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Pang Q, Ma S, Han H, Jin X, Liu X, Su T, Qi Q. Phage Enzyme-Assisted Direct In Vivo DNA Assembly in Multiple Microorganisms. ACS Synth Biol 2022; 11:1477-1487. [PMID: 35298132 DOI: 10.1021/acssynbio.1c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of DNA fragments is extremely important for molecular biology. Increasing numbers of studies have focused on streamlining the laborious and costly protocols via in vivo DNA assembly. However, the existing methods were mainly developed for Escherichia coli or Saccharomyces cerevisiae, whereas there are few direct in vivo DNA assembly methods for other microorganisms. The use of shuttle vectors and tedious plasmid extraction and transformation procedures make DNA cloning in other microorganisms laborious and inefficient, especially for DNA library construction. In this study, we developed a "phage enzyme-assisted in vivo DNA assembly" (PEDA) method via combinatorial expression of T5 exonuclease and T4 DNA ligase. PEDA facilitated the in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and it is applicable to multiple microorganisms, such as Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. The cloning efficiency of optimized PEDA is much higher than that of the existing in vivo DNA assembly methods and comparable to that of in vitro DNA assembly, making it extremely suitable for DNA library cloning. Collectively, PEDA will boost the application of in vivo DNA assembly in various microorganisms.
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Affiliation(s)
- Qingxiao Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Hao Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Xiaoqin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
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Cui Z, Jiang Z, Zhang J, Zheng H, Jiang X, Gong K, Liang Q, Wang Q, Qi Q. Stable and Efficient Biosynthesis of 5-Aminolevulinic Acid Using Plasmid-Free Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1478-1483. [PMID: 30644739 DOI: 10.1021/acs.jafc.8b06496] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
5-Aminolevulinic acid (5-ALA) is a key metabolic intermediate of the heme biosynthesis pathway, which has broad application prospects in agriculture and medicine. However, segregational instability of plasmid-based expression systems and low yield have hampered large-scale manufacture of 5-ALA. In this study, two important genes of the 5-ALA C5 biosynthesis pathway, hemA and hemL, were integrated into Escherichia coli MG1655 for chemically induced chromosomal evolution (CIChE). The highest hemA and hemL copy-number, 98 per genome, was obtained in CIChE strain MG136. The 5-ALA titer of this strain reached 2724 mg/L in optimized condition. Then, after undergoing adaptative evolution and the deletion of recA, strain MG136a ΔrecA::FRT could stably produce 4550 mg/L 5-ALA from glucose, 450 times the amount produced by hemA- hemL single copy strain MG1655-hemAL. This study constructed a plasmid-free E. coli strain for 5-ALA production, which will provide the basis for further manipulation of metabolic regulation and optimization of fermentation.
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Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Zhennan Jiang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Jinhong Zhang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Huihui Zheng
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Xin Jiang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Kai Gong
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center , Shandong University , Qingdao 266237 , P. R. China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology , Chinese Academy of Sciences , Qingdao 266101 , P. R. China
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Lee SQE, Tan TS, Kawamukai M, Chen ES. Cellular factories for coenzyme Q 10 production. Microb Cell Fact 2017; 16:39. [PMID: 28253886 PMCID: PMC5335738 DOI: 10.1186/s12934-017-0646-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/10/2017] [Indexed: 04/20/2023] Open
Abstract
Coenzyme Q10 (CoQ10), a benzoquinone present in most organisms, plays an important role in the electron-transport chain, and its deficiency is associated with various neuropathies and muscular disorders. CoQ10 is the only lipid-soluble antioxidant found in humans, and for this, it is gaining popularity in the cosmetic and healthcare industries. To meet the growing demand for CoQ10, there has been considerable interest in ways to enhance its production, the most effective of which remains microbial fermentation. Previous attempts to increase CoQ10 production to an industrial scale have thus far conformed to the strategies used in typical metabolic engineering endeavors. However, the emergence of new tools in the expanding field of synthetic biology has provided a suite of possibilities that extend beyond the traditional modes of metabolic engineering. In this review, we cover the various strategies currently undertaken to upscale CoQ10 production, and discuss some of the potential novel areas for future research.
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Affiliation(s)
- Sean Qiu En Lee
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Tsu Soo Tan
- School of Chemical & Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Makoto Kawamukai
- Faculty of Life and Environmental Science, Shimane University, Matsue, 690-8504, Japan
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore, Singapore. .,National University Health System (NUHS), Singapore, Singapore. .,NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore. .,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore.
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Genome engineering Escherichia coli for L-DOPA overproduction from glucose. Sci Rep 2016; 6:30080. [PMID: 27417146 PMCID: PMC4945936 DOI: 10.1038/srep30080] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/29/2016] [Indexed: 12/26/2022] Open
Abstract
Genome engineering has become a powerful tool for creating useful strains in research and industry. In this study, we applied singleplex and multiplex genome engineering approaches to construct an E. coli strain for the production of L-DOPA from glucose. We first used the singleplex genome engineering approach to create an L-DOPA-producing strain, E. coli DOPA-1, by deleting transcriptional regulators (tyrosine repressor tyrR and carbon storage regulator A csrA), altering glucose transport from the phosphotransferase system (PTS) to ATP-dependent uptake and the phosphorylation system overexpressing galactose permease gene (galP) and glucokinase gene (glk), knocking out glucose-6-phosphate dehydrogenase gene (zwf) and prephenate dehydratase and its leader peptide genes (pheLA) and integrating the fusion protein chimera of the downstream pathway of chorismate. Then, multiplex automated genome engineering (MAGE) based on 23 targets was used to further improve L-DOPA production. The resulting strain, E. coli DOPA-30N, produced 8.67 g/L of L-DOPA in 60 h in a 5 L fed-batch fermentation. This titer is the highest achieved in metabolically engineered E. coli having PHAH activity from glucose.
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Li XR, Tian GQ, Shen HJ, Liu JZ. Metabolic engineering of Escherichia coli to produce zeaxanthin. J Ind Microbiol Biotechnol 2014; 42:627-36. [PMID: 25533633 DOI: 10.1007/s10295-014-1565-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/09/2014] [Indexed: 01/06/2023]
Abstract
Zeaxanthin is a high-value carotenoid that is used in nutraceuticals, cosmetics, food, and animal feed industries. Zeaxanthin is chemically synthesized or purified from microorganisms as a natural product; however, increasing demand requires development of alternative sources such as heterologous biosynthesis by recombinant bacteria. For this purpose, we molecularly engineered Escherichia coli to optimize the synthesis of zeaxanthin from lycopene using fusion protein-mediated substrate channeling as well as by the introduction of tunable intergenic regions. The tunable intergenic regions approach was more efficient compared with protein fusion for coordinating expression of lycopene β-cyclase gene crtY and β-carotene 3-hydroxylase gene crtZ. The influence of the substrate channeling effect suggests that the reaction catalyzed by CrtZ is the rate-limiting step in zeaxanthin biosynthesis. Then Pantoea ananatis, Pantoea agglomerans and Haematococcus pluvialis crtZ were compared. Because P. ananatis crtZ is superior to that of P. agglomerans or H. pluvialis for zeaxanthin production, we used it to generate a recombinant strain of E. coli BETA-1 containing pZSPBA-2(P37-crtZPAN) that produced higher amounts of zeaxanthin (11.95 ± 0.21 mg/g dry cell weight) than other engineered E. coli strains described in the literature.
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Affiliation(s)
- Xi-Ran Li
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
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