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Gu P, Li F, Huang Z. Engineering Escherichia coli for Isobutanol Production from Xylose or Glucose-Xylose Mixture. Microorganisms 2023; 11:2573. [PMID: 37894231 PMCID: PMC10609591 DOI: 10.3390/microorganisms11102573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Aiming to overcome the depletion of fossil fuels and serious environmental pollution, biofuels such as isobutanol have garnered increased attention. Among different synthesis methods, the microbial fermentation of isobutanol from raw substrate is a promising strategy due to its low cost and environmentally friendly and optically pure products. As an important component of lignocellulosics and the second most common sugar in nature, xylose has become a promising renewable resource for microbial production. However, bottlenecks in xylose utilization limit its wide application as substrates. In this work, an isobutanol synthetic pathway from xylose was first constructed in E. coli MG1655 through the combination of the Ehrlich and Dahms pathways. The engineering of xylose transport and electron transport chain complexes further improved xylose assimilation and isobutanol production. By optimizing xylose supplement concentration, the recombinant E. coli strain BWL4 could produce 485.35 mg/L isobutanol from 20 g/L of xylose. To our knowledge, this is the first report related to isobutanol production using xylose as a sole carbon source in E. coli. Additionally, a glucose-xylose mixture was utilized as the carbon source. The Entner-Doudorof pathway was used to assimilate glucose, and the Ehrlich pathway was applied for isobutanol production. After carefully engineering the recombinant E. coli, strain BWL9 could produce 528.72 mg/L isobutanol from a mixture of 20 g/L glucose and 10 g/L xylose. The engineering strategies applied in this work provide a useful reference for the microbial production of isobutanol from xylose or glucose-xylose mixture.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
| | - Fangfang Li
- Yantai Food and Drug Control and Test Center, Yantai 264003, China;
| | - Zhaosong Huang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China;
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2
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Boecker S, Schulze P, Klamt S. Growth-coupled anaerobic production of isobutanol from glucose in minimal medium with Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:148. [PMID: 37789464 PMCID: PMC10548627 DOI: 10.1186/s13068-023-02395-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND The microbial production of isobutanol holds promise to become a sustainable alternative to fossil-based synthesis routes for this important chemical. Escherichia coli has been considered as one production host, however, due to redox imbalance, growth-coupled anaerobic production of isobutanol from glucose in E. coli is only possible if complex media additives or small amounts of oxygen are provided. These strategies have a negative impact on product yield, productivity, reproducibility, and production costs. RESULTS In this study, we propose a strategy based on acetate as co-substrate for resolving the redox imbalance. We constructed the E. coli background strain SB001 (ΔldhA ΔfrdA ΔpflB) with blocked pathways from glucose to alternative fermentation products but with an enabled pathway for acetate uptake and subsequent conversion to ethanol via acetyl-CoA. This strain, if equipped with the isobutanol production plasmid pIBA4, showed robust exponential growth (µ = 0.05 h-1) under anaerobic conditions in minimal glucose medium supplemented with small amounts of acetate. In small-scale batch cultivations, the strain reached a glucose uptake rate of 4.8 mmol gDW-1 h-1, a titer of 74 mM and 89% of the theoretical maximal isobutanol/glucose yield, while secreting only small amounts of ethanol synthesized from acetate. Furthermore, we show that the strain keeps a high metabolic activity also in a pulsed fed-batch bioreactor cultivation, even if cell growth is impaired by the accumulation of isobutanol in the medium. CONCLUSIONS This study showcases the beneficial utilization of acetate as a co-substrate and redox sink to facilitate growth-coupled production of isobutanol under anaerobic conditions. This approach holds potential for other applications with different production hosts and/or substrate-product combinations.
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Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
- University of Applied Sciences Berlin, Seestr. 64, 13347, Berlin, Germany
| | - Peter Schulze
- Physical and Chemical Foundations of Process Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Steffen Klamt
- Analysis and Redesign of Biological Networks, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.
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3
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Carranza-Saavedra D, Torres-Bacete J, Blázquez B, Sánchez Henao CP, Zapata Montoya JE, Nogales J. System metabolic engineering of Escherichia coli W for the production of 2-ketoisovalerate using unconventional feedstock. Front Bioeng Biotechnol 2023; 11:1176445. [PMID: 37152640 PMCID: PMC10158823 DOI: 10.3389/fbioe.2023.1176445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Replacing traditional substrates in industrial bioprocesses to advance the sustainable production of chemicals is an urgent need in the context of the circular economy. However, since the limited degradability of non-conventional carbon sources often returns lower yields, effective exploitation of such substrates requires a multi-layer optimization which includes not only the provision of a suitable feedstock but the use of highly robust and metabolically versatile microbial biocatalysts. We tackled this challenge by means of systems metabolic engineering and validated Escherichia coli W as a promising cell factory for the production of the key building block chemical 2-ketoisovalerate (2-KIV) using whey as carbon source, a widely available and low-cost agro-industrial waste. First, we assessed the growth performance of Escherichia coli W on mono and disaccharides and demonstrated that using whey as carbon source enhances it significantly. Second, we searched the available literature and used metabolic modeling approaches to scrutinize the metabolic space of E. coli and explore its potential for overproduction of 2-KIV identifying as basic strategies the block of pyruvate depletion and the modulation of NAD/NADP ratio. We then used our model predictions to construct a suitable microbial chassis capable of overproducing 2-KIV with minimal genetic perturbations, i.e., deleting the pyruvate dehydrogenase and malate dehydrogenase. Finally, we used modular cloning to construct a synthetic 2-KIV pathway that was not sensitive to negative feedback, which effectively resulted in a rerouting of pyruvate towards 2-KIV. The resulting strain shows titers of up to 3.22 ± 0.07 g/L of 2-KIV and 1.40 ± 0.04 g/L of L-valine in 24 h using whey in batch cultures. Additionally, we obtained yields of up to 0.81 g 2-KIV/g substrate. The optimal microbial chassis we present here has minimal genetic modifications and is free of nutritional autotrophies to deliver high 2-KIV production rates using whey as a non-conventional substrate.
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Affiliation(s)
- Darwin Carranza-Saavedra
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
| | - Blas Blázquez
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
| | - Claudia Patricia Sánchez Henao
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - José Edgar Zapata Montoya
- Faculty of Pharmaceutical and Food Sciences, Nutrition and Food Technology Group, University of Antioquia, Medellín, Colombia
| | - Juan Nogales
- Department of Systems Biology, National Centre for Biotechnology (CSIC), Systems Biotechnology Group, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC), Madrid, Spain
- *Correspondence: Juan Nogales,
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4
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Lakshmi NM, Binod P, Sindhu R, Awasthi MK, Pandey A. Microbial engineering for the production of isobutanol: current status and future directions. Bioengineered 2021; 12:12308-12321. [PMID: 34927549 PMCID: PMC8809953 DOI: 10.1080/21655979.2021.1978189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Fermentation-derived alcohols have gained much attention as an alternate fuel due to its minimal effects on atmosphere. Besides its application as biofuel it is also used as raw material for coating resins, deicing fluid, additives in polishes, etc. Among the liquid alcohol type of fuels, isobutanol has more advantage than ethanol. Isobutanol production is reported in native yeast strains, but the production titer is very low which is about 200 mg/L. In order to improve the production, several genetic and metabolic engineering approaches have been carried out. Genetically engineered organism has been reported to produce maximum of 50 g/L of isobutanol which is far more than the native strain without any modification. In bacteria mostly last two steps in Ehrlich pathway, catalyzed by enzymes ketoisovalerate decarboxylase and alcohol dehydrogenase, are heterologously expressed to improve the production. Native Saccharomyces cerevisiae can produce isobutanol in negligible amount since it possesses the pathway for its production through valine degradation pathway. Further modifications in the existing pathways made the improvement in isobutanol production in many microbial strains. Fermentation using cost-effective lignocellulosic biomass and an efficient downstream process can yield isobutanol in environment friendly and sustainable manner. The present review describes the various genetic and metabolic engineering practices adopted to improve the isobutanol production in microbial strains and its downstream processing.
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Affiliation(s)
- Nair M Lakshmi
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (Csir-niist), Thiruvananthapuram Kerala, India.,Academy of Scientific and Innovative Research (Acsir), Ghaziabad, Uttar Pradesh India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (Csir-niist), Thiruvananthapuram Kerala, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (Csir-niist), Thiruvananthapuram Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West a & F University, Yangling, Shaanxi China
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research (Csir-iitr), Lucknow India.,Centre for Energy and Environmental Sustainability, Lucknow Uttar Pradesh, India
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5
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Dynamic metabolic engineering of Escherichia coli improves fermentation for the production of pyruvate and its derivatives. J Biosci Bioeng 2021; 133:56-63. [PMID: 34674961 DOI: 10.1016/j.jbiosc.2021.09.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022]
Abstract
Pyruvate is a key intermediate that is involved in various synthetic metabolic pathways for microbial chemical and fuel production. It is widely used in the food, chemical, and pharmaceutical industries. However, the microbial production of pyruvate and its derivatives compete with microbial cell growth, as pyruvate is an important metabolic intermediate that serves as a hub for various endogenous metabolic pathways, including gluconeogenesis, amino acid synthesis, TCA cycle, and fatty acid biosynthesis. To achieve a more efficient bioprocess for the production of pyruvate and its derivatives, it is necessary to reduce the metabolic imbalance between cell growth and target chemical production. For this purpose, we devised a dynamic metabolic engineering strategy within an Escherichia coli model, in which a metabolic toggle switch (MTS) was employed to redirect metabolic flux from the endogenous pathway toward the target synthetic pathway. Through a combination of TCA cycle interruption through MTS and reduction of pyruvate consumption in endogenous pathways, we achieved a drastic improvement (163 mM, 26-fold) in pyruvate production. In addition, we demonstrated the redirection of metabolic flux from excess pyruvate toward isobutanol production. The final isobutanol production titer of the strain harboring MTS was 26% improved compared with that of the control strain.
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6
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Kim J, Hwang S, Lee SM. Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass. Metab Eng 2021; 71:2-12. [PMID: 34626808 DOI: 10.1016/j.ymben.2021.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/16/2021] [Accepted: 10/03/2021] [Indexed: 01/01/2023]
Abstract
The petrochemical industry has grown to meet the need for massive production of energy and commodities along with an explosive population growth; however, serious side effects such as greenhouse gas emissions and global warming have negatively impacted the environment. Lignocellulosic biomass with myriad quantities on Earth is an attractive resource for the production of carbon-neutral fuels and chemicals through environmentally friendly processes of microbial fermentation. This review discusses metabolic engineering efforts to achieve economically feasible industrial production of fuels and chemicals from microbial cell factories using the carbohydrate portion of lignocellulosic biomass as substrates. The combined knowledge of systems biology and metabolic engineering has been applied to construct robust platform microorganisms with maximum conversion of monomeric sugars, such as glucose and xylose, derived from lignocellulosic biomass. By comprehensively revisiting carbon conversion pathways, we provide a rationale for engineering strategies, as well as their features, feasibility, and recent representative studies. In addition, we briefly discuss how tools in systems biology can be applied in the field of metabolic engineering to accelerate the development of microbial cell factories that convert lignocellulosic biomass into carbon-neutral fuels and chemicals with economic feasibility.
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Affiliation(s)
- Jiwon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sungmin Hwang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Clean Energy and Chemical Engineering, University of Science and Technology, Daejeon, 34113, Republic of Korea; Green School (Graduate School of Energy and Environment), Korea University, Seoul, 02841, Republic of Korea.
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7
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Metabolic engineering of Escherichia coli for the production of isobutanol: a review. World J Microbiol Biotechnol 2021; 37:168. [PMID: 34487256 DOI: 10.1007/s11274-021-03140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
With the ongoing depletion of fossil fuel resources and emerging environmental issues, increasing research effort is being dedicated to producing biofuels from renewable substrates. With its advantages over ethanol in terms of energy density, octane number, and hygroscopicity, isobutanol is considered a potential alternative to traditional gasoline. However, as wild-type microorganisms cannot achieve the production of isobutanol with high titers and yields, rational genetic engineering has been employed to enhance its production. Herein, we review the latest developments in the metabolic engineering of Escherichia coli for the production of isobutanol, including those related to the utilization of diverse carbon sources, balancing the redox state, improving isobutanol tolerance, and application of synthetic biology circuits and tools.
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8
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Jojima T, Igari T, Noburyu R, Watanabe A, Suda M, Inui M. Coexistence of the Entner-Doudoroff and Embden-Meyerhof-Parnas pathways enhances glucose consumption of ethanol-producing Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:45. [PMID: 33593398 PMCID: PMC7888142 DOI: 10.1186/s13068-021-01876-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/07/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND It is interesting to modify sugar metabolic pathways to improve the productivity of biocatalysts that convert sugars to value-added products. However, this attempt often fails due to the tight control of the sugar metabolic pathways. Recently, activation of the Entner-Doudoroff (ED) pathway in Escherichia coli has been shown to enhance glucose consumption, though the mechanism underlying this phenomenon is poorly understood. In the present study, we investigated the effect of a functional ED pathway in metabolically engineered Corynebacterium glutamicum that metabolizes glucose via the Embden-Meyerhof-Parnas (EMP) pathway to produce ethanol under oxygen deprivation. This study aims to provide further information on metabolic engineering strategies that allow the Entner-Doudoroff and Embden-Meyerhof-Parnas pathways to coexist. RESULTS Three genes (zwf, edd, and eda) encoding glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydratase, and 2-keto-3-deoxy-6-phosphogluconate aldolase from Zymomonas mobilis were expressed in a genetically modified strain, C. glutamicum CRZ2e, which produces pyruvate decarboxylase and alcohol dehydrogenase from Z. mobilis. A 13C-labeling experiment using [1-13C] glucose indicated a distinctive 13C distribution of ethanol between the parental and the ED-introduced strains, which suggested an alteration of carbon flux as a consequence of ED pathway introduction. The ED-introduced strain, CRZ2e-ED, consumed glucose 1.5-fold faster than the parental strain. A pfkA deletion mutant of CRZ2e-ED (CRZ2e-EDΔpfkA) was also constructed to evaluate the effects of EMP pathway inactivation, which showed an almost identical rate of glucose consumption compared to that of the parental CRZ2e strain. The introduction of the ED pathway did not alter the intracellular NADH/NAD+ ratio, whereas it resulted in a slight increase in the ATP/ADP ratio. The recombinant strains with simultaneous overexpression of the genes for the EMP and ED pathways exhibited the highest ethanol productivity among all C. glutamicum strains ever constructed. CONCLUSIONS The increased sugar consumption observed in ED-introduced strains was not a consequence of cofactor balance alterations, but rather the crucial coexistence of two active glycolytic pathways for enhanced glucose consumption. Coexistence of the ED and EMP pathways is a good strategy for improving biocatalyst productivity even when NADPH supply is not a limiting factor for fermentation.
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Affiliation(s)
- Toru Jojima
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
- Faculty of Agriculture, Department of Environmental Management, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Takafumi Igari
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Ryoji Noburyu
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Akira Watanabe
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.
- Division of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, 8916-5, Nara, 630-0101, Japan.
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9
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Huang C, Guo L, Wang J, Wang N, Huo YX. Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering. Appl Microbiol Biotechnol 2020; 104:7943-7956. [PMID: 32794018 DOI: 10.1007/s00253-020-10819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. .,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China.
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10
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Liang S, Jiang W, Song Y, Zhou SF. Improvement and Metabolomics-Based Analysis of d-Lactic Acid Production from Agro-Industrial Wastes by Lactobacillus delbrueckii Submitted to Adaptive Laboratory Evolution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7660-7669. [PMID: 32603099 DOI: 10.1021/acs.jafc.0c00259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To decrease d-lactic acid production cost, sugarcane molasses and soybean meal, low-cost agro-industrial wastes, were selected as feedstock. First, sugarcane molasses was used directly by Lactobacillus delbrueckii S-NL31, and the nutrients were released from soybean meal by protease hydrolysis. Subsequently, to ensure intensive substrate utilization and enhanced d-lactic acid production from sugarcane molasses and soybean meal, adaptation of L. delbrueckii S-NL31 to substrates was performed through adaptive laboratory evolution. After two-phase adaptive laboratory evolution, the evolved strain L. delbrueckii S-NL31-CM3-SBM with improved cell growth and d-lactic acid production on sugarcane molasses and soybean meal was obtained. To decipher the potential reasons for improved fermentation performance, a metabolomics-based approach was developed to profile the differences of intracellular metabolism between initial and evolved strain. The in-depth analysis elucidated how the key factors exerted influence on d-lactic acid biosynthesis. The results revealed that the enhancement of glycolysis pathway and cofactor supply was directly associated with increased lactic acid production, and the reinforcement of pentose phosphate pathway, amino acid metabolism, and oleic acid uptake improved cell survival and growth. These might be the main reasons for significantly improved d-lactic acid production by adaptive laboratory evolution. Finally, fed-batch simultaneous enzymatic hydrolysis of soybean meal and fermentation process by evolved strain resulted in d-lactic acid levels of 112.3 g/L, with an average production efficiency of 2.4 g/(L × h), a yield of 0.98 g/g sugar, and optical purity of 99.6%. The results show the applicability of d-lactic acid production in L. delbrueckii fed on agro-industrial wastes through adaptive laboratory evolution.
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Affiliation(s)
- Shaoxiong Liang
- College of Chemical Engineering, Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Wei Jiang
- College of Chemical Engineering, Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Yibo Song
- College of Chemical Engineering, Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
| | - Shu-Feng Zhou
- College of Chemical Engineering, Huaqiao University, 668 Jimei Boulevard, Xiamen, Fujian 361021, P. R. China
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11
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Abstract
Metabolic engineering is crucial in the development of production strains for platform chemicals, pharmaceuticals and biomaterials from renewable resources. The central carbon metabolism (CCM) of heterotrophs plays an essential role in the conversion of biomass to the cellular building blocks required for growth. Yet, engineering the CCM ultimately aims toward a maximization of flux toward products of interest. The most abundant dissimilative carbohydrate pathways amongst prokaryotes (and eukaryotes) are the Embden-Meyerhof-Parnas (EMP) and the Entner-Doudoroff (ED) pathways, which build the basics for heterotrophic metabolic chassis strains. Although the EMP is regarded as the textbook example of a carbohydrate pathway owing to its central role in production strains like Escherichia coli, Saccharomyces cerevisiae and Bacillus subtilis, it is either modified, complemented or even replaced by alternative carbohydrate pathways in different organisms. The ED pathway also plays key roles in biotechnological relevant bacteria, like Zymomonas mobilis and Pseudomonas putida, and its importance was recently discovered in photoautotrophs and marine microorganisms. In contrast to the EMP, the ED pathway and its variations are not evolutionary optimized for high ATP production and it differs in key principles such as protein cost, energetics and thermodynamics, which can be exploited in the construction of unique metabolic designs. Single ED pathway enzymes and complete ED pathway modules have been used to rewire carbon metabolisms in production strains and for the construction of cell-free enzymatic pathways. This review focuses on the differences of the ED and EMP pathways including their variations and discusses the use of alternative pathway strategies for in vivo and cell-free metabolic engineering.
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Affiliation(s)
- Dominik Kopp
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
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12
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Liang L, Liu R, Freed EF, Eckert CA. Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2-C6 Bioalcohol Production. Front Bioeng Biotechnol 2020; 8:710. [PMID: 32719784 PMCID: PMC7347752 DOI: 10.3389/fbioe.2020.00710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022] Open
Abstract
Biofuel production from renewable and sustainable resources is playing an increasingly important role within the fuel industry. Among biofuels, bioethanol has been most widely used as an additive for gasoline. Higher alcohols can be blended at a higher volume compared to ethanol and generate lower greenhouse gas (GHG) emissions without a need to change current fuel infrastructures. Thus, these fuels have the potential to replace fossil fuels in support of more environmentally friendly processes. This review summarizes the efforts to enhance bioalcohol production in engineered Escherichia coli over the last 5 years and analyzes the current challenges for increasing productivities for industrial applications.
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Affiliation(s)
- Liya Liang
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
- National Renewable Energy Laboratory, Golden, CO, United States
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Xu L, Han F, Dong Z, Wei Z. Engineering Improves Enzymatic Synthesis of L-Tryptophan by Tryptophan Synthase from Escherichia coli. Microorganisms 2020; 8:microorganisms8040519. [PMID: 32260519 PMCID: PMC7232222 DOI: 10.3390/microorganisms8040519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022] Open
Abstract
To improve the thermostability of tryptophan synthase, the molecular modification of tryptophan synthase was carried out by rational molecular engineering. First, B-FITTER software was used to analyze the temperature factor (B-factor) of each amino acid residue in the crystal structure of tryptophan synthase. A key amino acid residue, G395, which adversely affected the thermal stability of the enzyme, was identified, and then, a mutant library was constructed by site-specific saturation mutation. A mutant (G395S) enzyme with significantly improved thermal stability was screened from the saturated mutant library. Error-prone PCR was used to conduct a directed evolution of the mutant enzyme (G395S). Compared with the parent, the mutant enzyme (G395S /A191T) had a Km of 0.21 mM and a catalytic efficiency kcat/Km of 5.38 mM−1∙s−1, which was 4.8 times higher than that of the wild-type strain. The conditions for L-tryptophan synthesis by the mutated enzyme were a L-serine concentration of 50 mmol/L, a reaction temperature of 40 °C, pH of 8, a reaction time of 12 h, and an L-tryptophan yield of 81%. The thermal stability of the enzyme can be improved by using an appropriate rational design strategy to modify the correct site. The catalytic activity of tryptophan synthase was increased by directed evolution.
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Affiliation(s)
- Lisheng Xu
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
- Correspondence: ; Tel.: +86-557-287-1681
| | - Fangkai Han
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
| | - Zeng Dong
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
| | - Zhaojun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China;
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Noda S, Mori Y, Oyama S, Kondo A, Araki M, Shirai T. Reconstruction of metabolic pathway for isobutanol production in Escherichia coli. Microb Cell Fact 2019; 18:124. [PMID: 31319852 PMCID: PMC6637570 DOI: 10.1186/s12934-019-1171-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 07/02/2019] [Indexed: 01/10/2023] Open
Abstract
Background The microbial production of useful fuels and chemicals has been widely studied. In several cases, glucose is used as the raw material, and almost all microbes adopt the Embden–Meyerhof (EM) pathway to degrade glucose into compounds of interest. Recently, the Entner–Doudoroff (ED) pathway has been gaining attention as an alternative strategy for microbial production. Results In the present study, we attempted to apply the ED pathway for isobutanol production in Escherichia coli because of the complete redox balance involved. First, we generated ED pathway-dependent isobutanol-producing E. coli. Thereafter, the inactivation of the genes concerning organic acids as the byproducts was performed to improve the carbon flux to isobutanol from glucose. Finally, the expression of the genes concerning the ED pathway was modified. Conclusions The optimized isobutanol-producing E. coli produced 15.0 g/L of isobutanol as the final titer, and the yield from glucose was 0.37 g/g (g-glucose/g-isobutanol). Electronic supplementary material The online version of this article (10.1186/s12934-019-1171-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yutaro Mori
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Sachiko Oyama
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Michihiro Araki
- Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Syogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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Tsuge Y, Kato N, Yamamoto S, Suda M, Jojima T, Inui M. Metabolic engineering of Corynebacterium glutamicum for hyperproduction of polymer-grade L- and D-lactic acid. Appl Microbiol Biotechnol 2019; 103:3381-3391. [PMID: 30877357 DOI: 10.1007/s00253-019-09737-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 01/22/2023]
Abstract
Strain development is critical for microbial production of bio-based chemicals. The stereo-complex form of polylactic acid, a complex of poly-L- and poly-D-lactic acid, is a promising polymer candidate due to its high thermotolerance. Here, we developed Corynebacterium glutamicum strains producing high amounts of L- and D-lactic acid through intensive metabolic engineering. Chromosomal overexpression of genes encoding the glycolytic enzymes, glucokinase, glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase, triosephosphate isomerase, and enolase, increased L- and D-lactic acid concentration by 146% and 56%, respectively. Chromosomal integration of two genes involved in the Entner-Doudoroff pathway (6-phosphogluconate dehydratase and 2-dehydro-3-deoxyphosphogluconate aldolase), together with a gene encoding glucose-6-phosphate dehydrogenase from Zymomonas mobilis, to bypass the carbon flow from glucose, further increased L- and D-lactic acid concentration by 11% and 44%, respectively. Finally, additional chromosomal overexpression of a gene encoding NADH dehydrogenase to modulate the redox balance resulted in the production of 212 g/L L-lactic acid with a 97.9% yield and 264 g/L D-lactic acid with a 95.0% yield. The optical purity of both L- and D-lactic acid was 99.9%. Because the constructed metabolically engineered strains were devoid of plasmids and antibiotic resistance genes and were cultivated in mineral salts medium, these strains could contribute to the cost-effective production of the stereo-complex form of polylactic acid in practical scale.
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Affiliation(s)
- Yota Tsuge
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan
| | - Naoto Kato
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Shogo Yamamoto
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Toru Jojima
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan. .,Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0101, Japan.
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