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Handayani CV, Laksmi FA, Andriani A, Nuryana I, Mubarik NR, Agustriana E, Dewi KS, Purnawan A. Expression of soluble moloney murine leukemia virus-reverse transcriptase in Escherichia coli BL21 star (DE3) using autoinduction system. Mol Biol Rep 2024; 51:628. [PMID: 38717629 DOI: 10.1007/s11033-024-09583-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/23/2024] [Indexed: 06/07/2024]
Abstract
Autoinduction systems in Escherichia coli can control the production of proteins without the addition of a particular inducer. In the present study, we optimized the heterologous expression of Moloney Murine Leukemia Virus derived Reverse Transcriptase (MMLV-RT) in E. coli. Among 4 autoinduction media, media Imperial College resulted the highest MMLV-RT overexpression in E. coli BL21 Star (DE3) with incubation time 96 h. The enzyme was produced most optimum in soluble fraction of lysate cells. The MMLV-RT was then purified using the Immobilized Metal Affinity Chromatography method and had specific activity of 629.4 U/mg. The system resulted lower specific activity and longer incubation of the enzyme than a classical Isopropyl ß-D-1-thiogalactopyranoside (IPTG)-induction system. However, the autoinduction resulted higher yield of the enzyme than the conventional induction (27.8%). Techno Economic Analysis revealed that this method could produce MMLV-RT using autoinduction at half the cost of MMLV-RT production by IPTG-induction. Bioprocessing techniques are necessary to conduct to obtain higher quality of MMLV-RT under autoinduction system.
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Affiliation(s)
- Christina Vivid Handayani
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
- Biotechnology Program, Graduate School, IPB University, Bogor, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia.
| | - Ade Andriani
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia.
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| | - Nisa Rachmania Mubarik
- Department of Biology, Faculty of Mathematic and Natural Science, IPB University, Bogor, Indonesia
| | - Eva Agustriana
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
| | - Awan Purnawan
- Research Center for Applied Microbiology, National Agency for Research and Innovation, Jl. Raya Bogor, Km. 46, Cibinong, Bogor, 16911, Indonesia
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Nugraha Y, Laksmi FA, Nuryana I, Helbert, Khasna FN. Production of reverse transcriptase from Moloney murine Leukemia virus in Escherichia coli expression system. Prep Biochem Biotechnol 2024:1-9. [PMID: 38411149 DOI: 10.1080/10826068.2024.2317311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Reverse transcriptase (RT) is one of the most important enzymes used in molecular biology applications, enabling the conversion of RNA into complementary DNA (cDNA) that is used in reverse transcription-polymerase chain reaction (RT-PCR). The high demand of RT enzymes in biotechnological applications making the production optimization of RT is crucial for meeting the growing demand in industrial settings. Conventionally, the expression of recombinant RT is T7-induced promoter using IPTG in Escherichia coli expression systems, which is not cost-efficient. Here, we successfully made an alternative procedure for RT expression from Moloney murine leukemia virus (M-MLV) using autoinduction method in chemically defined medium. The optimization of carbon source composition (glucose, lactose, and glycerol) was analyzed using Response Surface Methodology (RSM). M-MLV RT was purified for further investigation on its activity. A total of 32.8 mg/L purified M-MLV RT was successfully obtained when glucose, glycerol, and lactose were present at concentration of 0.06%, 0.9%, and 0.5% respectively, making a 3.9-fold improvement in protein yield. In addition, the protein was produced in its active form by displaying 7462.50 U/mg of specific activity. This study provides the first step of small-scale procedures of M-MLV RT production that make it a cost-effective and industrially applicable strategy.
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Affiliation(s)
- Yudhi Nugraha
- Research Center for Molecular Biology Eijkman, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
| | - Firyal Nida Khasna
- Research Center for Applied Microbiology, National Research and Innovation Agency, Cibinong, Bogor, West Java, Indonesia
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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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Dangerfield TL, Huang NZ, Johnson KA. Remdesivir Is Effective in Combating COVID-19 because It Is a Better Substrate than ATP for the Viral RNA-Dependent RNA Polymerase. iScience 2020; 23:101849. [PMID: 33283177 PMCID: PMC7695572 DOI: 10.1016/j.isci.2020.101849] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/30/2020] [Accepted: 11/18/2020] [Indexed: 01/18/2023] Open
Abstract
COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is currently being treated using Remdesivir, a nucleoside analog that inhibits the RNA-dependent-RNA polymerase (RdRp). However, the enzymatic mechanism and efficiency of Remdesivir have not been determined, and reliable screens for new inhibitors are urgently needed. Here we present our work to optimize expression in E. coli, followed by purification and kinetic analysis of an untagged NSP12/7/8 RdRp complex. Pre-steady-state kinetic analysis shows that our reconstituted RdRp catalyzes fast (kcat = 240–680 s−1) and processive (koff = 0.013 s−1) RNA polymerization. The specificity constant (kcat/Km) for Remdesivir triphosphate (RTP) incorporation (1.29 μM−1s−1) is higher than that for the competing ATP (0.74 μM−1 s−1). This work provides the first robust analysis of RNA polymerization and RTP incorporation by the SARS-CoV-2 RdRp and sets the standard for development of informative enzyme assays to screen for new inhibitors. Co-expression of NSP12/7/8 with chaperones in E. coli gives soluble SARS CoV2 RdRp Tag-free RdRp complex catalyzes fast and processive RNA polymerization Polymerization rates are sufficient to replicate the 30 kb genome in 2 min Remdesivir is incorporated with a specificity constant twice that observed for ATP
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Affiliation(s)
- Tyler L Dangerfield
- Department of Molecular Biosciences, The University of Texas at Austin, 100 W. 24th Street, Stop 5000, MBB 3.122, Austin, TX 78712, USA
| | - Nathan Z Huang
- Department of Molecular Biosciences, The University of Texas at Austin, 100 W. 24th Street, Stop 5000, MBB 3.122, Austin, TX 78712, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, 100 W. 24th Street, Stop 5000, MBB 3.122, Austin, TX 78712, USA
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Lai MT, Tawa P, Auger A, Wang D, Su HP, Yan Y, Hazuda DJ, Miller MD, Asante-Appiah E, Melnyk RA. Identification of novel bifunctional HIV-1 reverse transcriptase inhibitors. J Antimicrob Chemother 2018; 73:109-117. [PMID: 29029095 DOI: 10.1093/jac/dkx332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/12/2017] [Indexed: 02/01/2023] Open
Abstract
Objectives The increasing prevalence of mutations in HIV-1 reverse transcriptase (RT) that confer resistance to existing NRTIs and NNRTIs underscores the need to develop RT inhibitors with novel mode-of-inhibition and distinct resistance profiles. Methods Biochemical assays were employed to identify inhibitors of RT activity and characterize their mode of inhibition. The antiviral activity of the inhibitors was assessed by cell-based assays using laboratory HIV-1 isolates and MT4 cells. RT variants were purified via avidin affinity columns. Results Compound A displayed equal or greater potency against many common NNRTI-resistant RTs (K103N and Y181C RTs) relative to WT RT. Despite possessing certain NNRTI-like properties, such as being unable to inhibit an engineered variant of RT lacking an NNRTI-binding pocket, we found that compound A was dependent on Mg2+ for binding to RT. Optimization of compound A led to more potent analogues, which retained similar activities against WT and K103N mutant viruses with submicromolar potency in a cell-based assay. One of the analogues, compound G, was crystallized in complex with RT and the structure was determined at 2.6 Å resolution. The structure indicated that compound G simultaneously interacts with the active site (Asp186), the highly conserved primer grip region (Leu234 and Trp229) and the NNRTI-binding pocket (Tyr188). Conclusions These findings reveal a novel class of RT bifunctional inhibitors that are not sensitive to the most common RT mutations, which can be further developed to address the deficiency of current RT inhibitors.
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Affiliation(s)
- Ming-Tain Lai
- Department of Antiviral Research, MRL, West Point, PA 19486, USA
| | - Paul Tawa
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
| | - Anick Auger
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
| | - Deping Wang
- Department of Modeling, MRL, West Point, PA 19486, USA
| | - Hua-Poo Su
- Department of Structure Determination, MRL, West Point, PA 19486, USA
| | - Youwei Yan
- Department of Structure Determination, MRL, West Point, PA 19486, USA
| | - Daria J Hazuda
- Department of Antiviral Research, MRL, West Point, PA 19486, USA
| | - Michael D Miller
- Department of Antiviral Research, MRL, West Point, PA 19486, USA
| | - Ernest Asante-Appiah
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
| | - Roman A Melnyk
- Department of Antiviral Research, Merck Frosst Center for Therapeutic Research, Pointe-Claire - Dorval H9R 4P8, Canada
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Mechanistic Study of Common Non-Nucleoside Reverse Transcriptase Inhibitor-Resistant Mutations with K103N and Y181C Substitutions. Viruses 2016; 8:v8100263. [PMID: 27669286 PMCID: PMC5086599 DOI: 10.3390/v8100263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/30/2022] Open
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a mainstay of therapy for human immunodeficiency type 1 virus (HIV-1) infections. However, their effectiveness can be hampered by the emergence of resistant mutations. To aid in designing effective NNRTIs against the resistant mutants, it is important to understand the resistance mechanism of the mutations. Here, we investigate the mechanism of the two most prevalent NNRTI-associated mutations with K103N or Y181C substitution. Virus and reverse transcriptase (RT) with K103N/Y188F, K103A, or K103E substitutions and with Y181F, Y188F, or Y181F/Y188F substitutions were employed to study the resistance mechanism of the K103N and Y181C mutants, respectively. Results showed that the virus and RT with K103N/Y188F substitutions displayed similar resistance levels to the virus and RT with K103N substitution versus NNRTIs. Virus and RT containing Y181F, Y188F, or Y181F/Y188F substitution exhibited either enhanced or similar susceptibility to NNRTIs compared with the wild type (WT) virus. These results suggest that the hydrogen bond between N103 and Y188 may not play an important role in the resistance of the K103N variant to NNRTIs. Furthermore, the results from the studies with the Y181 or Y188 variant provide the direct evidence that aromatic π-π stacking plays a crucial role in the binding of NNRTIs to RT.
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Katano Y, Hisayoshi T, Kuze I, Okano H, Ito M, Nishigaki K, Takita T, Yasukawa K. Expression of moloney murine leukemia virus reverse transcriptase in a cell-free protein expression system. Biotechnol Lett 2016; 38:1203-11. [PMID: 27053084 DOI: 10.1007/s10529-016-2097-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To characterize Moloney murine leukemia virus (MMLV) reverse transcriptases (RTs) expressed in a cell-free system and in Escherichia coli. RESULTS We previously expressed MMLV RT using an E. coli expression system and generated a highly thermostable quadruple variant MM4 (E286R/E302K/L435R/D524A) by site-directed mutagenesis. In this study, we expressed the wild-type MMLV RT (WT) and MM4 using a cell-free protein expression system from insect cells. WT exhibited DNA polymerase and RNase H activities, while MM4, in which the catalytic residue for RNase H activity, Asp524 is changed into Ala, exhibited only DNA polymerase activity. MM4, when held at 60 °C for 10 min, retained DNA polymerase activity, while WT, held at 54 °C for 10 min, lost this activity. In the cDNA synthesis reaction (0.5 μl) in which WT or MM4 were exposed to various temperatures and amounts of target RNA in a microarray chip, MM4 exhibited higher thermostability than WT. CONCLUSION MMLV RT expressed in the cell-free system is indistinguishable from that expressed in E. coli.
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Affiliation(s)
- Yuta Katano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tetsuro Hisayoshi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ikumi Kuze
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Okano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masaaki Ito
- Okinawa National College of Technology, Nago, Japan
| | - Koichi Nishigaki
- Saitama-Bio-Monodukuri-Network Research Organization, Saitama University, Saitama, Japan.,National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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Kato E, Tsuji H, Kawabata J. Selective purification of intestinal maltase complex by affinity chromatography employing an uncompetitive inhibitor as the ligand. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Guan D, Chen Z. Challenges and recent advances in affinity purification of tag-free proteins. Biotechnol Lett 2014; 36:1391-406. [DOI: 10.1007/s10529-014-1509-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 03/03/2014] [Indexed: 12/19/2022]
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Wu D, Feng F, Xie D, Chen Y, Tan W, Schanze KS. Helical Conjugated Polyelectrolyte Aggregation Induced by Biotin-Avidin Interaction. J Phys Chem Lett 2012; 3:1711-5. [PMID: 26285733 DOI: 10.1021/jz300452t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is applied to demonstrate avidin-induced cross-linking in a system consisting of a helical anionic conjugated polyelectrolyte (P1) and a biotin-tetramethylrhodamine (TMR) conjugate (2). In a previous study, we used fluorescence spectroscopy to demonstrate that 2 binds to P1 via intercalation of the TMR chromophore into the P1 helix. Addition of avidin to the P1/2 complex induces little change in the fluorescence of the system; however, FCS reveals a remarkable increase in the diffusion time of the P1/2 complex in the presence of avidin. This change is attributed to supramolecular polymer aggregates produced by cross-link formation between the biotin unit of intercalated 2 and avidin. Atomic force microscopy imaging provides evidence supporting the existence of these aggregates. The highly sensitive FCS method is used to develop a novel sensor for the biotin-avidin interaction, with a detection limit of <100 pM for avidin.
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Affiliation(s)
- Danlu Wu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Fude Feng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Dongping Xie
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yan Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Weihong Tan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Kirk S Schanze
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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