1
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Yamaguchi R, Yamamoto T, Umeno D, Kamiya K, Kawai-Noma S. Imparting As(III) Responsiveness to the Choline Response Transcriptional Regulator BetI. ACS Omega 2024; 9:16035-16043. [PMID: 38617678 PMCID: PMC11007814 DOI: 10.1021/acsomega.3c09604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/23/2024] [Accepted: 02/26/2024] [Indexed: 04/16/2024]
Abstract
The development of a low-cost and user-friendly sensor using microorganisms to monitor the presence of As(III) on earth has garnered significant attention. In conventional research on microbial As(III) sensors, the focus has been on transcription factor ArsR, which plays a role in As(III) metabolism. However, we recently discovered that LuxR, a quorum-sensing control factor in Vibrio fischeri that contains multiple cysteine residues, acted as an As(III) sensor despite having no role in As(III) metabolism. This finding suggested that any protein could be an As(III) sensor if cysteine residues were incorporated. In this study, we aimed to confer As(III) responsiveness to BetI, a transcriptional repressor of the TetR family involved in osmotic regulation of the choline response, unrelated to As(III) metabolism. Based on the BetI structure constructed using molecular dynamics calculations, we generated a series of mutants in which each of the three amino acids not critical for function was substituted with cysteine. Subsequent examination of their response to As(III) revealed that the cysteine-substituted mutant, incorporating all three substitutions, demonstrated As(III) responsiveness. This was evidenced by the fluorescence intensity of the downstream reporter superfolder green fluorescent protein expression regulated by the operator region. Intriguingly, the BetI cysteine mutant maintained its binding responsiveness to the natural ligand choline. We successfully engineered an OR logic gate capable of responding to two orthogonal ligands using a single protein.
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Affiliation(s)
- Ryo Yamaguchi
- Department
of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Tetsuaki Yamamoto
- Department
of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department
of Applied Chemistry, Waseda University, Tokyo 169-8555, Japan
| | - Katsumasa Kamiya
- Center
for Basic Education and Integrated Learning, Kanagawa Institute of Technology, Atsugi, Kanagawa 243-0292, Japan
| | - Shigeko Kawai-Noma
- Department
of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
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2
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Watanabe T, Kimura Y, Umeno D. MetJ-Based Mutually Interfering SAM-ON/SAM-OFF Biosensors. ACS Synth Biol 2024; 13:624-633. [PMID: 38286030 DOI: 10.1021/acssynbio.3c00621] [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] [Indexed: 01/31/2024]
Abstract
SAM (S-adenosylmethionine) is an important metabolite that operates as a major donor of methyl groups and is a controller of various physiological processes. Its availability is also believed to be a major bottleneck in the biological production of numerous high-value metabolites. Here, we constructed SAM-sensing systems using MetJ, an SAM-dependent transcriptional regulator, as a core component. SAM is a corepressor of MetJ, which suppresses the MetJ promoter with an increasing cellular concentration of SAM (SAM-OFF sensor). The application of transcriptional interference and evolutionary tuning effectively inverted its response, yielding a SAM-ON sensor (signal increases with increasing SAM concentration). By linking two genes encoding fluorescent protein reporters in such a way that their transcription events interfere with each other's and by placing one of them under the control of MetJ, we could increase the effective signal-to-noise ratio of the SAM sensor while decreasing the batch-to-batch deviation in signal output, likely by canceling out the growth-associated fluctuation in translational resources. By taking the ratio of SAM-ON/SAM-OFF signals and by resetting the default pool size of SAM, we could rapidly identify SAM synthetase (MetK) mutants with increased cellular activity from a random library. The strategy described herein should be widely applicable for identifying activity mutants, which would be otherwise overlooked because of the strong homeostasis of metabolic networks.
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Affiliation(s)
- Taro Watanabe
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Kirin Central Research Institute, Kirin Holdings Company, Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Yuki Kimura
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
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3
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Watanabe T, Kimura Y, Umeno D. Systematic promoter design for plasmid-encoded S-adenosylmethionine sensing systems. J GEN APPL MICROBIOL 2024:2024.01.002. [PMID: 38281753 DOI: 10.2323/jgam.2024.01.002] [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] [Indexed: 01/30/2024]
Abstract
S-adenosylmethionine (SAM) is an important biomolecule that mainly acts as a methyl donor and plays many roles in a variety of biological functions. SAM is also required for the biosynthesis of valuable methylated compounds, but its supply is a bottleneck for these biosynthetic pathways. To overcome this bottleneck and to reconfigure SAM homeostasis, a high-throughput sensing system for changes in intracellular SAM availability is required. We constructed a plasmid that can detect the factors that can alter SAM availability using minimal components. It does so by placing a fluorescent protein under a promoter controlled by endogenous MetJ, a transcription factor that represses its own regulons upon binding with SAM. Next, to validate SAM-responsive behavior, we systematically reconstructed 10 synthetic promoters with different positions and with different number of metbox sites, sequences of MetJ binding. We found that a position between the -35 box and the -10 box was the most effective for repression and that this setup was suitable for detecting the genetic or environmental factors that can deplete and recover the intracellular SAM availability. Overall, the response patterns of the synthetic MetJ-regulated promoters characterized in this study may be useful for the development of further SAM biosensing systems.
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Affiliation(s)
- Taro Watanabe
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
- Kirin Central Research Institute, Kirin Holdings Company, Limited
| | - Yuki Kimura
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
| | - Daisuke Umeno
- Department of Applied Chemistry, Faculty of Science, and Engineering, Waseda University
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4
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Sugaya K, Yasuda S, Sato S, Sisi C, Yamamoto T, Umeno D, Matsuura T, Hayashi T, Ogasawara S, Kinoshita M, Murata T. A methodology for creating thermostabilized mutants of G‐protein coupled receptors by combining statistical thermodynamics and evolutionary molecular engineering. Protein Sci 2022. [DOI: 10.1002/pro.4404] [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] [Indexed: 11/08/2022]
Affiliation(s)
- Kanna Sugaya
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
| | - Shingo Sato
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Chen Sisi
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
| | - Taisei Yamamoto
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
| | - Daisuke Umeno
- Department of Applied Chemistry Waseda University Tokyo Japan
| | - Tomoaki Matsuura
- Earth‐Life Science Institute Tokyo Institute of Technology Tokyo Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology, and Art and Sports Sciences, Faculty of Engineering Niigata University Niigata Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
- Institute for Advanced Academic Research Chiba University Chiba Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Institute of Advanced Energy Kyoto University Kyoto Japan
- Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto‐shi Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science Chiba University Chiba Japan
- Membrane Protein Research Center Chiba University Chiba Japan
- Molecular Chirality Research Center Chiba University Chiba Japan
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5
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Otani Y, Maoka T, Kawai-Noma S, Saito K, Umeno D. A novel carotenoid biosynthetic route via oxidosqualene. Biochem Biophys Res Commun 2022; 599:75-80. [PMID: 35176628 DOI: 10.1016/j.bbrc.2022.01.105] [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: 11/16/2021] [Revised: 01/04/2022] [Accepted: 01/26/2022] [Indexed: 11/02/2022]
Abstract
Over 800 known carotenoids are synthesized from phytoene or 4,4'-diapophytoene (dehydrosqualene) characterized by three conjugated double bonds. In this paper, we report that carotenoid desaturase CrtN from Staphylococcus aureus and Methylomonas can accept oxidosqualene, which is the precursor for plant- or animal-type triterpenoids, yielding the yellow carotenoid pigments with 8, 9, or 10 conjugated double bonds. The resulting pathway is the second nonnatural route for carotenoid pigments and the first pathway for carotenoid pigments not biosynthesized via (diapo)phytoene.
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Affiliation(s)
- Yusuke Otani
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan; Department of Applied Chemistry, Waseda University, Tokyo, Japan.
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6
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Furubayashi M, Umeno D. Use of directed enzyme evolution to create novel biosynthetic pathways for production of rare or non-natural carotenoids. Methods Enzymol 2022; 671:351-382. [DOI: 10.1016/bs.mie.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Abstract
One of the most prominent features of genetically encoded biosensors (GEBs) is their evolvability-the ability to invent new sensory functions using mutations. Among the GEBs, the transcription factor-based biosensors (TF-biosensors) is the focus of this review. We also discuss how this class of sensors can be highly evolvable and how we can exploit it. With an established platform for directed evolution, researchers can create, or evolve, new TF-biosensors. Directed evolution experiments have revealed the TF-biosensors' evolvability, which is based partially on their characteristic physicochemical properties.
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Affiliation(s)
- Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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8
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Tominaga M, Nozaki K, Umeno D, Ishii J, Kondo A. Robust and flexible platform for directed evolution of yeast genetic switches. Nat Commun 2021; 12:1846. [PMID: 33758180 PMCID: PMC7988172 DOI: 10.1038/s41467-021-22134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/26/2021] [Indexed: 01/31/2023] Open
Abstract
A wide repertoire of genetic switches has accelerated prokaryotic synthetic biology, while eukaryotic synthetic biology has lagged in the model organism Saccharomyces cerevisiae. Eukaryotic genetic switches are larger and more complex than prokaryotic ones, complicating the rational design and evolution of them. Here, we present a robust workflow for the creation and evolution of yeast genetic switches. The selector system was designed so that both ON- and OFF-state selection of genetic switches is completed solely by liquid handling, and it enabled parallel screen/selection of different motifs with different selection conditions. Because selection threshold of both ON- and OFF-state selection can be flexibly tuned, the desired selection conditions can be rapidly pinned down for individual directed evolution experiments without a prior knowledge either on the library population. The system's utility was demonstrated using 20 independent directed evolution experiments, yielding genetic switches with elevated inducer sensitivities, inverted switching behaviours, sensory functions, and improved signal-to-noise ratio (>100-fold induction). The resulting yeast genetic switches were readily integrated, in a plug-and-play manner, into an AND-gated carotenoid biosynthesis pathway.
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Affiliation(s)
- Masahiro Tominaga
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kenta Nozaki
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Daisuke Umeno
- grid.136304.30000 0004 0370 1101Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, Chiba, Japan
| | - Jun Ishii
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Engineering Biology Research Center, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Department of Chemical Science and Engineering, Faculty of Engineering, Kobe University, Kobe, Japan ,grid.7597.c0000000094465255Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
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9
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Kimura Y, Kawai-Noma S, Saito K, Umeno D. Directed Evolution of the Stringency of the LuxR Vibrio fischeri Quorum Sensor without OFF-State Selection. ACS Synth Biol 2020; 9:567-575. [PMID: 31999435 DOI: 10.1021/acssynbio.9b00444] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/01/2023]
Abstract
Stringency (low leak) is one of the most important specifications required for genetic circuits and induction systems, but it is challenging to evolve without sacrificing the maximum output level. This problem also comes from the absence of truly tunable negative selection methods. This paper reports that stringently switching variants can sometimes emerge with surprising frequency upon mutations. We randomly mutated the previously generated leaky variants of LuxR, the quorum-sensing transcription activator from Vibrio fischeri, to restore the stringency. We found as much as 10-20% of the entire population exhibited significantly improved signal-to-noise ratios compared with their parents. This indicated that these mutants arose by the loss of folding capability by accumulating destabilizing mutations, not by introducing rare adaptive mutations, thereby becoming AHL-dependent folders. Only four rounds of mutagenesis and ON-state selection resulted in the domination of the entire population by the improved variants with low leak, without direct selection pressure for stringency. With this surprising frequency, conversion into the "ligand-addicted folders" should be one of the prevailing modes of evolving stringency both in the laboratory and in nature, and the workflow described here provides a rapid and versatile method of improving the signal-to-noise ratio of various genetic switches.
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Affiliation(s)
- Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
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10
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Mu T, Toyoda H, Kimura Y, Yamada M, Utoh R, Umeno D, Seki M. Laborless, Automated Microfluidic Tandem Cell Processor for Visualizing Intracellular Molecules of Mammalian Cells. Anal Chem 2020; 92:2580-2588. [PMID: 31822057 DOI: 10.1021/acs.analchem.9b04288] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Visualization and quantification of intracellular molecules of mammalian cells are crucial steps in clinical diagnosis, drug development, and basic biological research. However, conventional methods rely mostly on labor-intensive, centrifugation-based manual operations for exchanging the cell carrier medium and have limited reproducibility and recovery efficiency. Here we present a microfluidic cell processor that can perform four-step exchange of carrier medium, simply by introducing a cell suspension and fluid reagents into the device. The reaction time period for each reaction step, including fixation, membrane permeabilization, and staining, was tunable in the range of 2 to 15 min by adjusting the volume of the reaction tube connecting the neighboring exchanger modules. We double-stained the cell nucleus and cytoskeleton (F-actin) using the presented device with an overall reaction period of ∼30 min, achieving a high recovery ratio and high staining efficiency. Additionally, intracellular cytokine (IL-2) was visualized for T cells to demonstrate the feasibility of the device as a pretreatment system for downstream flow-cytometric analysis. The presented approach would facilitate the development of laborless, automated microfluidic systems that integrate cell processing and analysis operations and would pave a new path to high-throughput biological experiments.
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Affiliation(s)
- Tinglin Mu
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Hajime Toyoda
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Masumi Yamada
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Rie Utoh
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Minoru Seki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
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11
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Kimura Y, Umeno D. Directed evolution of transcriptional switches using dual-selector systems. Methods Enzymol 2020; 644:191-207. [DOI: 10.1016/bs.mie.2020.04.067] [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] [Indexed: 11/24/2022]
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12
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Shimada N, Okuda Y, Maeda K, Umeno D, Takaichi S, Ikeuchi M. Astaxanthin production in a model cyanobacterium Synechocystis sp. PCC 6803. J GEN APPL MICROBIOL 2020; 66:116-120. [DOI: 10.2323/jgam.2020.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Naoya Shimada
- Department of Life Sciences (Biology), The University of Tokyo
| | - Yukiko Okuda
- Department of Life Sciences (Biology), The University of Tokyo
| | - Kaisei Maeda
- Department of Life Sciences (Biology), The University of Tokyo
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Shinichi Takaichi
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), The University of Tokyo
- Faculty of Education and Integrated Arts and Sciences, Waseda University
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13
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Takemura M, Kubo A, Higuchi Y, Maoka T, Sahara T, Yaoi K, Ohdan K, Umeno D, Misawa N. Pathway engineering for efficient biosynthesis of violaxanthin in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:9393-9399. [PMID: 31673744 DOI: 10.1007/s00253-019-10182-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 07/29/2019] [Revised: 09/18/2019] [Accepted: 10/09/2019] [Indexed: 11/27/2022]
Abstract
Carotenoids are naturally synthesized in some species of bacteria, archaea, and fungi (including yeasts) as well as all photosynthetic organisms. Escherichia coli has been the most popular bacterial host for the heterologous production of a variety of carotenoids, including even xanthophylls unique to photosynthetic eukaryotes such as lutein, antheraxanthin, and violaxanthin. However, conversion efficiency of these epoxy-xanthophylls (antheraxanthin and violaxanthin) from zeaxanthin remained substantially low. We here examined several factors affecting their productivity in E. coli. Two sorts of plasmids were introduced into the bacterial host, i.e., a plasmid to produce zeaxanthin due to the presence of the Pantoea ananatis crtE, crtB, crtI, crtY, and crtZ genes in addition to the Haematococcus pluvialis IDI gene, and one containing each of zeaxanthin epoxidase (ZEP) genes originated from nine photosynthetic eukaryotes. It was consequently found that paprika (Capsicum annuum) ZEP (CaZEP) showed the highest conversion activity. Next, using the CaZEP gene, we performed optimization experiments in relation to E. coli strains as the production hosts, expression vectors, and ribosome-binding site (RBS) sequences. As a result, the highest productivity of violaxanthin (231 μg/g dry weight) was observed, when the pUC18 vector was used with CaZEP preceded by a RBS sequence of score 5000 in strain JM101(DE3).
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Affiliation(s)
- Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Akiko Kubo
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka, 555-8502, Japan
| | - Yuki Higuchi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
| | - Takashi Maoka
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
- Division of Food Function and Chemistry, Research Institute for Production Development, Kyoto, 606-0805, Japan
| | - Takehiko Sahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kohji Ohdan
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka, 555-8502, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, 263-8522, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, 921-8836, Japan
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14
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Abstract
Substrate tolerance of bacterial cyclases has been demonstrated in various contexts, but little is known about that of plant cyclases. Here, we tested two plant ε-cyclases to convert C50-lycopene, which we previously established by rounds of directed evolution. Unlike bacterial β-cyclases, two-end cyclase from lettuce exhibited complete specificity against this molecule, indicating that this enzyme has some mechanism that exerts size-specificity. Arabidopsis one-end cyclase At-y2 showed detectable activity to C50-lycopene. Interestingly, we found that it functions as a two-end cyclase in a C50 context. Based on this observation, a possible model for substrate discrimination of this enzyme is proposed.
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Affiliation(s)
- Yusuke Otani
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
- * E-mail:
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15
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Li L, Furubayashi M, Otani Y, Maoka T, Misawa N, Kawai-Noma S, Saito K, Umeno D. Nonnatural biosynthetic pathway for 2-hydroxylated xanthophylls with C 50-carotenoid backbone. J Biosci Bioeng 2019; 128:438-444. [PMID: 31029539 DOI: 10.1016/j.jbiosc.2019.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 12/02/2018] [Revised: 03/17/2019] [Accepted: 04/02/2019] [Indexed: 11/18/2022]
Abstract
Carotenoids are structurally diverse pigments with various important biological functions. There has been a large interest in the search for novel carotenoid structures, since only a slight structural changes can result in a drastic difference in their biological functions. Carotenoid-modifying enzymes show remarkable substrate promiscuity, allowing rapid access to a vast set of novel carotenoids by combinatorial biosynthesis. We previously constructed a nonnatural carotenoid biosynthetic pathway in Escherichia coli that can produce C50 carotenoids having a longer chain than their natural C40 counterparts. In this study, a carotenoid 2,2'-hydroxylase (crtG) from Brevundimonas sp. SD212 was coexpressed together with our laboratory-engineered C50-zeaxanthin and C50-astaxanthin biosynthetic pathways. We identified six novel nonnatural C50-xanthophylls, namely, C50-nostoxanthin, C50-caloxanthin, C50-adonixanthin, C50-4-ketonostoxanthin, C50-2-hydroxyastaxanthin, and C50-2,2'-dihydroxyastaxanthin.
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Affiliation(s)
- Ling Li
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Maiko Furubayashi
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Yusuke Otani
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto 606-0805, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa 921-8836, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba 263-8522, Japan.
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16
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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: 6] [Impact Index Per Article: 1.2] [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: 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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17
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Li L, Furubayashi M, Wang S, Maoka T, Kawai-Noma S, Saito K, Umeno D. Genetically engineered biosynthetic pathways for nonnatural C 60 carotenoids using C 5-elongases and C 50-cyclases in Escherichia coli. Sci Rep 2019; 9:2982. [PMID: 30814614 PMCID: PMC6393565 DOI: 10.1038/s41598-019-39289-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 11/22/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
While the majority of the natural carotenoid pigments are based on 40-carbon (C40) skeleton, some carotenoids from bacteria have larger C50 skeleton, biosynthesized by attaching two isoprene units (C5) to both sides of the C40 carotenoid pigment lycopene. Subsequent cyclization reactions result in the production of C50 carotenoids with diverse and unique skeletal structures. To produce even larger nonnatural novel carotenoids with C50 + C5 + C5 = C60 skeletons, we systematically coexpressed natural C50 carotenoid biosynthetic enzymes (lycopene C5-elongases and C50-cyclases) from various bacterial sources together with the laboratory-engineered nonnatural C50-lycopene pathway in Escherichia coli. Among the tested enzymes, the elongases and cyclases from Micrococcus luteus exhibited significant activity toward C50-lycopene, and yielded the novel carotenoids C60-flavuxanthin and C60-sarcinaxanthin. Moreover, coexpression of M. luteus elongase with Corynebacterium cyclase resulted in the production of C60-sarcinaxanthin, C60-sarprenoxanthin, and C60-decaprenoxanthin.
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Affiliation(s)
- Ling Li
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Maiko Furubayashi
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Shifei Wang
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan.
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18
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Yamagami K, Matsuura Y, Kawai-Noma S, Umeno D, Saito K, Fujiwara K, Sugo T, Yajima Y, Hioki J, Shiono T, Wakabayashi H. Adsorption of Caffeine onto Tannic Acid-Immobilized Fiber and its Elution with Hot Water. KAGAKU KOGAKU RONBUN 2018. [DOI: 10.1252/kakoronbunshu.44.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kazuma Yamagami
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Yuki Matsuura
- Department of Applied Chemistry and Biotechnology, Chiba University
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
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19
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Abstract
The cellular activities of gymnosperms monoterpene synthases are largely compromised due to their requirement for manganese, which is deficient in microbial cells. Through site-saturation mutagenesis of the residue adjacent to metal-binding glutamate, we found that pinene synthase is highly mutable at this position yet drastically alter their metal binding preference, thereby quickly improving the cellular performance in heterologous hosts.
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Affiliation(s)
- Miki Tashiro
- a Faculty of Engineering, Department of Applied Chemistry and Biotechnology , Chiba University Nishi-Chiba Campus (Administration Bureau) , Chiba-shi , Japan
| | - Koyo Ono
- a Faculty of Engineering, Department of Applied Chemistry and Biotechnology , Chiba University Nishi-Chiba Campus (Administration Bureau) , Chiba-shi , Japan
| | - Yuki Kimura
- a Faculty of Engineering, Department of Applied Chemistry and Biotechnology , Chiba University Nishi-Chiba Campus (Administration Bureau) , Chiba-shi , Japan
| | - Shigeko Kawai-Noma
- a Faculty of Engineering, Department of Applied Chemistry and Biotechnology , Chiba University Nishi-Chiba Campus (Administration Bureau) , Chiba-shi , Japan
| | - Kyoichi Saito
- a Faculty of Engineering, Department of Applied Chemistry and Biotechnology , Chiba University Nishi-Chiba Campus (Administration Bureau) , Chiba-shi , Japan
| | - Daisuke Umeno
- a Faculty of Engineering, Department of Applied Chemistry and Biotechnology , Chiba University Nishi-Chiba Campus (Administration Bureau) , Chiba-shi , Japan
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20
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Uchiyama S, Sasaki T, Ishihara R, Fujiwara K, Sugo T, Umeno D, Saito K. High-resolution separation of neodymium and dysprosium ions utilizing extractant-impregnated graft-type particles. J Chromatogr A 2018; 1533:10-16. [PMID: 29276081 DOI: 10.1016/j.chroma.2017.11.002] [Citation(s) in RCA: 3] [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: 09/01/2017] [Revised: 10/24/2017] [Accepted: 11/01/2017] [Indexed: 11/17/2022]
Abstract
An efficient method for rare metal recovery from environmental water and urban mines is in high demand. Toward rapid and high-resolution rare metal ion separation, a novel bis(2-ethylhexyl) phosphate (HDEHP)-impregnated graft-type particle as a filler for a chromatography column is proposed. To achieve rapid and high-resolution separation, a convection-flow-aided elution mode is required. The combination of 35 μm non-porous particles and a polymer-brush-rich particle structure minimizes the distance from metal ion binding sites to the convection flow in the column, resulting in minimized diffusional mass transfer resistance and the convection-flow-aided elution mode. The HDEHP-impregnated graft-type non-porous-particle-packed cartridge developed in this study exhibited a higher separation performance for model rare metals, neodymium (III) and dysprosium (III) ions, and a narrower peak at a higher linear velocity, than those of previous HDEHP-impregnated fiber-packed and commercially available Lewatit® VP OC 1026-packed cartridges.
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Affiliation(s)
- Shoichiro Uchiyama
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan
| | - Takaaki Sasaki
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan
| | - Ryo Ishihara
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan
| | - Kunio Fujiwara
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan; KJK Co., Ltd., 58-1 Yashima, Takasaki, Gunma 370-0849, Japan
| | - Takanobu Sugo
- KJK Co., Ltd., 58-1 Yashima, Takasaki, Gunma 370-0849, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan.
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21
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Kawamura R, Goto S, Matsuura Y, Kawai-Noma S, Umeno D, Saito K, Fujiwara K, Sugo T, Yajima Y, Kinoshita A, Kudo A, Hioki J, Wakabayashi H. Adsorption of Catechin in Green-Tea Extracts onto NVP-Grafted Fiber and Its Elution with NaOH. KAGAKU KOGAKU RONBUN 2018. [DOI: 10.1252/kakoronbunshu.44.99] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Shota Goto
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Yuki Matsuura
- Department of Applied Chemistry and Biotechnology, Chiba University
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
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22
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Matsuzaki Y, Kudo D, Kojima T, Kawai-Noma S, Umeno D, Saito K. Preparation of Cation-Exchange Fibers with High Protein-Binding Capacities by Pre-Irradiation Induced Emulsion Graft Polymerization. KAGAKU KOGAKU RONBUN 2017. [DOI: 10.1252/kakoronbunshu.43.88] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuka Matsuzaki
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Daiki Kudo
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Takashi Kojima
- Department of Applied Chemistry and Biotechnology, Chiba University
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
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23
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Tashiro M, Fujii A, Kawai-Noma S, Saito K, Umeno D. Directed evolution and expression tuning of geraniol synthase for efficient geraniol production in Escherichia coli. J GEN APPL MICROBIOL 2017; 63:287-295. [DOI: 10.2323/jgam.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Miki Tashiro
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Akira Fujii
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
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24
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Saeki K, Tominaga M, Kawai-Noma S, Saito K, Umeno D. Rapid Diversification of BetI-Based Transcriptional Switches for the Control of Biosynthetic Pathways and Genetic Circuits. ACS Synth Biol 2016; 5:1201-1210. [PMID: 26991155 DOI: 10.1021/acssynbio.5b00230] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 11/30/2022]
Abstract
Synthetic biologists are in need of genetic switches, or inducible sensor/promoter systems, that can be reliably integrated in multiple contexts. Using a liquid-based selection method, we systematically engineered the choline-inducible transcription factor BetI, yielding various choline-inducible and choline-repressive promoter systems with various input-output characteristics. In addition to having high stringency and a high maximum induction level, they underwent a graded and single-peaked response to choline. Taking advantage of these features, we demonstrated the utility of these systems for controlling the carotenoid biosynthetic pathway and for constructing two-input logic gates. Additionally, we demonstrated the rapidity, throughput, robustness, and cost-effectiveness of our selection method, which facilitates the conversion of natural genetic controlling systems into systems that are designed for various synthetic biology applications.
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Affiliation(s)
- Kazuya Saeki
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Masahiro Tominaga
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory Research
for Embryonic Science and Technology (PRESTO), Japan Science and Technology
Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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25
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Kimura Y, Tashiro Y, Saito K, Kawai-Noma S, Umeno D. Directed evolution of Vibrio fischeri LuxR signal sensitivity. J Biosci Bioeng 2016; 122:533-538. [DOI: 10.1016/j.jbiosc.2016.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/25/2016] [Accepted: 04/26/2016] [Indexed: 12/31/2022]
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26
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Tashiro M, Kiyota H, Kawai-Noma S, Saito K, Ikeuchi M, Iijima Y, Umeno D. Bacterial Production of Pinene by a Laboratory-Evolved Pinene-Synthase. ACS Synth Biol 2016; 5:1011-20. [PMID: 27247193 DOI: 10.1021/acssynbio.6b00140] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [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: 01/25/2023]
Abstract
Successful feeding of the substrate geranylpyrophosphate (GPP) to monoterpene synthase is critical to the efficient microbial production of monoterpenes. Overexpression of GPP synthases, metabolic channeling from GPP synthase to terpene synthases, and down-tuning of endogenous competitors have been successfully used to increase the production of monoterpene. Nevertheless, the production of monoterpenes has remained considerably lower than that of hemi-/sesqui-terpenoids. We tested whether it is effective to improve the cellular activity of monoterpene synthases. To this end, we developed a high-throughput screening system to monitor for elevated GPP consumption. Through a single round of mutagenesis and screening, we isolated a pinene synthase variant that outperformed the wild-type (parent) enzyme in multiple contexts in Escherichia coli and cyanobacteria. The purified variant exhibited drastically altered metal dependency, enabling to keep the activity in the cytosol that is manganese-deficient. Coexpression of this variant with mevalonate pathway enzymes, isopentenylpyrophosphate isomerase, and GPP synthase yielded 140 mg/L pinene in a flask culture.
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Affiliation(s)
- Miki Tashiro
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Hiroshi Kiyota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Masahiko Ikeuchi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Life
Sciences (Biology), Graduate School of Arts and Science, University of Tokyo, 3-8-1 Meguro-ku, Tokyo 153-8902, Japan
| | - Yoko Iijima
- Department of Nutrition
and Life Science, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory Research
for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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27
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Goto S, Umino S, Amakai W, Fujiwara K, Sugo T, Kojima T, Kawai-Noma S, Umeno D, Saito K. Impregnation structure of cobalt ferrocyanide microparticles by the polymer chain grafted onto nylon fiber. J NUCL SCI TECHNOL 2016. [DOI: 10.1080/00223131.2016.1143886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shota Goto
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
| | - Satoshi Umino
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
| | - Wataru Amakai
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
| | | | | | - Takashi Kojima
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, 1-33 Yayoi-cho, Chiba University, Chiba, Japan
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28
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Nakamura Y, Fujiwara K, Sugo T, Kawai-Noma S, Umeno D, Saito K. Preparation of Extractant-Impregnated Fiber for Recovery of Palladium from Hydrochloric Acid Solution. KAGAKU KOGAKU RONBUN 2016. [DOI: 10.1252/kakoronbunshu.42.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuki Nakamura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | | | | | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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29
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Tashiro Y, Kimura Y, Furubayashi M, Tanaka A, Terakubo K, Saito K, Kawai-Noma S, Umeno D. Directed evolution of the autoinducer selectivity of Vibrio fischeri LuxR. J GEN APPL MICROBIOL 2016; 62:240-247. [DOI: 10.2323/jgam.2016.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yohei Tashiro
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Chiba University
| | | | - Akira Tanaka
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kei Terakubo
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
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30
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Ike K, Arasawa Y, Koizumi S, Mihashi S, Kawai-Noma S, Saito K, Umeno D. Evolutionary Design of Choline-Inducible and -Repressible T7-Based Induction Systems. ACS Synth Biol 2015; 4:1352-60. [PMID: 26289535 DOI: 10.1021/acssynbio.5b00107] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
By assembly and evolutionary engineering of T7-phage-based transcriptional switches made from endogenous components of the bet operon on the Escherichia coli chromosome, genetic switches inducible by choline, a safe and inexpensive compound, were constructed. The functional plasticity of the BetI repressor was revealed by rapid and high-frequency identification of functional variants with various properties, including those with high stringency, high maximum expression level, and reversed phenotypes, from a pool of BetI mutants. The plasmid expression of BetI mutants resulted in the choline-inducible (Bet-ON) or choline-repressible (Bet-OFF) switching of genes under the pT7/betO sequence at unprecedentedly high levels, while keeping the minimal leaky expression in uninduced conditions.
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Affiliation(s)
- Kohei Ike
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Yusuke Arasawa
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Satoshi Koizumi
- Technology Development & Research Department, Kyowa Hakko Bio Co., Ltd., 1-6-1, Ohtemachi, Chiyoda-ku, Tokyo 100-8185, Japan
| | - Satoshi Mihashi
- Technology Development & Research Department, Kyowa Hakko Bio Co., Ltd., 1-6-1, Ohtemachi, Chiyoda-ku, Tokyo 100-8185, Japan
| | - Shigeko Kawai-Noma
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory
Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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31
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Tominaga M, Ike K, Kawai-Noma S, Saito K, Umeno D. Rapid and liquid-based selection of genetic switches using nucleoside kinase fused with aminoglycoside phosphotransferase. PLoS One 2015; 10:e0120243. [PMID: 25790096 PMCID: PMC4366196 DOI: 10.1371/journal.pone.0120243] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
The evolutionary design of genetic switches and circuits requires iterative rounds of positive (ON-) and negative (OFF-) selection. We previously reported a rapid OFF selection system based on the kinase activity of herpes simplex virus thymidine kinase (hsvTK) on the artificial mutator nucleoside dP. By fusing hsvTK with the kanamycin resistance marker aminoglycoside-(3')-phosphotransferase (APH), we established a novel selector system for genetic switches. Due to the bactericidal nature of kanamycin and nucleoside-based lethal mutagenesis, both positive and negative selection could be completed within several hours. Using this new selector system, we isolated a series of homoserine lactone-inducible genetic switches with different expression efficiencies from libraries of the Vibrio fischeri lux promoter in two days, using only liquid handling.
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Affiliation(s)
- Masahiro Tominaga
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1–33 Yayoi-Cyo, Inage-ku, Chiba, Japan
| | - Kohei Ike
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1–33 Yayoi-Cyo, Inage-ku, Chiba, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1–33 Yayoi-Cyo, Inage-ku, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1–33 Yayoi-Cyo, Inage-ku, Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1–33 Yayoi-Cyo, Inage-ku, Chiba, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4–1–8 Honcho, Kawaguchi, Saitama, Japan
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Tominaga M, Kawai-Noma S, Kawagishi I, Sowa Y, Saito K, Umeno D. Liquid-based iterative recombineering method tolerant to counter-selection escapes. PLoS One 2015; 10:e0119818. [PMID: 25775434 PMCID: PMC4361647 DOI: 10.1371/journal.pone.0119818] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
Selection-based recombineering is a flexible and proven technology to precisely modify bacterial genomes at single base resolution. It consists of two steps of homologous recombination followed by selection/counter-selection. However, the shortage of efficient counter-selectable markers limits the throughput of this method. Additionally, the emergence of ‘selection escapees’ can affect recombinant pools generated through this method, and they must be manually removed at each step of selection-based recombineering. Here, we report a series of efforts to improve the throughput and robustness of selection-based recombineering and to achieve seamless and automatable genome engineering. Using the nucleoside kinase activity of herpes simplex virus thymidine kinase (hsvTK) on the non-natural nucleoside dP, a highly efficient, rapid, and liquid-based counter-selection system was established. By duplicating hsvtk gene, combined with careful control of the population size for the subsequent round, we effectively eliminated selection escapes, enabling seamless and multiple insertions/replacement of gene-size fragments in the chromosome. Four rounds of recombineering could thus be completed in 10 days, requiring only liquid handling and without any need for colony isolation or genotype confirmation. The simplicity and robustness of our method make it broadly accessible for multi-locus chromosomal modifications.
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Affiliation(s)
- Masahiro Tominaga
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Ikuro Kawagishi
- Department of Frontier Bioscience, Hosei University, 3-7-2, Koganei, Tokyo 184-8584, Japan
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience, Hosei University, 3-7-2, Koganei, Tokyo 184-8584, Japan
- Research Center for Micro-Nano Technology, Hosei University, 3-11-15 Midori-cho, Tokyo 184-8584, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- * E-mail:
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Sasaki TA, Uchiyama S, Fujiwara K, Sugo T, Umeno D, Saito K. Nd/Dy Resolution by SPE-Based Elution Chromatography with Bis(2-ethylhexyl) Phosphate (HDEHP)-Impregnated Fiber-Packed Bed. KAGAKU KOGAKU RONBUN 2015. [DOI: 10.1252/kakoronbunshu.41.220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Taka-aki Sasaki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Shoichiro Uchiyama
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kunio Fujiwara
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
- KJK Co., Ltd
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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Furubayashi M, Li L, Katabami A, Saito K, Umeno D. Directed evolution of squalene synthase for dehydrosqualene biosynthesis. FEBS Lett 2014; 588:3375-81. [PMID: 25093296 DOI: 10.1016/j.febslet.2014.07.028] [Citation(s) in RCA: 7] [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: 06/20/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Squalene synthase (SQS) catalyzes the first step of sterol/hopanoid biosynthesis in various organisms. It has been long recognized that SQSs share a common ancestor with carotenoid synthases, but it is not known how these enzymes selectively produce their own product. In this study, SQSs from yeast, human, and bacteria were independently subjected to directed evolution for the production of the C30 carotenoid backbone, dehydrosqualene. This was accomplished via high-throughput screening with Pantoea ananatis phytoene desaturase, which can selectively convert dehydrosqualene into yellow carotenoid pigments. Genetic analysis of the resultant mutants revealed various mutations that could effectively convert SQS into a "dehydrosqualene synthase." All of these mutations are clustered around the residues that have been proposed to be important for NADPH binding.
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Affiliation(s)
- Maiko Furubayashi
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Ling Li
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Akinori Katabami
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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35
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Furubayashi M, Saito K, Umeno D. Evolutionary analysis of the functional plasticity of Staphylococcus aureus C30 carotenoid synthase. J Biosci Bioeng 2014; 117:431-6. [DOI: 10.1016/j.jbiosc.2013.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/16/2022]
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36
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Okamura Y, Fujiwara K, Ishihara R, Sugo T, Kojima T, Umeno D, Saito K. Cesium removal in freshwater using potassium cobalt hexacyanoferrate-impregnated fibers. Radiat Phys Chem Oxf Engl 1993 2014. [DOI: 10.1016/j.radphyschem.2013.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Sasaki TA, Uchiyama S, Fujiwara K, Sugo T, Umeno D, Saito K. Similarity of Rare Earth Extraction by Acidic Extractant Bis(2-ethylhexyl) Phosphate (HDEHP) Supported on a Dodecylamino-Group-Containing Graft Chain and by HDEHP Dissolved in Dodecane. KAGAKU KOGAKU RONBUN 2014. [DOI: 10.1252/kakoronbunshu.40.404] [Citation(s) in RCA: 5] [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] [Indexed: 11/11/2022]
Affiliation(s)
- Taka-aki Sasaki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Shoichiro Uchiyama
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kunio Fujiwara
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
- KJK Co., Ltd
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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Abstract
Ever-increasing repertories of RNA-based switching devices are enabling synthetic biologists to construct compact, self-standing, and easy-to-integrate regulatory circuits. However, it is rather rare that the existing RNA-based expression controllers happen to have the exact specification needed for particular applications from the beginning. Evolutionary design of is powerful strategy for quickly tuning functions/specification of genetic switches. Presented here are the steps required for rapid and efficient enrichment of genetic switches with desired specification using recently developed nucleoside kinase-based dual selection system. Here, the library of genetic switches, created by randomizing either the part or the entire sequence coding switching components, is subjected to OFF (negative) selection and ON (positive) selection in various conditions. The entire selection process is completed only by liquid handling, facilitating the parallel and continuous operations of multiple selection projects. This automation-liable platform for genetic selection of functional switches has potential applications for development of RNA-based biosensors, expression controllers, and their integrated forms (genetic circuits).
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Affiliation(s)
- Kohei Ike
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University, Chiba, Japan
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39
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Tanaka R, Ishihara R, Miyoshi K, Umeno D, Saito K, Asai S, Yamada S, Hirota H. Simple Method for High-Density Impregnation of Aliquat 336 onto Porous Sheet and Binding Performance of Resulting Sheet for Palladium Ions. SEP SCI TECHNOL 2013. [DOI: 10.1080/01496395.2013.829101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Furubayashi M, Li L, Katabami A, Saito K, Umeno D. Construction of carotenoid biosynthetic pathways using squalene synthase. FEBS Lett 2013; 588:436-42. [PMID: 24333579 DOI: 10.1016/j.febslet.2013.12.003] [Citation(s) in RCA: 19] [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: 10/26/2013] [Revised: 11/28/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
Abstract
The first committed steps of steroid/hopanoid pathways involve squalene synthase (SQS). Here, we report the Escherichia coli production of diaponeurosporene and diapolycopene, yellow C30 carotenoid pigments, by expressing human SQS and Staphylococcus aureus dehydrosqualene (C30 carotenoid) desaturase (CrtN). We suggest that the carotenoid pigments are synthesized mainly via the desaturation of squalene rather than the direct synthesis of dehydrosqualene through the non-reductive condensation of prenyl diphosphate precursors, indicating the possible existence of a "squalene route" and a "lycopersene route" for C30 and C40 carotenoids, respectively. Additionally, this finding yields a new method of colorimetric screening for the cellular activity of squalene synthases, which are major targets for cholesterol-lowering drugs.
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Affiliation(s)
- Maiko Furubayashi
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33, Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Ling Li
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33, Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Akinori Katabami
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33, Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33, Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33, Yayoi-cho, Inage, Chiba 263-8522, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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41
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Ishihara R, Uchiyama S, Ikezawa H, Yamada S, Hirota H, Umeno D, Saito K. Effect of Dose on Mole Percentages of Polymer Brush and Root Grafted onto Porous Polyethylene Sheet by Radiation-Induced Graft Polymerization. Ind Eng Chem Res 2013. [DOI: 10.1021/ie4011436] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryo Ishihara
- Department of Applied Chemistry
and Biotechnology, Chiba University, 1-33,
Yayoi-cho, Inage-ku, Chiba, Japan
| | - Shoichiro Uchiyama
- Department of Applied Chemistry
and Biotechnology, Chiba University, 1-33,
Yayoi-cho, Inage-ku, Chiba, Japan
| | - Hidekazu Ikezawa
- Department of Applied Chemistry
and Biotechnology, Chiba University, 1-33,
Yayoi-cho, Inage-ku, Chiba, Japan
| | - Shinsuke Yamada
- INOAC Corporation, 1-16-30, Sen-nen, Atsuta-ku,
Aichi, Japan
| | - Hideyuki Hirota
- INOAC Corporation, 1-16-30, Sen-nen, Atsuta-ku,
Aichi, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry
and Biotechnology, Chiba University, 1-33,
Yayoi-cho, Inage-ku, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry
and Biotechnology, Chiba University, 1-33,
Yayoi-cho, Inage-ku, Chiba, Japan
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42
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Iwanade A, Umeno D, Saito K, Sugo T. Dependence of protein binding capacity of dimethylamino-γ-butyric-acid (DMGABA)-immobilized porous membrane on composition of solvent used for DMGABA immobilization. Radiat Phys Chem Oxf Engl 1993 2013. [DOI: 10.1016/j.radphyschem.2013.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Wada G, Ishihara R, Miyoshi K, Umeno D, Saito K, Asai S, Yamada S, Hirota H. Crosslinked-Chelating Porous Sheet with High Dynamic Binding Capacity of Metal Ions. Solvent Extraction and Ion Exchange 2013. [DOI: 10.1080/07366299.2012.735555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Uchiyama S, Ishihara R, Umeno D, Saito K, Yamada S, Hirota H, Asai S. Determination of Mole Percentages of Brush and Root of Polymer Chain Grafted onto Porous Sheet. J Chem Eng Japan / JCEJ 2013. [DOI: 10.1252/jcej.12we274] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shoichiro Uchiyama
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Ryo Ishihara
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University
| | | | | | - Shiho Asai
- Division of Environment and Radiation Sciences, Japan Atomic Energy Agency
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45
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Sugiyama M, Ikeda K, Umeno D, Saito K, Kikuchi T, Ando K. Removal of Urea from Water Using Urease-Immobilized Fibers. J Chem Eng Japan / JCEJ 2013. [DOI: 10.1252/jcej.12we267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mai Sugiyama
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kohsuke Ikeda
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
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46
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Shimoda Y, Sekiya Y, Umeno D, Saito K, Furumoto G, Shirataki H, Shinohara N, Kubota N. Protein-Binding Characteristics of Anion-Exchange Particles Prepared by Radiation-Induced Graft Polymerization at Low Temperatures. J Chem Eng Japan / JCEJ 2013. [DOI: 10.1252/jcej.13we056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuichi Shimoda
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Yuta Sekiya
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Goro Furumoto
- Microza & Water Processing Division, Asahi Kasei Chemicals Corp
| | | | | | - Noboru Kubota
- Microza & Water Processing Division, Asahi Kasei Chemicals Corp
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47
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Hirayama Y, Okamura Y, Fujiwara K, Sugo T, Umeno D, Saito K. Effect of Salt Concentration of Cesium Solution on Cesium-Binding Capacity of Potassium Cobalt-Hexacyanoferrate-Impregnated Fiber. KAGAKU KOGAKU RONBUN 2013. [DOI: 10.1252/kakoronbunshu.39.28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuya Hirayama
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Yusuke Okamura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kunio Fujiwara
- KJK Co., Ltd
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | | | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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48
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Ishihara R, Asai S, Otosaka S, Yamada S, Hirota H, Miyoshi K, Umeno D, Saito K. Dependence of Lanthanide-Ion Binding Performance on HDEHP Concentration in HDEHP Impregnation to Porous Sheet. Solvent Extraction and Ion Exchange 2012. [DOI: 10.1080/07366299.2011.609382] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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49
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Abstract
The first step toward elucidating the mutagenic effects of chemicals and pathways is to determine the specificity of the mutations generated spontaneously or in response to treatment with mutagens. We constructed a set of plasmid-encoded probes for the specific detection of each type of base substitution mutation. Using these probes, we were able to quickly determine both the mutation rate and the specificity of the mutations caused by different types of mutagens and mutagenic conditions. We also developed a PCR-based method to rapidly and robustly determine the mutation spectrum in response to various mutagenic samples in parallel. This system allows one to not only analyze the mutation specificity of various chemicals, but also to search for novel genetic elements that promote the specific mutation events.
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Affiliation(s)
- Yohei Tashiro
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263–8522, Japan
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50
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Harayama T, Okamura Y, Shimoda Y, Umeno D, Saito K, Shinohara N, Kubota N. Protein Resolution in Elution Chromatography Using Novel Cation-Exchange Polymer-Brush-Immobilized Particles. J Chem Eng Japan / JCEJ 2012. [DOI: 10.1252/jcej.12we011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Takato Harayama
- Department of Applied Chemistry and Biotechnology, Chiba University
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Yusuke Okamura
- Department of Applied Chemistry and Biotechnology, Chiba University
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Yuichi Shimoda
- Department of Applied Chemistry and Biotechnology, Chiba University
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Naoyuki Shinohara
- Microza and Water Processing Division, Asahi Kasei Chemicals Corp
- Microza & Water Processing Division, Asahi Kasei Chemicals Corporation
| | - Noboru Kubota
- Microza and Water Processing Division, Asahi Kasei Chemicals Corp
- Microza & Water Processing Division, Asahi Kasei Chemicals Corporation
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