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Lu J, Lv X, Yu W, Zhang J, Lu J, Liu Y, Li J, Du G, Chen J, Liu L. Reshaping Phosphatase Substrate Preference for Controlled Biosynthesis Using a "Design-Build-Test-Learn" Framework. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309852. [PMID: 38504470 PMCID: PMC11165480 DOI: 10.1002/advs.202309852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Biosynthesis is the application of enzymes in microbial cell factories and has emerged as a promising alternative to chemical synthesis. However, natural enzymes with limited catalytic performance often need to be engineered to meet specific needs through a time-consuming trial-and-error process. This study presents a quantum mechanics (QM)-incorporated design-build-test-learn (DBTL) framework to rationally design phosphatase BT4131, an enzyme with an ambiguous substrate spectrum involved in N-acetylglucosamine (GlcNAc) biosynthesis. First, mutant M1 (L129Q) is designed using force field-based methods, resulting in a 1.4-fold increase in substrate preference (kcat/Km) toward GlcNAc-6-phosphate (GlcNAc6P). QM calculations indicate that the shift in substrate preference is caused by a 13.59 kcal mol-1 reduction in activation energy. Furthermore, an iterative computer-aided design is conducted to stabilize the transition state. As a result, mutant M4 (I49Q/L129Q/G172L) with a 9.5-fold increase in kcat-GlcNAc6P/Km-GlcNAc6P and a 59% decrease in kcat-Glc6P/Km-Glc6P is highly desirable compared to the wild type in the GlcNAc-producing chassis. The GlcNAc titer increases to 217.3 g L-1 with a yield of 0.597 g (g glucose)-1 in a 50-L bioreactor, representing the highest reported level. Collectively, this DBTL framework provides an easy yet fascinating approach to the rational design of enzymes for industrially viable biocatalysts.
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Affiliation(s)
- Jiangong Lu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jianing Zhang
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jianxing Lu
- Shandong Runde Biotechnology co., LTDTaian271200China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jianghua Li
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jian Chen
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
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Hu Q, Sun S, Zhang Z, Liu W, Yi X, He H, Scrutton NS, Chen GQ. Ectoine hyperproduction by engineered Halomonas bluephagenesis. Metab Eng 2024; 82:238-249. [PMID: 38401747 DOI: 10.1016/j.ymben.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Ectoine, a crucial osmoprotectant for salt adaptation in halophiles, has gained growing interest in cosmetics and medical industries. However, its production remains challenged by stringent fermentation process in model microorganisms and low production level in its native producers. Here, we systematically engineered the native ectoine producer Halomonas bluephagenesis for ectoine production by overexpressing ectABC operon, increasing precursors availability, enhancing product transport system and optimizing its growth medium. The final engineered H. bluephagenesis produced 85 g/L ectoine in 52 h under open unsterile incubation in a 7 L bioreactor in the absence of plasmid, antibiotic or inducer. Furthermore, it was successfully demonstrated the feasibility of decoupling salt concentration with ectoine synthesis and co-production with bioplastic P(3HB-co-4HB) by the engineered H. bluephagenesis. The unsterile fermentation process and significantly increased ectoine titer indicate that H. bluephagenesis as the chassis of Next-Generation Industrial Biotechnology (NGIB), is promising for the biomanufacturing of not only intracellular bioplastic PHA but also small molecular compound such as ectoine.
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Affiliation(s)
- Qitiao Hu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Simian Sun
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhongnan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wei Liu
- PhaBuilder Biotechnology Co. Ltd., Shunyi District, Beijing 101309, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hongtao He
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Manchester Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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Feng Y, Qiu M, Shao L, Jiang Y, Zhang W, Jiang W, Xin F, Jiang M. Strategies for the biological production of ectoine by using different chassis strains. Biotechnol Adv 2024; 70:108306. [PMID: 38157997 DOI: 10.1016/j.biotechadv.2023.108306] [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: 09/27/2023] [Revised: 11/27/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
As an amino acid derivative and a typical compatible solute, ectoine can assist microorganisms in resisting high osmotic pressure. Own to its long-term moisturizing effects, ectoine shows extensive applications in cosmetics, medicine and other fields. With the rapid development of synthetic biology and fermentation engineering, many biological strategies have been developed to improve the ectoine production and simplify the production process. Currently, the microbial fermentation has been widely used for large scaling ectoine production. Accordingly, this review will introduce the metabolic pathway for ectoine synthesis and also comprehensively evaluate both wild-type and genetically modified strains for ectoine production. Furthermore, process parameters affecting the ectoine production efficiency and adoption of low cost substrates will be evaluated. Lastly, future prospects on the improvement of ectoine production will be proposed.
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Affiliation(s)
- Yifan Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Lei Shao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211816, PR China
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