nanoparticles with two different Abs in a controllable ratio enabled the construction of a bispecific antibody mimic that redirected T lymphocytes specifically to cancer cells. Overall, we describe an easy and cost-effective strategy to produce multivalent, traceable protein nanostructures with the potential to be used for biomedical applications. STATEMENT OF SIGNIFICANCE: Functional inclusion bodies (IBs) are promising platforms for biomedical and biotechnological applications. These nanoparticles are usually sustained by amyloid-like interactions, which imposes some limitations on their use. In this work, we exploit the natural coiled-coil self-assembly properties to create highly functional, nonamyloid, and fluorescent IBs capable of capturing antibodies. These protein-based nanoparticles are successfully used to specifically and simultaneously target two unrelated cell types and bring them close together, becoming a technology with potential application in bioimaging and immunotherapy.
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Kamel S, Walczak MC, Kaspar F, Westarp S, Neubauer P, Kurreck A. Thermostable adenosine 5'-monophosphate phosphorylase from Thermococcus kodakarensis forms catalytically active inclusion bodies. Sci Rep 2021; 11:16880. [PMID: 34413335 PMCID: PMC8376864 DOI: 10.1038/s41598-021-96073-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Catalytically active inclusion bodies (CatIBs) produced in Escherichia coli are an interesting but currently underexplored strategy for enzyme immobilization. They can be purified easily and used directly as stable and reusable heterogenous catalysts. However, very few examples of CatIBs that are naturally formed during heterologous expression have been reported so far. Previous studies have revealed that the adenosine 5′-monophosphate phosphorylase of Thermococcus kodakarensis (TkAMPpase) forms large soluble multimers with high thermal stability. Herein, we show that heat treatment of soluble protein from crude extract induces aggregation of active protein which phosphorolyse all natural 5′-mononucleotides. Additionally, inclusion bodies formed during the expression in E. coli were found to be similarly active with 2–6 folds higher specific activity compared to these heat-induced aggregates. Interestingly, differences in the substrate preference were observed. These results show that the recombinant thermostable TkAMPpase is one of rare examples of naturally formed CatIBs.
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Affiliation(s)
- Sarah Kamel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Miriam C Walczak
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Felix Kaspar
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Sarah Westarp
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany. .,BioNukleo GmbH, Ackerstraße 76, 13355, Berlin, Germany.
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27
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The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure. Biomolecules 2021; 11:biom11081083. [PMID: 34439750 PMCID: PMC8392785 DOI: 10.3390/biom11081083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/30/2022] Open
Abstract
The complex topologies of large multi-domain globular proteins make the study of their folding and assembly particularly demanding. It is often characterized by complex kinetics and undesired side reactions, such as aggregation. The structural simplicity of tandem-repeat proteins, which are characterized by the repetition of a basic structural motif and are stabilized exclusively by sequentially localized contacts, has provided opportunities for dissecting their folding landscapes. In this study, we focus on the Erwinia chrysanthemi pectin methylesterase (342 residues), an all-β pectinolytic enzyme with a right-handed parallel β-helix structure. Chemicals and pressure were chosen as denaturants and a variety of optical techniques were used in conjunction with stopped-flow equipment to investigate the folding mechanism of the enzyme at 25 °C. Under equilibrium conditions, both chemical- and pressure-induced unfolding show two-state transitions, with average conformational stability (ΔG° = 35 ± 5 kJ·mol−1) but exceptionally high resistance to pressure (Pm = 800 ± 7 MPa). Stopped-flow kinetic experiments revealed a very rapid (τ < 1 ms) hydrophobic collapse accompanied by the formation of an extended secondary structure but did not reveal stable tertiary contacts. This is followed by three distinct cooperative phases and the significant population of two intermediate species. The kinetics followed by intrinsic fluorescence shows a lag phase, strongly indicating that these intermediates are productive species on a sequential folding pathway, for which we propose a plausible model. These combined data demonstrate that even a large repeat protein can fold in a highly cooperative manner.
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28
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Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
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Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
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29
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Singhvi P, Verma J, Panwar N, Wani TQ, Singh A, Qudratullah M, Chakraborty A, Saneja A, Sarkar DP, Panda AK. Molecular Attributes Associated With Refolding of Inclusion Body Proteins Using the Freeze-Thaw Method. Front Microbiol 2021; 12:618559. [PMID: 33959102 PMCID: PMC8093829 DOI: 10.3389/fmicb.2021.618559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/10/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the structure-function of inclusion bodies (IBs) in the last two decades has led to the development of several mild solubilization buffers for the improved recovery of bioactive proteins. The recently developed freeze-thaw-based inclusion body protein solubilization method has received a great deal of attention due to its simplicity and cost-effectiveness. The present report investigates the reproducibility, efficiency, and plausible mechanism of the freeze-thaw-based IB solubilization. The percentage recovery of functionally active protein species of human growth hormone (hGH) and L-asparaginase from their IBs in Escherichia coli and the quality attributes associated with the freeze-thaw-based solubilization method were analyzed in detail. The overall yield of the purified hGH and L-asparaginase protein was found to be around 14 and 25%, respectively. Both purified proteins had functionally active species lower than that observed with commercial proteins. Biophysical and biochemical analyses revealed that the formation of soluble aggregates was a major limitation in the case of tough IB protein like hGH. On the other hand, the destabilization of soft IB protein like L-asparaginase led to the poor recovery of functionally active protein species. Our study provides insight into the advantages, disadvantages, and molecular-structural information associated with the freeze-thaw-based solubilization method.
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Affiliation(s)
- Priyank Singhvi
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Juhi Verma
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Neha Panwar
- Product Development Cell, National Institute of Immunology, New Delhi, India.,Department of Biochemistry, University of Delhi, New Delhi, India
| | - Tabiya Qayoom Wani
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Akansha Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Md Qudratullah
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Arnab Chakraborty
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Ankit Saneja
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Debi P Sarkar
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology, New Delhi, India
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30
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Movahedpour A, Ahmadi N, Ghalamfarsa F, Ghesmati Z, Khalifeh M, Maleksabet A, Shabaninejad Z, Taheri-Anganeh M, Savardashtaki A. β-Galactosidase: From its source and applications to its recombinant form. Biotechnol Appl Biochem 2021; 69:612-628. [PMID: 33656174 DOI: 10.1002/bab.2137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of β-glycosidases found in higher plants, animals, and microorganisms. β-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. β-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. β-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of β-galactosidase for improving the production process are discussed. Since β-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.
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Affiliation(s)
- Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Ahmadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farideh Ghalamfarsa
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Ghesmati
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoomeh Khalifeh
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Shahid Arefian Hospital, Urmia, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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31
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Optimizing the Production of Recombinant Hydroperoxide Lyase in Escherichia coli Using Statistical Design. Catalysts 2021. [DOI: 10.3390/catal11020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Hydroperoxide lyase (HPL) catalyzes the synthesis of volatiles C6 or C9 aldehydes from fatty acid hydroperoxides. These short carbon chain aldehydes, known as green leaf volatiles (GLV), are widely used in cosmetic industries and as food additives because of their “fresh green” aroma. To meet the growing demand for natural GLVs, the use of recombinant HPL as a biocatalyst in enzyme-catalyzed processes appears to be an interesting application. Previously, we cloned and expressed a 13-HPL from olive fruit in Escherichia coli and showed high conversion rates (up to 94%) during the synthesis of C6 aldehydes. To consider a scale-up of this process, optimization of the recombinant enzyme production is necessary. In this study, four host-vector combinations were tested. Experimental design and response surface methodology (RSM) were used to optimize the expression conditions. Three factors were considered, i.e., temperature, inducer concentration and induction duration. The Box–Behnken design consisted of 45 assays for each expression system performed in deep-well microplates. The regression models were built and fitted well to the experimental data (R2 coefficient > 97%). The best response (production level of the soluble enzyme) was obtained with E. coli BL21 DE3 cells. Using the optimal conditions, 2277 U L−1of culture of the soluble enzyme was produced in microliter plates and 21,920 U L−1of culture in an Erlenmeyer flask, which represents a 79-fold increase compared to the production levels previously reported.
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32
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Urea titration of a lipase from Pseudomonas sp. reveals four different conformational states, with a stable partially folded state explaining its high aggregation propensity. Int J Biol Macromol 2021; 174:32-41. [PMID: 33508357 DOI: 10.1016/j.ijbiomac.2021.01.153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
The conversion of soluble proteins into amyloid fibrils has importance in protein chemistry, biology, biotechnology and medicine. A novel lipase from Pseudomonas sp. was previously shown to have an extremely high aggregation propensity. It was therefore herein studied to elucidate the physicochemical and structural determinants of this extreme behaviour. Amyloid-like structures were found to form in samples up to 2.5-3.0 M using Thioflavin T fluorescence and Congo red binding assays. However, dynamic light scattering (DLS), static light scattering and turbidimetry revealed the existence of aggregates up to 4.0 M urea, without amyloid-like structure. Two monomeric conformational states were detected with intrinsic fluorescence, 8-anilinonaphthalene-1-sulfonate (ANS) binding and circular dichroism. These were further characterized in 7.5 M and 4.5 M urea using enzymatic activity measurements, tryptophan fluorescence quenching, DLS and nuclear magnetic resonance (NMR) and were found to consist of a largely disordered and a partially folded state, respectively, with the latter appearing stable, cooperative, fairly compact, non-active, α-helical, with largely buried hydrophobic residues. The persistence of a stable structure up to high concentrations of urea, in the absence of sequence characteristics typical of a high intrinsic aggregation propensity, explains the high tendency of this enzyme to form amyloid-like structures.
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33
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Lim KYL, Mullally CA, Haese EC, Kibble EA, McCluskey NR, Mikucki EC, Thai VC, Stubbs KA, Sarkar-Tyson M, Kahler CM. Anti-Virulence Therapeutic Approaches for Neisseria gonorrhoeae. Antibiotics (Basel) 2021; 10:antibiotics10020103. [PMID: 33494538 PMCID: PMC7911339 DOI: 10.3390/antibiotics10020103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/15/2023] Open
Abstract
While antimicrobial resistance (AMR) is seen in both Neisseria gonorrhoeae and Neisseria meningitidis, the former has become resistant to commonly available over-the-counter antibiotic treatments. It is imperative then to develop new therapies that combat current AMR isolates whilst also circumventing the pathways leading to the development of AMR. This review highlights the growing research interest in developing anti-virulence therapies (AVTs) which are directed towards inhibiting virulence factors to prevent infection. By targeting virulence factors that are not essential for gonococcal survival, it is hypothesized that this will impart a smaller selective pressure for the emergence of resistance in the pathogen and in the microbiome, thus avoiding AMR development to the anti-infective. This review summates the current basis of numerous anti-virulence strategies being explored for N. gonorrhoeae.
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Affiliation(s)
- Katherine Y. L. Lim
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Christopher A. Mullally
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Ethan C. Haese
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Emily A. Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Nicolie R. McCluskey
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Edward C. Mikucki
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Van C. Thai
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, WA 6009, Australia;
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
| | - Charlene M. Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA 6009, Australia; (K.Y.L.L.); (C.A.M.); (E.C.H.); (E.A.K.); (N.R.M.); (E.C.M.); (V.C.T.); (M.S.-T.)
- Correspondence:
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Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s. Biochem J 2020; 477:2055-2069. [PMID: 32441748 DOI: 10.1042/bcj20200297] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Abstract
Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.
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35
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Gupta V, Sudhakaran IP, Islam Z, Vaikath NN, Hmila I, Lukacsovich T, Kolatkar PR, El-Agnaf OMA. Expression, purification and characterization of α-synuclein fibrillar specific scFv from inclusion bodies. PLoS One 2020; 15:e0241773. [PMID: 33156828 PMCID: PMC7647061 DOI: 10.1371/journal.pone.0241773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/20/2020] [Indexed: 12/31/2022] Open
Abstract
Aggregation of α-synuclein (α-syn) has been implicated in multiple neurodegenerative disorders including Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA), collectively grouped as synucleinopathies. Recently, recombinant antibody fragments (Fab, scFvs and diabodies) against α-syn have emerged as an alternative to the traditional full-length antibody in immunotherapeutic approaches owing to their advantages including smaller size and higher stability, specificity and affinity. However, most of the recombinant antibody fragments tend to be expressed as inclusion bodies (IBs) making its purification extremely challenging. In the current study, a single-chain variable fragment (scFv-F) antibody, targeting the pathogenic α-syn fibrils, was engineered and expressed in E. coli. Majority of the expressed scFv-F accumulated in insoluble aggregates as IBs. A variety of mild and harsh solubilizing conditions were tested to solubilize IBs containing scFv-F to obtain the active protein. To preserve secondary structure and bioactivity, a mild solubilizing protocol involving 100 mM Tris, pH 12.5 with 2 M urea was chosen to dissolve IBs. Slow on-column refolding method was employed to subsequently remove urea and obtain active scFv-F. A three-dimensional (3D) model was built using homology modeling and subjected to molecular docking with the known α-syn structure. Structural alignment was performed to delineate the potential binding pocket. The scFv-F thus purified demonstrated high specificity towards α-syn fibrils compared to monomers. Molecular modeling studies suggest that scFv-F shares the same structural topology with other known scFvs. We present evidence through structural docking and alignment that scFv-F binds to α-syn C-terminal region. In conclusion, mild solubilization followed by slow on-column refolding can be utilized as a generalized and efficient method for hard to purify disease relevant insoluble proteins and/or antibody molecules from IBs.
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Affiliation(s)
- Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Indulekha P. Sudhakaran
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Nishant N. Vaikath
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Issam Hmila
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | | | - Prasanna R. Kolatkar
- Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Omar M. A. El-Agnaf
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- * E-mail:
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36
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Umair S, Bouchet C, Palevich N, Simpson HV. Characterisation and structural analysis of glyoxylate cycle enzymes of Teladorsagia circumcincta. Mol Biochem Parasitol 2020; 240:111335. [PMID: 33058935 DOI: 10.1016/j.molbiopara.2020.111335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/22/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022]
Abstract
A 1332 bp full length cDNA encoding Teladorsagia circumcincta isocitrate lyase (TciICL) and a 1575 bp full length cDNA encoding T. circumcincta malate synthase (TciMS) were cloned, expressed in Escherichia coli and the recombinant proteins purified. The predicted TciICL protein of 444 amino acids was present as a single band of about 52 kDa on SDS-PAGE and the recombinant TciMS of 525 amino acids formed a single band about 62 kDa. Multiple alignments of the combined bifunctional TciICL-MS protein sequence with homologues from other nematodes showed that the greatest similarity (89-92 %) to the homologues of Ancylostoma ceylanicum, Haemonchus contortus and Haemonchus placei and 71-87 % similarity to the other nematode sequences. The 3-dimensional structures, binding and catalytic sites were determined for TciICL and TciMS and shown to be highly conserved. Substrate and metal ion binding sites were identified and were completely conserved in other homologues. TciICL was confirmed as a functional enzyme. At 30 °C, the optimum pH was pH 7.5, the Vmax was 275 ± 23 nmoles.min-1. mg-1 protein and the apparent Km for the substrate isocitrate was 0.7 ± 0.01μM (mean ± SEM, n = 3). Addition of 10 mM metal ions (except Mg2+) or 1 mM inhibitors reduced the recombinant TciICL activity by 60-90 %. Antibodies in both serum and saliva from field-immune, but not nematode-naïve, sheep recognised recombinant TciICL in ELISA, supporting similar antigenicity to that of the native enzyme.
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Affiliation(s)
- Saleh Umair
- AgResearch Ltd, Private Bag 11-008, Palmerston North, New Zealand.
| | | | - Nikola Palevich
- AgResearch Ltd, Private Bag 11-008, Palmerston North, New Zealand
| | - Heather V Simpson
- School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Roca-Pinilla R, Fortuna S, Natalello A, Sánchez-Chardi A, Ami D, Arís A, Garcia-Fruitós E. Exploring the use of leucine zippers for the generation of a new class of inclusion bodies for pharma and biotechnological applications. Microb Cell Fact 2020; 19:175. [PMID: 32887587 PMCID: PMC7650227 DOI: 10.1186/s12934-020-01425-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/11/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Inclusion bodies (IBs) are biologically active protein aggregates forming natural nanoparticles with a high stability and a slow-release behavior. Because of their nature, IBs have been explored to be used as biocatalysts, in tissue engineering, and also for human and animal therapies. To improve the production and biological efficiency of this nanomaterial, a wide range of aggregation tags have been evaluated. However, so far, the presence in the IBs of bacterial impurities such as lipids and other proteins coexisting with the recombinant product has been poorly studied. These impurities could strongly limit the potential of IB applications, being necessary to control the composition of these bacterial nanoparticles. Thus, we have explored the use of leucine zippers as alternative tags to promote not only aggregation but also the generation of a new type of IB-like protein nanoparticles with improved physicochemical properties. RESULTS Three different protein constructs, named GFP, J-GFP-F and J/F-GFP were engineered. J-GFP-F corresponded to a GFP flanked by two leucine zippers (Jun and Fos); J/F-GFP was formed coexpressing a GFP fused to Jun leucine zipper (J-GFP) and a GFP fused to a Fos leucine zipper (F-GFP); and, finally, GFP was used as a control without any tag. All of them were expressed in Escherichia coli and formed IBs, where the aggregation tendency was especially high for J/F-GFP. Moreover, those IBs formed by J-GFP-F and J/F-GFP constructs were smaller, rougher, and more amorphous than GFP ones, increasing surface/mass ratio and, therefore, surface for protein release. Although the lipid and carbohydrate content were not reduced with the addition of leucine zippers, interesting differences were observed in the protein specific activity and conformation with the addition of Jun and Fos. Moreover, J-GFP-F and J/F-GFP nanoparticles were purer than GFP IBs in terms of protein content. CONCLUSIONS This study proved that the use of leucine zippers strategy allows the formation of IBs with an increased aggregation ratio and protein purity, as we observed with the J/F-GFP approach, and the formation of IBs with a higher specific activity, in the case of J-GFP-F IBs. Thus, overall, the use of leucine zippers seems to be a good system for the production of IBs with more promising characteristics useful for pharma or biotech applications.
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Affiliation(s)
- Ramon Roca-Pinilla
- Department of Ruminant Production, Institute of Agriculture and Food Research and Technology (IRTA), 08140, Caldes de Montbui, Spain
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | - Alejandro Sánchez-Chardi
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona (UB), 08028, Barcelona, Spain
- Microscopy Service, Autonomous University of Barcelona (UAB), 08193, Cerdanyola del Vallès, Spain
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | - Anna Arís
- Department of Ruminant Production, Institute of Agriculture and Food Research and Technology (IRTA), 08140, Caldes de Montbui, Spain.
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institute of Agriculture and Food Research and Technology (IRTA), 08140, Caldes de Montbui, Spain.
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Jäger VD, Lamm R, Küsters K, Ölçücü G, Oldiges M, Jaeger KE, Büchs J, Krauss U. Catalytically-active inclusion bodies for biotechnology-general concepts, optimization, and application. Appl Microbiol Biotechnol 2020; 104:7313-7329. [PMID: 32651598 PMCID: PMC7413871 DOI: 10.1007/s00253-020-10760-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022]
Abstract
Bacterial inclusion bodies (IBs) have long been considered as inactive, unfolded waste material produced by heterologous overexpression of recombinant genes. In industrial applications, they are occasionally used as an alternative in cases where a protein cannot be expressed in soluble form and in high enough amounts. Then, however, refolding approaches are needed to transform inactive IBs into active soluble protein. While anecdotal reports about IBs themselves showing catalytic functionality/activity (CatIB) are found throughout literature, only recently, the use of protein engineering methods has facilitated the on-demand production of CatIBs. CatIB formation is induced usually by fusing short peptide tags or aggregation-inducing protein domains to a target protein. The resulting proteinaceous particles formed by heterologous expression of the respective genes can be regarded as a biologically produced bionanomaterial or, if enzymes are used as target protein, carrier-free enzyme immobilizates. In the present contribution, we review general concepts important for CatIB production, processing, and application. KEY POINTS: • Catalytically active inclusion bodies (CatIBs) are promising bionanomaterials. • Potential applications in biocatalysis, synthetic chemistry, and biotechnology. • CatIB formation represents a generic approach for enzyme immobilization. • CatIB formation efficiency depends on construct design and expression conditions.
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Affiliation(s)
- Vera D Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, Espoo, 02150, Finland
| | - Robin Lamm
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Kira Küsters
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Gizem Ölçücü
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Marco Oldiges
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Institute of Biotechnology, RWTH Aachen University, 52074, Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jochen Büchs
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Aachen, 52074, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
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Cardoso VM, Campani G, Santos MP, Silva GG, Pires MC, Gonçalves VM, de C. Giordano R, Sargo CR, Horta AC, Zangirolami TC. Cost analysis based on bioreactor cultivation conditions: Production of a soluble recombinant protein using Escherichia coli BL21(DE3). BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00441. [PMID: 32140446 PMCID: PMC7049567 DOI: 10.1016/j.btre.2020.e00441] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/06/2020] [Accepted: 02/21/2020] [Indexed: 12/20/2022]
Abstract
The impact of cultivation strategy on the cost of recombinant protein production is crucial for defining cost-effective bioreactor operation conditions. This paper presents a methodology to estimate and compare cost impacts related to utilities as well as medium composition, using simple design equations and accessible data. Data from batch bioreactor cultures were used as case study involving the production of pneumococcal surface protein A, a soluble recombinant protein, employing E. coli BL21(DE3). Cultivation strategies and corresponding process costs covered a wide range of operational conditions, including different media, inducers, and temperatures. The core expenses were related to the medium and cooling. When the price of peptone was above the threshold value of US$ 30/kg, defined medium became the best choice. IPTG and temperatures around 32 °C led to shorter cultures and lower PspA4Pro production costs. The procedure offers a simple, accessible theoretical tool to identify cost-effective production strategies using bioreactors.
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Affiliation(s)
- Valdemir M. Cardoso
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Gilson Campani
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
- Department of Engineering, Federal University of Lavras, 37200-000, Lavras, MG, Brazil
| | - Maurício P. Santos
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Gabriel G. Silva
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Manuella C. Pires
- Laboratory of Vaccine Development, Butantan Institute, Av. Vital Brasil 1500, 05508-900, São Paulo, SP, Brazil
| | - Viviane M. Gonçalves
- Laboratory of Vaccine Development, Butantan Institute, Av. Vital Brasil 1500, 05508-900, São Paulo, SP, Brazil
| | - Roberto de C. Giordano
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Cíntia R. Sargo
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, SP, Brazil
| | - Antônio C.L. Horta
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
| | - Teresa C. Zangirolami
- Graduate Program of Chemical Engineering (PPGEQ), Federal University of São Carlos (UFSCar), Rodovia Washington Luís, km 235, 13565-905, São Carlos, SP, Brazil
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Gil-Garcia M, Navarro S, Ventura S. Coiled-coil inspired functional inclusion bodies. Microb Cell Fact 2020; 19:117. [PMID: 32487230 PMCID: PMC7268670 DOI: 10.1186/s12934-020-01375-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recombinant protein expression in bacteria often leads to the formation of intracellular insoluble protein deposits, a major bottleneck for the production of soluble and active products. However, in recent years, these bacterial protein aggregates, commonly known as inclusion bodies (IBs), have been shown to be a source of stable and active protein for biotechnological and biomedical applications. The formation of these functional IBs is usually facilitated by the fusion of aggregation-prone peptides or proteins to the protein of interest, leading to the formation of amyloid-like nanostructures, where the functional protein is embedded. RESULTS In order to offer an alternative to the classical amyloid-like IBs, here we develop functional IBs exploiting the coiled-coil fold. An in silico analysis of coiled-coil and aggregation propensities, net charge, and hydropathicity of different potential tags identified the natural homo-dimeric and anti-parallel coiled-coil ZapB bacterial protein as an optimal candidate to form assemblies in which the native state of the fused protein is preserved. The protein itself forms supramolecular fibrillar networks exhibiting only α-helix secondary structure. This non-amyloid self-assembly propensity allows generating innocuous IBs in which the recombinant protein of interest remains folded and functional, as demonstrated using two different fluorescent proteins. CONCLUSIONS Here, we present a proof of concept for the use of a natural coiled-coil domain as a versatile tool for the production of functional IBs in bacteria. This α-helix-based strategy excludes any potential toxicity drawback that might arise from the amyloid nature of β-sheet-based IBs and renders highly active and homogeneous submicrometric particles.
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Affiliation(s)
- Marcos Gil-Garcia
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Schwaighofer A, Ablasser S, Lux L, Kopp J, Herwig C, Spadiut O, Lendl B, Slouka C. Production of Active Recombinant Hyaluronidase Inclusion Bodies from Apis mellifera in E. coli Bl21(DE3) and characterization by FT-IR Spectroscopy. Int J Mol Sci 2020; 21:E3881. [PMID: 32485932 PMCID: PMC7313074 DOI: 10.3390/ijms21113881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
The bacterium E. coli is one of the most important hosts for recombinant protein production. The benefits are high growth rates, inexpensive media, and high protein titers. However, complex proteins with high molecular weight and many disulfide bonds are expressed as inclusion bodies (IBs). In the last decade, the overall perception of these IBs being not functional proteins changed, as enzyme activity was found within IBs. Several applications for direct use of IBs are already reported in literature. While fluorescent proteins or protein tags are used for determination of IB activity to date, direct measurements of IB protein activity are scacre. The expression of recombinant hyaluronidase from Apis mellifera in E. coli BL21(DE3) was analyzed using a face centered design of experiment approach. Hyaluronidase is a hard to express protein and imposes a high metabolic burden to the host. Conditions giving a high specific IB titer were found at 25 °C at low specific substrate uptake rates and induction times of 2 to 4 h. The protein activity of hyaluronidase IBs was verified using (Fourier transform) FT-IR spectroscopy. Degradation of the substrate hyaluronan occurred at increased rates with higher IB concentrations. Active recombinant hyaluronidase IBs can be immediately used for direct degradation of hyaluronan without further down streaming steps. FT-IR spectroscopy was introduced as a method for tracking IB activity and showed differences in degradation behavior of hyaluronan dependent on the applied active IB concentration.
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Affiliation(s)
- Andreas Schwaighofer
- FG Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technology and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Wien, Austria; (A.S.); (L.L.); (B.L.)
| | - Sarah Ablasser
- FG Bioprocess Technology, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (S.A.); (J.K.); (C.H.)
| | - Laurin Lux
- FG Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technology and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Wien, Austria; (A.S.); (L.L.); (B.L.)
| | - Julian Kopp
- FG Bioprocess Technology, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (S.A.); (J.K.); (C.H.)
| | - Christoph Herwig
- FG Bioprocess Technology, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (S.A.); (J.K.); (C.H.)
| | - Oliver Spadiut
- FG Integrated Bioprocess Development, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria;
| | - Bernhard Lendl
- FG Environmental Analytics, Process Analytics and Sensors, Institute of Chemical Technology and Analytics, Vienna University of Technology, Getreidemarkt 9/164, 1060 Wien, Austria; (A.S.); (L.L.); (B.L.)
| | - Christoph Slouka
- FG Integrated Bioprocess Development, ICEBE, Vienna University of Technology, Gumpendorferstrasse 1a, 1060 Vienna, Austria;
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Lon Protease Is Important for Growth Under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani. Int J Mol Sci 2020; 21:ijms21103687. [PMID: 32456249 PMCID: PMC7279449 DOI: 10.3390/ijms21103687] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 01/08/2023] Open
Abstract
The Lon protein is a protease implicated in the virulence of many pathogenic bacteria, including some plant pathogens. However, little is known about the role of Lon in bacteria from genus Dickeya. This group of bacteria includes important potato pathogens, with the most aggressive species, D. solani. To determine the importance of Lon for pathogenicity and response to stress conditions of bacteria, we constructed a D. solani Δlon strain. The mutant bacteria showed increased sensitivity to certain stress conditions, in particular osmotic and high-temperature stresses. Furthermore, qPCR analysis showed an increased expression of the lon gene in D. solani under these conditions. The deletion of the lon gene resulted in decreased motility, lower activity of secreted pectinolytic enzymes and finally delayed onset of blackleg symptoms in the potato plants. In the Δlon cells, the altered levels of several proteins, including virulence factors and proteins associated with virulence, were detected by means of Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) analysis. These included components of the type III secretion system and proteins involved in bacterial motility. Our results indicate that Lon protease is important for D. solani to withstand stressful conditions and effectively invade the potato plant.
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Zhao Y, Xu B, Zhu B, Liu X, Yan D, Zhang Q. B subunit of cholera toxin fused with VP7 from GCRV (grass carp reovirus) was expressed in E. coli and folds into an active protein. Int J Biol Macromol 2020; 151:814-820. [PMID: 32097736 DOI: 10.1016/j.ijbiomac.2020.02.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 10/24/2022]
Abstract
Grass carp reovirus (GCRV) is one of the most serious pathogens threatening grass carp (Ctenopharyngodon idella) production and results in high mortality in China. To obtain a genetically engineered oral vaccine against GCRV, the cholera toxin B subunit (CTB) of Vibrio cholerae was fused to VP7 (CTB-VP7) and transformed into BL21(DE3) for expression. SDS-PAGE and Western blotting showed that the purified rCTB-VP7 fusion protein (rCTB-VP7) was approximately 49.0 kDa. The monomeric nature of rCTB-VP7 through multistage purification showed a binding affinity for GM1, a receptor for biologically active CTB. rCTB-VP7 is not vulnerable to disassembly by SDS but is vulnerable to disassembly by 2-mercaptoethanol. rCTB-VP7 is stable and highly active at room temperature. The binding affinity experiment between rCTB-VP7 and GM1 also confirms the effects of acid and alkalinity in solution on the structure of rCTB-VP7. rCTB-VP7 bound to GM1 with different affinities under different temperatures and pH values. Prokaryotic expression of rCTB-VP7 was characterized by high expression and easy purification and had a strong binding force with GM1 at 37 °C and pH 7.4. Our results suggest that rCTB-VP7 has the potential as an oral vaccine for protection against GCRV in aquaculture.
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Affiliation(s)
- Yan Zhao
- School of Agriculture, Ludong University, Middle Hongqi Road No.186, Yantai 264025, PR China
| | - Binglian Xu
- School of Mathematics and Statistics, Ludong University, Middle Hongqi Road No.186, Yantai 264025, PR China
| | - Borun Zhu
- School of Agriculture, Ludong University, Middle Hongqi Road No.186, Yantai 264025, PR China
| | - Xue Liu
- School of Agriculture, Ludong University, Middle Hongqi Road No.186, Yantai 264025, PR China
| | - Dongchun Yan
- School of Agriculture, Ludong University, Middle Hongqi Road No.186, Yantai 264025, PR China
| | - Qiusheng Zhang
- School of Agriculture, Ludong University, Middle Hongqi Road No.186, Yantai 264025, PR China.
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Singh A, Upadhyay V, Singh A, Panda AK. Structure-Function Relationship of Inclusion Bodies of a Multimeric Protein. Front Microbiol 2020; 11:876. [PMID: 32457730 PMCID: PMC7225587 DOI: 10.3389/fmicb.2020.00876] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022] Open
Abstract
High level expression of recombinant proteins in bacteria often results in their aggregation into inclusion bodies. Formation of inclusion bodies poses a major bottleneck in high-throughput recovery of recombinant protein. These aggregates have amyloid-like nature and can retain biological activity. Here, effect of expression temperature on the quality of Escherichia coli asparaginase II (a tetrameric protein) inclusion bodies was evaluated. Asparaginase was expressed as inclusion bodies at different temperatures. Purified inclusion bodies were checked for biological activities and analyzed for structural properties in order to establish a structure-activity relationship. Presence of activity in inclusion bodies showed the existence of properly folded asparaginase tetramers. Expression temperature affected the properties of asparaginase inclusion bodies. Inclusion bodies expressed at higher temperatures were characterized by higher biological activity and less amyloid content as evident by Thioflavin T binding and Fourier Transform Infrared (FTIR) spectroscopy. Complex kinetics of proteinase K digestion of asparaginase inclusion bodies expressed at higher temperatures indicate higher extent of conformational heterogeneity in these aggregates.
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Affiliation(s)
- Anupam Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Vaibhav Upadhyay
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Akansha Singh
- Product Development Cell, National Institute of Immunology, New Delhi, India
| | - Amulya K Panda
- Product Development Cell, National Institute of Immunology, New Delhi, India
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Chu LL, Montecillo JAV, Bae H. Recent Advances in the Metabolic Engineering of Yeasts for Ginsenoside Biosynthesis. Front Bioeng Biotechnol 2020; 8:139. [PMID: 32158753 PMCID: PMC7052115 DOI: 10.3389/fbioe.2020.00139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/03/2023] Open
Abstract
Ginsenosides are a group of glycosylated triterpenes isolated from Panax species. Ginsenosides are promising candidates for the prevention and treatment of cancer as well as food additives. However, owing to a lack of efficient approaches for ginsenoside production from plants and chemical synthesis, ginsenosides may not yet have reached their full potential as medicinal resources. In recent years, an alternative approach for ginsenoside production has been developed using the model yeast Saccharomyces cerevisiae and non-conventional yeasts such as Yarrowia lipolytica and Pichia pastoris. In this review, various metabolic engineering strategies, including heterologous gene expression, balancing, and increasing metabolic flux, and enzyme engineering, have been described as recent advanced engineering techniques for improving ginsenoside production. Furthermore, the usefulness of a systems approach and fermentation strategy has been presented. Finally, the present challenges and future research direction for industrial cell factories have been discussed.
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Affiliation(s)
- Luan Luong Chu
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
| | | | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
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Nekoufar S, Fazeli A, Fazeli MR. Solubilization of Human Interferon β-1b Inclusion Body Proteins by Organic Solvents. Adv Pharm Bull 2020; 10:233-238. [PMID: 32373491 PMCID: PMC7191233 DOI: 10.34172/apb.2020.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/07/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022] Open
Abstract
Purposes: Solubilization of inclusion bodies expressed in E. coli is a critical step during manufacturing of recombinant proteins expressed as inclusion bodies. So far, various methods have been used for solubilization and purification of inclusion body proteins to obtain active proteins with high purity and yield. The aim of this study was to examine the benefit of organic solvents such as alcohols in solubilization of recombinant interferon β-1b inclusion bodies.
Methods: Effect of important parameters inclusion pH, concentration and type of denaturant and concentration of alcoholic solvents were optimized to formulate a suitable solubilization buffer and investigate their effect on solubilization of interferon β-1b inclusion bodies.
Results: Our findings showed the acidic pH in the range of 2-3 is more suitable than alkaline pH >12 for solubilization and achieving higher content of interferon β-1beta and pure recombinant protein. We have also demonstrated that 1% SDS acts better than 2M urea to solubilize Inclusion body proteins of interferon β-1b at pH of 2-3. The interferon concentration was 2.35 mg per 100 mg IB when we used 40% (v/v) 1-propanol and 20% (v/v) 2-butanol into the buffer solution as well.
Conclusion: The optimized method provides gentile condition for solubilization of inclusion body at high protein concentration and purity with a degree of retention of native secondary structure which makes this method valuable to be used in production and research area.
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Affiliation(s)
- Samira Nekoufar
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Fazeli
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mohammad Reza Fazeli
- Department of Drug & Food Control, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
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Gardner QA, Hassan N, Hafeez S, Arif M, Akhtar M. Exploring the nature of inclusion bodies by MALDI mass spectrometry using recombinant proinsulin as a model protein. Int J Biol Macromol 2019; 139:647-653. [PMID: 31356950 DOI: 10.1016/j.ijbiomac.2019.07.131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/02/2019] [Accepted: 07/22/2019] [Indexed: 12/30/2022]
Abstract
The present study deals with mass spectrometric investigation to characterize the nature of proinsulin in inclusion bodies. Various derivatives of human proinsulin were cloned, expressed in E. coli and inclusion bodies prepared under weak acidic conditions (pH 6.5), which protected the native thiols. Non-reductive PAGE showed that proinsulin migrated as monomer (approximately 10 kDa). MALDI-MS protocol was developed for the direct analysis of proinsulin derivatives in inclusion bodies. It was found that the masses of the derivatives corresponded to polypeptides containing six cysteines in reduced form. Iodoacetamide or iodoacetic acid treatment of proinsulin inclusion bodies, in suspension under non-reducing conditions and without any chaotropic agents, showed six alkylations, suggesting that these cytoplasmic aggregates were assembled from reduced monomers, with their -SH groups pointing towards hydrophilic surface. The MALDI analysis of inclusion bodies was extended to a proinsulin derivatives labelled with 13C and 15N giving an excellent agreement between experimental and theoretical masses. These mass spectrometric studies also provide early information about post-translational modification as evident in one of the derivatives MTRR-pi showing N-terminal cleavage of methionine. This shows the potential value of the protocol for the accurate analysis of polypeptides, expressed as inclusion bodies, prior to undertaking further purification.
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Affiliation(s)
| | - Nadia Hassan
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Shakir Hafeez
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Muhammad Arif
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan; Biological Sciences, University of Southampton, SO17 1BJ, UK
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Pallarés I, Ventura S. Advances in the Prediction of Protein Aggregation Propensity. Curr Med Chem 2019; 26:3911-3920. [DOI: 10.2174/0929867324666170705121754] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/29/2022]
Abstract
Background:
Protein aggregation into β-sheet-enriched insoluble assemblies is being
found to be associated with an increasing number of debilitating human pathologies, such as Alzheimer’s
disease or type 2 diabetes, but also with premature aging. Furthermore, protein aggregation
represents a major bottleneck in the production and marketing of proteinbased therapeutics.
Thus, the development of methods to accurately forecast the aggregation propensity of a certain
protein is of much value.
Methods/Results:
A myriad of in vitro and in vivo aggregation studies have shown that the aggregation
propensity of a certain polypeptide sequence is highly dependent on its intrinsic properties
and, in most cases, driven by specific short regions of high aggregation propensity. These observations
have fostered the development of a first generation of algorithms aimed to predict protein
aggregation propensities from the protein sequence. A second generation of programs able to map
protein aggregation on protein structures is emerging. Herein, we review the most representative
online accessible predictive tools, emphasizing their main distinctive features and the range of
applications.
Conclusion:
In this review, we describe representative biocomputational approaches to evaluate
the aggregation properties of protein sequences and structures, while illustrating how they can
become very useful tools to target protein aggregation in biomedicine and biotechnology.
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Affiliation(s)
- Irantzu Pallarés
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Universitat Autonoma de Barcelona, 08193-Bellaterra (Barcelona), Spain
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Shibaei N, Majidi J, Bashir NS, Karkhaneh A, Razavi K. Production and Partial Purification of the Grapevine Fanleaf Virus Coat Protein 42 Polyclonal Antibody Against Inclusion Body Expressed in Escherichia coli. IRANIAN JOURNAL OF BIOTECHNOLOGY 2019; 16:e1525. [PMID: 31457029 PMCID: PMC6697837 DOI: 10.21859/ijb.1525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/05/2018] [Accepted: 06/12/2018] [Indexed: 11/27/2022]
Abstract
Background Expression of virus coat protein (CP) in Escherichia coli often leads to production of partially folded aggregated proteins which are called inclusion bodies. Grapevine fanleaf virus (GFLV) is one of the most serious and widespread grapevine virus diseases around the world and in Iran. Objective The main objective of this study was to find a simple and brief method for producing polyclonal antibodies (PAbs) to be used for immunodiagnosis of GFLV. Material and Methods An antigenic determinant in GFLV CP gene was inserted into pET-28a bacterial expression vector and the construct (pET-28a CP42) was cloned into E. coli strain BL21 (DE3). The recombinant coat protein of GFLV (CP42) was expressed and characterized by SDS-PAGE and western blot analysis using commercial anti-GFLV antibody. Expression of the CP was detected in the form of inclusion bodies in insoluble cytoplasmic fraction. Then, the inclusion bodies were isolated from the bacterial cells and injected into rabbits for PAbs production. The reaction of the antiserum was checked by ELISA assay. In order to analyze efficiency of the produced PAbs, first the infected and uninfected grapevine samples were confirmed based on morphological symptoms then the indirect plate- trapped antigen Enzyme-linked Immunosorbent Assay (IPTA-ELISA) was applied using the commercial anti GFLV antibody. In the next ELISA assay, efficiency of the raised polyclonal antibody was compared with commercial one. Results The expression of recombinant CP42 induced by IPTG was confirmed by the band of 42 kDa in SDS-PAGE and western blot. The antiserum of purified inclusion body immunized rabbit was reacted with CP42 and GFLV infected Grapevine samples. The results revealed an acceptable efficacy for prepared antibodies compared to that of commercial antibody. Conclusions It was evident that the recombinant coat protein in the form of inclusion bodies can be prepared and used as the antigen for immunizing animals in order to produce PAbs.
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Affiliation(s)
- Naeimeh Shibaei
- Department of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Jafar Majidi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Aliasghar Karkhaneh
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Khadijeh Razavi
- Department of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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Caballero AB, Espargaró A, Pont C, Busquets MA, Estelrich J, Muñoz-Torrero D, Gamez P, Sabate R. Bacterial Inclusion Bodies for Anti-Amyloid Drug Discovery: Current and Future Screening Methods. Curr Protein Pept Sci 2019; 20:563-576. [PMID: 30924417 DOI: 10.2174/1389203720666190329120007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/22/2022]
Abstract
Amyloid aggregation is linked to an increasing number of human disorders from nonneurological pathologies such as type-2 diabetes to neurodegenerative ones such as Alzheimer or Parkinson's diseases. Thirty-six human proteins have shown the capacity to aggregate into pathological amyloid structures. To date, it is widely accepted that amyloid folding/aggregation is a universal process present in eukaryotic and prokaryotic cells. In the last decade, several studies have unequivocally demonstrated that bacterial inclusion bodies - insoluble protein aggregates usually formed during heterologous protein overexpression in bacteria - are mainly composed of overexpressed proteins in amyloid conformation. This fact shows that amyloid-prone proteins display a similar aggregation propensity in humans and bacteria, opening the possibility to use bacteria as simple models to study amyloid aggregation process and the potential effect of both anti-amyloid drugs and pro-aggregative compounds. Under these considerations, several in vitro and in cellulo methods, which exploit the amyloid properties of bacterial inclusion bodies, have been proposed in the last few years. Since these new methods are fast, simple, inexpensive, highly reproducible, and tunable, they have aroused great interest as preliminary screening tools in the search for anti-amyloid (beta-blocker) drugs for conformational diseases. The aim of this mini-review is to compile recently developed methods aimed at tracking amyloid aggregation in bacteria, discussing their advantages and limitations, and the future potential applications of inclusion bodies in anti-amyloid drug discovery.
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Affiliation(s)
- Ana B Caballero
- Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Maria Antònia Busquets
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Joan Estelrich
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
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