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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nadhilah D, Andriani A, Agustriana E, Nuryana I, Mubarik NR, Dewi KS, Rahmani N, Yanto DHY, Ismayati M, Perwitasari U, Laksmi FA, Wijaya H. Co-catalysis of melanin degradation by laccase-manganese peroxidase complex from Trametes hirsuta OK271075 for application in whitening cosmetics. BIOCATAL BIOTRANSFOR 2023. [DOI: 10.1080/10242422.2023.2188995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Dini Nadhilah
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
- Department of Biology, Bogor Agricultural University, Bogor, Indonesia
| | - Ade Andriani
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
- Research Collaboration Center for Biomass-Based nano Cosmetics, Samarinda, Indonesia
| | - Eva Agustriana
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | - Isa Nuryana
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | | | - Kartika Sari Dewi
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | - Nanik Rahmani
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | - Dede Heri Yuli Yanto
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
- Research Collaboration Center for Biomass-Based nano Cosmetics, Samarinda, Indonesia
| | - Maya Ismayati
- Research Center for Biomass and Bioproducts, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | - Urip Perwitasari
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | - Fina Amreta Laksmi
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
| | - Hans Wijaya
- Research Centre for Applied Microbiology, National Agency for Research and Innovation, Cibinong, Bogor, Indonesia
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Agustriana E, Nuryana I, Laksmi FA, Dewi KS, Wijaya H, Rahmani N, Yudiargo DR, Ismadara A, Helbert, Hadi MI, Purnawan A, Cameliawati Djohan A. Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system. Prep Biochem Biotechnol 2022; 53:384-393. [PMID: 35792906 DOI: 10.1080/10826068.2022.2095573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Bst DNA polymerase is a DNA polymerase derived from Geobacillus stearothermophilus, has a strand-displacement activity, and is used in loop-mediated isothermal amplification (LAMP) for rapid detection of COVID-19. Despite its potential to be employed in the detection of COVID-19, using commercially available enzymes is not economically feasible. The use of noncommercial enzyme for routine use is desirable. However, research on Bst DNA polymerase is still limited in Indonesia. For those reasons, a preliminary study of scale-up production of recombinant Bst polymerase was conducted. Therefore, the optimization of expression conditions was performed. The optimum conditions for Bst polymerase expression were as follows: 1 mM of IPTG, post-induction incubation time of 6 h, and induction at OD600 1.1. Employing optimum conditions could result in 2.8 times increase in protein yield compared to the initial conditions. Subsequently, an operation in 1 L working volume by a lab-scale bioreactor had been performed, followed by purification and dialysis. The optimum result for a 1 L lab-scale bioreactor was achieved by applying 100 rpm and 3 vvm, giving 11.7 mg/L of protein yield. Bst polymerase was successfully purified showing 813.56 U/mg of polymerase activity.
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Affiliation(s)
- Eva Agustriana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Hans Wijaya
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Nanik Rahmani
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Danu Risqi Yudiargo
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | | | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Moch Irfan Hadi
- Department of Biology, Sunan Ampel State Islamic University, Surabaya, Indonesia
| | - Awan Purnawan
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Apridah Cameliawati Djohan
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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Dewi KS, Chairunnisa S, Swasthikawati S, Yuliawati, Agustiyanti DF, Mustopa AZ, Kusharyoto W, Ningrum RA. Production of codon-optimized Human papillomavirus type 52 L1 virus-like particles in Pichia pastoris BG10 expression system. Prep Biochem Biotechnol 2022; 53:148-156. [PMID: 35302435 DOI: 10.1080/10826068.2022.2048262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cervical cancer caused by Human papillomavirus (HPV) is one of the most common causes of cancer death in women worldwide. Even though the disease can be avoided by immunization, the expensive price of HPV vaccines makes it hard to be accessed by women in middle-low-income countries. Thus, the development of generic HPV vaccines is needed to address inequalities in life-saving access. This study aimed to develop the HPV52 L1 VLP-based recombinant vaccine using Pichia pastoris expression system. The l1 gene was codon-optimized based on P. pastoris codon usage resulting CAI value of 0.804. The gene was inserted into the pD902 plasmid under the regulation of the AOX1 promoter. The linear plasmid was transformed into P. pastoris BG10 genome and screened in YPD medium containing zeocin antibiotic. Colony of transformant that grown on highest zeocin concentration was characterized by genomic PCR and sequencing. The positive clone was selected and expressed using BMGY/BMMY medium induced with various methanol concentrations. The SDS-PAGE and Western blot analyses showed that 55 kDa L1 protein was successfully expressed using an optimum concentration of 1% methanol. The self-assembly of HPV52 L1 protein was also proven using TEM analysis. Moreover, we also analyzed the B-cell epitope of HPV52 L1 protein based on several criteria, including antigenicity, surface accessibility, flexibility, and hydrophilicity. We assumed that epitope 476GLQARPKLKRPASSAPRTSTKKKKV500 could be developed as an epitope-based vaccine with a neutralizing antibody response toward HPV52 infection. Finally, our study provided the alternative for developing low-cost HPV vaccines, either VLP or epitope-based.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Sheila Chairunnisa
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Sri Swasthikawati
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Yuliawati
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Dian Fitria Agustiyanti
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Apon Zainal Mustopa
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Wien Kusharyoto
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Ratih Asmana Ningrum
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
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Dewi KS, Fuad AM. Improving the Expression of Human Granulocyte Colony Stimulating Factor in Escherichia coli by Reducing the GC-content and Increasing mRNA Folding Free Energy at 5'-Terminal End. Adv Pharm Bull 2020; 10:610-616. [PMID: 33072539 PMCID: PMC7539321 DOI: 10.34172/apb.2020.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/24/2019] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Purpose: Strategy for improving the production of biopharmaceutical protein continues to develop due to increasing market demand. Human granulocyte colony stimulating factor (hG-CSF) is one of biopharmaceutical proteins that has many applications, and easily produced in Escherichia coli expression system. Previous studies reported that codon usage, rare codon, mRNA folding and GC-content at 5’-terminal end were crucial for protein production in E. coli. In the present study, the effect of reducing the GC-content and increasing the mRNA folding free energy at the 5’-terminal end on the expression level of hG-CSF proteins was investigated. Methods: Synonymous codon substitutions were performed to generate mutant variants of open reading frame (ORF) with lower GC-content at 5’-terminal ends. Oligoanalyzer tool was used to calculate the GC content of eight codons sequence after ATG. Whereas, mRNA folding free energy was predicted using KineFold and RNAfold tools. The template DNA was amplified using three variant forward primers and one same reverse primer. Those DNA fragments were individually cloned into pJexpress414 expression vector and were confirmed using restriction and DNA sequencing analyses. The confirmed constructs were transformed into E. coli NiCo21(DE3) host cells and the recombinant protein was expressed using IPTG-induction. Total protein obtained were characterized using SDS-PAGE, Western blot and ImageJ software analyses. Results: The result showed that the mutant variant with lower GC-content and higher mRNA folding free energy near the translation initiation region (TIR) could produce a higher amount of hG-CSF proteins compared to the original gene sequence. Conclusion: This study emphasized the important role of the nucleotide composition immediately downstream the start codon to achieve high-yield protein product on heterologous expression in E. coli.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia, 16911
| | - Asrul Muhamad Fuad
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia, 16911
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Dewi KS, Retnoningrum DS, Riani C, Fuad AM. Construction and Periplasmic Expression of the Anti-EGFRvIII ScFv Antibody Gene in Escherichia coli. Sci Pharm 2016; 84:141-52. [PMID: 27110505 PMCID: PMC4839555 DOI: 10.3797/scipharm.isp.2015.06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/15/2015] [Indexed: 12/13/2022] Open
Abstract
In the previous study, we constructed an expression vector carrying the anti-EGFRvIII scFv antibody gene with VH-linker-VL orientation. The proteins were successfully produced in the periplasmic space of Escherichia coli. In this study, we substituted the inserted DNA with VL-linker-VH orientation of the anti-EGFRvIII scFv gene and analyzed its expression in E. coli. The DNA fragment was amplified from its cloning vector (pTz-rscFv), subsequently cloned into a previous expression vector containing the pelB signal sequence and his-tag, and then transformed into E. coli TOP10. The recombinant plasmids were characterized by restriction, PCR, and DNA sequencing analyses. The new anti-EGFRvIII scFv antibody proteins have been successfully expressed in the periplasmic compartment of E. coli Nico21(DE3) using 0.1 mM final concentration of IPTG induction. Total proteins, soluble periplasmic and cytoplasmic proteins, solubilized inclusion bodies, and extracellular proteins were analyzed by SDS-PAGE and Western Blot analyses. The results showed that soluble scFv proteins were found in all fractions except from the cytoplasmic space.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km. 46, 16911, Cibinong, Bogor, Indonesia
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | | | - Catur Riani
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Asrul Muhamad Fuad
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km. 46, 16911, Cibinong, Bogor, Indonesia
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Widayanti CG, Dewi KS. Psychological Well-Being (Pwb) Dan Pengambilan Keputusan Untuk Mengikuti Konseling Genetika Pada Orangtua Anak Dengan Talasemia Mayor. psikologika 2012. [DOI: 10.20885/psikologika.vol17.iss2.art10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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