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Zhang L, Wang J, Gu S, Liu X, Hou M, Zhang J, Yang G, Zhao D, Dong R, Gao H. Biosynthesis of D-1,2,4-butanetriol promoted by a glucose-xylose dual metabolic channel system in engineered Escherichia coli. N Biotechnol 2024; 83:26-35. [PMID: 38936658 DOI: 10.1016/j.nbt.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
D-1,2,4-butanetriol (BT) is a widely used fine chemical that can be manufactured by engineered Escherichia coli expressing heterologous pathways and using xylose as a substrate. The current study developed a glucose-xylose dual metabolic channel system in an engineered E. coli and Combinatorially optimized it using multiple strategies to promote BT production. The carbon catabolite repression effects were alleviated by deleting the gene ptsG that encodes the major glucose transporter IICBGlc and mutating the gene crp that encodes the catabolite repressor protein, thereby allowing C-fluxes of both glucose and xylose into their respective metabolic channels separately and simultaneously, which increased BT production by 33% compared with that of the original MJ133K-1 strain. Then, the branch metabolic pathways of intermediates in the BT channel were investigated, the transaminase HisC, the ketoreductases DlD, OLD, and IlvC, and the aldolase MhpE and YfaU were identified as the enzymes for the branched metabolism of 2-keto-3-deoxy-xylonate, deletion of the gene hisC increased BT titer by 21.7%. Furthermore, the relationship between BT synthesis and the intracellular NADPH level was examined, and deletion of the gene pntAB that encodes a transhydrogenase resulted in an 18.1% increase in BT production. The combination of the above approaches to optimize the metabolic network increased BT production by 47.5%, resulting in 2.67 g/L BT in 24 deep-well plates. This study provides insights into the BT biosynthesis pathway and demonstrates effective strategies to increase BT production, which will promote the industrialization of the biosynthesis of BT.
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Affiliation(s)
- Lu Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jinbao Wang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Songhe Gu
- School of Life Science, Qufu Normal University, Qufu 273165, Shandong, China
| | - Xuedan Liu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Miao Hou
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jing Zhang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Ge Yang
- School of Life Science, Qufu Normal University, Qufu 273165, Shandong, China
| | - Dongxu Zhao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Runan Dong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haijun Gao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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2
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Lin Y, Liang M, Pang H, Wang Z, Bi H, Wei Y, Du L. Production of Gibberellins via a Non-Natural Pathway Using Steviol as a Substrate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:540-548. [PMID: 38131295 DOI: 10.1021/acs.jafc.3c06932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Gibberellins (GAs) are plant hormones widely used in agriculture. At present, GAs are produced by fermentation of the fungus Fusarium fujikuroi. However, fungal growth is too slow, resulting in slow fungal fermentation and a low yield. Here, to develop an alternative production source of GAs, an artificial pathway was engineered in Escherichia coli. By selecting and combining enzymes derived from plants and bacteria, a novel 4-enzyme pathway was successfully constructed to produce GAs using steviol, a readily available and less valuable byproduct during enzymatic refining of rebaudioside A, as a feedstock. Whole-cell biotransformation with E. coli strain expressing the novel pathway produced 71.17 ± 2.00 mg/L GA1 and a trace amount of GA3 from steviol in 48 h. This report presents a significant advancement in the fast production of GAs and establishes a method for the metabolism of terpenoids to produce target products in microbial hosts.
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Affiliation(s)
- Yu Lin
- Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning, Guangxi 530004, China
| | - Meng Liang
- Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning, Guangxi 530004, China
| | - Hao Pang
- Guangxi Key Laboratory of Bio-refinery, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Daling Road No. 98, Nanning, Guangxi 530007, China
| | - Zilong Wang
- Guangxi Key Laboratory of Bio-refinery, National Engineering Research Center for Non-Food Biorefinery, National Key Laboratory of Non-Food Biomass Energy Technology, Guangxi Academy of Sciences, Daling Road No. 98, Nanning, Guangxi 530007, China
| | - Hai Bi
- Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning, Guangxi 530004, China
| | - Yutuo Wei
- Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning, Guangxi 530004, China
| | - Liqin Du
- Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning, Guangxi 530004, China
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3
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Genetically Engineering Escherichia coli to Produce Xylitol from Corncob Hydrolysate without Lime Detoxification. Molecules 2023; 28:molecules28041550. [PMID: 36838538 PMCID: PMC9967598 DOI: 10.3390/molecules28041550] [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: 01/04/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Before fermentation with hemicellulosic hydrolysate as a substrate, it is generally necessary to detoxify the toxic substances that are harmful to microorganism growth. Cyclic AMP receptor protein (CRP) is a global regulator, and mutation of its key sites may have an important impact on E. coli virulence tolerance. Using corncob hydrolysate without ion-exchange or lime detoxification as the substrate, shake flask fermentation experiments showed that CRP mutant IS5-dG (I112L, T127G, A144T) produced 18.4 g/L of xylitol within 34 h, and the OD600 was 9.7 at 24 h; these values were 41.5% and 21.3% higher than those of the starting strain, IS5-d, respectively. This mutant produced 82 g/L of xylitol from corncob hydrolysate without ion-exchange or lime detoxification during fed-batch fermentation in a 15-L bioreactor, with a productivity of 1.04 g/L/h; these values were 173% and 174% higher than the starting strain, respectively. To our knowledge, this is the highest xylitol concentration and productivity produced by microbial fermentation using completely non-detoxified hemicellulosic hydrolysate as the substrate to date. This study also showed that alkali neutralization, high temperature sterilization, and fermentation of the hydrolysate had important effects on the xylose loss rate and xylitol production.
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Metabolomics and modelling approaches for systems metabolic engineering. Metab Eng Commun 2022; 15:e00209. [PMID: 36281261 PMCID: PMC9587336 DOI: 10.1016/j.mec.2022.e00209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering. Constraint-based models, such as genome scale models, have been used successfully to enhance the yield of desired compounds from engineered microbes, however, unlike kinetic or dynamic models, constraint-based models do not incorporate regulatory effects. Nevertheless, the lack of time-series metabolomic data generation has hindered the usefulness of dynamic models till today. In this review, we show that improvements in automation, dynamic real-time analysis and high throughput workflows can drive the generation of more quality data for dynamic models through time-series metabolomics data generation. Spatial metabolomics also has the potential to be used as a complementary approach to conventional metabolomics, as it provides information on the localization of metabolites. However, more effort must be undertaken to identify metabolites from spatial metabolomics data derived through imaging mass spectrometry, where machine learning approaches could prove useful. On the other hand, single-cell metabolomics has also seen rapid growth, where understanding cell-cell heterogeneity can provide more insights into efficient metabolic engineering of microbes. Moving forward, with potential improvements in automation, dynamic real-time analysis, high throughput workflows, and spatial metabolomics, more data can be produced and studied using machine learning algorithms, in conjunction with dynamic models, to generate qualitative and quantitative predictions to advance metabolic engineering efforts.
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5
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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] [Key Words] [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
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6
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Yuan X, Mao Y, Tu S, Lin J, Shen H, Yang L, Wu M. Increasing NADPH Availability for Xylitol Production via Pentose-Phosphate-Pathway Gene Overexpression and Embden-Meyerhof-Parnas-Pathway Gene Deletion in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9625-9631. [PMID: 34382797 DOI: 10.1021/acs.jafc.1c03283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cofactor availability is often a rate-limiting factor in the bioconversion of xylose to xylitol. The overexpression of pentose phosphate pathway genes and the deletion of Embden-Meyerhof-Parnas pathway genes can modulate the glucose metabolic flux and increase the intracellular NADPH supply, enabling Escherichia coli cells to produce xylitol from corncob hydrolysates. The effects of zwf and/or gnd overexpression and pfkA, pfkB, and/or pgi deletion on the intracellular redox environment and xylitol production were examined. The NADPH-enhanced strain 2bpgi produced 162 g/L xylitol from corncob hydrolysates after a 76 h fed-batch fermentation in a 15 L bioreactor, which was 13.3% greater than the 143 g/L xylitol produced by the IS5-d control strain. Additionally, the xylitol productivity and xylitol yield per glucose for 2bpgi were 2.13 g/L/h and 2.50 g/g, respectively. Thus, the genetic modifications in 2bpgi significantly enhanced NADPH regeneration, making 2bpgi a potentially useful strain for the industrial-scale production of xylitol from detoxified corncob hydrolysates.
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Affiliation(s)
- Xinsong Yuan
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230601, PR China
| | - Yudi Mao
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Shuai Tu
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230601, PR China
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Huahao Shen
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, PR China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, PR China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, PR China
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7
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Bañares AB, Nisola GM, Valdehuesa KNG, Lee WK, Chung WJ. Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds. Crit Rev Biotechnol 2021; 41:649-668. [PMID: 33563072 DOI: 10.1080/07388551.2021.1873243] [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] [Indexed: 12/16/2022]
Abstract
The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.
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Affiliation(s)
- Angelo B Bañares
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Grace M Nisola
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Kris N G Valdehuesa
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi, South Korea
| | - Wook-Jin Chung
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
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8
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Cao Z, Meng R, Wang P, Zhu G. Heterologous expression and enzymatic identification of two novel soluble pyridine nucleotide transhydrogenases from Acidobacteria bacterium KBS 146 and Nocardia jiangxiensis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1988708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zhengyu Cao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Rui Meng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
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9
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Immobilization of recombinant Escherichia coli on multi-walled carbon nanotubes for xylitol production. Enzyme Microb Technol 2020; 135:109495. [DOI: 10.1016/j.enzmictec.2019.109495] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/15/2022]
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10
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Deb SS, Reshamwala SMS, Lali AM. Activation of alternative metabolic pathways diverts carbon flux away from isobutanol formation in an engineered Escherichia coli strain. Biotechnol Lett 2019; 41:823-836. [PMID: 31093837 DOI: 10.1007/s10529-019-02683-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Metabolic engineering efforts are guided by identifying gene targets for overexpression and/or deletion. Isobutanol, a biofuel candidate, is biosynthesized using the valine biosynthesis pathway and enzymes of the Ehrlich pathway. Most reported studies for isobutanol production in Escherichia coli employ multicopy plasmids, an approach that suffers from disadvantages such as plasmid instability, increased metabolic burden, and use of antibiotics to maintain selection pressure. Cofactor imbalance is another issue that may limit production of isobutanol, as two enzymes of the pathway utilize NADPH as a cofactor. RESULTS To address these issues, we constructed E. coli strains with chromosomally-integrated, codon-optimized isobutanol pathway genes (ilvGM, ilvC, kivd, adh) selected on the basis of their cofactor preferences. Genes involved in diverting pyruvate flux toward fermentation byproducts were deleted. Metabolite analyses of the constructed strains revealed extracellular accumulation of significant amounts of isobutyraldehyde, a pathway intermediate, and the overflow metabolites 2,3-butanediol and acetol. CONCLUSIONS These results demonstrate that the genetic modifications carried out led to activation of alternative pathways that diverted carbon flux toward formation of unwanted metabolites. The present study highlights how precursor metabolites can be metabolized through enzymatic routes that have not been considered important in previous studies due to the different strategies employed therein. The insights gained from the present study will allow rational genetic modification of host cells for production of metabolites of interest.
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Affiliation(s)
- Shalini S Deb
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
| | - Shamlan M S Reshamwala
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India.
| | - Arvind M Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
- Department of Chemical Engineering, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
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11
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Yuan X, Wang J, Lin J, Yang L, Wu M. Efficient production of xylitol by the integration of multiple copies of xylose reductase gene and the deletion of Embden-Meyerhof-Parnas pathway-associated genes to enhance NADPH regeneration in Escherichia coli. J Ind Microbiol Biotechnol 2019; 46:1061-1069. [PMID: 31025135 DOI: 10.1007/s10295-019-02169-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/23/2019] [Indexed: 01/24/2023]
Abstract
Cofactor supply is a rate-limiting step in the bioconversion of xylose to xylitol. Strain WZ04 was first constructed by a novel simultaneous deletion-insertion strategy, replacing ptsG, xylAB and ptsF in wild-type Escherichia coli W3110 with three mutated xylose reductase genes (xr) from Neurospora crassa. Then, the pfkA, pfkB, pgi and/or sthA genes were deleted and replaced by xr to investigate the influence of carbon flux toward the pentose phosphate pathway and/or transhydrogenase activity on NADPH generation. The deletion of pfkA/pfkB significantly improved NADPH supply, but minimally influenced cell growth. The effects of insertion position and copy number of xr were examined by a quantitative real-time PCR and a shake-flask fermentation experiment. In a fed-batch fermentation experiment with a 15-L bioreactor, strain WZ51 produced 131.6 g L-1 xylitol from hemicellulosic hydrolysate (xylitol productivity: 2.09 g L-1 h-1). This study provided a potential approach for industrial-scale production of xylitol from hemicellulosic hydrolysate.
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Affiliation(s)
- Xinsong Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Jiping Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
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12
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On the bi-enzymatic behaviour of Saccharomyces cerevisiae -mediated stereoselective biotransformation of 2,6,6-trimethylcyclohex-2-ene-1,4-dione. MOLECULAR CATALYSIS 2018. [DOI: 10.1016/j.mcat.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Reynolds TS, Courtney CM, Erickson KE, Wolfe LM, Chatterjee A, Nagpal P, Gill RT. ROS mediated selection for increased NADPH availability in Escherichia coli. Biotechnol Bioeng 2017; 114:2685-2689. [PMID: 28710857 DOI: 10.1002/bit.26385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/21/2017] [Accepted: 07/12/2017] [Indexed: 11/10/2022]
Abstract
The economical production of chemicals and fuels by microbial processes remains an intense area of interest in biotechnology. A key limitation in such efforts concerns the availability of key co-factors, in this case NADPH, required for target pathways. Many of the strategies pursued for increasing NADPH availability in Escherichia coli involve manipulations to the central metabolism, which can create redox imbalances and overall growth defects. In this study we used a reactive oxygen species based selection to search for novel methods of increasing NADPH availability. We report a loss of function mutation in the gene hdfR appears to increase NADPH availability in E. coli. Additionally, we show this excess NADPH can be used to improve the production of 3HP in E. coli.
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Affiliation(s)
- Thomas S Reynolds
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Colleen M Courtney
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Keesha E Erickson
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado
| | - Lisa M Wolfe
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Prashant Nagpal
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado.,Materials Science and Engineering, University of Colorado, Boulder, Boulder, Colorado
| | - Ryan T Gill
- Chemical and Biological Engineering, University of Colorado, Boulder, Colorado.,Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado
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14
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Microbial secretion of lactate-enriched oligomers for efficient conversion into lactide: A biological shortcut to polylactide. J Biosci Bioeng 2017; 124:204-208. [DOI: 10.1016/j.jbiosc.2017.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/04/2017] [Indexed: 11/19/2022]
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15
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Wang C, Zhou Z, Cai H, Chen Z, Xu H. Redirecting carbon flux through pgi-deficient and heterologous transhydrogenase toward efficient succinate production in Corynebacterium glutamicum. J Ind Microbiol Biotechnol 2017; 44:1115-1126. [PMID: 28303352 DOI: 10.1007/s10295-017-1933-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/01/2017] [Indexed: 11/24/2022]
Abstract
Corynebacterium glutamicum is particularly known for its potentiality in succinate production. We engineered C. glutamicum for the production of succinate. To enhance C3-C4 carboxylation efficiency, chromosomal integration of the pyruvate carboxylase gene pyc resulted in strain NC-4. To increase intracellular NADH pools, the pntAB gene from Escherichia coli, encoding for transhydrogenase, was chromosomally integrated into NC-4, leading to strain NC-5. Furthermore, we deleted pgi gene in strain NC-5 to redirect carbon flux to the pentose phosphate pathway (PPP). To solve the drastic reduction of PTS-mediated glucose uptake, the ptsG gene from C. glutamicum, encoding for the glucose-specific transporter, was chromosomally integrated into pgi-deficient strain resulted in strain NC-6. In anaerobic batch fermentation, the production of succinate in pntAB-overexpressing strain NC-5 increased by 14% and a product yield of 1.22 mol/mol was obtained. In anaerobic fed-batch process, succinic acid concentration reached 856 mM by NC-6. The yields of succinate from glucose were 1.37 mol/mol accompanied by a very low level of by-products. Activating PPP and transhydrogenase in combination led to a succinate yield of 1.37 mol/mol, suggesting that they exhibited a synergistic effect for improving succinate yield.
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Affiliation(s)
- Chen Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhihui Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Heng Cai
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Zhongjun Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Hongtao Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China.,College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
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Su B, Zhang Z, Wu M, Lin J, Yang L. Construction of plasmid-free Escherichia coli for the production of arabitol-free xylitol from corncob hemicellulosic hydrolysate. Sci Rep 2016; 6:26567. [PMID: 27225023 PMCID: PMC4880924 DOI: 10.1038/srep26567] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/04/2016] [Indexed: 11/22/2022] Open
Abstract
High costs and low production efficiency are a serious constraint to bio-based xylitol production. For industrial-scale production of xylitol, a plasmid-free Escherichia coli for arabitol-free xylitol production from corncob hemicellulosic hydrolysate has been constructed. Instead of being plasmid and inducer dependent, this strain relied on multiple-copy integration of xylose reductase (XR) genes into the chromosome, where their expression was controlled by the constitutive promoter P43. In addition, to minimize the flux from L-arabinose to arabitol, two strategies including low XR total activity and high selectivity of XR has been adopted. Arabitol was significantly decreased using plasmid-free strain which had lower XR total activity and an eight point-mutations of XR with a 27-fold lower enzyme activity toward L-arabinose was achieved. The plasmid-free strain in conjunction with this mutant XR can completely eliminate arabitol formation in xylitol production. In fed-batch fermentation, this plasmid-free strain produced 143.8 g L(-1) xylitol at 1.84 g L(-1) h(-1) from corncob hemicellulosic hydrolysate. From these results, we conclude that this route by plasmid-free E. coli has potential to become a commercially viable process for xylitol production.
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Affiliation(s)
- Buli Su
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhe Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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Mienda BS, Shamsir MS, Md. Illias R. Model-assisted formate dehydrogenase-O (fdoH) gene knockout for enhanced succinate production in Escherichia coli from glucose and glycerol carbon sources. J Biomol Struct Dyn 2016; 34:2305-16. [DOI: 10.1080/07391102.2015.1113387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bashir Sajo Mienda
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, Skudai Johor Bahru 81310, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, Skudai Johor Bahru 81310, Malaysia
| | - Rosli Md. Illias
- Faculty of Chemical Engineering, Department of Bioprocess Engineering, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Malaysia
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Tan Z, Chen J, Zhang X. Systematic engineering of pentose phosphate pathway improves Escherichia coli succinate production. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:262. [PMID: 27980672 PMCID: PMC5134279 DOI: 10.1186/s13068-016-0675-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/24/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Succinate biosynthesis of Escherichia coli is reducing equivalent-dependent and the EMP pathway serves as the primary reducing equivalent source under anaerobic condition. Compared with EMP, pentose phosphate pathway (PPP) is reducing equivalent-conserving but suffers from low efficacy. In this study, the ribosome binding site library and modified multivariate modular metabolic engineering (MMME) approaches are employed to overcome the low efficacy of PPP and thus increase succinate production. RESULTS Altering expression levels of different PPP enzymes have distinct effects on succinate production. Specifically, increased expression of five enzymes, i.e., Zwf, Pgl, Gnd, Tkt, and Tal, contributes to increased succinate production, while the increased expression of two enzymes, i.e., Rpe and Rpi, significantly decreases succinate production. Modular engineering strategy is employed to decompose PPP into three modules according to position and function. Engineering of Zwf/Pgl/Gnd and Tkt/Tal modules effectively increases succinate yield and production, while engineering of Rpe/Rpi module decreases. Imbalance of enzymatic reactions in PPP is alleviated using MMME approach. Finally, combinational utilization of engineered PPP and SthA transhydrogenase enables succinate yield up to 1.61 mol/mol glucose, which is 94% of theoretical maximum yield (1.71 mol/mol) and also the highest succinate yield in minimal medium to our knowledge. CONCLUSIONS In summary, we systematically engineered the PPP for improving the supply of reducing equivalents and thus succinate production. Besides succinate, these PPP engineering strategies and conclusions can also be applicable to the production of other reducing equivalent-dependent biorenewables.
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Affiliation(s)
- Zaigao Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Park, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jing Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Park, 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, 32 XiQiDao, Tianjin Airport Economic Park, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
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Cao Y, Niu W, Guo J, Xian M, Liu H. Biotechnological production of 1,2,4-butanetriol: An efficient process to synthesize energetic material precursor from renewable biomass. Sci Rep 2015; 5:18149. [PMID: 26670289 PMCID: PMC4680960 DOI: 10.1038/srep18149] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/13/2015] [Indexed: 12/02/2022] Open
Abstract
1,2,4-Butanetriol (BT) is a valuable chemical with extensive applications in many different fields. The traditional chemical routes to synthesize BT suffer from many drawbacks, e.g., harsh reaction conditions, multiple steps and poor selectivity, limiting its industrial production. In this study, an engineered Escherichia coli strain was constructed to produce BT from xylose, which is a major component of the lignocellulosic biomass. Through the coexpression of a xylose dehydrogenase (CCxylB) and a xylonolactonase (xylC) from Caulobacter crescentus, native E. coli xylonate dehydratase (yjhG), a 2-keto acid decarboxylase from Pseudomonas putida (mdlC) and native E. coli aldehyde reductase (adhP) in E. coli BL21 star(DE3), the recombinant strain could efficiently convert xylose to BT. Furthermore, the competitive pathway responsible for xylose metabolism in E. coli was blocked by disrupting two genes (xylA and EcxylB) encoding xylose isomerase and xyloluse kinase. Under fed-batch conditions, the engineered strain BL21ΔxylAB/pE-mdlCxylBC&pA-adhPyjhG produced up to 3.92 g/L of BT from 20 g/L of xylose, corresponding to a molar yield of 27.7%. These results suggest that the engineered E. coli has a promising prospect for the large-scale production of BT.
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Affiliation(s)
- Yujin Cao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Wei Niu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Huizhou Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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Xu X, Chen J, Wang Q, Duan C, Li Y, Wang R, Yang S. Mutagenesis of Key Residues in the Binding Center of l-Aspartate-b-Semialdehyde Dehydrogenase from Escherichia coli Enhances Utilization of the Cofactor NAD(H). Chembiochem 2015; 17:56-64. [PMID: 26662025 DOI: 10.1002/cbic.201500534] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/07/2022]
Abstract
L-Aspartate-β-semialdehyde dehydrogenase (ASADH) is a key enzyme in the aspartate pathway. In bacteria, ASADH is highly specific for the cofactor NADP(+) rather than NAD(+). Limited information on cofactor utilization is available, and neither the wild-type protein nor the available mutants could utilize NAD(+) efficiently. In this study, we identified several residues crucial for cofactor utilization by Escherichia coli ASADH (ecASADH) by mutating residues within the cofactor binding center. Among the investigated mutants, ecASADH-Q350N and ecASADH-Q350N/H171A, which exhibited markedly improved NAD(+) utilization, were further investigated by various biochemical approaches and molecular modeling. Relative to the wild type, the two mutants showed approximately 44-fold and 66-fold increases, respectively, in the constant kcat /Km of NAD(+). As desired, they could also utilize NADH efficiently to synthesize l-homoserine in cascade reactions in vitro.
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Affiliation(s)
- Xiaoshu Xu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Jun Chen
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Qingzhuo Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Chunlan Duan
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Yan Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China. .,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 30 Meilong Road, Shanghai, 200237, China.
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22
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Pearsall SM, Rowley CN, Berry A. Advances in Pathway Engineering for Natural Product Biosynthesis. ChemCatChem 2015. [DOI: 10.1002/cctc.201500602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah M. Pearsall
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Christopher N. Rowley
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
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Lakshmanan M, Yu K, Koduru L, Lee DY. In silico model-driven cofactor engineering strategies for improving the overall NADP(H) turnover in microbial cell factories. J Ind Microbiol Biotechnol 2015; 42:1401-14. [PMID: 26254041 DOI: 10.1007/s10295-015-1663-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/23/2015] [Indexed: 02/03/2023]
Abstract
Optimizing the overall NADPH turnover is one of the key challenges in various value-added biochemical syntheses. In this work, we first analyzed the NADPH regeneration potentials of common cell factories, including Escherichia coli, Saccharomyces cerevisiae, Bacillus subtilis, and Pichia pastoris across multiple environmental conditions and determined E. coli and glycerol as the best microbial chassis and most suitable carbon source, respectively. In addition, we identified optimal cofactor specificity engineering (CSE) enzyme targets, whose cofactors when switched from NAD(H) to NADP(H) improve the overall NADP(H) turnover. Among several enzyme targets, glyceraldehyde-3-phosphate dehydrogenase was recognized as a global candidate since its CSE improved the NADP(H) regeneration under most of the conditions examined. Finally, by analyzing the protein structures of all CSE enzyme targets via homology modeling, we established that the replacement of conserved glutamate or aspartate with serine in the loop region could change the cofactor dependence from NAD(H) to NADP(H).
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Affiliation(s)
- Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668, Singapore
| | - Kai Yu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Lokanand Koduru
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668, Singapore. .,Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
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Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742. [PMID: 26284036 PMCID: PMC4518329 DOI: 10.3389/fmicb.2015.00742] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.
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Affiliation(s)
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen UniversityWageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
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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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Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metab Eng 2015; 29:86-96. [PMID: 25769287 DOI: 10.1016/j.ymben.2015.03.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/06/2015] [Accepted: 03/02/2015] [Indexed: 01/15/2023]
Abstract
NADPH is an essential cofactor for the biosynthesis of several high-value chemicals, including isoprenoids, fatty acid-based fuels, and biopolymers. Tunable control over all potentially rate-limiting steps, including the NADPH regeneration rate, is crucial to maximizing production titers. We have rationally engineered a synthetic version of the Entner-Doudoroff pathway from Zymomonas mobilis that increased the NADPH regeneration rate in Escherichia coli MG1655 by 25-fold. To do this, we combined systematic design rules, biophysical models, and computational optimization to design synthetic bacterial operons expressing the 5-enzyme pathway, while eliminating undesired genetic elements for maximum expression control. NADPH regeneration rates from genome-integrated pathways were estimated using a NADPH-binding fluorescent reporter and by the productivity of a NADPH-dependent terpenoid biosynthesis pathway. We designed and constructed improved pathway variants by employing the RBS Library Calculator to efficiently search the 5-dimensional enzyme expression space and by performing 40 cycles of MAGE for site-directed genome mutagenesis. 624 pathway variants were screened using a NADPH-dependent blue fluorescent protein, and 22 were further characterized to determine the relationship between enzyme expression levels and NADPH regeneration rates. The best variant exhibited 25-fold higher normalized mBFP levels when compared to wild-type strain. Combining the synthetic Entner-Doudoroff pathway with an optimized terpenoid pathway further increased the terpenoid titer by 97%.
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Affiliation(s)
- Chiam Yu Ng
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, United States
| | - Iman Farasat
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, United States
| | - Costas D Maranas
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, United States
| | - Howard M Salis
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, United States; Department of Biological Engineering, Pennsylvania State University, University Park, PA 16802, United States.
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Zhou Z, Wang C, Chen Y, Zhang K, Xu H, Cai H, Chen Z. Increasing available NADH supply during succinic acid production by Corynebacterium glutamicum. Biotechnol Prog 2014; 31:12-9. [PMID: 25311136 DOI: 10.1002/btpr.1998] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 10/09/2014] [Indexed: 11/06/2022]
Abstract
A critical factor in the biotechnological production of succinic acid with Corynebacterium glutamicum is the sufficient supply of NADH. It is conceivable that cofactor availability and the proportion of cofactor in the active form may play an important role in dictating the succinic acid yield. PntAB genes from Escherichia coli can directly catalyze the reversible hydride transfer and adjust the dynamic balance between NADP(H) and NAD(H). Hence, we studied the physiological effect of coenzyme systems by expressing the membrane-bound transhydrogenase pntAB genes. We have shown experimentally that the pntAB genes could function as an alternative source of NADH. In an anaerobic fermentation with C. glutamicum NC-3-pntAB, a 16% higher succinic acid yield and a 57% higher production from glucose were obtained by pntAB expression. Moreover, the formation of by-products was significantly decreased. The concomitant increase in the consumption of intracellular NADPH from 0.6 to 1.2 mmol/g CDW and the increased NADH/NAD(+) ratio resulted from introduction of pntAB, suggesting that the membrane-bound transhydrogenase converted excess NADPH to NADH for succinic acid production. Finally, we explored whether the transhydrogenase had different effects on the succinic acid formation on different carbon sources. The succinic acid yield was increased in the presence of pntAB by 16% on glucose, 7% on sucrose, and without large influence on fructose and xylose. The results of this study demonstrated that the effectiveness of cofactor manipulation could be a promising strategy applied in metabolic engineering.
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Affiliation(s)
- Zhihui Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, China
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Zhu X, Tan Z, Xu H, Chen J, Tang J, Zhang X. Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli. Metab Eng 2014; 24:87-96. [PMID: 24831708 DOI: 10.1016/j.ymben.2014.05.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/12/2014] [Accepted: 05/05/2014] [Indexed: 01/29/2023]
Abstract
Reducing equivalents are an important cofactor for efficient synthesis of target products. During metabolic evolution to improve succinate production in Escherichia coli strains, two reducing equivalent-conserving pathways were activated to increase succinate yield. The sensitivity of pyruvate dehydrogenase to NADH inhibition was eliminated by three nucleotide mutations in the lpdA gene. Pyruvate dehydrogenase activity increased under anaerobic conditions, which provided additional NADH. The pentose phosphate pathway and transhydrogenase were activated by increased activities of transketolase and soluble transhydrogenase SthA. These data suggest that more carbon flux went through the pentose phosphate pathway, thus leading to production of more reducing equivalent in the form of NADPH, which was then converted to NADH through soluble transhydrogenase for succinate production. Reverse metabolic engineering was further performed in a parent strain, which was not metabolically evolved, to verify the effects of activating these two reducing equivalent-conserving pathways for improving succinate yield. Activating pyruvate dehydrogenase increased succinate yield from 1.12 to 1.31mol/mol, whereas activating the pentose phosphate pathway and transhydrogenase increased succinate yield from 1.12 to 1.33mol/mol. Activating these two pathways in combination led to a succinate yield of 1.5mol/mol (88% of theoretical maximum), suggesting that they exhibited a synergistic effect for improving succinate yield.
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Affiliation(s)
- Xinna Zhu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Zaigao Tan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China; University of Chinese Academy of Sciences, China
| | - Hongtao Xu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Jing Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China; College of Biotechnology, Tianjin University of Science & Technology, China
| | - Jinlei Tang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China.
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King ZA, Feist AM. Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. Metab Eng 2014; 24:117-28. [PMID: 24831709 DOI: 10.1016/j.ymben.2014.05.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/06/2014] [Accepted: 05/06/2014] [Indexed: 01/30/2023]
Abstract
Maintaining cofactor balance is a critical function in microorganisms, but often the native cofactor balance does not match the needs of an engineered metabolic flux state. Here, an optimization procedure is utilized to identify optimal cofactor-specificity "swaps" for oxidoreductase enzymes utilizing NAD(H) or NADP(H) in the genome-scale metabolic models of Escherichia coli and Saccharomyces cerevisiae. The theoretical yields of all native carbon-containing molecules are considered, as well as theoretical yields of twelve heterologous production pathways in E. coli. Swapping the cofactor specificity of central metabolic enzymes (especially GAPD and ALCD2x) is shown to increase NADPH production and increase theoretical yields for native products in E. coli and yeast--including L-aspartate, L-lysine, L-isoleucine, L-proline, L-serine, and putrescine--and non-native products in E. coli-including 1,3-propanediol, 3-hydroxybutyrate, 3-hydroxypropanoate, 3-hydroxyvalerate, and styrene.
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Affiliation(s)
- Zachary A King
- Department of Bioengineering, University of California, 9500 Gilman Drive #0412, San Diego, La Jolla, CA 92093-0412, USA
| | - Adam M Feist
- Department of Bioengineering, University of California, 9500 Gilman Drive #0412, San Diego, La Jolla, CA 92093-0412, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
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Engineering class I cytochrome P450 by gene fusion with NADPH-dependent reductase and S. avermitilis host development for daidzein biotransformation. Appl Microbiol Biotechnol 2014; 98:8191-200. [DOI: 10.1007/s00253-014-5706-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/10/2014] [Accepted: 03/17/2014] [Indexed: 11/25/2022]
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Qi H, Li S, Zhao S, Huang D, Xia M, Wen J. Model-driven redox pathway manipulation for improved isobutanol production in Bacillus subtilis complemented with experimental validation and metabolic profiling analysis. PLoS One 2014; 9:e93815. [PMID: 24705866 PMCID: PMC3976320 DOI: 10.1371/journal.pone.0093815] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/06/2014] [Indexed: 12/05/2022] Open
Abstract
To rationally guide the improvement of isobutanol production, metabolic network and metabolic profiling analysis were performed to provide global and profound insights into cell metabolism of isobutanol-producing Bacillus subtilis. The metabolic flux distribution of strains with different isobutanol production capacity (BSUL03, BSUL04 and BSUL05) drops a hint of the importance of NADPH on isobutanol biosynthesis. Therefore, the redox pathways were redesigned in this study. To increase NADPH concentration, glucose-6-phosphate isomerase was inactivated (BSUL06) and glucose-6-phosphate dehydrogenase was overexpressed (BSUL07) successively. As expected, NADPH pool size in BSUL07 was 4.4-fold higher than that in parental strain BSUL05. However, cell growth, isobutanol yield and production were decreased by 46%, 22%, and 80%, respectively. Metabolic profiling analysis suggested that the severely imbalanced redox status might be the primary reason. To solve this problem, gene udhA of Escherichia coli encoding transhydrogenase was further overexpressed (BSUL08), which not only well balanced the cellular ratio of NAD(P)H/NAD(P)+, but also increased NADH and ATP concentration. In addition, a straightforward engineering approach for improving NADPH concentrations was employed in BSUL05 by overexpressing exogenous gene pntAB and obtained BSUL09. The performance for isobutanol production by BSUL09 was poorer than BSUL08 but better than other engineered strains. Furthermore, in fed-batch fermentation the isobutanol production and yield of BSUL08 increased by 11% and 19%, up to the value of 6.12 g/L and 0.37 C-mol isobutanol/C-mol glucose (63% of the theoretical value), respectively, compared with parental strain BSUL05. These results demonstrated that model-driven complemented with metabolic profiling analysis could serve as a useful approach in the strain improvement for higher bio-productivity in further application.
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Affiliation(s)
- Haishan Qi
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Shanshan Li
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Sumin Zhao
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Di Huang
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Menglei Xia
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Jianping Wen
- Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, People's Republic of China
- * E-mail:
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Wang X, Zhang C, Wang M, Lu W. Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for spinosad production improvement. Microb Cell Fact 2014; 13:41. [PMID: 24628959 PMCID: PMC4003821 DOI: 10.1186/1475-2859-13-41] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spinosad is a macrolide antibiotic produced by Saccharopolyspora spinosa with aerobic fermentation. However, the wild strain has a low productivity. In this article, a computational guided engineering approach was adopted in order to improve the yield of spinosad in S. spinosa. RESULTS Firstly, a genome-scale metabolic network reconstruction (GSMR) for S.spinosa based on its genome information, literature data and experimental data was established. The model was consists of 1,577 reactions, 1,726 metabolites, and 733 enzymes after manually refined. Then, amino acids supplying experiments were performed in order to test the capabilities of the model, and the results showed a high consistency. Subsequently, transhydrogenase (PntAB, EC 1.6.1.2) was chosen as the potential target for spinosad yield improvement based on the in silico metabolic network models. Furthermore, the target gene was manipulated in the parent strain in order to validate the model predictions. At last, shake flask fermentation was carried out which led to spinosad production of 75.32 mg/L, 86.5% higher than the parent strain (40.39 mg/L). CONCLUSIONS Results confirmed the model had a high potential in engineering S. spinosa for spinosad production. It is the first GSMM for S.spinosa, it has significance for a better understanding of the comprehensive metabolism and guiding strain designing of Saccharopolyspora spinosa in the future.
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Affiliation(s)
| | | | | | - Wenyu Lu
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
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Cheng H, Lv J, Wang H, Wang B, Li Z, Deng Z. Genetically engineered Pichia pastoris yeast for conversion of glucose to xylitol by a single-fermentation process. Appl Microbiol Biotechnol 2014; 98:3539-52. [PMID: 24419799 DOI: 10.1007/s00253-013-5501-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/10/2013] [Accepted: 12/24/2013] [Indexed: 12/22/2022]
Abstract
Xylitol is industrially synthesized by chemical reduction of D-xylose, which is more expensive than glucose. Thus, there is a growing interest in the production of xylitol from a readily available and much cheaper substrate, such as glucose. The commonly used yeast Pichia pastoris strain GS115 was shown to produce D-arabitol from glucose, and the derivative strain GS225 was obtained to produce twice amount of D-arabitol than GS115 by adaptive evolution during repetitive growth in hyperosmotic medium. We cloned the D-xylulose-forming D-arabitol dehydrogenase (DalD) gene from Klebsiella pneumoniae and the xylitol dehydrogenase (XDH) gene from Gluconobacter oxydans. Recombinant P. pastoris GS225 strains with the DalD gene only or with both DalD and XDH genes could produce xylitol from glucose in a single-fermentation process. Three-liter jar fermentation results showed that recombinant P. pastoris cells with both DalD and XDH converted glucose to xylitol with the highest yield of 0.078 g xylitol/g glucose and productivity of 0.29 g xylitol/L h. This was the first report to convert xylitol from glucose by the pathway of glucose-D-arabitol-D-xylulose-xylitol in a single process. The recombinant yeast could be used as a yeast cell factory and has the potential to produce xylitol from glucose.
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Affiliation(s)
- Hairong Cheng
- The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China,
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Chen X, Zhou L, Tian K, Kumar A, Singh S, Prior BA, Wang Z. Metabolic engineering of Escherichia coli: A sustainable industrial platform for bio-based chemical production. Biotechnol Adv 2013; 31:1200-23. [DOI: 10.1016/j.biotechadv.2013.02.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
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36
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Su B, Wu M, Lin J, Yang L. Metabolic engineering strategies for improving xylitol production from hemicellulosic sugars. Biotechnol Lett 2013; 35:1781-9. [DOI: 10.1007/s10529-013-1279-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/21/2013] [Indexed: 12/25/2022]
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Jan J, Martinez I, Wang Y, Bennett GN, San KY. Metabolic engineering and transhydrogenase effects on NADPH availability in Escherichia coli. Biotechnol Prog 2013; 29:1124-30. [PMID: 23794523 DOI: 10.1002/btpr.1765] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 04/08/2013] [Indexed: 11/08/2022]
Abstract
The synthesis of several industrially useful compounds are cofactor-dependent, requiring reducing equivalents like NADPH in enzymatic reactions leading up to the synthesis of high-value compounds like polymers, chiral alcohols, and antibiotics. However, NADPH is costly and has limited intracellular availability. This study focuses on the study of the effect of the two transhydrogenase enzymes of Escherichia coli, PntAB and UdhA (SthA) on reducing equivalents-dependent biosynthesis. The production of (S)-2-chloropropionate from 2-chloroacrylate is used as a model system for monitoring NADPH availability because 2-haloacrylate reductase, the enzyme catalyzing the one-step conversion to (S)-2-chloropropionate in the synthesis pathway, requires NADPH as a cofactor. Results suggest that the presence of UdhA increases product yield and NADPH availability while the presence of PntAB has the opposite effect. A maximum product yield of 1.4 mol product/mol glucose was achieved aerobically in a pnt-deletion strain with udhA overexpression, a 150% improvement over the wild-type control strain.
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Affiliation(s)
- Joanna Jan
- Dept. of Bioengineering, Rice University, Houston, TX
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38
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Wang Y, San KY, Bennett GN. Improvement of NADPH bioavailability in Escherichia coli through the use of phosphofructokinase deficient strains. Appl Microbiol Biotechnol 2013; 97:6883-93. [PMID: 23558585 DOI: 10.1007/s00253-013-4859-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 03/11/2013] [Accepted: 03/13/2013] [Indexed: 11/26/2022]
Abstract
NADPH-dependent reactions play important roles in production of industrially valuable compounds. In this study, we used phosphofructokinase (PFK)-deficient strains to direct fructose-6-phosphate to be oxidized through the pentose phosphate pathway (PPP) to increase NADPH generation. pfkA or pfkB single deletion and double-deletion strains were tested for their ability to produce lycopene. Since lycopene biosynthesis requires many NADPH, levels of lycopene were compared in a set of isogenic strains, with the pfkA single deletion strain showing the highest lycopene yield. Using another NADPH-requiring process, a one-step reduction reaction of 2-chloroacrylate to 2-chloropropionic acid by 2-haloacrylate reductase, the pfkA pfkB double-deletion strain showed the highest yield of 2-chloropropionic acid product. The combined effect of glucose-6-phosphate dehydrogenase overexpression or lactate dehydrogenase deletion with PFK deficiency on NADPH bioavailability was also studied. The results indicated that the flux distribution of fructose-6-phosphate between glycolysis and the pentose phosphate pathway determines the amount of NAPDH available for reductive biosynthesis.
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Affiliation(s)
- Yipeng Wang
- Department of Biochemistry and Cell Biology, MS-140, Rice University, 6100 Main Street, Houston, TX 77005-1892, USA
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Proline availability regulates proline-4-hydroxylase synthesis and substrate uptake in proline-hydroxylating recombinant Escherichia coli. Appl Environ Microbiol 2013; 79:3091-100. [PMID: 23455348 DOI: 10.1128/aem.03640-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial physiology plays a crucial role in whole-cell biotransformation, especially for redox reactions that depend on carbon and energy metabolism. In this study, regio- and enantio-selective proline hydroxylation with recombinant Escherichia coli expressing proline-4-hydroxylase (P4H) was investigated with respect to its interconnectivity to microbial physiology and metabolism. P4H production was found to depend on extracellular proline availability and on codon usage. Medium supplementation with proline did not alter p4h mRNA levels, indicating that P4H production depends on the availability of charged prolyl-tRNAs. Increasing the intracellular levels of soluble P4H did not result in an increase in resting cell activities above a certain threshold (depending on growth and assay temperature). Activities up to 5-fold higher were reached with permeabilized cells, confirming that host physiology and not the intracellular level of active P4H determines the achievable whole-cell proline hydroxylation activity. Metabolic flux analysis revealed that tricarboxylic acid cycle fluxes in growing biocatalytically active cells were significantly higher than proline hydroxylation rates. Remarkably, a catalysis-induced reduction of substrate uptake was observed, which correlated with reduced transcription of putA and putP, encoding proline dehydrogenase and the major proline transporter, respectively. These results provide evidence for a strong interference of catalytic activity with the regulation of proline uptake and metabolism. In terms of whole-cell biocatalyst efficiency, proline uptake and competition of P4H with proline catabolism are considered the most critical factors.
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40
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Iverson A, Garza E, Zhao J, Wang Y, Zhao X, Wang J, Manow R, Zhou S. Increasing reducing power output (NADH) of glucose catabolism for reduction of xylose to xylitol by genetically engineered Escherichia coli AI05. World J Microbiol Biotechnol 2013; 29:1225-32. [PMID: 23435875 DOI: 10.1007/s11274-013-1285-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Anaerobic homofermentative production of reduced products requires additional reducing power (NADH and/or NADPH) output from glucose catabolism. Previously, with an anaerobically expressed pyruvate dehydrogenase operon (aceEF-lpd), we doubled the reducing power output to four NADH per glucose (or 1.2 xylose) catabolized anaerobically, which satisfied the NADH requirement to establish a non-transgenic homoethanol pathway (1 glucose or 1.2 xylose --> 2 acetyl-CoA + 4 NADH --> 2 ethanol) in the engineered strain, Escherichia coli SZ420 (∆frdBC ∆ldhA ∆ackA ∆focA-pflB ∆pdhR::pflBp6-pflBrbs-aceEF-lpd). In this study, E. coli SZ420 was further engineered for reduction of xylose to xylitol by (1) deleting the alcohol dehydrogenase gene (adhE) to divert NADH from the ethanol pathway; (2) deleting the glucose-specific PTS permease gene (ptsG) to eliminate catabolite repression and allow simultaneous uptake of glucose and xylose; (3) cloning the aldose reductase gene (xylI) of Candida boidinii to reduce xylose to xylitol. The resulting strain, E. coli AI05 (pAGI02), could in theory simultaneously uptake glucose and xylose, and utilize glucose as a source of reducing power for the reduction of xylose to xylitol, with an expected yield of four xylitol for each glucose consumed (YRPG = 4) under anaerobic conditions. In resting cell fermentation tests using glucose and xylose mixtures, E. coli AI05 (pAGI02) achieved an actual YRPG value of ~3.6, with xylitol as the major fermentation product and acetate as the by-product.
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Affiliation(s)
- Andrew Iverson
- Key Laboratory of Fermentation Engineering, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan, 430068, People's Republic of China
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Lee WH, Kim MD, Jin YS, Seo JH. Engineering of NADPH regenerators in Escherichia coli for enhanced biotransformation. Appl Microbiol Biotechnol 2013; 97:2761-72. [PMID: 23420268 DOI: 10.1007/s00253-013-4750-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/30/2022]
Abstract
Efficient regeneration of NADPH is one of the limiting factors that constrain the productivity of biotransformation processes. In order to increase the availability of NADPH for enhanced biotransformation by engineered Escherichia coli, modulation of the pentose phosphate pathway and amplification of the transhydrogenases system have been conventionally attempted as primary solutions. Recently, other approaches for stimulating NADPH regeneration during glycolysis, such as replacement of native glyceradehdye-3-phosphate dehydrogenase (GAPDH) with NADP-dependent GAPDH from Clostridium acetobutylicum and introduction of NADH kinase catalyzing direct phosphorylation of NADH to NADPH from Saccharomyces cerevisiae, were attempted and resulted in remarkable impacts on NADPH-dependent bioprocesses. This review summarizes several metabolic engineering approaches used for improving the NADPH regenerating capacity in engineered E. coli for whole-cell-based bioprocesses and discusses the key features and progress of those attempts.
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Affiliation(s)
- Won-Heong Lee
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921, Korea
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42
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Nduko JM, Matsumoto K, Ooi T, Taguchi S. Effectiveness of xylose utilization for high yield production of lactate-enriched P(lactate-co-3-hydroxybutyrate) using a lactate-overproducing strain of Escherichia coli and an evolved lactate-polymerizing enzyme. Metab Eng 2013. [DOI: 10.1016/j.ymben.2012.11.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Lee WH, Kim JW, Park EH, Han NS, Kim MD, Seo JH. Effects of NADH kinase on NADPH-dependent biotransformation processes in Escherichia coli. Appl Microbiol Biotechnol 2012; 97:1561-9. [PMID: 23053084 DOI: 10.1007/s00253-012-4431-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 11/26/2022]
Abstract
Sufficient supply of NADPH is one of the most important factors affecting the productivity of biotransformation processes. In this study, construction of an efficient NADPH-regenerating system was attempted using direct phosphorylation of NADH by NADH kinase (Pos5p) from Saccharomyces cerevisiae for producing guanosine diphosphate (GDP)-L-fucose and ε-caprolactone in recombinant Escherichia coli. Expression of Pos5p in a fed-batch culture of recombinant E. coli producing GDP-L-fucose resulted in a maximum GDP-L-fucose concentration of 291.5 mg/l, which corresponded to a 51 % enhancement compared with the control strain. In a fed-batch Baeyer-Villiger (BV) oxidation of cyclohexanone using recombinant E. coli expressing Pos5p, a maximum ε-caprolactone concentration of 21.6 g/l was obtained, which corresponded to a 96 % enhancement compared with the control strain. Such an increase might be due to the enhanced availability of NADPH in recombinant E. coli expressing Pos5p. These results suggested that efficient regeneration of NADPH was possible by functional expression of Pos5p in recombinant E. coli, which can be applied to other NADPH-dependent biotransformation processes in E. coli.
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Affiliation(s)
- Won-Heong Lee
- Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul, 151-921, Korea
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De novo creation of MG1655-derived E. coli strains specifically designed for plasmid DNA production. Appl Microbiol Biotechnol 2012; 97:611-20. [PMID: 22885693 DOI: 10.1007/s00253-012-4308-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/13/2012] [Accepted: 07/13/2012] [Indexed: 12/20/2022]
Abstract
The interest in plasmid DNA (pDNA) as a biopharmaceutical has been increasing over the last several years, especially after the approval of the first DNA vaccines. New pDNA production strains have been created by rationally mutating genes selected on the basis of Escherichia coli central metabolism and plasmid properties. Nevertheless, the highly mutagenized genetic background of the strains used makes it difficult to ascertain the exact impact of those mutations. To explore the effect of strain genetic background, we investigated single and double knockouts of two genes, pykF and pykA, which were known to enhance pDNA synthesis in two different E. coli strains: MG1655 (wild-type genetic background) and DH5α (highly mutagenized genetic background). The knockouts were only effective in the wild-type strain MG1655, demonstrating the relevance of strain genetic background and the importance of designing new strains specifically for pDNA production. Based on the obtained results, we created a new pDNA production strain starting from MG1655 by knocking out the pgi gene in order to redirect carbon flux to the pentose phosphate pathway, enhance nucleotide synthesis, and, consequently, increase pDNA production. GALG20 (MG1655ΔendAΔrecAΔpgi) produced 25-fold more pDNA (19.1 mg/g dry cell weight, DCW) than its parental strain, MG1655ΔendAΔrecA (0.8 mg/g DCW), in glucose. For the first time, pgi was identified as an important target for constructing a high-yielding pDNA production strain.
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Molecular determinants of the cofactor specificity of ribitol dehydrogenase, a short-chain dehydrogenase/reductase. Appl Environ Microbiol 2012; 78:3079-86. [PMID: 22344653 DOI: 10.1128/aem.07751-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ribitol dehydrogenase from Zymomonas mobilis (ZmRDH) catalyzes the conversion of ribitol to d-ribulose and concomitantly reduces NAD(P)(+) to NAD(P)H. A systematic approach involving an initial sequence alignment-based residue screening, followed by a homology model-based screening and site-directed mutagenesis of the screened residues, was used to study the molecular determinants of the cofactor specificity of ZmRDH. A homologous conserved amino acid, Ser156, in the substrate-binding pocket of the wild-type ZmRDH was identified as an important residue affecting the cofactor specificity of ZmRDH. Further insights into the function of the Ser156 residue were obtained by substituting it with other hydrophobic nonpolar or polar amino acids. Substituting Ser156 with the negatively charged amino acids (Asp and Glu) altered the cofactor specificity of ZmRDH toward NAD(+) (S156D, [k(cat)/K(m)(,NAD)]/[k(cat)/K(m)(,NADP)] = 10.9, where K(m)(,NAD) is the K(m) for NAD(+) and K(m)(,NADP) is the K(m) for NADP(+)). In contrast, the mutants containing positively charged amino acids (His, Lys, or Arg) at position 156 showed a higher efficiency with NADP(+) as the cofactor (S156H, [k(cat)/K(m)(,NAD)]/[k(cat)/K(m)(,NADP)] = 0.11). These data, in addition to those of molecular dynamics and isothermal titration calorimetry studies, suggest that the cofactor specificity of ZmRDH can be modulated by manipulating the amino acid residue at position 156.
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Engineering yield and rate of reductive biotransformation in Escherichia coli by partial cyclization of the pentose phosphate pathway and PTS-independent glucose transport. Appl Microbiol Biotechnol 2011; 93:1459-67. [PMID: 22002070 PMCID: PMC3275745 DOI: 10.1007/s00253-011-3626-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/12/2011] [Accepted: 09/30/2011] [Indexed: 10/27/2022]
Abstract
Optimization of yields and productivities in reductive whole-cell biotransformations is an important issue for the industrial application of such processes. In a recent study with Escherichia coli, we analyzed the reduction of the prochiral β-ketoester methyl acetoacetate by an R-specific alcohol dehydrogenase (ADH) to the chiral hydroxy ester (R)-methyl 3-hydroxybutyrate (MHB) using glucose as substrate for the generation of NADPH. Deletion of the phosphofructokinase gene pfkA almost doubled the yield to 4.8 mol MHB per mole of glucose, and it was assumed that this effect was due to a partial cyclization of the pentose phosphate pathway (PPP). Here, this partial cyclization was confirmed by (13)C metabolic flux analysis, which revealed a negative net flux from glucose 6-phosphate to fructose 6-phosphate catalyzed by phosphoglucose isomerase. For further process optimization, the genes encoding the glucose facilitator (glf) and glucokinase (glk) of Zymomonas mobilis were overexpressed in recombinant E. coli strains carrying ADH and deletions of either pgi (phosphoglucose isomerase), or pfkA, or pfkA plus pfkB. In all cases, the glucose uptake rate was increased (30-47%), and for strains Δpgi and ΔpfkA also, the specific MHB production rate was increased by 15% and 20%, respectively. The yield of the latter two strains slightly dropped by 11% and 6%, but was still 73% and 132% higher compared to the reference strain with intact pgi and pfkA genes and expressing glf and glk. Thus, metabolic engineering strategies are presented for improving yield and rate of reductive redox biocatalysis by partial cyclization of the PPP and by increasing glucose uptake, respectively.
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Pandit AV, Mahadevan R. In silico characterization of microbial electrosynthesis for metabolic engineering of biochemicals. Microb Cell Fact 2011; 10:76. [PMID: 21967745 PMCID: PMC3215969 DOI: 10.1186/1475-2859-10-76] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 10/03/2011] [Indexed: 01/02/2023] Open
Abstract
Background A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates such as NADH. Bioelectrochemical techniques offer a novel and promising method to alleviate redox imbalances during the synthesis of biochemicals and biofuels. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell's redox balance. The cellular response to such redox changes and the additional reducing power available to the cell can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can be used to improve product yields and/or productivity. Results We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results in this paper elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity. Conclusions The results in this paper provide a systematic understanding of the benefits and limitations of bioelectrochemical techniques for biochemical production and highlight how electrical enhancement can impact cellular metabolism and biochemical production.
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Affiliation(s)
- Aditya V Pandit
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
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Bastian S, Liu X, Meyerowitz JT, Snow CD, Chen MMY, Arnold FH. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab Eng 2011; 13:345-52. [PMID: 21515217 DOI: 10.1016/j.ymben.2011.02.004] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/04/2011] [Accepted: 02/10/2011] [Indexed: 11/19/2022]
Abstract
2-methylpropan-1-ol (isobutanol) is a leading candidate biofuel for the replacement or supplementation of current fossil fuels. Recent work has demonstrated glucose to isobutanol conversion through a modified amino acid pathway in a recombinant organism. Although anaerobic conditions are required for an economically competitive process, only aerobic isobutanol production has been feasible due to an imbalance in cofactor utilization. Two of the pathway enzymes, ketol-acid reductoisomerase and alcohol dehydrogenase, require nicotinamide dinucleotide phosphate (NADPH); glycolysis, however, produces only nicotinamide dinucleotide (NADH). Here, we compare two solutions to this imbalance problem: (1) over-expression of pyridine nucleotide transhydrogenase PntAB and (2) construction of an NADH-dependent pathway, using engineered enzymes. We demonstrate that an NADH-dependent pathway enables anaerobic isobutanol production at 100% theoretical yield and at higher titer and productivity than both the NADPH-dependent pathway and transhydrogenase over-expressing strain. Our results show how engineering cofactor dependence can overcome a critical obstacle to next-generation biofuel commercialization.
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Affiliation(s)
- Sabine Bastian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Siedler S, Bringer S, Bott M. Increased NADPH availability in Escherichia coli: improvement of the product per glucose ratio in reductive whole-cell biotransformation. Appl Microbiol Biotechnol 2011; 92:929-37. [PMID: 21670981 DOI: 10.1007/s00253-011-3374-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/06/2011] [Accepted: 05/06/2011] [Indexed: 11/30/2022]
Abstract
A basic requirement for the efficiency of reductive whole-cell biotransformations is the reducing capacity of the host. Here, the pentose phosphate pathway (PPP) was applied for NADPH regeneration with glucose as the electron-donating co-substrate using Escherichia coli as host. Reduction of the prochiral β-keto ester methyl acetoacetate to the chiral hydroxy ester (R)-methyl 3-hydroxybutyrate (MHB) served as a model reaction, catalyzed by an R-specific alcohol dehydrogenase. The main focus was maximization of the reduced product per glucose yield of this pathway-coupled cofactor regeneration with resting cells. With a strain lacking the phosphoglucose isomerase, the yield of the reference strain was increased from 2.44 to 3.78 mol MHB/mol glucose. Even higher yields were obtained with strains lacking either phosphofructokinase I (4.79 mol MHB/mol glucose) or phosphofructokinase I and II (5.46 mol MHB/mol glucose). These results persuasively demonstrate the potential of NADPH generation by the PPP in whole-cell biotransformations.
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Affiliation(s)
- Solvej Siedler
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, 52425, Jülich, Germany
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Lee WH, Chin YW, Han NS, Kim MD, Seo JH. Enhanced production of GDP-L-fucose by overexpression of NADPH regenerator in recombinant Escherichia coli. Appl Microbiol Biotechnol 2011; 91:967-76. [PMID: 21538115 DOI: 10.1007/s00253-011-3271-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 03/19/2011] [Accepted: 03/23/2011] [Indexed: 11/29/2022]
Abstract
Biosynthesis of guanosine 5'-diphosphate-L-fucose (GDP-L-fucose) requires NADPH as a reducing cofactor. In this study, endogenous NADPH regenerating enzymes such as glucose-6-phosphate dehydrogenase (G6PDH), isocitrate dehydrogenase (Icd), and NADP(+)-dependent malate dehydrogenase (MaeB) were overexpressed to increase GDP-L-fucose production in recombinant Escherichia coli. The effects of overexpression of each NADPH regenerating enzyme on GDP-L-fucose production were investigated in a series of batch and fed-batch fermentations. Batch fermentations showed that overexpression of G6PDH was the most effective for GDP-L-fucose production. However, GDP-L-fucose production was not enhanced by overexpression of G6PDH in the glucose-limited fed-batch fermentation. Hence, a glucose feeding strategy was optimized to enhance GDP-L-fucose production. Fed-batch fermentation with a pH-stat feeding mode for sufficient supply of glucose significantly enhanced GDP-L-fucose production compared with glucose-limited fed-batch fermentation. A maximum GDP-L-fucose concentration of 235.2 ± 3.3 mg l(-1), corresponding to a 21% enhancement in the GDP-L-fucose production compared with the control strain overexpressing GDP-L-fucose biosynthetic enzymes only, was achieved in the pH-stat fed-batch fermentation of the recombinant E. coli overexpressing G6PDH. It was concluded that sufficient glucose supply and efficient NADPH regeneration are crucial for NADPH-dependent GDP-L-fucose production in recombinant E. coli.
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Affiliation(s)
- Won-Heong Lee
- Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, South Korea
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