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Kuznetsova AA, Kuznetsov NA. Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches. Bioengineering (Basel) 2023; 10:1150. [PMID: 37892880 PMCID: PMC10604792 DOI: 10.3390/bioengineering10101150] [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: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
DNA-dependent DNA polymerases have been intensively studied for more than 60 years and underlie numerous biotechnological and diagnostic applications. In vitro, DNA polymerases are used for DNA manipulations, including cloning, PCR, site-directed mutagenesis, sequencing, and others. Understanding the mechanisms of action of DNA polymerases is important for the creation of new enzymes possessing improved or modified properties. This review is focused on archaeal family B DNA polymerases. These enzymes have high fidelity and thermal stability and are finding many applications in molecular biological methods. Nevertheless, the search for and construction of new DNA polymerases with altered properties is constantly underway, including enzymes for synthetic biology. This brief review describes advances in the development of family B DNA polymerases for PCR, synthesis of xeno-nucleic acids, and reverse transcription.
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Affiliation(s)
- Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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Ahmad S, Ali SF, Iftikhar S, Rashid N. Engineering a DNA polymerase from Pyrobaculum calidifontis for improved activity, processivity and extension rate. Int J Biol Macromol 2023; 233:123545. [PMID: 36740112 DOI: 10.1016/j.ijbiomac.2023.123545] [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: 10/12/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Positively charged amino acids in the DNA polymerase domain are important for interaction with DNA. Two potential residues in the palm domain of Pca-Pol, a DNA polymerase from Pyrobaculum calidifontis, were identified and mutated to arginine in order to improve the properties of this enzyme. The mutant proteins were heterologously produced in Escherichia coli. Biochemical characterization revealed that there was no significant difference in pH, metal ion, buffer preferences, 3' - 5' exonuclease activity and error rate of the wild-type and the mutant enzymes. However, the specific activity, processivity and extension rate of the mutant enzymes increased significantly. Specific activity of one of the mutants (G522R-E555R) was nearly 9-fold higher than that of the wild-type enzyme. These properties make G522R-E555R mutant enzyme a potential candidate for commercial applications.
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Affiliation(s)
- Shazeel Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Syed Farhat Ali
- KAM-School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore 54600, Pakistan
| | - Saima Iftikhar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
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3
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Takahashi S, Oshige M, Katsura S, Nagahara Y. A new fluorescence labeling method for molecular analysis of double-stranded DNA. Anal Biochem 2023; 662:115000. [PMID: 36470466 DOI: 10.1016/j.ab.2022.115000] [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: 09/01/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
In this study, a double-stranded DNA (dsDNA) fluorescent labeling method was developed using the fusion proteins of fluorescent protein (FP), and 7 kDa DNA-binding family members including Sso7d from Sulfolobus solfataricus, Aho7c from Acidianus hospitalis, ATSV7 from Acidianus tailed spindle virus and Sto7 from Sulfolobus tokodaii. Using this fluorescent DNA labeling method, we succeeded in single-molecule imaging of bacteriophage λDNA molecules stretched on glass surfaces. The fluorescence of the λDNA with FP fusion proteins decayed 2.4- to 6.4-fold slower than that of the typical intercalating method with SYTOX Green (SxG). In addition, the dynamic behaviors of FP-fused Aho7c-λDNA were relaxed and stretched with and without buffer flow, respectively, in microflow channels and were similar to that with typical intercalating dye, such as YOYO-1 and SxG. this fluorescent DNA labeling method. This fluorescent DNA labeling method can solve the problem of rapid fluorescence decay due to the intercalating dyes and therefore can be expected as an alternative to compound-based fluorescent dye. Thus, this study establishes FP fusion proteins as useful fluorescent DNA probes at the single-molecule level.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan.
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Aramaki, Gunma, 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, 376-8515, Japan; Gunma University Center for Food Science and Wellness (GUCFW), Aramaki, Gunma, 371-8510, Japan
| | - Yukitoshi Nagahara
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama, 350-0394, Japan
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Zhang L, Jiang D, Shi H, Wu M, Gan Q, Yang Z, Oger P. Characterization and application of a family B DNA polymerase from the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans. Int J Biol Macromol 2020; 156:217-224. [PMID: 32229210 DOI: 10.1016/j.ijbiomac.2020.03.204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/07/2020] [Accepted: 03/24/2020] [Indexed: 11/19/2022]
Abstract
Thermococcus gammatolerans is anaerobic euryarchaeon which grows optimally at 88 °C and its genome encodes a family B DNA polymerase (Tga PolB). Herein, we cloned the gene of Tga PolB, expressed and purified the gene product, and characterized the enzyme biochemically. The recombinant Tga PolB can efficiently synthesize DNA at high temperature, and retain 93% activity after heated at 95 °C for 1.0 h, suggesting that the enzyme is thermostable. Furthermore, the optimal pH for the enzyme activity was measured to be 7.0-9.0. Tga PolB activity is dependent on a divalent cation, among which magnesium ion is optimal. NaCl at low concentration stimulates the enzyme activity but at high concentration inhibits enzyme activity. Interestingly, Tga PolB is able to efficiently bypass uracil in DNA, which is distinct from other archaeal family B DNA pols. By contrast, Tga PolB is halted by an AP site in DNA, as observed in other archaeal family B DNA polymerases. Furthermore, Tga PolB extends the mismatched ends with reduced efficiencies. The enzyme possesses 3'-5' exonuclease activity and this activity is inhibited by dNTPs. The DNA binding assays showed that Tga PolB can efficiently bind to ssDNA and primed DNA, and have a marked preference for primed DNA. Last, Tga PolB can be used in routine PCR.
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Affiliation(s)
- Likui Zhang
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China; Guangling College, Yangzhou University, China.
| | - Donghao Jiang
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Haoqiang Shi
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Mai Wu
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Qi Gan
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Zhihui Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding, City, Hebei Province 071001, China.
| | - Philippe Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France.
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Kalichuk V, Béhar G, Renodon-Cornière A, Danovski G, Obal G, Barbet J, Mouratou B, Pecorari F. The archaeal "7 kDa DNA-binding" proteins: extended characterization of an old gifted family. Sci Rep 2016; 6:37274. [PMID: 27853299 PMCID: PMC5112516 DOI: 10.1038/srep37274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/27/2016] [Indexed: 01/06/2023] Open
Abstract
The “7 kDa DNA-binding” family, also known as the Sul7d family, is composed of chromatin proteins from the Sulfolobales archaeal order. Among them, Sac7d and Sso7d have been the focus of several studies with some characterization of their properties. Here, we studied eleven other proteins alongside Sac7d and Sso7d under the same conditions. The dissociation constants of the purified proteins for binding to double-stranded DNA (dsDNA) were determined in phosphate-buffered saline at 25 °C and were in the range from 11 μM to 22 μM with a preference for G/C rich sequences. In accordance with the extremophilic origin of their hosts, the proteins were found highly stable from pH 0 to pH 12 and at temperatures from 85.5 °C to 100 °C. Thus, these results validate eight putative “7 kDa DNA-binding” family proteins and show that they behave similarly regarding both their function and their stability among various genera and species. As Sac7d and Sso7d have found numerous uses as molecular biology reagents and artificial affinity proteins, this study also sheds light on even more attractive proteins that will facilitate engineering of novel highly robust reagents.
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Affiliation(s)
- Valentina Kalichuk
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,Université catholique de Louvain, Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, Brussels, Belgium
| | - Ghislaine Béhar
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | - Georgi Danovski
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Gonzalo Obal
- Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay
| | - Jacques Barbet
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Barbara Mouratou
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Frédéric Pecorari
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
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Construction, Expression, and Characterization of Recombinant Pfu DNA Polymerase in Escherichia coli. Protein J 2016; 35:145-53. [PMID: 26920159 DOI: 10.1007/s10930-016-9651-4] [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: 10/22/2022]
Abstract
Pfu DNA polymerase (Pfu) is a DNA polymerase isolated from the hyperthermophilic archaeon Pyrococcus furiosus. With its excellent thermostability and high fidelity, Pfu is well known as one of the enzymes widely used in the polymerase chain reaction. In this study, the recombinant plasmid pLysS His6-tagged Pfu-pET28a was constructed. His-tagged Pfu was expressed in Escherichia coli BL21 (DE3) competent cells and then successfully purified with the ÄKTAprime plus compact one-step purification system by Ni(2+) chelating affinity chromatography after optimization of the purification conditions. The authenticity of the purified Pfu was further confirmed by peptide mass fingerprinting. A bio-assay indicated that its activity in the polymerase chain reaction was equivalent to that of commercial Pfu and its isoelectric point was found to be between 6.85 and 7.35. These results will be useful for further studies on Pfu and its wide application in the future.
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Huet S, Gorre H, Perrocheau A, Picot J, Cinier M. Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag. PLoS One 2015; 10:e0142304. [PMID: 26539718 PMCID: PMC4634965 DOI: 10.1371/journal.pone.0142304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022] Open
Abstract
With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant.
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Archaeal DNA polymerases in biotechnology. Appl Microbiol Biotechnol 2015; 99:6585-97. [DOI: 10.1007/s00253-015-6781-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
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Terpe K. Overview of thermostable DNA polymerases for classical PCR applications: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 2013; 97:10243-54. [DOI: 10.1007/s00253-013-5290-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/20/2013] [Accepted: 09/22/2013] [Indexed: 11/29/2022]
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