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Jin X, Li X, Zou L, Zheng Z, Ouyang J. Biological Valorization of Lignin-Derived Aromatics in Hydrolysate to Protocatechuic Acid by Engineered Pseudomonas putida KT2440. Molecules 2024; 29:1555. [PMID: 38611834 PMCID: PMC11013400 DOI: 10.3390/molecules29071555] [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: 02/14/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Alongside fermentable sugars, weak acids, and furan derivatives, lignocellulosic hydrolysates contain non-negligible amounts of lignin-derived aromatic compounds. The biological funnel of lignin offers a new strategy for the "natural" production of protocatechuic acid (PCA). Herein, Pseudomonas putida KT2440 was engineered to produce PCA from lignin-derived monomers in hydrolysates by knocking out protocatechuate 3,4-dioxygenase and overexpressing vanillate-O-demethylase endogenously, while acetic acid was used for cell growth. The sugar catabolism was further blocked to prevent the loss of fermentable sugar. Using the engineered strain, a total of 253.88 mg/L of PCA was obtained with a yield of 70.85% from corncob hydrolysate 1. The highest titer of 433.72 mg/L of PCA was achieved using corncob hydrolysate 2 without any additional nutrients. This study highlights the potential ability of engineered strains to address the challenges of PCA production from lignocellulosic hydrolysate, providing novel insights into the utilization of hydrolysates.
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Affiliation(s)
| | | | | | | | - Jia Ouyang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; (X.J.); (X.L.); (L.Z.); (Z.Z.)
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2
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Wang Y, Zheng J, Xue Y, Yu B. Engineering Pseudomonas putida KT2440 for Dipicolinate Production via the Entner-Doudoroff Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6500-6508. [PMID: 38470347 DOI: 10.1021/acs.jafc.4c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Dipicolinic acid (DPA), a cyclic diacid, has garnered significant interest due to its potential applications in antimicrobial agents, antioxidants, chelating reagents, and polymer precursors. However, its natural bioproduction is limited since DPA is only accumulated in Bacillus and Clostridium species during sporulation. Thus, heterologous production by engineered strains is of paramount importance for developing a sustainable biological route for DPA production. Pseudomonas putida KT2440 has emerged as a promising host for the production of various chemicals thanks to its robustness, metabolic versatility, and genetic tractability. The dominant Entner-Doudoroff (ED) pathway for glucose metabolism in this strain offers an ideal route for DPA production due to the advantage of NADPH generation and the naturally balanced flux between glyceraldehyde-3-phosphate and pyruvate, which are both precursors for DPA synthesis. In this study, DPA production via the ED pathway was in silico designed in P. putida KT2440. The systematically engineered strain produced dipicolinate with a titer of 11.72 g/L from glucose in a 5 L fermentor. This approach not only provides a sustainable green route for DPA production but also expands our understanding of the metabolic potential of the ED pathway in P. putida KT2440.
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Affiliation(s)
- Yihan Wang
- Department of Industrial Microbiology and Biotechnology, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Jie Zheng
- Department of Industrial Microbiology and Biotechnology, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yubin Xue
- Department of Industrial Microbiology and Biotechnology, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Yu
- Department of Industrial Microbiology and Biotechnology, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Li J, Lu X, Zou X, Ye BC. Recent Advances in Microbial Metabolic Engineering for Production of Natural Phenolic Acids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4538-4551. [PMID: 38377566 DOI: 10.1021/acs.jafc.3c07658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Phenolic acids are important natural bioactive compounds with varied physiological functions. They are extensively used in food, pharmaceutical, cosmetic, and other chemical industries and have attractive market prospects. Compared to plant extraction and chemical synthesis, microbial fermentation for phenolic acid production from renewable carbon sources has significant advantages. This review focuses on the structural information, physiological functions, current applications, and biosynthesis pathways of phenolic acids, especially advances in the development of metabolically engineered microbes for the production of phenolic acids. This review provides useful insights concerning phenolic acid production through metabolic engineering of microbial cell factories.
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Affiliation(s)
- Jin Li
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xiumin Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xiang Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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Wang M, Wang H, Gao C, Wei W, Liu J, Chen X, Hu G, Song W, Wu J, Zhang F, Liu L. Efficient production of protocatechuic acid using systems engineering of Escherichia coli. Metab Eng 2024; 82:134-146. [PMID: 38369051 DOI: 10.1016/j.ymben.2024.02.003] [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: 11/04/2023] [Revised: 01/21/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
Protocatechuic acid (3, 4-dihydroxybenzoic acid, PCA) is widely used in the pharmaceuticals, health food, and cosmetics industries owing to its diverse biological activities. However, the inhibition of 3-dehydroshikimate dehydratase (AroZ) by PCA and its toxicity to cells limit the efficient production of PCA in Escherichia coli. In this study, a high-level strain of 3-dehydroshikimate, E. coli DHS01, was developed by blocking the carbon flow from the shikimate-overproducing strain E. coli SA09. Additionally, the PCA biosynthetic pathway was established in DHS01 by introducing the high-activity ApAroZ. Subsequently, the protein structure and catalytic mechanism of 3-dehydroshikimate dehydratase from Acinetobacter pittii PHEA-2 (ApAroZ) were clarified. The variant ApAroZR363A, achieved by modulating the conformational dynamics of ApAroZ, effectively relieved product inhibition. Additionally, the tolerance of the strain E. coli PCA04 to PCA was enhanced by adaptive laboratory evolution, and a biosensor-assisted high-throughput screening method was designed and implemented to expedite the identification of high-performance PCA-producing strains. Finally, in a 5 L bioreactor, the final strain PCA05 achieved the highest PCA titer of 46.65 g/L, a yield of 0.23 g/g, and a productivity of 1.46 g/L/h for PCA synthesis from glucose using normal fed-batch fermentation. The strategies described herein serve as valuable guidelines for the production of other high-value and toxic products.
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Affiliation(s)
- Ming Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Haomiao Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Fan Zhang
- School of Life Sciences and Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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Li J, Fu J, Shang Y, Wei W, Zhang P, Wang X, Ye BC. Metabolic Engineering of Pseudomonas putida KT2440 for De Novo Biosynthesis of Vanillic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4217-4224. [PMID: 38356383 DOI: 10.1021/acs.jafc.3c07828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Vanillic acid (VA), as a plant-derived phenolic acid compound, has widespread applications and good market prospects. However, the traditional production process cannot meet market demand. In this study, Pseudomonas putida KT2440 was used for de novo biosynthesis of VA. Multiple metabolic engineering strategies were applied to construct these P. putida-based cell factories, including the introduction of a Hs-OMTopt, engineering the cofactor S-adenosylmethionine supply pathway through the overexpression of metX and metH, reforming solubility of Hs-OMTopt, increasing a second copy of Hs-OMTopt, and the optimization of the fermentation medium. The resulting strain, XCS17, de novo biosynthesized 5.4 g/L VA from glucose in a fed-batch fermentation system; this is the highest VA production titer reported up to recently. This study showed that P. putida KT2440 is a robust platform for achieving the effective production of phenolic acids.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianli Fu
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Zhang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xue Wang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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Pang AP, Wang Y, Zhang T, Gao F, Shen JD, Huang L, Zhou J, Zhang B, Liu ZQ, Zheng YG. Highly efficient production of rhamnolipid in P. putida using a novel sacB-based system and mixed carbon source. BIORESOURCE TECHNOLOGY 2024; 394:130220. [PMID: 38109979 DOI: 10.1016/j.biortech.2023.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Pseudomonas putida KT2440, a GRAS strain, has been used for synthesizing bulk and fine chemicals. However, the gene editing tool to metabolically engineer KT2440 showed low efficiency. In this study, a novel sacB-based system pK51mobsacB was established to improve the efficiency for marker-free gene disruption. Then the rhamnolipid synthetic pathway was introduced in KT2440 and genes of the competitive pathways were deleted to lower the metabolic burden based on pK51mobsacB. A series of endogenous and synthetic promoters were used for fine tuning rhlAB expression. The limited supply of dTDP-L-rhamnose was enhanced by heterologous rmlBDAC expression. Cell growth and rhamnolipid production were well balanced by using glucose/glycerol as mixed carbon sources. The final strain produced 3.64 g/L at shake-flask and 19.77 g/L rhamnolipid in a 5 L fermenter, the highest obtained among metabolically engineered KT2440, which implied the potential of KT2440 as a promising microbial cell factory for industrial rhamnolipid production.
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Affiliation(s)
- Ai-Ping Pang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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
| | - Yun Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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
| | - Teng Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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
| | - Feng Gao
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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
| | - Ji-Dong Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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
| | - Lianggang Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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
| | - Junping Zhou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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 Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral 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 Chiral 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 Chiral 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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Jiang H, Yu X, Guo J, Shang G, Dai Y. Rapid Degradation of Hazardous Amides by Immobilized Engineered Pseudomonas putida KT2440 Based on a Novel Gene Expression Vector. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2109-2119. [PMID: 38247140 DOI: 10.1021/acs.jafc.3c08124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The amides 4-trifluoromethylnicotinamide, acrylamide, and benzamide are widely used in agriculture and industry, posing hazards to the environment and animals. Immobilized bacteria are preferred in wastewater treatment, but degradation of these amides by immobilized engineered bacteria has not been explored. Here, engineered Pseudomonas putida KT2440 pLSJ15-amiA was constructed by introducing a new amidase gene expression vector into environmentally safe P. putida KT2440. P. putida KT2440 pLSJ15-amiA had high amidase activity, even at 80 °C. P. putida KT2440 pLSJ15-amiA immobilized with calcium alginate exhibited a greater environmental tolerance than free cells. The amides were rapidly degraded by the immobilized cells, but the activity was inhibited by high concentrations of substrates. The substrate inhibition model revealed that the optimum initial concentrations of 4-trifluoromethylnicotinamide, acrylamide, and benzamide for degradation by immobilized cells were 197.65, 350.76, and 249.40 μmol/L, respectively. This study develops a novel and excellent immobilized biocatalyst for remediation of wastewater containing hazardous amides.
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Affiliation(s)
- Huoyong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Xuexiu Yu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Jingjing Guo
- Nanjing Normal University Zhongbei College, Zhenjiang 212334, People's Republic of China
| | - Guangdong Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
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Li X, Chen S, Zeng J, Cai R, Liang Y, Chen C, Chen B, Li C. Database-aided UHPLC-Q-orbitrap MS/MS strategy putatively identifies 52 compounds from Wushicha Granule to propose anti-counterfeiting quality-markers for pharmacopoeia. Chin Med 2023; 18:116. [PMID: 37689743 PMCID: PMC10492348 DOI: 10.1186/s13020-023-00829-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023] Open
Abstract
Wushicha Granule, an over-the-counter-drug (OTC) prescription, consists of 19 traditional Chinese herbals medicines (CHMs), such as Chaihu, Hongcha, Chuanxiong, Houpo, and Gancao. The five however have not been effectively characterized by the quality-markers (Q-markers) system in current Pharmacopoeia. The study therefore established a novel database-aided ultra-high performance liquid chromatography-quadrupole-orbitrap mass spectrometry (UHPLC-Q-orbitrap MS/MS) strategy. The strategy has putatively identified 52 compounds from Wushicha Granule, mainly including flavonoids, saponins, alkaloid, lignins, and lactones. Especially, saponin "glycyrrhetinic acid" in the Granule was specifically identified as 18β-configuration (rather than 18α-configuration). Meanwhile, two pairs of isomers were fully discriminated, including vitexin vs isovitexin and daidzein vs 7,4'-dihydroxyflavone. 8β-Glycyrrhetinic acid, together with saponin saikosaponin A, alkaloid caffeine, lactone S-senkyunolide A, and lignin magnolol, were further studied using quantum chemical calculation, UV-vis spectra, and anti-counterfeiting validation experiment. In the validation experiment, they have successfully recognized 6 counterfeit Wushicha Granules, by means of a LC-MS equipped extraction software. Based on these results, 8β-glycyrrhetinic acid is recommended to replace the old Q-marker "glycyrrhetinic acid"; while saikosaponin A, caffeine, S-senkyunolide A, and magnolol are recommended as new Q-markers. These recommendations can not only recognize the counterfeits regarding Chaihu, Hongcha, Chuanxiong, Houpo, and Gancao, but also prevent the possible safety-incident. All these will greatly improve the efficiency and specificity of current Pharmacopoeia.
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Affiliation(s)
- Xican Li
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Shaoman Chen
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jingyuan Zeng
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Rongxin Cai
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yilan Liang
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chuanbin Chen
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ban Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), Hubei University of Technology, Wuhan, 430068, China
| | - Chunhou Li
- School of Chinese Herbal Medicines, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
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Higuchi Y, Ishimaru H, Yoshikawa T, Masuda T, Sakamoto C, Kamimura N, Masai E, Takeuchi D, Sonoki T. Successful selective production of vanillic acid from depolymerized sulfite lignin and its application to poly(ethylene vanillate) synthesis. BIORESOURCE TECHNOLOGY 2023:129450. [PMID: 37406831 DOI: 10.1016/j.biortech.2023.129450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Towards lignin upgrading, vanillic acid (VA), a lignin-derived guaiacyl compound, was produced from sulfite lignin for successfully synthesizing poly(ethylene vanillate), an aromatic polymer. The engineered Sphingobium sp. SYK-6-based strain in which the genes responsible for VA/3-O-methyl gallic acid O-demethylase and syringic acid O-demethylase were disrupted was able to produce vanillic acid (VA) from the mixture consisting of acetovanillone, vanillin, VA, and other low-molecular-weight aromatics obtained by Cu(OH)2-catalyzed alkaline depolymerization of sulfite lignin and membrane fractionation. From the bio-based VA, methyl-4-(2-hydroxyethoxy)-3-methoxybenzoate was synthesized via methylesterification, hydroxyethylation, and distillation, and then it was subjected to polymerization catalyzed by titanium tetraisopropoxide. The molecular weight of the obtained poly(ethylene vanillate) was evaluated to be Mw = 13,000 (Mw/Mn = 1.99) and its melting point was 261°C. The present work proved that poly(ethylene vanillate) is able to be synthesized using VA produced from lignin for the first time.
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Affiliation(s)
- Yudai Higuchi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Hiroya Ishimaru
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Takuya Yoshikawa
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan; Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Takao Masuda
- Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Chiho Sakamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Naofumi Kamimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Eiji Masai
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Daisuke Takeuchi
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Tomonori Sonoki
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.
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Li J, Fu J, Yue C, Shang Y, Ye BC. Highly Efficient Biosynthesis of Protocatechuic Acid via Recombinant Pseudomonas putida KT2440. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37365996 DOI: 10.1021/acs.jafc.3c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Owing to their physiological activities, plant-derived phenolic acids, such as protocatechuic acid (PCA), have extensive applications and market prospects. However, traditional production processes present numerous challenges and cannot meet increasing market demands. Hence, we aimed to biosynthesize PCA by constructing an efficient microbial factory via metabolic engineering of Pseudomonas putida KT2440. Glucose metabolism was engineered by deleting the genes for gluconate 2-dehydrogenase to enhance PCA biosynthesis. To increase the biosynthetic metabolic flux, one extra copy of the genes aroGopt, aroQ, and aroB was inserted into the genome. The resultant strain, KGVA04, produced 7.2 g/L PCA. By inserting the degradation tags GSD and DAS to decrease the amount of shikimate dehydrogenase, PCA biosynthesis was increased to 13.2 g/L in shake-flask fermentation and 38.8 g/L in fed-batch fermentation. To the best of our knowledge, this was the first use of degradation tags to adjust the amount of a key enzyme at the protein level in P. putida KT2440, evidencing the remarkable potential of this method for naturally producing phenolic acids.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianli Fu
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Cheng Yue
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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11
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Luo ZW, Choi KR, Lee SY. Improved terephthalic acid production from p-xylene using metabolically engineered Pseudomonas putida. Metab Eng 2023; 76:75-86. [PMID: 36693471 DOI: 10.1016/j.ymben.2023.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
Terephthalic acid (TPA) is an important commodity chemical used as a monomer of polyethylene terephthalate (PET). Since a large quantity of PET is routinely manufactured and consumed worldwide, the development of sustainable biomanufacturing processes for its monomers (i.e. TPA and ethylene glycol) has recently gained much attention. In a previous study, we reported the development of a metabolically engineered Escherichia coli strain producing 6.7 g/L of TPA from p-xylene (pX) with a productivity and molar conversion yield of 0.278 g/L/h and 96.7 mol%, respectively. Here, we report metabolic engineering of Pseudomonas putida KT2440, a microbial chassis particularly suitable for the synthesis of aromatic compounds, for improved biocatalytic conversion of pX to TPA. To develop a plasmid-free, antibiotic-free, and inducer-free biocatalytic process for cost-competitive TPA production, all heterologous genes required for the synthetic pX-to-TPA bioconversion pathway were integrated into the chromosome of P. putida KT2440 by RecET-based markerless recombineering and overexpressed under the control of constitutive promoters. Next, TPA production was enhanced by integrating multiple copies of the heterologous genes to the ribosomal RNA genes through iteration of recombineering-based random integration and subsequent screening of high-performance strains. Finally, fed-batch fermentation process was optimized to further improve the performance of the engineered P. putida strain. As a result, 38.25 ± 0.11 g/L of TPA was produced from pX with a molar conversion yield of 99.6 ± 0.6%, which is equivalent to conversion of 99.3 ± 0.8 g pX to 154.6 ± 0.5 g TPA. This superior pX-to-TPA biotransformation process based on the engineered P. putida strain will pave the way to the commercial biomanufacturing of TPA in an industrial scale.
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Affiliation(s)
- Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea; BioInformatics Research Center, KAIST Institute for the BioCentury, and KAIST Institute for Artificial Intelligence, KAIST, Daejeon, 34141, Republic of Korea.
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12
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Son J, Lim SH, Kim YJ, Lim HJ, Lee JY, Jeong S, Park C, Park SJ. Customized valorization of waste streams by Pseudomonas putida: State-of-the-art, challenges, and future trends. BIORESOURCE TECHNOLOGY 2023; 371:128607. [PMID: 36638894 DOI: 10.1016/j.biortech.2023.128607] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Preventing catastrophic climate events warrants prompt action to delay global warming, which threatens health and food security. In this context, waste management using engineered microbes has emerged as a long-term eco-friendly solution for addressing the global climate crisis and transitioning to clean energy. Notably, Pseudomonas putida can valorize industry-derived synthetic wastes including plastics, oils, food, and agricultural waste into products of interest, and it has been extensively explored for establishing a fully circular bioeconomy through the conversion of waste into bio-based products, including platform chemicals (e.g., cis,cis-muconic and adipic acid) and biopolymers (e.g., medium-chain length polyhydroxyalkanoate). However, the efficiency of waste pretreatment technologies, capability of microbial cell factories, and practicability of synthetic biology tools remain low, posing a challenge to the industrial application of P. putida. The present review discusses the state-of-the-art, challenges, and future prospects for divergent biosynthesis of versatile products from waste-derived feedstocks using P. putida.
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Affiliation(s)
- Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Hyun Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yu Jin Kim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye Jin Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yeon Lee
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seona Jeong
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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13
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Sheng Q, Yi L, Zhong B, Wu X, Liu L, Zhang B. Shikimic acid biosynthesis in microorganisms: Current status and future direction. Biotechnol Adv 2023; 62:108073. [PMID: 36464143 DOI: 10.1016/j.biotechadv.2022.108073] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.
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Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingxin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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14
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Ling C, Peabody GL, Salvachúa D, Kim YM, Kneucker CM, Calvey CH, Monninger MA, Munoz NM, Poirier BC, Ramirez KJ, St John PC, Woodworth SP, Magnuson JK, Burnum-Johnson KE, Guss AM, Johnson CW, Beckham GT. Muconic acid production from glucose and xylose in Pseudomonas putida via evolution and metabolic engineering. Nat Commun 2022; 13:4925. [PMID: 35995792 PMCID: PMC9395534 DOI: 10.1038/s41467-022-32296-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Muconic acid is a bioprivileged molecule that can be converted into direct replacement chemicals for incumbent petrochemicals and performance-advantaged bioproducts. In this study, Pseudomonas putida KT2440 is engineered to convert glucose and xylose, the primary carbohydrates in lignocellulosic hydrolysates, to muconic acid using a model-guided strategy to maximize the theoretical yield. Using adaptive laboratory evolution (ALE) and metabolic engineering in a strain engineered to express the D-xylose isomerase pathway, we demonstrate that mutations in the heterologous D-xylose:H+ symporter (XylE), increased expression of a major facilitator superfamily transporter (PP_2569), and overexpression of aroB encoding the native 3-dehydroquinate synthase, enable efficient muconic acid production from glucose and xylose simultaneously. Using the rationally engineered strain, we produce 33.7 g L−1 muconate at 0.18 g L−1 h−1 and a 46% molar yield (92% of the maximum theoretical yield). This engineering strategy is promising for the production of other shikimate pathway-derived compounds from lignocellulosic sugars. Muconic acid is a platform chemical with wide industrial applicability. Here, the authors report efficient muconate production from glucose and xylose by engineered Pseudomonas putida strain using adaptive laboratory evolution, metabolic modeling, and rational strain engineering strategies.
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Affiliation(s)
- Chen Ling
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - George L Peabody
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Young-Mo Kim
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Colin M Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher H Calvey
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michela A Monninger
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Nathalie Munoz Munoz
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Brenton C Poirier
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Peter C St John
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean P Woodworth
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jon K Magnuson
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Kristin E Burnum-Johnson
- Agile BioFoundry, Emeryville, CA, 94608, USA.,Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam M Guss
- Agile BioFoundry, Emeryville, CA, 94608, USA. .,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Agile BioFoundry, Emeryville, CA, 94608, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Agile BioFoundry, Emeryville, CA, 94608, USA.
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15
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High-Level Production of Catechol from Glucose by Engineered Escherichia coli. FERMENTATION 2022. [DOI: 10.3390/fermentation8070344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Catechol (CA) is an aromatic compound with important applications in the fine chemical and pharmaceutical fields. As an alternative strategy to petroleum-based chemical synthesis, the production of catechol by using microbial cell factories has attracted great interest. However, the toxicity of catechol to microbial cells significantly limits the efficient production of bio-based catechol via one-step fermentation. Therefore, in this study, a two-step strategy for the efficient synthesis of CA was designed. Protocatechuic acid (PCA) was first efficiently produced by the engineered Escherichia coli strain AAA01 via fermentation, and then PCA in the fermentative broth was converted into CA by the whole-cell biocatalyst AAA12 with PCA decarboxylase. By optimizing the expression of flavin isoprenyl transferases and protocatechuic acid decarboxylases, the titer of CA increased from 3.4 g/L to 15.8 g/L in 12 h through whole-cell biocatalysis, with a 365% improvement; after further optimizing the reaction conditions for whole-cell biocatalysis, the titer of CA achieved 17.7 g/L within 3 h, which is the highest titer reported so far. This work provides an effective strategy for the green biomanufacturing of toxic compounds by Escherichia coli cell factories.
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16
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Call SN, Andrews LB. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Front Genome Ed 2022; 4:892304. [PMID: 35813973 PMCID: PMC9260158 DOI: 10.3389/fgeed.2022.892304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/11/2022] [Indexed: 01/08/2023] Open
Abstract
CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) have become ubiquitous approaches to control gene expression in bacteria due to their simple design and effectiveness. By regulating transcription of a target gene(s), CRISPRi/a can dynamically engineer cellular metabolism, implement transcriptional regulation circuitry, or elucidate genotype-phenotype relationships from smaller targeted libraries up to whole genome-wide libraries. While CRISPRi/a has been primarily established in the model bacteria Escherichia coli and Bacillus subtilis, a growing numbering of studies have demonstrated the extension of these tools to other species of bacteria (here broadly referred to as non-model bacteria). In this mini-review, we discuss the challenges that contribute to the slower creation of CRISPRi/a tools in diverse, non-model bacteria and summarize the current state of these approaches across bacterial phyla. We find that despite the potential difficulties in establishing novel CRISPRi/a in non-model microbes, over 190 recent examples across eight bacterial phyla have been reported in the literature. Most studies have focused on tool development or used these CRISPRi/a approaches to interrogate gene function, with fewer examples applying CRISPRi/a gene regulation for metabolic engineering or high-throughput screens and selections. To date, most CRISPRi/a reports have been developed for common strains of non-model bacterial species, suggesting barriers remain to establish these genetic tools in undomesticated bacteria. More efficient and generalizable methods will help realize the immense potential of programmable CRISPR-based transcriptional control in diverse bacteria.
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Affiliation(s)
- Stephanie N. Call
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA, United States
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, United States
- *Correspondence: Lauren B. Andrews,
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17
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Volke DC, Martino RA, Kozaeva E, Smania AM, Nikel PI. Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing. Nat Commun 2022; 13:3026. [PMID: 35641501 PMCID: PMC9156665 DOI: 10.1038/s41467-022-30780-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
CRISPR/Cas technologies constitute a powerful tool for genome engineering, yet their use in non-traditional bacteria depends on host factors or exogenous recombinases, which limits both efficiency and throughput. Here we mitigate these practical constraints by developing a widely-applicable genome engineering toolset for Gram-negative bacteria. The challenge is addressed by tailoring a CRISPR base editor that enables single-nucleotide resolution manipulations (C·G → T·A) with >90% efficiency. Furthermore, incorporating Cas6-mediated processing of guide RNAs in a streamlined protocol for plasmid assembly supports multiplex base editing with >85% efficiency. The toolset is adopted to construct and deconstruct complex phenotypes in the soil bacterium Pseudomonas putida. Single-step engineering of an aromatic-compound production phenotype and multi-step deconstruction of the intricate redox metabolism illustrate the versatility of multiplex base editing afforded by our toolbox. Hence, this approach overcomes typical limitations of previous technologies and empowers engineering programs in Gram-negative bacteria that were out of reach thus far. Rapid engineering of bacterial genomes is a requisite for both fundamental and applied studies. Here the authors develop an enhanced, broad-host-range cytidine base editor that enables multiplexed and efficient genome editing of Gram-negative bacteria.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Román A Martino
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea M Smania
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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18
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Sarwar A, Nguyen LT, Lee EY. Bio-upgrading of ethanol to fatty acid ethyl esters by metabolic engineering of Pseudomonas putida KT2440. BIORESOURCE TECHNOLOGY 2022; 350:126899. [PMID: 35217159 DOI: 10.1016/j.biortech.2022.126899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Fatty acid ethyl esters (FAEEs) have gained increasing attention as a replacement for traditional fossil fuels in the recent years. Here, we report the efficient upgrading of ethanol to FAEEs from Pseudomonas putida KT2440, using ethanol as the sole carbon source. First, the wax synthase (WS) encoded by the atfA gene from Acinetobacter baylyi ADP1 was expressed in P. putida KT2440. Second, the flux from ethanol towards acetyl-CoA was increased by expression of the acetaldehyde dehydrogenase (ada) from Dickeya zeae. By using dodecane overlay to capture FAEEs, 1.2 g/L of FAEEs with a yield of 152.09 mg FAEEs/g ethanol were produced. Culture optimization enhanced the FAEEs contents up to 1.6 g/L in shake flask and 4.3 g/L in a fed-batch fermenter. In summary, our study provides a basis for combining the bioethanol production process with the efficient upgrading of ethanol to biodiesel.
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Affiliation(s)
- Arslan Sarwar
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Linh Thanh Nguyen
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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19
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Gómez-Álvarez H, Iturbe P, Rivero-Buceta V, Mines P, Bugg TDH, Nogales J, Díaz E. Bioconversion of lignin-derived aromatics into the building block pyridine 2,4-dicarboxylic acid by engineering recombinant Pseudomonas putida strains. BIORESOURCE TECHNOLOGY 2022; 346:126638. [PMID: 34971782 DOI: 10.1016/j.biortech.2021.126638] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
2,4 pyridine dicarboxylic acid (2,4 PDCA) is an analogue of terephthalate, and hence a target chemical in the field of bio-based plastics. Here, Pseudomonas putida KT2440 strains were engineered to efficiently drive the metabolism of lignin-derived monoaromatics towards 2,4 PDCA in a resting cells-based bioprocess that alleviates growth-coupled limitations and allows biocatalysts recycling. Native β-ketoadipate pathway was blocked by replacing protocatechuate 3,4-dioxygenase by the exogenous LigAB extradiol dioxygenase. Overexpression of pcaK encoding a transporter increased 8-fold 2,4 PDCA productivity from protocatechuate, reaching the highest value reported so far (0.58 g L-1h-1). Overexpression of the 4-hydroxybenzoate monooxygenase (pobA) speed up drastically the production of 2,4 PDCA from 4-hydroxybenzoate (0.056 g L-1h-1) or p-coumarate (0.012 g L-1h-1) achieving values 15-fold higher than those reported with Rhodococcus jostii biocatalysts. 2,4 PDCA was also bioproduced by using soda lignin as feedstock, paving the way for future polymeric lignin valorization approaches.
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Affiliation(s)
- Helena Gómez-Álvarez
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Iturbe
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain; Navarrabiomed, University of Navarra, Irunlarrea 3, 31008 Pamplona, Spain
| | - Virginia Rivero-Buceta
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Paul Mines
- Biome Bioplastics Ltd, North Road, Marchwood, Southampton SO40 4BL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Juan Nogales
- National Centre for Biotechnology, Spanish National Research Council, Darwin 3, 28049 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Eduardo Díaz
- Margarita Salas Center for Biological Research, Spanish National Research Council, Ramiro de Maeztu 9, 28040 Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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20
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Li J, Yue C, Wei W, Shang Y, Zhang P, Ye BC. Construction of a p-coumaric and ferulic acid auto-regulatory system in Pseudomonas putida KT2440 for protocatechuate production from lignin-derived aromatics. BIORESOURCE TECHNOLOGY 2022; 344:126221. [PMID: 34728357 DOI: 10.1016/j.biortech.2021.126221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Lignin is a robust and underutilized aromatic heteropolymer on earth. The effective valorization of lignin into value-added products is an attractive research topic in lignocellulosic biorefineries. However, a low bioconversion rate, high process cost, low yield, and high toxicity of substrates hinder its further applications. In this study, an auto-regulatory system was developed and identified as an effective solution to diminish these challenging bottlenecks. First, a lignin-derived standard model aromatic p-coumaric acid (p-CA)-responsive biosensor was successfully developed through a series of rational engineering approaches in Pseudomonas putida KT2440. Furthermore, an auto-regulatory system was established, which rapidly coexpressed key rate-limiting enzymes, 4-hydroxybenzoate hydroxylase, vanillate-O-demethylase, and transporter HcnK under the biosensor element, to convert the mixture of p-CA and ferulic acid into a value-added platform chemical protocatechuate with a titer of 12.7 g/L. This study demonstrated that the constructed auto-regulatory platform is effective and economical for lignin valorization.
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Affiliation(s)
- Jin Li
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Cheng Yue
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wenping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yanzhe Shang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ping Zhang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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21
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Nguyen LT, Tran MH, Lee EY. Co-upgrading of ethanol-assisted depolymerized lignin: A new biological lignin valorization approach for the production of protocatechuic acid and polyhydroxyalkanoic acid. BIORESOURCE TECHNOLOGY 2021; 338:125563. [PMID: 34284296 DOI: 10.1016/j.biortech.2021.125563] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
This study presents a promising biological co-upgrading of ethanol-assisted depolymerized lignin (EDL) into protocatechuic acid (PCA) and polyhydroxyalkanoic acid (PHA) without any separation process. A depolymerized alkali lignin containing various G-lignin-type monomers at a concentration of 77 mg/mL was used for co-upgrading. An engineered Pseudomonas putida KT2440 strain was constructed by knocking out the protocatechuate 3, 4-dioxygenase, expression of the formaldehyde utilization pathway, and the expression of aldehyde dehydrogenase to enhance the efficiency of the ethanol utilization pathway. The growth and production of value-added bioproducts have been promoted by the utilization of formaldehyde, resulted in 6.73 ± 0.26 mg/L of PCA with a 17.5% (w/w) yield of total lignin monomers, and 303.66 ± 26.75 mg/L of PHA with 21.26% (w/w) of dry cell weight from 0.5 mL EDL. Moreover, the ethanol solvent used for lignin depolymerization was also utilized along with depolymerized lignin for co-upgrading to value-added products.
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Affiliation(s)
- Linh Thanh Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - My Ha Tran
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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22
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Phale PS, Mohapatra B, Malhotra H, Shah BA. Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation. Environ Microbiol 2021; 24:2797-2816. [PMID: 34347343 DOI: 10.1111/1462-2920.15694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
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23
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Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways. Essays Biochem 2021; 65:319-336. [PMID: 34223620 PMCID: PMC8314020 DOI: 10.1042/ebc20200173] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/01/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.
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