1
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Huber LB, Betz K, Marx A. Reverse Transcriptases: From Discovery and Applications to Xenobiology. Chembiochem 2023; 24:e202200521. [PMID: 36354312 DOI: 10.1002/cbic.202200521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Reverse transcriptases are DNA polymerases that can use RNA as a template for DNA synthesis. They thus catalyze the reverse of transcription. Although discovered in 1970, reverse transcriptases are still of great interest and are constantly being further developed for numerous modern research approaches. They are frequently used in biotechnological and molecular diagnostic applications. In this review, we describe the discovery of these fascinating enzymes and summarize research results and applications ranging from molecular cloning, direct virus detection, and modern sequencing methods to xenobiology.
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Affiliation(s)
- Luisa B Huber
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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2
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Juma KM, Inoue E, Asada K, Fukuda W, Morimoto K, Yamagata M, Takita T, Kojima K, Suzuki K, Nakura Y, Yanagihara I, Fujiwara S, Yasukawa K. Recombinase polymerase amplification using novel thermostable strand-displacing DNA polymerases from Aeribacillus pallidus and Geobacillus zalihae. J Biosci Bioeng 2023; 135:282-290. [PMID: 36806411 DOI: 10.1016/j.jbiosc.2023.01.009] [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: 10/20/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/19/2023]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), and strand-displacing DNA polymerase (Pol). Component instability and the need to store commercial kits in a deep freezer until use are some limitations of RPA. In a previous study, Bacillus stearothermophilus Pol (Bst-Pol) was used as a thermostable strand-displacing DNA polymerase in RPA. Here, we attempted to optimize the lyophilization conditions for RPA with newly isolated thermostable DNA polymerases for storage at room temperature. We isolated novel two thermostable strand-displacing DNA polymerases, one from a thermophilic bacterium Aeribacillus pallidus (H1) and the other from Geobacillus zalihae (C1), and evaluated their performances in RPA reaction. Urease subunit β (UreB) DNA from Ureaplasma parvum serovar 3 was used as a model target for evaluation. The RPA reaction with H1-Pol or C1-Pol was performed at 41 °C with the in vitro synthesized standard UreB DNA. The minimal initial copy numbers of standard DNA from which the amplified products were observed were 600, 600, and 6000 copies for RPA with H1-Pol, C1-Pol, and Bst-Pol, respectively. Optimization was carried out using RPA components, showing that the lyophilized RPA reagents containing H1-Pol exhibited the same performance as the corresponding liquid RPA reagents. In addition, lyophilized RPA reagents with H1-Pol showed almost the same activity after two weeks of storage at room temperature as the freshly prepared liquid RPA reagents. These results suggest that lyophilized RPA reagents with H1-Pol are preferable to liquid RPA reagents for onsite use.
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Eisuke Inoue
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kengo Asada
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masaya Yamagata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka 565-0871, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi-shi, Osaka 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo 669-1330, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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3
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Nakura Y, Wu HN, Okamoto Y, Takeuchi M, Suzuki K, Tamura Y, Oba Y, Nishiumi F, Hatori N, Fujiwara S, Yasukawa K, Ida S, Yanagihara I. Development of an efficient one-step real-time reverse transcription polymerase chain reaction method for severe acute respiratory syndrome-coronavirus-2 detection. PLoS One 2021; 16:e0252789. [PMID: 34086827 PMCID: PMC8177496 DOI: 10.1371/journal.pone.0252789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
The general methods to detect the RNA of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in clinical diagnostic testing involve reverse transcriptases and thermostable DNA polymerases. In this study, we compared the detection of SARS-CoV-2 by a one-step real-time RT-PCR method using a heat-resistant reverse transcriptase variant MM4 from Moloney murine leukemia virus, two thermostable DNA polymerase variants with reverse transcriptase activity from Thermotoga petrophila K4 and Thermococcus kodakarensis KOD1, or a wild-type DNA polymerase from Thermus thermophilus M1. The highest performance was achieved by combining MM4 with the thermostable DNA polymerase from T. thermophilus M1. These enzymes efficiently amplified specific RNA using uracil-DNA glycosylase (UNG) to remove contamination and human RNase P RNA amplification as an internal control. The standard curve was obtained from 5 to 105 copies of synthetic RNA. The one-step real-time RT-PCR method’s sensitivity and specificity were 99.44% and 100%, respectively (n = 213), compared to those of a commercially available diagnostic kit. Therefore, our method will be useful for the accurate detection and quantification of SARS-CoV-2.
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Affiliation(s)
- Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
| | - Heng Ning Wu
- Department of Developmental Medicine, Research Institute, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
| | - Yuya Okamoto
- Department of Laboratory Medicine, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
| | - Muneyuki Takeuchi
- Department of Intensive Care Medicine, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University, Suita-city, Osaka, Japan
| | - Yoshitaka Tamura
- Department of Clinical Laboratory, Osaka Habikino Medical Center, Habikino-city, Osaka, Japan
| | - Yuichiro Oba
- Department of General Medicine, Osaka General Medical Center, Osaka-city, Osaka, Japan
| | - Fumiko Nishiumi
- Department of Developmental Medicine, Research Institute, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
| | - Nobuaki Hatori
- The Research Foundation for Microbial Diseases of Osaka University, Suita-city, Osaka, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda-city, Hyogo, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto-city, Kyoto, Japan
| | - Shinobu Ida
- Department of Laboratory Medicine, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
- Department of Laboratory Medicine, Osaka Women’s and Children’s Hospital, Izumi-city, Osaka, Japan
- * E-mail:
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4
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Oscorbin IP, Wong PF, Boyarskikh UA, Khrapov EA, Filipenko ML. The attachment of a DNA-binding Sso7d-like protein improves processivity and resistance to inhibitors of M-MuLV reverse transcriptase. FEBS Lett 2020; 594:4338-4356. [PMID: 32970841 DOI: 10.1002/1873-3468.13934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022]
Abstract
Reverse transcriptases (RTs) are a standard tool in both fundamental studies and diagnostics. RTs should possess elevated temperature optimum, high thermal stability, processivity and tolerance to contaminants. Here, we constructed a set of chimeric RTs, based on the combination of the Moloney murine leukaemia virus (M-MuLV) RT and either of two DNA-binding domains: the DNA-binding domain of the DNA ligase from Pyrococcus abyssi or the DNA-binding Sto7d protein from Sulfolobus tokodaii. The processivity and efficiency of cDNA synthesis of the chimeric RT with Sto7d at the C-end are increased several fold. The attachment of Sto7d enhances the tolerance of M-MuLV RT to the most common amplification inhibitors: NaCl, urea, guanidinium chloride, formamide, components of human whole blood and human blood plasma. Thus, fusing M-MuLV RT with an additional domain results in more robust and efficient RTs.
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Affiliation(s)
- Igor P Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Pei Fong Wong
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Ulyana A Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Evgeny A Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maksim L Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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5
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Yasukawa K, Yanagihara I, Fujiwara S. Alteration of enzymes and their application to nucleic acid amplification (Review). Int J Mol Med 2020; 46:1633-1643. [PMID: 33000189 PMCID: PMC7521554 DOI: 10.3892/ijmm.2020.4726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of polymerase chain reaction (PCR) in 1985, several methods have been developed to achieve nucleic acid amplification, and are currently used in various fields including clinical diagnosis and life science research. Thus, a wealth of information has accumulated regarding nucleic acid-related enzymes. In this review, some nucleic acid-related enzymes were selected and the recent advances in their modification along with their application to nucleic acid amplification were described. The discussion also focused on optimization of the corresponding reaction conditions. Using newly developed enzymes under well-optimized reaction conditions, the sensitivity, specificity, and fidelity of nucleic acid tests can be improved successfully.
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Affiliation(s)
- Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606‑8502, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka 594‑1101, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei‑Gakuin University, Sanda, Hyogo 669‑1337, Japan
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6
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Heller RC, Chung S, Crissy K, Dumas K, Schuster D, Schoenfeld TW. Engineering of a thermostable viral polymerase using metagenome-derived diversity for highly sensitive and specific RT-PCR. Nucleic Acids Res 2019; 47:3619-3630. [PMID: 30767012 PMCID: PMC6468311 DOI: 10.1093/nar/gkz104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 12/02/2022] Open
Abstract
Reverse transcription is an essential initial step in the analysis of RNA for most PCR-based amplification and detection methods. Despite advancements in these technologies, efficient conversion of RNAs that form stable secondary structures and double-stranded RNA targets remains challenging as retroviral-derived reverse transcriptases are often not sufficiently thermostable to catalyze synthesis at temperatures high enough to completely relax these structures. Here we describe the engineering and improvement of a thermostable viral family A polymerase with inherent reverse transcriptase activity for use in RT-PCR. Using the 3173 PyroPhage polymerase, previously identified from hot spring metagenomic sampling, and additional thermostable orthologs as a source of natural diversity, we used gene shuffling for library generation and screened for novel variants that retain high thermostability and display elevated reverse transcriptase activity. We then created a fusion enzyme between a high-performing variant polymerase and the 5′→3′ nuclease domain of Taq DNA polymerase that provided compatibility with probe-based detection chemistries and enabled highly sensitive detection of structured RNA targets. This technology enables a flexible single-enzyme RT-PCR system that has several advantages compared with standard heat-labile reverse transcription methods.
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Affiliation(s)
- Ryan C Heller
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Suhman Chung
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Katarzyna Crissy
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Kyle Dumas
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - David Schuster
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
| | - Thomas W Schoenfeld
- Department of Research and Development, QIAGEN Beverly, 100 Cummings Center, Suite 407J, Beverly, MA 01915, USA
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7
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Engineering Polymerases for New Functions. Trends Biotechnol 2019; 37:1091-1103. [PMID: 31003719 DOI: 10.1016/j.tibtech.2019.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 01/04/2023]
Abstract
DNA polymerases are critical tools in biotechnology, enabling efficient and accurate amplification of DNA templates, yet many desired functions are not readily available in natural DNA polymerases. New or improved functions can be engineered in DNA polymerases by mutagenesis or through the creation of protein chimeras. Engineering often necessitates the development of new techniques, such as selections in water-in-oil emulsions that connect genotype to phenotype and allow more flexibility in engineering than phage display. Engineering efforts have led to DNA polymerases that can withstand extreme conditions or the presence of inhibitors, as well as polymerases with the ability to copy modified DNA templates. In this review we discuss polymerases for biotechnology that have been reported along with tools to enable further development.
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8
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Identification of Thermus aquaticus DNA polymerase variants with increased mismatch discrimination and reverse transcriptase activity from a smart enzyme mutant library. Sci Rep 2019; 9:590. [PMID: 30679705 PMCID: PMC6345897 DOI: 10.1038/s41598-018-37233-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerases the key enzymes for several biotechnological applications. Obviously, nature has not evolved these enzymes to be compatible with applications in biotechnology. Thus, engineering of a natural scaffold of DNA polymerases may lead to enzymes improved for several applications. Here, we investigated a two-step approach for the design and construction of a combinatorial library of mutants of KlenTaq DNA polymerase. First, we selected amino acid sites for saturation mutagenesis that interact with the primer/template strands or are evolutionarily conserved. From this library, we identified mutations that little interfere with DNA polymerase activity. Next, these functionally active mutants were combined randomly to construct a second library with enriched sequence diversity. We reasoned that the combination of mutants that have minuscule effect on enzyme activity and thermostability, will result in entities that have an increased mutation load but still retain activity. Besides activity and thermostability, we screened the library for entities with two distinct properties. Indeed, we identified two different KlenTaq DNA polymerase variants that either exhibit increased mismatch extension discrimination or increased reverse transcription PCR activity, respectively.
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9
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Okano H, Baba M, Kawato K, Hidese R, Yanagihara I, Kojima K, Takita T, Fujiwara S, Yasukawa K. High sensitive RNA detection by one-step RT-PCR using the genetically engineered variant of DNA polymerase with reverse transcriptase activity from hyperthermophilies. J Biosci Bioeng 2018; 125:275-281. [PMID: 29100684 DOI: 10.1016/j.jbiosc.2017.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/03/2017] [Accepted: 10/07/2017] [Indexed: 01/14/2023]
Abstract
One-step RT-PCR has not been widely used even though some thermostable DNA polymerases with reverse transcriptase (RT) activity were developed from bacterial and archaeal polymerases, which is owing to low cDNA synthesis activity from RNA. In the present study, we developed highly-sensitive one-step RT-PCR using the single variant of family A DNA polymerase with RT activity, K4polL329A (L329A), from the hyperthermophilic bacterium Thermotoga petrophila K4 or the 16-tuple variant of family B DNA polymerase with RT activity, RTX, from the hyperthermophilic archaeon Thermococcus kodakarensis. Optimization of reaction condition revealed that the activities for cDNA synthesis and PCR of K4polL329A and RTX were highly affected by the concentrations of MgCl2 and Mn(OCOCH3)2 as well as those of K4polL329A or RTX. Under the optimized condition, 300 copies/μl of target RNA in 10 μl reaction volumes were successfully detected by the one-step RT-PCR with K4polL329A or RTX, which was almost equally sensitive enough compared with the current RT-PCR condition using retroviral RT and thermostable DNA polymerase. Considering that K4polL329A and RTX are stable even at 90-100°C, our results suggest that the one-step RT-PCR with K4polL329A or RTX is more advantageous than the current one.
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Affiliation(s)
- Hiroyuki Okano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Sakyo-ku, Kyoto 606-8502, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Sakyo-ku, Kyoto 606-8502, Japan
| | - Katsuhiro Kawato
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Ryota Hidese
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi 594-1101, Osaka, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Sakyo-ku, Kyoto 606-8502, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Sakyo-ku, Kyoto 606-8502, Japan.
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10
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Accurate fidelity analysis of the reverse transcriptase by a modified next-generation sequencing. Enzyme Microb Technol 2018; 115:81-85. [DOI: 10.1016/j.enzmictec.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 02/07/2023]
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11
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Sano S, Miyamoto S, Kawamoto S. Rapid multiplex nucleic acid amplification test developed using paper chromatography chip and azobenzene-modified oligonucleotides. J Biosci Bioeng 2018; 126:397-403. [PMID: 29673986 DOI: 10.1016/j.jbiosc.2018.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/09/2018] [Accepted: 03/23/2018] [Indexed: 11/17/2022]
Abstract
Although nucleic acid amplification test (NAT) is widely used for pathogen detection, rapid NAT systems that do not require special and expensive instruments must be developed in order to enable point of care (POC)-NATs, which contribute to early initiation of treatment. As a POC-NAT system, Kaneka DNA chromatography chip (KDCC), developed using DNA tag-bound primer through modified substance, was shown to be suitable for POC testing, due to the rapid detection time, simple procedures, and low manufacturing costs. However, owing to some modifications in primer, the detection performance and amplification speed were shown to be reduced when using KDCC, counteracting the increased speed of detection. To solve these issues and improve the speed of this NAT system, we investigated a better modification substance for KDCC. Here, azobenzene-modified primers were shown to have the highest amplification speed and detection performance in KDCC, of all modifications tested in this study, showing 10-100-fold lower detection limit but maintaining the same reaction time. Additionally, rapid herpes simplex virus detection system with azobenzene modified primers was developed. We believed that this breakthrough will contribute toward enabling greater utilization of POC-NATs for medical care, especially in developing countries and clinics.
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Affiliation(s)
- Sotaro Sano
- Medical Devices Solutions Vehicle, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan; Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
| | - Shigehiko Miyamoto
- Medical Devices Solutions Vehicle, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Seiji Kawamoto
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
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12
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Yasukawa K, Iida K, Okano H, Hidese R, Baba M, Yanagihara I, Kojima K, Takita T, Fujiwara S. Next-generation sequencing-based analysis of reverse transcriptase fidelity. Biochem Biophys Res Commun 2017; 492:147-153. [PMID: 28778390 DOI: 10.1016/j.bbrc.2017.07.169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 07/31/2017] [Indexed: 01/22/2023]
Abstract
In this study, we devised a simple and rapid method to analyze fidelity of reverse transcriptase (RT) using next-generation sequencing (NGS). The method comprises a cDNA synthesis reaction from standard RNA with a primer containing a tag of 14 randomized bases and the RT to be tested, PCR using high-fidelity DNA polymerase, and NGS. By comparing the sequence of each read with the reference sequence, mutations were identified. The mutation can be identified to be due to an error introduced by either cDNA synthesis, PCR, or NGS based on whether the sequence reads with the same tag contain the same mutation or not. The error rates in cDNA synthesis with Moloney murine leukemia virus (MMLV) RT thermostable variant MM4 or the recently developed 16-tuple variant of family B DNA polymerase with RT activity, RTX, from Thermococcus kodakarensis, were 0.75-1.0 × 10-4 errors/base, while that in the reaction with the wild-type human immunodeficiency virus type 1 (HIV-1) RT was 2.6 × 10-4 errors/base. Overall, our method could precisely evaluate the fidelity of various RTs with different reaction conditions in a high-throughput manner without the use of expensive optics and troublesome adaptor ligation.
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Affiliation(s)
- Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Kei Iida
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Okano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryota Hidese
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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13
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Okano H, Baba M, Yamasaki T, Hidese R, Fujiwara S, Yanagihara I, Ujiiye T, Hayashi T, Kojima K, Takita T, Yasukawa K. High sensitive one-step RT-PCR using MMLV reverse transcriptase, DNA polymerase with reverse transcriptase activity, and DNA/RNA helicase. Biochem Biophys Res Commun 2017; 487:128-133. [DOI: 10.1016/j.bbrc.2017.04.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 04/07/2017] [Indexed: 02/01/2023]
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Kumar S, Arumugam N, Permaul K, Singh S. Chapter 5 Thermostable Enzymes and Their Industrial Applications. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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15
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Okano H, Katano Y, Baba M, Fujiwara A, Hidese R, Fujiwara S, Yanagihara I, Hayashi T, Kojima K, Takita T, Yasukawa K. Enhanced detection of RNA by MMLV reverse transcriptase coupled with thermostable DNA polymerase and DNA/RNA helicase. Enzyme Microb Technol 2016; 96:111-120. [PMID: 27871370 DOI: 10.1016/j.enzmictec.2016.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 10/20/2022]
Abstract
Detection of mRNA is a valuable method for monitoring the specific gene expression. In this study, we devised a novel cDNA synthesis method using three enzymes, the genetically engineered thermostable variant of reverse transcriptase (RT), MM4 (E286R/E302K/L435R/D524A) from Moloney murine leukemia virus (MMLV), the genetically engineered variant of family A DNA polymerase with RT activity, K4polL329A from thermophilic Thermotoga petrophila K4, and the DNA/RNA helicase Tk-EshA from a hyperthermophilic archaeon Thermococcus kodakarensis. By optimizing assay conditions for three enzymes using Taguchi's method, 100 to 1000-fold higher sensitivity was achieved for cDNA synthesis than conventional assay condition using only RT. Our results suggest that DNA polymerase with RT activity and DNA/RNA helicase are useful to increase the sensitivity of cDNA synthesis.
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Affiliation(s)
- Hiroyuki Okano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuta Katano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ayako Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Ryota Hidese
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Tsukasa Hayashi
- Kainos Laboratories, Inc., 38-18, Hongo 2-chome, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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Yasukawa K, Konishi A, Shinomura M, Nagaoka E, Fujiwara S. Kinetic analysis of reverse transcriptase activity of bacterial family A DNA polymerases. Biochem Biophys Res Commun 2012; 427:654-8. [PMID: 23026053 DOI: 10.1016/j.bbrc.2012.09.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/21/2012] [Indexed: 11/26/2022]
Abstract
Some bacterial thermostable, wild-type or genetically engineered family A DNA polymerases have reverse transcriptase activity. However, difference in reverse transcriptase activities of family A DNA polymerases and retroviral reverse transcriptases (RTs) is unclear. In this study, comparative kinetic analysis was performed for the reverse transcriptase activities of the wild-type enzyme of family A DNA polymerase (M1pol(WT)) from Thermus thermophilus M1 and the variant enzyme of family A DNA polymerase (K4pol(L329A)), in which the mutation of Leu329→Ala is undertaken, from Thermotoga petrophila K4. In the incorporation of dTTP into poly(rA)-p(dT)(45), the reaction rates of K4pol(L329A) and M1pol(WT) exhibited a saturated profile of the Michaelis-Menten kinetics for dTTP concentrations but a substrate inhibition profile for poly(rA)-p(dT)(45) concentrations. In contrast, the reaction rates of Moloney murine leukemia virus (MMLV) RT exhibited saturated profiles for both dTTP and poly(rA)-p(dT)(45) concentrations. This suggests that high concentrations of DNA-primed RNA template decrease the efficiency of cDNA synthesis with bacterial family A DNA polymerases.
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Affiliation(s)
- Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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Pinheiro VB, Holliger P. The XNA world: progress towards replication and evolution of synthetic genetic polymers. Curr Opin Chem Biol 2012; 16:245-52. [PMID: 22704981 DOI: 10.1016/j.cbpa.2012.05.198] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/16/2012] [Accepted: 05/21/2012] [Indexed: 01/25/2023]
Abstract
Life's diversity is built on the wide range of properties and functions that can be encoded in natural biopolymers such as polypeptides and nucleic acids. However, despite their versatility, the range of chemical functionalities is limited, particularly in the case of nucleic acids. Chemical modification of nucleic acids can greatly increase their functional diversity but access to the full phenotypic potential of such polymers requires a system of replication. Here we review progress in the chemical and enzymatic synthesis, replication and evolution of unnatural nucleic acid polymers, which promises to enable the exploration of a vast sequence space not accessible to nature and deliver ligands, catalysts and materials based on this new class of biopolymers.
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Affiliation(s)
- Vitor B Pinheiro
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
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