Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system

References

• Jiang, M.; Pan, W.; Arasthfer, A.; Fang, W.; Ling, L.; Fang, H.; Daneshnia, F.; Yu, J.; Liao, W.; Pei, H.; et al. Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High-Throughput Screening of COVID-19. Front. Cell. Infect. Microbiol. 2020, 10, 331–336. DOI: 10.3389/fcimb.2020.00331.
   PubMed Web of Science ®Google Scholar
• Lu, R.; Wu, X.; Wan, Z.; Li, Y.; Zuo, L.; Qin, J.; Jin, X.; Zhang, C. Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2. Virol. Sin. 2020, 35, 344–347. DOI: 10.1007/s12250-020-00218-1.
   PubMed Web of Science ®Google Scholar
• Notomi, T.; Okayama, H.; Masubuchi, H.; Yonekawa, T.; Watanabe, K.; Amino, N.; Hase, T. Loop-Mediated Isothermal Amplification of DNA. Nucleic Acids Res. 2000, 28 (12).
   Web of Science ®Google Scholar
• Parida, M.; Sannarangaiah, S.; Dash, P. K.; Rao, P. V. L.; Morita, K. Loop Mediated Isothermal Amplification (LAMP): A New Generation of Innovative Gene Amplification Technique; Perspectives in Clinical Diagnosis of Infectious Diseases. Rev. Med. Virol. 2008, 18, 407–421. DOI: 10.1002/rmv.593.
   PubMed Web of Science ®Google Scholar
• Chander, Y.; Koelbl, J.; Puckett, J.; Moser, M. J.; Klingele, A. J.; Liles, M. R.; Carrias, A.; Mead, D. A.; Schoenfeld, T. W.; England, N. A Novel Thermostable Polymerase for RNA and DNA Loop-Mediated Isothermal Amplification (LAMP). Front. Microbiol. 2014, 5, 395–311. DOI: 10.3389/fmicb.2014.00395.
   PubMed Web of Science ®Google Scholar
• Lee, S. H.; Baek, Y. H.; Kim, Y.-H.; Choi, Y.-K.; Song, M.-S.; Ahn, J.-Y. One-Pot Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting MERS-CoV. Front. Microbiol. 2016, 7, 2166–2113. DOI: 10.3389/fmicb.2016.02166.
   PubMed Web of Science ®Google Scholar
• Alekseenko, A.; Barrett, D.; Sanchez, Y. P.; Howard, R. J.; Strandback, E.; Korsah, H. A.; Rovšnik, U.; Veliz, S. Z.; Klenov, A.; Malloo, J.; et al. Direct Detection of SARS-CoV-2 Using Non-Commercial RT-LAMP Reagents on Heat-Inactivated Samples. Sci. Rep 2021, 11, 1–10. DOI: 10.1038/s41598-020-80352-8.
   PubMedGoogle Scholar
• Kitajima, H.; Tamura, Y.; Yoshida, H.; Kinoshita, H.; Katsuta, H.; Matsui, C.; Matsushita, A.; Arai, T.; Hashimoto, S.; Iuchi, A.; et al. Clinical COVID-19 Diagnostic Methods: Comparison of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) and Quantitative. J. Clin. Virol. 2021, 139, 104813. DOI: 10.1016/j.jcv.2021.104813.
   PubMedGoogle Scholar
• Kiefer, J. R.; Mao, C.; Hansen, C. J.; Basehore, S. L.; Hogrefe, H. H.; Braman, J. C.; Beese, L. S. Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 Å Resolution. Structure 1997, 5, 95–108. DOI: 10.1016/S0969-2126(97)00169-X.
   PubMed Web of Science ®Google Scholar
• Ma, Y.; Zhang, B.; Wang, M.; Ou, Y.; Wang, J.; Li, S. Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site. Biomed Res. Int. 2016, 2016, 2906484. DOI: 10.1155/2016/2906484.
   PubMed Web of Science ®Google Scholar
• Aviel-ronen, S.; Zhu, C. Q.; Coe, B. P.; Liu, N.; Watson, S. K.; Lam, W. L.; Tsao, M. S. Large Fragment Bst DNA Polymerase for Whole Genome Amplification of DNA from Formalin-Fixed Paraffin-Embedded Tissues. BMC Genomics 2006, 10, 1–10. DOI: 10.1186/1471-2164-7-312.
   Google Scholar
• Babiker, A.; Myers, C. W.; Hill, C. E.; Guarner, J. SARS-CoV-2 Testing: Trials and Tribulations. Am. J. Clin. Pathol. 2020, 153, 706–708. DOI: 10.1093/ajcp/aqaa052.
   PubMedGoogle Scholar
• Bin, L.; Jufang, W.; Yi, M.; Beilei, Z. Method for Improving Activity of Large-fragment Geobacillus stearothermophilus (Bst) DNA polymerase through Point Mutation and Application. CN 106399299A, January 29, 2019.
   Google Scholar
• Chung, C. T.; Niemela, S. L.; Miller, R. H. One-Step Preparation of Competent Escherichia coli: transformation and Storage of Bacterial Cells in the Same Solution. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 2172–2175. DOI: 10.1073/pnas.86.7.2172.
   PubMed Web of Science ®Google Scholar
• Laemmli, U. K. Cleavage of Structural Proteins During the Assembly of the Head of Bacteriophage T4. Nature 1970, 227, 680–685. DOI: 10.1038/227680a0.
   PubMed Web of Science ®Google Scholar
• Fitri Kusuma, S. A.; Parwati, I.; Rostinawati, T.; Yusuf, M.; Fadhlillah, M.; Ahyudanari, R. R.; Rukayadi, Y.; Subroto, T. Optimization of Culture Conditions for Mpt64 Synthetic Gene Expression in Escherichia coli BL21 (DE3) Using Surface Response Methodology. Heliyon 2019, 5, e02741. DOI: 10.1016/j.heliyon.2019.e02741.
   PubMedGoogle Scholar
• Puigbò, P.; Guzmán, E.; Romeu, A.; Garcia-Vallvé, S. OPTIMIZER: A Web Server for Optimizing the Codon Usage of DNA Sequences. Nucleic Acids Res. 2007, 35, W126–W131. DOI: 10.1093/nar/gkm219.
   PubMed Web of Science ®Google Scholar
• Puigbò, P.; Bravo, I. G.; Garcia-Vallve, S. CAIcal: A Combined Set of Tools to Assess Codon Usage Adaptation. Biol. Direct. 2008, 3, 38. DOI: 10.1186/1745-6150-3-38.
   PubMed Web of Science ®Google Scholar
• Li, P.; Amenov, A.; Kalendar, R.; Abeldenov, S.; Khassenov, B. Cloning and Purification of Large Fragment of DNA Polymerase I from Geobacillus stearothermophilus and Application in Isothermal DNA Amplification. Eurasian j. app. biotechnol. 2017, 1..
   Google Scholar
• Suppan, M.; Shamsuddin, S.; Ismail, A.; Balakrishnan, V. PCR-Based Gene Synthesis, Cloning, Expression, Purification and Characterization of Bst DNA Polymerase in E. coli Cells. Curr. Synthetic Sys. Biol. 2015, 3, 126. DOI: 10.4172/2332-0737.1000126.
   Google Scholar
• Steitz, T. A. DNA Polymerases: Structural Diversity and Common Mechanisms. J. Biol. Chem. 1999, 274, 17395–17398. DOI: 10.1074/jbc.274.25.17395.
   PubMed Web of Science ®Google Scholar
• Phang, S. M.; Teo, C. Y.; Lo, E.; Wong, V. W. Cloning and Complete Sequence of the DNA Polymerase-Encoding Gene (BstpolI) and Characterisation of the Klenow-like Fragment from Bacillus stearothermophilus. Gene 1995, 163, 65–68. DOI: 10.1016/0378-1119(95)00387-l.
   PubMedGoogle Scholar
• Lawyer, F. C.; Stoffel, S.; Saiki, R. K.; Chang, S. Y.; Landre, P. A.; Abramson, R. D.; Gelfand, D. H. High-Level Expression, Purification, and Enzymatic Characterization of Full-Length Thermus aquaticus DNA Polymerase and a Truncated Form Deficient in 5’ to 3’ Exonuclease Activity. Genome Res. 1993, 2, 275–287. DOI: 10.1101/gr.2.4.275.
   Google Scholar
• Vincent, M.; Xu, Y.; Kong, H. Helicase-Dependent Isothermal DNA Amplification. EMBO Rep. 2004, 5, 795–800. DOI: 10.1038/sj.embor.7400200.
   PubMed Web of Science ®Google Scholar
• Kornberg, A.; Baker, T. DNA Replication. 2nd ed.; WH Freeman and Company: New York, NY, 1992.
   Google Scholar
• Oscorbin, I. P.; Boyarskikh, U. A.; Filipenko, M. L. Large Fragment of DNA Polymerase I from Geobacillus Sp. 777: Cloning and Comparison with DNA Polymerases I in Practical Applications. Mol. Biotechnol. 2015, 57, 947–959. DOI: 10.1007/s12033-015-9886-x.
   PubMedGoogle Scholar
• Donovan, R. S.; Robinson, C. W.; Glick, B. R. Review : Optimizing Inducer and Culture Conditions for Expression of Foreign Proteins Under the Control of the Lac Promoter. J. Ind. Microbiol. 1996, 16, 145–154.
   PubMedGoogle Scholar
• Bandaiphet, C.; Prasertsan, P. Effect of Aeration and Agitation Rates and Scale-up on Oxygen Transfer Coefficient, KLa in Exopolysaccharide Production from Enterobacter cloacae WD7. Carbohydr. Polym. 2006, 66, 216–228. DOI: 10.1016/j.carbpol.2006.03.004.
   Google Scholar
• Rastgoo, N.; Sadeghizadeh, M.; Bambaei, B.; Hosseinkhani, S. Restoring 3’-5’ Exonuclease Activity of Thermophilic Geobacillus DNA Polymerase I Using Site-Directed Mutagenesis in Active Site. J. Biotechnol. 2009, 144, 245–252. DOI: 10.1016/j.jbiotec.2009.09.006.
   PubMedGoogle Scholar