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Willems T, Hectors W, Rombaut J, De Rop AS, Goegebeur S, Delmulle T, De Mol ML, De Maeseneire SL, Soetaert WK. An exploratory in silico comparison of open-source codon harmonization tools. Microb Cell Fact 2023; 22:227. [PMID: 37932726 PMCID: PMC10626681 DOI: 10.1186/s12934-023-02230-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Not changing the native constitution of genes prior to their expression by a heterologous host can affect the amount of proteins synthesized as well as their folding, hampering their activity and even cell viability. Over the past decades, several strategies have been developed to optimize the translation of heterologous genes by accommodating the difference in codon usage between species. While there have been a handful of studies assessing various codon optimization strategies, to the best of our knowledge, no research has been performed towards the evaluation and comparison of codon harmonization algorithms. To highlight their importance and encourage meaningful discussion, we compared different open-source codon harmonization tools pertaining to their in silico performance, and we investigated the influence of different gene-specific factors. RESULTS In total, 27 genes were harmonized with four tools toward two different heterologous hosts. The difference in %MinMax values between the harmonized and the original sequences was calculated (ΔMinMax), and statistical analysis of the obtained results was carried out. It became clear that not all tools perform similarly, and the choice of tool should depend on the intended application. Almost all biological factors under investigation (GC content, RNA secondary structures and choice of heterologous host) had a significant influence on the harmonization results and thus must be taken into account. These findings were substantiated using a validation dataset consisting of 8 strategically chosen genes. CONCLUSIONS Due to the size of the dataset, no complex models could be developed. However, this initial study showcases significant differences between the results of various codon harmonization tools. Although more elaborate investigation is needed, it is clear that biological factors such as GC content, RNA secondary structures and heterologous hosts must be taken into account when selecting the codon harmonization tool.
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Affiliation(s)
- Thomas Willems
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Wim Hectors
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Jeltien Rombaut
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Anne-Sofie De Rop
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Stijn Goegebeur
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Tom Delmulle
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Maarten L De Mol
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
| | - Sofie L De Maeseneire
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium.
| | - Wim K Soetaert
- Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, 9000, Belgium
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Chen YS, Wu HC, Lin JR, Yang JL, Kuo TY. High-level expression of functional Pfu DNA polymerase recombinant protein by mimicking the enhanced green fluorescence protein gene codon usage. Biotechnol Appl Biochem 2023; 70:97-105. [PMID: 35179798 DOI: 10.1002/bab.2331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/05/2022] [Indexed: 11/08/2022]
Abstract
Pfu DNA polymerase is a vital enzyme in PCR-related experiments. However, it is not easy to achieve high-level expression and high purity through one-step purification. This paper illustrates the method to acquire the full-length open reading frame of Pfu DNA polymerase. Without altering its amino acids, we have modified the codon usage, based on that of the enhanced green fluorescence protein (eGFP), and named it rPfu. The synthesized rPfu gene has been subcloned into the pET28a plasmid and expressed in four Escherichia coli strains without the pLysS plasmid. Three strains have expressed a high level of soluble Pfu DNA polymerase. With the aid of Ni-NTA His•Bind® resin, we could obtain high purity (>95%) soluble recombinant protein. Compared with the commercial, proofreading DNA polymerase, rPfu's bioactivity was 12,987 U/mg; that is, 88,311 U of rPfu could be obtained from 50 mL cultured E. coli. The purified rPfu was able to amplify the length of DNA fragments at least 5.5 kb. The method of increasing soluble protein's yield using the eGFP codon usage may introduce a new possibility to the expression of other soluble recombinant proteins.
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Affiliation(s)
| | - Hsing-Chieh Wu
- International Degree Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Jin-Ru Lin
- Department of Foreign Languages and Literatures, National Taiwan University, Taipei, Taiwan
| | - Jia-Ling Yang
- Department of Veterinary medicine, National Taiwan University, Taipei, Taiwan
| | - Tsun-Yung Kuo
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
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Fox DM, Branson KM, Walker RC. mRNA codon optimization with quantum computers. PLoS One 2021; 16:e0259101. [PMID: 34714834 PMCID: PMC8555812 DOI: 10.1371/journal.pone.0259101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/12/2021] [Indexed: 11/19/2022] Open
Abstract
Reverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. A Quantum Annealer (QA) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The QA is found to be competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.
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Affiliation(s)
- Dillion M. Fox
- Data and Computational Science, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Kim M. Branson
- Artificial Intelligence and Machine Learning, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
| | - Ross C. Walker
- Data and Computational Science, Medicinal Sciences and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, United States of America
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, La Jolla, California, United States of America
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Fu H, Liang Y, Zhong X, Pan Z, Huang L, Zhang H, Xu Y, Zhou W, Liu Z. Codon optimization with deep learning to enhance protein expression. Sci Rep 2020; 10:17617. [PMID: 33077783 PMCID: PMC7572362 DOI: 10.1038/s41598-020-74091-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/21/2020] [Indexed: 02/05/2023] Open
Abstract
Heterologous expression is the main approach for recombinant protein production ingenetic synthesis, for which codon optimization is necessary. The existing optimization methods are based on biological indexes. In this paper, we propose a novel codon optimization method based on deep learning. First, we introduce the concept of codon boxes, via which DNA sequences can be recoded into codon box sequences while ignoring the order of bases. Then, the problem of codon optimization can be converted to sequence annotation of corresponding amino acids with codon boxes. The codon optimization models for Escherichia Coli were trained by the Bidirectional Long-Short-Term Memory Conditional Random Field. Theoretically, deep learning is a good method to obtain the distribution characteristics of DNA. In addition to the comparison of the codon adaptation index, protein expression experiments for plasmodium falciparum candidate vaccine and polymerase acidic protein were implemented for comparison with the original sequences and the optimized sequences from Genewiz and ThermoFisher. The results show that our method for enhancing protein expression is efficient and competitive.
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Affiliation(s)
- Hongguang Fu
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yanbing Liang
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Xiuqin Zhong
- University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - ZhiLing Pan
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Huang
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - HaiLin Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Xu
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Wei Zhou
- University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Zhong Liu
- Chengdu Institute of Computer Applications, Chinese Academy of Sciences, Chengdu, 610041, China
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Hosts for Hostile Protein Production: The Challenge of Recombinant Immunotoxin Expression. Biomedicines 2019; 7:biomedicines7020038. [PMID: 31108917 PMCID: PMC6630761 DOI: 10.3390/biomedicines7020038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022] Open
Abstract
For the recombinant expression of toxin-based drugs, a crucial step lies not only in the choice of the production host(s) but also in the accurate design of the protein chimera. These issues are particularly important since such products may be toxic to the expressing host itself. To avoid or limit the toxicity to productive cells while obtaining a consistent yield in chimeric protein, several systems from bacterial to mammalian host cells have been employed. In this review, we will discuss the development of immunotoxin (IT) expression, placing special emphasis on advantages and on potential drawbacks, as one single perfect host for every chimeric protein toxin or ligand does not exist.
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"CodonWizard" - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts. Protein Expr Purif 2019; 160:84-93. [PMID: 30953700 DOI: 10.1016/j.pep.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 11/22/2022]
Abstract
Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during commercial gene synthesis and thus unfortunately remains a black box for many researchers. The presented software program "CodonWizard" offers scientists a powerful but easy-to-use tool for customizable codon optimization: The intuitive graphical user interface empowers even scientists inexperienced in the art to straightforward design, modify, test and save complex codon optimization strategies and to publicly share successful otimization strategies among the scientific community. "Codon Wizard" provides highly flexible features for sequence analysis and completely customizable modification/optimization of codon usage of any given input sequence data (DNA/RNA/peptide) using freely combinable algorithms, allowing for implementation of contemporary, well-established optimization strategies as well as novel, proprietary ones alike. Contrary to comparable tools, "Codon Wizard" thus finally opens up ways for an empirical approach to codon optimization and may also >be used completely offline to protect resulting intellectual property. As a benchmark, the reliability, intuitiveness and utility of the application could be demonstrated by increasing the yield of recombinant TEV-protease expressed in E. coli by several orders of magnitude after codon optimization using "CodonWizard" - Permanently available for download on the web at http://schwalbe.org.chemie.uni-frankfurt.de/node/3324.
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Al-Hawash AB, Zhang X, Ma F. Strategies of codon optimization for high-level heterologous protein expression in microbial expression systems. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Xu J, Zhong F, Zhang Y, Zhang J, Huo S, Lin H, Wang L, Cui D, Li X. Construction of Bacillus subtilis strain engineered for expression of porcine β-defensin-2/cecropin P1 fusion antimicrobial peptides and its growth-promoting effect and antimicrobial activity. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:576-584. [PMID: 27383796 PMCID: PMC5394845 DOI: 10.5713/ajas.16.0207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/19/2016] [Accepted: 06/30/2016] [Indexed: 01/31/2023]
Abstract
Objective To generate recombinant Bacillus subtilis (B. subtilis) engineered for expression of porcine β-defensin-2 (pBD-2) and cecropin P1 (CP1) fusion antimicrobial peptide and investigate their anti-bacterial activity in vitro and their growth-promoting and disease resisting activity in vivo. Methods The pBD-2 and CP1 fused gene was synthesized using the main codons of B. subtilis and inserted into plasmid pMK4 vector to construct their expression vector. The fusion peptide-expressing B. subtilis was constructed by transformation with the vector. The expressed fusion peptide was detected with Western blot. The antimicrobial activity of the expressed fusion peptide and the recovered pBD-2 and CP1 by enterokinase digestion in vitro was analyzed by the bacterial growth-inhibitory activity assay. To analyze the engineered B. subtilis on growth promotion and disease resistance, the weaned piglets were fed with basic diet supplemented with the recombinant B. subtilis. Then the piglets were challenged by enteropathogenic Escherichia coli (E. coli). The weight gain and diarrhea incidence of piglets were measured after challenge. Results The recombinant B. subtilis engineered for expression of pBD-2/CP1 fusion peptide was successfully constructed using the main codons of the B. subtilis. Both expressed pBD-2/CP1 fusion peptide and their individual peptides recovered from parental fusion peptide by enterokinase digestion possessed the antimicrobial activities to a variety of the bacteria, including gram-negative bacteria (E. coli, Salmonella typhimurium, and Haemophilus parasuis) and gram-positive bacteria (Staphylococcus aureus). Supplementing the engineered B. subtilis to the pig feed could significantly promote the piglet growth and reduced diarrhea incidence of the piglets. Conclusion The generated B. subtilis strain can efficiently express pBD-2/CP1 fusion antimicrobial peptide, the recovered pBD-2 and CP1 peptides possess potent antimicrobial activities to a variety of bacterial species in vitro. Supplementation of the engineered B. subtilis in pig feed obviously promote piglet growth and resistance to the colibacillosis.
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Affiliation(s)
- Jian Xu
- Department of Biotechnology, College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China.,Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Fei Zhong
- Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Yonghong Zhang
- Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Jianlou Zhang
- Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Shanshan Huo
- Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Hongyu Lin
- Department of Biotechnology, College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Liyue Wang
- Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Dan Cui
- Laboratory of Molecular Virology and Immunology, College of Veterinary Medicine, Agricultural University of Hebei, Hebei Engineering and Technology Research Center of Veterinary Biotechnology, Baoding 071000, China
| | - Xiujin Li
- Department of Biotechnology, College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, China
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Extracellular production of Pseudozyma (Candida) antarctica lipase B with genuine primary sequence in recombinant Escherichia coli. J Biosci Bioeng 2015; 121:303-9. [PMID: 26272415 DOI: 10.1016/j.jbiosc.2015.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/22/2015] [Accepted: 07/06/2015] [Indexed: 11/21/2022]
Abstract
An Escherichia coli expression system was established to produce recombinant extracellular Pseudozyma (Candida) antarctica lipase B (CALB). With the aim of producing the genuine CALB without additional amino acid residues, the mature portion of the CALB gene was fused seamlessly to a pelB signal sequence and expressed in E. coli BL21(DE3) using the pET system. Inducing gene expression at low temperature (20°C) was crucial for the production of active CALB; higher temperatures caused inclusion body formation. Prolonged induction for 48 h at 20°C allowed for the enzyme to be released into the culture medium, with more than half of the activity detected in the culture supernatant. A catalytically inactive CALB mutant (S105A) protein was similarly released, suggesting that the lipid-hydrolyzing activity of the enzyme was not the reason for the release. The CALB production level was further improved by optimizing the culture medium. Under the optimized conditions, the CALB in the culture supernatant amounted to 550 mg/L. The recombinant CALB was purified from the culture supernatant, yielding 5.67 mg of purified CALB from 50 mL of culture. N-terminal sequencing and ESI-MS analyses showed proper removal of the pelB signal sequence and the correct molecular weight of the protein, respectively, confirming the structural integrity of the recombinant CALB. The kinetic parameters towards p-nitrophenylbutyrate and the enantiomeric selectivity on rac-1-phenylethylacetate of the recombinant CALB were consistent with those of the authentic CALB. This is the first example of E. coli-based extracellular production of a CALB enzyme without extra amino acid residues.
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Fang B, Jiang W, Zhou Q, Wang S. Codon-Optimized NADH Oxidase Gene Expression and Gene Fusion with Glycerol Dehydrogenase for Bienzyme System with Cofactor Regeneration. PLoS One 2015; 10:e0128412. [PMID: 26115038 PMCID: PMC4482596 DOI: 10.1371/journal.pone.0128412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/27/2015] [Indexed: 11/30/2022] Open
Abstract
NADH oxidases (NOXs) play an important role in maintaining balance of NAD+/NADH by catalyzing cofactors regeneration. The expression of nox gene from Lactobacillus brevis in Escherichia coli BL21 (BL21 (DE3)) was studied. Two strategies, the high AT-content in the region adjacent to the initiation codon and codon usage of the whole gene sequence consistent with the host, obtained the NOX activity of 59.9 U/mg and 73.3 U/mg (crude enzyme), with enhanced expression level of 2.0 and 2.5-folds, respectively. Purified NOX activity was 213.8 U/mg. Gene fusion of glycerol dehydrogenase (GDH) and NOX formed bifuctional multi-enzymes for bioconversion of glycerol coupled with coenzyme regeneration. Kinetic parameters of the GDH-NOX for each substrate, glycerol and NADH, were calculated as Vmax(Glycerol) 20 μM/min, Km(Glycerol) 19.4 mM, Vmax (NADH) 12.5 μM/min and Km (NADH) 51.3 μM, respectively, which indicated the potential application of GDH-NOX for quick glycerol analysis and dioxyacetone biosynthesis.
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Affiliation(s)
- Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
- The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian, 361005, China
| | - Wei Jiang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Qiang Zhou
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
- * E-mail:
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Farshadpour F, Taherkhani R, Makvandi M, Rajabi Memari H, Samarbafzadeh AR. Codon-Optimized Expression and Purification of Truncated ORF2 Protein of Hepatitis E Virus in Escherichia coli. Jundishapur J Microbiol 2014; 7:e11261. [PMID: 25368796 PMCID: PMC4216576 DOI: 10.5812/jjm.11261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/01/2013] [Accepted: 06/25/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Hepatitis E virus (HEV) is a causative agent of acute hepatitis among people of different age groups and has high mortality rate of up to 30% among pregnant women. Therefore, primary prevention of HEV infection is essential. OBJECTIVES The aim of this study was to obtain the highly purified truncated open reading frames 2 (ORF2) protein, which might be a future HEV vaccine candidate. MATERIALS AND METHODS The truncated orf2 gene (orf2.1), encoding the 112-660 amino acid of HEV capsid protein sequence, was optimized, synthesized, and cloned into pBluescript II SK(+) vector. After subcloning into expression vector pET-30a (+), a 193-nucleotide fragment was deleted from the construct and the recombinant plasmid pET-30a-ORF2.2 (orf2.2 encodes 112-608 amino acid sequence of HEV capsid protein) was constructed and used for transformation of Escherichia coli BL21 cells. After induction with isopropyl-β-D-thiogalactopyranoside (IPTG) and optimizing the conditions of expression, the target protein was highly expressed and purified by Ni(2+)-chelate affinity chromatography. The expressed and purified protein was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. RESULTS The subcloning was confirmed by PCR, restriction enzyme digestion, and DNA sequencing of recombinant plasmid pET30a-ORF2.2. The results obtained from optimizing the expression conditions showed that the highest expression of the protein was obtained by adding IPTG at a final concentration of 1 mM at 37℃ for four hours. The expression and purification of truncated ORF2 protein was confirmed by SDS-PAGE and western blotting. SDS-PAGE analysis showed a protein band of about 55 kDa. SDS-PAGE of the purified protein revealed that the highest amount of target protein in elution buffer at the pH of 4.5 was obtained. The yield of the purified protein was about 1 mg/L of culture media. CONCLUSIONS In this study, the optimized truncated ORF2 protein was expressed in E. coli successfully and the highly purified protein was obtained, which can be a potential vaccine candidate and as an antigen in ELISA to diagnose HEV infections.
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Affiliation(s)
- Fatemeh Farshadpour
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Reza Taherkhani
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
| | - Manoochehr Makvandi
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Corresponding author: Manoochehr Makvandi, Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran; Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran. Tel: +98-9166181683, Fax: +98-6113738313, E-mail:
| | - Hamid Rajabi Memari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Ahvaz Shahid Chamran University, Ahvaz, IR Iran
| | - Ali Reza Samarbafzadeh
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, IR Iran
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Taherkhani R, Makvandi M, Farshadpour F. Development of enzyme-linked immunosorbent assays using 2 truncated ORF2 proteins for detection of IgG antibodies against hepatitis E virus. Ann Lab Med 2014; 34:118-26. [PMID: 24624347 PMCID: PMC3948824 DOI: 10.3343/alm.2014.34.2.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/12/2013] [Accepted: 10/02/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Without appropriate culture systems for hepatitis E virus (HEV), sufficient natural viral proteins are difficult to generate for use in serological tests. Therefore, it is important to produce large amounts of HEV recombinant proteins in an economical way. The present study developed ELISAs using 2 truncated forms of the HEV open reading frame (ORF) 2 protein in order to detect anti-HEV IgG in serum samples. METHODS Two truncated forms of the ORF2 protein were expressed in Escherichia coli and were purified by Ni(2+)-chelate-affinity chromatography (Qiagen, Germany). Two ELISAs were developed using these proteins and were compared with DIA.PRO HEV IgG ELISA kit (DIA.PRO. Italy) in 220 serum samples. RESULTS High yields of the target proteins were obtained through codon optimization. The concentration and purity of the proteins were improved with Amicon filters (EMD Millipore, USA). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting analysis of the resultant proteins showed a protein band of approximately 60 kDa corresponding to ORF2.1 (amino acids 112-660) and a protein band of approximately 55 kDa corresponding to ORF2.2 (amino acids 112-607). Positive agreement, negative agreement, and concordance of the 2 in-house ELISAs compared with DIA.PRO HEV IgG ELISA kit were 87%, 99.5%, and 98.1%, respectively (kappa=0.899, P=0.625). CONCLUSIONS The newly developed ELISAs are useful for detecting anti-HEV IgG in serum samples and are highly concordant with DIA.PRO HEV IgG ELISA kit.
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Affiliation(s)
- Reza Taherkhani
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Scien, Ahvaz, Iran. ; Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Scien, Ahvaz, Iran. ; Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Farshadpour
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Scien, Ahvaz, Iran. ; Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Elena C, Ravasi P, Castelli ME, Peirú S, Menzella HG. Expression of codon optimized genes in microbial systems: current industrial applications and perspectives. Front Microbiol 2014; 5:21. [PMID: 24550894 PMCID: PMC3912506 DOI: 10.3389/fmicb.2014.00021] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/14/2014] [Indexed: 11/24/2022] Open
Abstract
The efficient production of functional proteins in heterologous hosts is one of the major bases of modern biotechnology. Unfortunately, many genes are difficult to express outside their original context. Due to their apparent “silent” nature, synonymous codon substitutions have long been thought to be trivial. In recent years, this dogma has been refuted by evidence that codon replacement can have a significant impact on gene expression levels and protein folding. In the past decade, considerable advances in the speed and cost of gene synthesis have facilitated the complete redesign of entire gene sequences, dramatically improving the likelihood of high protein expression. This technology significantly impacts the economic feasibility of microbial-based biotechnological processes by, for example, increasing the volumetric productivities of recombinant proteins or facilitating the redesign of novel biosynthetic routes for the production of metabolites. This review discusses the current applications of this technology, particularly those regarding the production of small molecules and industrially relevant recombinant enzymes. Suggestions for future research and potential uses are provided as well.
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Affiliation(s)
- Claudia Elena
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - Pablo Ravasi
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - María E Castelli
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - Salvador Peirú
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
| | - Hugo G Menzella
- Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet Rosario, Argentina
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Taherkhani R, Makvandi M, Farshadpour F. Development of Enzyme-Linked Immunosorbent Assays Using 2 Truncated ORF2 Proteins for Detection of IgG Antibodies Against Hepatitis E Virus. Ann Lab Med 2014. [DOI: 10.3343/alm.2014.34.2.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Reza Taherkhani
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Scien, Ahvaz, Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Scien, Ahvaz, Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Farshadpour
- Health Research Institute, Infectious and Tropical Disease Research Center, Ahvaz Jundishapur University of Medical Scien, Ahvaz, Iran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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15
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Codon preference optimization increases prokaryotic cystatin C expression. J Biomed Biotechnol 2012; 2012:732017. [PMID: 23093857 PMCID: PMC3471025 DOI: 10.1155/2012/732017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/14/2012] [Accepted: 08/22/2012] [Indexed: 02/06/2023] Open
Abstract
Gene expression is closely related to optimal vector-host system pairing in many prokaryotes. Redesign of the human cystatin C (cysC) gene using the preferred codons of the prokaryotic system may significantly increase cysC expression in Escherichia coli (E. coli). Specifically, cysC expression may be increased by removing unstable sequences and optimizing GC content. According to E. coli expression system codon preferences, the gene sequence was optimized while the amino acid sequence was maintained. The codon-optimized cysC (co-cysC) and wild-type cysC (wt-cysC) were expressed by cloning the genes into a pET-30a plasmid, thus transforming the recombinant plasmid into E. coli BL21. Before and after the optimization process, the prokaryotic expression vector and host bacteria were examined for protein expression and biological activation of CysC. The recombinant proteins in the lysate of the transformed bacteria were purified using Ni(2+)-NTA resin. Recombinant protein expression increased from 10% to 46% based on total protein expression after codon optimization. Recombinant CysC purity was above 95%. The significant increase in cysC expression in E. coli expression produced by codon optimization techniques may be applicable to commercial production systems.
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Gao B, Zhangsun D, Wu Y, Lin B, Zhu X, Luo S. Expression, renaturation and biological activity of recombinant conotoxin GeXIVAWT. Appl Microbiol Biotechnol 2012; 97:1223-30. [PMID: 22825834 DOI: 10.1007/s00253-012-4287-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 12/22/2022]
Abstract
Conotoxins are a diverse array of small peptides mostly with multiple disulfide bridges. These peptides become an increasing significant source of neuro-pharmacological probes and drugs as a result of the high selectivity for ion channels and receptors. Conotoxin GeXIVAWT (CTX-GeXIVAWT) is a 28-amino acid peptide containing five cysteines isolated from the venom of Conus generalis. Here, we present a simple and fast strategy of producing disulfide-rich conotoxins via recombinant expression. The codes of novel conotoxin gene GeXIVAWT were optimized and generated two pairs of primers by chemical synthesis for construction of expression vector. Recombinant expression vector pET22b(+)-GeXIVAWT fused with pelB leader and His-tag was successfully expressed as an insoluble body in Escherichia coli BL21(DE3) cells. Recombinant conotoxin GeXIVAWT (rCTX-GeXIVAWT) was obtained by dissolving the insoluble bodies and purifying with a Ni-NTA affinity column, which was further purified using reverse-phase high-performance liquid chromatography and identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. The rCTX-GeXIVAWT renatured in vitro could inhibited the growth of Sf9 cell with biological activity assay. This expression system may prove valuable for future structure-function studies of conotoxins.
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Affiliation(s)
- Bingmiao Gao
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
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Seok JH, Kim HS, Hatada Y, Nam SW, Kim YH. Construction of an expression system for the secretory production of recombinant α-agarase in yeast. Biotechnol Lett 2012; 34:1041-9. [DOI: 10.1007/s10529-012-0864-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/26/2012] [Indexed: 11/24/2022]
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18
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Menzella HG. Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli. Microb Cell Fact 2011; 10:15. [PMID: 21371320 PMCID: PMC3056764 DOI: 10.1186/1475-2859-10-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 03/03/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variations in codon usage between species are one of the major causes affecting recombinant protein expression levels, with a significant impact on the economy of industrial enzyme production processes. The use of codon-optimized genes may overcome this problem. However, designing a gene for optimal expression requires choosing from a vast number of possible DNA sequences and different codon optimization methods have been used in the past decade. Here, a comparative study of the two most common methods is presented using calf prochymosin as a model. RESULTS Seven sequences encoding calf prochymosin have been designed, two using the "one amino acid-one codon" method and five using a "codon randomization" strategy. When expressed in Escherichia coli, the variants optimized by the codon randomization approach produced significantly more proteins than the native sequence including one gene that produced an increase of 70% in the amount of prochymosin accumulated. On the other hand, no significant improvement in protein expression was observed for the variants designed with the one amino acid-one codon method. The use of codon-optimized sequences did not affect the quality of the recovered inclusion bodies. CONCLUSIONS The results obtained in this study indicate that the codon randomization method is a superior strategy for codon optimization. A significant improvement in protein expression was obtained for the largely established process of chymosin production, showing the power of this strategy to reduce production costs of industrial enzymes in microbial hosts.
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Affiliation(s)
- Hugo G Menzella
- Genetic Engineering & Fermentation Technology, CONICET, Facultad de Ciencias Bioquimicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531 Rosario 2000, Republica Argentina.
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