1
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Soma Y, Tominaga S, Tokito K, Imado Y, Naka K, Hanai T, Takahashi M, Izumi Y, Bamba T. Trace impurities in sodium phosphate influences the physiological activity of Escherichia coli in M9 minimal medium. Sci Rep 2023; 13:17396. [PMID: 37833342 PMCID: PMC10576033 DOI: 10.1038/s41598-023-44526-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/09/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of applied microbiology, reproducibility and experimental variability are important factors that influence both basic research as well as process development for industrial applications. Experimental reproducibility and accuracy depend not only on culture conditions such as temperature and aeration but also on raw materials and procedures used for media preparation. The M9 minimal medium is one of the most common synthetic media for culturing Escherichia coli and other bacteria. This synthetic medium can be used to observe and evaluate the physiological activity of microbes under minimal nutritional requirements and determine the limiting factor for the desired phenotype. Although one of the advantages using the M9 medium is that its composition can be modulated, it is difficult to control presence of trace components and impurities from the reagents for preparing this medium. Herein, we showed that trace ingredients present in the reagents used for M9 media preparation affect the bacterial physiological activities (e.g., cell growth, substrate consumption, and byproduct formation). Additionally, we systematically identified the trace ingredient that influenced phenotypic differences. Our results showed that the selection of reagents and accuracy during reagent preparation is important for experimental reproducibility in the field of bio-engineering and systems biology focused on the systematic and continuous development of biomolecular systems (e.g., biorefinery, metabolic engineering, and synthetic biology).
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Affiliation(s)
- Yuki Soma
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Laboratory for Synthetic Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, W5-729, 819-0395, Japan
| | - Saki Tominaga
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kanako Tokito
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yuri Imado
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kosuke Naka
- Shimadzu Corporation, 1, Nishinokyo-Kuwabara-cho, Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Taizo Hanai
- Laboratory for Synthetic Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, W5-729, 819-0395, Japan
| | - Masatomo Takahashi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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2
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Imada T, Yamamoto C, Toyoshima M, Toya Y, Shimizu H. Effect of light fluctuations on photosynthesis and metabolic flux in Synechocystis sp. PCC 6803. Biotechnol Prog 2023; 39:e3326. [PMID: 36700527 DOI: 10.1002/btpr.3326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/07/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
In nature, photosynthetic organisms are exposed to fluctuating light, and their physiological systems must adapt to this fluctuation. To maintain homeostasis, these organisms have a light fluctuation photoprotective mechanism, which functions in both photosystems and metabolism. Although the photoprotective mechanisms functioning in the photosystem have been studied, it is unclear how metabolism responds to light fluctuations within a few seconds. In the present study, we investigated the metabolic response of Synechocystis sp. PCC 6803 to light fluctuations using 13 C-metabolic flux analysis. The light intensity and duty ratio were adjusted such that the total number of photons or the light intensity during the low-light phase was equal. Light fluctuations affected cell growth and photosynthetic activity under the experimental conditions. However, metabolic flux distributions and cofactor production rates were not affected by the light fluctuations. Furthermore, the estimated ATP and NADPH production rates in the photosystems suggest that NADPH-consuming electron dissipation occurs under fluctuating light conditions. Although we focused on the water-water cycle as the electron dissipation path, no growth effect was observed in an flv3-disrupted strain under fluctuating light, suggesting that another path contributes to electron dissipation under these conditions.
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Affiliation(s)
- Tatsumi Imada
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Chiaki Yamamoto
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Masakazu Toyoshima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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3
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Jeung K, Kim S, Yeon Lee J, Yeol Jung G. Optimization of mevalonate production using acetate by precursor balancing and flux redistribution in Escherichia coli. J IND ENG CHEM 2023. [DOI: 10.1016/j.jiec.2022.12.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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4
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Sano M, Tanaka R, Kamata K, Hirono-Hara Y, Ishii J, Matsuda F, Hara KY, Shimizu H, Toya Y. Conversion of Mevalonate to Isoprenol Using Light Energy in Escherichia coli without Consuming Sugars for ATP Supply. ACS Synth Biol 2022; 11:3966-3972. [PMID: 36441576 DOI: 10.1021/acssynbio.2c00313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioconversion of key intermediate metabolites such as mevalonate into various useful chemicals is a promising strategy for microbial production. However, the conversion of mevalonate into isoprenoids requires a supply of adenosine triphosphate (ATP). Light-driven ATP regeneration using microbial rhodopsin is an attractive module for improving the intracellular ATP supply. In the present study, we demonstrated the ATP-consuming conversion of mevalonate to isoprenol using rhodopsin-expressing Escherichia coli cells as a whole-cell catalyst in a medium that does not contain energy cosubstrate, such as glucose. Heterologous genes for the synthesis of isoprenol from mevalonate, which requires three ATP molecules for the series of reactions, and a delta-rhodopsin gene derived from Haloterrigena turkmenica were cointroduced into E. coli. To evaluate the conversion efficiency of mevalonate to isoprenol, the cells were suspended in a synthetic medium containing mevalonate as the sole carbon source and incubated under dark or light illumination (100 μmol m-2 s-1). The specific isoprenol production rates were 10.0 ± 0.9 and 20.4 ± 0.7 μmol gDCW-1 h-1 for dark and light conditions, respectively. The conversion was successfully enhanced under the light condition. Furthermore, the conversion efficiency increased with increasing illumination intensity, suggesting that ATP regenerated by the proton motive force generated by rhodopsin using light energy can drive ATP-consuming reactions in the whole-cell catalyst.
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Affiliation(s)
- Mikoto Sano
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Ryo Tanaka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka422-8526, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo657-8501, Japan.,Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo657-8501, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka422-8526, Japan.,Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka422-8526, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka565-0871, Japan
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5
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Toya Y, Shimizu H. Metabolic pathway engineering for the non-growth-associated succinate production in Escherichia coli based on flux solution space. J Biosci Bioeng 2022; 134:29-33. [DOI: 10.1016/j.jbiosc.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 10/18/2022]
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6
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Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng 2022; 72:227-236. [PMID: 35346842 DOI: 10.1016/j.ymben.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/06/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
In microbial fermentative production, ATP regeneration, while crucial for cellular processes, conflicts with efficient target chemical production because ATP regeneration exhausts essential carbon sources also required for target chemical biosynthesis. To wrestle with this dilemma, we harnessed the power of microbial rhodopsins with light-driven proton pumping activity to supplement with ATP, thereby facilitating the bioproduction of various chemicals. We first demonstrated a photo-driven ATP supply and redistribution of metabolic carbon flows to target chemical synthesis by installing already-known delta rhodopsin (dR) in Escherichia coli. In addition, we identified novel rhodopsins with higher proton pumping activities than dR, and created an engineered cell for in vivo self-supply of the rhodopsin-activator, all-trans-retinal. Our concept exploiting the light-powering ATP supplier offers a potential increase in carbon use efficiency for microbial productions through metabolic reprogramming.
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Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hidenobu Hirayama
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Tanaka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikoto Sano
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Kikukawa
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
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7
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Kawai R, Toya Y, Miyoshi K, Murakami M, Niide T, Horinouchi T, Maeda T, Shibai A, Furusawa C, Shimizu H. Acceleration of target production in co-culture by enhancing intermediate consumption through adaptive laboratory evolution. Biotechnol Bioeng 2021; 119:936-945. [PMID: 34914093 DOI: 10.1002/bit.28007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/23/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
Co-culture is a promising way to alleviate metabolic burden by dividing the metabolic pathways into several modules and sharing the conversion processes with multiple strains. Since an intermediate is passed from the donor to the recipient via the extracellular environment, it is inevitably diluted. Therefore, enhancing the intermediate consumption rate is important for increasing target productivity. In the present study, we demonstrated the enhancement of mevalonate consumption in Escherichia coli by adaptive laboratory evolution and applied the evolved strain to isoprenol production in an E. coli (upstream: glucose to mevalonate)-E. coli (downstream: mevalonate to isoprenol) co-culture. An engineered mevalonate auxotroph strain was repeatedly sub-cultured in a synthetic medium supplemented with mevalonate, where the mevalonate concentration was decreased stepwise from 100 to 20 µM. In five parallel evolution experiments, all growth rates gradually increased, resulting in five evolved strains. Whole-genome re-sequencing and reverse engineering identified three mutations involved in enhancing mevalonate consumption. After introducing nudF gene for producing isoprenol, the isoprenol-producing parental and evolved strains were respectively co-cultured with a mevalonate-producing strain. At an inoculation ratio of 1:3 (upstream:downstream), isoprenol production using the evolved strain was 3.3 times higher than that using the parental strain.
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Affiliation(s)
- Ryutaro Kawai
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Kenta Miyoshi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Manami Murakami
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | - Teppei Niide
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
| | | | - Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Atsushi Shibai
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,Department of Physics, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, Japan
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8
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Shimizu H, Toya Y. Recent advances in metabolic engineering-integration of in silico design and experimental analysis of metabolic pathways. J Biosci Bioeng 2021; 132:429-436. [PMID: 34509367 DOI: 10.1016/j.jbiosc.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/07/2021] [Indexed: 11/29/2022]
Abstract
Microorganisms are widely used to produce valuable compounds. Because thousands of metabolic reactions occur simultaneously and many metabolic reactions are related to target production and cell growth, the development of a rational design method for metabolic pathway modification to optimize target production is needed. In this paper, recent advances in metabolic engineering are reviewed, specifically considering computational pathway modification design and experimental evaluation of metabolic fluxes by 13C-metabolic flux analysis. Computational tools for seeking effective gene deletion targets and recruiting heterologous genes are described in flux balance analysis approaches. A kinetic model and adaptive laboratory evolution were applied to identify and eliminate the rate-limiting step in metabolic pathways. Data science-based approaches for process monitoring and control are described to maximize the performance of engineered cells in bioreactors.
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Affiliation(s)
- Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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9
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Matsuda F, Maeda K, Taniguchi T, Kondo Y, Yatabe F, Okahashi N, Shimizu H. mfapy: An open-source Python package for 13C-based metabolic flux analysis. Metab Eng Commun 2021; 13:e00177. [PMID: 34354925 PMCID: PMC8322459 DOI: 10.1016/j.mec.2021.e00177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/01/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022] Open
Abstract
13C-based metabolic flux analysis (13C-MFA) is an essential tool for estimating intracellular metabolic flux levels in metabolic engineering and biology. In 13C-MFA, a metabolic flux distribution that explains the observed isotope labeling data was computationally estimated using a non-linear optimization method. Herein, we report the development of mfapy, an open-source Python package developed for more flexibility and extensibility for 13C-MFA. mfapy compels users to write a customized Python code by describing each step in the data analysis procedures of the isotope labeling experiments. The flexibility and extensibility provided by mfapy can support trial-and-error performance in the routine estimation of metabolic flux distributions, experimental design by computer simulations of 13C-MFA experiments, and development of new data analysis techniques for stable isotope labeling experiments. mfapy is available to the public from the Github repository (https://github.com/fumiomatsuda/mfapy). An open-source Python package, mfapy, is developed for 13C-MFA. mfapy enables users to write Python codes for data analysis procedures of 13C-MFA. mfapy has a flexibility and extensibility to support various data analysis procedures. Computer simulations of 13C-MFA experiments is supported for experimental design.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeo Taniguchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuya Kondo
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Futa Yatabe
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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10
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Bao SH, Jiang H, Zhu LY, Yao G, Han PG, Wan XK, Wang K, Song TY, Liu CJ, Wang S, Zhang ZY, Zhang DY, Meng E. A dynamic and multilocus metabolic regulation strategy using quorum-sensing-controlled bacterial small RNA. Cell Rep 2021; 36:109413. [PMID: 34289355 DOI: 10.1016/j.celrep.2021.109413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/30/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Metabolic regulation strategies have been developed to redirect metabolic fluxes to production pathways. However, it is difficult to screen out target genes that, when repressed, improve yield without affecting cell growth. Here, we report a strategy using a quorum-sensing system to control small RNA transcription, allowing cell-density-dependent repression of target genes. This strategy is shown with convenient operation, dynamic repression, and availability for simultaneous regulation of multiple genes. The parameters Ai, Am, and RA (3-oxohexanoyl-homoserine lactone [AHL] concentrations at which half of the maximum repression and the maximum repression were reached and value of the maximum repression when AHL was added manually, respectively) are defined and introduced to characterize repression curves, and the variant LuxRI58N is identified as the most suitable tuning factor for shake flask culture. Moreover, it is shown that dynamic overexpression of the Hfq chaperone is the key to combinatorial repression without disruptions on cell growth. To show a broad applicability, the production titers of pinene, pentalenene, and psilocybin are improved by 365.3%, 79.5%, and 302.9%, respectively, by applying combinatorial dynamic repression.
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Affiliation(s)
- Shao-Heng Bao
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Hui Jiang
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Ling-Yun Zhu
- College of Arts and Sciences, National University of Defense Technology, Changsha, PRC
| | - Ge Yao
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Peng-Gang Han
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Xiu-Kun Wan
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Kang Wang
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Tian-Yu Song
- State Key Laboratory of NBC Protection for Civilian, Beijing, PRC
| | - Chang-Jun Liu
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC
| | - Shan Wang
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC
| | - Zhe-Yang Zhang
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC
| | - Dong-Yi Zhang
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC; College of Arts and Sciences, National University of Defense Technology, Changsha, PRC.
| | - Er Meng
- Hunan Key Laboratory of Economic Crops, Genetic Improvement, and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, Hunan 411201, PRC.
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11
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Wang Y, Wu J, Lv M, Shao Z, Hungwe M, Wang J, Bai X, Xie J, Wang Y, Geng W. Metabolism Characteristics of Lactic Acid Bacteria and the Expanding Applications in Food Industry. Front Bioeng Biotechnol 2021; 9:612285. [PMID: 34055755 PMCID: PMC8149962 DOI: 10.3389/fbioe.2021.612285] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/16/2021] [Indexed: 12/31/2022] Open
Abstract
Lactic acid bacteria are a kind of microorganisms that can ferment carbohydrates to produce lactic acid, and are currently widely used in the fermented food industry. In recent years, with the excellent role of lactic acid bacteria in the food industry and probiotic functions, their microbial metabolic characteristics have also attracted more attention. Lactic acid bacteria can decompose macromolecular substances in food, including degradation of indigestible polysaccharides and transformation of undesirable flavor substances. Meanwhile, they can also produce a variety of products including short-chain fatty acids, amines, bacteriocins, vitamins and exopolysaccharides during metabolism. Based on the above-mentioned metabolic characteristics, lactic acid bacteria have shown a variety of expanded applications in the food industry. On the one hand, they are used to improve the flavor of fermented foods, increase the nutrition of foods, reduce harmful substances, increase shelf life, and so on. On the other hand, they can be used as probiotics to promote health in the body. This article reviews and prospects the important metabolites in the expanded application of lactic acid bacteria from the perspective of bioengineering and biotechnology.
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Affiliation(s)
- Yaqi Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jiangtao Wu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Mengxin Lv
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Zhen Shao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Meluleki Hungwe
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jinju Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaojia Bai
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jingli Xie
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yanping Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Weitao Geng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
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12
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Yamamoto C, Toyoshima M, Kitamura S, Ueno Y, Akimoto S, Toya Y, Shimizu H. Estimation of linear and cyclic electron flows in photosynthesis based on 13C-metabolic flux analysis. J Biosci Bioeng 2020; 131:277-282. [PMID: 33229211 DOI: 10.1016/j.jbiosc.2020.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 11/25/2022]
Abstract
Photosynthetic organisms produce ATP and NADPH using light as an energy source and further utilize these cofactors during metabolism. Photosynthesis involves linear and cyclic electron flows; as the cyclic electron flow produces ATP more effectively than the linear electron flow without NADPH, the cell efficiently adjusts ATP and NADPH production using the two different pathways. Nevertheless, direct measurement of ATP and NADPH production during photosynthesis has been difficult. In the present study, the photosynthetic ATP and NADPH production rates of Synechocystis sp. PCC 6803 under three different single peak wavelength lights (blue: 470 nm, R630: 630 nm, and R680: 680 nm) were evaluated based on 13C-metabolic flux analysis (13C-MFA) by considering the mass balance of ATP and NADPH between photosynthesis and metabolism. The ratios of ATP/NADPH production via photosynthesis were estimated as 3.13, 1.70, and 2.10 under blue, R630, and R680 light conditions, respectively. Moreover, the linear and cyclic electron flow ratios were estimated to be 1.1-2.2, 0.2-0.5, and 0.5-1.0 under blue, R630, and R680 light conditions, respectively. The predicted linear and cyclic electron flow ratios were consistent with the excitation ratio between photosystems I and II, as observed in the steady-state fluorescence spectra.
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Affiliation(s)
- Chiaki Yamamoto
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masakazu Toyoshima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshifumi Ueno
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Seiji Akimoto
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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13
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Wang Y, Wondisford FE, Song C, Zhang T, Su X. Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes. Metabolites 2020; 10:metabo10110447. [PMID: 33172051 PMCID: PMC7694648 DOI: 10.3390/metabo10110447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/02/2023] Open
Abstract
Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates’ labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.
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Affiliation(s)
- Yujue Wang
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Fredric E. Wondisford
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
| | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH 43210, USA;
| | - Teng Zhang
- Department of Mathematics, University of Central Florida, Orlando, FL 32816, USA;
| | - Xiaoyang Su
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Correspondence: ; Tel.: +1-732-235-5447
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14
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Application of a Pyruvate-Producing Escherichia coli Strain LAFCPCPt-accBC-aceE: A Case Study for d-Lactate Production. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6030070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pyruvate, a potential precursor of various chemicals, is one of the fundamental chemicals produced by the fermentation process. We previously reported a pyruvate-producing Escherichia coli strain LAFCPCPt-accBC-aceE (PYR) that has the potential to be applied to the industrial production of pyruvate. In this study, the availability of the PYR strain for the production of pyruvate-derivative chemicals was evaluated using a d-lactate-producing strain (LAC) based on the PYR strain. The LAC strain expresses a d-lactate dehydrogenase-encoding gene from Lactobacillus bulgaricus under the control of a T7 expression system. The d-lactate productivity of the LAC strain was further improved by limiting aeration and changing the induction period for the expression of d-lactate dehydrogenase-encoding gene expression. Under combined conditions, the LAC strain produced d-lactate at 21.7 ± 1.4 g·L−1, which was compatible with the pyruvate production by the PYR strain (26.1 ± 0.9 g·L−1). These results suggest that we have succeeded in the effective conversion of pyruvate to d-lactate in the LAC strain, demonstrating the wide versatility of the parental PYR strain as basal strain for various chemicals production.
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15
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Yang D, Park SY, Park YS, Eun H, Lee SY. Metabolic Engineering of Escherichia coli for Natural Product Biosynthesis. Trends Biotechnol 2020; 38:745-765. [DOI: 10.1016/j.tibtech.2019.11.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/27/2022]
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16
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Im D, Hong J, Gu B, Sung C, Oh M. 13
C Metabolic Flux Analysis of
Escherichia coli
Engineered for Gamma‐Aminobutyrate Production. Biotechnol J 2020; 15:e1900346. [DOI: 10.1002/biot.201900346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/12/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Dae‐Kyun Im
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Jaeseung Hong
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Boncheol Gu
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Changmin Sung
- Doping Control CenterKorea Institute of Science and Technology 5 Hwarang‐ro 14‐gil, Seongbuk‐gu Seoul 02792 Korea
| | - Min‐Kyu Oh
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
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17
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Matsuoka Y, Kurata H. Computer-Aided Rational Design of Efficient NADPH Production System by Escherichia coli pgi Mutant Using a Mixture of Glucose and Xylose. Front Bioeng Biotechnol 2020; 8:277. [PMID: 32318559 PMCID: PMC7154054 DOI: 10.3389/fbioe.2020.00277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/16/2020] [Indexed: 12/02/2022] Open
Abstract
Lignocellulosic biomass can be hydrolyzed into two major sugars of glucose and xylose, and thus the strategy for the efficient consumption of both sugars is highly desirable. NADPH is the essential molecule for the production of industrially important value-added chemicals, and thus its availability is quite important. Escherichia coli mutant lacking the pgi gene encoding phosphoglucose isomerase (Pgi) has been preferentially used to overproduce the NADPH. However, there exists a disadvantage that the cell growth rate becomes low for the mutant grown on glucose. This limits the efficient NADPH production, and therefore, it is quite important to investigate how addition of different carbon source such as xylose (other than glucose) effectively improves the NADPH production. In this study, we have developed a kinetic model to propose an efficient NADPH production system using E. coli pgi-knockout mutant with a mixture of glucose and xylose. The proposed system adds xylose to glucose medium to recover the suppressed growth of the pgi mutant, and determines the xylose content to maximize the NADPH productivity. Finally, we have designed a mevalonate (MVA) production system by implementing ArcA overexpression into the pgi-knockout mutant using a mixture of glucose and xylose. In addition to NADPH overproduction, the accumulation of acetyl-CoA (AcCoA) is necessary for the efficient MVA production. In the present study, therefore, we considered to overexpress ArcA, where ArcA overexpression suppresses the TCA cycle, causing the overflow of AcCoA, a precursor of MVA. We predicted the xylose content that maximizes the MVA production. This approach demonstrates the possibility of a great progress in the computer-aided rational design of the microbial cell factories for useful metabolite production.
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Affiliation(s)
- Yu Matsuoka
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan.,Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Japan
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18
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Matsuda F, Maeda K, Okahashi N. Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming. Sci Rep 2020; 10:286. [PMID: 31937835 PMCID: PMC6959353 DOI: 10.1038/s41598-019-57146-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
Measurement of metabolic flux levels using stable isotope labeling has been successfully used to investigate metabolic redirection and reprogramming in living cells or tissues. The metabolic flux ratio between two reactions can be estimated from the 13C-labeling patterns of a few metabolites combined with the knowledge of atom mapping in the complicated metabolic network. However, it remains unclear whether an observed change in the labeling pattern of the metabolites is sufficient evidence of a shift in flux ratio between two metabolic states. In this study, a data analysis method was developed for the quantitative assessment of metabolic reprogramming. The Metropolis-Hastings algorithm was used with an in silico metabolic model to generate a probability distribution of metabolic flux levels under a condition in which the 13C-labeling pattern was observed. Reanalysis of literature data demonstrated that the developed method enables analysis of metabolic redirection using whole 13C-labeling pattern data. Quantitative assessment by Cohen’s effect size (d) enables a more detailed read-out of metabolic reprogramming information. The developed method will enable future applications of the metabolic isotopomer analysis to various targets, including cultured cells, whole tissues, and organs.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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19
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Liu C, He M, Wang Z, Xu J. Integrative Analysis of Terpenoid Profiles and Hormones from Fruits of Red-Flesh Citrus Mutants and Their Wild Types. Molecules 2019; 24:molecules24193456. [PMID: 31547628 PMCID: PMC6804237 DOI: 10.3390/molecules24193456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/16/2019] [Accepted: 09/21/2019] [Indexed: 12/21/2022] Open
Abstract
In citrus color mutants, the levels of carotenoid constituents and other secondary metabolites are different in their corresponding wild types. Terpenoids are closely related to coloration, bitterness, and flavor. In this study, terpenoid profiles and hormones in citrus fruits of two red-flesh mutants—Red Anliu orange and Red-flesh Guanxi pummelo—and their corresponding wild types were investigated using GC/MS, HPLC, and LC-MS/MS. Results showed that Red Anliu orange (high in carotenoids) and Anliu orange (low in carotenoids) accumulated low levels of limonoid aglycones but high levels of monoterpenoids; conversely, Red-flesh Guanxi pummelo (high in carotenoids) and Guanxi pummelo (deficient in carotenoids) accumulated high levels of limonoid aglycones but low levels of monoterpenoids. However, isopentenyl diphosphate was present at similar levels. A correlation analysis indicated that jasmonic and salicylic acids might play important roles in regulating terpenoid biosynthesis. Additionally, the similarities of carotenoid and volatile profiles between each mutant and its corresponding wild type were greater than those between the two mutants or the two wild types. The flux balance of terpenoid metabolism in citrus fruit tends toward stability among various citrus genera that have different terpenoid profiles. Bud mutations could influence metabolite profiles of citrus fruit to a limited extent.
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Affiliation(s)
- Cuihua Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, China.
| | - Min He
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zhuang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, China.
| | - Juan Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan 430070, China.
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20
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Yuan W, Lv S, Chen L, Zhao Y, Deng Z, Hong K. Production of sesterterpene ophiobolin by a bifunctional terpene synthase in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:8785-8797. [DOI: 10.1007/s00253-019-10103-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/05/2019] [Accepted: 08/26/2019] [Indexed: 12/01/2022]
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21
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Senoo S, Tandar ST, Kitamura S, Toya Y, Shimizu H. Light‐inducible flux control of triosephosphate isomerase on glycolysis in
Escherichia coli. Biotechnol Bioeng 2019; 116:3292-3300. [DOI: 10.1002/bit.27148] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/24/2019] [Accepted: 08/15/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Sachie Senoo
- Department of Bioinformatic Engineering, Graduate School of Information Science and TechnologyOsaka University Osaka Japan
| | - Sebastian Tommi Tandar
- Department of Bioinformatic Engineering, Graduate School of Information Science and TechnologyOsaka University Osaka Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and TechnologyOsaka University Osaka Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and TechnologyOsaka University Osaka Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and TechnologyOsaka University Osaka Japan
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22
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Optogenetic switch for controlling the central metabolic flux of Escherichia coli. Metab Eng 2019; 55:68-75. [DOI: 10.1016/j.ymben.2019.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/28/2019] [Accepted: 06/12/2019] [Indexed: 01/09/2023]
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23
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Ward VCA, Chatzivasileiou AO, Stephanopoulos G. Metabolic engineering of Escherichia coli for the production of isoprenoids. FEMS Microbiol Lett 2019; 365:4953741. [PMID: 29718190 DOI: 10.1093/femsle/fny079] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/25/2018] [Indexed: 12/22/2022] Open
Abstract
Metabolic engineering is the practice of using directed genetic manipulations to rewire cellular metabolism primarily with the aim to transform the organism into a single-celled chemical factory. Using biological processes, we can produce more complex chemicals in a more sustainable way. This is particularly important for chemicals which are hard to synthesize using traditional chemistry. However, cells have evolved for growth and must be engineered to produce a single chemical at commercially viable levels. This review focuses on the strategies used to rewire cellular metabolism to produce chemicals using isoprenoid production in Escherichia coli as an example that illustrates many of the challenges faced in metabolic engineering.
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Affiliation(s)
- Valerie C A Ward
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemical Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | | | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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GC-MS-based 13C metabolic flux analysis resolves the parallel and cyclic glucose metabolism of Pseudomonas putida KT2440 and Pseudomonas aeruginosa PAO1. Metab Eng 2019; 54:35-53. [DOI: 10.1016/j.ymben.2019.01.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 01/05/2023]
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25
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Kamiura R, Toya Y, Matsuda F, Shimizu H. Theophylline-inducible riboswitch accurately regulates protein expression at low level in Escherichia coli. Biotechnol Lett 2019; 41:743-751. [PMID: 30953309 DOI: 10.1007/s10529-019-02672-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/31/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Fine-tuning of enzyme expression at low levels is an important challenge for metabolic engineers. Here, theophylline-inducible riboswitch for translational regulation was evaluated. The background expression, translation rate, and time delay for its induction was reported. RESULTS To evaluate the effect of the amount of mRNA on its translation rate, transcription of the riboswitch RNA with red fluorescent protein (RFP) was controlled by the lac system with addition of isopropyl β-D-1-thiogalactopyranoside in Escherichia coli. Regardless of the amount of riboswitch mRNA, the translation of RFP was completely suppressed without theophylline during both growth and stationary phases. Furthermore, a strong positive correlation between theophylline concentration (0 to 1 mM) and specific RFP production rate was observed. The specific RFP production rate with the riboswitch was approximately 2.3% of that without the riboswitch. Furthermore, 60 min of time delay for RFP expression was observed after adding theophylline during the stationary phase. CONCLUSION Theophylline-inducible riboswitch precisely controls protein translation at low expression levels with significantly low background expression. It can emerge as a powerful tool for fine tuning of enzyme expression.
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Affiliation(s)
- Rikuto Kamiura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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26
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Kitamura S, Toya Y, Shimizu H. 13C-Metabolic Flux Analysis Reveals Effect of Phenol on Central Carbon Metabolism in Escherichia coli. Front Microbiol 2019; 10:1010. [PMID: 31134035 PMCID: PMC6514248 DOI: 10.3389/fmicb.2019.01010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/23/2019] [Indexed: 11/13/2022] Open
Abstract
Phenol is an important chemical product that can be used in a wide variety of applications, and it is currently produced from fossil resources. Fermentation production of phenol from renewable biomass resources by microorganisms is highly desirable for sustainable development. However, phenol toxicity hampers phenol production in industrial microorganisms such as Escherichia coli. In the present study, it was revealed that culturing E. coli in the presence of phenol not only decreased growth rate, but also biomass yield. This suggests that phenol affects the carbon flow of the metabolism, but the mechanism is unknown. To investigate the effect of phenol on the flux distribution of central carbon metabolism, 13C-metabolic flux analysis (13C-MFA) was performed on cells grown under different phenol concentrations (0, 0.1, and 0.15%). 13C-MFA revealed that the TCA cycle flux reduced by 25% increased acetate production from acetyl-CoA by 30% in the presence of 0.1% phenol. This trend of flux changes was emphasized at a phenol concentration of 0.15%. Although the expression level of citrate synthase, which catalyzes the first reaction of the TCA cycle, does not change regardless of phenol concentrations, the in vitro enzyme activity assay shows that the reaction was inhibited by phenol. These results suggest that the TCA cycle flux decreased due to phenol inhibition of citrate synthase; therefore, ATP could not be sufficiently produced by respiration, and growth rate decreased. Furthermore, since carbon was lost as acetate due to overflow metabolism, the biomass yield became low in the presence of phenol.
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Affiliation(s)
- Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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27
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Guo J, Cao Y, Liu H, Zhang R, Xian M, Liu H. Improving the production of isoprene and 1,3-propanediol by metabolically engineered Escherichia coli through recycling redox cofactor between the dual pathways. Appl Microbiol Biotechnol 2019; 103:2597-2608. [PMID: 30719552 DOI: 10.1007/s00253-018-09578-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/01/2018] [Accepted: 12/11/2018] [Indexed: 01/08/2023]
Abstract
The biosynthesis of isoprene by microorganisms is a promising green route. However, the yield of isoprene is limited due to the generation of excess NAD(P)H via the mevalonate (MVA) pathway, which converts more glucose into CO2 or undesired reduced by-products. The production of 1,3-propanediol (1,3-PDO) from glycerol is a typical NAD(P)H-consuming process, which restricts 1,3-PDO yield to ~ 0.7 mol/mol. In this study, we propose a strategy of redox cofactor balance by coupling the production of isoprene with 1,3-PDO fermentation. With the introduction and optimization of the dual pathways in an engineered Escherichia coli, ~ 85.2% of the excess NADPH from isoprene pathway was recycled for 1,3-PDO production. The best strain G05 simultaneously produced 665.2 mg/L isoprene and 2532.1 mg/L 1,3-PDO under flask fermentation conditions. The yields were 0.3 mol/mol glucose and 1.0 mol/mol glycerol, respectively, showing 3.3- and 4.3-fold improvements relative to either pathway independently. Since isoprene is a volatile organic compound (VOC) whereas 1,3-PDO is separated from the fermentation broth, their coproduction process does not increase the complexity or cost for the separation from each other. Hence, the presented strategy will be especially useful for developing efficient biocatalysts for other biofuels and biochemicals, which are driven by cofactor concentrations.
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Affiliation(s)
- Jing Guo
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujin Cao
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China
| | - Hui Liu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China
| | - Rubing Zhang
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China.
| | - Huizhou Liu
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Rd., Qingdao, 266101, China.
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Kamata K, Toya Y, Shimizu H. Effect of precise control of flux ratio between the glycolytic pathways on mevalonate production in Escherichia coli. Biotechnol Bioeng 2019; 116:1080-1088. [PMID: 30636280 DOI: 10.1002/bit.26923] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/19/2018] [Accepted: 01/09/2019] [Indexed: 12/14/2022]
Abstract
Mevalonate is a useful metabolite synthesized from three molecules of acetyl-CoA, consuming two molecules of NADPH. Escherichia coli ( E. coli) catabolizes glucose to acetyl-CoA via several routes, such as the Embden-Meyerhof-Parnas (EMP) and the oxidative pentose phosphate (oxPP) pathways. Although the oxPP pathway supplies NADPH, it is disadvantageous in terms of acetyl-CoA supply, compared with the EMP pathway. In this study, the optimal flux ratio between the EMP and oxPP pathways on the mevalonate yield was investigated. Expression level of pgi was controlled by isopropyl β-D-1-thiogalactopyranoside (IPTG) inducible promoter in an engineered mevalonate-producing E. coli strain. The relationship between the flux ratio and mevalonate yield was evaluated by changing the flux ratio by varying IPTG concentration. At the stationary phase, the mevalonate yield was maximum at an EMP flux of 39.7%, and was increased by 25% compared with that with no flux control (EMP flux of 70.4%). The optimal flux ratio was consistent with the theoretical value based on the mass balance of NADPH. The flux ratio between EMP and oxPP pathways affects the synthesis fluxes of mevalonate and acetate from acetyl-CoA. Fine tuning of the flux ratio would be necessary to achieve an optimized production of metabolites that require NADPH.
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Affiliation(s)
- Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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29
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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30
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Wang C, Liwei M, Park JB, Jeong SH, Wei G, Wang Y, Kim SW. Microbial Platform for Terpenoid Production: Escherichia coli and Yeast. Front Microbiol 2018; 9:2460. [PMID: 30369922 PMCID: PMC6194902 DOI: 10.3389/fmicb.2018.02460] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/25/2018] [Indexed: 11/13/2022] Open
Abstract
Terpenoids, also called isoprenoids, are a large and highly diverse family of natural products with important medical and industrial properties. However, a limited production of terpenoids from natural resources constrains their use of either bulk commodity products or high valuable products. Microbial production of terpenoids from Escherichia coli and yeasts provides a promising alternative owing to available genetic tools in pathway engineering and genome editing, and a comprehensive understanding of their metabolisms. This review summarizes recent progresses in engineering of industrial model strains, E. coli and yeasts, for terpenoids production. With advances of synthetic biology and systems biology, both strains are expected to present the great potential as a platform of terpenoid synthesis.
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Affiliation(s)
- Chonglong Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Mudanguli Liwei
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Ji-Bin Park
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Seong-Hee Jeong
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju, South Korea
| | - Gongyuan Wei
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yujun Wang
- Department of Marine Science, Qinzhou University, Qinzhou, China
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus), PMBBRC, Gyeongsang National University, Jinju, South Korea
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Nagai H, Masuda A, Toya Y, Matsuda F, Shimizu H. Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis. Metab Eng 2018; 47:1-9. [DOI: 10.1016/j.ymben.2018.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/07/2017] [Accepted: 02/25/2018] [Indexed: 01/07/2023]
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Ueda K, Nakajima T, Yoshikawa K, Toya Y, Matsuda F, Shimizu H. Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803. J Biosci Bioeng 2018; 126:38-43. [PMID: 29499995 DOI: 10.1016/j.jbiosc.2018.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 10/17/2022]
Abstract
The role of the oxidative pentose phosphate pathway (oxPPP) in Synechocystis sp. PCC 6803 under mixotrophic conditions was investigated by 13C metabolic flux analysis. Cells were cultured under low (10 μmol m-2 s-1) and high light intensities (100 μmol m-2 s-1) in the presence of glucose. The flux of CO2 fixation by ribulose bisphosphate carboxylase/oxygenase under the high light condition was approximately 3-fold higher than that under the low light condition. Although no flux of the oxPPP was observed under the high light condition, flux of 0.08-0.19 mmol gDCW-1 h-1 in the oxPPP was observed under the low light condition. The balance between the consumption and production of NADPH suggested that approximately 10% of the total NADPH production was generated by the oxPPP under the low light condition. The growth phenotype of a mutant with deleted zwf, which encodes glucose-6-phosphate dehydrogenase in the oxPPP, was compared to that of the parental strain under low and high light conditions. Growth of the Δzwf mutant nearly stopped during the late growth phase under the low light condition, whereas the growth rates of the two strains were identical under the high light condition. These results indicate that NADPH production in the oxPPP is essential for anabolism under low light conditions. The oxPPP appears to play an important role in producing NADPH from glucose and ATP to compensate for NADPH shortage under low light conditions.
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Affiliation(s)
- Kentaro Ueda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Tsubasa Nakajima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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33
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Masuda A, Toya Y, Shimizu H. Metabolic impact of nutrient starvation in mevalonate-producing Escherichia coli. BIORESOURCE TECHNOLOGY 2017; 245:1634-1640. [PMID: 28501379 DOI: 10.1016/j.biortech.2017.04.110] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work was to enhance mevalonate yield from glucose in Escherichia coli by essential nutrient starvations and to reveal these effects on the central carbon metabolism. Stationary phase culture without essential nutrients such as nitrogen, sulfur, and magnesium was evaluated using an engineered E. coli introducing mvaE and mvaS genes from Enterococcus faecalis. Sulfur starvation resulted in the highest mevalonate yield of 0.61C-molC-mol-1 from glucose. The metabolic impacts of nutrient starvation were investigated by 13C-metabolic flux analysis. Under nitrogen starvation, the flux of the TCA cycle was large, causing high CO2 production. This was caused by degradation of mevalonate synthesis pathway enzymes. Under magnesium starvation, NADPH production was decreased, which limited mevalonate synthesis and promoted an overflow of acetate. Sulfur starvation not only suppressed the TCA cycle flux, but also supplied NADPH for mevalonate synthesis.
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Affiliation(s)
- Ami Masuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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34
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35
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Matsuda F, Toya Y, Shimizu H. Learning from quantitative data to understand central carbon metabolism. Biotechnol Adv 2017; 35:971-980. [DOI: 10.1016/j.biotechadv.2017.09.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 09/01/2017] [Accepted: 09/14/2017] [Indexed: 12/23/2022]
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36
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Toya Y, Ohashi S, Shimizu H. Optimal 13C-labeling of glycerol carbon source for precise flux estimation in Escherichia coli. J Biosci Bioeng 2017; 125:301-305. [PMID: 29107627 DOI: 10.1016/j.jbiosc.2017.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/01/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
Abstract
Glycerol is a promising carbon source for bio-production and is particularly attractive because it is produced in excess as a biodiesel byproduct. Elucidating the flux distribution of glycerol catabolism would greatly aid metabolic engineering, but 13C-labeling of glycerol has not yet been optimized for precise flux estimations. In this study, an Escherichia coli wild type strain was aerobically cultured using glycerol as the sole carbon source. [1,3-13C], [2-13C], and [U-13C] glycerols were independently mixed with an equal amount of naturally labeled glycerol; these mixtures were used as 13C-labeled substrates, and flux distributions during exponential growth were estimated based on 13C-enrichment of proteinogenic amino acids. The glycerol catabolism pathway in E. coli has four branches: the oxidative pentose phosphate pathway (PP), Entner-Doudoroff pathway (ED), and malic enzyme (ME) pathways, and the glyoxylate shunt (GX). The 95% confidence intervals of these fluxes were compared across the 13C-labeling experiments. The [2-13C] and [U-13C] glycerols, but not [1,3-13C] glycerol allowed precise characterization of the PP, ED, and ME pathway fluxes. All three types of 13C-labeling aided in successfully determining the GX flux. Based on the above estimated flux distribution, various patterns of 13C-labeling of glycerol were computationally generated. These in silico experiments revealed that the sole use of [2-13C] glycerol or [1,3-13C] glycerol is optimal for precise flux estimation, where simultaneous using glycerols with different types of 13C-labeling failed to improve flux estimation as assessed by confidence intervals.
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Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shugo Ohashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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37
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Liu H, Cheng T, Zou H, Zhang H, Xu X, Sun C, Aboulnaga E, Cheng Z, Zhao G, Xian M. High titer mevalonate fermentation and its feeding as a building block for isoprenoids (isoprene and sabinene) production in engineered Escherichia coli. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.07.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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38
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The oxidative TCA cycle operates during methanotrophic growth of the Type I methanotroph Methylomicrobium buryatense 5GB1. Metab Eng 2017; 42:43-51. [DOI: 10.1016/j.ymben.2017.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/19/2017] [Accepted: 05/20/2017] [Indexed: 11/18/2022]
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39
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Metabolic engineering of Synechocystis sp. PCC 6803 for enhanced ethanol production based on flux balance analysis. Bioprocess Biosyst Eng 2017; 40:791-796. [DOI: 10.1007/s00449-017-1744-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
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