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Han S, Qin M, Wang Y, Gao C, Niu W, Han J, Wang H, Li Y. Quorum sensing signal autoinducer-2 promotes hydrogen peroxide degradation in water by Gram-positive bacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133582. [PMID: 38280328 DOI: 10.1016/j.jhazmat.2024.133582] [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: 09/10/2023] [Revised: 12/27/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
Hydrogen peroxide is widely used to remedy bacterial and parasitic infections, but its excessive use will cause severe damage to aquatic animals. Moreover, there is no safe, efficient and low-cost method to degrade residual hydrogen peroxide in water. Here we developed a hydrogen peroxide removal mechanism by which autoinducer-2 (AI-2), a quorum sensing signal molecule that can promote the hydrogen peroxide degradation by Gram-positive bacteria. Here, we investigated the promotion effect of AI-2 on hydrogen peroxide degradation by Deinococcus sp. Y35 and the response of the antioxidant system. We further sought to understand the key mechanism underlying the promotion effect of AI-2 on hydrogen peroxide degradation is that, AI-2 contributed to the resistance of strain Y35 to oxidative stress induced by hydrogen peroxide, and altered membrane permeability of strain Y35 that allowed more hydrogen peroxide to enter bacterial cells and be degraded. Additionally, AI-2 can also encourage multiple Gram-positive bacteria to degrade hydrogen peroxide. Accordingly, our study serves as a reference for the regulation mechanism of the signal molecule AI-2 and provides the development of new strategies for hydrogen peroxide degradation.
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Affiliation(s)
- Shuo Han
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Mengyuan Qin
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Yuqi Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Chao Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Wenfang Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China
| | - Jingjing Han
- College of Nursing and Health, Qingdao Huanghai University, Qingdao 266299, China
| | - Hailei Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China; Advanced Environmental Biotechnology Center, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Yi Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, Xinxiang 453007, China.
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Xie Y, Wu X, Fu C, Duan H, Shi J, Blamey JM, Sun J. Rational Design of an α-1,3-Fucosyltransferase for the Biosynthesis of 3-Fucosyllactose in Bacillus subtilis ATCC 6051a via De Novo GDP-l-Fucose Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1178-1189. [PMID: 38183288 DOI: 10.1021/acs.jafc.3c07604] [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: 01/08/2024]
Abstract
3-Fucosyllactose (3-FL) is an important oligosaccharide and nutrient in breast milk that can be synthesized in microbial cells by α-1,3-fucosyltransferase (α-1,3-FucT) using guanosine 5'-diphosphate (GDP)-l-fucose and lactose as substrates. However, the catalytic efficiency of known α-1,3-FucTs from various sources was limited due to their low solubility. To enhance the microbial production of 3-FL, the efficiencies of α-1,3-FucTs were evaluated and in Bacillus subtilis (B. subtilis) chassis cells that had been endowed with a heterologous synthetic pathway for GDP-l-fucose, revealing that the activity of FucTa from Helicobacter pylori (H. pylori) was higher than that of any of other reported homologues. To further improve the catalytic performance of FucTa, a rational design approach was employed, involving intracellular evaluation of the mutational sites of M32 obtained through directed evolution, analysis of the ligand binding site diversity, and protein structure simulation. Among the obtained variants, the FucTa-Y218 K variant exhibited the highest 3-FL yield, reaching 7.55 g/L in the shake flask growth experiment, which was 3.48-fold higher than that achieved by the wild-type enzyme. Subsequent fermentation optimization in a 5 L bioreactor resulted in a remarkable 3-FL production of 36.98 g/L, highlighting the great prospects of the designed enzyme and the strains for industrial applications.
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Affiliation(s)
- Yukang Xie
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinying Wu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Cong Fu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Duan
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas, 2280 Ñuñoa, Santiago, Chile
- Facultad de Química Y Biología, Universidad de Santiago de Chile, 3363 Alameda, Estación Central, Santiago, Chile
| | - Junsong Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
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Cheng YY, Chen Z, Cao X, Ross TD, Falbel TG, Burton BM, Venturelli OS. Programming bacteria for multiplexed DNA detection. Nat Commun 2023; 14:2001. [PMID: 37037805 PMCID: PMC10086068 DOI: 10.1038/s41467-023-37582-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023] Open
Abstract
DNA is a universal and programmable signal of living organisms. Here we develop cell-based DNA sensors by engineering the naturally competent bacterium Bacillus subtilis (B. subtilis) to detect specific DNA sequences in the environment. The DNA sensor strains can identify diverse bacterial species including major human pathogens with high specificity. Multiplexed detection of genomic DNA from different species in complex samples can be achieved by coupling the sensing mechanism to orthogonal fluorescent reporters. We also demonstrate that the DNA sensors can detect the presence of species in the complex samples without requiring DNA extraction. The modularity of the living cell-based DNA-sensing mechanism and simple detection procedure could enable programmable DNA sensing for a wide range of applications.
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Affiliation(s)
- Yu-Yu Cheng
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhengyi Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyun Cao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Tyler D Ross
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Tanya G Falbel
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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Fu C, Xu X, Xie Y, Liu Y, Liu M, Chen A, Blamey JM, Shi J, Zhao S, Sun J. Rational design of GDP‑D‑mannose mannosyl hydrolase for microbial L‑fucose production. Microb Cell Fact 2023; 22:56. [PMID: 36964553 PMCID: PMC10037897 DOI: 10.1186/s12934-023-02060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/11/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND L‑Fucose is a rare sugar that has beneficial biological activities, and its industrial production is mainly achieved with brown algae through acidic/enzymatic fucoidan hydrolysis and a cumbersome purification process. Fucoidan is synthesized through the condensation of a key substance, guanosine 5'‑diphosphate (GDP)‑L‑fucose. Therefore, a more direct approach for biomanufacturing L‑fucose could be the enzymatic degradation of GDP‑L‑fucose. However, no native enzyme is known to efficiently catalyze this reaction. Therefore, it would be a feasible solution to engineering an enzyme with similar function to hydrolyze GDP‑L‑fucose. RESULTS Herein, we constructed a de novo L‑fucose synthetic route in Bacillus subtilis by introducing heterologous GDP‑L‑fucose synthesis pathway and engineering GDP‑mannose mannosyl hydrolase (WcaH). WcaH displays a high binding affinity but low catalytic activity for GDP‑L‑fucose, therefore, a substrate simulation‑based structural analysis of the catalytic center was employed for the rational design and mutagenesis of selected positions on WcaH to enhance its GDP‑L‑fucose‑splitting efficiency. Enzyme mutants were evaluated in vivo by inserting them into an artificial metabolic pathway that enabled B. subtilis to yield L‑fucose. WcaHR36Y/N38R was found to produce 1.6 g/L L‑fucose during shake‑flask growth, which was 67.3% higher than that achieved by wild‑type WcaH. The accumulated L‑fucose concentration in a 5 L bioreactor reached 6.4 g/L. CONCLUSIONS In this study, we established a novel microbial engineering platform for the fermentation production of L‑fucose. Additionally, we found an efficient GDP‑mannose mannosyl hydrolase mutant for L‑fucose biosynthesis that directly hydrolyzes GDP‑L‑fucose. The engineered strain system established in this study is expected to provide new solutions for L‑fucose or its high value‑added derivatives production.
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Affiliation(s)
- Cong Fu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuexia Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Yukang Xie
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufei Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ai Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jenny M Blamey
- Fundación Biociencia, José Domingo Cañas, 2280, Ñuñoa, Santiago, Chile
- Facultad de Química Y Biología, Universidad de Santiago de Chile, 3363, Alameda, Estación Central, Santiago, Chile
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
| | - Junsong Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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