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Zhu J, Wang X, Zhao J, Ji F, Zeng J, Wei Y, Xu L, Dong G, Ma X, Wang C. Genomic characterization and related functional genes of γ- poly glutamic acid producing Bacillus subtilis. BMC Microbiol 2024; 24:125. [PMID: 38622505 PMCID: PMC11017564 DOI: 10.1186/s12866-024-03262-z] [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] [Accepted: 03/15/2024] [Indexed: 04/17/2024] Open
Abstract
γ- poly glutamic acid (γ-PGA), a high molecular weight polymer, is synthesized by microorganisms and secreted into the extracellular space. Due to its excellent performance, γ-PGA has been widely used in various fields, including food, biomedical and environmental fields. In this study, we screened natto samples for two strains of Bacillus subtilis N3378-2at and N3378-3At that produce γ-PGA. We then identified the γ-PGA synthetase gene cluster (PgsB, PgsC, PgsA, YwtC and PgdS), glutamate racemase RacE, phage-derived γ-PGA hydrolase (PghB and PghC) and exo-γ-glutamyl peptidase (GGT) from the genome of these strains. Based on these γ-PGA-related protein sequences from isolated Bacillus subtilis and 181 B. subtilis obtained from GenBank, we carried out genotyping analysis and classified them into types 1-5. Since we found B. amyloliquefaciens LL3 can produce γ-PGA, we obtained the B. velezensis and B. amyloliquefaciens strains from GenBank and classified them into types 6 and 7 based on LL3. Finally, we constructed evolutionary trees for these protein sequences. This study analyzed the distribution of γ-PGA-related protein sequences in the genomes of B. subtilis, B. velezensis and B. amyloliquefaciens strains, then the evolutionary diversity of these protein sequences was analyzed, which provided novel information for the development and utilization of γ-PGA-producing strains.
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Affiliation(s)
- Jiayue Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xue Wang
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jianan Zhao
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Fang Ji
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Jun Zeng
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yanwen Wei
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - LiLi Xu
- Union Biology (Shanghai) Co., Ltd, Shanghai, 201100, China
| | - Guoying Dong
- College of Global Change and Earth System Science, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Chengmin Wang
- Guangdong key Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China.
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Qiu Y, Xu D, Lei P, Li S, Xu H. Engineering functional homopolymeric amino acids: from biosynthesis to design. Trends Biotechnol 2024; 42:310-325. [PMID: 37775417 DOI: 10.1016/j.tibtech.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/08/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023]
Abstract
Homopolymeric amino acids (HPAs) are a class of microbial polymers that can be classified into two categories: anionic and cationic HPAs. Notable examples include γ-poly-glutamic acid (γ-PGA) and ε-poly-L-lysine (ε-PL) that have wide-ranging applications in medicine, food, and agriculture. The primary method of manufacture is through microbial synthesis. In recent decades significant efforts have been made to enhance the production of HPAs, specifically focusing on γ-PGA and ε-PL. We comprehensively review current advances in understanding the synthetic mechanisms as well as metabolic engineering and fermentation process techniques to improve the production of HPAs. In addition, we discuss the major challenges and solutions associated with desired structure regulation of HPAs and the development of novel structures.
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Affiliation(s)
- Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Delei Xu
- College of Biological and Food Engineering, Changshu Institute of Technology, 99 South Third Ring Road, Changshu 215500, PR China
| | - Peng Lei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China.
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, PR China; Nanjing Shineking Biotech Co. Ltd., Nanjing 210061, PR China.
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Xu G, Wang J, Shen J, Zhu Y, Liu W, Chen Y, Zha J, Zhang X, Zhang X, Shi J, Koffas MAG, Xu Z. Enhanced poly-γ-glutamic acid synthesis in Corynebacterium glutamicum by reconstituting PgsBCA complex and fermentation optimization. Metab Eng 2024; 81:238-248. [PMID: 38160746 DOI: 10.1016/j.ymben.2023.12.008] [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: 07/07/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Previously, a novel Corynebacterium glutamicum strain for the de novo biosynthesis of tailored poly-γ-glutamic acid (γ-PGA) has been constructed by our group. The strain was based on the γ-PGA synthetase complex, PgsBCA, which is the only polyprotein complex responsible for γ-PGA synthesis in Bacillus spp. In the present study, PgsBCA was reconstituted and overexpressed in C. glutamicum to further enhance γ-PGA synthesis. First, we confirmed that all the components (PgsB, PgsC, and PgsA) of γ-PGA synthetase derived from B. licheniformis are necessary for γ-PGA synthesis, and γ-PGA was detected only when PgsB, PgsC, and PgsA were expressed in combination in C. glutamicum. Next, the expression level of each pgsB, pgsC, and pgsA was tuned in order to explore the effect of expression of each of the γ-PGA synthetase subunits on γ-PGA production. Results showed that increasing the transcription levels of pgsB or pgsC and maintaining a medium-level transcription level of pgsA led to 35.44% and 76.53% increase in γ-PGA yield (γ-PGA yield-to-biomass), respectively. Notably, the expression level of pgsC had the greatest influence (accounting for 68.24%) on γ-PGA synthesis, followed by pgsB. Next, genes encoding for PgsC from four different sources (Bacillus subtilis, Bacillus anthracis, Bacillus methylotrophicus, and Bacillus amyloliquefaciens) were tested in order to identify the influence of PgsC-encoding orthologues on γ-PGA production, but results showed that in all cases the synthesis of γ-PGA was significantly inhibited. Similarly, we also explored the influence of gene orthologues encoding for PgsB on γ-PGA production, and found that the titer increased to 17.14 ± 0.62 g/L from 8.24 ± 0.10 g/L when PgsB derived from B. methylotrophicus replaced PgsB alone in PgsBCA from B. licheniformis. The resulting strain was chosen for further optimization, and we achieved a γ-PGA titer of 38.26 g/L in a 5 L fermentor by optimizing dissolved oxygen level. Subsequently, by supplementing glucose, γ-PGA titer increased to 50.2 g/L at 48 h. To the best of our knowledge, this study achieved the highest titer for de novo production of γ-PGA from glucose, without addition of L-glutamic acid, resulting in a novel strategy for enhancing γ-PGA production.
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Affiliation(s)
- Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China
| | - Jiyue Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Jiancheng Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China
| | - Yaxin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Wanjing Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China
| | - Yuhang Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China
| | - Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi, 710021, China
| | - Xiaomei Zhang
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China
| | - Xiaojuan Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Jinsong Shi
- Laboratory of Pharmaceutical Engineering, School of Life Science and Health Engineering, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - Zhenghong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214122, China; Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China; Yixing Institute of Food and Biotechnology, Yixing, 214200, China.
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Wei X, Chen Z, Liu A, Yang L, Xu Y, Cao M, He N. Advanced strategies for metabolic engineering of Bacillus to produce extracellular polymeric substances. Biotechnol Adv 2023; 67:108199. [PMID: 37330153 DOI: 10.1016/j.biotechadv.2023.108199] [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: 03/05/2023] [Revised: 05/24/2023] [Accepted: 06/11/2023] [Indexed: 06/19/2023]
Abstract
Extracellular polymeric substances are mainly synthesized via a variety of biosynthetic pathways in bacteria. Bacilli-sourced extracellular polymeric substances, such as exopolysaccharides (EPS) and poly-γ-glutamic acid (γ-PGA), can serve as active ingredients and hydrogels, and have other important industrial applications. However, the functional diversity and widespread applications of these extracellular polymeric substances, are hampered by their low yields and high costs. Biosynthesis of extracellular polymeric substances is very complex in Bacillus, and there is no detailed elucidation of the reactions and regulations among various metabolic pathways. Therefore, a better understanding of the metabolic mechanisms is required to broaden the functions and increase the yield of extracellular polymeric substances. This review systematically summarizes the biosynthesis and metabolic mechanisms of extracellular polymeric substances in Bacillus, providing an in-depth understanding of the relationships between EPS and γ-PGA synthesis. This review provides a better clarification of Bacillus metabolic mechanisms during extracellular polymeric substance secretion and thus benefits their application and commercialization.
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Affiliation(s)
- Xiaoyu Wei
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Zhen Chen
- College of Life Science, Xinyang Normal University, Xinyang 464000, China.
| | - Ailing Liu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Lijie Yang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Yiyuan Xu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China; Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China.
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen 361005, China.
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Motta Nascimento B, Nair NU. Characterization of a membrane enzymatic complex for heterologous production of poly-γ-glutamate in E. coli. Metab Eng Commun 2020; 11:e00144. [PMID: 32963960 PMCID: PMC7490850 DOI: 10.1016/j.mec.2020.e00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/10/2020] [Accepted: 08/20/2020] [Indexed: 11/06/2022] Open
Abstract
Poly-γ-glutamic acid (PGA) produced by many Bacillus species is a polymer with many distinct and desirable characteristics. However, the multi-subunit enzymatic complex responsible for its synthesis, PGA Synthetase (PGS), has not been well characterized yet, in native nor in recombinant contexts. Elucidating structural and functional properties are crucial for future engineering efforts aimed at altering the catalytic properties of this enzyme. This study focuses on expressing the enzyme heterologously in the Escherichia coli membrane and characterizing localization, orientation, and activity of this heterooligomeric enzyme complex. In E. coli, we were able to produce high molecular weight PGA polymers with minimal degradation at titers of approximately 13 mg/L in deep-well microtiter batch cultures. Using fusion proteins, we observed, for the first time, the association and orientation of the different subunits with the inner cell membrane. These results provide fundamental structural information on this poorly studied enzyme complex and will aid future fundamental studies and engineering efforts. Successfully expressed active poly-γ-glutamate synthetase (PGS) in E. coli. Confirmed PGS localization at inner membrane of E. coli. Elucidated topology of PGS components in E. coli membrane. Culture and expression in microplates might allow future screening of a high number of samples. Faster production of poly-γ-glutamate in E. coli supernatant compared to B. subtilis.
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Affiliation(s)
- Bruno Motta Nascimento
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA
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