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Sheremetieva M, Anufriev K, Khlebodarova T, Kolchanov N, Yanenko A. Rational metabolic engineering of Corynebacterium glutamicum to create a producer of L-valine. Vavilovskii Zhurnal Genet Selektsii 2022; 26:743-757. [PMID: 36694718 PMCID: PMC9834717 DOI: 10.18699/vjgb-22-90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 01/06/2023] Open
Abstract
L-Valine is one of the nine amino acids that cannot be synthesized de novo by higher organisms and must come from food. This amino acid not only serves as a building block for proteins, but also regulates protein and energy metabolism and participates in neurotransmission. L-Valine is used in the food and pharmaceutical industries, medicine and cosmetics, but primarily as an animal feed additive. Adding L-valine to feed, alone or mixed with other essential amino acids, allows for feeds with lower crude protein content, increases the quality and quantity of pig meat and broiler chicken meat, as well as improves reproductive functions of farm animals. Despite the fact that the market for L-valine is constantly growing, this amino acid is not yet produced in our country. In modern conditions, the creation of strains-producers and organization of L-valine production are especially relevant for Russia. One of the basic microorganisms most commonly used for the creation of amino acid producers, along with Escherichia coli, is the soil bacterium Corynebacterium glutamicum. This review is devoted to the analysis of the main strategies for the development of L- valine producers based on C. glutamicum. Various aspects of L-valine biosynthesis in C. glutamicum are reviewed: process biochemistry, stoichiometry and regulation, enzymes and their corresponding genes, export and import systems, and the relationship of L-valine biosynthesis with central cell metabolism. Key genetic elements for the creation of C. glutamicum-based strains-producers are identified. The use of metabolic engineering to enhance L-valine biosynthesis reactions and to reduce the formation of byproducts is described. The prospects for improving strains in terms of their productivity and technological characteristics are shown. The information presented in the review can be used in the production of producers of other amino acids with a branched side chain, namely L-leucine and L-isoleucine, as well as D-pantothenate.
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Affiliation(s)
| | - K.E. Anufriev
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
| | - T.M. Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N.A. Kolchanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.S. Yanenko
- NRC “Kurchatov Institute”, Kurchatov Genomic Center, Moscow, Russia
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Fu B, Yang L, Chen Q, Zhang Q, Zhang L, Yu P. Enhanced biosynthesis of physiologically active vitamin D3 by constructing recombinant Escherichia coli BL21 with a multienzyme system. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Golubyatnikov V, Akinshin A, Ayupova N, Minushkina L. Stratifications and foliations in phase portraits of gene network models. Vavilovskii Zhurnal Genet Selektsii 2022; 26:758-764. [PMID: 36694713 PMCID: PMC9837163 DOI: 10.18699/vjgb-22-91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Periodic processes of gene network functioning are described with good precision by periodic trajectories (limit cycles) of multidimensional systems of kinetic-type differential equations. In the literature, such systems are often called dynamical, they are composed according to schemes of positive and negative feedback between components of these networks. The variables in these equations describe concentrations of these components as functions of time. In the preparation of numerical experiments with such mathematical models, it is useful to start with studies of qualitative behavior of ensembles of trajectories of the corresponding dynamical systems, in particular, to estimate the highest likelihood domain of the initial data, to solve inverse problems of parameter identification, to list the equilibrium points and their characteristics, to localize cycles in the phase portraits, to construct stratification of the phase portraits to subdomains with different qualities of trajectory behavior, etc. Such an à priori geometric analysis of the dynamical systems is quite analogous to the basic section "Investigation of functions and plot of their graphs" of Calculus, where the methods of qualitative studies of shapes of curves determined by equations are exposed. In the present paper, we construct ensembles of trajectories in phase portraits of some dynamical systems. These ensembles are 2-dimensional surfaces invariant with respect to shifts along the trajectories. This is analogous to classical construction in analytic mechanics, i. e. the level surfaces of motion integrals (energy, kinetic moment, etc.). Such surfaces compose foliations in phase portraits of dynamical systems of Hamiltonian mechanics. In contrast with this classical mechanical case, the foliations considered in this paper have singularities: all their leaves have a non-empty intersection, they contain limit cycles on their boundaries. Description of the phase portraits of these systems at the level of their stratifications, and that of ensembles of trajectories allows one to construct more realistic gene network models on the basis of methods of statistical physics and the theory of stochastic differential equations.
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Affiliation(s)
- V.P. Golubyatnikov
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - A.A. Akinshin
- Huawei Russian Research Institute, St. Petersburg, Russia
| | - N.B. Ayupova
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun 2022; 13:7282. [PMID: 36435948 PMCID: PMC9701214 DOI: 10.1038/s41467-022-35021-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/15/2022] [Indexed: 11/28/2022] Open
Abstract
Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN+) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN+-based reducing power. This is based on an orthogonal, NMN+-dependent glycolytic pathway in Escherichia coli which can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN+. With a throughput of >106 variants per iteration, the growth selection discovers a Lactobacillus pentosus NADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme's global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme's access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Sarah Maxel
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
| | - Yulai Zhang
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
| | - Karissa C Kenney
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Youtian Cui
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Emma Luu
- Genome Center, University of California Davis, Davis, CA, 95616, USA
| | - Justin B Siegel
- Genome Center, University of California Davis, Davis, CA, 95616, USA
- Department of Chemistry, Molecular Medicine University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine University of California, Davis, Davis, CA, USA
| | - Gregory A Weiss
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA
- Department Materials Science and Engineering, University of California Irvine, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA
| | - Han Li
- Department Chemical and Biomolecular Engineering University of California Irvine, Irvine, CA, 92697, USA.
- Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92697, USA.
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Kim YE, Cho KH, Bang I, Kim CH, Ryu YS, Kim Y, Choi EM, Nong LK, Kim D, Lee SK. Characterization of an Entner-Doudoroff pathway-activated Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:120. [PMID: 36352474 PMCID: PMC9648032 DOI: 10.1186/s13068-022-02219-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Escherichia coli have both the Embden-Meyerhof-Parnas pathway (EMPP) and Entner-Doudoroff pathway (EDP) for glucose breakdown, while the EDP primarily remains inactive for glucose metabolism. However, EDP is a more favorable route than EMPP for the production of certain products. RESULTS EDP was activated by deleting the pfkAB genes in conjunction with subsequent adaptive laboratory evolution (ALE). The evolved strains acquired mutations in transcriptional regulatory genes for glycolytic process (crp, galR, and gntR) and in glycolysis-related genes (gnd, ptsG, and talB). The genotypic, transcriptomic and phenotypic analyses of those mutations deepen our understanding of their beneficial effects on cellulosic biomass bio-conversion. On top of these scientific understandings, we further engineered the strain to produce higher level of lycopene and 3-hydroxypropionic acid. CONCLUSIONS These results indicate that the E. coli strain has innate capability to use EDP in lieu of EMPP for glucose metabolism, and this versatility can be harnessed to further engineer E. coli for specific biotechnological applications.
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Affiliation(s)
- Ye Eun Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kyung Hyun Cho
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Ina Bang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Chang Hee Kim
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea
| | - Young Shin Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yuchan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Eun Mi Choi
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Department of Biomedical Engineering, UNIST, Ulsan, 44919, Republic of Korea.
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Ghiffary MR, Prabowo CPS, Adidjaja JJ, Lee SY, Kim HU. Systems metabolic engineering of Corynebacterium glutamicum for the efficient production of β-alanine. Metab Eng 2022; 74:121-129. [DOI: 10.1016/j.ymben.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Bruno Bühler,
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Fine tuning the glycolytic flux ratio of EP-bifido pathway for mevalonate production by enhancing glucose-6-phosphate dehydrogenase (Zwf) and CRISPRi suppressing 6-phosphofructose kinase (PfkA) in Escherichia coli. Microb Cell Fact 2021; 20:32. [PMID: 33531004 PMCID: PMC7852082 DOI: 10.1186/s12934-021-01526-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Natural glycolysis encounters the decarboxylation of glucose partial oxidation product pyruvate into acetyl-CoA, where one-third of the carbon is lost at CO2. We previously constructed a carbon saving pathway, EP-bifido pathway by combining Embden-Meyerhof-Parnas Pathway, Pentose Phosphate Pathway and "bifid shunt", to generate high yield acetyl-CoA from glucose. However, the carbon conversion rate and reducing power of this pathway was not optimal, the flux ratio of EMP pathway and pentose phosphate pathway (PPP) needs to be precisely and dynamically adjusted to improve the production of mevalonate (MVA). RESULT Here, we finely tuned the glycolytic flux ratio in two ways. First, we enhanced PPP flux for NADPH supply by replacing the promoter of zwf on the genome with a set of different strength promoters. Compared with the previous EP-bifido strains, the zwf-modified strains showed obvious differences in NADPH, NADH, and ATP synthesis levels. Among them, strain BP10BF accumulated 11.2 g/L of MVA after 72 h of fermentation and the molar conversion rate from glucose reached 62.2%. Second, pfkA was finely down-regulated by the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system. The MVA yield of the regulated strain BiB1F was 8.53 g/L, and the conversion rate from glucose reached 68.7%. CONCLUSION This is the highest MVA conversion rate reported in shaken flask fermentation. The CRISPRi and promoter fine-tuning provided an effective strategy for metabolic flux redistribution in many metabolic pathways and promotes the chemicals production.
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Jiang Y, Sheng Q, Wu XY, Ye BC, Zhang B. l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process. Crit Rev Biotechnol 2020; 41:172-185. [PMID: 33153325 DOI: 10.1080/07388551.2020.1844625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As an important semi-essential amino acid, l-arginine is extensively used in the food and pharmaceutical fields. At present, l-arginine production depends on cost-effective, green, and sustainable microbial fermentation by using a renewable carbon source. To enhance its fermentative production, various metabolic engineering strategies have been employed, which provide valid paths for reducing the cost of l-arginine production. This review summarizes recent advances in molecular biology strategies for the optimization of l-arginine-producing strains, including manipulating the principal metabolic pathway, modulating the carbon metabolic pathway, improving the intracellular biosynthesis of cofactors and energy usage, manipulating the assimilation of ammonia, improving the transportation and membrane permeability, and performing biosensor-assisted high throughput screening, providing useful insight into the current state of l-arginine production.
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Affiliation(s)
- Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China
| | - Qi Sheng
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang, China.,College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, China
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Yu Y, Shao M, Li D, Fan F, Xu H, Lu F, Bi C, Zhu X, Zhang X. Construction of a carbon-conserving pathway for glycolate production by synergetic utilization of acetate and glucose in Escherichia coli. Metab Eng 2020; 61:152-159. [PMID: 32531344 DOI: 10.1016/j.ymben.2020.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/05/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Glycolate is a bulk chemical which has been widely used in textile, food processing, and pharmaceutical industries. Glycolate can be produced from sugars by microbial fermentation. However, when using glucose as the sole carbon source, the theoretical maximum carbon molar yield of glycolate is 0.67 mol/mol due to the loss of carbon as CO2. In this study, a synergetic system for simultaneous utilization of acetate and glucose was designed to increase the carbon yield. The main function of glucose is to provide NADPH while acetate to provide the main carbon backbone for glycolate production. Theoretically, 1 glucose and 5 acetate can produce 6 glycolate, and the carbon molar yield can be increased to 0.75 mol/mol. The whole synthetic pathway was divided into two modules, one for converting acetate to glycolate and another to utilize glucose to provide NADPH. After engineering module I through activation of acs, gltA, aceA and ycdW, glycolate titer increased from 0.07 to 2.16 g/L while glycolate yields increased from 0.04 to 0.35 mol/mol-acetate and from 0.03 to 1.04 mol/mol-glucose. Module II was then engineered to increase NADPH supply. Through deletion of pfkA, pfkB, ptsI and sthA genes as well as upregulating zwf, pgl and tktA, glycolate titer increased from 2.16 to 4.86 g/L while glycolate yields increased from 0.35 to 0.82 mol/mol-acetate and from 1.04 to 6.03 mol/mol-glucose. The activities of AceA and YcdW were further increased to pull the carbon flux to glycolate, which increased glycolate yield from 0.82 to 0.92 mol/mol-acetate. Fed-batch fermentation of the final strain NZ-Gly303 produced 73.3 g/L glycolate with a productivity of 1.04 g/(L·h). The acetate to glycolate yield was 0.85 mol/mol (1.08 g/g), while glucose to glycolate yield was 6.1 mol/mol (2.58 g/g). The total carbon molar yield was 0.60 mol/mol, which reached 80% of the theoretical value.
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Affiliation(s)
- Yong Yu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Mengyao Shao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Di Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hongtao Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Huang M, Zhao Y, Feng L, Zhu L, Zhan L, Chen X. Role of the ClpX from Corynebacterium crenatum involved in stress responses and energy metabolism. Appl Microbiol Biotechnol 2020; 104:5505-5517. [PMID: 32300856 DOI: 10.1007/s00253-020-10597-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 02/04/2023]
Abstract
ClpX and ClpP are involved in many important functions, including stress responses and energy metabolism, in microorganisms. However, the ClpX and ClpP of microbes used in industrial scale have rarely been studied. Industrial bacterial fermentation experiences a variety of stresses, and energy metabolism is extremely important for industrial bacteria. Thus, the role played by the ClpX and ClpP of industrial bacteria in fermentation should be investigated. Most microorganisms have a single clpP gene, while Corynebacterium crenatum AS 1.542 possesses two clpPs. Herein, the clpX, clpP1, and clpP2 of C. crenatum were cloned, and its fusion protein was expressed and characterized. We also constructed clpX deletion mutant and complementation strain. Results indicate that ClpX serves an important function in thermal, pH, and ethanol stresses. It is also involved in NADPH synthesis and glucose consumption during fermentation.
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Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China.,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China. .,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China.
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12
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Wu XY, Guo XY, Zhang B, Jiang Y, Ye BC. Recent Advances of L-ornithine Biosynthesis in Metabolically Engineered Corynebacterium glutamicum. Front Bioeng Biotechnol 2020; 7:440. [PMID: 31998705 PMCID: PMC6962107 DOI: 10.3389/fbioe.2019.00440] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/11/2019] [Indexed: 12/31/2022] Open
Abstract
L-ornithine, a valuable non-protein amino acid, has a wide range of applications in the pharmaceutical and food industries. Currently, microbial fermentation is a promising, sustainable, and environment-friendly method to produce L-ornithine. However, the industrial production capacity of L-ornithine by microbial fermentation is low and rarely meets the market demands. Various strategies have been employed to improve the L-ornithine production titers in the model strain, Corynebacterium glutamicum, which serves as a major indicator for improving the cost-effectiveness of L-ornithine production by microbial fermentation. This review focuses on the development of high L-ornithine-producing strains by metabolic engineering and reviews the recent advances in breeding strategies, such as reducing by-product formation, improving the supplementation of precursor glutamate, releasing negative regulation and negative feedback inhibition, increasing the supply of intracellular cofactors, modulating the central metabolic pathway, enhancing the transport system, and adaptive evolution for improving L-ornithine production.
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Affiliation(s)
- Xiao-Yu Wu
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiao-Yan Guo
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bin Zhang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yan Jiang
- Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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Tozlu C, Şahin E, Serencam H, Dertli E. Production of enantiomerically enriched chiral carbinols using Weissella paramesenteroides as a novel whole cell biocatalyst. BIOCATAL BIOTRANSFOR 2019. [DOI: 10.1080/10242422.2019.1568416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Caner Tozlu
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, Turkey
| | - Engin Şahin
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, Turkey
| | - Hüseyin Serencam
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, Turkey
| | - Enes Dertli
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, Turkey
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14
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Öksüz S, Şahin E, Dertli E. Synthesis of Enantiomerically Enriched Drug Precursors by Lactobacillus paracasei BD87E6 as a Biocatalyst. Chem Biodivers 2018; 15:e1800028. [PMID: 29667758 DOI: 10.1002/cbdv.201800028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/12/2018] [Indexed: 01/13/2023]
Abstract
Global sales of single enantiomeric drug products are growing at an alarming rate every year. A total of 7 bacterial strains were screened for their ability to reduce acetophenones to its corresponding alcohol. Among these strains Lactobacillus paracasei BD87E6 was found to be the most successful biocatalyst to reduce the ketones to the corresponding alcohols. The reaction conditions were systematically optimized for the reducing agent Lactobacillus paracasei BD87E6, which showed high enantioselectivity and conversion for the bioreduction. The preparative scale asymmetric reduction of 3-methoxyacetophenone (1h) by Lactobacillus paracasei BD87E6 gave (R)-1-(3-methoxyphenyl)ethanol (2h) with 92% yield and 99% enantiomeric excess. Compound 2h could be used for the synthesis of (S)-rivastigmine which has a great potential for the treatment of Alzheimer's disease. This study demonstrates that Lactobacillus paracasei BD87E6 can be used as a biocatalyst to obtain chiral carbinol with excellent yield and selectivity. The whole cell catalyzed the reductions of ketone substrates on the preparative scale, demonstrating that Lactobacillus paracasei BD87E6 would be a valuable biocatalyst for the preparation of chiral aromatic alcohols of pharmaceutical interest.
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Affiliation(s)
- Selda Öksüz
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, 69000, Turkey
| | - Engin Şahin
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, 69000, Turkey
| | - Enes Dertli
- Department of Food Engineering, Faculty of Engineering, Bayburt University, Bayburt, 69000, Turkey
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15
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Holistic bioengineering: rewiring central metabolism for enhanced bioproduction. Biochem J 2017; 474:3935-3950. [PMID: 29146872 PMCID: PMC5688466 DOI: 10.1042/bcj20170377] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/29/2022]
Abstract
What does it take to convert a living organism into a truly productive biofactory? Apart from optimizing biosynthesis pathways as standalone units, a successful bioengineering approach must bend the endogenous metabolic network of the host, and especially its central metabolism, to support the bioproduction process. In practice, this usually involves three complementary strategies which include tuning-down or abolishing competing metabolic pathways, increasing the availability of precursors of the desired biosynthesis pathway, and ensuring high availability of energetic resources such as ATP and NADPH. In this review, we explore these strategies, focusing on key metabolic pathways and processes, such as glycolysis, anaplerosis, the TCA (tricarboxylic acid) cycle, and NADPH production. We show that only a holistic approach for bioengineering — considering the metabolic network of the host organism as a whole, rather than focusing on the production pathway alone — can truly mold microorganisms into efficient biofactories.
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16
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Santhanam S, Patil S, Shanmugam R, Dronamraju V.L. S, Balasundaram U, Baburaj B. Enantioselective reduction of aryl and hetero aryl methyl ketones using plant cell suspension cultures of Vigna radiata. BIOCATAL BIOTRANSFOR 2017. [DOI: 10.1080/10242422.2017.1315412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Swati Patil
- Department of Genetic Engineering, SRM University, Kattankulathur, India
| | - Ramu Shanmugam
- Department of Chemistry, SRM University, Kattankulathur, India
| | | | - Usha Balasundaram
- Department of Genetic Engineering, SRM University, Kattankulathur, India
| | - Baskar Baburaj
- Department of Chemistry, SRM University, Kattankulathur, India
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17
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Liu C, Ding Y, Xian M, Liu M, Liu H, Ma Q, Zhao G. Malonyl-CoA pathway: a promising route for 3-hydroxypropionate biosynthesis. Crit Rev Biotechnol 2017; 37:933-941. [PMID: 28078904 DOI: 10.1080/07388551.2016.1272093] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
3-Hydroxypropionate (3HP) is an attractive platform chemical, serving as a precursor to a variety of commodity chemicals like acrylate and acrylamide, as well as a monomer of a biodegradable plastic. To establish a sustainable way to produce these commercially important chemicals and materials, fermentative production of 3HP is widely investigated in recent years. It is reported that 3HP can be produced from several intermediates, such as glycerol, malonyl-CoA, and β-alanine. Among all these biosynthetic routes, the malonyl-CoA pathway has some distinct advantages, including a broad feedstock spectrum, thermodynamic feasibility, and redox neutrality. To date, this pathway has been successfully constructed in various species including Escherichia coli, yeast and cyanobacteria, and optimized through carbon flux redirection, enzyme screening and engineering, and an increasing supply of energy and cofactors, resulting in significantly enhanced 3HP titer up to 40 g/L. These results show the feasibility of commercial manufacturing of 3HP and its derivatives in the future.
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Affiliation(s)
- Changshui Liu
- a CAS Key Lab of Biobased Materials , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China.,b Institute of Oceanology , Chinese Academy of Sciences , Qingdao , China
| | - Yamei Ding
- b Institute of Oceanology , Chinese Academy of Sciences , Qingdao , China
| | - Mo Xian
- a CAS Key Lab of Biobased Materials , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China
| | - Min Liu
- a CAS Key Lab of Biobased Materials , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China
| | - Huizhou Liu
- a CAS Key Lab of Biobased Materials , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China
| | - Qingjun Ma
- b Institute of Oceanology , Chinese Academy of Sciences , Qingdao , China
| | - Guang Zhao
- a CAS Key Lab of Biobased Materials , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao , China
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18
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Chen C, Hong M, Chu J, Huang M, Ouyang L, Tian X, Zhuang Y. Blocking the flow of propionate into TCA cycle through a mutB knockout leads to a significant increase of erythromycin production by an industrial strain of Saccharopolyspora erythraea. Bioprocess Biosyst Eng 2016; 40:201-209. [DOI: 10.1007/s00449-016-1687-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/23/2016] [Indexed: 11/28/2022]
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19
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Ma W, Wang J, Li Y, Hu X, Shi F, Wang X. Enhancing pentose phosphate pathway in Corynebacterium glutamicum to improve l-isoleucine production. Biotechnol Appl Biochem 2016; 63:877-885. [PMID: 27010514 DOI: 10.1002/bab.1442] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 08/26/2015] [Indexed: 11/09/2022]
Abstract
Three genes, gnd, pgl, and fbp, relevant to the pentose phosphate pathway (PPP) were overexpressed in Corynebacterium glutamicum IWJ001, leading to increase of l-isoleucine production. The transcriptional levels of gnd, pgl, and fbp significantly increased in IWJ001/pDXW-8-gnd-fbp-pgl. Compared with the control strain IWJ001/pDXW-8, intracellular NADPH/NADP+ ratios in IWJ001/pDXW-8-gnd and IWJ001/pDXW-8-gnd-fbp cells grown for 36 H increased threefold and fourfold, respectively, indicating that overexpression of gnd and fbp redirected the carbon flux to PPP. Intracellular NADPH/NADP+ ratio in IWJ001/pDXW-8-gnd-fbp-pgl grown for 36 H was similar to IWJ001/pDXW-8, suggesting that the NADPH produced by PPP could be quickly consumed for l-isoleucine production. 10.9 and 28.96 g/L of l-isoleucine was produced in IWJ001/pDXW-8-gnd-fbp-pgl in shake flask cultivation and fed-batch fermentation, respectively. In addition, IWJ001/pDXW-8-gnd-fbp-pgl grew fast, its dry cell weight reached 49 g/L after 48 H, whereas the start strain IWJ001/pDXW-8 reached only 40 g/L. After 96 H fermentation, l-isoleucine yield on glucose in IWJ001/pDXW-8-gnd-fbp-pgl reached 0.138 g/g. The results demonstrate that carbon flux redirection to PPP is an efficient approach to enhance l-isoleucine production in C. glutamicum.
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Affiliation(s)
- Wenjian Ma
- School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Jianli Wang
- School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Ye Li
- School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
| | - Xiaoqing Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, People's Republic of China
| | - Feng Shi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, People's Republic of China
| | - Xiaoyuan Wang
- School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, People's Republic of China
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20
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Knudsen JD, Hägglöf C, Weber N, Carlquist M. Increased availability of NADH in metabolically engineered baker's yeast improves transaminase-oxidoreductase coupled asymmetric whole-cell bioconversion. Microb Cell Fact 2016; 15:37. [PMID: 26879378 PMCID: PMC4754910 DOI: 10.1186/s12934-016-0430-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/25/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae can be engineered to perform a multitude of different chemical reactions that are not programmed in its original genetic code. It has a large potential to function as whole-cell biocatalyst for one-pot multistep synthesis of various organic molecules, and it may thus serve as a powerful alternative or complement to traditional organic synthetic routes for new chemical entities (NCEs). However, although the selectivity in many cases is high, the catalytic activity is often low which results in low space-time-yields. In the case for NADH-dependent heterologous reductive reactions, a possible constraint is the availability of cytosolic NADH, which may be limited due to competition with native oxidative enzymes that act to maintain redox homeostasis. In this study, the effect of increasing the availability of cytosolic NADH on the catalytic activity of engineered yeast for transamination-reduction coupled asymmetric one-pot conversion was investigated. RESULTS A series of active whole-cell biocatalysts were constructed by over-expressing the (S)-selective ω-transaminase (VAMT) from Capsicum chinense together with the NADH-dependent (S)-selective alcohol dehydrogenase (SADH) originating from Rhodococcus erythropolis in strains with or without deletion of glycerol-3-phosphate dehydrogenases 1 and 2 (GPD1 and GPD2). The yeast strains were evaluated as catalysts for simultaneous: (a) kinetic resolution of the racemic mixture to (R)-1-phenylethylamine, and (b) reduction of the produced acetophenone to (S)-1-phenylethanol. For the gpd1Δgpd2Δ strain, cell metabolism was effectively used for the supply of both amine acceptors and the co-factor pyridoxal-5'-phosphate (PLP) for the ω-transaminase, as well as for regenerating NADH for the reduction. In contrast, there was nearly no formation of (S)-1-phenylethanol when using the control strain with intact GPDs and over-expressing the VAMT-SADH coupling. It was found that a gpd1Δgpd2Δ strain over-expressing SADH had a 3-fold higher reduction rate and a 3-fold lower glucose requirement than the strain with intact GPDs over-expressing SADH. CONCLUSIONS Overall the results demonstrate that the deletion of the GPD1 and GPD2 genes significantly increases activity of the whole-cell biocatalyst, and at the same time reduces the co-substrate demand in a process configuration where only yeast and sugar is added to drive the reactions, i.e. without addition of external co-factors or prosthetic groups.
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Affiliation(s)
- Jan Dines Knudsen
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden.
- The Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 4, 20126, Milano (MI), Italy.
| | - Cecilia Hägglöf
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden.
| | - Nora Weber
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden.
- Evolva, Duggingerstrasse 23, 4153, Reinach, Switzerland.
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, PO Box 124, 221 00, Lund, Sweden.
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21
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Cheap and environmentally sustainable stereoselective arylketones reduction by Lactobacillus reuteri whole cells. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2015.11.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Heider SAE, Wendisch VF. Engineering microbial cell factories: Metabolic engineering ofCorynebacterium glutamicumwith a focus on non-natural products. Biotechnol J 2015. [DOI: 10.1002/biot.201400590] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism. PLoS One 2015; 10:e0129837. [PMID: 26086807 PMCID: PMC4472234 DOI: 10.1371/journal.pone.0129837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 05/13/2015] [Indexed: 01/18/2023] Open
Abstract
NADPH regeneration capacity is attracting growing research attention due to its important role in resisting oxidative stress. Besides, NADPH availability has been regarded as a limiting factor in production of industrially valuable compounds. The central carbon metabolism carries the carbon skeleton flux supporting the operation of NADPH-regenerating enzyme and offers flexibility in coping with NADPH demand for varied intracellular environment. To acquire an insightful understanding of its NADPH regeneration capacity, the elementary mode method was employed to compute all elementary flux modes (EFMs) of a network representative of central carbon metabolism. Based on the metabolic flux distributions of these modes, a cluster analysis of EFMs with high NADPH regeneration rate was conducted using the self-organizing map clustering algorithm. The clustering results were used to study the relationship between the flux of total NADPH regeneration and the flux in each NADPH producing enzyme. The results identified several reaction combinations supporting high NADPH regeneration, which are proven to be feasible in cells via thermodynamic analysis and coincident with a great deal of previous experimental report. Meanwhile, the reaction combinations showed some common characteristics: there were one or two decarboxylation oxidation reactions in the combinations that produced NADPH and the combination constitution included certain gluconeogenesis pathways. These findings suggested cyclization pathways as a powerful way for NADPH regeneration capacity of bacterial central carbon metabolism.
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24
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Metabolic engineering of Escherichia coli to enhance acetol production from glycerol. Appl Microbiol Biotechnol 2015; 99:7945-52. [PMID: 26078109 DOI: 10.1007/s00253-015-6732-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/17/2015] [Accepted: 05/27/2015] [Indexed: 12/22/2022]
Abstract
Acetol, a C3 keto alcohol, is an important intermediate used to produce polyols and acrolein. To enhance acetol production from glycerol by Escherichia coli, a mutant (HJ02) was constructed by replacing the native glpK gene with the allele from E. coli Lin 43 and overexpression of yqhD, which encodes aldehyde oxidoreductase YqhD that converts methylglyoxal to acetol. Compared to the control strain without the glpK replacement, HJ02 had 5.5 times greater acetol production and a 53.4 % higher glycerol consumption rate. Then, glucose was added as a co-substrate to enhance NADPH availability and the ptsG gene was deleted in HJ02 (HJ04) to alleviate carbon catabolite repression, which led to a 30 % increase in the NADPH level and NADPH/NADP(+). Consequently, HJ04 accumulated up to 1.20 g/L of acetol, which is 69.0 % higher than that of HJ02. Furthermore, the gapA gene in HJ04 was silenced by antisense RNA (HJ05) to further enhance acetol production. The acetol concentration produced by HJ05 reached 1.82 g/L, which was 2.1 and 1.5 times higher than that of HJ02 and HJ04.Real-time PCR analysis indicates that glucose catabolism was rerouted from glycolysis to the oxidative pentose phosphate pathway in HJ05.
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25
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Nguyen AQD, Schneider J, Reddy GK, Wendisch VF. Fermentative production of the diamine putrescine: system metabolic engineering of corynebacterium glutamicum. Metabolites 2015; 5:211-31. [PMID: 25919117 PMCID: PMC4495370 DOI: 10.3390/metabo5020211] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/08/2015] [Accepted: 04/13/2015] [Indexed: 11/16/2022] Open
Abstract
Corynebacterium glutamicum shows great potential for the production of the glutamate-derived diamine putrescine, a monomeric compound of polyamides. A genome-scale stoichiometric model of a C. glutamicum strain with reduced ornithine transcarbamoylase activity, derepressed arginine biosynthesis, and an anabolic plasmid-addiction system for heterologous expression of E. coli ornithine decarboxylase gene speC was investigated by flux balance analysis with respect to its putrescine production potential. Based on these simulations, enhancing glycolysis and anaplerosis by plasmid-borne overexpression of the genes for glyceraldehyde 3-phosphate dehydrogenase and pyruvate carboxylase as well as reducing 2-oxoglutarate dehydrogenase activity were chosen as targets for metabolic engineering. Changing the translational start codon of the chromosomal gene for 2-oxoglutarate dehydrogenase subunit E1o to the less preferred TTG and changing threonine 15 of OdhI to alanine reduced 2-oxoglutarate dehydrogenase activity about five fold and improved putrescine titers by 28%. Additional engineering steps improved further putrescine production with the largest contributions from preventing the formation of the by-product N-acetylputrescine by deletion of spermi(di)ne N-acetyltransferase gene snaA and from overexpression of the gene for a feedback-resistant N-acetylglutamate kinase variant. The resulting C. glutamicum strain NA6 obtained by systems metabolic engineering accumulated two fold more putrescine than the base strain, i.e., 58.1 ± 0.2 mM, and showed a specific productivity of 0.045 g·g-1·h-1 and a yield on glucose of 0.26 g·g-1.
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Affiliation(s)
- Anh Q D Nguyen
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Jens Schneider
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Gajendar Komati Reddy
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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26
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Metabolic engineering of an ATP-neutral Embden-Meyerhof-Parnas pathway in Corynebacterium glutamicum: growth restoration by an adaptive point mutation in NADH dehydrogenase. Appl Environ Microbiol 2015; 81:1996-2005. [PMID: 25576602 DOI: 10.1128/aem.03116-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium glutamicum uses the Embden-Meyerhof-Parnas pathway of glycolysis and gains 2 mol of ATP per mol of glucose by substrate-level phosphorylation (SLP). To engineer glycolysis without net ATP formation by SLP, endogenous phosphorylating NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was replaced by nonphosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GapN) from Clostridium acetobutylicum, which irreversibly converts glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3-PG) without generating ATP. As shown recently (S. Takeno, R. Murata, R. Kobayashi, S. Mitsuhashi, and M. Ikeda, Appl Environ Microbiol 76:7154-7160, 2010, http://dx.doi.org/10.1128/AEM.01464-10), this ATP-neutral, NADPH-generating glycolytic pathway did not allow for the growth of Corynebacterium glutamicum with glucose as the sole carbon source unless hitherto unknown suppressor mutations occurred; however, these mutations were not disclosed. In the present study, a suppressor mutation was identified, and it was shown that heterologous expression of udhA encoding soluble transhydrogenase from Escherichia coli partly restored growth, suggesting that growth was inhibited by NADPH accumulation. Moreover, genome sequence analysis of second-site suppressor mutants that were able to grow faster with glucose revealed a single point mutation in the gene of non-proton-pumping NADH:ubiquinone oxidoreductase (NDH-II) leading to the amino acid change D213G, which was shared by these suppressor mutants. Since related NDH-II enzymes accepting NADPH as the substrate possess asparagine or glutamine residues at this position, D213G, D213N, and D213Q variants of C. glutamicum NDH-II were constructed and were shown to oxidize NADPH in addition to NADH. Taking these findings together, ATP-neutral glycolysis by the replacement of endogenous NAD-dependent GAPDH with NADP-dependent GapN became possible via oxidation of NADPH formed in this pathway by mutant NADPH-accepting NDH-II(D213G) and thus by coupling to electron transport phosphorylation (ETP).
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27
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Chen Y, Xu D, Fan L, Zhang X, Tan T. Manipulating multi-system of NADPH regulation in Escherichia coli for enhanced S-adenosylmethionine production. RSC Adv 2015. [DOI: 10.1039/c5ra02937f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
NADPH regulation strategies were applied to increase the availability of NADPH in theS-adenosylmethionine biosynthesis, and they are also potentially applicable to various processes for enhancing the NADPH-dependent chemicals production.
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Affiliation(s)
- Yawei Chen
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing
- PR China
| | - Duanbin Xu
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing
- PR China
| | - Lihai Fan
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing
- PR China
| | - Xu Zhang
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing
- PR China
| | - Tianwei Tan
- National Energy R&D Center for Biorefinery
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing
- PR China
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29
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Wendisch VF. Microbial production of amino acids and derived chemicals: synthetic biology approaches to strain development. Curr Opin Biotechnol 2014; 30:51-8. [PMID: 24922334 DOI: 10.1016/j.copbio.2014.05.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/15/2014] [Accepted: 05/18/2014] [Indexed: 10/25/2022]
Abstract
Amino acids are produced at the multi-million-ton-scale with fermentative production of l-glutamate and l-lysine alone being estimated to amount to more than five million tons in the year 2013. Metabolic engineering constantly improves productivities of amino acid producing strains, mainly Corynebacterium glutamicum and Escherichia coli strains. Classical mutagenesis and screening have been accelerated by combination with intracellular metabolite sensing. Synthetic biology approaches have allowed access to new carbon sources to realize a flexible feedstock concept. Moreover, new pathways for amino acid production as well as fermentative production of non-native compounds derived from amino acids or their metabolic precursors were developed. These include dipeptides, α,ω-diamines, α,ω-diacids, keto acids, acetylated amino acids and ω-amino acids.
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Affiliation(s)
- Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Germany.
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30
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Klatte S, Wendisch VF. Redox self-sufficient whole cell biotransformation for amination of alcohols. Bioorg Med Chem 2014; 22:5578-85. [PMID: 24894767 DOI: 10.1016/j.bmc.2014.05.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/02/2014] [Accepted: 05/09/2014] [Indexed: 10/25/2022]
Abstract
Whole cell biotransformation is an upcoming tool to replace common chemical routes for functionalization and modification of desired molecules. In the approach presented here the production of various non-natural (di)amines was realized using the designed whole cell biocatalyst Escherichia coli W3110/pTrc99A-ald-adh-ta with plasmid-borne overexpression of genes for an l-alanine dehydrogenase, an alcohol dehydrogenase and a transaminase. Cascading alcohol oxidation with l-alanine dependent transamination and l-alanine dehydrogenase allowed for redox self-sufficient conversion of alcohols to the corresponding amines. The supplementation of the corresponding (di)alcohol precursors as well as amino group donor l-alanine and ammonium chloride were sufficient for amination and redox cofactor recycling in a resting buffer system. The addition of the transaminase cofactor pyridoxal-phosphate and the alcohol dehydrogenase cofactor NAD(+) was not necessary to obtain complete conversion. Secondary and cyclic alcohols, for example, 2-hexanol and cyclohexanol were not aminated. However, efficient redox self-sufficient amination of aliphatic and aromatic (di)alcohols in vivo was achieved with 1-hexanol, 1,10-decanediol and benzylalcohol being aminated best.
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Affiliation(s)
- Stephanie Klatte
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany.
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Reddy GK, Wendisch VF. Characterization of 3-phosphoglycerate kinase from Corynebacterium glutamicum and its impact on amino acid production. BMC Microbiol 2014; 14:54. [PMID: 24593686 PMCID: PMC3996851 DOI: 10.1186/1471-2180-14-54] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 02/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum cg1790/pgk encodes an enzyme active as a 3-phosphoglycerate kinase (PGK) (EC 2.7.2.3) catalyzing phosphoryl transfer from 1,3-biphosphoglycerate (bPG) to ADP to yield 3-phosphoglycerate (3-PG) and ATP in substrate chain phosphorylation. RESULTS C. glutamicum 3-phosphoglycerate kinase was purified to homogeneity from the soluble fraction of recombinant E. coli. PGK(His) was found to be active as a homodimer with molecular weight of 104 kDa. The enzyme preferred conditions of pH 7.0 to 7.4 and required Mg²⁺ for its activity. PGK(His) is thermo labile and it has shown maximal activity at 50-65°C. The maximal activity of PGK(His) was estimated to be 220 and 150 U mg-1 with KM values of 0.26 and 0.11 mM for 3-phosphoglycerate and ATP, respectively. A 3-phosphoglycerate kinase negative C. glutamicum strain ∆pgk was constructed and shown to lack the ability to grow under glycolytic or gluconeogenic conditions unless PGK was expressed from a plasmid to restore growth. When pgk was overexpressed in L-arginine and L-ornithine production strains the production increased by 8% and by 17.5%, respectively. CONCLUSION Unlike many bacterial PGKs, C. glutamicum PGK is active as a homodimer. PGK is essential for growth of C. glutamicum with carbon sources requiring glycolysis and gluconeogenesis. Competitive inhibition by ADP reveals the critical role of PGK in gluconeogenesis by energy charge. Pgk overexpression improved the productivity in L-arginine and L-ornithine production strains.
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Affiliation(s)
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, University of Bielefeld, Bielefeld 33615, Germany.
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Enhancement of L-ornithine production by disruption of three genes encoding putative oxidoreductases in Corynebacterium glutamicum. J Ind Microbiol Biotechnol 2014; 41:573-8. [PMID: 24402505 DOI: 10.1007/s10295-013-1398-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
Abstract
Recently, Corynebacterium glutamicum has been shown to exhibit gluconate bypass activity, with two key enzymes, glucose dehydrogenase (GDH) and gluconate kinase, that provides an alternate route to 6-phosphogluconate formation. In this study, gene disruption analysis was used to examine possible metabolic functions of three proteins encoded by open reading frames having significant sequence similarity to GDH of Bacillus subtilis. Chromosomal in-frame deletion of three genes (NCgl0281, NCgl2582, and NCgl2053) encoding putative NADP⁺-dependent oxidoreductases led to the absence of GDH activity and correlated with increased specific glucose 6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase activities. This finding suggested that enhanced carbon flux from glucose was directed toward the oxidative pentose phosphate (PP) pathway, when the mutant was cultivated with 6 % glucose. Consequently, the mutant showed 72.4 % increased intracellular NADPH and 66.3 % increased extracellular L-ornithine production. The enhanced activities of the oxidative PP pathway in the mutant explain both the increased intracellular NADPH and the high extracellular concentration of L-ornithine. Thus, the observed metabolic changes in this work corroborate the importance of NADPH in L-ornithine production from C. glutamicum.
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Lorenz E, Klatte S, Wendisch VF. Reductive amination by recombinant Escherichia coli: whole cell biotransformation of 2-keto-3-methylvalerate to L-isoleucine. J Biotechnol 2013; 168:289-94. [PMID: 23831557 DOI: 10.1016/j.jbiotec.2013.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/17/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
Abstract
A whole cell biotransformation system for reductive amination has been studied in recombinant Escherichia coli cells. Reductive amination of 2-keto-3-methylvalerate to L-isoleucine by a two-enzyme-cascade was achieved by overproduction of endogenous L-alanine dependent transaminase AvtA and heterologous L-alanine dehydrogenase from Bacillus subtilis in recombinant E. coli. Up to 100 mM L-isoleucine were produced from 100 mM 2-keto-3-methylvalerate and 100 mM ammonium sulfate. Regeneration of NADH as cofactor in the whole cell system was driven by glucose catabolism. The effects of defined gene deletions in the central carbon metabolism on biotransformation were tested. Strains lacking the NuoG subunit of NADH:ubiquinone oxidoreductase (complex I) or aceA encoding the glyoxylate cycle enzyme isocitrate lyase exhibited increased biotransformation rates.
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Affiliation(s)
- Elisabeth Lorenz
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
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Gao J, Xu YY, Li FW, Ding G. Production of S-acetoin from diacetyl by Escherichia coli transformant cells that express the diacetyl reductase gene of Paenibacillus polymyxa ZJ-9. Lett Appl Microbiol 2013; 57:274-81. [PMID: 23701367 DOI: 10.1111/lam.12107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/16/2013] [Accepted: 05/18/2013] [Indexed: 12/01/2022]
Abstract
UNLABELLED S-acetoin (S-AC) is an important four-carbon chiral compound that has unique industrial applications in the asymmetric synthesis of valuable chiral specialty chemicals. However, previous studies showed that the usually low yield and optical purity of S-AC as well as the very high substrate cost have hindered the application of this compound. In the current work, a gene encoding diacetyl reductase (DAR) from a Paenibacillus polymyxa strain ZJ-9 was cloned and expressed in Escherichia coli. Whole cells of the recombinant E. coli were used to produce S-AC from diacetyl (DA). Under optimal conditions, S-AC with high optical purity (purity >99·9%) was obtained with a yield of 13·5 ± 0·24 and 39·4 ± 0·38 g l(-1) under batch and fed-batch culture conditions, respectively. This process featured the biotransformation of DA into S-AC using whole cells of engineered E. coli. The result is a considerable increase in the yield and optical purity of S-AC, which in turn facilitated the practical application of the compound. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrated a highly efficient new method to produce S-acetoin with higher than 99·9% optical purity from diacetyl using whole cells of engineered Escherichia coli. It will therefore decrease the production cost of S-acetoin and highlight its application in asymmetric synthesis of highly valuable chiral compounds.
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Affiliation(s)
- J Gao
- Schol of Chemical and Biological Engineering, Yancheng Institute of Technology, Yancheng, China
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Zahoor A, Lindner SN, Wendisch VF. Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products. Comput Struct Biotechnol J 2012; 3:e201210004. [PMID: 24688664 PMCID: PMC3962153 DOI: 10.5936/csbj.201210004] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/19/2012] [Accepted: 10/24/2012] [Indexed: 01/05/2023] Open
Abstract
Corynebacterium glutamicum is well known as the amino acid-producing workhorse of fermentation industry, being used for multi-million-ton scale production of glutamate and lysine for more than 60 years. However, it is only recently that extensive research has focused on engineering it beyond the scope of amino acids. Meanwhile, a variety of corynebacterial strains allows access to alternative carbon sources and/or allows production of a wide range of industrially relevant compounds. Some of these efforts set new standards in terms of titers and productivities achieved whereas others represent a proof-of-principle. These achievements manifest the position of C. glutamicum as an important industrial microorganism with capabilities far beyond the traditional amino acid production. In this review we focus on the state of the art of metabolic engineering of C. glutamicum for utilization of alternative carbon sources, (e.g. coming from wastes and unprocessed sources), and construction of C. glutamicum strains for production of new products such as diamines, organic acids and alcohols
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Affiliation(s)
- Ahmed Zahoor
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, University of Bielefeld, 33615 Bielefeld, Germany
| | - Steffen N Lindner
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, University of Bielefeld, 33615 Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, University of Bielefeld, 33615 Bielefeld, Germany
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