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Yang H, Wang S, Zhao M, Liao Y, Wang F, Yin X. Metabolic engineering of Escherichia coli for seleno-methylselenocysteine production. J Biotechnol 2024; 395:S0168-1656(24)00248-7. [PMID: 39260702 DOI: 10.1016/j.jbiotec.2024.09.006] [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: 06/11/2024] [Revised: 08/04/2024] [Accepted: 09/04/2024] [Indexed: 09/13/2024]
Abstract
Selenium (Se) is an essential trace element for life. Seleno-methylselenocysteine (SeMCys) can serve as a Se supplement with anticarcinogenic activity and can improve cognitive deficits. We engineered Escherichia coli for microbial production of SeMCys. The genes involved in the synthesis of SeMCys were divided into three modules-the SeCys synthesis, methyl donor synthesis and SMT modules-and expressed in plasmids with different copy numbers. The higher copy number of the SeCys synthesis module facilitated SeMCys production. The major routes for SeCys degradation were then modified. Deletion of the cysteine desulfurase gene csdA or sufS improved SeMCys production the most, and the strain that knocked out both genes doubled SeMCys production. The addition of serine in the mid-logarithmic growth phase significantly improved SeMCys synthesis. When the serine synthetic pathway was enhanced, SeMCys production increased by 12.5%. Fed-batch culture for sodium selenite supplementation in the early stationary phase improved SeMCys production to 3.715mg/L. This is the first report of the metabolic engineering of E. coli for the production of SeMCys and provide information on Se metabolism.
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Affiliation(s)
- Hulin Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China; School of Light Industry, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China
| | - ShiZhuo Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China; School of Light Industry, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China
| | - Meiyi Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China; School of Light Industry, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China
| | - Yonghong Liao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China; School of Light Industry, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China
| | - Fenghuan Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China; School of Light Industry, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China
| | - Xian Yin
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China; School of Light Industry, Beijing Technology and Business University, Fucheng RD 11, Beijing 100048, China.
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2
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Zou S, Liu J, Zhao K, Zhu X, Zhang B, Liu Z, Zheng Y. Metabolic engineering of Escherichia coli for enhanced production of D-pantothenic acid. BIORESOURCE TECHNOLOGY 2024; 412:131352. [PMID: 39186986 DOI: 10.1016/j.biortech.2024.131352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/08/2024] [Accepted: 08/23/2024] [Indexed: 08/28/2024]
Abstract
D-pantothenic acid (D-PA) is an essential vitamin that has been widely used in various industries. However, the low productivity caused by slow D-PA production in fermentation hinders its potential applications. In this study, strategies of engineering the synthetic pathway combined with regulating methyl recycle were employed in E. coli to enhance D-PA production. First, a self-induced promoter-mediated dynamic regulation of D-PA degradation pathway was carried out to improve D-PA accumulation. Then, to drive more carbon flux into D-PA synthesis, the key nodes of the R-pantoate pathway which encoded the essential enzyme were integrated into the genome. Subsequently, the further increase in D-PA production was achieved by promoting the regeneration of methyl donor. The strain L11T produced 86.03 g/L D-PA with a productivity of 0.797 g/L/h, which presented the highest D-PA titer and productivity to date. The strategies could be applied to constructing cell factories for producing other bio-based products.
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Affiliation(s)
- Shuping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jinlong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Kuo Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xintao Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhiqiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China.
| | - Yuguo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou 310014, PR China
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3
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Wang L, Guo Y, Shen Y, Yang K, Cai X, Zhang B, Liu Z, Zheng Y. Microbial production of sulfur-containing amino acids using metabolically engineered Escherichia coli. Biotechnol Adv 2024; 73:108353. [PMID: 38593935 DOI: 10.1016/j.biotechadv.2024.108353] [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: 12/21/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
L-Cysteine and L-methionine, as the only two sulfur-containing amino acids among the canonical 20 amino acids, possess distinct characteristics and find wide-ranging industrial applications. The use of different organisms for fermentative production of L-cysteine and L-methionine is gaining increasing attention, with Escherichia coli being extensively studied as the preferred strain. This preference is due to its ability to grow rapidly in cost-effective media, its robustness for industrial processes, the well-characterized metabolism, and the availability of molecular tools for genetic engineering. This review focuses on the genetic and molecular mechanisms involved in the production of these sulfur-containing amino acids in E. coli. Additionally, we systematically summarize the metabolic engineering strategies employed to enhance their production, including the identification of new targets, modulation of metabolic fluxes, modification of transport systems, dynamic regulation strategies, and optimization of fermentation conditions. The strategies and design principles discussed in this review hold the potential to facilitate the development of strain and process engineering for direct fermentation of sulfur-containing amino acids.
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Affiliation(s)
- Lijuan Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Yingying Guo
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Yizhou Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Kun Yang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Zhiqiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China.
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
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Wang Y, Wu M, Zheng H, Wu D, Yao P, Li W, Jin K, Yu X. Biomanufacture of L-homoserine lactone building block: A strategy for preparing γ-substituted L-amino acids by modular reaction. Enzyme Microb Technol 2024; 176:110411. [PMID: 38377656 DOI: 10.1016/j.enzmictec.2024.110411] [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: 11/05/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024]
Abstract
A strain high-performance of esterase producing bacteria was screened from soil, which could selectively hydrolyze D-homoserine lactone from its racemate to achieve the resolution of L- homoserine lactone with more than 99% e.e. in 48% yield. L-homoserine lactone building block was then converted to L-α-amino-γ-bromobutyronic acid chiral blocks, which reacted with various nucleophilic reagent modules could to be applied to prepare L-γ- substituted α-amino acids such as L-selenomethionine, L-methionine, L-glufosinate and L-selenocystine. Its advantages included high selectivity of biocatalytic resolution reactions, high optical purity of products, racemic recycle of D-substrates and modular reaction, which simplified the production process of these products and highlighted the power of biological manufacturing.
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Affiliation(s)
- Yuguang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China; Jiangxi XinzhongyeTea Industry Biotechnology Co., Ltd, China; Zhejiang Caihe Biotechnology Co., Ltd, China
| | - Mengjing Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China
| | - Huifang Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China
| | - Dongmei Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China
| | - Panpan Yao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China
| | - Wenjing Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China
| | - Kexin Jin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China
| | - Xinjun Yu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, No.1 Gongda Road, Deqing, Zhejiang 313299, China.
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5
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Harting C, Teleki A, Braakmann M, Jankowitsch F, Takors R. Systemic intracellular analysis for balancing complex biosynthesis in a transcriptionally deregulated Escherichia coli l-Methionine producer. Microb Biotechnol 2024; 17:e14433. [PMID: 38528766 DOI: 10.1111/1751-7915.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
l-Methionine (l-Met) has gained remarkable interest due to its multifaceted and versatile applications in the fields of nutrition, pharmaceuticals and clinical practice. In this study, the fluxes of the challenging l-Met biosynthesis in the producer strain Escherichia coli (E. coli) DM2853 were fine-tuned to enable improved l-Met production. The potential bottlenecks identified in sulfur assimilation and l-Met synthesis downstream of O-succinyl-l-homoserine (OSHS) were addressed by overexpressing glutaredoxin 1 (grxA), thiosulfate sulfurtransferase (pspE) and O-succinylhomoserine lyase (metB). Although deemed as a straightforward target for improving glucose-to-Met conversion, the yields remained at approximately 12%-13% (g/g). Instead, intracellular l-Met pools increased by up to four-fold with accelerated kinetics. Overexpression of the Met exporter ygaZH may serve as a proper valve for releasing the rising internal Met pressure. Interestingly, the export kinetics revealed maximum saturated export rates already at low growth rates. This scenario is particularly advantageous for large-scale fermentation when product formation is ideally uncoupled from biomass formation to achieve maximum performance within the technical limits of large-scale bioreactors.
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6
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Wang Y, Bai Y, Zeng Q, Jiang Z, Liu Y, Wang X, Liu X, Liu C, Min W. Recent advances in the metabolic engineering and physiological opportunities for microbial synthesis of L-aspartic acid family amino acids: A review. Int J Biol Macromol 2023; 253:126916. [PMID: 37716660 DOI: 10.1016/j.ijbiomac.2023.126916] [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: 07/24/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
L-aspartic acid, L-threonine, L-isoleucine, l-lysine, and L-methionine constitute the l-aspartate amino acids (AFAAs). Except for L-aspartic acid, these are essential amino acids that cannot be synthesized by humans or animals themselves. E. coli and C. glutamicum are the main model organisms for AFAA production. It is necessary to reconstitute microbial cell factories and the physiological state of industrial fermentation cells for in-depth research into strains with higher AFAA production levels and optimal growth states. Considering that the anabolic pathways of the AFAAs and engineering modifications have rarely been reviewed in the latest progress, this work reviews the central metabolic pathways of two strains and strategies for the metabolic engineering of AFAA synthetic pathways. The challenges posed by microbial physiology in AFAA production and possible strategies to address them, as well as future research directions for constructing strains with high AFAA production levels, are discussed in this review article.
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Affiliation(s)
- Yusheng Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Yunlong Bai
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Qi Zeng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Zeyuan Jiang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Yuzhe Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Xiyan Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Xiaoting Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China
| | - Chunlei Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China.
| | - Weihong Min
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, PR China.
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7
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François JM. Progress advances in the production of bio-sourced methionine and its hydroxyl analogues. Biotechnol Adv 2023; 69:108259. [PMID: 37734648 DOI: 10.1016/j.biotechadv.2023.108259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
The essential sulphur-containing amino acid, methionine, is becoming a mass-commodity product with an annual production that exceeded 1,500,000 tons in 2018. This amino acid is today almost exclusively produced by chemical process from fossil resources. The environmental problems caused by this industrial process, and the expected scarcity of oil resources in the coming years, have recently accelerated the development of bioprocesses for producing methionine from renewable carbon feedstock. After a brief description of the chemical process and the techno-economic context that still justify the production of methionine by petrochemical processes, this review will present the current state of the art of biobased alternatives aiming at a sustainable production of this amino acid and its hydroxyl analogues from renewable carbon feedstock. In particular, this review will focus on three bio-based processes, namely a purely fermentative process based on the metabolic engineering of the natural methionine pathway, a mixed process combining the production of the O-acetyl/O-succinyl homoserine intermediate of this pathway by fermentation followed by an enzyme-based conversion of this intermediate into L-methionine and lately, a hybrid process in which the non-natural chemical synthon, 2,4-dihydroxybutyric acid, obtained by fermentation of sugars is converted by chemo-catalysis into hydroxyl methionine analogues. The industrial potential of these three bioprocesses, as well as the major technical and economic obstacles that remain to be overcome to reach industrial maturity are discussed. This review concludes by bringing up the assets of these bioprocesses to meet the challenge of the "green transition", with the accomplishment of the objective "zero carbon" by 2050 and how they can be part of a model of Bioeconomy enhancing local resources.
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Affiliation(s)
- Jean Marie François
- Toulouse Biotechnology Institute, UMR INSA -CNRS5504 and UMR INSA-INRAE 792, 135 avenue de Rangueil, 31077 Toulouse, France; Toulouse White Biotechnology, UMS INRAE-INSA-CNRS, 135 Avenue de Rangueil, 31077 Toulouse, France.
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8
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Cai M, Liu Z, Zhao Z, Wu H, Xu M, Rao Z. Microbial production of L-methionine and its precursors using systems metabolic engineering. Biotechnol Adv 2023; 69:108260. [PMID: 37739275 DOI: 10.1016/j.biotechadv.2023.108260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/11/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
L-methionine is an essential amino acid with versatile applications in food, feed, cosmetics and pharmaceuticals. At present, the production of L-methionine mainly relies on chemical synthesis, which conflicts with the concern over serious environmental problems and sustainable development goals. In recent years, microbial production of natural products has been amply rewarded with the emergence and rapid development of system metabolic engineering. However, efficient L-methionine production by microbial fermentation remains a great challenge due to its complicated biosynthetic pathway and strict regulatory mechanism. Additionally, the engineered production of L-methionine precursors, L-homoserine, O-succinyl-L-homoserine (OSH) and O-acetyl-L-homoserine (OAH), has also received widespread attention because they can be catalyzed to L-methionine via a high-efficiently enzymatic reaction in vitro, which is also a promising alternative to chemical route. This review provides a comprehensive overview on the recent advances in the microbial production of L-methionine and its precursors, highlighting the challenges and potential solutions for developing L-methionine microbial cell factories from the perspective of systems metabolic engineering, aiming to offer guidance for future engineering.
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Affiliation(s)
- Mengmeng Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhifei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Hongxuan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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9
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Chen L, Xin X, Zhang Y, Li S, Zhao X, Li S, Xu Z. Advances in Biosynthesis of Non-Canonical Amino Acids (ncAAs) and the Methods of ncAAs Incorporation into Proteins. Molecules 2023; 28:6745. [PMID: 37764520 PMCID: PMC10534643 DOI: 10.3390/molecules28186745] [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: 09/03/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The functional pool of canonical amino acids (cAAs) has been enriched through the emergence of non-canonical amino acids (ncAAs). NcAAs play a crucial role in the production of various pharmaceuticals. The biosynthesis of ncAAs has emerged as an alternative to traditional chemical synthesis due to its environmental friendliness and high efficiency. The breakthrough genetic code expansion (GCE) technique developed in recent years has allowed the incorporation of ncAAs into target proteins, giving them special functions and biological activities. The biosynthesis of ncAAs and their incorporation into target proteins within a single microbe has become an enticing application of such molecules. Based on that, in this study, we first review the biosynthesis methods for ncAAs and analyze the difficulties related to biosynthesis. We then summarize the GCE methods and analyze their advantages and disadvantages. Further, we review the application progress of ncAAs and anticipate the challenges and future development directions of ncAAs.
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Affiliation(s)
- Liang Chen
- College of Bioengineering, Beijing Polytechnic, Beijing 100176, China; (X.X.); (Y.Z.); (S.L.); (X.Z.); (S.L.); (Z.X.)
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10
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Gruzdev N, Hacham Y, Haviv H, Stern I, Gabay M, Bloch I, Amir R, Gal M, Yadid I. Conversion of methionine biosynthesis in Escherichia coli from trans- to direct-sulfurylation enhances extracellular methionine levels. Microb Cell Fact 2023; 22:151. [PMID: 37568230 PMCID: PMC10416483 DOI: 10.1186/s12934-023-02150-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023] Open
Abstract
Methionine is an essential amino acid in mammals and a precursor for vital metabolites required for the survival of all organisms. Consequently, its inclusion is required in diverse applications, such as food, feed, and pharmaceuticals. Although amino acids and other metabolites are commonly produced through microbial fermentation, high-yield biosynthesis of L-methionine remains a significant challenge due to the strict cellular regulation of the biosynthesis pathway. As a result, methionine is produced primarily synthetically, resulting in a racemic mixture of D,L-methionine. This study explores methionine bio-production in E. coli by replacing its native trans-sulfurylation pathway with the more common direct-sulfurylation pathway used by other bacteria. To this end, we generated a methionine auxotroph E. coli strain (MG1655) by simultaneously deleting metA and metB genes and complementing them with metX and metY from different bacteria. Complementation of the genetically modified E. coli with metX/metY from Cyclobacterium marinum or Deinococcus geothermalis, together with the deletion of the global repressor metJ and overexpression of the transporter yjeH, resulted in a substantial increase of up to 126 and 160-fold methionine relative to the wild-type strain, respectively, and accumulation of up to 700 mg/L using minimal MOPS medium and 2 ml culture. Our findings provide a method to study methionine biosynthesis and a chassis for enhancing L-methionine production by fermentation.
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Affiliation(s)
- Nadya Gruzdev
- Migal - Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Yael Hacham
- Migal - Galilee Research Institute, Kiryat Shmona, 11016, Israel
- Tel-Hai College, Upper Galilee, 1220800, Israel
| | - Hadar Haviv
- Migal - Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Inbar Stern
- Department of Oral Biology, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Matan Gabay
- Department of Oral Biology, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Itai Bloch
- Migal - Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Rachel Amir
- Migal - Galilee Research Institute, Kiryat Shmona, 11016, Israel
- Tel-Hai College, Upper Galilee, 1220800, Israel
| | - Maayan Gal
- Department of Oral Biology, Goldschleger School of Dental Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel.
| | - Itamar Yadid
- Migal - Galilee Research Institute, Kiryat Shmona, 11016, Israel.
- Tel-Hai College, Upper Galilee, 1220800, Israel.
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11
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Li Z, Liu Q, Sun J, Sun J, Li M, Zhang Y, Deng A, Liu S, Wen T. Multivariate modular metabolic engineering for enhanced L-methionine biosynthesis in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:101. [PMID: 37312226 DOI: 10.1186/s13068-023-02347-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND L-Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and strictly regulated biosynthesis, the development of microbial strains for high-level L-methionine production has remained challenging in recent years. RESULTS By strengthening the L-methionine terminal synthetic module via site-directed mutation of L-homoserine O-succinyltransferase (MetA) and overexpression of metAfbr, metC, and yjeH, L-methionine production was increased to 1.93 g/L in shake flask fermentation. Deletion of the pykA and pykF genes further improved L-methionine production to 2.51 g/L in shake flask fermentation. Computer simulation and auxotrophic experiments verified that during the synthesis of L-methionine, equimolar amounts of L-isoleucine were accumulated via the elimination reaction of cystathionine γ-synthetase MetB due to the insufficient supply of L-cysteine. To increase the supply of L-cysteine, the L-cysteine synthetic module was strengthened by overexpression of cysEfbr, serAfbr, and cysDN, which further increased the production of L-methionine by 52.9% and significantly reduced the accumulation of the byproduct L-isoleucine by 29.1%. After optimizing the addition of ammonium thiosulfate, the final metabolically engineered strain MET17 produced 21.28 g/L L-methionine in 64 h with glucose as the carbon source in a 5 L fermenter, representing the highest L-methionine titer reported to date. CONCLUSIONS In this study, a high-efficiency strain for L-methionine production was derived from wild-type Escherichia coli W3110 by rational metabolic engineering strategies, providing an efficient platform for the industrial production of L-methionine.
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Affiliation(s)
- Zhongcai Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiahui Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Jianjian Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingjie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aihua Deng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuwen Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
- China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100049, China.
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12
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Li B, Huang LG, Yang YF, Chen YY, Zhou XJ, Liu ZQ, Zheng YG. Metabolic engineering and pathway construction for O-acetyl-L-homoserine production in Escherichia coli. 3 Biotech 2023; 13:173. [PMID: 37188286 PMCID: PMC10170018 DOI: 10.1007/s13205-023-03564-5] [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: 10/31/2022] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
O-Acetyl-L-homoserine (OAH) is a potentially important platform metabolic intermediate for the production of homoserine lactone, methionine, 1,4-butanediol and 1,3-propanediol which have giant market value. Currently, multiple strategies have been adopted to explore sustainable production of OAH. However, the production of OAH by consuming cheap bio-based feedstocks with Escherichia coli as the chassis is still in its infancy. Construction of high yield OAH-producing strains is of great significance in industry. In this study, we introduced an exogenous metA from Bacillus cereus (metXbc) and engineered an OAH-producing strain by combinatorial metabolic engineering. Initially, exogenous metXs/metA were screened and used to reconstruct an initial biosynthesis pathway of OAH in E. coli. Subsequently, the disruption of degradation and competitive pathways combined with optimal expression of metXbc were carried out, accumulating 5.47 g/L OAH. Meanwhile, the homoserine pool was enriched by overexpressing metL with producing 7.42 g/L OAH. Lastly, the carbon flux of central carbon metabolism was redistributed to balance the metabolic flux of homoserine and acetyl coenzyme A (acetyl-CoA) in OAH biosynthesis with accumulating 8.29 g/L OAH. The engineered strain produced 24.33 g/L OAH with a yield of 0.23 g/g glucose in fed-batch fermentation. By these strategies, the key nodes for OAH synthesis were clarified and corresponding strategies were proposed. This study would lay a foundation for OAH bioproduction. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03564-5.
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Affiliation(s)
- Bo Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
| | - Liang-Gang Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
| | - Yu-Feng Yang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
| | - Yuan-Yuan Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
| | - Xiao-Jie Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014 People’s Republic of China
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13
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Shen ZY, Wang YF, Wang LJ, Wang Y, Liu ZQ, Zheng YG. Thorough research and modification of one-carbon units cycle for improving L-methionine production in Escherichia coli. 3 Biotech 2023; 13:203. [PMID: 37220602 PMCID: PMC10199968 DOI: 10.1007/s13205-023-03625-9] [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: 02/15/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Methionine is the only one of the essential amino acids that contain sulfur, widely used as a feed additive in agriculture. In this study, the availability of 5-methyl-tetrahydrofolate was confirmed as the main limitation in the complex multibranched biosynthetic pathway of L-methionine. The cycle of one-carbon units was thoroughly investigated and modified to supply 5-methyl-tetrahydrofolate for L-methionine production, such as enhancing the supply of precursor, expediting the conversion rate of the cycle, introducing exogenous serine hydroxymethyltransferase and increasing pool size of one-carbon units carrier. The final strain MYA/pAmFA-4 was able to produce 20.89 g/L L-methionine by fed-batch fermentation, which was the highest titer reported in the literatures. This study is instructive for other metabolites biosynthesized needing one-carbon units or having a complex multibranched biosynthetic pathway. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03625-9.
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Affiliation(s)
- Zhen-Yang Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yi-Feng Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Li-Juan Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Ying Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
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14
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Shen ZY, Wang YF, Wang LJ, Zhang B, Liu ZQ, Zheng YG. Construction of exogenous methanol, formate, and betaine modules for methyl donor supply in methionine biosynthesis. Front Bioeng Biotechnol 2023; 11:1170491. [PMID: 37064240 PMCID: PMC10102461 DOI: 10.3389/fbioe.2023.1170491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Methionine is an essential sulfur-containing amino acid that finds widespread applications in agriculture, medicine, and the food industry. However, the complex and multibranched biosynthetic pathway of methionine has posed significant challenges to its efficient fermentation production. In this study, we employed a modularized synthetic biology strategy to improve the weakest branched pathway of methionine biosynthesis. Three exogenous modules were constructed and assembled to provide methyl donors, which are the primary limiting factors in methionine biosynthesis. The first module utilized added methanol, which was converted into 5,10-methylene-tetrahydrofolate for methionine production but was hindered by the toxicity of methanol. To circumvent this issue, a non-toxic formate module was constructed, resulting in a visible improvement in the methionine titer. Finally, an exogenous betaine module was constructed, which could directly deliver methyl to methionine. The final strain produced 2.87 g/L of methionine in a flask, representing a 20% increase over the starting strain. This study presents a novel strategy for improving and balancing other metabolites that are synthesized through complex multibranched pathways.
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Affiliation(s)
- Zhen-Yang Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yi-Feng Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Li-Juan Wang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- *Correspondence: Zhi-Qiang Liu,
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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15
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Zhang X, Zhang H, Shen T, Pei J, Zhao L. Biotransformation to synthesize the methylated derivatives of baicalein using engineered Escherichia coli. Bioprocess Biosyst Eng 2023; 46:735-745. [PMID: 36932217 DOI: 10.1007/s00449-023-02860-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 03/04/2023] [Indexed: 03/19/2023]
Abstract
Oroxylin A and negletein are flavonoid compounds existing in plants, with excellent pharmacological activities such as anti-inflammatory, anti-viropexis, and anti-cancer. Nevertheless, the natural abundance of these compounds in plants is extremely low. Here, a biotransformation pathway was developed in engineered strains to synthesize oroxylin A and negletein from baicalin by using the crude extract of Scutellaria baicalensis as the substrate. Briefly, the precursor baicalin in this crude extract was hydrolyzed by a β-glucuronidase to form the intermediate baicalein, then O-methyltransferases utilize this intermediate to synthesize oroxylin A and negletein. Through screening strains and carbon sources, regulating intercellular S-adenosyl L-methionine synthesis, and optimizing culture conditions, the titers of the target products increased gradually, with 188.0 mg/L for oroxylin A and 222.7 mg/L for negletein finally. The study illustrates a convenient method to synthesize oroxylin A and negletein from a low-cost substrate, paving the way for the mass acquisition and further bioactivities development and utilization of these rare and high-value compounds.
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Affiliation(s)
- Xiaomeng Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China.,College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Haiyan Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China.,College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Tianyu Shen
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China.,College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jianjun Pei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China. .,College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China. .,College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
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16
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Shen ZY, Wang YF, Wang LJ, Wang Y, Liu ZQ, Zheng YG. Local metabolic response of Escherichia coli to the module genetic perturbations in l-methionine biosynthetic pathway. J Biosci Bioeng 2023; 135:217-223. [PMID: 36707399 DOI: 10.1016/j.jbiosc.2022.12.010] [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: 08/20/2022] [Revised: 11/16/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023]
Abstract
l-Methionine biosynthesis is through multilevel regulated and multibranched biosynthetic pathway (MRMBP). Because of the complex regulatory mechanism and the imbalanced metabolic flux between branched pathways, microbial production of l-methionine has not been commercialized. In this study, local metabolic response in MRMBP of l-methionine was investigated and various crucial genes in branched pathways were determined. In l-serine pathway, the crucial gene was serABC. In O-succinyl homoserine (OSH) pathway, which was the C4 backbone of l-methionine, metB and metL controlled the metabolic flux jointly. In l-cysteine pathway, the crucial gene cysEfbr could disturb the flux distribution of local network in l-methionine biosynthesis. However, no crucial gene for l-methionine production in 5-methyl tetrahydrofolate (CH3-THF) pathway was found. The relation between these pathways was also researched. l-Serine pathway, as the upstream pathway of l-cysteine and CH3-THF, played a crucial role in l-methionine biosynthesis. l-Cysteine pathway showed the strongest controlling force of the metabolic flux, and OSH pathway was second to l-cysteine pathway. In contrast, CH3-THF pathway was the weakest, which was probably the mainly limited steps at present and had great potential in further research. In addition, constructed W3110 IJAHFEBC/pA∗HAmL was able to produce 2.62 g/L l-methionine in flask. This study is instructive for l-methionine biosynthesis and provides a new research method of biosynthesizing other metabolic products in MRMBPs.
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Affiliation(s)
- Zhen-Yang Shen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China
| | - Yi-Feng Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China
| | - Li-Juan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China
| | - Ying Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, PR China
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [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: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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18
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Niu K, Fu Q, Mei ZL, Ge LR, Guan AQ, Liu ZQ, Zheng YG. High-Level Production of l-Methionine by Dynamic Deregulation of Metabolism with Engineered Nonauxotroph Escherichia coli. ACS Synth Biol 2023; 12:492-501. [PMID: 36701126 DOI: 10.1021/acssynbio.2c00481] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
l-Methionine is the only sulfur-containing amino acid among the essential amino acids, and it is mainly produced by the chemical method in industry so far. The fermentation production of l-methionine by genetically engineered strains is an attractive alternative. Due to the complex metabolic mechanism and multilevel regulation of the synthesis pathway in the organism, the fermentation production of l-methionine by genetically engineered strains was still not satisfied. In this study, the biosynthesis pathway of l-methionine was regulated based on the previous studies. As the competitive pathway and an essential amino acid for cell growth, the biosynthesis pathway of l-lysine was first repaired by complementation of the lysA gene in situ on the genome and then replaced the in situ promoter with the dynamically regulated promoter PfliA to construct a nonauxotroph strain. In addition, the central metabolic pathway and l-cysteine catabolism pathway were further modified to promote the cell growth and enhance the l-methionine production. Finally, the l-methionine fermentation yield in a 5 L bioreactor reached 17.74 g/L without adding exogenous amino acids. These strategies can effectively balance the contradiction between cell growth and l-methionine production and alleviate the complexity of fermentation operation and the cost with auxotroph strains, which provide a reference for the industrial production of l-methionine by microbial fermentation.
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Affiliation(s)
- Kun Niu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Qiang Fu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zi-Long Mei
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Li-Rong Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - An-Qi Guan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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Liang X, Deng H, Bai Y, Fan TP, Zheng X, Cai Y. Highly efficient biosynthesis of spermidine from L-homoserine and putrescine using an engineered Escherichia coli with NADPH self-sufficient system. Appl Microbiol Biotechnol 2022; 106:5479-5493. [PMID: 35931895 DOI: 10.1007/s00253-022-12110-x] [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: 06/02/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/30/2022]
Abstract
Spermidine is an important polyamine that can be used for the synthesis of various bioactive compounds in the food and pharmaceutical fields. In this study, a novel efficient whole-cell biocatalytic method with an NADPH self-sufficient cycle for spermidine biosynthesis was designed and constructed by co-expressing homoserine dehydrogenase (HSD), carboxyspermidine dehydrogenase (CASDH), and carboxyspermidine decarboxylase (CASDC). First, the enzyme-substrate coupled cofactor regeneration system from co-expression of NADP+-dependent ScHSD and NADPH-dependent AfCASDH exactly provides an efficient method for cofactor cycling. Second, we identified and characterized a putative CASDC with high decarboxylase activity from Butyrivibrio crossotus DSM 2876; it showed an optimum temperature of 35 °C and an optimum pH of 7.0, which make it better suited for the designed synthetic route. Subsequently, the protein expression level of each enzyme was optimized through the variation of the gene copy number, and a whole-cell catalyst with high catalytic efficiency was constructed successfully. Finally, a yield of 28.6 mM of spermidine was produced in a 1-L scale of E. coli whole-cell catalytic system with a 95.3% molar conversion rate after optimization of temperature, the ratio of catalyst-to-substrate, and the amount of NADP+, and a productivity of 0.17 g·L-1·h-1 was achieved. In summary, this novel pathway of constructing a whole-cell catalytic system from L-homoserine and putrescine could provide a green alternative method for the efficient synthesis of spermidine. KEY POINTS: • A novel pathway for spermidine biosynthesis was developed in Escherichia coli. • The enzyme-substrate coupled system provides an NADPH self-sufficient cycle. • Spermidine with 28.6 mM was obtained using an optimized whole-cell system.
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Affiliation(s)
- Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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20
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Sagong HY, Lee D, Kim IK, Kim KJ. Rational Engineering of Homoserine O-Succinyltransferase from Escherichia coli for Reduced Feedback Inhibition by Methionine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1571-1578. [PMID: 35084172 DOI: 10.1021/acs.jafc.1c07211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methionine is an essential amino acid in all living organisms and has been used in various industrial applications such as food and feed additives. However, inhibition of enzymes involved in methionine biosynthesis is considered to be a crucial bottleneck for an efficient bio-based methionine production process. Homoserine O-succinyltransferase fromEscherichia coli (EcHST) has been reported to be feedback inhibited by the final product methionine. To understand the regulation mechanism of the enzyme and generate a feedback-resistant mutant, we determined the crystal structure of EcHST and elucidated the binding site of homoserine and succinyl-CoA. The enzyme kinetic experiments of EcHST revealed that the enzyme is noncompetitively inhibited by methionine with a Ki value of 2.44 mM, and we also identified a putative inhibitor binding site located in the vicinity of the substrate binding site. We then generated the EcHSTT242A variant with reduced feedback inhibition with a Ki value of 17.40 mM.
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Affiliation(s)
- Hye-Young Sagong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Donghoon Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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21
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Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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22
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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23
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Wang P, Zhou HY, Li B, Ding WQ, Liu ZQ, Zheng YG. Multiplex modification of Escherichia coli for enhanced β-alanine biosynthesis through metabolic engineering. BIORESOURCE TECHNOLOGY 2021; 342:126050. [PMID: 34597803 DOI: 10.1016/j.biortech.2021.126050] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
β-Alanine is the only naturally occurring β-amino acid, widely used in the fine chemical and pharmaceutical fields. In this study, metabolic design strategies were attempted in Escherichia coli W3110 for enhancing β-alanine biosynthesis. Specifically, heterologous L-aspartate-α-decarboxylase was used, the aspartate kinase I and III involved in competitive pathways were down-regulated, the β-alanine uptake system was disrupted, the phosphoenolpyruvate carboxylase was overexpressed, and the isocitrate lyase repressor repressing glyoxylate cycle shunt was delete, the glucose uptake system was modified, and the regeneration of amino donor was up-regulated. On this basis, a plasmid harboring the heterologous panD and aspB was constructed. The resultant strain ALA17/pTrc99a-panDBS-aspBCG could yield 4.20 g/L β-alanine in shake flask and 43.94 g/L β-alanine (a yield of 0.20 g/g glucose) in 5-L bioreactor via fed-batch cultivation. These modification strategies were proved effective and the constructed β-alanine producer was a promising microbial cell factory for industrial production of β-alanine.
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Affiliation(s)
- Pei Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Hai-Yan Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Bo Li
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Wen-Qing Ding
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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24
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Xue C, Yi YC, Ng IS. Migration of glutamate decarboxylase by cold treatment on whole-cell biocatalyst triggered activity for 4-aminobutyric acid production in engineering Escherichia coli. Int J Biol Macromol 2021; 190:113-119. [PMID: 34480902 DOI: 10.1016/j.ijbiomac.2021.08.166] [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: 07/02/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 02/05/2023]
Abstract
Glutamate decarboxylase B (GadB) from Escherichia coli, an intrinsic pyridoxal 5'-phosphate (PLP)-dependent enzyme has been employed for 4-aminobutyric acid (GABA) biosynthesis, which involves the glutamate import and GABA export via a transporter located in the inner membrane as rate determined step of whole-cell (WC) biotransformation. Herein, GadB was cloned and overexpressed in E. coli under a constitutive promoter in a high copy number plasmid, and 46.9 g/L GABA was produced. It was observed that GadB migrated to the periplasm when the WC were subjected to -20 °C cold treatment for 24 h prior to the biotransformation. Kinetic studies indicated that the enzymatic turnover rate of WC increased 2-fold after cold treatment, which was correlated with the migration rate of GadB, and up to 88.6% of GadB. The export or possible migration of GadB mitigated the rate-limiting step of WC biotransformation, and a 100% conversion of substrate to GABA was obtained. Finally, we launched a promising strategy for GABA production of 850 g/L from cost-effective monosodium glutamate (MSG) by using WC biocatalysts with 10-times recycling.
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Affiliation(s)
- Chengfeng Xue
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
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25
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Zhu WY, Niu K, Liu P, Cai X, Liu ZQ, Zheng YG. Combining fermentation to produce O-succinyl-l-homoserine and enzyme catalysis for the synthesis of l-methionine in one pot. J Biosci Bioeng 2021; 132:451-459. [PMID: 34420895 DOI: 10.1016/j.jbiosc.2021.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 11/29/2022]
Abstract
The biosynthetic pathway of l-methionine in microorganisms was complex and regulated at multiple levels. In this study, a two-step method for l-methionine production combined fermentation and biocatalysis was realized in one pot. The O-succinyl-l-homoserine (OSH) producing strain Escherichia coli W3110(DE3) ΔIJB∗TrcmetL/pTrc-metAfbr-Trc-thrAfbr-yjeH (ΔIJB) was constructed initially. OSH in the fermentation supernatant was then converted to l-methionine in the presence of O-succinyl-l-homoserine sulfhydrylase (OSHS) and sodium methanethiol. The titer of l-methionine could reach 21.1 g/L after 88 h (84 h fermentation and 4 h catalysis) in a two-step method (process 1). In a one-pot two-strain system (process 2), two strains ΔIJB and E. coli BL21(DE3)/pET28b-OSHS-cutinase were co-cultured, and 8.24 g/L l-methionine was obtained. In another one-pot one-strain system (process 3), strain E. coli ΔIJB/pET28b-OSHS-cutinase could co-express OSHS and cutinase during ΔIJB fermentation at the same time, obtaining 13.6 g/L l-methionine in a 5 L fermentor after 84 h. By comparing the three processes for l-methionine production based on the process 1, the simplified process in process 3 provided in this study showed potent in the large-scale production of l-methionine with convenient handling and production efficiency, but further works still need to be carried out to improve the l-methionine production.
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Affiliation(s)
- Wen-Yuan Zhu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Kun Niu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Peng Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China.
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
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26
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Luo ZW, Ahn JH, Chae TU, Choi SY, Park SY, Choi Y, Kim J, Prabowo CPS, Lee JA, Yang D, Han T, Xu H, Lee SY. Metabolic Engineering of
Escherichia
coli. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Transcription of Cystathionine β-Lyase (MetC) Is Repressed by HeuR in Campylobacter jejuni, and Methionine Biosynthesis Facilitates Colonocyte Invasion. J Bacteriol 2021; 203:e0016421. [PMID: 34001558 DOI: 10.1128/jb.00164-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A previously identified transcriptional regulator in Campylobacter jejuni, termed HeuR, was found to positively regulate heme utilization. Additionally, transcriptomic work demonstrated that the putative operons CJJ81176_1390 to CJJ81176_1394 (CJJ81176_1390-1394) and CJJ81176_1214-1217 were upregulated in a HeuR mutant, suggesting that HeuR negatively regulates expression of these genes. Because genes within these clusters include a cystathionine β-lyase (metC) and a methionine synthase (metE), it appeared HeuR negatively regulates C. jejuni methionine biosynthesis. To address this, we confirmed mutation of HeuR reproducibly results in metC overexpression under nutrient-replete conditions but did not affect expression of metE, while metC expression in the wild type increased to heuR mutant levels during iron limitation. We subsequently determined that both gene clusters are operonic and demonstrated the direct interaction of HeuR with the predicted promoter regions of these operons. Using DNase footprinting assays, we were able to show that HeuR specifically binds within the predicted -35 region of the CJJ81176_1390-1394 operon. As predicted based on transcriptional results, the HeuR mutant was able to grow and remain viable in a defined medium with and without methionine, but we identified significant impacts on growth and viability in metC and metE mutants. Additionally, we observed decreased adherence, invasion, and persistence of metC and metE mutants when incubated with human colonocytes, while the heuR mutant exhibited increased invasion. Taken together, these results suggest that HeuR regulates methionine biosynthesis in an iron-responsive manner and that the ability to produce methionine is an important factor for adhering to and invading the gastrointestinal tract of a susceptible host. IMPORTANCE As the leading cause of bacterium-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health. Investigating colonization factors that allow C. jejuni to successfully infect a host furthers our understanding of genes and regulatory elements necessary for virulence. In this study, we have begun to characterize the role of the transcriptional regulatory protein, HeuR, on methionine biosynthesis in C. jejuni. When the ability to synthesize methionine is impaired, detrimental impacts on growth and viability are observed during growth in limited media lacking methionine and/or iron. Additionally, mutations in the methionine biosynthetic pathway result in decreased adhesion, invasion, and intracellular survival of C. jejuni when incubated with human colonocytes, indicating the importance of regulating methionine biosynthesis.
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28
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Zhu WY, Niu K, Liu P, Fan YH, Liu ZQ, Zheng YG. Identification and Characterization of an O-Succinyl-L-Homoserine Sulfhydrylase From Thioalkalivibrio sulfidiphilus. Front Chem 2021; 9:672414. [PMID: 33937207 PMCID: PMC8080516 DOI: 10.3389/fchem.2021.672414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
L-methionine is an important natural amino acid with broad application prospects. A novel gene encoding the enzyme with the ability to catalyze O-succinyl-L-homoserine (OSH) to L-methionine was screened and characterized. The recombinant O-succinyl-L-homoserine sulfhydrylase from Thioalkalivibrio sulfidiphilus (tsOSHS) exhibited maximum activity at 35°C and pH 6.5. OSHS displayed an excellent thermostability with a half-life of 21.72 h at 30°C. Furthermore, the activity of OSHS increased 115% after Fe2+ added. L-methionine was obtained with a total yield reaching 42.63 g/L under the concentration of O-succinyl-L-homoserine 400 mM (87.6 g/L). These results indicated that OSHS is a potential candidate for applying in the large-scale bioproduction of L-methionine.
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Affiliation(s)
- Wen-Yuan Zhu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Kun Niu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Peng Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Hang Fan
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China.,Key Laboratory of Bioorganic Synthesis of Zhejiang, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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29
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Zhang Y, Wei M, Zhao G, Zhang W, Li Y, Lin B, Li Y, Xu Q, Chen N, Zhang C. High-level production of l-homoserine using a non-induced, non-auxotrophic Escherichia coli chassis through metabolic engineering. BIORESOURCE TECHNOLOGY 2021; 327:124814. [PMID: 33592493 DOI: 10.1016/j.biortech.2021.124814] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
l-Homoserine is a valuable non-proteinogenic amino acid used in the synthesis of various important compounds. Microbial fermentation has potential value for producing l-homoserine on a large scale, but suffers from a low yield and the need for expensive additives. In this study, a non-induced, non-auxotrophic, plasmid-free Escherichia coli chassis for the high-efficiency production of l-homoserine was constructed. Initially, the l-homoserine degradation pathway was dynamically attenuated. Subsequently, systems metabolic engineering strategies were employed, including reinforcing the synthetic flux, improving NADPH generation, and elevating l-homoserine efflux. The constructed strain HOM-14, produced 60.1 g/L l-homoserine without additional supplements or inducers, which achieved the highest fermentative production efficiency of l-homoserine till date. Moreover, common byproducts, such as acetate, did not accumulate. The strategies presented here can be applied in the further engineering of chassis for the scale-up production of l-homoserine and derivatives.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Minhua Wei
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guihong Zhao
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenjie Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yingzi Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Beibei Lin
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qingyang Xu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chenglin Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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30
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Mohany NAM, Totti A, Naylor KR, Janovjak H. Microbial methionine transporters and biotechnological applications. Appl Microbiol Biotechnol 2021; 105:3919-3929. [PMID: 33929594 PMCID: PMC8140960 DOI: 10.1007/s00253-021-11307-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 11/07/2022]
Abstract
Methionine (Met) is an essential amino acid with commercial value in animal feed, human nutrition, and as a chemical precursor. Microbial production of Met has seen intensive investigation towards a more sustainable alternative to the chemical synthesis that currently meets the global Met demand. Indeed, efficient Met biosynthesis has been achieved in genetically modified bacteria that harbor engineered enzymes and streamlined metabolic pathways. Very recently, the export of Met as the final step during its fermentative production has been studied and optimized, primarily through identification and expression of microbial Met efflux transporters. In this mini-review, we summarize the current knowledge on four families of Met export and import transporters that have been harnessed for the production of Met and other valuable biomolecules. These families are discussed with respect to their function, gene regulation, and biotechnological applications. We cover methods for identification and characterization of Met transporters as the basis for the further engineering of these proteins and for exploration of other solute carrier families. The available arsenal of Met transporters from different species and protein families provides blueprints not only for fermentative production but also synthetic biology systems, such as molecular sensors and cell-cell communication systems. KEY POINTS: • Sustainable production of methionine (Met) using microbes is actively explored. • Met transporters of four families increase production yield and specificity. • Further applications include other biosynthetic pathways and synthetic biology.
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Affiliation(s)
- Nurul Amira Mohammad Mohany
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Clayton, Australia
- European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Melbourne, Clayton, Australia
| | - Alessandra Totti
- Department of Pharmacy and Biotechnology FaBiT, University of Bologna, Bologna, Italy
| | - Keith R Naylor
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Clayton, Australia
- European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Melbourne, Clayton, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Clayton, Australia.
- European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Melbourne, Clayton, Australia.
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31
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Wang T, Tague N, Whelan SA, Dunlop MJ. Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites. Nucleic Acids Res 2021; 49:1163-1172. [PMID: 33367820 PMCID: PMC7826281 DOI: 10.1093/nar/gkaa1234] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/12/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Nathan Tague
- Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Mary J Dunlop
- Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA 02215, USA.,Biological Design Center, Boston University, Boston, MA 02215, USA.,Biomedical Engineering, Boston University, Boston, MA 02215, USA
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32
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Zhu WY, Niu K, Liu P, Fan YH, Liu ZQ, Zheng YG. Enhanced O-succinyl-l-homoserine production by recombinant Escherichia coli ΔIJBB*TrcmetL/pTrc-metA fbr -Trc-thrA fbr -yjeH via multilevel fermentation optimization. J Appl Microbiol 2020; 130:1960-1971. [PMID: 33025634 DOI: 10.1111/jam.14884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/04/2020] [Accepted: 09/30/2020] [Indexed: 01/09/2023]
Abstract
AIMS Constructing a strain with high yield of O-succinyl-l-homoserine (OSH) and improving the titre through multilevel fermentation optimization. METHODS AND RESULTS OSH high-yielding strain was first constructed by deleting the thrB gene to block the threonine biosynthesis. Single-factor experiment was carried out, where a Plackett-Burman design was used to screen out three factors (glucose, yeast and threonine) from the original 11 factors that affected the titre of OSH. The Box-Behnken response surface method was used to optimize the fermentation conditions. Through gene editing and medium optimization, the titre of OSH increased from 7·20 to 8·70 g l-1 in 500 ml flask. Furthermore, the fermentation process and fed-batch fermentation conditions including pH, temperature, feeding strategy and feeding medium were investigated and optimized. Under the optimal conditions, the titre of OSH reached 102·5 g l-1 , which is 5·6 times higher than before (15·6 g l-1 ). CONCLUSIONS O-succinyl-l-homoserine fermentation process was established and the combination of response surface methodology and metabolic pathway analysis effectively improved the titre of OSH. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, the titre of OSH reached the needs for industrial production and the metabolic pathway of OSH was demonstrated for further optimization.
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Affiliation(s)
- W-Y Zhu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P.R.China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - K Niu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P.R.China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - P Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P.R.China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Y-H Fan
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P.R.China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Z-Q Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P.R.China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Y-G Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P.R.China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
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33
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Ting WW, Tan SI, Ng IS. Development of chromosome-based T7 RNA polymerase and orthogonal T7 promoter circuit in Escherichia coli W3110 as a cell factory. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00342-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
Orthogonal T7 RNA polymerase (T7RNAP) and T7 promoter is a powerful genetic element to mediate protein expression in different cells. Among all, Escherichia coli possess advantages of fast growth rate, easy for culture and comprehensive elements for genetic engineering. As E. coli W3110 owns the benefits of more heat shock proteins and higher tolerance to toxic chemicals, further execution of T7-based system in W3110 as cell factory is a conceivable strategy.
Results
Three novel W3110 strains, i.e., W3110:IL5, W3110::L5 and W3110::pI, were accomplished by chromosome-equipped T7RNAP. At first, the LacZ and T7RNAP with isopropyl-β-D-thiogalactopyranoside (IPTG) induction showed higher expression levels in W3110 derivatives than that in BL21(DE3). The plasmids with and without lacI/lacO repression were used to investigate the protein expression of super-fold green fluorescence protein (sfGFP), carbonic anhydrase (CA) for carbon dioxide uptake and lysine decarboxylase (CadA) to produce a toxic chemical cadaverine (DAP). All the proteins showed better expression in W3110::L5 and W3110::pI, respectively. As a result, the highest cadaverine production of 36.9 g/L, lysine consumption of 43.8 g/L and up to 100% yield were obtained in W3110::pI(−) with plasmid pSU-T7-CadA constitutively.
Conclusion
Effect of IPTG and lacI/lacO regulator has been investigated in three chromosome-based T7RNAP E. coli strains. The newly engineered W3110 strains possessed similar protein expression compared to commercial BL21(DE3). Furthermore, W3110::pI displays higher production of sfGFP, CA and CadA, due to it having the highest sensitivity to IPTG, thus it represents the greatest potential as a cell factory.
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Huang K, Zhang B, Shen ZY, Cai X, Liu ZQ, Zheng YG. Enhanced amphotericin B production by genetically engineered Streptomyces nodosus. Microbiol Res 2020; 242:126623. [PMID: 33189073 DOI: 10.1016/j.micres.2020.126623] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 10/09/2020] [Indexed: 11/26/2022]
Abstract
The antifungal agent amphotericin B (AmB) is a polyketide produced by Streptomyces nodosus. The synthetic precursors of the amphotericin macrolactone skeleton are acetyl-CoA, malonyl-CoA and methylmalonyl-CoA. The genome sequence of the wild type S. nodosus ATCC14899 revealed a type II polyketide synthase (PKS) competing for malonyl-CoA. The same competitive branch was sequenced and verified in a mutant named S. nodosus ZJB2016050 (S. nodosus N3) screened in our lab. The transcriptome of the secondary metabolic synthetic gene cluster comparisons suggested that type II PKS (PKS5) competition is a factor in low production. The deletion of the PKS5 gene led to the titer of AmB improved from 5.01 g/L to 6.32 g/L while the by-product amphotericin A (AmA) reduced from 0.51 g/L to 0.12 g/L. A sequence of genes including PKS amphA, acc1, mme and mcm were overexpressed in a ΔPKS5 mutant, resulting in improved production AmB from 5.01 g/L to 7.06 g/L in shake flasks at 96 h. The yield of AmB and AmA in a 5 L bioreactor at 144 h was 15.6 g/L and 0.36 g/L, respectively. The intracellular reducibility of the wild type, mutagenesis type and genetically engineered type were detected, which was first found to be related to the by-product AmA. The increment of skeleton biosynthesis may consume more NADPH and reduces AmphC ER5 domain reduction. This study can be implemented for other polyketides in industrial production.
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Affiliation(s)
- Kai Huang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Bo Zhang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Zhen-Yang Shen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Xue Cai
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China.
| | - Yu-Guo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China; Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China
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35
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Li N, Xu S, Du G, Chen J, Zhou J. Efficient production of L-homoserine in Corynebacterium glutamicum ATCC 13032 by redistribution of metabolic flux. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107665] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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36
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Schneider P, Klamt S. Characterizing and ranking computed metabolic engineering strategies. Bioinformatics 2020; 35:3063-3072. [PMID: 30649194 PMCID: PMC6735923 DOI: 10.1093/bioinformatics/bty1065] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/28/2018] [Accepted: 01/07/2019] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION The computer-aided design of metabolic intervention strategies has become a key component of an integrated metabolic engineering approach and a broad range of methods and algorithms has been developed for this task. Many of these algorithms enforce coupling of growth with product synthesis and may return thousands of possible intervention strategies from which the most suitable strategy must then be selected. RESULTS This work focuses on how to evaluate and rank, in a meaningful way, a given pool of computed metabolic engineering strategies for growth-coupled product synthesis. Apart from straightforward criteria, such as a preferably small number of necessary interventions, a reasonable growth rate and a high product yield, we present several new criteria useful to pick the most suitable intervention strategy. Among others, we investigate the robustness of the intervention strategies by searching for metabolites that may disrupt growth coupling when accumulated or secreted and by checking whether the interventions interrupt pathways at their origin (preferable) or at downstream steps. We also assess thermodynamic properties of the pathway(s) favored by the intervention strategy. Furthermore, strategies that have a significant overlap with alternative solutions are ranked higher because they provide flexibility in implementation. We also introduce the notion of equivalence classes for grouping intervention strategies with identical solution spaces. Our ranking procedure involves in total ten criteria and we demonstrate its applicability by assessing knockout-based intervention strategies computed in a genome-scale model of E.coli for the growth-coupled synthesis of l-methionine and of the heterologous product 1,4-butanediol. AVAILABILITY AND IMPLEMENTATION The MATLAB scripts that were used to characterize and rank the example intervention strategies are available at http://www2.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Philipp Schneider
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Analysis and Redesign of Biological Networks, Magdeburg, Germany
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37
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Zhou HY, Wu WJ, Xu YY, Zhou B, Niu K, Liu ZQ, Zheng YG. Calcium Carbonate Addition Improves L-Methionine Biosynthesis by Metabolically Engineered Escherichia coli W3110-BL. Front Bioeng Biotechnol 2020; 8:300. [PMID: 32426336 PMCID: PMC7212366 DOI: 10.3389/fbioe.2020.00300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/20/2020] [Indexed: 12/02/2022] Open
Abstract
L-Methionine (L-Met) is a sulfur-containing amino acid, which is one of the eight essential amino acids to human body. In this work, the fermentative production of L-Met with genetically engineered Escherichia coli W3110-BL in a 5-L fermentor was enhanced through supplement of Ca2+ into the fermentation medium. With the addition of 30 g/L calcium carbonate (CaCO3), the titer of L-Met and yield against glucose reached 1.48 g/L and 0.09 mol/mol glucose, 57.45% higher than those of the control, respectively. The flux balance analysis (FBA) revealed that addition of CaCO3 strengthened the tricarboxylic acid cycle and increased the intracellular ATP concentration by 39.28%. The re-distribution of carbon, ATP, and cofactors flux may collaborate to improve L-Met biosynthesis with E. coli W3110-BL. The regulation of citrate synthase and oxidative phosphorylation pathway was proposed to be important for overproduction of L-Met. These foundations provide helpful reference in the following metabolic modification or fermentation control for further improvement of L-Met biosynthesis.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Wang-Jie Wu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yue-Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Bin Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Kun Niu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification, Ministry of Education, Zhejiang University of Technology, Hangzhou, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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38
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Chen J, Liu P, Chu X, Chen J, Zhang H, Rowley DC, Wang H. Metabolic Pathway Construction and Optimization of Escherichia coli for High-Level Ectoine Production. Curr Microbiol 2020; 77:1412-1418. [DOI: 10.1007/s00284-020-01888-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/14/2020] [Indexed: 01/05/2023]
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39
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Effect of dissolved oxygen on L-methionine production from glycerol by Escherichia coli W3110BL using metabolic flux analysis method. J Ind Microbiol Biotechnol 2020; 47:287-297. [PMID: 32052230 DOI: 10.1007/s10295-020-02264-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/30/2020] [Indexed: 12/15/2022]
Abstract
L-Methionine is an essential amino acid in humans, which plays an important role in the synthesis of some important amino acids and proteins. In this work, metabolic flux of batch fermentation of L-methionine with recombinant Escherichia coli W3110BL was analyzed using the flux balance analysis method, which estimated the intracellular flux distributions under different dissolved oxygen conditions. The results revealed the producing L-methionine flux of 4.8 mmol/(g cell·h) [based on the glycerol uptake flux of 100 mmol/(g cell·h)] was obtained at 30% dissolved oxygen level which was higher than that of other dissolved oxygen levels. The carbon fluxes for synthesizing L-methionine were mainly obtained from the pathway of phosphoenolpyruvate to oxaloacetic acid [15.6 mmol/(g cell·h)] but not from the TCA cycle. Hence, increasing the flow from phosphoenolpyruvate to oxaloacetic acid by enhancing the enzyme activity of phosphoenolpyruvate carboxylase might be conducive to the production of L-methionine. Additionally, pentose phosphate pathway could provide a large amount of reducing power NADPH for the synthesis of amino acids and the flux could increase from 41 mmol/(g cell·h) to 51 mmol/(g cell·h) when changing the dissolved oxygen levels, thus meeting the requirement of NADPH for L-methionine production and biomass synthesis. Therefore, the following modification of the strains should based on the improvement of the key pathway and the NAD(P)/NAD(P)H metabolism.
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40
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Regulation of homoserine O-succinyltransferase for efficient production of L-methionine in engineered Escherichia coli. J Biotechnol 2020; 309:53-58. [PMID: 31891734 DOI: 10.1016/j.jbiotec.2019.12.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/07/2019] [Accepted: 12/26/2019] [Indexed: 01/08/2023]
Abstract
l-Methionine biosynthesis in Eschericha coli consists of multiple unit modules with various enzymes involved and the imbalance between different modules always restricted its productivity. In this study, the key enzymes participating in the pathway were investigated for their effect on l-methionine production and the pivotal enzyme homoserine O-succinyltransferase (MetA) was designed to be regulated. The surface amino acid residues of MetA were effectively modified through site-saturation mutagenesis and single mutants L63F, A28V, P298L and double mutant L63F/A28V were obtained with improved l-methionine productivity. The structure analysis revealed that the involved residues were on the surface loop regions, which was proposed to be conducive to the refolding of MetA and thus reduce the inhibition effect caused by l-methionine. After expression of the selected single mutant L63F in engineered E. coli ΔIJA-HFEBC strain with l-methionine efflux pump and mutated 3-phosphoglycerate dehydrogenase, the l-methionine production was significantly improved, with a final yield of 3528 mg/L. The results demonstrated the efficiency of MetA regulation for enhanced production of l-methionine and meanwhile provided important guidance for further engineering of MetA with increased l-methionine productivity.
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Zhang B, Zhou YT, Jiang SX, Zhang YH, Huang K, Liu ZQ, Zheng YG. Amphotericin B biosynthesis in Streptomyces nodosus: quantitative analysis of metabolism via LC-MS/MS based metabolomics for rational design. Microb Cell Fact 2020; 19:18. [PMID: 32005241 PMCID: PMC6995120 DOI: 10.1186/s12934-020-1290-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 01/21/2020] [Indexed: 01/19/2023] Open
Abstract
Background Amphotericin B (AmB) is widely used against fungal infection and produced mainly by Streptomyces nodosus. Various intracellular metabolites of S. nodosus were identified during AmB fermentation, and the key compounds that related to the cell growth and biosynthesis of AmB were analyzed by principal component analysis (PCA) and partial least squares (PLS). Results Rational design that based on the results of metabolomics was employed to improve the AmB productivity of Streptomyces nodosus, including the overexpression of genes involved in oxygen-taking, precursor-acquiring and product-exporting. The AmB yield of modified strain S. nodosus VMR4A was 6.58 g/L, which was increased significantly in comparison with that of strain S. nodosus ZJB2016050 (5.16 g/L). This was the highest yield of AmB reported so far, and meanwhile, the amount of by-product amphotericin A (AmA) was decreased by 45%. Moreover, the fermentation time of strain S. nodosus VMR4A was shortened by 24 h compared with that of strain. The results indicated that strain S. nodosus VMR4A was an excellent candidate for the industrial production of AmB because of its high production yield, low by-product content and the fast cell growth. Conclusions This study would lay the foundation for improving the AmB productivity through metabolomics analysis and overexpression of key enzymes.![]()
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yi-Teng Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Sheng-Xian Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yu-Han Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Kai Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Enhanced production of L-methionine in engineered Escherichia coli with efficient supply of one carbon unit. Biotechnol Lett 2019; 42:429-436. [PMID: 31865476 DOI: 10.1007/s10529-019-02786-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/14/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVE L-methionine is an important sulfur-containing amino acid essential for humans and animals. Its biosynthesis pathway is complex and highly regulated. This study aims to explore the bottleneck limiting the improvement of L-methionine productivity and apply efficient strategies to increase L-methionine production in engineered E. coli. RESULTS The enzyme O-succinylhomoserine sulfhydrylase involved in thiolation of OSH to form homocysteine was overexpressed in the engineered strain E. coli W3110 IJAHFEBC/PAm, resulting in L-methionine production increased from 2.8 to 3.22 g/L in shake flask cultivation. By exogenous addition of L-glycine as the precursor of one carbon unit, the titer of L-methionine was increased to 3.68 g/L. The glycine cleavage system was further strengthened for the efficient one carbon unit supply and a L-methionine titer of 3.96 g/L was obtained, which was increased by 42% compared with that of the original strain. CONCLUSIONS Insufficient supply of one carbon unit was found to be the issue limiting the improvement of L-methionine productivity and its up-regulation significantly promoted the L-methionine production in the engineered E. coli.
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43
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Promoter engineering strategies for the overproduction of valuable metabolites in microbes. Appl Microbiol Biotechnol 2019; 103:8725-8736. [PMID: 31630238 DOI: 10.1007/s00253-019-10172-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 12/16/2022]
Abstract
Promoter engineering is an enabling technology in metabolic engineering and synthetic biology. As an indispensable part of synthetic biology, the promoter is a key factor in regulating genetic circuits and in coordinating multi-gene biosynthetic pathways. In this review, we summarized the recent progresses in promoter engineering in microbes. Specifically, the endogenous promoters are firstly discussed, followed by the statement of the influence of nucleotides exchange on the strength of promoters explored by site-selective mutagenesis. We then introduced the promoter libraries with a wide range of strength, which are constructed focusing on core promoter regions and upstream activating sequences by rational designs. Finally, the application of promoter libraries in the optimization of multi-gene metabolic pathways for high-yield production of metabolites was illustrated with a couple of recent examples.
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Zhang B, Zhang XM, Wang W, Liu ZQ, Zheng YG. Metabolic engineering of Escherichia coli for d-pantothenic acid production. Food Chem 2019; 294:267-275. [DOI: 10.1016/j.foodchem.2019.05.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/22/2019] [Accepted: 05/07/2019] [Indexed: 02/04/2023]
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Ruan L, Li L, Zou D, Jiang C, Wen Z, Chen S, Deng Y, Wei X. Metabolic engineering of Bacillus amyloliquefaciens for enhanced production of S-adenosylmethionine by coupling of an engineered S-adenosylmethionine pathway and the tricarboxylic acid cycle. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:211. [PMID: 31516550 PMCID: PMC6732833 DOI: 10.1186/s13068-019-1554-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND S-Adenosylmethionine (SAM) is a critical cofactor involved in many biochemical reactions. However, the low fermentation titer of SAM in methionine-free medium hampers commercial-scale production. The SAM synthesis pathway is specially related to the tricarboxylic acid (TCA) cycle in Bacillus amyloliquefaciens. Therefore, the SAM synthesis pathway was engineered and coupled with the TCA cycle in B. amyloliquefaciens to improve SAM production in methionine-free medium. RESULTS Four genes were found to significantly affect SAM production, including SAM2 from Saccharomyces cerevisiae, metA and metB from Escherichia coli, and native mccA. These four genes were combined to engineer the SAM pathway, resulting in a 1.42-fold increase in SAM titer using recombinant strain HSAM1. The engineered SAM pathway was subsequently coupled with the TCA cycle through deletion of succinyl-CoA synthetase gene sucC, and the resulted HSAM2 mutant produced a maximum SAM titer of 107.47 mg/L, representing a 0.59-fold increase over HSAM1. Expression of SAM2 in this strain via a recombinant plasmid resulted in strain HSAM3 that produced 648.99 mg/L SAM following semi-continuous flask batch fermentation, a much higher yield than previously reported for methionine-free medium. CONCLUSIONS This study reports an efficient strategy for improving SAM production that can also be applied for generation of SAM cofactors supporting group transfer reactions, which could benefit metabolic engineering, chemical biology and synthetic biology.
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Affiliation(s)
- Liying Ruan
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lu Li
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Dian Zou
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cong Jiang
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhiyou Wen
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Department of Food Science and Human Nutrition, Iowa State University, Ames, 50011 USA
| | - Shouwen Chen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, Wuxi, 214122 China
| | - Xuetuan Wei
- Key Laboratory of Environment Correlative Dietology (Ministry of Education), College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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Wang W, Wang J, Wu S, Dong X, Guo C, Zhang H, Qi G. Bioavailability ofl-methionine relative todl-methionine in Broiler chickens. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1641433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Weiwei Wang
- Risk Assessment Laboratory of Feed Derived Factors to Animal Product Quality Safety of Ministry of Agriculture & Rural Affairs, National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wang
- Risk Assessment Laboratory of Feed Derived Factors to Animal Product Quality Safety of Ministry of Agriculture & Rural Affairs, National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shugeng Wu
- Risk Assessment Laboratory of Feed Derived Factors to Animal Product Quality Safety of Ministry of Agriculture & Rural Affairs, National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Dong
- CJ CheilJedang (Shanghai) Trading Co. Ltd, Shanghai, China
| | - Chunyan Guo
- CJ CheilJedang (Shanghai) Trading Co. Ltd, Shanghai, China
| | - Haijun Zhang
- Risk Assessment Laboratory of Feed Derived Factors to Animal Product Quality Safety of Ministry of Agriculture & Rural Affairs, National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanghai Qi
- Risk Assessment Laboratory of Feed Derived Factors to Animal Product Quality Safety of Ministry of Agriculture & Rural Affairs, National Engineering Research Center of Biological Feed, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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In-Cell Synthesis of Bioorthogonal Alkene Tag S-Allyl-Homocysteine and Its Coupling with Reprogrammed Translation. Int J Mol Sci 2019; 20:ijms20092299. [PMID: 31075919 PMCID: PMC6539321 DOI: 10.3390/ijms20092299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/22/2022] Open
Abstract
In this study, we report our initial results on in situ biosynthesis of S-allyl-l-homocysteine (Sahc) by simple metabolic conversion of allyl mercaptan in Escherichia coli, which served as the host organism endowed with a direct sulfhydration pathway. The intracellular synthesis we describe in this study is coupled with the direct incorporation of Sahc into proteins in response to methionine codons. Together with O-acetyl-homoserine, allyl mercaptan was added to the growth medium, followed by uptake and intracellular reaction to give Sahc. Our protocol efficiently combined the in vivo synthesis of Sahc via metabolic engineering with reprogrammed translation, without the need for a major change in the protein biosynthesis machinery. Although the system needs further optimisation to achieve greater intracellular Sahc production for complete protein labelling, we demonstrated its functional versatility for photo-induced thiol-ene coupling and the recently developed phosphonamidate conjugation reaction. Importantly, deprotection of Sahc leads to homocysteine-containing proteins-a potentially useful approach for the selective labelling of thiols with high relevance in various medical settings.
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Xiong N, Yu R, Chen T, Xue YP, Liu ZQ, Zheng YG. Separation and purification of l-methionine from E. coli fermentation broth by macroporous resin chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1110-1111:108-115. [DOI: 10.1016/j.jchromb.2019.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/12/2019] [Accepted: 02/14/2019] [Indexed: 02/02/2023]
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Enhanced L-methionine production by genetically engineered Escherichia coli through fermentation optimization. 3 Biotech 2019; 9:96. [PMID: 30800607 DOI: 10.1007/s13205-019-1609-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
Microbial fermentation for L-methionine (L-Met) production based on natural renewable resources is attractive and challenging. In this work, the effects of medium composition and fermentation conditions were investigated to improve L-Met production by genetically engineered Escherichia coli MET-3. Statistical optimization techniques including Plackett-Burman (PB) design and Box-Behnken design (BBD) were adopted first to optimize the culture medium. Results of PB-designed experiments indicated that the culture medium components including glucose, yeast extract, KH2PO4, and MgSO4.7H2O had significant effects on L-Met biosynthesis. With their best-predicted concentration established by BBD (glucose 37.43 g/L, yeast extract 0.95 g/L, KH2PO4 1.82 g/L, and MgSO4.7H2O 4.51 g/L), L-Met titer was increased to 3.04 g/L from less than 2.0 g/L. For further enhancement of L-Met biosynthesis, the fermentation conditions of batch cultivation carried out in a 5-L fermentor were optimized, and the optimum results were obtained at an agitation rate of 300 rpm, medium pH of 7.0, and induction temperature of 28 °C. Based on the optimization parameters, fed-batch fermentation with the modified medium was conducted. As a result, great improvement of L-Met titer (12.80 g/L) and yield (0.13 mol/mol) were achieved, with an increase of 38.53% and 30.0% compared with those of the basal medium, respectively. Furthermore, higher L-Met productivity of 0.261 g/L/h was obtained, representing 2.13-fold higher in comparison to the original medium. The results may provide a helpful reference for further study on strain improvement and fermentation control.
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Xu JM, Li JQ, Zhang B, Liu ZQ, Zheng YG. Fermentative production of the unnatural amino acid L-2-aminobutyric acid based on metabolic engineering. Microb Cell Fact 2019; 18:43. [PMID: 30819198 PMCID: PMC6393993 DOI: 10.1186/s12934-019-1095-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/25/2019] [Indexed: 01/13/2023] Open
Abstract
Background l-2-aminobutyric acid (l-ABA) is an unnatural amino acid that is a key intermediate for the synthesis of several important pharmaceuticals. To make the biosynthesis of l-ABA environmental friendly and more suitable for the industrial-scale production. We expand the nature metabolic network of Escherichia coli using metabolic engineering approach for the production of l-ABA. Results In this study, Escherichia coli THR strain with a modified pathway for threonine-hyperproduction was engineered via deletion of the rhtA gene from the chromosome. To redirect carbon flux from 2-ketobutyrate (2-KB) to l-ABA, the ilvIH gene was deleted to block the l-isoleucine pathway. Furthermore, the ilvA gene from Escherichia coli W3110 and the leuDH gene from Thermoactinomyces intermedius were amplified and co-overexpressed. The promoter was altered to regulate the expression strength of ilvA* and leuDH. The final engineered strain E. coli THR ΔrhtAΔilvIH/Gap-ilvA*-Pbs-leuDH was able to produce 9.33 g/L of l-ABA with a yield of 0.19 g/L/h by fed-batch fermentation in a 5 L bioreactor. Conclusions This novel metabolically tailored strain offers a promising approach to fulfill industrial requirements for production of l-ABA. Electronic supplementary material The online version of this article (10.1186/s12934-019-1095-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian-Miao Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jian-Qiang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, China
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