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Wang Y, Zhou J, Zhang Z, Huang L, Zhang B, Liu Z, Zheng Y. Efficient carbon flux allocation towards D-pantothenic acid production via growth-decoupled strategy in Escherichia coli. BIORESOURCE TECHNOLOGY 2024; 411:131325. [PMID: 39179135 DOI: 10.1016/j.biortech.2024.131325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
For industrial strain construction, rational allocation of carbon flux is of paramount importance especially for decoupling cell growth and chemical productions to get maximum titer, rate, yield (TRY), which become Gordian Knot. Here, a temperature-sensitive switch and genetic circuits was used for effectively decoupling cell growth from D-pantothenic acid (DPA) production, along with systematically metabolic engineering including blocking redundant pathways of pyruvate and enhancing DPA driving force. Afterwards, rapid biomass accumulation only happened during growth stage, and subsequent high-efficient DPA production was initiated with reducing fermentation temperature. Finally, 97.20 g/L DPA and 0.64 g/g glucose conversion rate were achieved in 5-liter fed-batch fermentation. These undisputedly represent a milestone for the biosynthesis of DPA. With using strategies for decoupling cell growth from chemical productions, it would serve as "Alexander's sword" to cut Gordian Knot to get industrial chassis cells with excellent TRY for de novo biosynthesis of valuable chemicals.
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Affiliation(s)
- Yihong Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Junping Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zheng Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lianggang Huang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhiqiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
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Wu W, Chen M, Li C, Zhong J, Xie R, Pan Z, Lin J, Qi F. Efficient production of phenyllactic acid in Escherichia coli via metabolic engineering and fermentation optimization strategies. Front Microbiol 2024; 15:1457628. [PMID: 39247693 PMCID: PMC11377314 DOI: 10.3389/fmicb.2024.1457628] [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: 07/01/2024] [Accepted: 08/14/2024] [Indexed: 09/10/2024] Open
Abstract
Phenyllactic acid (PhLA), an important natural organic acid, can be used as a biopreservative, monomer of the novel polymeric material poly (phenyllactic acid), and raw material for various medicines. Herein, we achieved a high-level production of PhLA in Escherichia coli through the application of metabolic engineering and fermentation optimization strategies. First, the PhLA biosynthetic pathway was established in E. coli CGSC4510, and the phenylalanine biosynthetic pathway was disrupted to improve the carbon flux toward PhLA biosynthesis. Then, we increased the copy number of the key genes involved in the synthesis of the PhLA precursor phenylpyruvic acid. Concurrently, we disrupted the tryptophan biosynthetic pathway and enhanced the availability of phosphoenolpyruvate and erythrose 4-phosphate, thereby constructing the genetically engineered strain MG-P10. This strain was capable of producing 1.42 ± 0.02 g/L PhLA through shake flask fermentation. Furthermore, after optimizing the dissolved oxygen feedback feeding process and other conditions, the PhLA yield reached 52.89 ± 0.25 g/L in a 6 L fermenter. This study successfully utilized metabolic engineering and fermentation optimization strategies to lay a foundation for efficient PhLA production in E. coli as an industrial application.
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Affiliation(s)
- Weibin Wu
- Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Maosen Chen
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Chenxi Li
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jie Zhong
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Rusheng Xie
- Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Zhibin Pan
- Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Junhan Lin
- Fujian Vocational College of Bioengineering, Fuzhou, China
| | - Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
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Rajpurohit H, Eiteman MA. Citrate synthase variants improve yield of acetyl-CoA derived 3-hydroxybutyrate in Escherichia coli. Microb Cell Fact 2024; 23:173. [PMID: 38867236 PMCID: PMC11167817 DOI: 10.1186/s12934-024-02444-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The microbial chiral product (R)-3-hydroxybutyrate (3-HB) is a gateway to several industrial and medical compounds. Acetyl-CoA is the key precursor for 3-HB, and several native pathways compete with 3-HB production. The principal competing pathway in wild-type Escherichia coli for acetyl-CoA is mediated by citrate synthase (coded by gltA), which directs over 60% of the acetyl-CoA into the tricarboxylic acid cycle. Eliminating citrate synthase activity (deletion of gltA) prevents growth on glucose as the sole carbon source. In this study, an alternative approach is used to generate an increased yield of 3-HB: citrate synthase activity is reduced but not eliminated by targeted substitutions in the chromosomally expressed enzyme. RESULTS Five E. coli GltA variants were examined for 3-HB production via heterologous overexpression of a thiolase (phaA) and NADPH-dependent acetoacetyl-CoA reductase (phaB) from Cupriavidus necator. In shake flask studies, four variants showed nearly 5-fold greater 3-HB yield compared to the wild-type, although pyruvate accumulated. Overexpression of either native thioesterases TesB or YciA eliminated pyruvate formation, but diverted acetyl-CoA towards acetate formation. Overexpression of pantothenate kinase similarly decreased pyruvate formation but did not improve 3-HB yield. Controlled batch studies at the 1.25 L scale demonstrated that the GltA[A267T] variant produced the greatest 3-HB titer of 4.9 g/L with a yield of 0.17 g/g. In a phosphate-starved repeated batch process, E. coli ldhA poxB pta-ackA gltA::gltA[A267T] generated 15.9 g/L 3-HB (effective concentration of 21.3 g/L with dilution) with yield of 0.16 g/g from glucose as the sole carbon source. CONCLUSIONS This study demonstrates that GltA variants offer a means to affect the generation of acetyl-CoA derived products. This approach should benefit a wide range of acetyl-CoA derived biochemical products in E. coli and other microbes. Enhancing substrate affinity of the introduced pathway genes like thiolase towards acetyl-CoA will likely further increase the flux towards 3-HB while reducing pyruvate and acetate accumulation.
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Affiliation(s)
| | - Mark A Eiteman
- School of Chemical, Materials and Biomedical Engineering, Athens, GA, USA.
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Hao Y, Pan X, You J, Li G, Xu M, Rao Z. Microbial production of branched chain amino acids: Advances and perspectives. BIORESOURCE TECHNOLOGY 2024; 397:130502. [PMID: 38417463 DOI: 10.1016/j.biortech.2024.130502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Branched-chain amino acids (BCAAs) such as L-valine, L-leucine, and L-isoleucine are widely used in food and feed. To comply with sustainable development goals, commercial production of BCAAs has been completely replaced with microbial fermentation. However, the efficient production of BCAAs by microorganisms remains a serious challenge due to their staggered metabolic networks and cell growth. To overcome these difficulties, systemic metabolic engineering has emerged as an effective and feasible strategy for the biosynthesis of BCAA. This review firstly summarizes the research advances in the microbial synthesis of BCAAs and representative engineering strategies. Second, systematic methods, such as high-throughput screening, adaptive laboratory evolution, and omics analysis, can be used to analyses the synthesis of BCAAs at the whole-cell level and further improve the titer of target chemicals. Finally, new tools and engineering strategies that may increase the production output and development direction of the microbial production of BCAAs are discussed.
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Affiliation(s)
- Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guomin Li
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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Zhang B, Zhang YQ, He ZL, Xiao YY, Tang MN, Zhou JP, Liu ZQ, Zheng YG. Engineered E. coli for D-pantothenic acid production with an acetolactate isomeroreductase mutant. 3 Biotech 2024; 14:117. [PMID: 38524241 PMCID: PMC10959892 DOI: 10.1007/s13205-024-03931-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/11/2024] [Indexed: 03/26/2024] Open
Abstract
D-Pantothenic acid, as a momentous vitamin, is extensively applied to feed, medicine, cosmetics and other fields. However, there are still limitations to produce D-pantothenic acid by microbial fermentation at present. In this paper, we constructed a recombinant strain for D-pantothenic acid production by blocking the organic acid pathway, boosting pyruvate biosynthesis, relieving feedback inhibition of acetolactate synthase, improving glucose intake capacity, and modifying essential genes in the metabolic pathway. In addition, a new acetolactate isomeroreductase mutant V412A origin from Escherichia coli (EcAHAIR) encoded by ilvC was obtained to explore its substrate promiscuity. Compared with the wild type, the variant EcAHAIR-V412A has reduced steric hindrance and enhanced intermolecular forces, resulting in a high affinity for 2-acetolactate. Eventually, the fermentation production of the final strain DPAN19/trc-ilvCV412A reached 4.65 g/L, increased by 192.5% compared with strain DPA8 in shake flask cultivation and produced 62.82 g/L D-pantothenic acid in a 5 L bioreactor. The metabolic engineering strategies and enzyme modification approaches described in this paper provide a particular perspective for the bio-manufacturing of D-pantothenic acid, branched-chain amino acids and its derivates.
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Affiliation(s)
- Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu-Qiong Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Zhou-Lin He
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yun-Ying Xiao
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Meng-Na Tang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Jun-Ping Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
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Zhao K, Tang H, Zhang B, Zou S, Liu Z, Zheng Y. Microbial production of vitamin B5: current status and prospects. Crit Rev Biotechnol 2023; 43:1172-1192. [PMID: 36210178 DOI: 10.1080/07388551.2022.2104690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 07/01/2022] [Indexed: 11/03/2022]
Abstract
Vitamin B5, also called D-pantothenic acid (D-PA), is a necessary micronutrient that plays an essential role in maintaining the physiological function of an organism. It is widely used in: food, medicine, feed, cosmetics, and other fields. Currently, the production of D-PA in industry heavily relies on chemical processes and enzymatic catalysis. With an increasing demand on the market, replacing chemical-based production of D-PA with microbial fermentation utilizing renewable resources is necessary. In this review, the physiological role and applications of D-PA were firstly introduced, after which the biosynthesis pathways and enzymes will be summarized. Subsequently, a series of cell factory development strategies for excessive D-PA production are analyzed and discussed. Finally, the prospect of microbial production of D-PA production has been prospected.
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Affiliation(s)
- Kuo Zhao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Bo Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Zhiqiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, PR China
- College of Biotechnology and Bioengineering, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, Zhejiang University of Technology, Hangzhou, PR China
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Kim WJ, Lee Y, Kim HU, Ryu JY, Yang JE, Lee SY. Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes. Cell Syst 2023; 14:990-1001.e5. [PMID: 37935194 DOI: 10.1016/j.cels.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/23/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023]
Abstract
In metabolic engineering, predicting gene overexpression targets remains challenging because both endogenous and heterologous genes in a large metabolic space can be candidates, in contrast to gene knockout targets that are confined to endogenous genes. We report the development of iBridge that identifies positive and negative metabolites exerting positive and negative impacts on product formation, respectively, based on the sum of covariances of their outgoing (consuming) reaction fluxes for a target chemical. Then, "bridge" reactions converting negative metabolites to positive metabolites are identified as overexpression targets, while the opposites as downregulation targets. Using iBridge, overexpression and downregulation targets are suggested for the production of 298 chemicals and validated for 36 chemicals experimentally demonstrated in previous studies. Finally, iBridge is employed to engineer Escherichia coli strains capable of producing 10.3 g/L of D-panthenol, a compound not previously produced, as well as putrescine and 4-hydroxyphenyllactate at enhanced titers, 63.7 and 8.3 g/L, respectively.
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Affiliation(s)
- Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Youngjoon Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
| | - Jae Yong Ryu
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jung Eun Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea.
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Carranza-Saavedra D, Torres-Bacete J, Blázquez B, Sánchez Henao CP, Zapata Montoya JE, Nogales J. System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock. Front Bioeng Biotechnol 2023; 11:1176445. [PMID: 37152640 PMCID: PMC10158823 DOI: 10.3389/fbioe.2023.1176445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Replacing traditional substrates in industrial bioprocesses to advance the sustainable production of chemicals is an urgent need in the context of the circular economy. However, since the limited degradability of non-conventional carbon sources often returns lower yields, effective exploitation of such substrates requires a multi-layer optimization which includes not only the provision of a suitable feedstock but the use of highly robust and metabolically versatile microbial biocatalysts. We tackled this challenge by means of systems metabolic engineering and validated Escherichia coli W as a promising cell factory for the production of the key building block chemical 2-ketoisovalerate (2-KIV) using whey as carbon source, a widely available and low-cost agro-industrial waste. First, we assessed the growth performance of Escherichia coli W on mono and disaccharides and demonstrated that using whey as carbon source enhances it significantly. Second, we searched the available literature and used metabolic modeling approaches to scrutinize the metabolic space of E. coli and explore its potential for overproduction of 2-KIV identifying as basic strategies the block of pyruvate depletion and the modulation of NAD/NADP ratio. We then used our model predictions to construct a suitable microbial chassis capable of overproducing 2-KIV with minimal genetic perturbations, i.e., deleting the pyruvate dehydrogenase and malate dehydrogenase. Finally, we used modular cloning to construct a synthetic 2-KIV pathway that was not sensitive to negative feedback, which effectively resulted in a rerouting of pyruvate towards 2-KIV. The resulting strain shows titers of up to 3.22 ± 0.07 g/L of 2-KIV and 1.40 ± 0.04 g/L of L-valine in 24 h using whey in batch cultures. Additionally, we obtained yields of up to 0.81 g 2-KIV/g substrate. The optimal microbial chassis we present here has minimal genetic modifications and is free of nutritional autotrophies to deliver high 2-KIV production rates using whey as a non-conventional substrate.
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Affiliation(s)
- Darwin Carranza-Saavedra
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
| | - Blas Blázquez
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Claudia Patricia Sánchez Henao
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - José Edgar Zapata Montoya
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - Juan Nogales
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- *Correspondence: Juan Nogales,
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Pan X, Tang M, You J, Hao Y, Zhang X, Yang T, Rao Z. A Novel Method to Screen Strong Constitutive Promoters in Escherichia coli and Serratia marcescens for Industrial Applications. BIOLOGY 2022; 12:biology12010071. [PMID: 36671763 PMCID: PMC9855843 DOI: 10.3390/biology12010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/18/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Promoters serve as the switch of gene transcription, playing an important role in regulating gene expression and metabolites production. However, the approach to screening strong constitutive promoters in microorganisms is still limited. In this study, a novel method was designed to identify strong constitutive promoters in E. coli and S. marcescens based on random genomic interruption and fluorescence-activated cell sorting (FACS) technology. First, genomes of E. coli, Bacillus subtilis, and Corynebacterium glutamicum were randomly interrupted and inserted into the upstream of reporter gene gfp to construct three promoter libraries, and a potential strong constitutive promoter (PBS) suitable for E. coli was screened via FACS technology. Second, the core promoter sequence (PBS76) of the screened promoter was identified by sequence truncation. Third, a promoter library of PBS76 was constructed by installing degenerate bases via chemical synthesis for further improving its strength, and the intensity of the produced promoter PBS76-100 was 59.56 times higher than that of the promoter PBBa_J23118. Subsequently, promoters PBBa_J23118, PBS76, PBS76-50, PBS76-75, PBS76-85, and PBS76-100 with different strengths were applied to enhance the metabolic flux of L-valine synthesis, and the L-valine yield was significantly improved. Finally, a strong constitutive promoter suitable for S. marcescens was screened by a similar method and applied to enhance prodigiosin production by 34.81%. Taken together, the construction of a promoter library based on random genomic interruption was effective to screen the strong constitutive promoters for fine-tuning gene expression and reprogramming metabolic flux in various microorganisms.
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Affiliation(s)
- Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mi Tang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-510-85916881
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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10
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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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11
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Wang Q, Gu J, Shu L, Jiang W, Mojovic L, Knezevic-Jugovic Z, Shi J, Baganz F, Lye GJ, Xiang W, Hao J. Blocking the 2,3-butanediol synthesis pathway of Klebsiella pneumoniae resulted in L-valine production. World J Microbiol Biotechnol 2022; 38:81. [PMID: 35348886 DOI: 10.1007/s11274-022-03266-9] [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: 02/01/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022]
Abstract
Klebsiella pneumoniae is a 2,3-butanediol producing bacterium. Nevertheless, a design and construction of L-valine production strain was studied in this paper. The first step of 2,3-butanediol synthesis and branched-chain amino acid synthesis pathways share the same step of α-acetolactate synthesis from pyruvate. However, the two pathways are existing in parallel and do not interfere with each other in the wild-type strain. A knockout of budA blocked the 2,3-butanediol synthesis pathway and resulted in the L-valine production. The budA coded an α-acetolactate decarboxylase and catalyzed the acetoin formation from α-acetolactate. Furthermore, blocking the lactic acid synthesis by knocking out of ldhA, which is encoding a lactate dehydrogenase, improved the L-valine synthesis. 2-Ketoisovalerate is the precursor of L-valine, it is also an intermediate of the isobutanol synthesis pathway, while indole-3-pyruvate decarboxylase (ipdC) is responsible for isobutyraldehyde formation from 2-ketoisovalerate. Production of L-valine has been improved by knocking out of ipdC. On the other side, the ilvE, encoding a transaminase B, reversibly transfers one amino group from glutamate to α-ketoisovalerate. Overexpression of ilvE exhibited a distinct improvement of L-valine production. The brnQ encodes a branched-chain amino acid transporter, and L-valine production was further improved by disrupting brnQ. It is also revealed that weak acidic and aerobic conditions favor L-valine production. Based on these findings, L-valine production by metabolically engineered K. pneumonia was examined. In fed-batch fermentation, 22.4 g/L of L-valine was produced by the engineered K. pneumoniae ΔbudA-ΔldhA-ΔipdC-ΔbrnQ-ilvE after 55 h of cultivation, with a substrate conversion ratio of 0.27 mol/mol glucose.
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Affiliation(s)
- Qinghui Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.,Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Jinjie Gu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Lin Shu
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Weiyan Jiang
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Ljiljana Mojovic
- Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
| | | | - Jiping Shi
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China
| | - Frank Baganz
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Gary J Lye
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
| | - Jian Hao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99 Haike Road, Pudong, Shanghai, 201210, People's Republic of China. .,Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK.
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12
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Li B, Zhang B, Wang P, Cai X, Tang YQ, Jin JY, Liang JX, Liu ZQ, Zheng YG. Targeting metabolic driving and minimization of by-products synthesis for high-yield production of D-pantothenate in Escherichia coli. Biotechnol J 2021; 17:e2100431. [PMID: 34705325 DOI: 10.1002/biot.202100431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 01/02/2023]
Abstract
BACKGROUND d-Pantothenate (DPA) is an important functional chemical that has been widely applied in healthcare, cosmetics, animal food, and feed industries. METHODS AND RESULTS In this study, a high-yield DPA-producing strain was constructed by metabolic engineering strategies with targeting metabolic driving and by-products minimization. The metabolic driving force of push and pull was firstly obtained to improve the production of DPA via enrichment of precursor pool and synthetic pathway, accumulating 4.29 g L-1 DPA in shake flask fermentation. To eliminate the metabolic pressure on DPA production, an amino throttling system was proposed and successfully attenuated the synthesis of four competitive amino acids by a single-step regulation of gdhA. Further minimization of acetate was carried out by pta deletion, and utilization of β-alanine was improved via enhancing its uptake system with producing 5.78 g L-1 DPA. Finally, the engineered strain produced 66.39 g L-1 DPA with β-alanine addition in fermentor under fed-batch fermentation. CONCLUSION This study paved a foundation for the industrial production of DPA.
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Affiliation(s)
- Bo Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Pei Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Xue Cai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Qun Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Jie-Yi Jin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Jin-Xi Liang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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13
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Strengthening the (R)-pantoate pathway to produce D-pantothenic acid based on systematic metabolic analysis. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Carranza-Saavedra D, Sánchez Henao CP, Zapata Montoya JE. Kinetic analysis and modeling of L-valine production in fermentation batch from E. coli using glucose, lactose and whey as carbon sources. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 31:e00642. [PMID: 34150530 PMCID: PMC8193114 DOI: 10.1016/j.btre.2021.e00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022]
Abstract
In this study the effect of the carbon source on L-valine production kinetics using genetically modified E. coli was researched. Glucose, lactose, Whey (W) and deproteinized whey (DW) were tested as carbon sources, keeping the carbon/nitrogen (C/N) ratio constant. Biomass generation and substrate consumption were modeled with Contois and Mass Conservation models, respectively, whereas Mass Conservation Balance and Luedeking-Piret models were used for product obtaining. Results showed that L-valine production is partially associated to growth, with values of 0.485 g L-valine/(g dry cell weight.h), and a product loss effect at a specific rate (β) of 0.019 g L-valine/(g dry cell weight.h) with W. The yield of this product increased 36 % using W concerning glucose or lactose as carbon sources. On the other hand, Mass Balance and Luedeking-Piret models adjust properly to experimental data (R2 >0.90). In conclusion whey is a promising substrate for obtaining L-valine using genetically-modified E. coli.
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Affiliation(s)
- Darwin Carranza-Saavedra
- Grupo Nutrición y Tecnología de Alimentos, Universidad de Antioquia, Medellín 050010, Colombia
- Departamento de Producción y Sanidad Vegetal, Facultad de Ingeniería Agronómica, Universidad Del Tolima, Ibagué 730006299, Colombia
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15
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Gao H, Tuyishime P, Zhang X, Yang T, Xu M, Rao Z. Engineering of microbial cells for L-valine production: challenges and opportunities. Microb Cell Fact 2021; 20:172. [PMID: 34461907 PMCID: PMC8406616 DOI: 10.1186/s12934-021-01665-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and special nutrients in pharmaceutical and agriculture fields. Currently, fermentation with the aid of model organisms, is a major method for the production of L-valine. However, achieving the optimal production has often been limited because of the metabolic imbalance in recombinant strains. In this review, the constrains in L-valine biosynthesis are discussed first. Then, we summarize the current advances in engineering of microbial cell factories that have been developed to address and overcome major challenges in the L-valine production process. Future prospects for enhancing the current L-valine production strategies are also discussed.
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Affiliation(s)
- Hui Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Philibert Tuyishime
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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16
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L-valine production in Corynebacterium glutamicum based on systematic metabolic engineering: progress and prospects. Amino Acids 2021; 53:1301-1312. [PMID: 34401958 DOI: 10.1007/s00726-021-03066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
L-valine is an essential branched-chain amino acid that cannot be synthesized by the human body and has a wide range of applications in food, medicine and feed. Market demand has stimulated people's interest in the industrial production of L-valine. At present, the mutagenized or engineered Corynebacterium glutamicum is an effective microbial cell factory for producing L-valine. Because the biosynthetic pathway and metabolic network of L-valine are intricate and strictly regulated by a variety of key enzymes and genes, highly targeted metabolic engineering can no longer meet the demand for efficient biosynthesis of L-valine. In recent years, the development of omics technology has promoted the upgrading of traditional metabolic engineering to systematic metabolic engineering. This whole-cell-scale transformation strategy has become a productive method for developing L-valine producing strains. This review provides an overview of the biosynthesis and regulation mechanism of L-valine, and summarizes the current metabolic engineering techniques and strategies for constructing L-valine high-producing strains. Finally, the opinion of constructing a cell factory for efficiently biosynthesizing L-valine was proposed.
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17
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Improved production of D-pantothenic acid in Escherichia coli by integrated strain engineering and fermentation strategies. J Biotechnol 2021; 339:65-72. [PMID: 34352344 DOI: 10.1016/j.jbiotec.2021.07.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 11/23/2022]
Abstract
D-pantothenic acid (D-PA) is an essential vitamin that has been widely used in medicine, food, and animal feed. Microbial production of D-PA from natural renewable resources is attractive and challenging. In this study, both strain improvements and fermentation process strategies were applied to achieve high-level D-PA production in Escherichia coli. First, a D-PA-producing strain was developed through deletion of the aceF and mdh genes combined with the overexpression of the gene ppnk. The obtained engineered E. coli DPA02/pT-ppnk accumulated 6.89 ± 0.11 g/L of D-PA in shake flask fermentation, which was 79.9 % higher than the control strain. Moreover, the cultivation process contributed greatly to D-PA production with respect to titer and productivity by betaine supplementation and dissolved oxygen (DO)-feedback feeding framework. Under optimal conditions, 68.3 g/L of D-PA, the specific productivity of 0.794 g/L h and the yield of 0.36 g/g glucose in 5 L fermenter were achieved. Overall, this research successfully exploited advanced strategies to lay the foundation for bio-based D-PA production in industrial applications.
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18
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Luo ZW, Ahn JH, Chae TU, Choi SY, Park SY, Choi Y, Kim J, Prabowo CPS, Lee JA, Yang D, Han T, Xu H, Lee SY. Metabolic Engineering of
Escherichia
coli. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Kumar P, Adamczyk PA, Zhang X, Andrade RB, Romero PA, Ramanathan P, Reed JL. Active and machine learning-based approaches to rapidly enhance microbial chemical production. Metab Eng 2021; 67:216-226. [PMID: 34229079 DOI: 10.1016/j.ymben.2021.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/12/2021] [Accepted: 06/29/2021] [Indexed: 10/20/2022]
Abstract
In order to make renewable fuels and chemicals from microbes, new methods are required to engineer microbes more intelligently. Computational approaches, to engineer strains for enhanced chemical production typically rely on detailed mechanistic models (e.g., kinetic/stoichiometric models of metabolism)-requiring many experimental datasets for their parameterization-while experimental methods may require screening large mutant libraries to explore the design space for the few mutants with desired behaviors. To address these limitations, we developed an active and machine learning approach (ActiveOpt) to intelligently guide experiments to arrive at an optimal phenotype with minimal measured datasets. ActiveOpt was applied to two separate case studies to evaluate its potential to increase valine yields and neurosporene productivity in Escherichia coli. In both the cases, ActiveOpt identified the best performing strain in fewer experiments than the case studies used. This work demonstrates that machine and active learning approaches have the potential to greatly facilitate metabolic engineering efforts to rapidly achieve its objectives.
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Affiliation(s)
- Prashant Kumar
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI, 53706, USA; ZS Associates, 1560 Sherman Ave, Evanston, IL, 60201, USA
| | - Paul A Adamczyk
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI, 53706, USA
| | - Xiaolin Zhang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI, 53706, USA
| | - Ramon Bonela Andrade
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI, 53706, USA
| | - Philip A Romero
- Department of Biochemistry, University of Wisconsin-Madison, 440 Henry Mall, Madison, WI, 53706, USA
| | - Parameswaran Ramanathan
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI, 53706, USA.
| | - Jennifer L Reed
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr., Madison, WI, 53706, USA
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20
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Salazar S, Gutiérrez N, Sánchez O, Ramos E, González A, Acosta J, Ramos T, Altamirano C, Toledo J, Montesino R. Establishment of a production process for a novel vaccine candidate against Lawsonia intracellularis. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications. Methods Mol Biol 2021; 2189:217-229. [PMID: 33180304 DOI: 10.1007/978-1-0716-0822-7_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genome-scale metabolic modeling is and will continue to play a central role in computational systems metabolic engineering and synthetic biology applications for the productions of chemicals and antibiotics. To that end, a survey and workflows of methods used for the development of high-quality genome-scale metabolic models (GEMs) and chassis design for synthetic biology are described here. The chapter consists of two parts (a) the methods of development of GEMs (Escherichia coli as a case study) and (b) E. coli chassis design for synthetic production of 1,4-butanediol (BDO). The methods described here can guide existing and future development of GEMs coupled with host chassis design for synthetic productions of novel antibiotics.
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22
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Hao Y, Ma Q, Liu X, Fan X, Men J, Wu H, Jiang S, Tian D, Xiong B, Xie X. High-yield production of L-valine in engineered Escherichia coli by a novel two-stage fermentation. Metab Eng 2020; 62:198-206. [DOI: 10.1016/j.ymben.2020.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/24/2020] [Accepted: 09/16/2020] [Indexed: 01/27/2023]
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23
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Tran KNT, Eom GT, Hong SH. Improving L-serine production in Escherichia coli via synthetic protein scaffold of SerB, SerC, and EamA. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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24
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Geraskina NV, Sycheva EV, Samsonov VV, Eremina NS, Hook CD, Serebrianyi VA, Stoynova NV. Engineering Escherichia coli for autoinducible production of L-valine: An example of an artificial positive feedback loop in amino acid biosynthesis. PLoS One 2019; 14:e0215777. [PMID: 31022249 PMCID: PMC6483228 DOI: 10.1371/journal.pone.0215777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Artificial metabolically regulated inducible expression systems are often used for the production of essential compounds. In most cases, the application of such systems enables regulating the expression of an entire group of genes in response to any internal signal such as an aerobic/anaerobic switch, a transition to stationary phase, or the exhausting of essential compounds. In this work, we demonstrate an example of another type of artificial autoinducible module, denoted a positive feedback module. This positive feedback module generates an inducer molecule that in turn enhances its own synthesis, promoting an activation signal. Due to the use of acetolactate, an intermediate of the L-valine biosynthetic pathway, as a specific inducer molecule, we realized a positive feedback loop in the biosynthetic pathway of branched chain amino acids. Such positive feedback was demonstrated to improve the production of a target compound.
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Affiliation(s)
| | - Elena V. Sycheva
- Ajinomoto-Genetika Research Institute, Moscow, Russian Federation
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25
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Savrasova EA, Stoynova NV. Application of leucine dehydrogenase Bcd from Bacillus subtilis for l-valine synthesis in Escherichia coli under microaerobic conditions. Heliyon 2019; 5:e01406. [PMID: 30993221 PMCID: PMC6449708 DOI: 10.1016/j.heliyon.2019.e01406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/05/2019] [Accepted: 03/20/2019] [Indexed: 12/02/2022] Open
Abstract
Microaerobic cultivation conditions have been shown experimentally and theoretically to improve the performance of a number of bioproduction systems. However, under these conditions, the production of l-valine by Escherichia coli is decreased mainly because of a redox cofactor imbalance and a decreased l-glutamate supply. The synthesis of one mole of l-valine from one mole of glucose generates two moles of NADH via glycolysis but consumes a total of two moles of NADPH, one in the ketol-acid reductoisomerase (KARI) reaction and the other in the regeneration of l-glutamate as an amino group donor for the branched-chain amino acid aminotransferase (BCAT) reaction. The improvement of l-valine synthesis under oxygen deprivation may be due to solving these problems. Increased l-valine synthesis under oxygen deprivation conditions was previously shown in Corynebacterium glutamicum (Hasegawa et al., 2012). In this study, we have proposed the use of NADH-dependent leucine dehydrogenase (LeuDH; EC 1.4.1.9) Bcd from B. subtilis instead of the native NADPH-dependent pathway including aminotransferase encoded by ilvE to improve l-valine production in E. coli under microaerobic conditions. We have created l-valine-producing strains on the base of the aminotransferase B-deficient strain V1 (B-7 ΔilvBN ΔilvIH ΔilvGME::PL-ilvBNN17KDA) by introducing one chromosomal copy of the bcd gene or the ilvE gene. Evaluation of the l-valine production by the obtained strains under microaerobic and aerobic conditions revealed that leucine dehydrogenase Bcd had a higher potential for l-valine production under microaerobic conditions. The Bcd-possessing strain exhibited 2.2-fold higher l-valine accumulation (up to 9.1 g/L) and 2.0-fold higher yield (up to 35.3%) under microaerobic conditions than the IlvE-possessing strain. The obtained results could be interpreted as follows: an altering of redox cofactor balance in the l-valine biosynthesis pathway increased the production and yield by E. coli cells under microaerobic conditions. Thus, the effective synthesis of l-valine by means of “valine fermentation” was shown in E. coli. This methodology has the advantages of being an economical and environmentally friendly process.
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26
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Adaptive laboratory evolution of a genome-reduced Escherichia coli. Nat Commun 2019; 10:935. [PMID: 30804335 PMCID: PMC6389913 DOI: 10.1038/s41467-019-08888-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain's systems biology.
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Zhang X, Zhang D, Zhu J, Liu W, Xu G, Zhang X, Shi J, Xu Z. High-yield production of L-serine from glycerol by engineered Escherichia coli. J Ind Microbiol Biotechnol 2019; 46:221-230. [PMID: 30600411 DOI: 10.1007/s10295-018-2113-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/20/2018] [Indexed: 01/19/2023]
Abstract
L-Serine is widely used in pharmaceutical, food and cosmetic industries, and the direct fermentation to produce L-serine from cheap carbon sources such as glycerol is greatly desired. The production of L-serine by engineered Escherichia coli from glycerol has not been achieved so far. In this study, E. coli was engineered to efficiently produce L-serine from glycerol. To this end, three L-serine deaminase genes were deleted in turn, and all of the deletions caused the maximal accumulation of L-serine at 0.06 g/L. Furthermore, removal of feedback inhibition by L-serine resulted in a titer of 1.1 g/L. Additionally, adaptive laboratory evolution was employed to improve glycerol utilization in combination with the overexpression of the cysteine/acetyl serine transporter gene eamA, leading to 2.36 g/L L-serine (23.6% of the theoretical yield). In 5-L bioreactor, L-serine titer could reach up to 7.53 g/L from glycerol, demonstrating the potential of the established strain and bioprocess.
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Affiliation(s)
- Xiaomei Zhang
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science, Jiangnan University, Wuxi, People's Republic of China
| | - Dong Zhang
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science, Jiangnan University, Wuxi, People's Republic of China
| | - Jiafen Zhu
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science, Jiangnan University, Wuxi, People's Republic of China
| | - Wang Liu
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science, Jiangnan University, Wuxi, People's Republic of China
| | - Guoqiang Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Xiaojuan Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Jinsong Shi
- Laboratory of Pharmaceutical Engineering, School of Pharmaceutics Science, Jiangnan University, Wuxi, People's Republic of China
| | - Zhenghong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, People's Republic of China. .,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China.
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Westbrook AW, Ren X, Moo‐Young M, Chou CP. Metabolic engineering ofBacillus subtilisforl‐valine overproduction. Biotechnol Bioeng 2018; 115:2778-2792. [DOI: 10.1002/bit.26789] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Adam W. Westbrook
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
| | - Xiang Ren
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
| | - Murray Moo‐Young
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
| | - C. Perry Chou
- Department of Chemical EngineeringUniversity of WaterlooWaterloo Ontario Canada
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Genome shuffling and high-throughput screening of Brevibacterium flavum MDV1 for enhanced l-valine production. World J Microbiol Biotechnol 2018; 34:121. [DOI: 10.1007/s11274-018-2502-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 07/10/2018] [Indexed: 11/25/2022]
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30
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Tsipa A, Koutinas M, Usaku C, Mantalaris A. Optimal bioprocess design through a gene regulatory network - Growth kinetic hybrid model: Towards replacing Monod kinetics. Metab Eng 2018; 48:129-137. [PMID: 29729316 DOI: 10.1016/j.ymben.2018.04.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/14/2018] [Accepted: 04/30/2018] [Indexed: 01/01/2023]
Abstract
Currently, design and optimisation of biotechnological bioprocesses is performed either through exhaustive experimentation and/or with the use of empirical, unstructured growth kinetics models. Whereas, elaborate systems biology approaches have been recently explored, mixed-substrate utilisation is predominantly ignored despite its significance in enhancing bioprocess performance. Herein, bioprocess optimisation for an industrially-relevant bioremediation process involving a mixture of highly toxic substrates, m-xylene and toluene, was achieved through application of a novel experimental-modelling gene regulatory network - growth kinetic (GRN-GK) hybrid framework. The GRN model described the TOL and ortho-cleavage pathways in Pseudomonas putida mt-2 and captured the transcriptional kinetics expression patterns of the promoters. The GRN model informed the formulation of the growth kinetics model replacing the empirical and unstructured Monod kinetics. The GRN-GK framework's predictive capability and potential as a systematic optimal bioprocess design tool, was demonstrated by effectively predicting bioprocess performance, which was in agreement with experimental values, when compared to four commonly used models that deviated significantly from the experimental values. Significantly, a fed-batch biodegradation process was designed and optimised through the model-based control of TOL Pr promoter expression resulting in 61% and 60% enhanced pollutant removal and biomass formation, respectively, compared to the batch process. This provides strong evidence of model-based bioprocess optimisation at the gene level, rendering the GRN-GK framework as a novel and applicable approach to optimal bioprocess design. Finally, model analysis using global sensitivity analysis (GSA) suggests an alternative, systematic approach for model-driven strain modification for synthetic biology and metabolic engineering applications.
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Affiliation(s)
- Argyro Tsipa
- Department of Chemical Engineering, South Kensington Campus, Imperial College London, London, United Kingdom
| | - Michalis Koutinas
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kuprianou Str., Limassol, Cyprus
| | - Chonlatep Usaku
- Department of Chemical Engineering, South Kensington Campus, Imperial College London, London, United Kingdom; Department of Biotechnology, Silpakorn University, Nakorn Pathom 73000, Thailand
| | - Athanasios Mantalaris
- Department of Chemical Engineering, South Kensington Campus, Imperial College London, London, United Kingdom.
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31
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Wang X, Zhang H, Quinn PJ. Production of l-valine from metabolically engineered Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:4319-4330. [DOI: 10.1007/s00253-018-8952-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 01/25/2023]
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Abstract
Systems metabolic engineering, which recently emerged as metabolic engineering integrated with systems biology, synthetic biology, and evolutionary engineering, allows engineering of microorganisms on a systemic level for the production of valuable chemicals far beyond its native capabilities. Here, we review the strategies for systems metabolic engineering and particularly its applications in Escherichia coli. First, we cover the various tools developed for genetic manipulation in E. coli to increase the production titers of desired chemicals. Next, we detail the strategies for systems metabolic engineering in E. coli, covering the engineering of the native metabolism, the expansion of metabolism with synthetic pathways, and the process engineering aspects undertaken to achieve higher production titers of desired chemicals. Finally, we examine a couple of notable products as case studies produced in E. coli strains developed by systems metabolic engineering. The large portfolio of chemical products successfully produced by engineered E. coli listed here demonstrates the sheer capacity of what can be envisioned and achieved with respect to microbial production of chemicals. Systems metabolic engineering is no longer in its infancy; it is now widely employed and is also positioned to further embrace next-generation interdisciplinary principles and innovation for its upgrade. Systems metabolic engineering will play increasingly important roles in developing industrial strains including E. coli that are capable of efficiently producing natural and nonnatural chemicals and materials from renewable nonfood biomass.
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Huang Z, Lee DY, Yoon S. Quantitative intracellular flux modeling and applications in biotherapeutic development and production using CHO cell cultures. Biotechnol Bioeng 2017; 114:2717-2728. [DOI: 10.1002/bit.26384] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 06/07/2017] [Accepted: 07/12/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Zhuangrong Huang
- Department of Chemical Engineering, University of Massachusetts Lowell; One University Avenue; Lowell Massachusetts
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering; National University of Singapore; Singapore Singapore
- Bioprocessing Technology Institute; Agency for Science, Technology and Research (A*STAR); Singapore Singapore
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell; One University Avenue; Lowell Massachusetts
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Ming LC, Halim M, Rahim RA, Wan HY, Ariff AB. Strategies in fed-batch cultivation on the production performance of Lactobacillus salivarius I 24 viable cells. Food Sci Biotechnol 2016; 25:1393-1398. [PMID: 30263421 PMCID: PMC6049257 DOI: 10.1007/s10068-016-0217-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/02/2016] [Accepted: 06/15/2016] [Indexed: 10/20/2022] Open
Abstract
The potential use of fed-batch cultivation (FBC) for improvement of the production of Lactobacillus salivarius I 24 biomass for subsequent use as probiotics was studied using a 2-L stirredtank bioreactor. Three different constant feeding rates (0.1, 0.05, and 0.033 L/h) were applied in FBCs and their effect on carbon metabolism was evaluated. The carbon flux for cell built-up with reduction in lactic acid synthesis was observed in the fed-batch as compared to the batch cultivation mode. The viable cell number obtained in the constant FBC (CFBC) operated at a feeding rate of 0.05 L/h was 8 times higher (10.7×1010 CFU/mL) than that recorded in the batch cultivation. This gave the viable cell yield based on glucose consumed for CFBC of 26 times higher (11.3×1012 CFU/gGlucose) than the batch cultivation. This study demonstrated CFBC, which is simple with minimal use of process control equipment, has an industrial potential for improvement of probiotic production.
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Affiliation(s)
- Lim Chi Ming
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Murni Halim
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Bioprocessing and Biomanufacturing Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raha Abd Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Ho Yin Wan
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Arbakariya Bin Ariff
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Bioprocessing and Biomanufacturing Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Yang JE, Kim JW, Oh YH, Choi SY, Lee H, Park AR, Shin J, Park SJ, Lee SY. Biosynthesis of poly(2-hydroxyisovalerate-co-lactate) by metabolically engineeredEscherichia coli. Biotechnol J 2016; 11:1572-1585. [DOI: 10.1002/biot.201600420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/22/2016] [Accepted: 09/06/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Jung Eun Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Je Woong Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Young Hoon Oh
- Center for Bio-based Chemistry, Division of Convergence Chemistry; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyuk Lee
- Division of Drug Discovery Research; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - A-Reum Park
- Division of Drug Discovery Research; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - Jihoon Shin
- Center for Bio-based Chemistry, Division of Convergence Chemistry; Korea Research Institute of Chemical Technology; Daejeon Republic of Korea
| | - Si Jae Park
- Department of Environmental Engineering and Energy; Myongji University; Gyeonggido Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
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Recent advances in amino acid production by microbial cells. Curr Opin Biotechnol 2016; 42:133-146. [PMID: 27151315 DOI: 10.1016/j.copbio.2016.04.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 12/25/2022]
Abstract
Amino acids have been utilized for the production of foods, animal feeds and pharmaceuticals. After the discovery of the glutamic acid-producing bacterium Corynebacterium glutamicum by Japanese researchers, the production of amino acids, which are primary metabolites, has been achieved using various microbial cells as hosts. Recently, metabolic engineering studies on the rational design of amino acid-producing microbial cells have been successfully conducted. Moreover, the technology of systems biology has been applied to metabolic engineering for the creation of amino acid-producing microbial cells. Currently, new technologies including synthetic biology, single-cell analysis, and evolutionary engineering have been utilized to create amino acid-producing microbial cells. In addition, useful compounds from amino acids have been produced by microbial cells. Here, current researches into the metabolic engineering of microbial cells toward production of amino acids and amino acid-related compounds are reviewed.
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McCloskey D, Young JD, Xu S, Palsson BO, Feist AM. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Anal Chem 2016; 88:3844-52. [DOI: 10.1021/acs.analchem.5b04914] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Douglas McCloskey
- Department
of Bioengineering, University of California, San Diego, California 92093, United States
| | | | - Sibei Xu
- Department
of Bioengineering, University of California, San Diego, California 92093, United States
| | - Bernhard O. Palsson
- Department
of Bioengineering, University of California, San Diego, California 92093, United States
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Adam M. Feist
- Department
of Bioengineering, University of California, San Diego, California 92093, United States
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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38
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Gu P, Su T, Qi Q. Novel technologies provide more engineering strategies for amino acid-producing microorganisms. Appl Microbiol Biotechnol 2016; 100:2097-105. [PMID: 26754821 DOI: 10.1007/s00253-015-7276-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/20/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
Traditionally, amino acid-producing strains were obtained by random mutagenesis and subsequent selection. With the development of genetic and metabolic engineering techniques, various microorganisms with high amino acid production yields are now constructed by rational design of targeted biosynthetic pathways. Recently, novel technologies derived from systems and synthetic biology have emerged and open a new promising avenue towards the engineering of amino acid production microorganisms. In this review, these approaches, including rational engineering of rate-limiting enzymes, real-time sensing of end-products, pathway optimization on the chromosome, transcription factor-mediated strain improvement, and metabolic modeling and flux analysis, were summarized with regard to their application in microbial amino acid production.
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Affiliation(s)
- Pengfei Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
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Rebouillat S, Pla F. Recent Strategies for the Development of Biosourced-Monomers, Oligomers and Polymers-Based Materials: A Review with an Innovation and a Bigger Data Focus. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/jbnb.2016.74017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Yoshikawa K, Aikawa S, Kojima Y, Toya Y, Furusawa C, Kondo A, Shimizu H. Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction. PLoS One 2015; 10:e0144430. [PMID: 26640947 PMCID: PMC4671677 DOI: 10.1371/journal.pone.0144430] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/18/2015] [Indexed: 11/18/2022] Open
Abstract
Arthrospira (Spirulina) platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful method that can be used to design metabolic engineering strategies for the improvement of target molecule production. In this study, we constructed a genome-scale metabolic model of A. platensis NIES-39 including 746 metabolic reactions and 673 metabolites, and developed novel strategies to improve the production of valuable metabolites, such as glycogen and ethanol. The simulation results obtained using the metabolic model showed high consistency with experimental results for growth rates under several trophic conditions and growth capabilities on various organic substrates. The metabolic model was further applied to design a metabolic network to improve the autotrophic production of glycogen and ethanol. Decreased flux of reactions related to the TCA cycle and phosphoenolpyruvate reaction were found to improve glycogen production. Furthermore, in silico knockout simulation indicated that deletion of genes related to the respiratory chain, such as NAD(P)H dehydrogenase and cytochrome-c oxidase, could enhance ethanol production by using ammonium as a nitrogen source.
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Affiliation(s)
- Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3–5 Sanbancho, Chiyoda-ku, Tokyo 102–0075, Japan
| | - Shimpei Aikawa
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3–5 Sanbancho, Chiyoda-ku, Tokyo 102–0075, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1–1 Rokkodai, Nada-ku, Kobe 657–8501, Japan
| | - Yuta Kojima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3–5 Sanbancho, Chiyoda-ku, Tokyo 102–0075, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan
| | - Chikara Furusawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3–5 Sanbancho, Chiyoda-ku, Tokyo 102–0075, Japan
- Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565–0874, Japan
| | - Akihiko Kondo
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3–5 Sanbancho, Chiyoda-ku, Tokyo 102–0075, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1–1 Rokkodai, Nada-ku, Kobe 657–8501, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka 565–0871, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 3–5 Sanbancho, Chiyoda-ku, Tokyo 102–0075, Japan
- * E-mail:
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41
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Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering. Biotechnol Adv 2015; 33:1455-66. [DOI: 10.1016/j.biotechadv.2014.11.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/23/2014] [Accepted: 11/09/2014] [Indexed: 11/22/2022]
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42
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Systems strategies for developing industrial microbial strains. Nat Biotechnol 2015; 33:1061-72. [DOI: 10.1038/nbt.3365] [Citation(s) in RCA: 357] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022]
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43
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Advancing metabolic engineering through systems biology of industrial microorganisms. Curr Opin Biotechnol 2015; 36:8-15. [PMID: 26318074 DOI: 10.1016/j.copbio.2015.08.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 11/21/2022]
Abstract
Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further.
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Co-evolution of strain design methods based on flux balance and elementary mode analysis. Metab Eng Commun 2015; 2:85-92. [PMID: 34150512 PMCID: PMC8193246 DOI: 10.1016/j.meteno.2015.04.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/17/2015] [Accepted: 04/29/2015] [Indexed: 01/16/2023] Open
Abstract
More than a decade ago, the first genome-scale metabolic models for two of the most relevant microbes for biotechnology applications, Escherichia coli and Saccaromyces cerevisiae, were published. Shortly after followed the publication of OptKnock, the first strain design method using bilevel optimization to couple cellular growth with the production of a target product. This initiated the development of a family of strain design methods based on the concept of flux balance analysis. Another family of strain design methods, based on the concept of elementary mode analysis, has also been growing. Although the computation of elementary modes is hindered by computational complexity, recent breakthroughs have allowed applying elementary mode analysis at the genome scale. Here we review and compare strain design methods and look back at the last 10 years of in silico strain design with constraint-based models. We highlight some features of the different approaches and discuss the utilization of these methods in successful in vivo metabolic engineering applications. Computational strain design methods are divided into two main families. We trace the evolutionary history of these two families. Surveyed successful cases of model-guided strain design for industrial applications. Most proposed methods have not yet been tested in real applications. Agreement between in silico and in vivo results shows potential of tested methods.
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45
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Sun J, Alper HS. Metabolic engineering of strains: from industrial-scale to lab-scale chemical production. ACTA ACUST UNITED AC 2015; 42:423-36. [DOI: 10.1007/s10295-014-1539-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022]
Abstract
Abstract
A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5–50 g/L), and lab-scale (0–5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.
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Affiliation(s)
- Jie Sun
- grid.89336.37 0000000419369924 McKetta Department of Chemical Engineering The University of Texas at Austin 200 E Dean Keeton St. Stop C0400 78712 Austin TX USA
| | - Hal S Alper
- grid.89336.37 0000000419369924 McKetta Department of Chemical Engineering The University of Texas at Austin 200 E Dean Keeton St. Stop C0400 78712 Austin TX USA
- grid.89336.37 0000000419369924 Institute for Cellular and Molecular Biology The University of Texas at Austin 2500 Speedway Avenue 78712 Austin TX USA
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Becker J, Wittmann C. Advanced Biotechnology: Metabolically Engineered Cells for the Bio-Based Production of Chemicals and Fuels, Materials, and Health-Care Products. Angew Chem Int Ed Engl 2015; 54:3328-50. [DOI: 10.1002/anie.201409033] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 12/16/2022]
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47
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Biotechnologie von Morgen: metabolisch optimierte Zellen für die bio-basierte Produktion von Chemikalien und Treibstoffen, Materialien und Gesundheitsprodukten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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48
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Kiparissides A, Pistikopoulos EN, Mantalaris A. On the model-based optimization of secreting mammalian cell (GS-NS0) cultures. Biotechnol Bioeng 2014; 112:536-48. [DOI: 10.1002/bit.25457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/01/2014] [Accepted: 09/05/2014] [Indexed: 12/16/2022]
Affiliation(s)
- A. Kiparissides
- Centre for Process Systems Engineering; Department of Chemical Engineering; Imperial College London; London SW7 2AZ UK
| | - E. N. Pistikopoulos
- Centre for Process Systems Engineering; Department of Chemical Engineering; Imperial College London; London SW7 2AZ UK
| | - A. Mantalaris
- Centre for Process Systems Engineering; Department of Chemical Engineering; Imperial College London; London SW7 2AZ UK
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Zobel S, Kumpfmüller J, Süssmuth RD, Schweder T. Bacillus subtilis as heterologous host for the secretory production of the non-ribosomal cyclodepsipeptide enniatin. Appl Microbiol Biotechnol 2014; 99:681-91. [PMID: 25398283 PMCID: PMC4306738 DOI: 10.1007/s00253-014-6199-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 01/11/2023]
Abstract
The heterologous expression of genes or gene clusters in microbial hosts, followed by metabolic engineering of biosynthetic pathways, is key to access industrially and pharmaceutically relevant compounds in an economically affordable and sustainable manner. Therefore, platforms need to be developed, which provide tools for the controlled synthesis of bioactive compounds. The Gram-positive bacterium Bacillus subtilis is a promising candidate for such applications, as it is generally regarded as a safe production host, its physiology is well investigated and a variety of tools is available for its genetic manipulation. Furthermore, this industrially relevant bacterium provides a high secretory potential not only for enzymes but also for primary and secondary metabolites. In this study, we present the first heterologous expression of an eukaryotic non-ribosomal peptide synthetase gene (esyn) coding for the biosynthesis of the small molecule enniatin in B. subtilis. Enniatin is a pharmaceutically used cyclodepsipeptide for treatment of topical bacterial and fungal infections. We generated various enniatin-producing B. subtilis strains, allowing for either single chromosomal or plasmid-based multi-copy expression of the esyn cluster under the control of an acetoin-inducible promoter system. Optimization of cultivation conditions, combined with modifications of the genetic background and multi-copy plasmid-based esyn expression, resulted in a secretory production of enniatin B. This work presents B. subtilis as a suitable host for the expression of heterologous eukaryotic non-ribosomal peptide synthetases (NRPS) clusters.
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Affiliation(s)
- Sophia Zobel
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Jana Kumpfmüller
- Institut für Pharmazie, Ernst-Moritz-Arndt-Universität, Felix-Hausdorff-Strasse 3, 17489 Greifswald, Germany
| | - Roderich D. Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Thomas Schweder
- Institut für Pharmazie, Ernst-Moritz-Arndt-Universität, Felix-Hausdorff-Strasse 3, 17489 Greifswald, Germany
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50
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Gu P, Yang F, Su T, Li F, Li Y, Qi Q. Construction of an L-serine producing Escherichia coli via metabolic engineering. J Ind Microbiol Biotechnol 2014; 41:1443-50. [PMID: 24997624 DOI: 10.1007/s10295-014-1476-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/16/2014] [Indexed: 12/14/2022]
Abstract
L-Serine is a nonessential amino acid, but plays a crucial role as a building block for cell growth. Currently, L-serine production is mainly dependent on enzymatic or cellular conversion. In this study, we constructed a recombinant Escherichia coli that can fermentatively produce L-serine from glucose. To accumulate L-serine, sdaA encoding the L-serine dehydratase, iclR encoding the isocitrate lyase regulator, and arcA encoding the aerobic respiration control protein were deleted in turn. In batch fermentation, the engineered E. coli strain YF-5 exhibited obvious L-serine accumulation but poor cell growth. To restore cell growth, aceB encoding the malate synthase was knocked out, and the engineered strain was then transformed with plasmid that overexpressed serA (FR) , serB, and serC genes. The resulting strain YF-7 produced 4.5 g/L L-serine in batch cultivation and 8.34 g/L L-serine in fed-batch cultivation.
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Affiliation(s)
- Pengfei Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
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