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Wu R, Li D, Chen Q, Luo Z, Zhou J, Mao J. Optimization of vanillin biosynthesis in Escherichia coli K12 MG1655 through metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 411:131189. [PMID: 39127360 DOI: 10.1016/j.biortech.2024.131189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Vanillin is an important flavouring agent applied in food, spices, pharmaceutical industries and other fields. Microbial biosynthesis of vanillin is considered a sustainable and economically feasible alternative to traditional chemical synthesis. In this study, Escherichia coli K12 MG1655 was used for the de novo synthesis of VAN by screening highly active carboxylic acid reductases and catechol O-methyltransferases, optimising the protocatechuic acid pathway, and regulating competitive metabolic pathways. Additionally, major alcohol by-products were identified and decreased by deleting three endogenous aldo-keto reductases and three alcohol dehydrogenases. Finally, a highest VAN titer was achieved to 481.2 mg/L in a 5 L fermenter from glucose. This work provides a valuable example of pathway engineering and screens several enzyme variants for the first time in E. coli.
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Affiliation(s)
- Renga Wu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Dong Li
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qihang Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhengshan Luo
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Mao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Jiangnan University (Shaoxing) Industrial Technology Research Institute, National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine Co., Ltd., Shaoxing, Zhejiang 312000, China.
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Guo X, Farag M, Qian N, Yu X, Ni A, Ma Y, Yu W, King MR, Liu V, Lee J, Zare RN, Min W, Pappu RV, Dai Y. Biomolecular condensates can function as inherent catalysts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602359. [PMID: 39026887 PMCID: PMC11257451 DOI: 10.1101/2024.07.06.602359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We report the discovery that chemical reactions such as ATP hydrolysis can be catalyzed by condensates formed by intrinsically disordered proteins (IDPs), which themselves lack any intrinsic ability to function as enzymes. This inherent catalytic feature of condensates derives from the electrochemical environments and the electric fields at interfaces that are direct consequences of phase separation. The condensates we studied were capable of catalyzing diverse hydrolysis reactions, including hydrolysis and radical-dependent breakdown of ATP whereby ATP fully decomposes to adenine and multiple carbohydrates. This distinguishes condensates from naturally occurring ATPases, which can only catalyze the dephosphorylation of ATP. Interphase and interfacial properties of condensates can be tuned via sequence design, thus enabling control over catalysis through sequence-dependent electrochemical features of condensates. Incorporation of hydrolase-like synthetic condensates into live cells enables activation of transcriptional circuits that depend on products of hydrolysis reactions. Inherent catalytic functions of condensates, which are emergent consequences of phase separation, are likely to affect metabolic regulation in cells.
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Affiliation(s)
- Xiao Guo
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Xia Yu
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Anton Ni
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Yuefeng Ma
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Wen Yu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Matthew R. King
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Vicky Liu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Joonho Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130
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Lee CY, Chen KW, Chiang CL, Kao HY, Yu HC, Lee HC, Chen WL. Improved production of β-carotene in light-powered Escherichia coli by co-expression of Gloeobacter rhodopsin expression. Microb Cell Fact 2023; 22:207. [PMID: 37817206 PMCID: PMC10563301 DOI: 10.1186/s12934-023-02212-0] [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: 05/25/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Providing sufficient and usable energy for the cell factory has long been a heated issue in biosynthesis as solar energy has never been rooted out from the strategy for improvement, and turning Escherichia coli (E. coli) into a phototrophic host has multiple captivating qualities for biosynthesis. In this study, β-carotene was a stable compound for production in E. coli with the expression of four enzymes (CrtE, CrtB, CrtI, CrtY) for production due to its light-harvesting feature as an antenna pigment and as an antioxidant and important precursor for human health. The expression of Gloeobacter rhodopsin (GR) in microbial organisms was proved to have potential for application. RESULTS The expression of fusion protein, GR-GFP, in E. coli showed visible GFP signal under fluorescent microscopy, and its in vivo proton pumping activity signal can be detected in induced photocurrent by electrodes on the chip under intervals of illumination. To assess the phototrophic synthesis ability of the host strain compared to wild-type and vector control strain in chemostat batch with illumination, the expression of red fluorescent protein (RFP) as a target protein showed its yield improvement in protein assay and also reflected its early dominance in RFP fluorescence signal during the incubation, whereas the synthesis of β-carotene also showed yield increase by 1.36-fold and 2.32-fold compared with its wildtype and vector control strain. To investigate the effect of GR-GFP on E. coli, the growth of the host showed early rise into the exponential phase compared to the vector control strain and glucose turnover rate was elevated in increased glucose intake rate and upregulation of ATP-related genes in glycolysis (PtsG, Pgk, Pyk). CONCLUSION We reported the first-time potential application of GR in the form of fusion protein GR-GFP. Expression of GR-GFP in E. coli improved the production of β-carotene and RFP. Our work provides a strain of E. coli harboring phototrophic metabolism, thus paving path to a more sustainable and scalable production of biosynthesis.
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Affiliation(s)
- Chao-Yu Lee
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Kai-Wen Chen
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Chih-Lu Chiang
- Department of Civil Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hsuan-Yu Kao
- Department of Mechanical Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
- Department of Civil Engineering, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hao-Cheng Yu
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Hsiao-Ching Lee
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan
| | - Wen-Liang Chen
- Institute of Molecular Medicine and Bioengineering, Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan.
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García-Calvo L, Rane DV, Everson N, Humlebrekk ST, Mathiassen LF, Mæhlum AHM, Malmo J, Bruheim P. Central carbon metabolite profiling reveals vector-associated differences in the recombinant protein production host Escherichia coli BL21. FRONTIERS IN CHEMICAL ENGINEERING 2023. [DOI: 10.3389/fceng.2023.1142226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
The Gram-negative bacterium Escherichia coli is the most widely used host for recombinant protein production, both as an industrial expression platform and as a model system at laboratory scale. The recombinant protein production industry generates proteins with direct applications as biopharmaceuticals and in technological processes central to a plethora of fields. Despite the increasing economic significance of recombinant protein production, and the importance of E. coli as an expression platform and model organism, only few studies have focused on the central carbon metabolic landscape of E. coli during high-level recombinant protein production. In the present work, we applied four targeted CapIC- and LC-MS/MS methods, covering over 60 metabolites, to perform an in-depth metabolite profiling of the effects of high-level recombinant protein production in strains derived from E. coli BL21, carrying XylS/Pm vectors with different characteristics. The mass-spectrometric central carbon metabolite profiling was complemented with the study of growth kinetics and protein production in batch bioreactors. Our work shows the robustness in E. coli central carbon metabolism when introducing increased plasmid copy number, as well as the greater importance of induction of recombinant protein production as a metabolic challenge, especially when strong promoters are used.
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Zhang ZX, Nong FT, Wang YZ, Yan CX, Gu Y, Song P, Sun XM. Strategies for efficient production of recombinant proteins in Escherichia coli: alleviating the host burden and enhancing protein activity. Microb Cell Fact 2022; 21:191. [PMID: 36109777 PMCID: PMC9479345 DOI: 10.1186/s12934-022-01917-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli, one of the most efficient expression hosts for recombinant proteins (RPs), is widely used in chemical, medical, food and other industries. However, conventional expression strains are unable to effectively express proteins with complex structures or toxicity. The key to solving this problem is to alleviate the host burden associated with protein overproduction and to enhance the ability to accurately fold and modify RPs at high expression levels. Here, we summarize the recently developed optimization strategies for the high-level production of RPs from the two aspects of host burden and protein activity. The aim is to maximize the ability of researchers to quickly select an appropriate optimization strategy for improving the production of RPs.
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Pasini M, Fernández-Castané A, Caminal G, Overton TW, Ferrer P. Process Intensification at the expression system level for the production of 1-phosphate aldolase in antibiotic-free E. coli fed-batch cultures. J Ind Microbiol Biotechnol 2022; 49:6601392. [PMID: 35657374 PMCID: PMC9339150 DOI: 10.1093/jimb/kuac018] [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] [Received: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 12/03/2022]
Abstract
To successfully design expression systems for industrial biotechnology and biopharmaceutical applications; plasmid stability, efficient synthesis of the desired product and the use of selection markers acceptable to regulatory bodies are of utmost importance. In this work we demonstrate the application of a set of IPTG-inducible protein expression systems -- harboring different features namely, antibiotic vs auxotrophy marker; two-plasmids vs single plasmid expression system; expression levels of the repressor protein (LacI) and the auxotrophic marker (glyA) -- in high-cell density cultures to evaluate their suitability in bioprocess conditions that resemble industrial settings. Results revealed that the first generation of engineered strain showed a 50% reduction in the production of the model recombinant protein fuculose-1-phosphate aldolase (FucA) compared to the reference system from QIAGEN. The over-transcription of glyA was found to be a major factor responsible for the metabolic burden. The second- and third-generation of expression systems presented an increase in FucA production and advantageous features. In particular, the third-generation expression system is antibiotic-free, autotrophy-selection based and single-plasmid and, is capable to produce FucA at similar levels compared to the original commercial expression system. These new tools open new avenues for high-yield and robust expression of recombinant proteins in E. coli.
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Affiliation(s)
- Martina Pasini
- Aston institute of Photonic technologies (AiPT), Aston University, Birmingham, B4 7ET, UK.,Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
| | - Alfred Fernández-Castané
- Aston Institute of Materials Research, Aston University, Birmingham, B4 7ET, UK.,Energy and Bioproducts Research Institute, Aston University, Birmingham, B4 7ET, UK
| | - Gloria Caminal
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain.,Institute of Advanced Chemical of Catalonia, IQAC-CSIC, 08034, Barcelona, Spain
| | - Tim W Overton
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute for Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès) 08193, Catalonia, Spain
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Li Z, Nees M, Bettenbrock K, Rinas U. Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. Microb Cell Fact 2022; 21:67. [PMID: 35449049 PMCID: PMC9027384 DOI: 10.1186/s12934-022-01787-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/26/2022] [Indexed: 12/20/2022] Open
Abstract
Background Escherichia coli adapted to carbon-limiting conditions is generally geared for energy-efficient carbon utilization. This includes also the efficient utilization of glucose, which serves as a source for cellular building blocks as well as energy. Thus, catabolic and anabolic functions are balanced under these conditions to minimize wasteful carbon utilization. Exposure to glucose excess interferes with the fine-tuned coupling of anabolism and catabolism leading to the so-called carbon overflow metabolism noticeable through acetate formation and eventually growth inhibition. Results Cellular adaptations towards sudden but timely limited carbon excess conditions were analyzed by exposing slow-growing cells in steady state glucose-limited continuous culture to a single glucose pulse. Concentrations of metabolites as well as time-dependent transcriptome alterations were analyzed and a transcriptional network analysis performed to determine the most relevant transcription and sigma factor combinations which govern these adaptations. Down-regulation of genes related to carbon catabolism is observed mainly at the level of substrate uptake and downstream of pyruvate and not in between in the glycolytic pathway. It is mainly accomplished through the reduced activity of CRP-cAMP and through an increased influence of phosphorylated ArcA. The initiated transcriptomic change is directed towards down-regulation of genes, which contribute to active movement, carbon uptake and catabolic carbon processing, in particular to down-regulation of genes which contribute to efficient energy generation. Long-term changes persisting after glucose depletion and consumption of acetete encompassed reduced expression of genes related to active cell movement and enhanced expression of genes related to acid resistance, in particular acid resistance system 2 (GABA shunt) which can be also considered as an inefficient bypass of the TCA cycle. Conclusions Our analysis revealed that the major part of the trancriptomic response towards the glucose pulse is not directed towards enhanced cell proliferation but towards protection against excessive intracellular accumulation of potentially harmful concentration of metabolites including among others energy rich compounds such as ATP. Thus, resources are mainly utilized to cope with “overfeeding” and not for growth including long-lasting changes which may compromise the cells future ability to perform optimally under carbon-limiting conditions (reduced motility and ineffective substrate utilization). Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01787-4.
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Affiliation(s)
- Zhaopeng Li
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany
| | - Markus Nees
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany. .,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany.
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