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Schiefelbein K, Lang J, Schuster M, Grigglestone CE, Striga R, Bigler L, Schuman MC, Zerbe O, Li Y, Hartrampf N. Merging Flow Synthesis and Enzymatic Maturation to Expand the Chemical Space of Lasso Peptides. J Am Chem Soc 2024; 146:17261-17269. [PMID: 38759637 DOI: 10.1021/jacs.4c03898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Many peptidic natural products, such as lasso peptides, cyclic peptides, and cyclotides, are conformationally constrained and show biological stability, making them attractive scaffolds for drug development. Although many peptides can be synthesized and modified through chemical methods, knot-like lasso peptides such as microcin J25 (MccJ25) and their analogues remain elusive. As the chemical space of MccJ25 analogues accessible through purely biological methods is also limited, we proposed a hybrid approach: flow-based chemical synthesis of non-natural precursor peptides, followed by in vitro transformation with recombinant maturation enzymes, to yield a more diverse array of lasso peptides. Herein, we established the rapid, flow-based synthesis of chemically modified MccJ25 precursor peptides (57 amino acids). Heterologous expression of enzymes McjB and McjC was extensively optimized to improve yields and facilitate the synthesis of multiple analogues of MccJ25, including the incorporation of non-canonical tyrosine and histidine derivatives into the lasso scaffold. Finally, using our chemoenzymatic strategy, we produced a biologically active analogue containing three d-amino acids in the loop region and incorporated backbone N-methylations. Our method provides rapid access to chemically modified lasso peptides that could be used to investigate structure-activity relationships, epitope grafting, and the improvement of therapeutic properties.
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Affiliation(s)
- Kevin Schiefelbein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jakob Lang
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Claire E Grigglestone
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Robin Striga
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM). UMR7245, CNRS-Muséum National d'Histoire Naturelle (MNHN), Alliance Sorbonne Université, 57 rue Cuvier, 75005 Paris, France
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Meredith C Schuman
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Yanyan Li
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM). UMR7245, CNRS-Muséum National d'Histoire Naturelle (MNHN), Alliance Sorbonne Université, 57 rue Cuvier, 75005 Paris, France
| | - Nina Hartrampf
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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2
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Val DS, Di Nardo L, Marchisio F, Peiru S, Castelli ME, Abriata LA, Menzella HG, Rasia RM. Thermal Stabilization of a Bacterial Zn(II)-Dependent Phospholipase C through Consensus Sequence Design. Biochemistry 2024; 63:348-354. [PMID: 38206322 DOI: 10.1021/acs.biochem.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Proteins' extraordinary performance in recognition and catalysis has led to their use in a range of applications. However, proteins obtained from natural sources are oftentimes not suitable for direct use in industrial or diagnostic setups. Natural proteins, evolved to optimally perform a task in physiological conditions, usually lack the stability required to be used in harsher conditions. Therefore, the alteration of the stability of proteins is commonly pursued in protein engineering studies. Here, we achieved a substantial thermal stabilization of a bacterial Zn(II)-dependent phospholipase C by consensus sequence design. We retrieved and analyzed sequenced homologues from different sources, selecting a subset of examples for expression and characterization. A non-natural consensus sequence showed the highest stability and activity among those tested. Comparison of the stability parameters of this stabilized mutant and other natural variants bearing similar mutations allows us to pinpoint the sites most likely to be responsible for the enhancement. Point mutations in these sites alter the unfolding process of the consensus sequence. We show that the stabilized version of the protein retains full activity even in harsh oil degumming conditions, making it suitable for industrial applications.
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Affiliation(s)
- Diego S Val
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | - Luisina Di Nardo
- Instituto de Biología Celular y Molecular de Rosario (IBR), FbioyF-UNR-CONICET. Ocampo y Esmeralda, 2000 Rosario, Argentina
| | - Fiorela Marchisio
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | | | - María Eugenia Castelli
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | | | - Hugo G Menzella
- Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), FbioyF-UNR-CONICET. Mitre 1998, 2000 Rosario, Argentina
| | - Rodolfo M Rasia
- Instituto de Biología Celular y Molecular de Rosario (IBR), FbioyF-UNR-CONICET. Ocampo y Esmeralda, 2000 Rosario, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica, Ocampo y Esmeralda, 2000 Rosario, Argentina
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3
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Nuryana I, Laksmi FA, Dewi KS, Akbar FR, Nurhayati, Harmoko R. Codon optimization of a gene encoding DNA polymerase from Pyrococcus furiosus and its expression in Escherichia coli. J Genet Eng Biotechnol 2023; 21:129. [PMID: 37987973 PMCID: PMC10663413 DOI: 10.1186/s43141-023-00605-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND DNA polymerase is an essential component in PCR assay for DNA synthesis. Improving DNA polymerase with characteristics indispensable for a powerful assay is crucial because it can be used in wide-range applications. Derived from Pyrococcus furiosus, Pfu DNA polymerase (Pfu pol) is one of the excellent polymerases due to its high fidelity. Therefore, we aimed to develop Pfu pol from a synthetic gene with codon optimization to increase its protein yield in Escherichia coli. RESULTS Recombinant Pfu pol was successfully expressed and purified with a two-step purification process using nickel affinity chromatography, followed by anion exchange chromatography. Subsequently, the purified Pfu pol was confirmed by Western blot analysis, resulting in a molecular weight of approximately 90 kDa. In the final purification process, we successfully obtained a large amount of purified enzyme (26.8 mg/L). Furthermore, the purified Pfu pol showed its functionality and efficiency when tested for DNA amplification using the standard PCR. CONCLUSIONS Overall, a high-level expression of recombinant Pfu pol was achieved by employing our approach in the present study. In the future, our findings will be useful for studies on synthesizing recombinant DNA polymerase in E. coli expression system.
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Affiliation(s)
- Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia.
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
| | - Faiz Raihan Akbar
- Department of Biology, Faculty of Sciences and Mathematics, Universitas Diponegoro, Jalan Prof Soedarto, SH, Kampus UNDIP Tembalang, Semarang, 50275, Indonesia
| | - Nurhayati
- Department of Biology, Faculty of Sciences and Mathematics, Universitas Diponegoro, Jalan Prof Soedarto, SH, Kampus UNDIP Tembalang, Semarang, 50275, Indonesia
| | - Rikno Harmoko
- Research Center for Genetic Engineering, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
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4
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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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5
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Lewin LE, Daniels KG, Hurst LD. Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation. PLoS Comput Biol 2023; 19:e1011581. [PMID: 37878567 PMCID: PMC10599525 DOI: 10.1371/journal.pcbi.1011581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023] Open
Abstract
In many species highly expressed genes (HEGs) over-employ the synonymous codons that match the more abundant iso-acceptor tRNAs. Bacterial transgene codon randomization experiments report, however, that enrichment with such "translationally optimal" codons has little to no effect on the resultant protein level. By contrast, consistent with the view that ribosomal initiation is rate limiting, synonymous codon usage following the 5' ATG greatly influences protein levels, at least in part by modifying RNA stability. For the design of bacterial transgenes, for simple codon based in silico inference of protein levels and for understanding selection on synonymous mutations, it would be valuable to computationally determine initiation optimality (IO) scores for codons for any given species. One attractive approach is to characterize the 5' codon enrichment of HEGs compared with the most lowly expressed genes, just as translational optimality scores of codons have been similarly defined employing the full gene body. Here we determine the viability of this approach employing a unique opportunity: for Escherichia coli there is both the most extensive protein abundance data for native genes and a unique large-scale transgene codon randomization experiment enabling objective definition of the 5' codons that cause, rather than just correlate with, high protein abundance (that we equate with initiation optimality, broadly defined). Surprisingly, the 5' ends of native genes that specify highly abundant proteins avoid such initiation optimal codons. We find that this is probably owing to conflicting selection pressures particular to native HEGs, including selection favouring low initiation rates, this potentially enabling high efficiency of ribosomal usage and low noise. While the classical HEG enrichment approach does not work, rendering simple prediction of native protein abundance from 5' codon content futile, we report evidence that initiation optimality scores derived from the transgene experiment may hold relevance for in silico transgene design for a broad spectrum of bacteria.
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Affiliation(s)
- Loveday E. Lewin
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Kate G. Daniels
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Laurence D. Hurst
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
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6
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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7
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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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8
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Cloning, Exogenous Expression and Function Analysis of Interferon–γ from Gadus macrocephalus. Viruses 2022; 14:v14102304. [PMID: 36298859 PMCID: PMC9610899 DOI: 10.3390/v14102304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/30/2022] Open
Abstract
Interferon γ (IFN–γ) is now considered to be one of the key molecules in the regulation of innate and adaptive immunity. The function of IFN–γ is best described in humans, but less of IFN–γ in fish species has been described at protein level. In the present study, IFN–γ from Gadus macrocephalus (GmIFN–γ) has been examined in terms of bioinformatics, prokaryotic expression, yeast expression, antiviral activity and immune regulatory function. The cDNA of GmIFN–γ contains an open reading frame of 570 nucleotides, coding 189 amino acids. The mature protein contains a nuclear localization signal motif and an obvious IFN–γ signature sequence at the C-terminal. GmIFN–γ is very similar to that of Atlantic cod, with homology up to 89.89%, but less than 32% to other species. GmIFN–γ can be detected in the gills, spleen, intestine, brain and kidney. Interestingly, during early development, a strong signal of GmIFN–γ was not detected until 40 days post hatching. Prokaryotic expression plasmid pET–32a–GmIFN–γ was constructed, and the expression products in BL21 were confirmed by Mass Spectrometry. Meanwhile, the plasmid pGAPZA–GmIFN–γ with Myc tag was constructed and transmitted into Pichia pastoris yeast GS115, and the products were tested using Western blot. The purified GmIFN–γ from either BL21 or yeast has a strong antivirus (Spring viremia of carp virus) effect. The vector of pcDNA3.1–GmIFN–γ was expressed in EPC cell lines; high transcript levels of MHC class I chain-related protein A (MICA) gene were detected; and the exogenous GmIFN–γ protein could also induce MICA expression, indicating that GmIFN–γ could stimulate immune response. The yeast GS115 with GmIFN–γ protein, which is an inclusion body, was given to zebrafish orally, and the transcript of zebrafish IFN–γ was upregulated significantly; however, genes of the interferon type–I signal pathway were not well stimulated.
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9
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Razali R, Fahrudin FA, Subbiah VK, Takano K, Budiman C. Heterologous Expression and Catalytic Properties of Codon-Optimized Small-Sized Bromelain from MD2 Pineapple. Molecules 2022; 27:molecules27186031. [PMID: 36144767 PMCID: PMC9502857 DOI: 10.3390/molecules27186031] [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: 06/14/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Bromelain is a unique enzyme-based bioactive complex containing a mixture of cysteine proteases specifically found in the stems and fruits of pineapple (Ananas comosus) with a wide range of applications. MD2 pineapple harbors a gene encoding a small bromelain cysteine protease with the size of about 19 kDa, which might possess unique properties compared to the other cysteine protease bromelain. This study aims to determine the expressibility and catalytic properties of small-sized (19 kDa) bromelain from MD2 pineapple (MD2-SBro). Accordingly, the gene encoding MD2-SBro was firstly optimized in its codon profile, synthesized, and inserted into the pGS-21a vector. The insolubly expressed MD2-SBro was then resolubilized and refolded using urea treatment, followed by purification by glutathione S-transferase (GST) affinity chromatography, yielding 14 mg of pure MD2-SBro from 1 L of culture. The specific activity and catalytic efficiency (kcat/Km) of MD2-SBro were 3.56 ± 0.08 U mg−1 and 4.75 ± 0.23 × 10−3 µM−1 s−1, respectively, where optimally active at 50 °C and pH 8.0, and modulated by divalent ions. The MD2-SBro also exhibited the ability to scavenge the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) with an IC50 of 0.022 mg mL−1. Altogether, this study provides the production feasibility of active and functional MD2-Bro as a bioactive compound.
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Affiliation(s)
- Rafida Razali
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Fikran Aranda Fahrudin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
- Correspondence:
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10
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Expression of Codon-Optimized Gene Encoding Murine Moloney Leukemia Virus Reverse Transcriptase in Escherichia coli. Protein J 2022; 41:515-526. [PMID: 35933571 PMCID: PMC9362449 DOI: 10.1007/s10930-022-10066-5] [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] [Accepted: 07/10/2022] [Indexed: 10/27/2022]
Abstract
Moloney murine leukemia virus reverse transcriptase (MMLV-RT) is the most frequently used enzyme in molecular biology for cDNA synthesis. To date, reverse transcription coupled with Polymerase Chain Reaction, known as RT-PCR, has been popular as an excellent approach for the detection of SARS-CoV-2 during the COVID-19 pandemic. In this study, we aimed to improve the enzymatic production and performance of MMLV-RT by optimizing both codon and culture conditions in E. coli expression system. By applying the optimized codon and culture conditions, the enzyme was successfully overexpressed and increased at high level based on the result of SDS-PAGE and Western blotting. The total amount of MMLV-RT has improved 85-fold from 0.002 g L-1 to 0.175 g L-1 of culture. One-step purification by nickel affinity chromatography has been performed to generate the purified enzyme for further analysis of qualitative and quantitative RT activity. Overall, our investigation provides useful strategies to enhance the recombinant enzyme of MMLV-RT in both production and performance. More importantly, the enzyme has shown promising activity to be used for RT-PCR assay.
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11
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Santos SP, Garcés LFS, Silva FS, Santiago LF, Pinheiro CS, Alcantara-Neves NM, Pacheco LG. Engineering an optimized expression operating unit for improved recombinant protein production in Escherichia coli. Protein Expr Purif 2022; 199:106150. [DOI: 10.1016/j.pep.2022.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 10/31/2022]
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12
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Daya T, Jeje O, Maake R, Aloke C, Khoza T, Achilonu I. Expression, Purification, and Biophysical Characterization of Klebsiella Pneumoniae Nicotinate Nucleotide Adenylyltransferase. Protein J 2022; 41:141-156. [DOI: 10.1007/s10930-021-10037-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 10/19/2022]
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13
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Markou GC, Sarkar CA. A cell-free approach to identify binding hotspots in plant immune receptors. Sci Rep 2022; 12:501. [PMID: 35017559 PMCID: PMC8752824 DOI: 10.1038/s41598-021-04259-8] [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: 06/29/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
Plant immune receptors are often difficult to express heterologously, hindering study of direct interactions between these receptors and their targets with traditional biochemical approaches. The cell-free method ribosome display (RD) enables expression of such recalcitrant proteins by keeping each nascent polypeptide chain tethered to its ribosome, which can enhance protein folding by virtue of its size and solubility. Moreover, in contrast to an in planta readout of receptor activity such as a hypersensitive response that conflates binding and signaling, RD enables direct probing of the interaction between plant immune receptors and their targets. Here, we demonstrate the utility of this approach using tomato recognition of Trichoderma viride ethylene-inducing xylanase (EIX) as a case study. Leveraging the modular nature of the tomato LeEIX2 and LeEIX1 leucine-rich repeat (LRR) receptors, we applied an entropy-informed algorithm to maximize the information content in our receptor segmentation RD experiments to identify segments implicated in EIX binding. Unexpectedly, two distinct EIX-binding hotspots were discovered on LeEIX2 and both hotspots are shared with decoy LeEIX1, suggesting that their contrasting receptor functions are not due to differential modes of ligand binding. Given that most plant immune receptors are thought to engage targets via their LRR sequences, this approach should be of broad utility in rapidly identifying their binding hotspots.
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Affiliation(s)
- George C Markou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455, USA.
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14
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Abulmagd S, Khattab AENA, Zedan H. Expression of full and fragment-B of diphtheria toxin genes in Escherichia coli for generating of recombinant diphtheria vaccines. Clin Exp Vaccine Res 2022; 11:12-29. [PMID: 35223662 PMCID: PMC8844665 DOI: 10.7774/cevr.2022.11.1.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/21/2021] [Accepted: 12/18/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose In the present study, whole diphtheria toxin (dt) and fragment B (dtb) genes from Corynebacterium diphtheriae Park William were cloned into Escherichia coli, the purified expressed proteins were evaluated for ultimately using as a candidate vaccine. Materials and Methods The dt and dtb genes were isolated from bacterial strain ATCC (American Type Culture Collection) no. 13812. Plasmid pET29a+ was extracted by DNA-spin TM plasmid purification kit where genes were inserted using BamHI and HindIII-HF. Cloned pET29a+dt and pET29a+dtb plasmids were transformed into E. coli BL21(DE3)PlysS as expression host. The identity of the sequences was validated by blasting the sequence (BLASTn) against all the reported nucleotide sequences in the NCBI (National Center for Biotechnology Information) GenBank. Production of proteins in high yield by different types and parameters of fermentation to determine optimal conditions. Lastly, the purified concentrated rdtx and rdtb were injected to BALB/c mice and antibody titers were detected. Results The genetic transformation of E. coli DH5α and E. coli BL21 with the pET-29a(+) carrying the dt and dtb genes was confirmed by colony polymerase chain reaction assay and were positive to grow on Luria-Bertani/kanamycin medium. The open reading frame of dt and dtb sequences consisted of 1,600 bp and 1,000 bp, were found to be 100% identical to dt and dtb sequence of C. diphtheriae (accession number KX702999.1 and KX702993.1) respectively. The optimal condition for high cell density is fed-batch fermentation production to express the rdtx and rdtb at 280 and 240 Lf/mL, dissolved oxygen was about 24% and 22% and the dry cell weight of bacteria was 2.41 g/L and 2.18 g/L, respectively. Conclusion This study concluded with success in preparing genetically modified two strains for the production of a diphtheria vaccine, and to reach ideal production conditions to achieve the highest productivity.
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Affiliation(s)
| | | | - Hamdallah Zedan
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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15
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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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16
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Yi YC, Shih IT, Yu TH, Lee YJ, Ng IS. Challenges and opportunities of bioprocessing 5-aminolevulinic acid using genetic and metabolic engineering: a critical review. BIORESOUR BIOPROCESS 2021; 8:100. [PMID: 38650260 PMCID: PMC10991938 DOI: 10.1186/s40643-021-00455-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
5-Aminolevulinic acid (5-ALA), a non-proteinogenic five-carbon amino acid, has received intensive attentions in medicine due to its approval by the US Food and Drug Administration (FDA) for cancer diagnosis and treatment as photodynamic therapy. As chemical synthesis of 5-ALA performed low yield, complicated processes, and high cost, biosynthesis of 5-ALA via C4 (also called Shemin pathway) and C5 pathway related to heme biosynthesis in microorganism equipped more advantages. In C4 pathway, 5-ALA is derived from condensation of succinyl-CoA and glycine by 5-aminolevulic acid synthase (ALAS) with pyridoxal phosphate (PLP) as co-factor in one-step biotransformation. The C5 pathway involves three enzymes comprising glutamyl-tRNA synthetase (GltX), glutamyl-tRNA reductase (HemA), and glutamate-1-semialdehyde aminotransferase (HemL) from α-ketoglutarate in TCA cycle to 5-ALA and heme. In this review, we describe the recent results of 5-ALA production from different genes and microorganisms via genetic and metabolic engineering approaches. The regulation of different chassis is fine-tuned by applying synthetic biology and boosts 5-ALA production eventually. The purification process, challenges, and opportunities of 5-ALA for industrial applications are also summarized.
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Affiliation(s)
- Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - I-Tai Shih
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Tzu-Hsuan Yu
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Yen-Ju Lee
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
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17
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Functional expression of an echinocandin B deacylase from Actinoplanes utahensis in Escherichia coli. Int J Biol Macromol 2021; 187:850-857. [PMID: 34339787 DOI: 10.1016/j.ijbiomac.2021.07.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/10/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022]
Abstract
Echinocandin B deacylase (ECBD) from Actinoplanes utahensis can be applied to produce echinocandin B nucleus (ECBN), an essential intermediate of the echinocandins antifungal drugs such as anidulafungin. To date, the expression of ECBD has been limited to Streptomyces. To achieve the active expression of ECBD in Escherichia coli (E. coli), we constructed a plasmid carrying two subunits of ECBD for T7 RNA polymerase driven transcription of dicistron messenger after codon optimization. Subsequently, the introduction of peptide tags in the recombinant ECBD was adopted to reduce the formation of inclusion bodies and enhance the ECBD solubility. The peptide tags with the opposite electrostatic charge, hexa-lysine (6K) and GEGEG (GE), exhibited the best positive effect, which was verified by activity assay and structural simulation. After that, optimization of culture conditions and characterization of ECBD were conducted, the optimal pH and temperature were 7.0 and 60 °C. It is the first report concerning the functional expression of ECBD in the host E. coli. Our results reported here can provide a reference for the high-level expression of other deacylases with respect to a possible industrial application.
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18
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Bourgade B, Minton NP, Islam MA. Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms. FEMS Microbiol Rev 2021; 45:fuab008. [PMID: 33595667 PMCID: PMC8351756 DOI: 10.1093/femsre/fuab008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Unabated mining and utilisation of petroleum and petroleum resources and their conversion to essential fuels and chemicals have drastic environmental consequences, contributing to global warming and climate change. In addition, fossil fuels are finite resources, with a fast-approaching shortage. Accordingly, research efforts are increasingly focusing on developing sustainable alternatives for chemicals and fuels production. In this context, bioprocesses, relying on microorganisms, have gained particular interest. For example, acetogens use the Wood-Ljungdahl pathway to grow on single carbon C1-gases (CO2 and CO) as their sole carbon source and produce valuable products such as acetate or ethanol. These autotrophs can, therefore, be exploited for large-scale fermentation processes to produce industrially relevant chemicals from abundant greenhouse gases. In addition, genetic tools have recently been developed to improve these chassis organisms through synthetic biology approaches. This review will focus on the challenges of genetically and metabolically modifying acetogens. It will first discuss the physical and biochemical obstacles complicating successful DNA transfer in these organisms. Current genetic tools developed for several acetogens, crucial for strain engineering to consolidate and expand their catalogue of products, will then be described. Recent tool applications for metabolic engineering purposes to allow redirection of metabolic fluxes or production of non-native compounds will lastly be covered.
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Affiliation(s)
- Barbara Bourgade
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, University of Nottingham, Nottingham, Nottinghamshire, NG7 2RD, UK
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
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19
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Xu J, Dong F, Wu M, Tao R, Yang J, Wu M, Jiang Y, Yang S, Yang L. Vibrio natriegens as a pET-Compatible Expression Host Complementary to Escherichia coli. Front Microbiol 2021; 12:627181. [PMID: 33679648 PMCID: PMC7933001 DOI: 10.3389/fmicb.2021.627181] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022] Open
Abstract
Efficient and novel recombinant protein expression systems can further reduce the production cost of enzymes. Vibrio natriegens is the fastest growing free-living bacterium with a doubling time of less than 10 min, which makes it highly attractive as a protein expression host. Here, 196 pET plasmids with different genes of interest (GOIs) were electroporated into the V. natriegens strain VnDX, which carries an integrated T7 RNA polymerase expression cassette. As a result, 65 and 75% of the tested GOIs obtained soluble expression in V. natriegens and Escherichia coli, respectively, 20 GOIs of which showed better expression in the former. Furthermore, we have adapted a consensus "what to try first" protocol for V. natriegens based on Terrific Broth medium. Six sampled GOIs encoding biocatalysts enzymes thus achieved 50-128% higher catalytic efficiency under the optimized expression conditions. Our study demonstrated V. natriegens as a pET-compatible expression host with a spectrum of highly expressed GOIs distinct from E. coli and an easy-to-use consensus protocol, solving the problem that some GOIs cannot be expressed well in E. coli.
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Affiliation(s)
- Jiaqi Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Feng Dong
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China
| | - Meixian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rongsheng Tao
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China.,Huzhou Yisheng Biotechnology Co., Ltd., Huzhou, China
| | - Junjie Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mianbin Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China.,Shanghai Taoyusheng Biotechnology Co., Ltd., Shanghai, China
| | - Sheng Yang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes for Biological Sciences, Huzhou, China.,Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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20
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Stepwise optimization of recombinant protein production in Escherichia coli utilizing computational and experimental approaches. Appl Microbiol Biotechnol 2020; 104:3253-3266. [DOI: 10.1007/s00253-020-10454-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
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21
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Hui CY, Guo Y, Liu L, Zheng HQ, Gao CX, Zhang W. Construction of a RFP-lacZα bicistronic reporter system and its application in lead biosensing. PLoS One 2020; 15:e0228456. [PMID: 31999769 PMCID: PMC6991944 DOI: 10.1371/journal.pone.0228456] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/15/2020] [Indexed: 01/12/2023] Open
Abstract
The combination of a fluorescent reporter and enzymatic reporter provides a flexible and versatile way for the study of diverse biological processes, such as the detection of transcription and translation. Thus, there is an urgent need to develop this novel bifunctional reporter system. This study reports the design, construction, and validation of a new dicistronic mCherry-lacZα reporter system by artificial lac operon and pbr operon models in lacZM15-producing E. coli. It allows two reporter genes to be co-transcribed into a dicistronic mRNA strand, followed by coupled expression of mCherry and lacZα. In artificial lac operons, expression of the downstream lacZα was demonstrated to be positively related to expression of the upstream ORF. In artificial pbr operons, compared with the insertion of downstream full-length lacZ, the insertion of downstream lacZα exerted a slight effect on the response from the upstream mCherry. Furthermore, the downstream lacZα reporter showed stronger response to Pb(II) than the downstream full-length lacZ. Importantly, the response sensitivity of downstream lacZα was still higher than that of upstream mCherry in a dual RFP-lacZα reporter construct. The highly efficient expression profile of the reporter lacZα peptide makes it a preferred downstream reporter in polycistronic constructs. This novel bifunctional reporter system offers a robust tool for biological studies.
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Affiliation(s)
- Chang-ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- Department of Science & Education, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Institute of Translational Medicine, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Hao-qu Zheng
- Department of Science & Education, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Chao-xian Gao
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Wen Zhang
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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22
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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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23
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Costa DAL, Filho EXF. Microbial β-mannosidases and their industrial applications. Appl Microbiol Biotechnol 2018; 103:535-547. [PMID: 30426153 DOI: 10.1007/s00253-018-9500-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/18/2022]
Abstract
Heteropolymers of mannan are polysaccharide components of the plant cell wall of gymnosperms and some angiosperms, including palm trees (Arecales and Monocot). Degradation of the complex structure of these polysaccharides requires the synergistic action of enzymes that disrupt the internal carbon skeleton of mannan and accessory enzymes that remove side chain substituents. However, complete degradation of these polysaccharides is carried out by an exo-hydrolase termed β-mannosidase. Microbial β-mannosidases belong to families 1, 2, and 5 of glycosyl hydrolases, and catalyze the hydrolysis of non-reducing ends of mannose oligomers. Besides, these enzymes are also involved in transglycosylation reactions. Because of their activity at different temperatures and pH values, these enzymes are used in a variety of industrial applications and the pharmaceutical, food, and biofuel industries.
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24
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Efficient Conversion of Acetate to 3-Hydroxypropionic Acid by Engineered Escherichia coli. Catalysts 2018. [DOI: 10.3390/catal8110525] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Acetate, which is an abundant carbon source, is a potential feedstock for microbial processes that produce diverse value-added chemicals. In this study, we produced 3-hydroxypropionic acid (3-HP) from acetate with engineered Escherichia coli. For the efficient conversion of acetate to 3-HP, we initially introduced heterologous mcr (encoding malonyl-CoA reductase) from Chloroflexus aurantiacus. Then, the acetate assimilating pathway and glyoxylate shunt pathway were activated by overexpressing acs (encoding acetyl-CoA synthetase) and deleting iclR (encoding the glyoxylate shunt pathway repressor). Because a key precursor malonyl-CoA is also consumed for fatty acid synthesis, we decreased carbon flux to fatty acid synthesis by adding cerulenin. Subsequently, we found that inhibiting fatty acid synthesis dramatically improved 3-HP production (3.00 g/L of 3-HP from 8.98 g/L of acetate). The results indicated that acetate can be used as a promising carbon source for microbial processes and that 3-HP can be produced from acetate with a high yield (44.6% of the theoretical maximum yield).
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25
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Müller C, Ulrich R, Franzke K, Müller M, Köllner B. Crude extracts of recombinant baculovirus expressing rabbit hemorrhagic disease virus 2 VLPs from both insect and rabbit cells protect rabbits from rabbit hemorrhagic disease caused by RHDV2. Arch Virol 2018; 164:137-148. [PMID: 30291504 DOI: 10.1007/s00705-018-4032-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/14/2018] [Indexed: 12/19/2022]
Abstract
Vaccines against viral pathogens are often composed of recombinant proteins expressed in different systems. Such proteins expressed by recombinant baculoviruses have been proven to be effective for vaccination. Especially, after codon usage optimization high amounts of recombinant viral proteins can be obtained which can assemble to virus like particles (VLPs) spontaneously. In this study we compared two different codon usages of RHDV2-VP1 to improve the expression of recombinant VP1 of RHDV2 by recombinant baculoviruses after infection of insect SF9 cells or transduction of mammalian RK13 cells in order to gain high protein yields. Also the influence on the auto-assembly of RHDV2-VP1 to VLPs was investigated. Finally, the immunogenic potential of such recombinant vaccines against RHDV2 to induce a protective immune response in rabbits against RHDV2 should be characterized. There was no influence of different codon usages on RHDV2-VP1 gene expression in the respective cell lines detected. However, in insect cell line SF9 higher rates of recombinant VP1 were measured in comparison to the transduction of mammalian cells RK13. Auto-assembly of RHDV2-VP1 to VLPs was observed in both cell systems by electron microscopy. Finally, both RHDV-VP1 VLPs derived from mammalian and insect cells were able to induce a protective humoral immune response in rabbits against RHDV2.
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Affiliation(s)
- Claudia Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany
| | - Reiner Ulrich
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany
| | - Marcus Müller
- IDT Biologika (Riems), Greifswald-Insel Riems, Germany
| | - Bernd Köllner
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany.
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26
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Du MZ, Wei W, Qin L, Liu S, Zhang AY, Zhang Y, Zhou H, Guo FB. Co-adaption of tRNA gene copy number and amino acid usage influences translation rates in three life domains. DNA Res 2018; 24:623-633. [PMID: 28992099 PMCID: PMC5726483 DOI: 10.1093/dnares/dsx030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/15/2017] [Indexed: 12/01/2022] Open
Abstract
Although more and more entangled participants of translation process were realized, how they cooperate and co-determine the final translation efficiency still lacks details. Here, we reasoned that the basic translation components, tRNAs and amino acids should be consistent to maximize the efficiency and minimize the cost. We firstly revealed that 310 out of 410 investigated genomes of three domains had significant co-adaptions between the tRNA gene copy numbers and amino acid compositions, indicating that maximum efficiency constitutes ubiquitous selection pressure on protein translation. Furthermore, fast-growing and larger bacteria are found to have significantly better co-adaption and confirmed the effect of this pressure. Within organism, highly expressed proteins and those connected to acute responses have higher co-adaption intensity. Thus, the better co-adaption probably speeds up the growing of cells through accelerating the translation of special proteins. Experimentally, manipulating the tRNA gene copy number to optimize co-adaption between enhanced green fluorescent protein (EGFP) and tRNA gene set of Escherichia coli indeed lifted the translation rate (speed). Finally, as a newly confirmed translation rate regulating mechanism, the co-adaption reflecting translation rate not only deepens our understanding on translation process but also provides an easy and practicable method to improve protein translation rates and productivity.
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Affiliation(s)
| | - Wen Wei
- School of Life Science and Technology
| | - Lei Qin
- School of Life Science and Technology
| | - Shuo Liu
- School of Life Science and Technology
| | - An-Ying Zhang
- School of Life Science and Technology.,Centre for Informational Biology
| | - Yong Zhang
- School of Life Science and Technology.,Centre for Informational Biology
| | - Hong Zhou
- School of Life Science and Technology.,Centre for Informational Biology
| | - Feng-Biao Guo
- School of Life Science and Technology.,Centre for Informational Biology.,Key Laboratory for Neuroinformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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27
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Kumar N, Pandey R, Prabhu AA, Venkata Dasu V. Genetic and substrate-level modulation of Bacillus subtilis physiology for enhanced extracellular human interferon gamma production. Prep Biochem Biotechnol 2018; 48:391-401. [PMID: 29688129 DOI: 10.1080/10826068.2018.1446157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Human interferon-gamma (hIFNG) production is limited by various gene-level bottlenecks including translation, protein folding, and secretion which depends upon the physiological state of the organism. In this study gene-level and substrate-level modulations have been used to control Bacillus subtilis physiology for >15 fold extracellular soluble hIFNG production. Two variants of the native human interferon-gamma gene (hifng) were designed and synthesized, namely, cohifnghis and cohifng having codon adaptation index 25.33 and 26.89% higher than the native gene, respectively. BScoIFNG and BScoIFNGhis with ΔG of -100.0 and -113.7 kcal mol-1 resulted in 30 and 6.5% higher hIFNG compared to the native gene in complex medium. BScoIFNG produced 1.53 fold higher hIFNG using glucose-based defined medium as compared to the complex medium by modulating the physiological parameter growth rate from 0.35 to 0.26 hr-1. Further modulatory effect of various phosphotransferase transport system (PTS) and no-PTS sugars, sugar alcohols, and organic acids was quantified on the physiology of B. subtilis WB800N for extracellular hIFNG production. Sorbitol and glycerol emerged as the best hIFNG producers with lowest growth and substrate consumption rates. BScoIFNG produced maximum 3.15 mg L-1 hIFNG at 50 g L-1 glycerol with highest hIFNG yield (Yp/x = 0.136) and lowest substrate uptake rate (qs = 0.26).
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Affiliation(s)
- Nitin Kumar
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
| | - Rajat Pandey
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
| | - Ashish Anand Prabhu
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
| | - Veeranki Venkata Dasu
- a Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering , Indian Institute of Technology Guwahati , Guwahati , Assam , India
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28
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Ohmori T, Mizukami H, Katakai Y, Kawai S, Nakamura H, Inoue M, Shu T, Sugimoto H, Sakata Y. Safety of intra-articular transplantation of lentivirally transduced mesenchymal stromal cells for haemophilic arthropathy in a non-human primate. Int J Hematol 2018; 108:239-245. [PMID: 29737459 DOI: 10.1007/s12185-018-2465-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/01/2022]
Abstract
Joint bleeding and resultant arthropathy are major determinants of quality of life in haemophilia patients. We previously developed a mesenchymal stromal cell (MSC)-based treatment approach for haemophilic arthropathy in a mouse model of haemophilia A. Here, we evaluated the long-term safety of intra-articular injection of lentivirally transduced autologous MSCs in non-human primates. Autologous bone-marrow-derived MSCs transduced with a lentiviral vector expressing coagulation factor VIII (FVIII) were injected into the left knee joint of cynomolgus monkeys. We first conducted codon optimization to increase FVIII production in the cells. Lentiviral transduction of autologous MSCs resulted in a significant increase of FVIII in the culture supernatant before transplantation. We did not find any tumour generation around the knee structure at 11-16 months after injection by magnetic resonance imaging. The proviral sequence of the simian immunodeficiency virus lentiviral vector was not detected in the heart, lungs, spleen, liver, testis, or bone marrow by real-time quantitative PCR. We confirmed the long-term safety of intra-articular injection of transduced MSCs in a non-human primate. The procedure may be an attractive therapeutic approach for joint diseases in haemophilia patients.
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Affiliation(s)
- Tsukasa Ohmori
- Department of Biochemistry, Jichi Medical University School of Medicine, 3111-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan.
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yuko Katakai
- The Corporation for Production and Research of Laboratory Primates, 1-16-2 Sakura, Tsukuba, Ibaraki, 305-0003, Japan
| | - Sho Kawai
- Department of Radiology, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hitoyasu Nakamura
- Department of Radiology, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Makoto Inoue
- ID Pharma Inc., 6 Okubo, Tsukuba, Ibaraki, 300-2611, Japan
| | - Tsugumine Shu
- ID Pharma Inc., 6 Okubo, Tsukuba, Ibaraki, 300-2611, Japan
| | - Hideharu Sugimoto
- Department of Radiology, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yoichi Sakata
- Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan
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Mignon C, Mariano N, Stadthagen G, Lugari A, Lagoutte P, Donnat S, Chenavas S, Perot C, Sodoyer R, Werle B. Codon harmonization - going beyond the speed limit for protein expression. FEBS Lett 2018; 592:1554-1564. [PMID: 29624661 DOI: 10.1002/1873-3468.13046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 12/14/2022]
Abstract
Codon usage distribution has been soundly used by nature to fine tune protein biogenesis. Alteration of the mRNA structure or sequential scheduling of codons can profoundly affect translation, thus altering protein yield, functionality, solubility, and proper folding. Building on these observations, here, we present an evaluation of different recently designed algorithms of sequence adaptation based on Codon Adaptation Index (CAI) profiling. The first algorithm globally harmonizes synonymous codons in the original sequence in full respect to the heterologous expression host codon usage. The second recodes the sequence in accordance with the native sequence CAI profile. Our data, generated on three model proteins, highlights the importance to consider gene recoding as a parameter itself for recombinant protein expression improvement.
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Affiliation(s)
- Charlotte Mignon
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | - Natacha Mariano
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | | | - Adrien Lugari
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | | | - Stéphanie Donnat
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
| | | | | | | | - Bettina Werle
- Protein and Expression System Engineering Unit, BIOASTER, Lyon, France
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Ahmad I, Nawaz N, Darwesh NM, ur Rahman S, Mustafa MZ, Khan SB, Patching SG. Overcoming challenges for amplified expression of recombinant proteins using Escherichia coli. Protein Expr Purif 2018; 144:12-18. [DOI: 10.1016/j.pep.2017.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 11/28/2022]
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Afriat-Jurnou L, Cohen R, Paluy I, Ben-Adiva R, Yadid I. Directed evolution of an endoinulinase from Talaromyces purpureogenus
toward efficient production of inulooligosaccharides. Biotechnol Prog 2018; 34:868-877. [DOI: 10.1002/btpr.2618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/25/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Livnat Afriat-Jurnou
- MIGAL- Galilee Research Institute; Kiryat-Shmona 11016 Israel
- Faculty of Sciences and Technology; Tel-Hai Academic College; Upper Galilee 12208 Israel
| | - Rami Cohen
- MIGAL- Galilee Research Institute; Kiryat-Shmona 11016 Israel
| | - Irina Paluy
- MIGAL- Galilee Research Institute; Kiryat-Shmona 11016 Israel
| | - Ran Ben-Adiva
- MIGAL- Galilee Research Institute; Kiryat-Shmona 11016 Israel
| | - Itamar Yadid
- MIGAL- Galilee Research Institute; Kiryat-Shmona 11016 Israel
- Faculty of Sciences and Technology; Tel-Hai Academic College; Upper Galilee 12208 Israel
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Wu D, Cai G, Li X, Li B, Lu J. Cloning and expression of ferulic acid esterase gene and its effect on wort filterability. Biotechnol Lett 2018; 40:711-717. [PMID: 29435688 DOI: 10.1007/s10529-018-2511-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/08/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To optimize the expression of type A ferulic acid esterase (FaeA) from Aspergillus niger in Pichia pastoris X-33 using codon optimization. RESULTS Recombinant FaeA was purified from the fermentation broth, with the maximum specific activity of 48.4 ± 0.1 U mg-1. Adding it during mashing process for beer brewing raised the filtration rate by 14.5% while the turbidity and viscosity declined by 22 and 6.9%, respectively. Addition of FaeA increased the concentrations of free ferulic acid (FA) and arabinoxylan (AX) in the wort, while the polymeric arabinoxylans content declined significantly. CONCLUSIONS Recombinant FaeA was capable to prevent the oxidative gelation of PAX formation by breaking the cross-linking of FA among AX chains and improve the filtration performance of wort.
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Affiliation(s)
- Dianhui Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guolin Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaomin Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bing Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jian Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, China.
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Yaakob Y, Rodrigues KF, Opook F, William T, John DV. Recombinant LipL32 Protein Developed Using a Synthetic Gene Detects Leptospira-specific Antibodies in Human Serum Samples. Malays J Med Sci 2018; 24:44-51. [PMID: 29386971 DOI: 10.21315/mjms2017.24.5.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/13/2017] [Indexed: 10/18/2022] Open
Abstract
Background Synthetic biology is emerging as a viable alternative for the production of recombinant antigens for diagnostic applications. It offers a safe alternative for the synthesis of antigenic principles derived from organisms that pose a high biological risk. Methods Here, we describe an enzyme-linked immunosorbent assay (ELISA) using the synthetic recombinant LipL32 (rLipL32) protein expressed in Escherichia coli for the detection of Leptospira-specific antibodies in human serum samples. The rLipL32-based ELISA was compared with a microscopic agglutination test (MAT), which is currently used as the gold standard for the diagnosis of leptospirosis. Results Our results showed that all the MAT-positive serum samples were positive for Leptospira-specific IgG in an ELISA, while 65% (n = 13) of these samples were also positive for Leptospira-specific IgM. In the MAT-negative serum samples, 80% and 55% of the samples were detected as negative by an ELISA for Leptospira-specific IgM and IgG, respectively. Conclusion An ELISA using the synthetic rLipL32 antigen was able to distinguish Leptospira-specific IgM (sensitivity 65% and specificity 80%) and IgG (sensitivity 100% and specificity 55%) in human serum samples and has the potential to serve as a rapid diagnostic test for leptospirosis.
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Affiliation(s)
- Yuszniahyati Yaakob
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | | | - Fernandes Opook
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | | | - Daisy Vanitha John
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
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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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Rodríguez-Álvarez Y, Martínez-Cordovez K, Llopiz-Arzuaga A, Ramos-Gómez Y, Besada-Pérez V, García-Lines D, Santos-Savio A. Obtention and characterization of the recombinant simian Interleukin-15 in Escherichia coli for the preclinical assessment of an IL-15-based therapeutic vaccine. Prep Biochem Biotechnol 2017; 47:889-900. [PMID: 28816622 DOI: 10.1080/10826068.2017.1365238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Recombinant simian IL-15 (siIL-15) was obtained for the preclinical assessment of an anti-human IL-15 vaccine. For this purpose, the cDNA from peripheral blood mononuclear cells of a Macaca fascicularis monkey was cloned into a pIL-2 vector. The siIL-15 was expressed in Escherichia coli strain W3110 as an insoluble protein which accounted for 13% of the total cellular proteins. Inclusion bodies were solubilized in an 8 M urea solution, which was purified by ion exchange and reverse phase chromatography up to 92% purity. The protein identity was validated by electrospray ionization-mass spectrometry, confirming the presence of the amino acids which distinguish the siIL-15 from human IL-15. The purified siIL-15 stimulates the proliferation of cytotoxic T-lymphocytes line (CTLL)-2 and Kit 225 cells with EC50 values of 3.1 and 32.5 ng/mL, respectively. Antisera from modified human IL-15-immunized macaques were reactive to human and simian IL-15 in enzyme-linked immunosorbent assays. Moreover, the anti-human IL-15 antibodies from immune sera inhibited siIL-15 activity in CTLL-2 and Kit 225 cells, supporting the activity and purity of recombinant siIL-15. These results indicate that the recombinant siIL-15 is biologically active in two IL-15-dependent cell lines, and it is also suitable for the preclinical evaluation of an IL-15-based therapeutic vaccine.
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Affiliation(s)
| | | | - Alexey Llopiz-Arzuaga
- b Chemistry and Physics Division , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Yassel Ramos-Gómez
- b Chemistry and Physics Division , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Vladimir Besada-Pérez
- b Chemistry and Physics Division , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Dayana García-Lines
- b Chemistry and Physics Division , Center for Genetic Engineering and Biotechnology , Havana , Cuba
| | - Alicia Santos-Savio
- a Pharmaceutical Division , Center for Genetic Engineering and Biotechnology , Havana , Cuba
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36
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Thermostable proteins bioprocesses: The activity of restriction endonuclease-methyltransferase from Thermus thermophilus (RM.TthHB27I) cloned in Escherichia coli is critically affected by the codon composition of the synthetic gene. PLoS One 2017; 12:e0186633. [PMID: 29040308 PMCID: PMC5645126 DOI: 10.1371/journal.pone.0186633] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/04/2017] [Indexed: 11/25/2022] Open
Abstract
Obtaining thermostable enzymes (thermozymes) is an important aspect of biotechnology. As thermophiles have adapted their genomes to high temperatures, their cloned genes’ expression in mesophiles is problematic. This is mainly due to their high GC content, which leads to the formation of unfavorable secondary mRNA structures and codon usage in Escherichia coli (E. coli). RM.TthHB27I is a member of a family of bifunctional thermozymes, containing a restriction endonuclease (REase) and a methyltransferase (MTase) in a single polypeptide. Thermus thermophilus HB27 (T. thermophilus) produces low amounts of RM.TthHB27I with a unique DNA cleavage specificity. We have previously cloned the wild type (wt) gene into E. coli, which increased the production of RM.TthHB27I over 100-fold. However, its enzymatic activities were extremely low for an ORF expressed under a T7 promoter. We have designed and cloned a fully synthetic tthHB27IRM gene, using a modified ‘codon randomization’ strategy. Codons with a high GC content and of low occurrence in E. coli were eliminated. We incorporated a stem-loop circuit, devised to negatively control the expression of this highly toxic gene by partially hiding the ribosome-binding site (RBS) and START codon in mRNA secondary structures. Despite having optimized 59% of codons, the amount of produced RM.TthHB27I protein was similar for both recombinant tthHB27IRM gene variants. Moreover, the recombinant wt RM.TthHB27I is very unstable, while the RM.TthHB27I resulting from the expression of the synthetic gene exhibited enzymatic activities and stability equal to the native thermozyme isolated from T. thermophilus. Thus, we have developed an efficient purification protocol using the synthetic tthHB27IRM gene variant only. This suggests the effect of co-translational folding kinetics, possibly affected by the frequency of translational errors. The availability of active RM.TthHB27I is of practical importance in molecular biotechnology, extending the palette of available REase specificities.
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37
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Efficient genetic approaches for improvement of plasmid based expression of recombinant protein in Escherichia coli : A review. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cerminati S, Eberhardt F, Elena CE, Peirú S, Castelli ME, Menzella HG. Development of a highly efficient oil degumming process using a novel phosphatidylinositol-specific phospholipase C enzyme. Appl Microbiol Biotechnol 2017; 101:4471-4479. [PMID: 28238084 DOI: 10.1007/s00253-017-8201-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/31/2017] [Accepted: 02/14/2017] [Indexed: 11/27/2022]
Abstract
Enzymatic degumming using phospholipase C (PLC) enzymes may be used in environmentally friendly processes with improved oil recovery yields. In this work, phosphatidylinositol-specific phospholipase C (PIPLC) candidates obtained from an in silico analysis were evaluated for oil degumming. A PIPLC from Lysinibacillus sphaericus was shown to efficiently remove phosphatidylinositol from crude oil, and when combined with a second phosphatidylcholine and phosphatidylethanolamine-specific phospholipase C, the three major phospholipids were completely hydrolyzed, providing an extra yield of oil greater than 2.1%, compared to standard methods. A remarkably efficient fed-batch Escherichia coli fermentation process producing ∼14 g/L of the recombinant PIPLC enzyme was developed, which may facilitate the adoption of this cost-effective oil-refining process.
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Affiliation(s)
- Sebastián Cerminati
- CONICET y Departamento de Tecnología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), Suipacha 531, 2000, Rosario, Argentina
| | - Florencia Eberhardt
- CONICET y Departamento de Tecnología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), Suipacha 531, 2000, Rosario, Argentina
| | | | - Salvador Peirú
- CONICET y Departamento de Tecnología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), Suipacha 531, 2000, Rosario, Argentina.,Keclon S.A., Tucumán 7180, 2000, Rosario, Argentina
| | - María E Castelli
- CONICET y Departamento de Tecnología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), Suipacha 531, 2000, Rosario, Argentina.,Keclon S.A., Tucumán 7180, 2000, Rosario, Argentina
| | - Hugo G Menzella
- CONICET y Departamento de Tecnología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Instituto de Procesos Biotecnológicos y Químicos (IPROBYQ), Suipacha 531, 2000, Rosario, Argentina. .,Keclon S.A., Tucumán 7180, 2000, Rosario, Argentina.
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Tuan-Anh T, Ly LT, Viet NQ, Bao PT. Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. BMC Bioinformatics 2017; 18:100. [PMID: 28187713 PMCID: PMC5303253 DOI: 10.1186/s12859-017-1517-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 02/01/2017] [Indexed: 11/18/2022] Open
Abstract
Background Since the recombinant protein was discovered, it has become more popular in many aspects of life science. The value of global pharmaceutical market was $87 billion in 2008 and the sales for industrial enzyme exceeded $4 billion in 2012. This is strong evidence showing the great potential of recombinant protein. However, native genes introduced into a host can cause incompatibility of codon usage bias, GC content, repeat region, Shine-Dalgarno sequence with host’s expression system, so the yields can fall down significantly. Hence, we propose novel methods for gene optimization based on neural network, Bayesian theory, and Euclidian distance. Result The correlation coefficients of our neural network are 0.86, 0.73, and 0.90 in training, validation, and testing process. In addition, genes optimized by our methods seem to associate with highly expressed genes and give reasonable codon adaptation index values. Furthermore, genes optimized by the proposed methods are highly matched with the previous experimental data. Conclusion The proposed methods have high potential for gene optimization and further researches in gene expression. We built a demonstrative program using Matlab R2014a under Mac OS X. The program was published in both standalone executable program and Matlab function files. The developed program can be accessed from http://www.math.hcmus.edu.vn/~ptbao/paper_soft/GeneOptProg/.
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Affiliation(s)
- Tran Tuan-Anh
- Faculty of Mathematics and Computer Science, VNUHCM-University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Le Thi Ly
- School of Biotechnology, VNUHCM-International University, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Ngo Quoc Viet
- Faculty of Information Technology, Ho Chi Minh City University of Pedagogy, 280 An Duong Vuong Street, Ward 4, District 5, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Faculty of Mathematics and Computer Science, VNUHCM-University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam.
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Vazquez-Albacete D, Cavaleiro AM, Christensen U, Seppälä S, Møller BL, Nørholm MHH. An expression tag toolbox for microbial production of membrane bound plant cytochromes P450. Biotechnol Bioeng 2016; 114:751-760. [PMID: 27748524 DOI: 10.1002/bit.26203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/11/2022]
Abstract
Membrane-associated Cytochromes P450 (P450s) are one of the most important enzyme families for biosynthesis of plant-derived medicinal compounds. However, the hydrophobic nature of P450s makes their use in robust cell factories a challenge. Here, we explore a small library of N-terminal expression tag chimeras of the model plant P450 CYP79A1 in different Escherichia coli strains. Using a high-throughput screening platform based on C-terminal GFP fusions, we identify several highly expressing and robustly performing chimeric designs. Analysis of long-term cultures by flow cytometry showed homogeneous populations for some of the conditions. Three chimeric designs were chosen for a more complex combinatorial assembly of a multigene pathway consisting of two P450s and a redox partner. Cells expressing these recombinant enzymes catalyzed the conversion of the substrate to highly different ratios of the intermediate and the final product of the pathway. Finally, the effect of a robustly performing expression tag was explored with a library of 49 different P450s from medicinal plants and nearly half of these were improved in expression by more than twofold. The developed toolbox serves as a platform to tune P450 performance in microbial cells, thereby facilitating recombinant production of complex plant P450-derived biochemicals. Biotechnol. Bioeng. 2017;114: 751-760. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Dario Vazquez-Albacete
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Ana Mafalda Cavaleiro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Ulla Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Susanna Seppälä
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for Synthetic Biology: bioSYNergy, University of Copenhagen, Copenhagen, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle allé 6, Hørsholm, Denmark.,Center for Synthetic Biology: bioSYNergy, University of Copenhagen, Copenhagen, Denmark
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Expression of Codon-Optimized Plant Glycosyltransferase UGT72B14 in Escherichia coli Enhances Salidroside Production. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9845927. [PMID: 27597978 PMCID: PMC5002478 DOI: 10.1155/2016/9845927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 11/18/2022]
Abstract
Salidroside, a plant secondary metabolite in Rhodiola, has been demonstrated to have several adaptogenic properties as a medicinal herb. Due to the limitation of plant source, microbial production of salidroside by expression of plant uridine diphosphate glycosyltransferase (UGT) is promising. However, glycoside production usually remains hampered by poor expression of plant UGTs in microorganisms. Herein, we achieved salidroside production by expression of Rhodiola UGT72B14 in Escherichia coli (E. coli) and codon optimization was accordingly applied. UGT72B14 expression was optimized by changing 278 nucleotides and decreasing the G+C content to 51.05% without altering the amino acid sequence. The effect of codon optimization on UGT72B14 catalysis for salidroside production was assessed both in vitro and in vivo. In vitro, salidroside production by codon-optimized UGT72B14 is enhanced because of a significantly improved protein yield (increased by 4.8-fold) and an equivalently high activity as demonstrated by similar kinetic parameters (KM and Vmax), compared to that by wild-type protein. In vivo, both batch and fed-batch cultivation using the codon-optimized gene resulted in a significant increase in salidroside production, which was up to 6.7 mg/L increasing 3.2-fold over the wild-type UGT72B14.
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Critical reflections on synthetic gene design for recombinant protein expression. Curr Opin Struct Biol 2016; 38:155-62. [DOI: 10.1016/j.sbi.2016.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/17/2022]
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Purification and characterization of thermostable serine proteases encoded by the genes ttha0099 and ttha01320 from Thermus thermophilus HB8. Extremophiles 2016; 20:493-502. [DOI: 10.1007/s00792-016-0839-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
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Ang KS, Kyriakopoulos S, Li W, Lee DY. Multi-omics data driven analysis establishes reference codon biases for synthetic gene design in microbial and mammalian cells. Methods 2016; 102:26-35. [PMID: 26850284 DOI: 10.1016/j.ymeth.2016.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 01/08/2016] [Accepted: 01/19/2016] [Indexed: 11/19/2022] Open
Abstract
In this study, we analyzed multi-omics data and subsets thereof to establish reference codon usage biases for codon optimization in synthetic gene design. Specifically, publicly available genomic, transcriptomic, proteomic and translatomic data for microbial and mammalian expression hosts, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Chinese hamster ovary (CHO) cells, were compiled to derive their individual codon and codon pair frequencies. Then, host dependent and -omics specific codon biases were generated and compared by principal component analysis and hierarchical clustering. Interestingly, our results indicated the similar codon bias patterns of the highly expressed transcripts, highly abundant proteins, and efficiently translated mRNA in microbial cells, despite the general lack of correlation between mRNA and protein expression levels. However, for CHO cells, the codon bias patterns among various -omics subsets are not distinguishable, forming one cluster. Thus, we further investigated the effect of different input codon biases on codon optimized sequences using the codon context (CC) and individual codon usage (ICU) design parameters, via in silico case study on the expression of human IFNγ sequence in CHO cells. The results supported that CC is more robust design parameter than ICU for improved heterologous gene design.
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Affiliation(s)
- Kok Siong Ang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Sarantos Kyriakopoulos
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore
| | - Wei Li
- Sangon Biotech (Shanghai) Co., Ltd., 698 Xiangmin Road, SongJiang District, Shanghai 201611, China
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668, Singapore.
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Peiru S, Aguirre A, Eberhardt F, Braia M, Cabrera R, Menzella HG. An industrial scale process for the enzymatic removal of steryl glucosides from biodiesel. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:223. [PMID: 26697112 PMCID: PMC4687101 DOI: 10.1186/s13068-015-0405-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Biodiesels produced from transesterification of vegetable oils have a major quality problem due to the presence of precipitates, which need to be removed to avoid clogging of filters and engine failures. These precipitates have been reported to be mostly composed of steryl glucosides (SGs), but so far industrial cost-effective methods to remove these compounds are not available. Here we describe a novel method for the efficient removal of SGs from biodiesel, based on the hydrolytic activity of a thermostable β-glycosidase obtained from Thermococcus litoralis. RESULTS A steryl glucosidase (SGase) enzyme from T. litoralis was produced and purified from Escherichia coli cultures expressing a synthetic gene, and used to treat soybean-derived biodiesel. Several optimization steps allowed for the selection of optimal reaction conditions to finally provide a simple and efficient process for the removal of SGs from crude biodiesel. The resulting biodiesel displayed filterability properties similar to distilled biodiesel according to the total contamination (TC), the cold soak filtration test (CSFT), filter blocking tendency (FBT), and cold soak filter blocking tendency (CSFBT) tests. The process was successfully scaled up to a 20 ton reactor, confirming its adaptability to industrial settings. CONCLUSIONS The results presented in this work provide a novel path for the removal of steryl glucosides from biodiesel using a cost-effective, environmentally friendly and scalable enzymatic process, contributing to the adoption of this renewable fuel.
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Affiliation(s)
- Salvador Peiru
- />Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet, Suipacha 531, Rosario, 2000 Argentina
- />Keclon S.A., Tucuman 7180, Rosario, 2000 Argentina
| | - Andres Aguirre
- />Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet, Suipacha 531, Rosario, 2000 Argentina
- />Keclon S.A., Tucuman 7180, Rosario, 2000 Argentina
| | - Florencia Eberhardt
- />Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet, Suipacha 531, Rosario, 2000 Argentina
| | - Mauricio Braia
- />Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet, Suipacha 531, Rosario, 2000 Argentina
| | - Rodolfo Cabrera
- />Unitec Bio S.A., Batalla del Quebracho s/n, Pto. Gral, San Martín, 2202 Argentina
| | - Hugo G. Menzella
- />Genetic Engineering and Fermentation Technology, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario-Conicet, Suipacha 531, Rosario, 2000 Argentina
- />Keclon S.A., Tucuman 7180, Rosario, 2000 Argentina
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Ravasi P, Braia M, Eberhardt F, Elena C, Cerminati S, Peirú S, Castelli ME, Menzella HG. High-level production of Bacillus cereus phospholipase C in Corynebacterium glutamicum. J Biotechnol 2015; 216:142-8. [DOI: 10.1016/j.jbiotec.2015.10.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/15/2015] [Accepted: 10/22/2015] [Indexed: 11/15/2022]
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Rahmen N, Schlupp CD, Mitsunaga H, Fulton A, Aryani T, Esch L, Schaffrath U, Fukuzaki E, Jaeger KE, Büchs J. A particular silent codon exchange in a recombinant gene greatly influences host cell metabolic activity. Microb Cell Fact 2015; 14:156. [PMID: 26438243 PMCID: PMC4595056 DOI: 10.1186/s12934-015-0348-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombinant protein production using Escherichia coli as expression host is highly efficient, however, it also induces strong host cell metabolic burden. Energy and biomass precursors are withdrawn from the host's metabolism as they are required for plasmid replication, heterologous gene expression and protein production. Rare codons in a heterologous gene may be a further drawback. This study aims to investigate the influence of particular silent codon exchanges within a heterologous gene on host cell metabolic activity. Silent mutations were introduced into the coding sequence of a model protein to introduce all synonymous arginine or leucine codons at two randomly defined positions, as well as substitutions leading to identical amino acid exchanges with different synonymous codons. The respective E. coli clones were compared during cultivation in a mineral autoinduction medium using specialized online and offline measuring techniques to quantitatively analyze effects on respiration, biomass and protein production, as well as on carbon source consumption, plasmid copy number, intracellular nucleobases and mRNA content of each clone. RESULTS Host stain metabolic burden correlates with recombinant protein production. Upon heterologous gene expression, tremendous differences in respiration, biomass and protein production were observed. According to their different respiration activity the E. coli clones could be classified into two groups, Type A and Type B. Type A clones tended to higher product formation, Type B clones showed stronger biomass formation. Whereas codon usage and intracellular nucleobases had no influence on the Type-A-Type-B-behavior, plasmid copy number, mRNA content and carbon source consumption strongly differed between the two groups. CONCLUSIONS Particular silent codon exchanges in a heterologous gene sequence led to differences in initial growth of Type A and Type B clones. Thus, the biomass concentration at the time point of induction varied. In consequence, not only plasmid copy number and expression levels differed between the two groups, but also the kinetics of lactose and glycerol consumption. Even though the underlying molecular mechanisms are not yet identified we observed the astonishing phenomenon that particular silent codon exchanges within a heterologous gene tremendously affect host cell metabolism and recombinant protein production. This could have great impact on codon optimization of heterologous genes, screening procedures for improved variants, and biotechnological protein production processes.
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Affiliation(s)
- Natalie Rahmen
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Christian D Schlupp
- Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Hitoshi Mitsunaga
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Japan.
| | - Alexander Fulton
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
| | - Tita Aryani
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
| | - Lara Esch
- Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
| | - Eiichiro Fukuzaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, 565-0871, Japan.
| | - Karl-Erich Jaeger
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany. .,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany.
| | - Jochen Büchs
- AVT, Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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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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Ihssen J, Reiss R, Luchsinger R, Thöny-Meyer L, Richter M. Biochemical properties and yields of diverse bacterial laccase-like multicopper oxidases expressed in Escherichia coli. Sci Rep 2015; 5:10465. [PMID: 26068013 PMCID: PMC4464401 DOI: 10.1038/srep10465] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 04/15/2015] [Indexed: 11/09/2022] Open
Abstract
Laccases are multi-copper oxidases that oxidize a broad range of substrates at the expense of molecular oxygen, without any need for co-factor regeneration. These enzymes bear high potential for the sustainable synthesis of fine chemicals and the modification of (bio)polymers. Here we describe cloning and expression of five novel bacterial laccase-like multi copper oxidases (LMCOs) of diverse origin which were identified by homology searches in online databases. Activity yields under different expression conditions and temperature stabilities were compared to three previously described enzymes from Bacillus subtilis, Bacillus pumilus and Bacillus clausii. In almost all cases, a switch to oxygen-limited growth conditions after induction increased volumetric activity considerably. For proteins with predicted signal peptides for secretion, recombinant expression with and without signal sequence was investigated. Bacillus CotA-type LMCOs outperformed enzymes from Streptomyces and Gram-negative bacteria with respect to activity yields in Escherichia coli and application relevant biochemical properties. The novel Bacillus coagulans LMCO combined high activity yields in E. coli with unprecedented activity at strong alkaline pH and high storage stability, making it a promising candidate for further development.
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Affiliation(s)
- Julian Ihssen
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Renate Reiss
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Ronny Luchsinger
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Linda Thöny-Meyer
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
| | - Michael Richter
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biointerfaces, Lerchenfeldstr.5, 9014 St. Gallen, Switzerland
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