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Li L, Zhou X, Gao Z, Xiong P, Liu X. Production of succinate with two CO 2 fixation reactions from fatty acids in Cupriavidus necator H16. Microb Cell Fact 2024; 23:194. [PMID: 38970033 PMCID: PMC11225152 DOI: 10.1186/s12934-024-02470-6] [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: 12/18/2023] [Accepted: 07/02/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Biotransformation of CO2 into high-value-added carbon-based products is a promising process for reducing greenhouse gas emissions. To realize the green transformation of CO2, we use fatty acids as carbon source to drive CO2 fixation to produce succinate through a portion of the 3-hydroxypropionate (3HP) cycle in Cupriavidus necator H16. RESULTS This work can achieve the production of a single succinate molecule from one acetyl-CoA molecule and two CO2 molecules. It was verified using an isotope labeling experiment utilizing NaH13CO3. This implies that 50% of the carbon atoms present in succinate are derived from CO2, resulting in a twofold increase in efficiency compared to prior methods of succinate biosynthesis that relied on the carboxylation of phosphoenolpyruvate or pyruvate. Meanwhile, using fatty acid as a carbon source has a higher theoretical yield than other feedstocks and also avoids carbon loss during acetyl-CoA and succinate production. To further optimize succinate production, different approaches including the optimization of ATP and NADPH supply, optimization of metabolic burden, and optimization of carbon sources were used. The resulting strain was capable of producing succinate to a level of 3.6 g/L, an increase of 159% from the starting strain. CONCLUSIONS This investigation established a new method for the production of succinate by the implementation of two CO2 fixation reactions and demonstrated the feasibility of ATP, NADPH, and metabolic burden regulation strategies in biological carbon fixation.
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Affiliation(s)
- Linqing Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China
| | - Xiuyuan Zhou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China
| | - Zhuoao Gao
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China.
| | - Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China.
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2
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Liu X, Li L, Zhao G, Xiong P. Optimization strategies for CO 2 biological fixation. Biotechnol Adv 2024; 73:108364. [PMID: 38642673 DOI: 10.1016/j.biotechadv.2024.108364] [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: 09/18/2023] [Revised: 04/07/2024] [Accepted: 04/14/2024] [Indexed: 04/22/2024]
Abstract
Global sustainable development faces a significant challenge in effectively utilizing CO2. Meanwhile, CO2 biological fixation offers a promising solution. CO2 has the highest oxidation state (+4 valence state), whereas typical multi‑carbon chemicals have lower valence states. The Gibbs free energy (ΔG) changes of CO2 reductive reactions are generally positive and this renders it necessary to input different forms of energy. Although biological carbon fixation processes are friendly to operate, the thermodynamic obstacles must be overcome. To make this reaction occur favorably and efficiently, diverse strategies to enhance CO2 biological fixation efficiency have been proposed by numerous researchers. This article reviews recent advances in optimizing CO2 biological fixation and intends to provide new insights into achieving efficient biological utilization of CO2. It first outlines the thermodynamic characteristics of diverse carbon fixation reactions and proposes optimization directions for CO2 biological fixation. A comprehensive overview of the catalytic mechanisms, optimization strategies, and challenges encountered by common carbon-fixing enzymes is then provided. Subsequently, potential routes for improving the efficiency of biological carbon fixation are discussed, including the ATP supply, reducing power supply, energy supply, reactor design, and carbon enrichment system modules. In addition, effective artificial carbon fixation pathways were summarized and analyzed. Finally, prospects are made for the research direction of continuously improving the efficiency of biological carbon fixation.
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Affiliation(s)
- Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China.
| | - Linqing Li
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China.
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, 255000 Zibo, China; International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, 255000 Zibo, China.
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3
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Zhang Y, Zhang G, Zhang H, Tian Y, Li J, Yun J, Zabed HM, Qi X. Efficient Fermentative Production of β-Alanine from Glucose through Multidimensional Engineering of Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14274-14283. [PMID: 38867465 DOI: 10.1021/acs.jafc.4c03492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
β-Alanine, a valuable β-type amino acid, is experiencing increased demand due to its multifaceted applications in food flavoring, nutritional supplements, pharmaceuticals, and the chemical industry. Nevertheless, the sustainable biosynthesis of β-alanine currently faces challenges due to the scarcity of robust strains, attributed to the complexities of modulating multiple genes and the inherent physiological constraints. Here, systems metabolic engineering was implemented in Escherichia coli to overcome these limitations. First, an efficient l-aspartate-α-decarboxylase (ADC) was recruited for β-alanine biosynthesis. To conserve phosphoenolpyruvate flux, we subsequently modified the endogenous glucose assimilation system by inactivating the phosphotransferase system (PTS) and introducing an alternative non-PTS system, which increased β-alanine production to 1.70 g/L. The supply of key precursors, oxaloacetate and l-aspartate, was synergistically improved through comprehensive modulation, including strengthening main flux and blocking bypass metabolism, which significantly increased the β-alanine titer to 3.43 g/L. Next, the expression of ADC was optimized by promoter and untranslated region (UTR) engineering. Further transport engineering, which involved disrupting β-alanine importer CycA and heterologously expressing β-alanine exporter NCgI0580, improved β-alanine production to 8.48 g/L. Additionally, corn steep liquor was used to develop a cost-effective medium. The final strain produced 74.03 g/L β-alanine with a yield of 0.57 mol/mol glucose during fed-batch fermentation.
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Affiliation(s)
- Yufei Zhang
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, P. R. China
| | - Guoyan Zhang
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, P. R. China
| | - Huifang Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, P. R. China
| | - Yuehui Tian
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
| | - Jia Li
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
| | - Junhua Yun
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
| | - Hossain M Zabed
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, Guangdong, P. R. China
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu, P. R. China
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4
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Yu L, Gao Y, He Y, Liu Y, Shen J, Liang H, Gong R, Duan H, Price NPJ, Song X, Deng Z, Chen W. Developing the E. coli platform for efficient production of UMP-derived chemicals. Metab Eng 2024; 83:61-74. [PMID: 38522576 DOI: 10.1016/j.ymben.2024.03.004] [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: 11/03/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
5-Methyluridine (5-MU) is a prominent intermediate for industrial synthesis of several antiviral-drugs, however, its availability over the past decades has overwhelmingly relied on chemical and enzymatic strategies. Here, we have realized efficient production of 5-MU in E. coli, for the first time, via a designer artificial pathway consisting of a two-enzyme cascade (UMP 5-methylase and phosphatase). More importantly, we have engineered the E. coli cell factory to boost 5-MU production by systematic evaluation of multiple strategies, and as a proof of concept, we have further developed an antibiotic-free fermentation strategy to realize 5-MU production (10.71 g/L) in E. coli MB229 (a ΔthyA strain). Remarkably, we have also established a versatile and robust platform with exploitation of the engineered E. coli for efficient production of diversified UMP-derived chemicals. This study paves the way for future engineering of E. coli as a synthetic biology platform for acceleratively accessing UMP-derived chemical diversities.
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Affiliation(s)
- Le Yu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yaojie Gao
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yuanyuan He
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yang Liu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jianning Shen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Han Liang
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - He Duan
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xuemin Song
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenqing Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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5
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Godar AG, Chase T, Conway D, Ravichandran D, Woodson I, Lai YJ, Song K, Rittmann BE, Wang X, Nielsen DR. 'Dark' CO 2 fixation in succinate fermentations enabled by direct CO 2 delivery via hollow fiber membrane carbonation. Bioprocess Biosyst Eng 2024; 47:223-233. [PMID: 38142425 DOI: 10.1007/s00449-023-02957-3] [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: 09/18/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Abstract
Anaerobic succinate fermentations can achieve high-titer, high-yield performance while fixing CO2 through the reductive branch of the tricarboxylic acid cycle. To provide the needed CO2, conventional media is supplemented with significant (up to 60 g/L) bicarbonate (HCO3-), and/or carbonate (CO32-) salts. However, producing these salts from CO2 and natural ores is thermodynamically unfavorable and, thus, energetically costly, which reduces the overall sustainability of the process. Here, a series of composite hollow fiber membranes (HFMs) were first fabricated, after which comprehensive CO2 mass transfer measurements were performed under cell-free conditions using a novel, constant-pH method. Lumen pressure and total HFM surface area were found to be linearly correlated with the flux and volumetric rate of CO2 delivery, respectively. Novel HFM bioreactors were then constructed and used to comprehensively investigate the effects of modulating the CO2 delivery rate on succinate fermentations by engineered Escherichia coli. Through appropriate tuning of the design and operating conditions, it was ultimately possible to produce up to 64.5 g/L succinate at a glucose yield of 0.68 g/g; performance approaching that of control fermentations with directly added HCO3-/CO32- salts and on par with prior studies. HFMs were further found to demonstrate a high potential for repeated reuse. Overall, HFM-based CO2 delivery represents a viable alternative to the addition of HCO3-/CO32- salts to succinate fermentations, and likely other 'dark' CO2-fixing fermentations.
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Affiliation(s)
- Amanda G Godar
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Timothy Chase
- School for Engineering of Matter, Transport and Energy, Arizona State University, BDC C499C, Tempe, AZ, 85282, USA
| | - Dalton Conway
- School for Engineering of Matter, Transport and Energy, Arizona State University, BDC C499C, Tempe, AZ, 85282, USA
| | | | - Isaiah Woodson
- School for Engineering of Matter, Transport and Energy, Arizona State University, BDC C499C, Tempe, AZ, 85282, USA
| | - Yen-Jung Lai
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
| | - Kenan Song
- School of Manufacturing Systems and Networks, Arizona State University, Tempe, AZ, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - David R Nielsen
- School for Engineering of Matter, Transport and Energy, Arizona State University, BDC C499C, Tempe, AZ, 85282, USA.
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6
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Zhou S, Ding N, Han R, Deng Y. Metabolic engineering and fermentation optimization strategies for producing organic acids of the tricarboxylic acid cycle by microbial cell factories. BIORESOURCE TECHNOLOGY 2023; 379:128986. [PMID: 37001700 DOI: 10.1016/j.biortech.2023.128986] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
The organic acids of the tricarboxylic acid (TCA) pathway are important platform compounds and are widely used in many areas. The high-productivity strains and high-efficient and low-cost fermentation are required to satisfy a huge market size. The high metabolic flux of the TCA pathway endows microorganisms potential to produce high titers of these organic acids. Coupled with metabolic engineering and fermentation optimization, the titer of the organic acids has been significantly improved in recent years. Herein, we discuss and compare the recent advances in synthetic pathway engineering, cofactor engineering, transporter engineering, and fermentation optimization strategies to maximize the biosynthesis of organic acids. Such engineering strategies were mainly based on the TCA pathway and glyoxylate pathway. Furthermore, organic-acid-secretion enhancement and renewable-substrate-based fermentation are often performed to assist the biosynthesis of organic acids. Further strategies are also discussed to construct high-productivity and acid-resistant strains for industrial large-scale production.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Nana Ding
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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7
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Ceron-Chafla P, de Vrieze J, Rabaey K, van Lier JB, Lindeboom REF. Steering the product spectrum in high-pressure anaerobic processes: CO 2 partial pressure as a novel tool in biorefinery concepts. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:27. [PMID: 36803622 PMCID: PMC9938588 DOI: 10.1186/s13068-023-02262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 01/05/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Elevated CO2 partial pressure (pCO2) has been proposed as a potential steering parameter for selective carboxylate production in mixed culture fermentation. It is anticipated that intermediate product spectrum and production rates, as well as changes in the microbial community, are (in)directly influenced by elevated pCO2. However, it remains unclear how pCO2 interacts with other operational conditions, namely substrate specificity, substrate-to-biomass (S/X) ratio and the presence of an additional electron donor, and what effect pCO2 has on the exact composition of fermentation products. Here, we investigated possible steering effects of elevated pCO2 combined with (1) mixed substrate (glycerol/glucose) provision; (2) subsequent increments in substrate concentration to increase the S/X ratio; and (3) formate as an additional electron donor. RESULTS Metabolite predominance, e.g., propionate vs. butyrate/acetate, and cell density, depended on interaction effects between pCO2-S/X ratio and pCO2-formate. Individual substrate consumption rates were negatively impacted by the interaction effect between pCO2-S/X ratio and were not re-established after lowering the S/X ratio and adding formate. The product spectrum was influenced by the microbial community composition, which in turn, was modified by substrate type and the interaction effect between pCO2-formate. High propionate and butyrate levels strongly correlated with Negativicutes and Clostridia predominance, respectively. After subsequent pressurized fermentation phases, the interaction effect between pCO2-formate enabled a shift from propionate towards succinate production when mixed substrate was provided. CONCLUSIONS Overall, interaction effects between elevated pCO2, substrate specificity, high S/X ratio and availability of reducing equivalents from formate, rather than an isolated pCO2 effect, modified the proportionality of propionate, butyrate and acetate in pressurized mixed substrate fermentations at the expense of reduced consumption rates and increased lag-phases. The interaction effect between elevated pCO2 and formate was beneficial for succinate production and biomass growth with a glycerol/glucose mixture as the substrate. The positive effect may be attributed to the availability of extra reducing equivalents, likely enhanced carbon fixating activity and hindered propionate conversion due to increased concentration of undissociated carboxylic acids.
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Affiliation(s)
- Pamela Ceron-Chafla
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands.
| | - Jo de Vrieze
- grid.5342.00000 0001 2069 7798Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Korneel Rabaey
- grid.5342.00000 0001 2069 7798Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium ,grid.510907.aCenter for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Coupure Links 653, 9000 Ghent, Belgium
| | - Jules B. van Lier
- grid.5292.c0000 0001 2097 4740Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Ralph E. F. Lindeboom
- grid.5292.c0000 0001 2097 4740Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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8
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Re-designing Escherichia coli for high-yield production of β-alanine by metabolic engineering. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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9
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Jiang S, Otero-Muras I, Banga JR, Wang Y, Kaiser M, Krasnogor N. OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production. ACS Synth Biol 2022; 11:1531-1541. [PMID: 35389631 PMCID: PMC9016760 DOI: 10.1021/acssynbio.1c00610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Computational
tools have been widely adopted for strain optimization
in metabolic engineering, contributing to numerous success stories
of producing industrially relevant biochemicals. However, most of
these tools focus on single metabolic intervention strategies (either
gene/reaction knockout or amplification alone) and rely on hypothetical
optimality principles (e.g., maximization of growth) and precise gene
expression (e.g., fold changes) for phenotype prediction. This paper
introduces OptDesign, a new two-step strain design strategy. In the
first step, OptDesign selects regulation candidates that have a noticeable
flux difference between the wild type and production strains. In the
second step, it computes optimal design strategies with limited manipulations
(combining regulation and knockout), leading to high biochemical production.
The usefulness and capabilities of OptDesign are demonstrated for
the production of three biochemicals in Escherichia
coli using the latest genome-scale metabolic model
iML1515, showing highly consistent results with previous studies while
suggesting new manipulations to boost strain performance. The source
code is available at https://github.com/chang88ye/OptDesign.
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Affiliation(s)
- Shouyong Jiang
- Department of Computing Science, University of Aberdeen, Aberdeen AB24 3FX, U.K
| | - Irene Otero-Muras
- Institute for Integrative Systems Biology, UV-CSIC, Valencia 46980, Spain
| | - Julio R. Banga
- Computational Biology Lab, MBG-CSIC, Pontevedra 36143, Spain
| | - Yong Wang
- School of Automation, Central South University, Changsha 410083, China
| | - Marcus Kaiser
- School of Medicine, University of Nottingham, Nottingham NG7 2RD, U.K
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10
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Liu X, Zhao G, Sun S, Fan C, Feng X, Xiong P. Biosynthetic Pathway and Metabolic Engineering of Succinic Acid. Front Bioeng Biotechnol 2022; 10:843887. [PMID: 35350186 PMCID: PMC8957974 DOI: 10.3389/fbioe.2022.843887] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/16/2022] [Indexed: 11/25/2022] Open
Abstract
Succinic acid, a dicarboxylic acid produced as an intermediate of the tricarboxylic acid (TCA) cycle, is one of the most important platform chemicals for the production of various high value-added derivatives. As traditional chemical synthesis processes suffer from nonrenewable resources and environment pollution, succinic acid biosynthesis has drawn increasing attention as a viable, more environmentally friendly alternative. To date, several metabolic engineering approaches have been utilized for constructing and optimizing succinic acid cell factories. In this review, different succinic acid biosynthesis pathways are summarized, with a focus on the key enzymes and metabolic engineering approaches, which mainly include redirecting carbon flux, balancing NADH/NAD+ ratios, and optimizing CO2 supplementation. Finally, future perspectives on the microbial production of succinic acid are discussed.
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Affiliation(s)
- Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Guang Zhao
- State Key Lab of Microbial Technology, Shandong University, Qingdao, China
| | - Shengjie Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Chuanle Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Xinjun Feng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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11
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Miao L, Li Y, Zhu T. Metabolic engineering of methylotrophic Pichia pastoris for the production of β-alanine. BIORESOUR BIOPROCESS 2021; 8:89. [PMID: 38650288 PMCID: PMC10991944 DOI: 10.1186/s40643-021-00444-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/08/2021] [Indexed: 11/10/2022] Open
Abstract
β-Alanine (3-aminopropionic acid) is the only naturally occurring β-amino acid and an important precursor for the synthesis of a variety of nitrogen-containing chemicals. Fermentative production of β-alanine from renewable feedstocks such as glucose has attracted significant interest in recent years. Methanol has become an emerging and promising renewable feedstock for biomanufacturing as an alternative to glucose. In this work, we demonstrated the feasibility of β-alanine production from methanol using Pichia pastoris (Komagataella phaffii) as a methylotrophic cell factory. L-Aspartate-α-decarboxylases (ADCs) from different sources were screened and expressed in P. pastoris, followed by the optimization of aspartate decarboxylation by increasing the ADC copy number and C4 precursor supply via the overexpression of aspartate dehydrogenase. The production potential of the best strain was further evaluated in a 1-L fermenter, and a β-alanine titer of 5.6 g/L was obtained. To our best knowledge, this is the highest metabolite production titer ever reached in P. pastoris using methanol as the substrate.
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Affiliation(s)
- Liangtian Miao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
| | - Taicheng Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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12
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Zhu T, Yao D, Li D, Xu H, Jia S, Bi C, Cai J, Zhu X, Zhang X. Multiple strategies for metabolic engineering of Escherichia coli for efficient production of glycolate. Biotechnol Bioeng 2021; 118:4699-4707. [PMID: 34491579 DOI: 10.1002/bit.27934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/12/2023]
Abstract
Glycolate is a bulk chemical with wide applications in the textile, food processing, and pharmaceutical industries. Glycolate can be produced from glucose via the glycolysis and glyoxylate shunt pathways, followed by reduction to glycolate. However, two problems limit the productivity and yield of glycolate when using glucose as the sole carbon source. The first is a cofactor imbalance in the production of glycolate from glucose via the glycolysis pathway, since NADPH is required for glycolate production, while glycolysis generates NADH. To rectify this imbalance, the NADP+ -dependent glyceraldehyde 3-phosphate dehydrogenase GapC from Clostridium acetobutylicum was introduced to generate NADPH instead of NADH in the oxidation of glyceraldehyde 3-phosphate during glycolysis. The soluble transhydrogenase SthA was further eliminated to conserve NADPH by blocking its conversion into NADH. The second problem is an unfavorable carbon flux distribution between the tricarboxylic acid cycle and the glyoxylate shunt. To solve this problem, isocitrate dehydrogenase (ICDH) was eliminated to increase the carbon flux of glyoxylate and thereby improve the glycolate titer. After engineering through the integration of gapC, combined with the inactivation of ICDH, SthA, and by-product pathways, as well as the upregulation of the two key enzymes isocitrate lyase (encoding by aceA), and glyoxylate reductase (encoding by ycdW), the glycolate titer increased to 5.3 g/L with a yield of 1.89 mol/mol glucose. Moreover, an optimized fed-batch fermentation reached a titer of 41 g/L with a yield of 1.87 mol/mol glucose after 60 h.
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Affiliation(s)
- Tong Zhu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese of Academy of Sciences, Tianjin, China
| | - Die Yao
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Di Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese of Academy of Sciences, Tianjin, China
| | - Hongtao Xu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese of Academy of Sciences, Tianjin, China
| | - Shiru Jia
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jun Cai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese of Academy of Sciences, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese of Academy of Sciences, Tianjin, China
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13
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Serek P, Lewandowski Ł, Dudek B, Pietkiewicz J, Jermakow K, Kapczyńska K, Krzyżewska E, Bednarz-Misa I. Klebsiella pneumoniae enolase-like membrane protein interacts with human plasminogen. Int J Med Microbiol 2021; 311:151518. [PMID: 34237624 DOI: 10.1016/j.ijmm.2021.151518] [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: 03/02/2021] [Revised: 05/14/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022] Open
Abstract
Many models assessing the risk of sepsis utilize the knowledge of the constituents of the plasminogen system, as it is proven that some species of bacteria can activate plasminogen, as a result of interactions with bacterial outer membrane proteins. However, much is yet to be discovered about this interaction since there is little information regarding some bacterial species. This study is aimed to check if Klebsiella pneumoniae, one of the major factors of nosocomial pneumonia and a factor for severe sepsis, has the ability to bind to human plasminogen. The strain used in this study, PCM 2713, acted as a typical representative of the species. With use of various methods, including: electron microscopy, 2-dimensional electrophoresis, immunoblotting and peptide fragmentation fingerprinting, it is shown that Klebsiella pneumoniae binds to human plasminogen, among others, due to plasminogen-bacterial enolase-like protein interaction, occurring on the outer membrane of the bacterium. Moreover, the study reveals, that other proteins, such as: phosphoglucomutase, and phosphoenolpyruvate carboxykinase act as putative plasminogen-binding factors. These information may virtually act as a foundation for future studies investigating: the: pathogenicity of Klebsiella pneumoniae and means for prevention from the outcomes of Klebsiella-derived sepsis.
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Affiliation(s)
- Paweł Serek
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland
| | - Łukasz Lewandowski
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland
| | - Bartłomiej Dudek
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63-77, 51-148, Wroclaw, Poland
| | - Jadwiga Pietkiewicz
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland
| | - Katarzyna Jermakow
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, Chałubińskiego 4, 50-368, Wrocław, Poland
| | - Katarzyna Kapczyńska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Eva Krzyżewska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114, Wrocław, Poland
| | - Iwona Bednarz-Misa
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chałubińskiego 10, 50-368, Wroclaw, Poland.
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14
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Hao T, Li G, Zhou S, Deng Y. Engineering the Reductive TCA Pathway to Dynamically Regulate the Biosynthesis of Adipic Acid in Escherichia coli. ACS Synth Biol 2021; 10:632-639. [PMID: 33687200 DOI: 10.1021/acssynbio.0c00648] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid is a versatile aliphatic dicarboxylic acid. It is applied mainly in the polymerization of nylon-6,6, which accounts for 50.8% of the global consumption market of adipic acid. The microbial production of adipic acid avoids the usage of petroleum resources and the emission of harmful nitrogen oxides that are generated by traditional chemical synthetic approaches. However, in the fermentation process, the low theoretical yield and the usage of expensive inducers hinders the large-scale industrial production of adipic acid. To overcome these challenges, we established an oxygen-dependent dynamic regulation (ODDR) system to control the expression of key genes (sucD, pyc, mdh, and frdABCD) that could be induced to enhance the metabolic flux of the reductive TCA pathway under anaerobic conditions. Coupling of the constitutively expressed adipic acid synthetic pathway not only avoids the use of inducers but also increases the theoretical yield by nearly 50%. After the gene combination and operon structure were optimized, the reaction catalyzed by frdABCD was found to be the rate-limiting step. Further optimizing the relative expression levels of sucD, pyc, and frdABCD improved the titer of adipic acid 41.62-fold compared to the control strain Mad1415, demonstrating the superior performance of our ODDR system.
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Affiliation(s)
- Tingting Hao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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15
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Su HY, Li HY, Xie CY, Fei Q, Cheng KK. Co-production of acetoin and succinic acid by metabolically engineered Enterobacter cloacae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:26. [PMID: 33468210 PMCID: PMC7816431 DOI: 10.1186/s13068-021-01878-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Renewable chemicals have attracted attention due to increasing interest in environmental concerns and resource utilization. Biobased production of industrial compounds from nonfood biomass has become increasingly important as a sustainable replacement for traditional petroleum-based production processes depending on fossil resources. Therefore, we engineered an Enterobacter cloacae budC and ldhA double-deletion strain (namely, EC∆budC∆ldhA) to redirect carbon fluxes and optimized the culture conditions to co-produce succinic acid and acetoin. RESULTS In this work, E. cloacae was metabolically engineered to enhance its combined succinic acid and acetoin production during fermentation. Strain EC∆budC∆ldhA was constructed by deleting 2,3-butanediol dehydrogenase (budC), which is involved in 2,3-butanediol production, and lactate dehydrogenase (ldhA), which is involved in lactic acid production, from the E. cloacae genome. After redirecting and fine-tuning the E. cloacae metabolic flux, succinic acid and acetoin production was enhanced, and the combined production titers of acetoin and succinic acid from glucose were 17.75 and 2.75 g L-1, respectively. Moreover, to further improve acetoin and succinic acid production, glucose and NaHCO3 modes and times of feeding were optimized during fermentation of the EC∆budC∆ldhA strain. The maximum titers of acetoin and succinic acid were 39.5 and 20.3 g L-1 at 72 h, respectively. CONCLUSIONS The engineered strain EC∆budC∆ldhA is useful for the co-production of acetoin and succinic acid and for reducing microbial fermentation costs by combining processes into a single step.
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Affiliation(s)
- Hsiang-Yen Su
- Engineering Research Center of Health Food Design & Nutrition Regulation, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, 523808 China
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
- China-Latin America Joint Laboratory for Clean Energy and Climate Change, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, 523808 China
| | - Hua-Ying Li
- China-Latin America Joint Laboratory for Clean Energy and Climate Change, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, 523808 China
| | - Cai-Yun Xie
- China-Latin America Joint Laboratory for Clean Energy and Climate Change, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, 523808 China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Ke-Ke Cheng
- Engineering Research Center of Health Food Design & Nutrition Regulation, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, 523808 China
- China-Latin America Joint Laboratory for Clean Energy and Climate Change, School of Chemical Engineering and Energy Technology, Dongguan University of Technology, Dongguan, 523808 China
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16
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Li Y, Yang S, Ma D, Song W, Gao C, Liu L, Chen X. Microbial engineering for the production of C 2-C 6 organic acids. Nat Prod Rep 2021; 38:1518-1546. [PMID: 33410446 DOI: 10.1039/d0np00062k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C2-C6 organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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17
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Gong Z, Wang H, Tang J, Bi C, Li Q, Zhang X. Coordinated Expression of Astaxanthin Biosynthesis Genes for Improved Astaxanthin Production in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14917-14927. [PMID: 33289384 DOI: 10.1021/acs.jafc.0c05379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Astaxanthin has great potential commercial value in the feed, cosmetics, and nutraceutical industries due to its strong antioxidant capacity. In this study, the Escherichia coli strain CAR026 with completely balanced metabolic flow was selected as the starting strain for the production of astaxanthin. The expression of β-carotene ketolase (CrtW) and β-carotene hydroxylase (CrtZ), which catalyze the conversion of β-carotene to astaxanthin, was coordinated, and a bottleneck was eliminated by increasing the copy number of crtY in CAR026. The resulting strain Ast007 produced 21.36 mg/L and 4.6 mg/g DCW of astaxanthin in shake flasks. In addition, the molecular chaperone genes groES-groEL were regulated to further improve the astaxanthin yield. The best strain Gro-46 produced 26 mg/L astaxanthin with a yield of 6.17 mg/g DCW in shake flasks and 1.18 g/L astaxanthin after 60 h of fermentation under fed-batch conditions. To the best of our knowledge, this is the highest astaxanthin obtained using engineered E. coli to date.
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Affiliation(s)
- Zhongkuo Gong
- School of Chemistry and Life Science, Changchun University of Technology, Changchun 130012, China
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Honglei Wang
- School of Chemistry and Life Science, Changchun University of Technology, Changchun 130012, China
| | - Jinlei Tang
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100071, China
| | - Qingyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100071, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100071, China
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18
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Characterization and directed evolution of propionyl-CoA carboxylase and its application in succinate biosynthetic pathway with two CO2 fixation reactions. Metab Eng 2020; 62:42-50. [DOI: 10.1016/j.ymben.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/18/2020] [Accepted: 08/24/2020] [Indexed: 11/20/2022]
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19
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Zhan T, Chen Q, Zhang C, Bi C, Zhang X. Constructing a Novel Biosynthetic Pathway for the Production of Glycolate from Glycerol in Escherichia coli. ACS Synth Biol 2020; 9:2600-2609. [PMID: 32794740 DOI: 10.1021/acssynbio.0c00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glycolate is an important α-hydroxy acid with a wide range of industrial applications. The current industrial production of glycolate mainly depends on chemical synthesis, but biochemical production from renewable resources using engineered microorganisms is increasingly viewed as an attractive alternative. Crude glycerol is an abundant byproduct of biodiesel production and a widely investigated potential sustainable feedstock. Here, we constructed a novel biosynthetic pathway for the production of glycolate from glycerol in Escherichia coli. The pathway starts from the oxidation of glycerol to d-glycerate by alditol oxidase, followed by sequential enzymatic dehydrogenation and decarboxylation as well as reduction reactions. We screened and characterized the catalytic activity of candidate enzymes, and a variant of alditol oxidase from Streptomyces coelicolor A3(2), 2-hydroxyglutarate-pyruvate transhydrogenase from Saccharomyces cerevisiae, α-ketoisovalerate decarboxylase from Lactococcus lactis, and aldehyde dehydrogenase from Escherichia coli were selected and assembled to create an artificial operon for the biosynthetic production of glycolate from glycerol. We also characterized the native strong constitutive promoter Plpp from E. coli and compared it with the PT7 promoter, which was employed to express the artificial operon on the plasmid pSC105-ADKA. To redirect glycerol flux toward glycolate synthesis, we deleted key genes of the native glycerol assimilation pathways and other branches of native E. coli metabolism, and we introduced a second plasmid expressing Dld3 to reduce the accumulation of the intermediate d-glycerate. Finally, the engineered strain TZ-108 harboring pSC105-ADKA and pACYC184-Plpp-Dld3 produced 0.64 g/L glycolate in shake flasks, which was increased to 4.74 g/L in fed-batch fermentation. This study provides an alternative pathway for glycolate synthesis and demonstrates the potential for producing other commodity chemicals by redesigning glycerol metabolism.
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Affiliation(s)
- Tao Zhan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qian Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chao Zhang
- College of Chemistry and Life Sciences, Changchun University of Technology, Changchun, Jilin 130012, China
| | - Changhao Bi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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20
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Yu Y, Shao M, Li D, Fan F, Xu H, Lu F, Bi C, Zhu X, Zhang X. Construction of a carbon-conserving pathway for glycolate production by synergetic utilization of acetate and glucose in Escherichia coli. Metab Eng 2020; 61:152-159. [PMID: 32531344 DOI: 10.1016/j.ymben.2020.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/05/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Glycolate is a bulk chemical which has been widely used in textile, food processing, and pharmaceutical industries. Glycolate can be produced from sugars by microbial fermentation. However, when using glucose as the sole carbon source, the theoretical maximum carbon molar yield of glycolate is 0.67 mol/mol due to the loss of carbon as CO2. In this study, a synergetic system for simultaneous utilization of acetate and glucose was designed to increase the carbon yield. The main function of glucose is to provide NADPH while acetate to provide the main carbon backbone for glycolate production. Theoretically, 1 glucose and 5 acetate can produce 6 glycolate, and the carbon molar yield can be increased to 0.75 mol/mol. The whole synthetic pathway was divided into two modules, one for converting acetate to glycolate and another to utilize glucose to provide NADPH. After engineering module I through activation of acs, gltA, aceA and ycdW, glycolate titer increased from 0.07 to 2.16 g/L while glycolate yields increased from 0.04 to 0.35 mol/mol-acetate and from 0.03 to 1.04 mol/mol-glucose. Module II was then engineered to increase NADPH supply. Through deletion of pfkA, pfkB, ptsI and sthA genes as well as upregulating zwf, pgl and tktA, glycolate titer increased from 2.16 to 4.86 g/L while glycolate yields increased from 0.35 to 0.82 mol/mol-acetate and from 1.04 to 6.03 mol/mol-glucose. The activities of AceA and YcdW were further increased to pull the carbon flux to glycolate, which increased glycolate yield from 0.82 to 0.92 mol/mol-acetate. Fed-batch fermentation of the final strain NZ-Gly303 produced 73.3 g/L glycolate with a productivity of 1.04 g/(L·h). The acetate to glycolate yield was 0.85 mol/mol (1.08 g/g), while glucose to glycolate yield was 6.1 mol/mol (2.58 g/g). The total carbon molar yield was 0.60 mol/mol, which reached 80% of the theoretical value.
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Affiliation(s)
- Yong Yu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Mengyao Shao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Di Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hongtao Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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21
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Bai Y, Mansell TJ. Production and Sensing of Butyrate in a Probiotic Escherichia coli Strain. Int J Mol Sci 2020; 21:ijms21103615. [PMID: 32443851 PMCID: PMC7279287 DOI: 10.3390/ijms21103615] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
The short-chain fatty acid butyrate plays critical roles in human gut health, affecting immunomodulation, cell differentiation, and apoptosis, while also serving as the preferred carbon source for colon cells. In this work, we have engineered a model probiotic organism, Escherichia coli Nissle 1917 (EcN, serotype O6:K5:H1), to produce butyrate from genomic loci up to approximately 1 g/L (11 mM). Then, for real-time monitoring of butyrate production in cultures, we developed a high-throughput biosensor that responds to intracellular butyrate concentrations, with green fluorescent protein as the reporter. This work provides a foundation for studies of butyrate for therapeutic applications.
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22
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Bharathiraja B, Selvakumari IAE, Jayamuthunagai J, Kumar RP, Varjani S, Pandey A, Gnansounou E. Biochemical conversion of biodiesel by-product into malic acid: A way towards sustainability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:136206. [PMID: 31905567 DOI: 10.1016/j.scitotenv.2019.136206] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Crude glycerol, one of the ever-growing by-product of biodiesel industry and is receiving the closest review in recent times because direct disposal of crude glycerol may emerge ecological issues. The renewability, bioavailability and typical structure of glycerol, therefore, discover conceivable application in serving the role of carbon and energy source for microbial biosynthesis of high value products. This conceivable arrangement could find exploitation of crude glycerol as a renewable building block for bio-refineries as it is economically as well as environmentally profitable. In this review, we summarize the uptake and catabolism of crude glycerol by different wild and recombinant microorganism. The chemical and biochemical transformation of crude glycerol into high esteem malic acid by various microbial pathways is also additionally discussed. An extensive investigation in the synthesis of high-value malic acid production from various feed stock which finds applications in cosmeceutical and chemical industries, food and beverages, and to some extent in the field of medical science is also likewise studied. Finally, the open doors for unrefined crude glycerol in serving as a promising abundant energy source for malic acid production in near future have been highlighted.
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Affiliation(s)
- B Bharathiraja
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai 600 062, India
| | | | - J Jayamuthunagai
- Centre for Biotechnology, Anna University, Chennai 600 025, India
| | - R Praveen Kumar
- Department of Biotechnology, Arunai Engineering College, Thiruvannaamalai 606 603, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar 382 010, Gujarat, India.
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, India; Frontier Research Lab, Yonsei University, Sinchon-dong, Seodaemun-gu, Seoul, South Korea.
| | - Edgard Gnansounou
- Bioenergy and Energy Planning Research Group, Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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23
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Braga A, Faria N. Bioprocess Optimization for the Production of Aromatic Compounds With Metabolically Engineered Hosts: Recent Developments and Future Challenges. Front Bioeng Biotechnol 2020; 8:96. [PMID: 32154231 PMCID: PMC7044121 DOI: 10.3389/fbioe.2020.00096] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022] Open
Abstract
The most common route to produce aromatic chemicals - organic compounds containing at least one benzene ring in their structure - is chemical synthesis. These processes, usually starting from an extracted fossil oil molecule such as benzene, toluene, or xylene, are highly environmentally unfriendly due to the use of non-renewable raw materials, high energy consumption and the usual production of toxic by-products. An alternative way to produce aromatic compounds is extraction from plants. These extractions typically have a low yield and a high purification cost. This motivates the search for alternative platforms to produce aromatic compounds through low-cost and environmentally friendly processes. Microorganisms are able to synthesize aromatic amino acids through the shikimate pathway. The construction of microbial cell factories able to produce the desired molecule from renewable feedstock becomes a promising alternative. This review article focuses on the recent advances in microbial production of aromatic products, with a special emphasis on metabolic engineering strategies, as well as bioprocess optimization. The recent combination of these two techniques has resulted in the development of several alternative processes to produce phenylpropanoids, aromatic alcohols, phenolic aldehydes, and others. Chemical species that were unavailable for human consumption due to the high cost and/or high environmental impact of their production, have now become accessible.
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Affiliation(s)
- Adelaide Braga
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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24
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Kim HJ, Jeong H, Lee SJ. Short-Term Adaptation Modulates Anaerobic Metabolic Flux to Succinate by Activating ExuT, a Novel D-Glucose Transporter in Escherichia coli. Front Microbiol 2020; 11:27. [PMID: 32038601 PMCID: PMC6989600 DOI: 10.3389/fmicb.2020.00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/08/2020] [Indexed: 11/18/2022] Open
Abstract
The sugar phosphotransferase system (PTS) is an essential energy-saving mechanism, particularly under anaerobic conditions. Since the PTS consumes equimolar phosphoenolpyruvate to phosphorylate each molecule of internalized glucose in the process of pyruvate generation, its absence can adversely affect the mixed acid fermentation profile and cell growth under anaerobic conditions. In this study, we report that the ΔptsG mutant cells of Escherichia coli K-12 strain exhibited inefficient glucose utilization, produced a significant amount of succinate, and exhibited a low growth rate. However, cells adapted soon after and started to grow rapidly in the same batch culture. As a result, the adapted ΔptsG cells showed the same mixed acid fermentation profiles as the wild-type cells, which was attributed to the mutation of the mlc gene, a repressor of the D-mannose PTS, another transporter for D-glucose. Similar adaptations were observed in the cells with ΔptsGΔmanX and the cells with ΔptsI that resulted in the production of a substantial amount of succinate and fast growth rate. The genome sequencing showed the presence of null mutations in the exuR gene, which encodes a modulator of exuT-encoded non-PTS sugar transporter, in adapted ΔptsGΔmanX and ΔptsI strains. Results from the RT-qPCR analysis and genetic test confirmed that the enhanced expression of ExuT, a non-PTS sugar transporter, was responsible for the uptake of D-glucose, increased succinate production, and fast growth of adapted cells. In conclusion, our study showed that the regulatory network of sugar transporters can be modulated by short-term adaptation and that downstream metabolic flux could be significantly determined by the choice of sugar transporters.
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Affiliation(s)
- Hyun Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Haeyoung Jeong
- Gwanggyo R&D Center, Medytox Inc., Suwon, South Korea.,Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
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25
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Efficient whole-cell catalysis for 5-aminovalerate production from L-lysine by using engineered Escherichia coli with ethanol pretreatment. Sci Rep 2020; 10:990. [PMID: 31969619 PMCID: PMC6976619 DOI: 10.1038/s41598-020-57752-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/31/2019] [Indexed: 01/22/2023] Open
Abstract
Microorganisms can utilize biomass to produce valuable chemicals, showing sustainable, renewable and economic advantages compared with traditional chemical synthesis. As a potential five-carbon platform polymer monomer, 5-aminovalerate has been widely used in industrial fields such as clothes and disposable goods. Here we establish an efficient whole-cell catalysis for 5-aminovalerate production with ethanol pretreatment. In this study, the metabolic pathway from L-lysine to 5-aminovalerate was constructed at the cellular level by introducing L-lysine α-oxidase. The newly produced H2O2 and added ethanol both are toxic to the cells, obviously inhibiting their growth. Here, a promising strategy of whole-cell catalysis with ethanol pretreatment is proposed, which greatly improves the yield of 5-aminovalerate. Subsequently, the effects of ethanol pretreatment, substrate concentration, reaction temperature, pH value, metal ion additions and hydrogen peroxide addition on the whole-cell biocatalytic efficiency were investigated. Using 100 g/L of L-lysine hydrochloride as raw material, 50.62 g/L of 5-aminovalerate could be excellently produced via fed-batch bioconversion with the yield of 0.84 mol/mol. The results show that a fast, environmentally friendly and efficient production of 5-aminovalerate was established after introducing the engineered whole-cell biocatalysts. This strategy, combined with ethanol pretreatment, can not only greatly enhance the yield of 5-aminovalerate but also be applied to the biosynthesis of other valuable chemicals.
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26
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Construction of an energy-conserving glycerol utilization pathways for improving anaerobic succinate production in Escherichia coli. Metab Eng 2019; 56:181-189. [DOI: 10.1016/j.ymben.2019.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 10/02/2019] [Accepted: 10/05/2019] [Indexed: 02/07/2023]
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27
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Kurgan G, Sievert C, Flores A, Schneider A, Billings T, Panyon L, Morris C, Taylor E, Kurgan L, Cartwright R, Wang X. Parallel experimental evolution reveals a novel repressive control of GalP on xylose fermentation in Escherichia coli. Biotechnol Bioeng 2019; 116:2074-2086. [PMID: 31038200 PMCID: PMC11161036 DOI: 10.1002/bit.27004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/28/2019] [Accepted: 04/25/2019] [Indexed: 12/25/2022]
Abstract
Efficient xylose utilization will facilitate microbial conversion of lignocellulosic sugar mixtures into valuable products. In Escherichia coli, xylose catabolism is controlled by carbon catabolite repression (CCR). However, in E. coli such as the succinate-producing strain KJ122 with disrupted CCR, xylose utilization is still inhibited under fermentative conditions. To probe the underlying genetic mechanisms inhibiting xylose utilization, we evolved KJ122 to enhance its xylose fermentation abilities in parallel and characterized the potential convergent genetic changes shared by multiple independently evolved strains. Whole-genome sequencing revealed that convergent mutations occurred in the galactose regulon during adaptive laboratory evolution potentially decreasing the transcriptional level or the activity of GalP, a galactose permease. We showed that deletion of galP increased xylose utilization in both KJ122 and wild-type E. coli, demonstrating a common repressive role of GalP for xylose fermentation. Concomitantly, induced expression of galP from a plasmid repressed xylose fermentation. Transcriptome analysis using RNA sequencing indicates that galP inactivation increases transcription levels of many catabolic genes for secondary sugars including xylose and arabinose. The repressive role of GalP for fermenting secondary sugars in E. coli suggests that utilization of GalP as a substitute glucose transporter is undesirable for conversion of lignocellulosic sugar mixtures.
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Affiliation(s)
- Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Christian Sievert
- School of Life Sciences, Arizona State University, Tempe, Arizona
- The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Andrew Flores
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona
| | - Aidan Schneider
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Thomas Billings
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Larry Panyon
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Chandler Morris
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Eric Taylor
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Logan Kurgan
- School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Reed Cartwright
- School of Life Sciences, Arizona State University, Tempe, Arizona
- The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, Arizona
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28
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Metabolic Engineering and Fermentation Process Strategies for L-Tryptophan Production by Escherichia coli. Processes (Basel) 2019. [DOI: 10.3390/pr7040213] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
L-tryptophan is an essential aromatic amino acid that has been widely used in medicine, food, and animal feed. Microbial biosynthesis of L-tryptophan through metabolic engineering approaches represents a sustainable, cost-effective, and environmentally friendly route compared to chemical synthesis. In particular, metabolic pathway engineering allows enhanced product titers by inactivating/blocking the competing pathways, increasing the intracellular level of essential precursors, and overexpressing rate-limiting enzymatic steps. Based on the route of the l-tryptophan biosynthesis pathway, this review presents a systematic and detailed summary of the contemporary metabolic engineering approaches employed for l-tryptophan production. In addition to the engineering of the l-tryptophan biosynthesis pathway, the metabolic engineering modification of carbon source uptake, by-product formation, key regulatory factors, and the polyhydroxybutyrate biosynthesis pathway in l-tryptophan biosynthesis are discussed. Moreover, fermentation bioprocess optimization strategies used for l-tryptophan overproduction are also delineated. Towards the end, the review is wrapped up with the concluding remarks, and future strategies are outlined for the development of a high l-tryptophan production strain.
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29
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Wu Z, Wang J, Liu J, Wang Y, Bi C, Zhang X. Engineering an electroactive Escherichia coli for the microbial electrosynthesis of succinate from glucose and CO 2. Microb Cell Fact 2019; 18:15. [PMID: 30691454 PMCID: PMC6348651 DOI: 10.1186/s12934-019-1067-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/20/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Electrochemical energy is a key factor of biosynthesis, and is necessary for the reduction or assimilation of substrates such as CO2. Previous microbial electrosynthesis (MES) research mainly utilized naturally electroactive microbes to generate non-specific products. RESULTS In this research, an electroactive succinate-producing cell factory was engineered in E. coli T110(pMtrABC, pFccA-CymA) by expressing mtrABC, fccA and cymA from Shewanella oneidensis MR-1, which can utilize electricity to reduce fumarate. The electroactive T110 strain was further improved by incorporating a carbon concentration mechanism (CCM). This strain was fermented in an MES system with neutral red as the electron carrier and supplemented with HCO3+, which produced a succinate yield of 1.10 mol/mol glucose-a 1.6-fold improvement over the parent strain T110. CONCLUSIONS The strain T110(pMtrABC, pFccA-CymA, pBTCA) is to our best knowledge the first electroactive microbial cell factory engineered to directly utilize electricity for the production of a specific product. Due to the versatility of the E. coli platform, this pioneering research opens the possibility of engineering various other cell factories to utilize electricity for bioproduction.
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Affiliation(s)
- Zaiqiang Wu
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Junsong Wang
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Jun Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Yan Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Changhao Bi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
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30
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Rerouting carbon flux for optimized biosynthesis of mesaconate in Escherichia coli. Appl Microbiol Biotechnol 2018; 102:7377-7388. [DOI: 10.1007/s00253-018-9135-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/09/2018] [Accepted: 05/15/2018] [Indexed: 11/26/2022]
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31
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An economically and environmentally acceptable synthesis of chiral drug intermediate l-pipecolic acid from biomass-derived lysine via artificially engineered microbes. ACTA ACUST UNITED AC 2018; 45:405-415. [DOI: 10.1007/s10295-018-2044-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/29/2018] [Indexed: 12/29/2022]
Abstract
Abstract
Deficiency in petroleum resources and increasing environmental concerns have pushed a bio-based economy to be built, employing a highly reproducible, metal contaminant free, sustainable and green biomanufacturing method. Here, a chiral drug intermediate l-pipecolic acid has been synthesized from biomass-derived lysine. This artificial bioconversion system involves the coexpression of four functional genes, which encode l-lysine α-oxidase from Scomber japonicus, glucose dehydrogenase from Bacillus subtilis, Δ1-piperideine-2-carboxylase reductase from Pseudomonas putida, and lysine permease from Escherichia coli. Besides, a lysine degradation enzyme has been knocked out to strengthen the process in this microbe. The overexpression of LysP improved the l-pipecolic acid titer about 1.6-folds compared to the control. This engineered microbial factory showed the highest l-pipecolic acid production of 46.7 g/L reported to date and a higher productivity of 2.41 g/L h and a yield of 0.89 g/g. This biotechnological l-pipecolic acid production is a simple, economic, and green technology to replace the presently used chemical synthesis.
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32
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Dai Z, Zhou H, Zhang S, Gu H, Yang Q, Zhang W, Dong W, Ma J, Fang Y, Jiang M, Xin F. Current advance in biological production of malic acid using wild type and metabolic engineered strains. BIORESOURCE TECHNOLOGY 2018; 258:345-353. [PMID: 29550171 DOI: 10.1016/j.biortech.2018.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
Malic acid (2-hydroxybutanedioic acid) is a four-carbon dicarboxylic acid, which has attracted great interest due to its wide usage as a precursor of many industrially important chemicals in the food, chemicals, and pharmaceutical industries. Several mature routes for malic acid production have been developed, such as chemical synthesis, enzymatic conversion and biological fermentation. With depletion of fossil fuels and concerns regarding environmental issues, biological production of malic acid has attracted more attention, which mainly consists of three pathways, namely non-oxidative pathway, oxidative pathway and glyoxylate cycle. In recent decades, metabolic engineering of model strains, and process optimization for malic acid production have been rapidly developed. Hence, this review comprehensively introduces an overview of malic acid producers and highlight some of the successful metabolic engineering approaches.
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Affiliation(s)
- Zhongxue Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Huiyuan Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Honglian Gu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Qiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Yan Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
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33
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Guo L, Zhang F, Zhang C, Hu G, Gao C, Chen X, Liu L. Enhancement of malate production through engineering of the periplasmic rTCA pathway in Escherichia coli. Biotechnol Bioeng 2018; 115:1571-1580. [PMID: 29476618 DOI: 10.1002/bit.26580] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/18/2018] [Accepted: 02/20/2018] [Indexed: 12/13/2022]
Abstract
The compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency; however, prokaryotes are unicellular organisms that lack membrane-bound organelles. To mimic this natural compartmentalization, we present here the targeting of the reductive tricarboxylic acid (rTCA) pathway to the periplasm to enhance the production of malate. A multigene combination knockout strategy was used to construct a phosphoenolpyruvate (PEP) pool. Then, the genes encoding phosphoenolpyruvate carboxykinase and malate dehydrogenase were combinatorially overexpressed to construct a cytoplasmic rTCA pathway for malate biosynthesis; however, the efficiency of malate production was low. To further enhance malate production, the rTCA pathway was targeted to the periplasm, which led to a 100% increase in malate production to 18.8 mM. Next, dual metabolic engineering regulation was adopted to balance the cytoplasmic and periplasmic pathways, leading to an increase in malate production to 58.8 mM. The final engineered strain, GL2306, produced 193 mM malate with a yield of 0.53 mol/mol in 5 L of pH-stat fed-batch culture. The strategy described here paves the way for the development of metabolic engineering and synthetic biology in the microbial production of chemicals.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Fan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Can Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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34
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Current advances of succinate biosynthesis in metabolically engineered Escherichia coli. Biotechnol Adv 2017; 35:1040-1048. [DOI: 10.1016/j.biotechadv.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/19/2023]
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35
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Balanced activation of IspG and IspH to eliminate MEP intermediate accumulation and improve isoprenoids production in Escherichia coli. Metab Eng 2017; 44:13-21. [DOI: 10.1016/j.ymben.2017.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 03/30/2017] [Accepted: 08/28/2017] [Indexed: 11/20/2022]
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36
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Tan Z, Khakbaz P, Chen Y, Lombardo J, Yoon JM, Shanks JV, Klauda JB, Jarboe LR. Engineering Escherichia coli membrane phospholipid head distribution improves tolerance and production of biorenewables. Metab Eng 2017; 44:1-12. [DOI: 10.1016/j.ymben.2017.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/26/2017] [Accepted: 08/29/2017] [Indexed: 12/27/2022]
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37
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Xiao M, Zhu X, Bi C, Ma Y, Zhang X. Improving Succinate Productivity by Engineering a Cyanobacterial CO2
Concentrating System (CCM) in Escherichia coli. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/16/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Mengyong Xiao
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
- Key Laboratory of Systems Microbial Biotechnology; Chinese Academy of Sciences; Tianjin China
- University of Chinese Academy of Sciences; Beijing China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
- Key Laboratory of Systems Microbial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
- Key Laboratory of Systems Microbial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; Tianjin China
- Key Laboratory of Systems Microbial Biotechnology; Chinese Academy of Sciences; Tianjin China
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38
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Zhu X, Zhao D, Qiu H, Fan F, Man S, Bi C, Zhang X. The CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique and its application to improve the Escherichia coli xylose utilization pathway. Metab Eng 2017; 43:37-45. [PMID: 28800965 DOI: 10.1016/j.ymben.2017.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 01/09/2023]
Abstract
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome. To implement it, two plasmids were employed to target Cas9 to regulatory sequences of pathway genes, and a donor DNA plasmid library was constructed containing a regulator pool to modulate the expression of these genes. A modularized plasmid construction strategy was used to enable the assembly of a complex donor DNA plasmid library. After genome editing using this technique, a combinatorial library was obtained with variably expressed pathway genes. As a demonstration, the CFPO technique was applied to the xylose metabolic pathway genes in E. coli to improve xylose utilization. Three transcriptional units containing a total of four genes were modulated simultaneously with 70% efficiency, and improved strains were selected from the resulting combinatorial library by growth enrichment. The best strain, HQ304, displayed a 3-fold increase of the xylose-utilization rate. Finally, the xylose-utilization pathway of HQ304 was analyzed enzymologically to determine the optimal combination of enzyme activities.
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Affiliation(s)
- Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Huanna Qiu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Shuli Man
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China.
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Liu J, Xie Z, Shin HD, Li J, Du G, Chen J, Liu L. Rewiring the reductive tricarboxylic acid pathway and L-malate transport pathway of Aspergillus oryzae for overproduction of L-malate. J Biotechnol 2017; 253:1-9. [DOI: 10.1016/j.jbiotec.2017.05.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/09/2017] [Accepted: 05/12/2017] [Indexed: 12/13/2022]
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40
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Cui Z, Gao C, Li J, Hou J, Lin CSK, Qi Q. Engineering of unconventional yeast Yarrowia lipolytica for efficient succinic acid production from glycerol at low pH. Metab Eng 2017. [PMID: 28627452 DOI: 10.1016/j.ymben.2017.06.007] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Yarrowia lipolytica is considered as a potential candidate for succinic acid production because of its innate ability to accumulate citric acid cycle intermediates and its tolerance to acidic pH. Previously, a succinate-production strain was obtained through the deletion of succinate dehydrogenase subunit encoding gene Ylsdh5. However, the accumulation of by-product acetate limited further improvement of succinate production. Meanwhile, additional pH adjustment procedure increased the downstream cost in industrial application. In this study, we identified for the first time that acetic acid overflow is caused by CoA-transfer reaction from acetyl-CoA to succinate in mitochondria rather than pyruvate decarboxylation reaction in SDH negative Y. lipolytica. The deletion of CoA-transferase gene Ylach eliminated acetic acid formation and improved succinic acid production and the cell growth. We then analyzed the effect of overexpressing the key enzymes of oxidative TCA, reductive carboxylation and glyoxylate bypass on succinic acid yield and by-products formation. The best strain with phosphoenolpyruvate carboxykinase (ScPCK) from Saccharomyces cerevisiae and endogenous succinyl-CoA synthase beta subunit (YlSCS2) overexpression improved succinic acid titer by 4.3-fold. In fed-batch fermentation, this strain produced 110.7g/L succinic acid with a yield of 0.53g/g glycerol without pH control. This is the highest succinic acid titer achieved at low pH by yeast reported worldwide, to date, using defined media. This study not only revealed the mechanism of acetic acid overflow in SDH negative Y. lipolytica, but it also reported the development of an efficient succinic acid production strain with great industrial prospects.
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Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Cuijuan Gao
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China; School of Life Science, Linyi University, Linyi 276000, China
| | - Jiaojiao Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, China.
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Osmotolerance in Escherichia coli Is Improved by Activation of Copper Efflux Genes or Supplementation with Sulfur-Containing Amino Acids. Appl Environ Microbiol 2017; 83:AEM.03050-16. [PMID: 28115377 DOI: 10.1128/aem.03050-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/09/2017] [Indexed: 11/20/2022] Open
Abstract
Improvement in the osmotolerance of Escherichia coli is essential for the production of high titers of various bioproducts. In this work, a cusS mutation that was identified in the previously constructed high-succinate-producing E. coli strain HX024 was investigated for its effect on osmotolerance. CusS is part of the two-component system CusSR that protects cells from Ag(I) and Cu(I) toxicity. Changing cusS from strain HX024 back to its original sequence led to a 24% decrease in cell mass and succinate titer under osmotic stress (12% glucose). When cultivated with a high initial glucose concentration (12%), introduction of the cusS mutation into parental strain Suc-T110 led to a 21% increase in cell mass and a 40% increase in succinate titer. When the medium was supplemented with 30 g/liter disodium succinate, the cusS mutation led to a 120% increase in cell mass and a 492% increase in succinate titer. Introducing the cusS mutation into the wild-type strain ATCC 8739 led to increases in cell mass of 87% with 20% glucose and 36% using 30 g/liter disodium succinate. The cusS mutation increased the expression of cusCFBA, and gene expression levels were found to be positively related to osmotolerance abilities. Because high osmotic stress has been associated with deleterious accumulation of Cu(I) in the periplasm, activation of CusCFBA may alleviate this effect by transporting Cu(I) out of the cells. This hypothesis was confirmed by supplementing sulfur-containing amino acids that can chelate Cu(I). Adding methionine or cysteine to the medium increased the osmotolerance of E. coli under anaerobic conditions.IMPORTANCE In this work, an activating Cus copper efflux system was found to increase the osmotolerance of E. coli In addition, new osmoprotectants were identified. Supplementation with methionine or cysteine led to an increase in osmotolerance of E. coli under anaerobic conditions. These new strategies for improving osmotolerance will be useful for improving the production of chemicals in industrial bioprocesses.
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Tan Z, Black W, Yoon JM, Shanks JV, Jarboe LR. Improving Escherichia coli membrane integrity and fatty acid production by expression tuning of FadL and OmpF. Microb Cell Fact 2017; 16:38. [PMID: 28245829 PMCID: PMC5331629 DOI: 10.1186/s12934-017-0650-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/22/2017] [Indexed: 11/26/2022] Open
Abstract
Background Construction of microbial biocatalysts for the production of biorenewables at economically viable yields and titers is frequently hampered by product toxicity. Membrane damage is often deemed as the principal mechanism of this toxicity, particularly in regards to decreased membrane integrity. Previous studies have attempted to engineer the membrane with the goal of increasing membrane integrity. However, most of these works focused on engineering of phospholipids and efforts to identify membrane proteins that can be targeted to improve fatty acid production have been unsuccessful. Results Here we show that deletion of outer membrane protein ompF significantly increased membrane integrity, fatty acid tolerance and fatty acid production, possibly due to prevention of re-entry of short chain fatty acids. In contrast, deletion of fadL resulted in significantly decreased membrane integrity and fatty acid production. Consistently, increased expression of fadL remarkably increased membrane integrity and fatty acid tolerance while also increasing the final fatty acid titer. This 34% increase in the final fatty acid titer was possibly due to increased membrane lipid biosynthesis. Tuning of fadL expression showed that there is a positive relationship between fadL abundance and fatty acid production. Combinatorial deletion of ompF and increased expression of fadL were found to have an additive role in increasing membrane integrity, and was associated with a 53% increase the fatty acid titer, to 2.3 g/L. Conclusions These results emphasize the importance of membrane proteins for maintaining membrane integrity and production of biorenewables, such as fatty acids, which expands the targets for membrane engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0650-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zaigao Tan
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - William Black
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.,Department of Chemical Engineering and Materials Sciences, University of California, 916 Engineering Tower Irvine, Irvine, CA, 92697-2575, USA
| | - Jong Moon Yoon
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Jacqueline V Shanks
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Laura R Jarboe
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
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43
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Lie AAY, Liu Z, Terrado R, Tatters AO, Heidelberg KB, Caron DA. Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp. BMC Genomics 2017; 18:163. [PMID: 28196482 PMCID: PMC5310065 DOI: 10.1186/s12864-017-3549-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/02/2017] [Indexed: 12/21/2022] Open
Abstract
Background Ochromonas is a genus of mixotrophic chrysophytes that is found ubiquitously in many aquatic environments. Species in this genus can be important consumers of bacteria but vary in their ability to perform photosynthesis. We studied the effect of light and bacteria on growth and gene expression of a predominantly phagotrophic Ochromonas species. Axenic cultures of Ochromonas sp. were fed with heat-killed bacteria (HKB) and grown in constant light or darkness. RNA was extracted from cultures in the light or in the dark with HKB present (Light + HKB; Dark + HKB), and in the light after HKB were depleted (Light + depleted HKB). Results There were no significant differences in the growth or bacterial ingestion rates between algae grown in light or dark conditions. The availability of light led to a differential expression of only 8% of genes in the transcriptome. A number of genes associated with photosynthesis, phagotrophy, and tetrapyrrole synthesis was upregulated in the Light + HKB treatment compared to Dark + HKB. Conversely, the comparison between the Light + HKB and Light + depleted HKB treatments revealed that the presence of HKB led to differential expression of 59% of genes, including the majority of genes involved in major carbon and nitrogen metabolic pathways. Genes coding for unidirectional enzymes for the utilization of glucose were upregulated in the presence of HKB, implying increased glycolytic activities during phagotrophy. Algae without HKB upregulated their expression of genes coding for ammonium transporters, implying uptake of inorganic nitrogen from the culture medium when prey were unavailable. Conclusions Transcriptomic results agreed with previous observations that light had minimal effect on the population growth of Ochromonas sp. However, light led to the upregulation of a number of phototrophy- and phagotrophy-related genes, while the availability of bacterial prey led to prominent changes in major carbon and nitrogen metabolic pathways. Our study demonstrated the potential of transcriptomic approaches to improve our understanding of the trophic physiologies of complex mixotrophs, and revealed responses in Ochromonas sp. not apparent from traditional culture studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3549-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alle A Y Lie
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA.
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Ramon Terrado
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Avery O Tatters
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
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Xiao M, Zhu X, Xu H, Tang J, Liu R, Bi C, Fan F, Zhang X. A novel point mutation in RpoB improves osmotolerance and succinic acid production in Escherichia coli. BMC Biotechnol 2017; 17:10. [PMID: 28193207 PMCID: PMC5307762 DOI: 10.1186/s12896-017-0337-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/10/2017] [Indexed: 11/29/2022] Open
Abstract
Background Escherichia coli suffer from osmotic stress during succinic acid (SA) production, which reduces the performance of this microbial factory. Results Here, we report that a point mutation leading to a single amino acid change (D654Y) within the β-subunit of DNA-dependent RNA polymerase (RpoB) significantly improved the osmotolerance of E. coli. Importation of the D654Y mutation of RpoB into the parental strain, Suc-T110, increased cell growth and SA production by more than 40% compared to that of the control under high glucose osmolality. The transcriptome profile, determined by RNA-sequencing, showed two distinct stress responses elicited by the mutated RpoB that counterbalanced the osmotic stress. Under non-stressed conditions, genes involved in the synthesis and transport of compatible solutes such as glycine-betaine, glutamate or proline were upregulated even without osmotic stimulation, suggesting a “pre-defense” mechanism maybe formed in the rpoB mutant. Under osmotic stressed conditions, genes encoding diverse sugar transporters, which should be down-regulated in the presence of high osmotic pressure, were derepressed in the rpoB mutant. Additional genetic experiments showed that enhancing the expression of the mal regulon, especially for genes that encode the glycoporin LamB and maltose transporter, contributed to the osmotolerance phenotype. Conclusions The D654Y single amino acid substitution in RpoB rendered E. coli cells resistant to osmotic stress, probably due to improved cell growth and viability via enhanced sugar uptake under stressed conditions, and activated a potential “pre-defense” mechanism under non-stressed conditions. The findings of this work will be useful for bacterial host improvement to enhance its resistance to osmotic stress and facilitate bio-based organic acids production. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0337-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengyong Xiao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Hongtao Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Jinlei Tang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Ru Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China.
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Tomita Y, Yoshioka K, Iijima H, Nakashima A, Iwata O, Suzuki K, Hasunuma T, Kondo A, Hirai MY, Osanai T. Succinate and Lactate Production from Euglena gracilis during Dark, Anaerobic Conditions. Front Microbiol 2016; 7:2050. [PMID: 28066371 PMCID: PMC5174102 DOI: 10.3389/fmicb.2016.02050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/07/2016] [Indexed: 01/01/2023] Open
Abstract
Euglena gracilis is a eukaryotic, unicellular phytoflagellate that has been widely studied in basic science and applied science. Under dark, anaerobic conditions, the cells of E. gracilis produce a wax ester that can be converted into biofuel. Here, we demonstrate that under dark, anaerobic conditions, E. gracilis excretes organic acids, such as succinate and lactate, which are bulk chemicals used in the production of bioplastics. The levels of succinate were altered by changes in the medium and temperature during dark, anaerobic incubation. Succinate production was enhanced when cells were incubated in CM medium in the presence of NaHCO3. Excretion of lactate was minimal in the absence of external carbon sources, but lactate was produced in the presence of glucose during dark, anaerobic incubation. E. gracilis predominantly produced L-lactate; however, the percentage of D-lactate increased to 28.4% in CM medium at 30°C. Finally, we used a commercial strain of E. gracilis for succinate production and found that nitrogen-starved cells, incubated under dark, anaerobic conditions, produced 869.6 mg/L succinate over a 3-day incubation period, which was 70-fold higher than the amount produced by nitrogen-replete cells. This is the first study to demonstrate organic acid excretion by E. gracilis cells and to reveal novel aspects of primary carbon metabolism in this organism.
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Affiliation(s)
- Yuko Tomita
- School of Agriculture, Meiji University Kawasaki, Japan
| | | | - Hiroko Iijima
- School of Agriculture, Meiji University Kawasaki, Japan
| | | | | | | | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University Kobe, Japan
| | | | - Takashi Osanai
- School of Agriculture, Meiji UniversityKawasaki, Japan; RIKEN Center for Sustainable Resource ScienceYokohama, Japan
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46
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Wei LN, Zhu LW, Tang YJ. Succinate production positively correlates with the affinity of the global transcription factor Cra for its effector FBP in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:264. [PMID: 27980674 PMCID: PMC5146860 DOI: 10.1186/s13068-016-0679-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Effector binding is important for transcription factors, affecting both the pattern and function of transcriptional regulation to alter cell phenotype. Our previous work suggested that the affinity of the global transcription factor catabolite repressor/activator (Cra) for its effector fructose-1,6-bisphosphate (FBP) may contribute to succinate biosynthesis. To support this hypothesis, single-point and three-point mutations were proposed through the semi-rational design of Cra to improve its affinity for FBP. RESULTS For the first time, a positive correlation between succinate production and the affinity of Cra for FBP was revealed in Escherichia coli. Using the best-fit regression function, a cubic equation was used to examine and describe the relationship between succinate production and the affinity of Cra for FBP, demonstrating a significant positive correlation between the two factors (coefficient of determination R2 = 0.894, P = 0.000 < 0.01). The optimal mutant strain was Tang1683, which provided the lowest mutation energy of -4.78 kcal/mol and the highest succinate concentration of 92.7 g/L, which was 34% higher than that obtained using an empty vector control. The parameters for the interaction between Cra and DNA showed that Cra bound to the promoter regions of pck and aceB to activate the corresponding genes. Normally, Cra-regulated operons under positive control are deactivated in the presence of FBP. Therefore, theoretically, the enhanced affinity of Cra for FBP will inhibit the activation of pck and aceB. However, the activation of genes involved in CO2 fixation and the glyoxylate pathway was further improved by the Cra mutant, ultimately contributing to succinate biosynthesis. CONCLUSIONS Enhanced binding of Cra to FBP or active site mutations may eliminate the repressive effect caused by FBP, thus leading to increased activation of genes associated with succinate biosynthesis in the Cra mutant. This work demonstrates an important transcriptional regulation strategy in the metabolic engineering of succinate production and provides useful information for better understanding of the regulatory mechanisms of transcription factors.
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Affiliation(s)
- Li-Na Wei
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, 430068 China
| | - Li-Wen Zhu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, 430068 China
| | - Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, 430068 China
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Ye L, Zhang C, Bi C, Li Q, Zhang X. Combinatory optimization of chromosomal integrated mevalonate pathway for β-carotene production in Escherichia coli. Microb Cell Fact 2016; 15:202. [PMID: 27905930 PMCID: PMC5134235 DOI: 10.1186/s12934-016-0607-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/26/2016] [Indexed: 01/04/2023] Open
Abstract
Background Plasmid expression is a popular method in studies of MVA pathway for isoprenoid production in Escherichia coli. However, heterologous gene expression with plasmid is often not stable and might burden growth of host cells, decreases cell mass and product yield. In this study, MVA pathway was divided into three modules, and two heterologous modules were integrated into the E. coli chromosome. These modules were individually modulated with regulatory parts to optimize efficiency of the pathway in terms of downstream isoprenoid production. Results MVA pathway modules Hmg1-erg12 operon and mvaS-mvaA-mavD1 operon were integrated into E. coli chromosome followed by modulation with promoters with varied strength. Along with activation of atoB, a 26% increase of β-carotene production with no effect on cell growth was obtained. With a combinatory modulation of two key enzymes mvas and Hmg1 with degenerate RBS library, β-carotene showed a further increase of 51%. Conclusions Our study provides a novel strategy for improving production of a target compound through integration and modulation of heterologous pathways in both transcription and translation level. In addition, a genetically hard-coded chassis with both efficient MEP and MVA pathways for isoprenoid precursor supply was constructed in this work. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0607-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lijun Ye
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Qingyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
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48
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Zhu LW, Xia ST, Wei LN, Li HM, Yuan ZP, Tang YJ. Enhancing succinic acid biosynthesis in Escherichia coli by engineering its global transcription factor, catabolite repressor/activator (Cra). Sci Rep 2016; 6:36526. [PMID: 27811970 PMCID: PMC5109907 DOI: 10.1038/srep36526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 10/17/2016] [Indexed: 11/09/2022] Open
Abstract
This study was initiated to improve E. coli succinate production by engineering the E. coli global transcription factor, Cra (catabolite repressor/activator). Random mutagenesis libraries were generated through error-prone PCR of cra. After re-screening and mutation site integration, the best mutant strain was Tang1541, which provided a final succinate concentration of 79.8 ± 3.1 g/L: i.e., 22.8% greater than that obtained using an empty vector control. The genes and enzymes involved in phosphoenolpyruvate (PEP) carboxylation and the glyoxylate pathway were activated, either directly or indirectly, through the mutation of Cra. The parameters for interaction of Cra and DNA indicated that the Cra mutant was bound to aceBAK, thereby activating the genes involved in glyoxylate pathway and further improving succinate production even in the presence of its effector fructose-1,6-bisphosphate (FBP). It suggested that some of the negative effect of FBP on Cra might have been counteracted through the enhanced binding affinity of the Cra mutant for FBP or the change of Cra structure. This work provides useful information about understanding the transcriptional regulation of succinate biosynthesis.
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Affiliation(s)
- Li-Wen Zhu
- School of Public Health, Wuhan University, Wuhan 430071 China.,Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Shi-Tao Xia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Li-Na Wei
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Hong-Mei Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Zhan-Peng Yuan
- School of Public Health, Wuhan University, Wuhan 430071 China
| | - Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
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49
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Metabolic engineering of cyanobacteria for the photosynthetic production of succinate. Metab Eng 2016; 38:483-493. [PMID: 27989804 DOI: 10.1016/j.ymben.2016.10.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
Abstract
Succinate is an important commodity chemical currently used in the food, pharmaceutical, and polymer industries. It can also be chemically converted into other major industrial chemicals such as 1,4-butanediol, butadiene, and tetrahydrofuran. Here we metabolically engineered a model cyanobacterium Synechococcus elongatus PCC 7942 to photosynthetically produce succinate. We expressed the genes encoding for α-ketoglutarate decarboxylase and succinate semialdehyde dehydrogenase in S. elongatus PCC 7942, resulting in a strain capable of producing 120mg/L of succinate. However, this recombinant strain exhibited severe growth retardation upon induction of the genes encoding for the succinate producing pathway, potentially due to the depletion of α-ketoglutarate. To replenish α-ketoglutarate, we expressed the genes encoding for phosphoenolpyruvate carboxylase and citrate synthase from Corynebacterium glutamicum into the succinate producing strain. The resulting strain successfully restored the growth phenotype and produced succinate with a titer of 430mg/L in 8 days. These results demonstrated the possibility of photoautotrophic succinate production.
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Meng J, Wang B, Liu D, Chen T, Wang Z, Zhao X. High-yield anaerobic succinate production by strategically regulating multiple metabolic pathways based on stoichiometric maximum in Escherichia coli. Microb Cell Fact 2016; 15:141. [PMID: 27520031 PMCID: PMC4983090 DOI: 10.1186/s12934-016-0536-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 08/02/2016] [Indexed: 12/03/2022] Open
Abstract
Background Succinate has been identified by the U.S. Department of Energy as one of the top 12 building block chemicals, which can be used as a specialty chemical in the agricultural, food, and pharmaceutical industries. Escherichia coli are now one of the most important succinate producing candidates. However, the stoichiometric maximum succinate yield under anaerobic conditions through the reductive branch of the TCA cycle is restricted by NADH supply in E. coli. Results In the present work, we report a rational approach to increase succinate yield by regulating NADH supply via pentose phosphate (PP) pathway and enhancing flux towards succinate. The deregulated genes zwf243 (encoding glucose-6-phosphate dehydrogenase) and gnd361 (encoding 6-phosphogluconate dehydrogenase) involved in NADPH generation from Corynebacterium glutamicum were firstly introduced into E. coli for succinate production. Co-expression of beneficial mutated dehydrogenases, which removed feedback inhibition in the oxidative part of the PP pathway, increased succinate yield from 1.01 to 1.16 mol/mol glucose. Three critical genes, pgl (encoding 6-phosphogluconolactonase), tktA (encoding transketolase) and talB (encoding transaldolase) were then overexpressed to redirect more carbon flux towards PP pathway and further improved succinate yield to 1.21 mol/mol glucose. Furthermore, introducing Actinobacillus succinogenes pepck (encoding phosphoenolpyruvate carboxykinase) together with overexpressing sthA (encoding soluble transhydrogenase), further increased succinate yield to 1.31 mol/mol glucose. In addition, removing byproduct formation through inactivating acetate formation genes ackA-pta and heterogenously expressing pyc (encoding pyruvate carboxylase) from C. glutamicum led to improved succinate yield to 1.4 mol/mol glucose. Finally, synchronously overexpressing dcuB and dcuC encoding succinate exporters enhanced succinate yield to 1.54 mol/mol glucose, representing 52 % increase relative to the parent strain and amounting to 90 % of the strain-specific stoichiometric maximum (1.714 mol/mol glucose). Conclusions It’s the first time to rationally regulate pentose phosphate pathway to improve NADH supply for succinate synthesis in E. coli. 90 % of stoichiometric maximum succinate yield was achieved by combining further flux increase towards succinate and engineering its export. Regulation of NADH supply via PP pathway is therefore recommended for the production of products that are NADH-demanding in E. coli. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0536-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiao Meng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Baiyun Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Dingyu Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.,Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan, 430068, People's Republic of China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China.
| | - Xueming Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
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