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Ikeda Y, Nishimoto S, Qiao Y, Yano H, Minami H, Ito M, Kimura T, Takita T, Yasukawa K. Use of human Caco-2 cells and HPAE-PAD for α-glucosidase assay. J Pharmacol Toxicol Methods 2024:107508. [PMID: 38670388 DOI: 10.1016/j.vascn.2024.107508] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/28/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
To measure α-glucosidase activity, rat intestinal acetone powder is commonly used as a source of α-glucosidase, and the mutarotase-glucose oxidase (GOD) methods commonly used to quantitate glucose produced by enzymatic hydrolysis of the substrates. In this study, we compared human Caco-2 cell extracts with rat intestinal acetone powder extracts. We also compared high-performance anion-exchange chromatography with pulsed amperometric detection (HPAE-PAD) with the mutarotase-GOD method. The sensitivity of HPAE-PAD was higher than that of mutarotase-GOD. The glucose concentration quantified by HPAE-PAD was similar to that quantified using the mutarotase-GOD method. In the maltase reaction, 1-deoxynojirimycin (1-DNJ) exerted a more potent inhibitory effect on human enzymes than on rat enzymes. This order was reversed during the sucrase reaction. These results suggested that the combined use of Caco-2 cell extracts and HPAE-PAD is advantageous for use in α-glucosidase-related basic research.
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Affiliation(s)
- Yuki Ikeda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - So Nishimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ying Qiao
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruna Yano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideaki Minami
- Kyoto Municipal Institute of Industrial Technology and Culture, Shimogyo-ku, Kyoto 600-8815, Japan
| | - Masaaki Ito
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Henoko, Nago 905-2192, Japan
| | - Toshiyuki Kimura
- Research Center of Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8642, 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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2
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Kuramochi M, Nakamura M, Takahashi H, Komoriya T, Takita T, Pham NTK, Yasukawa K, Yoshimune K. Adenosine triphosphate induces amorphous aggregation of amyloid β by increasing Aβ dynamics. Sci Rep 2024; 14:8134. [PMID: 38584155 PMCID: PMC10999452 DOI: 10.1038/s41598-024-58773-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/03/2024] [Indexed: 04/09/2024] Open
Abstract
Amyloid β (Aβ) aggregates into two distinct fibril and amorphous forms in the brains of patients with Alzheimer's disease. Adenosine triphosphate (ATP) is a biological hydrotrope that causes Aβ to form amorphous aggregates and inhibit fibril formation at physiological concentrations. Based on diffracted X-ray blinking (DXB) analysis, the dynamics of Aβ significantly increased immediately after ATP was added compared to those in the absence and presence of ADP and AMP, and the effect diminished after 30 min as the aggregates formed. In the presence of ATP, the β-sheet content of Aβ gradually increased from the beginning, and in the absence of ATP, the content increased rapidly after 180 min incubation, as revealed by a time-dependent thioflavin T fluorescence assay. Images of an atomic force microscope revealed that ATP induces the formation of amorphous aggregates with an average diameter of less than 100 nm, preventing fibrillar formation during 4 days of incubation at 37 °C. ATP may induce amorphous aggregation by increasing the dynamics of Aβ, and as a result, the other aggregation pathway is omitted. Our results also suggest that DXB analysis is a useful method to evaluate the inhibitory effect of fibrillar formation.
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Affiliation(s)
- Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
| | - Momoka Nakamura
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Hiroto Takahashi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
| | - Tomoe Komoriya
- Department of Sustainable Engineering, College of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ngan Thi Kim Pham
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kazuaki Yoshimune
- Department of Applied Molecular Chemistry, Graduate School of Industrial Technology, Nihon University, 1-2-1, Izumichou, Narashino, Chiba, 275-8575, Japan.
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3
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Nakamura T, Takita T, Kuwata K, Mizutani K, Mikami B, Nakamura S, Yasukawa K. Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR. Sci Rep 2024; 14:7767. [PMID: 38565938 PMCID: PMC10987496 DOI: 10.1038/s41598-024-57819-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
XynR is a thermostable alkaline GH10 xylanase, for which we have previously examined the effects of saturation mutagenesis at position 315 on enzyme alkaliphily, and found that at pH 10, the activities of variants could be ordered as follows: T315Q > T315S = T315N > T315H = wild-type XynR (WT) > 15 other variants. In this study, we sought to elucidate the mechanisms underlying the variable activity of these different variants. Crystallographic analysis revealed that the Ca2+ ion near position 315 in WT was absent in the T315Q variant. We accordingly hypothesized that the enhancement of alkaliphily in T315Q, and probably also in the T315H, T315N, and T315S variants, could be ascribed to an activity-stability trade-off associated with a reduction in stability due to the lack of this Ca2+ ion. Consistent with expectations, the alkaline resistance of T315H, T315N, T315Q, and T315S, evaluated through the pH-dependence of stability at 0 mM CaCl2 under alkaline conditions, was found to be lower than that of WT: the residual activity at pH 11 of WT was 78% while those of T315H, T315N, T315Q, and T315S were 0, 9, 0, and 43%, respectively. In addition, the thermostabilities of these four variants, as assessed using the denaturing temperatures (Tm) at 0 mM CaCl2 based on ellipticity at 222 nm in circular dichroism measurements, were lower than that of WT by 2-8 °C. Furthermore, the Tm values of WT and variants at 5 mM CaCl2 were higher than those at 0 mM CaCl2 by 6-11 °C. Collectively, our findings in this study indicate that mutation of the T residue at position 315 of XynR to H, N, Q, and S causes an increase in the alkaliphily of this enzyme, thereby reducing its stability.
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Affiliation(s)
- Tomoka Nakamura
- 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
| | - Kohei Kuwata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kimihiko Mizutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Satoshi Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, 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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4
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Morimoto K, Juma KM, Yamagata M, Takita T, Kojima K, Suzuki K, Yanagihara I, Fujiwara S, Yasukawa K. Increase in the solubility of uvsY using a site saturation mutagenesis library for application in a lyophilized reagent for recombinase polymerase amplification. Mol Biol Rep 2024; 51:367. [PMID: 38411701 PMCID: PMC10899321 DOI: 10.1007/s11033-024-09367-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Recombinase uvsY from bacteriophage T4, along with uvsX, is a key enzyme for recombinase polymerase amplification (RPA), which is used to amplify a target DNA sequence at a constant temperature. uvsY, though essential, poses solubility challenges, complicating the lyophilization of RPA reagents. This study aimed to enhance uvsY solubility. METHODS Our hypothesis centered on the C-terminal region of uvsY influencing solubility. To test this, we generated a site-saturation mutagenesis library for amino acid residues Lys91-Glu134 of the N-terminal (His)6-tagged uvsY. RESULTS Screening 480 clones identified A116H as the variant with superior solubility. Lyophilized RPA reagents featuring the uvsY variant A116H demonstrated enhanced performance compared to those with wild-type uvsY. CONCLUSIONS The uvsY variant A116H emerges as an appealing choice for RPA applications, offering improved solubility and heightened lyophilization feasibility.
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Affiliation(s)
- Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Masaya Yamagata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, 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
| | - 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, Kyoto, 606-8502, Japan.
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5
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Juma KM, Morimoto K, Sharma V, Sharma K, Biyani R, Biyani M, Takita T, Yasukawa K. Detection of SARS-CoV-2 spike protein D614G mutation using μTGGE. Mol Biol Rep 2024; 51:289. [PMID: 38329653 DOI: 10.1007/s11033-023-09065-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/02/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND The accurate and expeditious detection of SARS-CoV-2 mutations is critical for monitoring viral evolution, assessing its impact on transmission, virulence, and vaccine efficacy, and formulating public health interventions. In this study, a detection system utilizing micro temperature gradient gel electrophoresis (μTGGE) was developed for the identification of the D614 and G614 variants of the SARS-CoV-2 spike protein. METHODS The in vitro synthesized D614 and G614 gene fragments of the SARS-CoV-2 spike protein were amplified via polymerase chain reaction and subjected to μTGGE analysis. RESULTS The migration patterns exhibited by the D614 and G614 variants on the polyacrylamide gel were distinctly dissimilar and readily discernible by μTGGE. In particular, the mid-melting pattern of D614 was shorter than that of G614. CONCLUSIONS Our results demonstrate the capability of μTGGE for the rapid, precise, and cost-effective detection of SARS-CoV-2 spike protein D614 and G614 variants without the need for sequencing. Therefore, this approach holds considerable potential for use in point-of-care mutation assays for SARS-CoV-2 and other pathogens.
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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
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Vishnu Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
- Biyani BioSolutions Pvt. Ltd., R-4, Sector 3, Vidhyadharnagar, Jaipur, 302023, India
| | - Kirti Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Radhika Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Manish Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Lab, Ashahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan.
- Biyani BioSolutions Pvt. Ltd., R-4, Sector 3, Vidhyadharnagar, Jaipur, 302023, India.
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, 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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6
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Tanakura Y, Uekawa Y, Shige Y, Fukuda W, Ikuta S, Wu HN, Yasukawa K, Yanagihara I, Fujiwara S. Expression of a recombinant protein by an acetic acid bacterial host. J Biotechnol 2024; 380:38-50. [PMID: 38135188 DOI: 10.1016/j.jbiotec.2023.12.009] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
We evaluated the suitability of Komagataeibacter europaeus, a vinegar production organism adept at synthetic media growth, as a host for heterologous gene expression. Cryptic plasmids (pGE1 and pGE2 derivatives) from K. europaeus strain KGMA0119 were employed as vectors for heterologous gene expression. The focus was placed on the groES promoter as a potential inducible switch. The groES promoter was fused with the EGFP gene and introduced into a pGE1 derivative to assess its suitability. Ethanol, acetic acid, and heat stresses were examined under various conditions for induction. EGFP transcription surged 600-fold when late logarithmic phase K. europaeus cells, cultured at 30 °C, endured heat stress at 40 °C, coupled with 20% acetic acid and 30% ethanol stress after an additional 6-hour cultivation. This robust induction system was then applied to express two proteins, Tth pol from the thermophilic bacterium Thermus thermophilus strain M1 and UPV230, a restriction enzyme from the acid-tolerant microorganism Ureaplasma parvum, known to cause vaginal infections and miscarriages. Both Tth pol and UPV230 were successfully expressed in K. europaeus cells and purified. The recovery of Tth pol from K. europaeus cells (480 µg protein per liter culture) was approximately half that from E. coli (960 µg protein per liter culture). In contrast, UPV230 recovery from K. europaeus cells (640 µg protein per liter culture) was nearly 10 times higher than that from Escherichia coli (66 µg protein per liter). The data highlights the potential of acetic acid bacteria as a host for producing acidophilic proteins. The shift in recognition from a 6-base sequence to a 4-base sequence of UPV230 was observed, accompanied by a change in structure as the pH transitioned from acidic pH to near-neutral pH.
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Affiliation(s)
- Yuya Tanakura
- Department of Biosciences, Graduate School of Science and Technology, Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Yasuyoshi Uekawa
- Department of Biosciences, Graduate School of Science and Technology, Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Yuki Shige
- Department of Biosciences, Graduate School of Science and Technology, Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Soichiro Ikuta
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan
| | - Heng Ning Wu
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Izumi, Osaka 594-1101, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, 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 Biosciences, Graduate School of Science and Technology, Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan; Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan.
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7
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Kojima K, Morimoto K, Juma KM, Takita T, Saito K, Yanagihara I, Fujiwara S, Yasukawa K. Application of recombinant human pyruvate kinase in recombinase polymerase amplification. J Biosci Bioeng 2023; 136:341-346. [PMID: 37718149 DOI: 10.1016/j.jbiosc.2023.08.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41°C using recombinase (Rec), single-stranded DNA-binding protein (SSB), strand-displacing DNA polymerase (Pol), and an ATP-regenerating enzyme. In this study, we attempted to use pyruvate kinase instead of creatine kinase (CK) that has been consistently used as an ATP-regenerating enzyme in RPA. Human pyruvate kinase M1 (PKM) was expressed in Escherichia coli and purified from the cells. RPA with PKM was performed at 41°C with the in vitro synthesized urease subunit β (ureB) DNA from Ureaplasma parvum serovar 3 as a standard DNA. The optimal concentrations of PKM and phosphoenolpyruvate were 20 ng/μL and 10 mM, respectively. The RPA reaction with PKM was more sensitive than that with CK. PKM exhibited higher thermostability than CK, suggesting that the RPA reagents with PKM are preferable to those with CK for onsite use.
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Affiliation(s)
- Kenji Kojima
- Division of Bioanalytical Chemistry, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, Japan
| | - Kenta Morimoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kevin Maafu Juma
- 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
| | - Kazuki Saito
- Division of Bioanalytical Chemistry, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo 670-8524, 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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8
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Ueshima S, Yasumoto M, Kitagawa Y, Akazawa K, Takita T, Tanaka K, Hattori S, Mizutani K, Mikami B, Yasukawa K. Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses. FEBS Lett 2023; 597:2473-2483. [PMID: 37698340 DOI: 10.1002/1873-3468.14732] [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: 06/28/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023]
Abstract
Grimontia hollisae collagenase (Ghcol) exhibits high collagen-degrading activity. To explore its catalytic mechanism, its substrate (Gly-Pro-Hyp-Gly-Pro-Hyp, GPOGPO)-complexed crystal structure was determined at 2.0 Å resolution. A water molecule was observed near the active-site zinc ion. Since this water was not observed in the product (GPO)-complexed Ghcol, it was hypothesized that the GPOGPO-complexed Ghcol structure reflects a Michaelis complex, providing a structural basis for understanding the catalytic mechanism. Analyses of the active-site geometry and site-directed mutagenesis of the active-site tyrosine residues revealed that Glu493 and Tyr564 were essential for catalysis, suggesting that Glu493 functions as an acid and base catalyst while Tyr564 stabilizes the tetrahedral complex in the transition state. These results shed light on the catalytic mechanism of bacterial collagenase.
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Affiliation(s)
- Saori Ueshima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Mizuki Yasumoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Yuto Kitagawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Kaho Akazawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | | | | | - Kimihiko Mizutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Japan
- Institute of Advanced Energy, Kyoto University, Uji, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
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9
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Hara H, Yano H, Akazawa K, Kamoda K, Kandabashi M, Baba M, Takita T, Yasukawa K. Construction and characterization of ribonuclease H2 C subunit-knockout NIH3T3 cells. Biosci Biotechnol Biochem 2023:7192426. [PMID: 37291694 DOI: 10.1093/bbb/zbad077] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mammalian ribonuclease (RNase) H2 is a trimer consisting of catalytic A and accessory B and C subunits. RNase H2 is involved in the removal of misincorporated ribonucleotides from genomic DNA. In humans, mutations in RNase H2 gene cause a severe neuroinflammatory disorder, Aicardi-Goutières syndrome (AGS). Here, we constructed RNase H2 C subunit (RH2C)-knockout mouse fibroblast NIH3T3 cells. Compared with the wild-type NIH3T3 cells, the knockout cells exhibited a decreased single ribonucleotide-hydrolyzing activity and an increased accumulation of ribonucleotides in genomic DNA. Transient expression of wild-type RH2C in the knockout cells increased this activity and decreased this ribonucleotide accumulation. Same events were observed when RH2C variants with an AGS-causing mutation, R69W or K145I, were expressed. These results corresponded with our previous results on the RNase H2 A subunit (RH2A)-knockout NIH3T3 cells and the expression of wild-type RH2A or RH2A variants with an AGS-causing mutation, N213I and R293H, in the RH2A-knockout cells.
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Affiliation(s)
- Haruka Hara
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruna Yano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kaho Akazawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kana Kamoda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mako Kandabashi
- 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
| | - 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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10
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Tokonami M, Horiguchi A, Ueshima N, Takita T, Takahashi T, Nishimura K, Yasukawa K. Purification and characterization of a serine protease from the fruit of Ficus carica cultivar Masui Dauphine. Biosci Biotechnol Biochem 2023; 87:532-540. [PMID: 37037773 DOI: 10.1093/bbb/zbad028] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/18/2023] [Indexed: 04/12/2023]
Abstract
Ficus carica produces, in addition to the cysteine protease ficin, a serine protease (FSP). Here, we purified FSP to homogeneity from the fruit of F. carica cultivar Masui Dauphine. An 81-fold enrichment in specific activity of FSP with 2.1% recovery was attained. Three protein bands (70, 62, and 60 kDa) were identified on SDS-PAGE. Each band was identified as a subtilisin-like protease (661 amino acids) by trypsin digestion and LC-MS/MS analysis, and the partial N-terminal amino-acid sequence analysis. Gelatin zymography revealed that the active FSP exists as a dimer. The optimum hydrolysis pH of FSP was 7.5, and the pHs at which the enzyme retained its initial activity by 70% in 24 h were 8.0-11.0. The optimum hydrolysis temperature of FSP was 50-60ºC, and the temperature required to reduce the initial activity by 50% in 15 min was 70ºC. These results will inform the industrial use of FSP.
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Affiliation(s)
- Mizuki Tokonami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Akari Horiguchi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Naoki Ueshima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Toru Takahashi
- Toyo Institute of Food Technology, 4-23-2, Minami-Hanayashiki, Kawanishi, Hyogo, Japan
| | - Kosaku Nishimura
- Toyo Institute of Food Technology, 4-23-2, Minami-Hanayashiki, Kawanishi, Hyogo, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Yoshimura M, Shimizu K, Nakura Y, Kawahara K, Katano H, Motooka D, Takeuchi M, Nagamune K, Imamura Y, Nakamura S, Yasukawa K, Hasegawa H, Yoshida Y, Yanagihara I. A fatal case of hemophagocytic lymphohistiocytosis associated with gestational psittacosis without symptoms of pneumonia. J Obstet Gynaecol Res 2022; 48:3325-3330. [PMID: 36097654 DOI: 10.1111/jog.15429] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]
Abstract
Psittacosis is a zoonotic infection caused by Chlamydia psittaci. Most patients present with acute respiratory symptoms and systemic illness. When C. psittaci infects pregnant women, it causes severe clinical manifestations called gestational psittacosis. Here we report a case of gestational psittacosis. Our patient lacked respiratory symptoms, and pathological postmortem examinations revealed severe placentitis. Both DNA and immunohistochemical analyses were positive for C. psittaci from formalin-fixed paraffin-embedded tissues. The chlamydial DNA in the placenta was about 100 times more abundant than that in the lungs; therefore, the placenta rather than the lungs was the probable target of the C. psittaci infection during this pregnancy. We could not identify the source of infection. Gestational psittacosis should be considered in the differential diagnosis for fever of unknown origin during pregnancy, even in cases lacking respiratory symptoms.
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Affiliation(s)
- Michinobu Yoshimura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kanako Shimizu
- Department of Obstetrics and Gynecology, Maizuru Kyosai Hospital, Kyoto, Japan.,Department of Obstetrics and Gynecology, University of Fukui, Fukui, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kazumi Kawahara
- Department of Obstetrics and Gynecology, Maizuru Kyosai Hospital, Kyoto, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Makoto Takeuchi
- Department of Pathology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kisaburo Nagamune
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiaki Imamura
- Division of Diagnostic Pathology/Surgical Pathology, University of Fukui, Fukui, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshio Yoshida
- Department of Obstetrics and Gynecology, University of Fukui, Fukui, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka, Japan
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13
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Kandabashi M, Yano H, Hara H, Ogawa S, Kamoda K, Ishibashi S, Himeda K, Baba M, Takita T, Yasukawa K. Analysis of ribonucleotide content in the genomic DNA of ribonuclease H2 A subunit (RH2A)-knockout NIH3T3 cells after transient expression of wild-type RH2A or RH2A variants with an Aicardi-Goutières syndrome-causing mutation. J Biochem 2022; 172:225-231. [DOI: 10.1093/jb/mvac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/03/2022] [Indexed: 11/13/2022] Open
Abstract
Summary
Ribonuclease (RNase) H2 is involved in the removal of ribonucleotides embedded in genomic DNA. Eukaryotic RNase H2 is a heterotrimer consisting of the catalytic A subunit (RH2A) and the accessory B and C subunits. This study aimed to compare the cellular activities of wild-type ribonuclease (RNase) H2 and its variants with a mutation causing neuroinflammatory autoimmune disease, Aicardi-Goutières syndrome (AGS). We first analyzed cellular RNase H2 activity and ribonucleotide content in the genomic DNA of RH2A-knockout (KO) mouse fibroblast NIH3T3 cells after transfection with a transient expression plasmid encoding mouse wild-type RH2A. From four hours after transfection, the RNase H2 activity increased, and the amount of ribonucleotides decreased, as compared with the corresponding non-transfected RH2A-KO cells. This demonstrated the rapidness of ribonucleotide turnover in mammalian genomic DNA and the importance of continuous expression of RNase H2 to maintain the ribonucleotide amount low. Next, we expressed mouse RH2A variants with a mutation corresponding to a human AGS-causing mutation in RH2A-KO NIH3T3 cells. Neither increase in RNase H2 activity nor decrease in ribonucleotide amount were observed for G37S; however, both conditions were observed for N213I and R293H. This corresponded with our previous results on the activity of recombinant human RNase H2 variants.
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Affiliation(s)
- Mako Kandabashi
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruna Yano
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruka Hara
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Saori Ogawa
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kana Kamoda
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shu Ishibashi
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kohei Himeda
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Misato Baba
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kiyoshi Yasukawa
- Graduate School of Agriculture Division of Food Science and Biotechnology, , Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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14
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Takita T, Sakuma H, Ohashi R, Nilouyal S, Nemoto S, Wada M, Yogo Y, Yasuda K, Ikushiro S, Sakaki T, Yasukawa K. Comparison of the stability of CYP105A1 and its variants engineered for production of active forms of vitamin D. Biosci Biotechnol Biochem 2022; 86:444-454. [PMID: 35134837 DOI: 10.1093/bbb/zbac019] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/21/2022] [Indexed: 11/14/2022]
Abstract
CYP105A1 from Streptomyces griseolus converts vitamin D3 to its biologically active form, 1α,25-dihydroxy vitamin D3. R73A/R84A mutation enhanced the 1α- and 25-hydroxylation activity for vitamin D3, while M239A mutation generated the 1α-hydroxylation activity for vitamin D2. In this study, the stability of six CYP105A1 enzymes, including 5 variants (R73A/R84A, M239A, R73A/R84A/M239A (=TriA), TriA/E90A, and TriA/E90D), was examined. Circular dichroism analysis revealed that M239A markedly reduces the enzyme stability. Protein fluorescence analysis disclosed that these mutations, especially M239A, induce large changes in the local conformation around Trp residues. Strong stabilizing effect of glycerol was observed. Nondenaturing PAGE analysis showed that CYP105A1 enzymes are prone to self-association. Fluorescence analysis using a hydrophobic probe 8-anilino-1-naphthalenesulfonic acid suggested that M239A mutation enhances self-association and that E90A and E90D mutations, in cooperation with M239A, accelerate self-association with little effect on the stability.
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Affiliation(s)
- Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hiro Sakuma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Ren Ohashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Somaye Nilouyal
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sho Nemoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Moeka Wada
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuya Yogo
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Kaori Yasuda
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan.,Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Toshiyuki Sakaki
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan.,Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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15
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Qiao Y, Ikeda Y, Ito M, Kimura T, Ikeuchi T, Takita T, Yasukawa K. Inhibition of α‐amylase and α‐glucosidase by
Morus australis
fruit extract and its components iminosugar, anthocyanin, and glucose. J Food Sci 2022; 87:1672-1683. [DOI: 10.1111/1750-3841.16098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Qiao
- Divison of Food Science and Biotechnology, Graduate School of Agriculture Kyoto University Sakyo‐ku Japan
| | - Yuki Ikeda
- Divison of Food Science and Biotechnology, Graduate School of Agriculture Kyoto University Sakyo‐ku Japan
| | - Masaaki Ito
- Department of Bioresources Engineering, National Institute of Technology Okinawa College Nago Japan
| | - Toshiyuki Kimura
- Research Center of Advanced Analysis National Agriculture and Food Research Organization (NARO) Tsukuba Japan
| | - Takeaki Ikeuchi
- Divison of Food Science and Biotechnology, Graduate School of Agriculture Kyoto University Sakyo‐ku Japan
| | - Teisuke Takita
- Divison of Food Science and Biotechnology, Graduate School of Agriculture Kyoto University Sakyo‐ku Japan
| | - Kiyoshi Yasukawa
- Divison of Food Science and Biotechnology, Graduate School of Agriculture Kyoto University Sakyo‐ku Japan
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16
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Yogo Y, Yasuda K, Takita T, Yasukawa K, Iwai Y, Nishikawa M, Sugimoto H, Ikushiro S, Sakaki T. Metabolism of non-steroidal anti-inflammatory drugs (NSAIDs) by Streptomyces griseolus CYP105A1 and its variants. Drug Metab Pharmacokinet 2022; 45:100455. [DOI: 10.1016/j.dmpk.2022.100455] [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] [Received: 09/14/2021] [Revised: 02/08/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
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17
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Juma KM, Takita T, Yamagata M, Ishitani M, Hayashi K, Kojima K, Suzuki K, Ando Y, Fukuda W, Fujiwara S, Nakura Y, Yanagihara I, Yasukawa K. Modified uvsY by N-terminal hexahistidine tag addition enhances efficiency of recombinase polymerase amplification to detect SARS-CoV-2 DNA. Mol Biol Rep 2022; 49:2847-2856. [PMID: 35098395 PMCID: PMC8801280 DOI: 10.1007/s11033-021-07098-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/16/2021] [Indexed: 11/28/2022]
Abstract
Background Methods Results Conclusions Supplementary Information
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Affiliation(s)
- Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Masaya Yamagata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Mika Ishitani
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kaichi Hayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- 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
| | - Yuri Ando
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669‑1337, Japan
| | - Wakao Fukuda
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669‑1337, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, Sanda, Hyogo, 669‑1337, 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
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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18
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Biyani R, Sharma K, Kojima K, Biyani M, Sharma V, Kumawat T, Juma KM, Yanagihara I, Fujiwara S, Kodama E, Takamura Y, Takagi M, Yasukawa K, Biyani M. Development of robust isothermal RNA amplification assay for lab-free testing of RNA viruses. Sci Rep 2021; 11:15997. [PMID: 34362977 PMCID: PMC8346491 DOI: 10.1038/s41598-021-95411-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/26/2021] [Indexed: 11/30/2022] Open
Abstract
Simple tests of infectiousness that return results in minutes and directly from samples even with low viral loads could be a potential game-changer in the fight against COVID-19. Here, we describe an improved isothermal nucleic acid amplification assay, termed the RICCA (RNA Isothermal Co-assisted and Coupled Amplification) reaction, that consists of a simple one-pot format of ‘sample-in and result-out’ with a primary focus on the detection of low copy numbers of RNA virus directly from saliva without the need for laboratory processing. We demonstrate our assay by detecting 16S rRNA directly from E. coli cells with a sensitivity as low as 8 CFU/μL and RNA fragments from a synthetic template of SARS-CoV-2 with a sensitivity as low as 1740 copies/μL. We further demonstrate the applicability of our assay for real-time testing at the point of care by designing a closed format for paper-based lateral flow assay and detecting heat-inactivated SARS-COV-2 virus in human saliva at concentrations ranging from 28,000 to 2.8 copies/μL with a total assay time of 15–30 min.
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Affiliation(s)
- Radhika Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kirti Sharma
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Madhu Biyani
- BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan.,Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Vishnu Sharma
- Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Tarun Kumawat
- Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, 840 Murodocho, Izumi, Osaka, 594-1101, Japan
| | - Shinsuke Fujiwara
- Department of Biosciences, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Eiichi Kodama
- Division of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryocho Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Masahiro Takagi
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa, 923-1292, Japan. .,BioSeeds Corporation, JAIST Venture Business Laboratory, Ishikawa Create Labo, Asahidai 2-13, Nomi City, Ishikawa, 923-1211, Japan. .,Biyani BioSolutions Pvt. Ltd., Biyani Group of Colleges Venture Business Laboratory, R-4, Sector 3, Vidhyadhar Nagar, Jaipur, 302039, India.
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19
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Kuwata K, Suzuki M, Takita T, Yatsunami R, Nakamura S, Yasukawa K. The mutation of Thr315 to Asn of GH10 xylanase XynR increases the alkaliphily but decreases the alkaline resistance. Biosci Biotechnol Biochem 2021; 85:1853-1860. [PMID: 34077498 DOI: 10.1093/bbb/zbab102] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022]
Abstract
XynR is a thermophilic and alkaline GH10 xylanase, identified in the culture broth of alkaliphilic and thermophilic Bacillus sp. strain TAR-1. We previously selected S92E as a thermostable variant from a site saturation mutagenesis library. Here, we attempted to select the alkaliphilic XynR variant from the library and isolated T315N. In the hydrolysis of beechwood xylan, T315N and S92E/T315N exhibited a broader bell-shaped pH-dependent activity than the wild-type (WT) XynR and S92E. The optimal pH values of T315N and S92E/T315N were 6.5-9.5 while those of WT and S92E were 6.5-8.5. On the other hand, T315N and S92E/T315N exhibited a narrower bell-shaped pH dependence of stability: the pHs at which the activity was stable after the incubation at 37 °C for 24 h were 6.0-8.5 for T315N and S92E/T315N, but 6.0-10.0 for WT and S92E. These results indicated that the mutation of Thr315 to Asn increased the alkaliphily but decreased the alkaline resistance.
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Affiliation(s)
- Kohei Kuwata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Manami Suzuki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Rie Yatsunami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan.,National Institute of Technology, Numazu College, Ooka, Numazu, Shizuoka, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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20
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Notake T, Shimizu A, Kubota K, Ikehara T, Hayashi H, Yasukawa K, Kobayashi A, Yamada A, Fujinaga Y, Soejima Y. Hepatocellular uptake index obtained with gadoxetate disodium-enhanced magnetic resonance imaging in the assessment future liver remnant function after major hepatectomy for biliary malignancy. BJS Open 2021; 5:6319789. [PMID: 34254117 PMCID: PMC8275880 DOI: 10.1093/bjsopen/zraa048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/06/2020] [Indexed: 12/19/2022] Open
Abstract
Background Functional assessment of the future liver remnant (FLR) after major hepatectomy is essential but often difficult in patients with biliary malignancy, owing to obstructive jaundice and portal vein embolization. This study evaluated whether a novel index using gadoxetate disodium-enhanced MRI (EOB-MRI) could predict posthepatectomy liver failure (PHLF) after major hepatectomy for biliary malignancy. Methods The remnant hepatocellular uptake index (rHUI) was calculated in patients undergoing EOB-MRI before major hepatectomy for biliary malignancy. Receiver operating characteristic (ROC) curve analyses were used to evaluate the accuracy of rHUI for predicting PHLF grade B or C, according to International Study Group of Liver Surgery criteria. Multivariable logistic regression analyses comprised stepwise selection of parameters, including rHUI and other conventional indices. Results This study included 67 patients. The rHUI accurately predicted PHLF (area under the curve (AUC) 0.896). A cut-off value for rHUI of less than 0.410 predicted all patients who developed grade B or C PHLF. In multivariable analysis, only rHUI was an independent risk factor for grade B or C PHLF (odds ratio 2.0 × 103, 95 per cent c.i. 19.6 to 3.8 × 107; P < 0.001). In patients who underwent preoperative portal vein embolization, rHUI accurately predicted PHLF (AUC 0.885), whereas other conventional indices, such as the plasma disappearance rate of indocyanine green of the FLR and FLR volume, did not. Conclusion The rHUI is potentially a useful predictor of PHLF after major hepatectomy for biliary malignancy.
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Affiliation(s)
- T Notake
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - A Shimizu
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - K Kubota
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - T Ikehara
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - H Hayashi
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - K Yasukawa
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - A Kobayashi
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - A Yamada
- Department of Radiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Y Fujinaga
- Department of Radiology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Y Soejima
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Paediatric Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
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21
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Qiao Y, Ito M, Kimura T, Ikeuchi T, Takita T, Yasukawa K. Inhibitory effect of Morus australis leaf extract and its component iminosugars on intestinal carbohydrate-digesting enzymes. J Biosci Bioeng 2021; 132:226-233. [PMID: 34148793 DOI: 10.1016/j.jbiosc.2021.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/24/2022]
Abstract
α-Amylase and α-glucosidase are central enzymes involved in the digestion of carbohydrates. α-Glucosidase includes maltase-glucoamylase and sucrase-isomaltase. We have previously performed the kinetic analysis of the inhibitory effects of powdered or roasted Morus australis leaf extract and its component iminosugars, such as 1-deoxynojirimycin (1-DNJ), fagomine, and 2-O-α-d-galactopyranosyl deoxynojirimycin (GAL-DNJ) on the activity of maltase. In this study, we analyzed the inhibitory effects of the aforementioned compounds against α-amylase, glucoamylase, sucrase, and isomaltase. At pH 6.0 and 37 °C, each leaf extract sample inhibited glucoamylase, sucrase, and isomaltase but not α-amylase. 1-DNJ and fagomine showed weak α-amylase inhibitory activity while GAL-DNJ exhibited none. 1-DNJ showed a strong glucoamylase, sucrase, and isomaltase inhibitory potential. The inhibitory potential against these three enzymes was 18-500 and 1500-3000-fold higher in the case of 1-DNJ than that observed in the case of fagomine and GAL-DNJ, respectively. We also observed that the indigestible dextrin could considerably inhibit α-amylase. When the powdered M. australis leaf extract was blended with indigestible dextrin, the mixture inhibited α-amylase, as well as maltase, glucoamylase, sucrase, and isomaltase. These results suggest that the ingestion of the leaf extract blended with indigestible dextrin might have the potential to efficiently suppress the postprandial blood glucose level increase.
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Affiliation(s)
- Ying Qiao
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masaaki Ito
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905 Henoko, Nago 905-2192, Japan
| | - Toshiyuki Kimura
- Food Research Institute (NFRI), National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Takeaki Ikeuchi
- 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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Nishimura K, Higashiya K, Ueshima N, Kojima K, Takita T, Abe T, Takahashi T, Yasukawa K. Insight into the collagen-degrading activity of a serine protease in the latex of Ficus carica cultivar Masui Dauphine. Biosci Biotechnol Biochem 2021; 85:1147-1156. [PMID: 33580958 DOI: 10.1093/bbb/zbab025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/05/2021] [Indexed: 02/02/2023]
Abstract
Ficus carica produces, in addition to the cysteine protease ficin, a serine protease. Earlier study on a serine protease from F. carica cultivar Brown Turkey showed that it specifically degraded collagen. In this study, we characterized the collagenolytic activity of a serine protease in the latex of F. carica cultivar Masui Dauphine. The serine protease degraded denatured, but not undenatured, acid-solubilized type I collagen. It also degraded bovine serum albumin, while the collagenase from Clostridium histolyticum did not. These results indicated that the serine protease in Masui Dauphine is not collagen-specific. The protease was purified to homogeneity by two-dimensional gel electrophoresis, and its partial amino acid sequence was determined by liquid chromatography-tandem mass spectrometry. BLAST searches against the Viridiplantae (green plants) genome database revealed that the serine protease was a subtilisin-like protease. Our results contrast with the results of the earlier study stating that the serine protease from F. carica is collagen-specific.
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Affiliation(s)
- Kosaku Nishimura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Toyo Institute of Food Technology, Kawanishi, Hyogo, Japan
| | - Keisuke Higashiya
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Naoki Ueshima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tatsuya Abe
- Toyo Institute of Food Technology, Kawanishi, Hyogo, Japan
| | - Toru Takahashi
- Toyo Institute of Food Technology, Kawanishi, Hyogo, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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24
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Suzuki M, Takita T, Kuwata K, Nakatani K, Li T, Katano Y, Kojima K, Mizutani K, Mikami B, Yatsunami R, Nakamura S, Yasukawa K. Insight into the mechanism of thermostabilization of GH10 xylanase from Bacillus sp. strain TAR-1 by the mutation of S92 to E. Biosci Biotechnol Biochem 2021; 85:386-390. [PMID: 33604642 DOI: 10.1093/bbb/zbaa003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/02/2020] [Indexed: 11/12/2022]
Abstract
The mechanism of thermostabilization of GH10 xylanase, XynR, from Bacillus sp. strain TAR-1 by the mutation of S92 to E was investigated. Thermodynamic analysis revealed that thermostabilization was driven by the decrease in entropy change of activation for thermal inactivation. Crystallographic analysis suggested that this mutation suppressed the fluctuation of the amino acid residues at position 92-95.
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Affiliation(s)
- Manami Suzuki
- 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
| | - Kohei Kuwata
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kota Nakatani
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tongyang Li
- 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
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kimihiko Mizutani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.,Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Rie Yatsunami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.,National Institute of Technology, Numazu College, Ooka, Numazu, Shizuoka 410-8501, 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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25
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Narukawa Y, Kandabashi M, Li T, Baba M, Hara H, Kojima K, Iida K, Hiyama T, Yokoe S, Yamazaki T, Takita T, Yasukawa K. Improvement of Moloney murine leukemia virus reverse transcriptase thermostability by introducing a disulfide bridge in the ribonuclease H region. Protein Eng Des Sel 2021; 34:6213763. [PMID: 33825883 DOI: 10.1093/protein/gzab006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 11/14/2022] Open
Abstract
Moloney murine leukemia virus (MMLV) reverse transcriptase (RT) is widely used in research and clinical diagnosis. Improvement of MMLV RT thermostability has been an important topic of research for increasing the efficiency of cDNA synthesis. In this study, we attempted to increase MMLV RT thermostability by introducing a disulfide bridge in its RNase H region using site-directed mutagenesis. Five variants were designed, focusing on the distance between the two residues to be mutated into cysteine. The variants were expressed in Escherichia coli and purified. A551C/T662C was determined to be the most thermostable variant.
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Affiliation(s)
- Yutaro Narukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mako Kandabashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tongyang Li
- 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
| | - Haruka Hara
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- 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
| | - Takayoshi Hiyama
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd. 10-24 Toyo-cho, Tsuruga 914-8550, Japan
| | - Sho Yokoe
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd. 10-24 Toyo-cho, Tsuruga 914-8550, Japan
| | - Tomomi Yamazaki
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd. 10-24 Toyo-cho, Tsuruga 914-8550, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, 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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26
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Kojima K, Juma KM, Akagi S, Hayashi K, Takita T, O'Sullivan CK, Fujiwara S, Nakura Y, Yanagihara I, Yasukawa K. Solvent engineering studies on recombinase polymerase amplification. J Biosci Bioeng 2020; 131:219-224. [PMID: 33177003 DOI: 10.1016/j.jbiosc.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 11/24/2022]
Abstract
Recombinase polymerase amplification (RPA) is a technique that is used to specifically amplify a target nucleic acid sequence. Unlike the polymerase chain reaction (PCR), RPA is performed at a constant temperature between 37 and 42°C. Therefore, it can be potentially used for the onsite detection of various pathogens when combined with DNA extraction and amplicon detection techniques. In this study, we prepared recombinant recombinase and single-stranded DNA-binding protein from T4 phage and used them to examine the effects of reaction conditions and additives on the efficiency of RPA. The results revealed that the optimal pH was 7.5-8.0, optimal potassium acetate concentration was 40-80 mM, and optimal reaction temperature was 37-45°C although dimethyl sulfoxide at 5% v/v and formamide at 5% v/v inhibited the reaction. Our results suggest that RPA could be conducted using a wider range of optimal reaction conditions than those required for PCR and that RPA is highly suitable for point-of-care use.
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Affiliation(s)
- Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shihomi Akagi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kaichi Hayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, Hyogo 669-1337, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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27
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Qiao Y, Nakayama J, Ikeuchi T, Ito M, Kimura T, Kojima K, Takita T, Yasukawa K. Kinetic analysis of inhibition of α-glucosidase by leaf powder from Morus australis and its component iminosugars. Biosci Biotechnol Biochem 2020; 84:2149-2156. [DOI: 10.1080/09168451.2020.1783991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Abstract
Mulberry leaves contain iminosugars, such as 1-deoxynojirimycin (1-DNJ), fagomine, and 2-O-α-D-galactopyranosyl deoxynojirimycin (GAL-DNJ) that inhibit α-glucosidase. In this study, we quantified iminosugars in Morus australis leaves and made the kinetic analysis in the hydrolysis of maltose by α-glucosidase. By LC-MS/MS, the concentrations of 1-DNJ, fagomine, and GAL-DNJ in the powdered leaves were 4.0, 0.46, and 2.5 mg/g, respectively, and those in the roasted ones were 1.0, 0.24, and 0.73 mg/g, respectively, suggesting that the roasting process degraded iminosugars. Steady-state kinetic analysis revealed that the powdered and roasted leaves exhibited competitive inhibition. At pH 6.0 at 37ºC, the IC50 values of the extracts from the boiled powdered or roasted leaves were 0.36 and 1.1 mg/mL, respectively. At the same condition, the IC50 values of 1-DNJ, fagomine, and GAL-DNJ were 0.70 μg/mL, 0.18 mg/mL, and 2.9 mg/mL, respectively. These results suggested that in M. australis, 1-DNJ is a major inhibitor of α-glucosidase.
Abbreviations
1-DNJ: 1-deoxynojirimycin; GAL-DNJ: 2-O-α-D-galactopyranosyl-DNJ
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Affiliation(s)
- Ying Qiao
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Juri Nakayama
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takeaki Ikeuchi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masaaki Ito
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago, Japan
| | - Toshiyuki Kimura
- Food Research Institute (NFRI), National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 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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28
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Hayashi K, Ikeuchi T, Morishita R, Qian J, Kojima K, Takita T, Tanaka K, Hattori S, Yasukawa K. The roles of histidine and tyrosine residues in the active site of collagenase in Grimontia hollisae. J Biochem 2020; 168:385-392. [PMID: 32386303 DOI: 10.1093/jb/mvaa055] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/30/2020] [Indexed: 11/13/2022] Open
Abstract
Collagenase from the Grimontia hollisae strain 1706B (Ghcol) is a zinc metalloproteinase with the zinc-binding motif H492EXXH496. It exhibits higher collagen-degrading activity than the collagenase from Clostridium histolyticum, which is widely used in industry. We previously examined the pH and temperature dependencies of Ghcol activity; Glu493 was thought to contribute acidic pKa (pKe1), while no residue was assigned to contribute alkaline pKa (pKe2). In this study, we introduced nine single mutations at the His or Tyr residues in and near the active site. Our results showed that H412A, H485A, Y497A, H578A and H737A retained the activities to hydrolyze collagen and gelatin, while H426A, H492A, H496A and Y568A lacked them. Purification of active variants H412A, H485A, H578A and H737A, along with inactive variants H492A and H496A, were successful. H412A preferred (7-methoxycoumarin-4-yl)acetyl-L-Lys-L-Pro-L-Leu-Gly-L-Leu-[N3-(2,4-dinitrophenyl)-L-2,3-diaminopropionyl]-L-Ala-L-Arg-NH2 to collagen, while H485A preferred collagen to the peptide, suggesting that His412 and His485 are important for substrate specificity. Purification of the active variant Y497A and inactive variants H426A and Y568A were unsuccessful, suggesting that these three residues were important for stability. Based on the reported crystal structure of clostridial collagenase, Tyr568 of Ghcol is suggested to be involved in catalysis and may be the ionizable residue for pKe2.
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Affiliation(s)
- Kaichi Hayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takeaki Ikeuchi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryo Morishita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Qian
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, 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
| | - Keisuke Tanaka
- Research Institute of Biomatrix, Nippi, Incorporated, 520-11, Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Shunji Hattori
- Research Institute of Biomatrix, Nippi, Incorporated, 520-11, Kuwabara, Toride, Ibaraki 302-0017, 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, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Baba M, Kojima K, Nishimura T, Sugiura T, Takita T, Uehara R, Crouch RJ, Yasukawa K. Val143 of human ribonuclease H2 is not critical for, but plays a role in determining catalytic activity and substrate specificity. PLoS One 2020; 15:e0228774. [PMID: 32069311 PMCID: PMC7028304 DOI: 10.1371/journal.pone.0228774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 11/18/2022] Open
Abstract
Ribonuclease H2 (RNase H2) exhibits both single ribonucleotide excision activity (activity A) and RNA strand degrading activity (activity B). Val143 of human RNase H2 is located at the active site and is conserved in eukaryotic RNase H2. In this study, we explored the role of Val143 in catalytic activity and substrate specificity. Nineteen single variants at amino acid position 143 were expressed in E. coli, and all variants except for V143C and V143M were purified from the cells. When the activity of the wild-type human RNase H2 (WT) was set as 100%, the relative activities A and B of the 17 variants were in the range of 0.05–130 and 0.02–42%, respectively. When the ratio of the relative activity A to the relative activity B of WT was set as 1, the ratios of the 17 variants were in the range of 0.2–5.7. This indicates that valine is optimal for balancing the two activities. The ratios for V143Y and V143W were relatively high (5.6 and 5.5, respectively), suggesting that the bulky residues like tyrosine and tryptophan at position 143 caused steric hindrance with the 2’-OH of the sugar moiety of the ribonucleotide at the 5’ side of the scissile phosphodiester bond. The ratio for V143Q was relatively low (0.2). These results suggested that Val143 is not critical for, but plays a role in determining catalytic activity and substrate specificity.
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Affiliation(s)
- Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takuto Nishimura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takuya Sugiura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ryo Uehara
- Section on Formation of RNA, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Noji-higashi, Shiga, Japan
| | - Robert J. Crouch
- Section on Formation of RNA, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- * E-mail:
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31
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Nishimura K, Higashiya K, Ueshima N, Abe T, Yasukawa K. Characterization of proteases activities in Ficus carica cultivars. J Food Sci 2020; 85:535-544. [PMID: 32027028 DOI: 10.1111/1750-3841.15028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
In this study, we characterized protease activities of 23 Ficus carica cultivars. Extracts of fruit, branch, and leaf of Masui Dauphine, one of the most representative F. carica cultivars in Japan, exhibited gelatin-hydrolyzing activity, both in the absence and presence of a cysteine protease-specific inhibitor, E-64, suggesting that not only ficin (classified as cysteine protease) but also collagenase (classified as serine protease) were involved in the digestion of gelatin. In the hydrolysis of (7-methoxycoumarin-4-yl)acetyl-l-Lys-l-Pro-l-Leu-Gly-l-Leu-[N3 -(2,4-dinitrophenyl)-l-2,3-diaminopropionyl]-l-Ala-l-Arg-NH2 , all branch extracts of 23 F. carica cultivars exhibited the activity both in the absence and presence of cysteine protease-specific inhibitor E-64, indicating that they contain ficin and collagenase. During digestion of acid-solubilized type I collagen by the branch extract of Masui Dauphine at 40-55 °C, collagen was completely digested in the absence of E-64, while it was partially digested in the presence of the inhibitor, indicating that the manner of digestion differed between ficin and collagenase contained in the extract. These results suggest that F. carica is attractive for industrial use to digest collagen. PRACTICAL APPLICATION: The industrial use of F. carica might be enhanced by efficiently utilizing these proteases and/or selecting the appropriate F. carica cultivar. Collagen is one of the targets to which our results might be applied. It is widely accepted today that collagen and its digestion products could be useful as functional food. F. carica is a potential candidate for use in not only complete but also partial digestion of collagen.
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Affiliation(s)
- Kosaku Nishimura
- Div. of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto Univ., Sakyo-ku, Kyoto, 606-8502, Japan.,Toyo Inst. of Food Technology, 4-23-2, Minami-Hanayashiki, Kawanishi, Hyogo, 666-0026, Japan
| | - Keisuke Higashiya
- Div. of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto Univ., Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naoki Ueshima
- Div. of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto Univ., Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tatsuya Abe
- Toyo Inst. of Food Technology, 4-23-2, Minami-Hanayashiki, Kawanishi, Hyogo, 666-0026, Japan
| | - Kiyoshi Yasukawa
- Div. of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto Univ., Sakyo-ku, Kyoto, 606-8502, Japan
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Nishimura T, Baba M, Ogawa S, Kojima K, Takita T, Crouch RJ, Yasukawa K. Characterization of six recombinant human RNase H2 bearing Aicardi-Goutiéres syndrome causing mutations. J Biochem 2019; 166:537-545. [PMID: 31529068 DOI: 10.1093/jb/mvz073] [Citation(s) in RCA: 5] [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] [Received: 04/02/2019] [Accepted: 09/02/2019] [Indexed: 01/18/2023] Open
Abstract
Mammalian RNase H2 is a heterotrimeric enzyme consisting of one catalytic subunit (A) and two accessory subunits (B and C). RNase H2 is involved in the removal of a single ribonucleotide embedded in genomic DNA and removal of RNA of RNA/DNA hybrids. In humans, mutation of the RNase H2 gene causes a severe neuroinflammatory disorder Aicardi-Goutières syndrome (AGS). Here, we examined the activity and stability of six recombinant human RNase H2 variants bearing one AGS-causing mutation, A-G37S (Gly37 in the A subunit is replaced with Ser), A-N212I, A-R291H, B-A177T, B-V185G, or C-R69W. The activity of A-G37S was 0.3-1% of that of the wild-type RNase H2 (WT), while those of other five variants were 51-120%. In circular dichroism measurement, the melting temperatures of variants were 50-53°C, lower than that of WT (56°C). These results suggested that A-G37S had decreased activity and stability than WT, while other five variants had decreased stability but retained activity. In gel filtration chromatography of the purified enzyme preparation, WT migrated as a heterotrimer, while A-R291H eluted in two separate peaks containing either the heterotrimer or only the A subunit, suggesting that some AGS-causing mutations affect the heterotrimer-forming stability of RNase H2.
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Affiliation(s)
- Takuto Nishimura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan
| | - Saori Ogawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan
| | - Robert J Crouch
- Section on Formation of RNA, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyoku, Kyoto 606-8502, Japan
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Takita T, Nakatani K, Katano Y, Suzuki M, Kojima K, Saka N, Mikami B, Yatsunami R, Nakamura S, Yasukawa K. Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis. Enzyme Microb Technol 2019; 130:109363. [DOI: 10.1016/j.enzmictec.2019.109363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/29/2019] [Accepted: 06/17/2019] [Indexed: 10/26/2022]
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Tsukiashi M, Baba M, Kojima K, Himeda K, Takita T, Yasukawa K. Construction and characterization of ribonuclease H2 knockout NIH3T3 cells. J Biochem 2019; 165:249-256. [PMID: 30481312 DOI: 10.1093/jb/mvy101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 11/13/2018] [Indexed: 11/13/2022] Open
Abstract
Ribonuclease H (RNase H) specifically hydrolyzes the 5'-phosphodiester bonds of the RNA of RNA/DNA hybrid. Both types 1 and 2 RNases H act on the RNA strand of the hybrid, while only type 2 acts on the single ribonucleotide embedded in DNA duplex. In this study, to explore the role of mammalian type 2 RNase H (RNase H2) in cells, we constructed the RNase H2 knockout NIH3T3 cells (KO cells) by CRISPR/Cas9 system. KO cells hydrolyzed RNA strands in RNA/DNA hybrid, but not single ribonucleotides in DNA duplex, while wild-type NIH3T3 cells (WT cells) hydrolyzed both. Genomic DNA in the KO cells was more heavily hydrolyzed than in the WT cells by the alkaline or RNase H2 treatment, suggesting that the KO cells contained more ribonucleotides in genomic DNA than the WT cells. The growth rate of the KO cells was 60% of that of the WT cells. Expression of interferon-stimulated genes (ISGs) in the KO cells was not markedly elevated compared with the WT cells. These results suggest that in NIH3T3 cells, RNase H2 is crucial for suppressing the accumulation of ribonucleotides in genomic DNA but not for the expression of ISGs.
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Affiliation(s)
- Motoki Tsukiashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kohei Himeda
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Abstract
Ribonuclease H (RNase H) [EC 3.1.26.4] is an enzyme that specifically degrades RNA from RNA/DNA hybrids. Since its discovery in 1969, the enzyme has been extensively studied for its catalytic mechanism and physiological role. RNase H has been classified into two major families, Type 1 and Type 2. Type 1 enzymes are designated RNase HI in prokaryotes and RNase H1 in eukaryotes, while Type 2 enzymes are designated RNase HII in prokaryotes and RNase H2 in eukaryotes. Type 2 enzymes are able to cleave the 5′-phosphodiester bond of one ribonucleotide embedded in a DNA double strand. Recent studies have shown that RNase H2 is involved in excision of a single ribonucleotide embedded in genomic DNA and removal of an R-loop formed in cells. It is also involved in double-strand break of DNA and its repair. In this review, we aim to outline the structures recognized by RNase H2.
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Affiliation(s)
- Kenji Kojima
- Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Misato Baba
- Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Takita T, Qian J, Geng H, He Z, Nemoto S, Mori M, Tanaka K, Hattori S, Kojima K, Yasukawa K. Comparative studies on the activities of collagenases from Grimontia hollisae and Clostridium hystoliticum in the hydrolysis of synthetic substrates. J Biochem 2018; 163:425-431. [DOI: 10.1093/jb/mvy009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/14/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Qian
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hongmin Geng
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Zejian He
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sho Nemoto
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mariko Mori
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Keisuke Tanaka
- Nippi Research Institute of Biomatrix, 520-11, Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Shunji Hattori
- Nippi Research Institute of Biomatrix, 520-11, Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Kenji Kojima
- 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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Hidese R, Kawato K, Nakura Y, Fujiwara A, Yasukawa K, Yanagihara I, Fujiwara S. Thermostable DNA helicase improves the sensitivity of digital PCR. Biochem Biophys Res Commun 2017; 495:2189-2194. [PMID: 29233693 DOI: 10.1016/j.bbrc.2017.12.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
DNA/RNA helicases, which catalyze the unwinding of duplex nucleic acids using the energy of ATP hydrolysis, contribute to various biological functions involving DNA or RNA. Euryarchaeota-specific helicase Tk-EshA (superfamily 2) from the hyperthermophilic archaeon Thermococcus kodakarensis has been used to decrease generation of mis-amplified products (noise DNAs) during PCR. In this study, we focused on another type (superfamily 1B) of helicase, Tk-Upf1 (TK0178) from T. kodakarensis, and compared its effectiveness in PCR and digital PCR with that of Tk-EshA. For this purpose, we obtained Tk-Upf1 as a recombinant protein and assessed its enzymatic characteristics. Among various double-stranded DNA (dsDNA) substrates (forked, 5' overhung, 3' overhung, and blunt-ended duplex), Tk-Upf1 had the highest unwinding activity toward 5' overhung DNAs. Noise DNAs were also eliminated in the presence of Tk-Upf1 at concentrations 10-fold lower than those required to yield a comparable reduction with Tk-EshA. When a 5' or 3' overhung mis-annealed primer was included as a competitive primer along with specific primers, noise DNAs derived from the mis-annealed primer were eliminated in the presence of Tk-Upf1. In digital PCR, addition of Tk-EshA or Tk-Upf1 increased fluorescent intensities and improved separation between common and risk allele clusters, indicating that both helicases functioned as signal enhancers. In comparison with Tk-EshA, a smaller amount of Tk-Upf1 was required to improve the performance of digital PCR.
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Affiliation(s)
- Ryota Hidese
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Katsuhiro Kawato
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Ayako Fujiwara
- Department of Bioscience, Graduate 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, 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
| | - Shinsuke Fujiwara
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan.
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Katano Y, Li T, Baba M, Nakamura M, Ito M, Kojima K, Takita T, Yasukawa K. Generation of thermostable Moloney murine leukemia virus reverse transcriptase variants using site saturation mutagenesis library and cell-free protein expression system. Biosci Biotechnol Biochem 2017; 81:2339-2345. [DOI: 10.1080/09168451.2017.1394790] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
We attempted to increase the thermostability of Moloney murine leukemia virus (MMLV) reverse transcriptase (RT). The eight-site saturation mutagenesis libraries corresponding to Ala70−Arg469 in the whole MMLV RT (Thr24−Leu671), in each of which 1 out of 50 amino acid residues was replaced with other amino acid residue, were constructed. Seven-hundred and sixty eight MMLV RT clones were expressed using a cell-free protein expression system, and their thermostabilities were assessed by the temperature of thermal treatment at which they retained cDNA synthesis activity. One clone D200C was selected as the most thermostable variant. The highest temperature of thermal treatment at which D200C exhibited cDNA synthesis activity was 57ºC, which was higher than for WT (53ºC). Our results suggest that a combination of site saturation mutagenesis library and cell-free protein expression system might be useful for generation of thermostable MMLV RT in a short period of time for expression and selection.
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Affiliation(s)
- Yuta Katano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tongyang Li
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Miyo Nakamura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masaaki Ito
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, Nago, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, 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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Kumari P, Gautam SG, Baba M, Tsukiashi M, Matsuoka K, Yasukawa K, Nishigaki K. DNA-based mutation assay GPMA (genome profiling-based mutation assay): reproducibility, parts-per-billion scale sensitivity, and introduction of a mammalian-cell-based approach. J Biochem 2017; 162:395-401. [PMID: 29186523 DOI: 10.1093/jb/mvx043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/28/2017] [Indexed: 11/12/2022] Open
Abstract
Genome profiling-based mutation assay (GPMA) is, to date, the only DNA sequence-based mutation assay that directly measures DNA alterations induced by mutagens. Here, the all-important congruence of mutagen assignment between DNA-based GPMA and the phenotype-based Ames test (the gold standard of mutagen assays) was confirmed qualitatively and semi-quantitatively by means of 94 chemical species (including previously examined 64). The high sensitivity (on the order of 10 ppb) and reproducibility of GPMA were also corroborated by the match between virtually independent experiments conducted in the distant past (10 years ago) and recently. Meanwhile, a standard experimental framework was established: the conditions of 100 parts per billion (ppb) concentration of a chemical and 15-generation culture of Escherichia coli. Moreover, a mammalian cell line (NIH 3T3) was shown to be suitable as a tester organism for the GPMA approach. Preliminary experimental results suggested that this approach can provide a qualitatively equivalent and quantitatively different mutagen assay results relative to the bacteria-based GPMA (renamed as bGPMA). This finding confirmed the effectiveness of the GPMA approach and indicates that mGPMA is a promising way to detect mammalian-cell mutagens.
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Affiliation(s)
- Parmila Kumari
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Sunita Ghimire Gautam
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Motoki Tsukiashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Koji Matsuoka
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.,Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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41
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Baba M, Kojima K, Nakase R, Imai S, Yamasaki T, Takita T, Crouch RJ, Yasukawa K. Effects of neutral salts and pH on the activity and stability of human RNase H2. J Biochem 2017; 162:211-219. [PMID: 28402412 DOI: 10.1093/jb/mvx021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 11/14/2022] Open
Abstract
Ribonuclease H (RNase H) specifically degrades the RNA of RNA/DNA hybrid. Recent study has shown that a single ribonucleotide is embedded in DNA double strand at every few thousand base pairs in human genome, and human RNase H2 is involved in its removal. Here, we examined the effects of neutral salts and pH on the activity and stability of human RNase H2. NaCl, KCl, RbCl and NaBr increased the activity to 170-390% at 10-60 mM, while LiCl, LiBr and CsCl inhibited it, suggesting that species of cation, but not anion, is responsible for the effect on activity. NaCl and KCl increased the stability by decreasing the first-order rate constant of the inactivation to 50-60% at 60-80 mM. The activity at 25-35 °C exhibited a narrow bell-shaped pH-dependence with the acidic and alkaline pKe (pKe1 and pKe2) values of 7.3 - 7.6 and 8.1 - 8.8, respectively. Enthalpy changes (ΔH°) of deprotonation were 5 ± 21 kJ mol-1 for pKe1 and 68 ± 25 kJ mol-1 for pKe2. These results suggest that the ionizable groups responsible for pKe1 may be two out of Asp34, Glu35 and Asp141 of DEDD motif, and that for pKe2 may be Lys69 of DSK motif.
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Affiliation(s)
- Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Rihoko Nakase
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shota Imai
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tomomi Yamasaki
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Robert J Crouch
- Section on Formation of RNA, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Oiwakecho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Baba M, Kakue R, Leucht C, Rasor P, Walch H, Ladiges D, Bell C, Kojima K, Takita T, Yasukawa K. Further increase in thermostability of Moloney murine leukemia virus reverse transcriptase by mutational combination. Protein Eng Des Sel 2017; 30:551-557. [PMID: 28967961 DOI: 10.1093/protein/gzx046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/15/2017] [Indexed: 11/13/2022] Open
Abstract
We previously generated a highly thermostable triple variant of Moloney murine leukemia virus reverse transcriptase, MM3 (E286R/E302K/L435R), by introducing positive charges by site-directed mutagenesis at positions that have been implicated in the interaction with template-primer (Yasukawa et al., (2010) J. Biotechnol., 150, 299-306). In this study, we attempted to further increase the thermostability of MM3. Twenty-nine mutations were newly designed, focusing on the number of surface charge, stabilization of hydrophobic core, and introduction of salt bridge. The corresponding 29 single variants were produced in Escherichia coli and characterized for activity and stability. Six mutations (A32V, L41D, L72R, I212R, L272E and W388R) were selected as the candidates for further stabilize MM3. Fifteen multiple variants were designed by combining two or more of the six mutations with the MM3 mutations, produced and characterized. The sextuple variant MM3.14 (A32V/L72R/E286R/E302K/W388R/L435R) exhibited higher thermostability than MM3.
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Affiliation(s)
- Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryota Kakue
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Christoph Leucht
- Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, 82377 Penzberg, Germany
| | - Peter Rasor
- Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, 82377 Penzberg, Germany
| | - Heiko Walch
- Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, 82377 Penzberg, Germany
| | - Daniel Ladiges
- Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, 82377 Penzberg, Germany
| | - Christian Bell
- Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, 82377 Penzberg, Germany
| | - 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, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yasuda K, Sugimoto H, Hayashi K, Takita T, Yasukawa K, Ohta M, Kamakura M, Ikushiro S, Shiro Y, Sakaki T. Protein engineering of CYP105s for their industrial uses. Biochim Biophys Acta Proteins Proteom 2017; 1866:23-31. [PMID: 28583351 DOI: 10.1016/j.bbapap.2017.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/20/2017] [Accepted: 05/27/2017] [Indexed: 12/26/2022]
Abstract
Cytochrome P450 enzymes belonging to the CYP105 family are predominantly found in bacteria belonging to the phylum Actinobacteria and the order Actinomycetales. In this review, we focused on the protein engineering of P450s belonging to the CYP105 family for industrial use. Two Arg substitutions to Ala of CYP105A1 enhanced its vitamin D3 25- and 1α-hydroxylation activities by 400 and 100-fold, respectively. The coupling efficiency between product formation and NADPH oxidation was largely improved by the R84A mutation. The quintuple mutant Q87W/T115A/H132L/R194W/G294D of CYP105AB3 showed a 20-fold higher activity than the wild-type enzyme. Amino acids at positions 87 and 191 were located at the substrate entrance channel, and that at position 294 was located close to the heme group. Semi-rational engineering of CYP105A3 selected the best performing mutant, T85F/T119S/V194N/N363Y, for producing pravastatin. The T119S and N363Y mutations synergistically had remarkable effects on the interaction between CYP105A3 and putidaredoxin. Although wild-type CYP105AS1 hydroxylated compactin to 6-epi-pravastatin, the quintuple mutant I95T/Q127R/A180V/L236I/A265N converted almost all compactin to pravastatin. Five amino acid substitutions by two rounds of mutagenesis almost completely changed the stereo-selectivity of CYP105AS1. These results strongly suggest that the protein engineering of CYP105 enzymes greatly increase their industrial utility. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Kaori Yasuda
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Hiroshi Sugimoto
- RIKEN Spring-8 Center, Harima Institute, Sayo, Hyogo 679-5148, Japan
| | - Keiko Hayashi
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Teisuke Takita
- Division of Food Science and Technology, Graduate School of Agriculture, Kyoto University, KitashirakawaOiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Technology, Graduate School of Agriculture, Kyoto University, KitashirakawaOiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Miho Ohta
- Department of Food and Nutrition Management Studies, Faculty of Human Development, Soai University, 4-4-1 Nanko-naka, Suminoe-ku, Osaka 559-0033, Japan
| | - Masaki Kamakura
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yoshitsugu Shiro
- RIKEN Spring-8 Center, Harima Institute, Sayo, Hyogo 679-5148, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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45
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Martrette JM, Egloff C, Clément C, Yasukawa K, Thornton SN, Trabalon M. Effects of prolonged exposure to CO 2 on behaviour, hormone secretion and respiratory muscles in young female rats. Physiol Behav 2017; 177:257-262. [PMID: 28501558 DOI: 10.1016/j.physbeh.2017.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/07/2017] [Accepted: 05/04/2017] [Indexed: 11/28/2022]
Abstract
Atmospheric CO2 concentrations increased significantly over the last century and continuing increases are expected to have significant effects on current ecosystems. This study evaluated the behavioural and physiological (hormone status, muscle structure) effects of prolonged CO2 exposure in young female Wistar rats exposed at 700ppm of CO2 during 6h a day for 15days. Prolonged CO2 exposure, though not continuous, produced significant disturbances in behaviour with an increase in drinking, grooming and resting, and a reduction in rearing, jumping-play and locomotor activity. Furthermore, CO2 exposure was accompanied by increased plasma levels of corticosterone, suggesting that prolonged exposure to CO2 was stressful. The muscular structure can also be modified also when respiratory working conditions change. The expression of myosin heavy chain was significantly affected in the diaphragm and oral respiratory muscles: Masseter Superficialis and Anterior Digastric. Modified behaviour and hormonal changes both appear to be at the origin of the observed muscular adaptation.
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Affiliation(s)
- J M Martrette
- EA 3450 DevAH, Université de Lorraine, 54505 Vandœuvre-lès-Nancy, France
| | - C Egloff
- UMR 7039 CNRS, Université de Lorraine, 54505 Vandœuvre-lès-Nancy, France.
| | - C Clément
- EA 3450 DevAH, Université de Lorraine, 54505 Vandœuvre-lès-Nancy, France
| | - K Yasukawa
- EA 3450 DevAH, Université de Lorraine, 54505 Vandœuvre-lès-Nancy, France
| | - S N Thornton
- INSERM U_1116, Université de Lorraine, 54505 Vandœuvre-lès-Nancy, France
| | - M Trabalon
- UMR 6552 CNRS, Université de Rennes 1, 35042 Rennes, France
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 04/07/2017] [Indexed: 02/01/2023]
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47
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Yasuda K, Yogo Y, Sugimoto H, Mano H, Takita T, Ohta M, Kamakura M, Ikushiro S, Yasukawa K, Shiro Y, Sakaki T. Production of an active form of vitamin D 2 by genetically engineered CYP105A1. Biochem Biophys Res Commun 2017; 486:336-341. [DOI: 10.1016/j.bbrc.2017.03.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/12/2017] [Indexed: 12/29/2022]
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48
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Nakayama H, Mori M, Takita T, Yasukawa K, Tanaka K, Hattori S, Aikawa H, Hasegawa O, Okamura T, Takegami K, Motokawa S, Kuwahara M, Amano K. Development of immersion vaccine for bacterial cold-water disease in ayu Plecoglossus altivelis. Biosci Biotechnol Biochem 2017; 81:608-613. [PMID: 28051913 DOI: 10.1080/09168451.2016.1268041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 10/20/2022]
Abstract
Flavobacterium psychrophilum (F. psychrophilum) is the causative agent of bacterial cold-water disease (BCWD) that occurs in ayu Plecoglossus altivelis. Formalin-killed cell of F. psychrophilum has long been studied as an immersion vaccine for BCWD. In this study, we explored the possibility of F. psychrophilum collagenase (fpcol) for use as the immersion vaccine. BCWD convalescent ayu sera contained specific IgM antibodies against somatic F. psychrophilum and fpcol, meaning that fpcol is a promising antigen for the vaccine development. The recombinant fpcol was successfully expressed in Escherichia coli and Brevibacillus chosinensis (B. chosinensis). The culture supernatant of the B. chosinensis was used as an immersion vaccine solution. The vaccinated ayu were then challenged by soaking into F. psychrophilum culture. In two experimental groups, the relative percentages of survivals were 63 and 38%, respectively, suggesting that fpcol is promising as the immersion vaccine for ayu-BCWD.
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Affiliation(s)
- Hitoshi Nakayama
- a Department of Freshwater Fisheries , Wakayama Prefectural Fisheries Experimental Station , Kinokawa-shi , Japan
| | - Mariko Mori
- b Division of Food Science and Biotechnology, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | - Teisuke Takita
- b Division of Food Science and Biotechnology, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | - Kiyoshi Yasukawa
- b Division of Food Science and Biotechnology, Graduate School of Agriculture , Kyoto University , Kyoto , Japan
| | - Keisuke Tanaka
- c Nippi Research Institute of Biomatrix , Toride-shi , Japan
| | - Shunji Hattori
- c Nippi Research Institute of Biomatrix , Toride-shi , Japan
| | - Hideaki Aikawa
- d Kanagawa Prefectural Fisheries Technology Center Freshwater Experiment Station , Sagamihara-shi , Japan
| | - Osamu Hasegawa
- d Kanagawa Prefectural Fisheries Technology Center Freshwater Experiment Station , Sagamihara-shi , Japan
| | - Takashi Okamura
- e Shiga Prefectural Fisheries Experiment Station , Hikone-shi , Japan
| | - Kentarou Takegami
- e Shiga Prefectural Fisheries Experiment Station , Hikone-shi , Japan
| | - Shogo Motokawa
- f Matsuken Pharmaceutical Industry Co., Ltd. , Koganei-shi , Japan
| | | | - Kenichi Amano
- f Matsuken Pharmaceutical Industry Co., Ltd. , Koganei-shi , Japan
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Qian J, Ito S, Satoh J, Geng H, Tanaka K, Hattori S, Kojima K, Takita T, Yasukawa K. The cleavage site preference of the porcine pepsin on the N-terminal α1 chain of bovine type I collagen: a focal analysis with mass spectrometry. Biosci Biotechnol Biochem 2016; 81:514-522. [PMID: 27931164 DOI: 10.1080/09168451.2016.1263146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 10/20/2022]
Abstract
Bovine type I collagen consists of two α1 and one α2 chains, containing the internal triple helical regions and the N- and C-terminal telopeptides. In industries, it is frequently digested with porcine pepsin to produce a triple helical collagen without the telopeptides. However, the digestion mechanism is not precisely understood. Here, we performed a mass spectrometric analysis of the pepsin digest of the N-terminal telopeptide pQLSYGYDEKSTGISVP (1-16) in the α1 chain. When purified collagen was digested, pQLSYGY (1-6) and pQLSYGYDEKSTG (1-12) were identified, while DEKSTG (7-12) was not. When the N-terminal telopeptide mimetic synthetic peptide pQLSK(MOCAc)GYDEKSTGISK(Dnp)P-NH2 was digested, pQLSK(MOCAc)GYDEKSTG (1-12) and ISK(Dnp)P-NH2 (13-16) were readily identified, pQLSK(MOCAc)GY (1-6) and DEKSTGISK(Dnp)P-NH2 (7-16) were weakly detected, and DEKSTG (7-12) was hardly identified. These results suggest that pepsin preferentially cleaves Tyr6-Asp7 and less preferentially Gly12-Ile13. They also suggest that the former cleavage requires native collagen structure, while the latter cleavage does not.
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Affiliation(s)
- Jun Qian
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Shinji Ito
- b Medical Research Support Center, Graduate School of Medicine , Kyoto University , Kyoto , Japan
| | - Junko Satoh
- b Medical Research Support Center, Graduate School of Medicine , Kyoto University , Kyoto , Japan
| | - Hongmin Geng
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Keisuke Tanaka
- c Nippi Research Institute of Biomatrix , Toride , Japan
| | - Shunji Hattori
- c Nippi Research Institute of Biomatrix , Toride , Japan
| | - Kenji Kojima
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Teisuke Takita
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
| | - Kiyoshi Yasukawa
- a Division of Food Science and Biotechnology , Graduate School of Agriculture, Kyoto University , Kyoto , Japan
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50
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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