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He F, Liu X, Tang M, Wang H, Wu Y, Liang S. CRISETR: an efficient technology for multiplexed refactoring of biosynthetic gene clusters. Nucleic Acids Res 2024:gkae781. [PMID: 39271125 DOI: 10.1093/nar/gkae781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 08/16/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
The efficient refactoring of natural product biosynthetic gene clusters (BGCs) for activating silent BGCs is a central challenge for the discovery of new bioactive natural products. Herein, we have developed a simple and robust CRISETR (CRISPR/Cas9 and RecET-mediated Refactoring) technique, combining clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 and RecET, for the multiplexed refactoring of natural product BGCs. By this approach, natural product BGCs can be refactored through the synergistic interaction between RecET-mediated efficient homologous recombination and the CRISPR/Cas9 system. We first performed a proof-of-concept validation of the ability of CRISETR, and CRISETR can achieve simultaneous replacement of four promoter sites and marker-free replacement of single promoter site in natural product BGCs. Subsequently, we applied CRISETR to the promoter engineering of the 74-kb daptomycin BGC containing a large number of direct repeat sequences for enhancing the heterologous production of daptomycin. We used combinatorial design to build multiple refactored daptomycin BGCs with diverse combinations of promoters different in transcriptional strengths, and the yield of daptomycin was improved 20.4-fold in heterologous host Streptomyces coelicolor A3(2). In general, CRISETR exhibits enhanced tolerance to repetitive sequences within gene clusters, enabling efficient refactoring of diverse and complex BGCs, which would greatly accelerate discovery of novel bioactive metabolites present in microorganism.
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Affiliation(s)
- Fuqiang He
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Xinpeng Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Min Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Haiyi Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Yun Wu
- Department of Cell Biology, College of Life Science, Sichuan Normal University, Chengdu, Sichuan, 610101, P.R. China
| | - Shufang Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
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Yang K, Jing D, Kong W, Shi Z, Jing G, Li W, Li S, Wang Q. Quantifying the energy-material-pollution nexus in a typical fine chemical industry: A sustainable development-oriented support for collaborative emission reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166826. [PMID: 37673253 DOI: 10.1016/j.scitotenv.2023.166826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/31/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
The fine chemical industry is currently facing challenges in energy saving, material conservation, and pollution reduction due to the dual policy pressure of precise system management and collaborative pollution and carbon reduction. However, the interweaving of materials and energy input-output was not well understood due to the incomplete coverage and the lack of a generic framework. Therefore, a methodology based on the energy-material-pollution (E-M-P) coupling nexus was proposed to quantitatively assess multi-level coupling. According to the selected generic 32 coupling units, two representative glyphosate (PMG) production processes were taken as case studies. Quantification results showed that the solvent element and the material system had a higher priority. Moreover, Process 2 owned a greater optimization potential as the coupling relationship pairs were 2.55 compared to 2.32 for Process 1, and the correlation proportions of material systems reached 69.26 % and 56.92 %, respectively. In addition, assessment results indicated that Process 2 was more environmentally friendly because of the lower ecological indexes (9.7 GPt vs. 15.8 GPt) and weaker carbon footprint (CF) (1.16E+08 vs. 2.32E+08). Combined coupling nexus and environmental assessment organically, methanol had the most optimization potential and was beneficial for the measures such as solvent substitution. This work offered theory and practice guidance with demonstrative value to support the sustainable development of precise system management.
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Affiliation(s)
- Kexuan Yang
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, Institute of Industrial Ecology and Environment, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Deji Jing
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, Institute of Industrial Ecology and Environment, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Weixin Kong
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, Institute of Industrial Ecology and Environment, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhanhong Shi
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, Institute of Industrial Ecology and Environment, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Guohua Jing
- Department of Environmental Science & Engineering, College of Chemical Engineering, Huaqiao University, Xiamen 361021, China
| | - Wei Li
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, Institute of Industrial Ecology and Environment, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Sujing Li
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, Institute of Industrial Ecology and Environment, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Qiaoli Wang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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Li J, Li L, Gao J. Redefining the Glyphosate Sector: Harmonizing Inventiveness and Sustainable Practices for a Better World. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14393-14395. [PMID: 37768014 DOI: 10.1021/acs.jafc.3c04755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
The glyphosate industry has long been a critical player in global agriculture, providing effective and economical solutions for weed control. However, growing concerns over environmental and health impacts have led to increased scrutiny and calls for more sustainable practices. This Viewpoint focuses on the scientific aspects of greener glyphosate synthesis strategies, discussing recent advancements in biobased pathways and catalytic methods, challenges such as scalability and technical hurdles, and future prospects for the herbicide industry. By embracing these new techniques, we can ensure a more sustainable future for herbicide production and contribute to a healthier world.
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Affiliation(s)
- Jinhuan Li
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P. R. China
| | - Jiangtao Gao
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, P. R. China
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Zhao C, Wang XH, Lu XY, Zong H, Zhuge B. Metabolic Engineering of Candida glycerinogenes for Sustainable Production of Geraniol. ACS Synth Biol 2023; 12:1836-1844. [PMID: 37271978 DOI: 10.1021/acssynbio.3c00195] [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] [Indexed: 06/06/2023]
Abstract
Geraniol is a class of natural products that are widely used in the aroma industry due to their unique aroma. Here, to achieve the synthesis of geraniol and alleviate the intense competition from the yeast ergosterol pathway, a transcription factor-mediated ergosterol feedback system was developed in this study to autonomously regulate ergosterol metabolism and redirect carbon flux to geraniol synthesis. In addition, the modification of ergosterol-responsive promoters, the optimization of transcription factor expression intensity, and stepwise metabolic engineering resulted in a geraniol titer of 531.7 mg L-1. For sustainable production of geraniol, we constructed a xylose assimilation pathway in Candida glycerinogenes (C. glycerinogenes). Then, the xylose metabolic capacity was ameliorated and the growth of the engineered strain was rescued by activating the pentose phosphate (PP) pathway. Finally, we obtained 1091.6, 862.4, and 921.8 mg L-1 of geraniol in a 5 L bioreactor by using pure glucose, simulated wheat straw hydrolysates, and simulated sugarcane bagasse hydrolysates, with yields of 47.5, 57.9, and 59.1 mg g-1 DCW, respectively. Our study demonstrated that C. glycerinogenes has the potential to produce geraniol from lignocellulosic biomass, providing a powerful tool for the sustainable synthesis of other valuable monoterpenes.
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Affiliation(s)
- Cui Zhao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xi-Hui Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xin-Yao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Yu Z, Li W, Ge C, Sun X, Wang J, Shen X, Yuan Q. Functional expansion of the natural inorganic phosphorus starvation response system in Escherichia coli. Biotechnol Adv 2023; 66:108154. [PMID: 37062526 DOI: 10.1016/j.biotechadv.2023.108154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 04/18/2023]
Abstract
Phosphorus, an indispensable nutrient, plays an essential role in cell composition, metabolism, and signal transduction. When inorganic phosphorus (Pi) is scarce, the Pi starvation response in E. coli is activated to increase phosphorus acquisition and drive the cells into a non-growing state to reduce phosphorus consumption. In the six decades of research history, the initiation, output, and shutdown processes of the Pi starvation response have been extensively studied. Simultaneously, Pi starvation has been used in biosensor development, recombinant protein production, and natural product biosynthesis. In this review, we focus on the output process and the applications of the Pi starvation response that have not been summarized before. Meanwhile, based on the current status of mechanistic studies and applications, we propose practical strategies to develop the natural Pi starvation response into a multifunctional and standardized regulatory system in four aspects, including response threshold, temporal expression, intensity range, and bifunctional regulation, which will contribute to its broader application in more fields such as industrial production, medical analysis, and environmental protection.
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Affiliation(s)
- Zheng Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenna Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Ge
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Makris C, Carmichael JR, Zhou H, Butler A. C-Diazeniumdiolate Graminine in the Siderophore Gramibactin Is Photoreactive and Originates from Arginine. ACS Chem Biol 2022; 17:3140-3147. [PMID: 36354305 PMCID: PMC9679993 DOI: 10.1021/acschembio.2c00593] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022]
Abstract
Siderophores are synthesized by microbes to facilitate iron acquisition required for growth. Catecholate, hydroxamate, and α-hydroxycarboxylate groups comprise well-established ligands coordinating Fe(III) in siderophores. Recently, a C-type diazeniumdiolate ligand in the newly identified amino acid graminine (Gra) was found in the siderophore gramibactin (Gbt) produced by Paraburkholderia graminis DSM 17151. The N-N bond in the diazeniumdiolate is a distinguishing feature of Gra, yet the origin and reactivity of this C-type diazeniumdiolate group has remained elusive until now. Here, we identify l-arginine as the direct precursor to l-Gra through the isotopic labeling of l-Arg, l-ornithine, and l-citrulline. Furthermore, these isotopic labeling studies establish that the N-N bond in Gra must be formed between the Nδ and Nω of the guanidinium group in l-Arg. We also show the diazeniumdiolate groups in apo-Gbt are photoreactive, with loss of nitric oxide (NO) and H+ from each d-Gra yielding E/Z oxime isomers in the photoproduct. With the loss of Gbt's ability to chelate Fe(III) upon exposure to UV light, our results hint at this siderophore playing a larger ecological role. Not only are NO and oximes important in plant biology for communication and defense, but so too are NO-releasing compounds and oximes attractive in medicinal applications.
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Affiliation(s)
| | | | - Hongjun Zhou
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Alison Butler
- Department of Chemistry &
Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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