1
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Guan Z, Song Y, de Vries M, Permentier H, Tepper P, van Merkerk R, Setroikromo R, Quax WJ. The Promiscuity of Squalene Synthase-Like Enzyme: Dehydrosqualene Synthase, a Natural Squalene Hyperproducer? JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3017-3024. [PMID: 38315649 PMCID: PMC10870770 DOI: 10.1021/acs.jafc.3c05770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Dehydrosqualene synthase (CrtM), as a squalene synthase-like enzyme from Staphylococcus aureus, can naturally utilize farnesyl diphosphate to produce dehydrosqualene (C30H48). However, no study has documented the natural production of squalene (C30H50) by CrtM. Here, based on an HPLC-Q-Orbitrap-MS/MS study, we report that the expression of crtM in vitro or in Bacillus subtilis 168 both results in the output of squalene, dehydrosqualene, and phytoene (C40H64). Notably, wild-type CrtM exhibits a significantly higher squalene yield compared to squalene synthase (SQS) from Bacillus megaterium with an approximately 2.4-fold increase. Moreover, the examination of presqualene diphosphate's stereostructures in both CrtM and SQS enzymes provides further understanding into the presence of multiple identified terpenoids. In summary, this study not only provides insights into the promiscuity demonstrated by squalene synthase-like enzymes but also highlights a new strategy of utilizing CrtM as a potential replacement for SQS in cell factories, thereby enhancing squalene production.
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Affiliation(s)
- Zheng Guan
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Yafeng Song
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
- Guangdong
Provincial Key Laboratory of Microbial Culture Collection and Application,
State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou510070, China
| | - Marcel de Vries
- Interfaculty
Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Hjalmar Permentier
- Interfaculty
Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Pieter Tepper
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Ronald van Merkerk
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Rita Setroikromo
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
| | - Wim J. Quax
- Department
of Chemical and Pharmaceutical Biology, Groningen Research Institute
of Pharmacy, University of Groningen, Groningen9713 AV, The Netherlands
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2
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Zhang N, Yang Y, Li W, Zhou S, Li W, Peng Y, Zheng J. Asparagine and Glutamine Residues Participate in Protein Covalent Binding by Epoxide Metabolite of 8-Epidiosbulbin E Acetate In Vitro and In Vivo. Chem Res Toxicol 2022; 35:1821-1830. [PMID: 35839447 DOI: 10.1021/acs.chemrestox.2c00130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dioscorea Bulbifera L. (DBL), an effective traditional Chinese medicine, has been restricted because of multiple reports that it can cause severe hepatotoxicity. 8-Epidiosbulbin E acetate (EEA), one of the main components of DBL, can induce severe liver injury. It has been reported that EEA can be metabolized by CYP3A to the corresponding cis-enedial intermediate which alkylates the lysine residues of proteins to form pyrroline derivatives. The present study unexpectedly found that the reactive intermediate reacted with the amide groups of asparagine (Asn) and glutamine (Gln) residues of hepatic proteins of mice treated with EEA. The amide-derived protein modification increased with the increase in the dose administered. Like the adduction of the primary amine of lysine residues, the electrophilic metabolite reacted with the amide groups of Asn and Gln residues to offer the corresponding pyrrolines. The structures of the pyrrolines were confirmed by mass spectrometry and nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- Na Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China
| | - Yi Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China
| | - Wei Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China
| | - Shenzhi Zhou
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou 550025, PR China
| | - Ying Peng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China
| | - Jiang Zheng
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, PR China.,State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou 550025, PR China
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3
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Zhang L, Zhang X, Min J, Liu B, Huang JW, Yang Y, Liu W, Dai L, Yang Y, Chen CC, Guo RT. Structural insights to a bi-functional isoprenyl diphosphate synthase that can catalyze head-to-tail and head-to-middle condensation. Int J Biol Macromol 2022; 214:492-499. [PMID: 35764165 DOI: 10.1016/j.ijbiomac.2022.06.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/05/2022]
Abstract
Isoprenoids represent the largest group of natural products, whose basal skeletons are synthesized by various isoprenyl diphosphate synthases (IDSs). As majority of IDSs catalyze head-to-tail reaction to produce linear form isoprenoids, some catalyze head-to-middle reaction to produce branched form products. In a previous study, an IDS termed MA1831 from Methanosarcina acetivorans was found to be capable of catalyzing both types of reaction. In addition to the canonical linear product of C35 in length, MA1831 also catalyzes head-to-middle condensation of farnesyl diphosphate (FPP) and dimethylallyl diphosphate (DMAPP) to produce geranyllavandulyl diphosphate. In order to investigate the mechanism of action of MA1831, we determined its crystal structures in apo-form and in complex with substrates and analogues. The complex structures that contain isopentenyl S-thiolodiphosphate and DMAPP as homoallylic substrates were also reported, which should represent the reaction modes of MA1831-mediated head-to-tail and head-to-middle reaction, respectively. Based on the structural information, the mechanism of MA1831 catalyze head-to-tail and head-to-middle condensation reaction was proposed.
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Affiliation(s)
- Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Xiaowen Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Beibei Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Weidong Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Yunyun Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, PR China.
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4
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Okada M, Unno H, Emi KI, Matsumoto M, Hemmi H. A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. J Biol Chem 2021; 296:100679. [PMID: 33872599 PMCID: PMC8131916 DOI: 10.1016/j.jbc.2021.100679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
Polyprenyl groups, products of isoprenoid metabolism, are utilized in peptidoglycan biosynthesis, protein N-glycosylation, and other processes. These groups are formed by cis-prenyltransferases, which use allylic prenyl pyrophosphates as prenyl-donors to catalyze the C-prenylation of the general acceptor substrate, isopentenyl pyrophosphate. Repetition of this reaction forms (Z,E-mixed)-polyprenyl pyrophosphates, which are converted later into glycosyl carrier lipids, such as undecaprenyl phosphate and dolichyl phosphate. MM_0014 from the methanogenic archaeon Methanosarcina mazei is known as a versatile cis-prenyltransferase that accepts both isopentenyl pyrophosphate and dimethylallyl pyrophosphate as acceptor substrates. To learn more about this enzyme’s catalytic activity, we determined the X-ray crystal structures of MM_0014 in the presence or absence of these substrates. Surprisingly, one structure revealed a complex with O-prenylglycerol, suggesting that the enzyme catalyzed the prenylation of glycerol contained in the crystallization buffer. Further analyses confirmed that the enzyme could catalyze the O-prenylation of small alcohols, such as 2-propanol, expanding our understanding of the catalytic ability of cis-prenyltransferases.
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Affiliation(s)
- Miyako Okada
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hideaki Unno
- Graduate School of Engineering, Nagasaki University, Nagasaki, Nagasaki, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Koh-Ichi Emi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Mayuko Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan.
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5
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Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase. Nat Commun 2021; 12:2079. [PMID: 33824320 PMCID: PMC8024262 DOI: 10.1038/s41467-021-22290-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022] Open
Abstract
Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O2•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn3+ and Mn2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pKas, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn3+ and Mn2+ redox states. Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn3+SOD and Mn2+SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.
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6
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Voice AT, Tresadern G, Twidale RM, van Vlijmen H, Mulholland AJ. Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations. Chem Sci 2021; 12:5511-5516. [PMID: 33995994 PMCID: PMC8097726 DOI: 10.1039/d0sc06122k] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ibrutinib is the first covalent inhibitor of Bruton's tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition will aid in the design of safer and more selective covalent inhibitors that target BTK. The mechanism of covalent inhibition in BTK has been uncertain because there is no appropriate residue nearby that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. We investigate several mechanisms of covalent modification of C481 in BTK by ibrutinib using combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics reaction simulations. The lowest energy pathway involves direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto-enol tautomerisation step (ΔG ‡ = 10.5 kcal mol-1) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and other similar targets.
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Affiliation(s)
- Angus T Voice
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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7
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Chen CC, Malwal SR, Han X, Liu W, Ma L, Zhai C, Dai L, Huang JW, Shillo A, Desai J, Ma X, Zhang Y, Guo RT, Oldfield E. Terpene Cyclases and Prenyltransferases: Structures and Mechanisms of Action. ACS Catal 2020. [DOI: 10.1021/acscatal.0c04710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Satish R. Malwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xu Han
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Weidong Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Alli Shillo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Janish Desai
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xianqiang Ma
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yonghui Zhang
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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8
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Kurokawa H, Ambo T, Takahashi S, Koyama T. Crystal structure of Thermobifida fusca cis-prenyltransferase reveals the dynamic nature of its RXG motif-mediated inter-subunit interactions critical for its catalytic activity. Biochem Biophys Res Commun 2020; 532:459-465. [PMID: 32892948 DOI: 10.1016/j.bbrc.2020.08.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 11/17/2022]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze consecutive condensations of isopentenyl diphosphate to an allylic diphosphate acceptor to produce a linear polyprenyl diphosphate of designated length. Dimer formation is a prerequisite for cis-PTs to catalyze all cis-prenyl condensation reactions. The structure-function relationship of a conserved C-terminal RXG motif in cis-PTs that forms inter-subunit interactions and has a role in catalytic activity has attracted much attention. Here, we solved the crystal structure of a medium-chain cis-PT from Thermobifida fusca that produces dodecaprenyl diphosphate as a polyprenoid glycan carrier for cell wall synthesis. The structure revealed a characteristic dimeric architecture of cis-PTs in which a rigidified RXG motif of one monomer formed inter-subunit hydrogen bonds with the catalytic site of the other monomer, while the RXG motif of the latter remained flexible. Careful analyses suggested the existence of a possible long-range negative cooperativity between the two catalytic sites on the two monomeric subunits that allowed the binding of one subunit to stabilize the formation of the enzyme-substrate ternary complex and facilitated the release of Mg-PPi and subsequent intra-molecular translocation at the counter subunit so that the condensation reaction could occur in consecutive cycles. The current structure reveals the dynamic nature of the RXG motif and provides a rationale for pursuing further investigations to elucidate the inter-subunit cooperativity of cis-PTs.
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Affiliation(s)
- Hirofumi Kurokawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
| | - Takanori Ambo
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki Aza Aoba 6-6-11, Aoba-ku, Sendai, 980-8579, Japan
| | - Tanetoshi Koyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
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9
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Fiebig T, Cramer JT, Bethe A, Baruch P, Curth U, Führing JI, Buettner FFR, Vogel U, Schubert M, Fedorov R, Mühlenhoff M. Structural and mechanistic basis of capsule O-acetylation in Neisseria meningitidis serogroup A. Nat Commun 2020; 11:4723. [PMID: 32948778 PMCID: PMC7501274 DOI: 10.1038/s41467-020-18464-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/20/2020] [Indexed: 02/08/2023] Open
Abstract
O-Acetylation of the capsular polysaccharide (CPS) of Neisseria meningitidis serogroup A (NmA) is critical for the induction of functional immune responses, making this modification mandatory for CPS-based anti-NmA vaccines. Using comprehensive NMR studies, we demonstrate that O-acetylation stabilizes the labile anomeric phosphodiester-linkages of the NmA-CPS and occurs in position C3 and C4 of the N-acetylmannosamine units due to enzymatic transfer and non-enzymatic ester migration, respectively. To shed light on the enzymatic transfer mechanism, we solved the crystal structure of the capsule O-acetyltransferase CsaC in its apo and acceptor-bound form and of the CsaC-H228A mutant as trapped acetyl-enzyme adduct in complex with CoA. Together with the results of a comprehensive mutagenesis study, the reported structures explain the strict regioselectivity of CsaC and provide insight into the catalytic mechanism, which relies on an unexpected Gln-extension of a classical Ser-His-Asp triad, embedded in an α/β-hydrolase fold.
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Affiliation(s)
- Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
| | | | - Andrea Bethe
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Petra Baruch
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Jana I Führing
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Fraunhofer International Consortium for Anti-Infective Research (iCAIR), Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Ulrich Vogel
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Roman Fedorov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Martina Mühlenhoff
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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10
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Chen CC, Zhang L, Yu X, Ma L, Ko TP, Guo RT. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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11
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Lin M, Tan J, Xu Z, Huang J, Tian Y, Chen B, Wu Y, Tong Y, Zhu Y. Computational design of enhanced detoxification activity of a zearalenone lactonase from Clonostachys rosea in acidic medium. RSC Adv 2019; 9:31284-31295. [PMID: 35527979 PMCID: PMC9072336 DOI: 10.1039/c9ra04964a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/27/2019] [Indexed: 11/21/2022] Open
Abstract
Computational design of pH-activity profiles for enzymes is of great importance in industrial applications. In this research, a computational strategy was developed to engineer the pH-activity profile of a zearalenone lactonase (ZHD101) from Clonostachys rosea to promote its activity in acidic medium. The active site pK a values of ZHD101 were computationally designed by introducing positively charged lysine mutations on the enzyme surface, and the experimental results showed that two variants, M2(D157K) and M9(E171K), increased the catalytic efficiencies of ZHD101 modestly under acidic conditions. Moreover, two variants, M8(D133K) and M9(E171K), were shown to increase the turnover numbers by 2.73 and 2.06-fold with respect to wild type, respectively, though their apparent Michaelis constants were concomitantly increased. These results imply that the active site pK a value change might affect the pH-activity profile of the enzyme. Our computational strategy for pH-activity profile engineering considers protein stability; therefore, limited experimental validation is needed to discover beneficial mutations under shifted pH conditions.
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Affiliation(s)
- Min Lin
- Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Jian Tan
- Nutrition & Health Research Institute, China National Cereals, Oils and Foodstuffs Corporation (COFCO) Beijing 102209 China
- Beijing Key Lab of Nutrition, Health and Food Safety Beijing 102209 China
- Beijing Livestock Products Quality and Safety Source Control Engineering Technology Research Center Beijing 102209 China
| | - Zhaobin Xu
- Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Jin Huang
- Nutrition & Health Research Institute, China National Cereals, Oils and Foodstuffs Corporation (COFCO) Beijing 102209 China
- Beijing Key Lab of Nutrition, Health and Food Safety Beijing 102209 China
- Beijing Livestock Products Quality and Safety Source Control Engineering Technology Research Center Beijing 102209 China
| | - Ye Tian
- Department of Chemical Engineering, Tsinghua University Beijing 100084 China
| | - Bo Chen
- Nutrition & Health Research Institute, China National Cereals, Oils and Foodstuffs Corporation (COFCO) Beijing 102209 China
- Beijing Key Lab of Nutrition, Health and Food Safety Beijing 102209 China
- Beijing Livestock Products Quality and Safety Source Control Engineering Technology Research Center Beijing 102209 China
| | - Yandong Wu
- National Engineering Research Center of Corn Deep Processing Changchun 130033 Jilin China
| | - Yi Tong
- National Engineering Research Center of Corn Deep Processing Changchun 130033 Jilin China
| | - Yushan Zhu
- Department of Chemical Engineering, Tsinghua University Beijing 100084 China
- MOE Key Lab of Industrial Biocatalysis, Tsinghua University Beijing 100084 China
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12
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Ma J, Ko TP, Yu X, Zhang L, Ma L, Zhai C, Guo RT, Liu W, Li H, Chen CC. Structural insights to heterodimeric cis-prenyltransferases through yeast dehydrodolichyl diphosphate synthase subunit Nus1. Biochem Biophys Res Commun 2019; 515:621-626. [DOI: 10.1016/j.bbrc.2019.05.135] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022]
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13
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Ko TP, Xiao X, Guo RT, Huang JW, Liu W, Chen CC. Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase. Acta Crystallogr F Struct Biol Commun 2019; 75:212-216. [PMID: 30950820 PMCID: PMC6450523 DOI: 10.1107/s2053230x19001213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/22/2019] [Indexed: 12/03/2022] Open
Abstract
Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.
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Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Xiansha Xiao
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
| | - Weidong Liu
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People’s Republic of China
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14
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Li L, Furubayashi M, Hosoi T, Seki T, Otani Y, Kawai-Noma S, Saito K, Umeno D. Construction of a Nonnatural C 60 Carotenoid Biosynthetic Pathway. ACS Synth Biol 2019; 8:511-520. [PMID: 30689939 DOI: 10.1021/acssynbio.8b00385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Longer-chain carotenoids have interesting physiological and electronic/photonic properties due to their extensive polyene structures. Establishing nonnatural biosynthetic pathways for longer-chain carotenoids in engineerable microorganisms will provide a platform to diversify and explore the potential of these molecules. We have previously reported the biosynthesis of nonnatural C50 carotenoids by engineering a C30-carotenoid backbone synthase (CrtM) from Staphylococcus aureus. In the present work, we conducted a series of experiments to engineer C60 carotenoid pathways. Stepwise introduction of cavity-expanding mutations together with stabilizing mutations progressively shifted the product size specificity of CrtM toward efficient synthases for C60 carotenoids. By coexpressing these CrtM variants with hexaprenyl diphosphate synthase, we observed that C60-phytoene accumulated together with a small amount of C65-phytoene, which is the largest carotenoid biosynthesized to date. Although these carotenoids failed to serve as a substrate for carotene desaturases, the C25-half of the C55-phytoene was accepted by the variant of phytoene desaturase CrtI, leading to accumulation of the largest carotenoid-based pigments. Continuing effort should further expand the scope of carotenoids, which are promising components for various biological (light-harvesting, antioxidant, and communicating) and nonbiological (photovoltaic, photonic, and field-effect transistor) systems.
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Affiliation(s)
- Ling Li
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Maiko Furubayashi
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Takuya Hosoi
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Takahiro Seki
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Yusuke Otani
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, 263-8522 Chiba, Japan
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15
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Nagel R, Schmidt A, Peters RJ. Isoprenyl diphosphate synthases: the chain length determining step in terpene biosynthesis. PLANTA 2019; 249:9-20. [PMID: 30467632 DOI: 10.1007/s00425-018-3052-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/14/2018] [Indexed: 05/07/2023]
Abstract
This review summarizes the recent developments in the study of isoprenyl diphosphate synthases with an emphasis on analytical techniques, product length determination, and the physiological consequences of manipulating expression in planta. The highly diverse structures of all terpenes are synthesized from the five carbon precursors dimethylallyl diphosphate and a varying number of isopentenyl diphosphate units through 1'-4 alkylation reactions. These elongation reactions are catalyzed by isoprenyl diphosphate synthases (IDS). IDS are classified depending on the configuration of the ensuing double bond as trans- and cis-IDS. In addition, IDS are further stratified by the length of their prenyl diphosphate product. This review discusses analytical techniques for the determination of product length and the factors that control product length, with an emphasis on alternative mechanisms. With recent advances in analytics, multiple IDS of Arabidopsis thaliana have been recently reinvestigated and demonstrated to yield products of different lengths than originally reported, which is summarized here. As IDS dictate prenyl diphosphate length and thereby which class of terpenes is ultimately produced, another focus of this review is the impact that altering IDS expression has on terpenoid natural product accumulation. Finally, recent findings regarding the ability of a few IDS to not catalyze 1'-4 alkylation reactions, but instead produce irregular products, with unusual connectivity, or act as terpene synthases, are also discussed.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
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16
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Ko TP, Huang CH, Lai SJ, Chen Y. Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2018; 74:765-769. [PMID: 30511669 PMCID: PMC6277960 DOI: 10.1107/s2053230x18012931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/13/2018] [Indexed: 04/06/2024] Open
Abstract
Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side chains of the catalytic aspartate and serine. These observations may provide a structural basis for inhibitor design against AbUPPS.
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Affiliation(s)
- Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chi-Hung Huang
- Department of Biotechnology, HungKuang University, Taichung, Taiwan
| | - Shu-Jung Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yeh Chen
- Department of Biotechnology, HungKuang University, Taichung, Taiwan
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17
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Kobayashi M, Kuzuyama T. Structural and Mechanistic Insight into Terpene Synthases that Catalyze the Irregular Non‐Head‐to‐Tail Coupling of Prenyl Substrates. Chembiochem 2018; 20:29-33. [DOI: 10.1002/cbic.201800510] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Masaya Kobayashi
- Biotechnology Research CenterThe University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research CenterThe University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of Tokyo 1-1-1 Yayoi Bunkyo-ku Tokyo 113-8657 Japan
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