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Li D, Wang X, Huo L, Zeng W, Li J, Zhou J. Computer-Aided Semi-Rational Design to Enhance the Activity of l-Sorbosone Dehydrogenase from Gluconobacter oxidans WSH-004. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10995-11001. [PMID: 38701424 DOI: 10.1021/acs.jafc.3c08365] [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: 05/05/2024]
Abstract
The titer of the microbial fermentation products can be increased by enzyme engineering. l-Sorbosone dehydrogenase (SNDH) is a key enzyme in the production of 2-keto-l-gulonic acid (2-KLG), which is the precursor of vitamin C. Enhancing the activity of SNDH may have a positive impact on 2-KLG production. In this study, a computer-aided semirational design of SNDH was conducted. Based on the analysis of SNDH's substrate pocket and multiple sequence alignment, three modification strategies were established: (1) expanding the entrance of SNDH's substrate pocket, (2) engineering the residues within the substrate pocket, and (3) enhancing the electron transfer of SNDH. Finally, mutants S453A, L460V, and E471D were obtained, whose specific activity was increased by 20, 100, and 10%, respectively. In addition, the ability of Gluconobacter oxidans WSH-004 to synthesize 2-KLG was improved by eliminating H2O2. This study provides mutant enzymes and metabolic engineering strategies for the microbial-fermentation-based production of 2-KLG.
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Affiliation(s)
- Dong Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lin Huo
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
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Liu Q, Liu M, Chen W, Yuan H, Jiang Y, Huang D, Liu H, Wang T. Recent Advances in 2-Keto-l-gulonic Acid Production Using Mixed-Culture Fermentation and Future Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1419-1428. [PMID: 38206567 DOI: 10.1021/acs.jafc.3c08189] [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: 01/12/2024]
Abstract
Vitamin C, also known as ascorbic acid, is an essential vitamin that cannot be synthesized by the human body and must be acquired through our diet. At present, the precursor of vitamin C, 2-keto-l-gulonic acid (2-KGA), is typically produced via a two-step fermentation process utilizing three bacterial strains. The second step of this traditional two-step fermentation method involves mixed-culture fermentation employing 2-KGA-producing bacteria (Ketogulonicigenium vulgare) along with associated bacteria. Because K. vulgare has defects in various metabolic pathways, associated bacteria are needed to provide key substances to promote K. vulgare growth and 2-KGA production. Unlike previous reviews where the main focus was the interaction between associated bacteria and K. vulgare, this Review presents the latest scientific research from the perspective of the metabolic pathways associated with 2-KGA production by K. vulgare and the mechanism underlying the interaction between K. vulgare and the associated bacteria. In addition, the dehydrogenases that are responsible for 2-KGA production, the 2-KGA synthesis pathway, strategies for simplifying 2-KGA production via a one-step fermentation route, and, finally, future prospects and research goals in vitamin C production are also presented.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Meng Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Wenhu Chen
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Yi Jiang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Di Huang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Hongling Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
| | - Tengfei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
- Key Laboratory of Shandong Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, Shandong, People's Republic of China
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Li F, Wang CY, Wu YC, Zhang MY, Wang YJ, Zhou XY, Zhang YX. Enhancing the biosynthesis of 2-keto-L-gulonic acid through multi-strategy metabolic engineering in Pseudomonas putida KT2440. BIORESOURCE TECHNOLOGY 2024; 392:130014. [PMID: 37956951 DOI: 10.1016/j.biortech.2023.130014] [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: 10/11/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
2-KGA, a precursor for the synthesis of Vitamin C, is currently produced in China utilizing the "two-step fermentation" technique. Nevertheless, this method exhibits many inherent constraints. This study presents a comprehensive metabolic engineering strategy to establish and optimize a one-step 2-KGA fermentation process from D-sorbitol in Pseudomonas putida KT2440. In general, the endogenous promoters were screened to identify promoter P1 for subsequent heterologous gene expression in KT2440. Following the screening and confirmation of suitable heterologous gene elements such as sldh, sdh, cytc551, pqqAB, and irrE, genetic recombination was performed in KT2440. In comparison to the initial achievement of expressing only sldh and sdh in KT2440, a yield of merely 0.42 g/L was obtained. However, by implementing four metabolic engineering strategies, the recombinant strain KT20 exhibited a significant enhancement in its ability to produce 2-KGA with a remarkable yield of up to 6.5 g/L - representing an impressive 15.48-fold improvement.
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Affiliation(s)
- Fan Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Ying-Cai Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yi-Jin Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xun-Yong Zhou
- Sinobiotech (Shenzhen) Limited Company, Shenzhen 518001, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
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Li D, Wang X, Qin Z, Yu S, Chen J, Zhou J. Combined engineering of l-sorbose dehydrogenase and fermentation optimization to increase 2-keto-l-gulonic acid production in Escherichia coli. BIORESOURCE TECHNOLOGY 2023; 372:128672. [PMID: 36702324 DOI: 10.1016/j.biortech.2023.128672] [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: 12/20/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
One-step fermentation to produce 2-keto-l-gulonic acid (2-KLG), the precursor of vitamin C, is a long-term goal. Improvement of the enzyme's activity through engineering could benefit 2-KLG production. This study aimed to conduct a semi-rational design of l-sorbose dehydrogenase (SDH) through structure-directed, to screen mutants that could enhance the 2-KLG titer. First, the predicted structure of SDH was obtained using AlphaFold2. The key mutation sites in the substrate pocket were identified by Ala scanning. Subsequently, the mutant V336I/V368A was obtained by iterative saturation mutagenesis, which increased the yield of 2-KLG 1.9-fold. Finally, 5.03 g/L of 2-KLG was obtained by a two-stage temperature control fermentation method, and the conversion rate was 50%. Furthermore, experiments showed that knockdown of the l-sorbose-associated phosphotransferase system delays 2-KLG production. The results show that the production of 2-KLG was effectively increased through a combination of SDH engineering and fermentation optimization.
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Affiliation(s)
- Dong Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xinglong Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Zhijie Qin
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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5
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Wang CY, Liu LC, Wu YC, Zhang YX. Identification and Validation of Four Novel Promoters for Gene Engineering with Broad Suitability across Species. J Microbiol Biotechnol 2021; 31:1154-1162. [PMID: 34226414 PMCID: PMC9706022 DOI: 10.4014/jmb.2103.03049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/15/2022]
Abstract
The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (Pk.rtufB, Pk.r1, Pk.r2, and Pk.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with Pk.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by Pk.r1 and Pk.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.
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Affiliation(s)
- Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Li-Cheng Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Ying-Cai Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, P.R. China,Corresponding author Phone: +86-024-43520921 E-mail:
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6
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Zhou M, Bi Y, Ding M, Yuan Y. One-Step Biosynthesis of Vitamin C in Saccharomyces cerevisiae. Front Microbiol 2021; 12:643472. [PMID: 33717042 PMCID: PMC7947327 DOI: 10.3389/fmicb.2021.643472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Vitamin C (VC) is comprehensively applied in foods, cosmetics, pharmaceuticals, and especially clinical medicine. Nowadays, the industrial production of VC mainly relies on the classic two-step fermentation route, and researchers have explored the way for one-step fermentation of VC in recent years. In this study, a VC biosynthesis pathway that directly produced VC from glucose was reconstructed in Saccharomyces cerevisiae, and the protein engineering and metabolic engineering strategies were adopted to improve it. First, five exogenous modules from Arabidopsis were introduced into the chassis cells by synthetic biology approaches to obtain the strain YLAA harboring VC biosynthesis. In addition, L-galactose dehydrogenase (L-GalDH) and L-galactono-1,4-lactone dehydrogenase (L-GLDH) were fused and expressed in S. cerevisiae cells for the first time, which increased the intracellular VC accumulation by 2.78-fold, reaching 9.97 ± 0.09 mg/L. Through copy number engineering, it was further confirmed that the last step catalyzed by L-GLDH is the rate-limiting step. GDP-L-galactose phosphorylase (GPP) encoded by vtc2 is another rate-limiting enzyme confirmed by GAL1p overexpression results. Finally, by balancing gene expression and cell growth, the highest production strain with overexpressing vtc2 by multicopy plasmids was constructed. The VC accumulation reached 24.94 ± 1.16 mg/L, which was currently the highest production from glucose in S. cerevisiae. The production of the recombinant strain reached nearly 44 mg/L with the exogenous addition of L-galactose or glutathione. The results further emphasized the importance of the step catalyzed by GPP. The investigation provided experience for the efficient biosynthesis of VC and the determination of rate-limiting steps.
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Affiliation(s)
- Mengyu Zhou
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yanhui Bi
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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7
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Ma Q, Gao X, Tu L, Han Q, Zhang X, Guo Y, Yan W, Shen Y, Wang M. Enhanced Chitin Deacetylase Production Ability of Rhodococcus equi CGMCC14861 by Co-culture Fermentation With Staphylococcus sp. MC7. Front Microbiol 2020; 11:592477. [PMID: 33362742 PMCID: PMC7758288 DOI: 10.3389/fmicb.2020.592477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Chitin deacetylase (CDA) can hydrolyze the acetamido group of chitin polymers and its deacetylated derivatives to produce chitosan, an industrially important biopolymer. Compared with traditional chemical methods, biocatalysis by CDA is more environment-friendly and easy to control. However, most reported CDA-producing microbial strains show low CDA producing capabilities. Thus, the enhancement of CDA production has always been a challenge. In this study, we report co-culture fermentation to significantly promote the CDA production of Rhodococcus equi CGMCC14861 chitin deacetylase (ReCDA). Due to co-culture fermentation with Staphylococcus sp. MC7, ReCDA yield increased to 21.74 times that of pure culture of R. equi. Additionally, the enhancement was demonstrated to be cell-independent by adding cell-free extracts and the filtrate obtained by 10 kDa ultrafiltration of Staphylococcus sp. MC7. By preliminary characterization, we found extracellular, thermosensitive signal substances produced by Staphylococcus that were less than 10 kDa. We investigated the mechanism of promotion of ReCDA production by transcriptomic analysis. The data showed that 328 genes were upregulated and 1,258 genes were downregulated. The transcription level of the gene encoding ReCDA increased 2.3-fold. These findings provide new insights into the research of co-culture fermentation for the production of CDA and quorum sensing regulation.
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Affiliation(s)
- Qinyuan Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Xiuzhen Gao
- School of Life Sciences, Shandong University of Technology, Zibo, China
| | - Linna Tu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qi Han
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Xing Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yabo Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wenqin Yan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yanbing Shen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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8
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Zeng W, Wang P, Li N, Li J, Chen J, Zhou J. Production of 2-keto-L-gulonic acid by metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2020; 318:124069. [PMID: 32916460 DOI: 10.1016/j.biortech.2020.124069] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
The 2-keto-L-gulonic acid (2-KLG) is the direct precursor for industrial vitamin C production. The main biosynthetic method for 2-KLG production is the classical two-step fermentation route. However, disadvantages of this method are emerging, including high consumption of energy, difficulties in strain screening, complex operation, and poor stability. In this study, five recombinant Escherichia coli strains overexpressing different sorbose/sorbosone dehydrogenases were constructed and used for 2-KLG production. By optimizing catalytic conditions and further expressing pyrroloquinoline quinone in the recombinant strain, the titer of 2-KLG reached 72.4 g/L, with a conversion ratio from L-sorbose of 71.2% in a 5-L bioreactor. To achieve direct biosynthesis of 2-KLG from D-sorbitol, a co-culture system consisting of Gluconobacter oxydans and recombinant E. coli was designed. With this co-culture system, 16.8 g/L of 2-KLG was harvested, with a conversion ratio from D-sorbitol of 33.6%. The approaches developed here provide alternative routes for the efficient biosynthesis of 2-KLG.
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Affiliation(s)
- Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Panpan Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ning Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jianghua Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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9
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Gao L, Wu X, Xia X, Jin Z. Fine-tuning ethanol oxidation pathway enzymes and cofactor PQQ coordinates the conflict between fitness and acetic acid production by Acetobacter pasteurianus. Microb Biotechnol 2020; 14:643-655. [PMID: 33174682 PMCID: PMC7936290 DOI: 10.1111/1751-7915.13703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/23/2020] [Accepted: 10/22/2020] [Indexed: 12/28/2022] Open
Abstract
The very high concentrations required for industrial production of free acetic acid create toxicity and low pH values, which usually conflict with the host cell growth, leading to a poor productivity. Achieving a balance between cell fitness and product synthesis is the key challenge to improving acetic acid production efficiency in metabolic engineering. Here, we show that the synergistic regulation of alcohol/aldehyde dehydrogenase expression and cofactor PQQ level could not only efficiently relieve conflict between increased acetic acid production and compromised cell fitness, but also greatly enhance acetic acid tolerance of Acetobacter pasteurianus to a high initial concentration (3% v/v) of acetic acid. Combinatorial expression of adhA and pqqABCDE greatly shortens the duration of starting‐up process from 116 to 99 h, leading to a yield of 69 g l‐1 acetic acid in semi‐continuous fermentation. As a final result, average acetic acid productivity has been raised to 0.99 g l‐1 h‐1, which was 32% higher than the parental A. pasteurianus. This study is of great significance for decreasing cost of semi‐continuous fermentation for producing high‐strength acetic acid industrially. We envisioned that this strategy will be useful for production of many other desired organic acids, especially those involving cofactor reactions.
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Affiliation(s)
- Ling Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.,State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaole Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
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10
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Enhanced 2-keto-L-gulonic acid production by a mixed culture of Ketogulonicigenium vulgare and Bacillus megaterium using three-stage temperature control strategy. Braz J Microbiol 2020; 52:257-265. [PMID: 33145708 DOI: 10.1007/s42770-020-00396-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
As a key precursor of vitamin C, 2-keto-L-gulonic acid (2-KLG) was mainly produced from L-sorbose by mixed fermentation of Ketogulonicigenium vulgare and a helper strain (Bacillus spp.) with a low conversion rate for decades. The aim of this study was to enhance the 2-KLG production by co-culturing K. vulgare and Bacillus megaterium using three-stage temperature control (TSTC) strategy. By investigating the temperature effect on the 2-KLG fermentation, the optimum temperatures for the growths of K. vulgare and B. megaterium were 32 °C and 29 °C, respectively, while the optimum temperature for 2-KLG production was 35 °C. We developed a TSTC process: the temperature was kept at 32 °C during the first 16 h of fermentation, then decreased to 29 °C for the following 14 h, and maintained at 35 °C to the end of fermentation. By using this new process, the productivity and yield of 2-KLG from L-sorbose were obtained at 2.19 ± 0.19 g/L/h and 92.91 ± 1.02 g/L in 20-L fermentors for 5 batches, respectively, which were 22.35% and 6.02% higher than that of the control treatment (the single temperature of 29 °C). The increased cell density of K. vulgare during the exponential phase and the enhanced SDH activity (increased by 25.18% at 36 h, 17.14% at 44 h) in the production stage might be the reasons for enhanced 2-KLG conversion rate and yield. Our results demonstrated the feasibility of the TSTC strategy for 2-KLG production.
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11
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Liu D, Ke X, Hu ZC, Zheng YG. Combinational expression of D-sorbitol dehydrogenase and pyrroloquinoline quinone increases 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose production by Gluconobacter oxydans through cofactor manipulation. Enzyme Microb Technol 2020; 141:109670. [PMID: 33051020 DOI: 10.1016/j.enzmictec.2020.109670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/21/2020] [Accepted: 09/10/2020] [Indexed: 11/29/2022]
Abstract
6-(N-hydroxyethyl)-amino-6-deoxy-l-sorbofuranose (6NSL), a key precursor in the synthesis of miglitol, is produced from N-2-hydroxyethyl-glucamine (NHEG) by the regioselective oxidation of Gluconobacter oxydans. The limitation of PQQ biosynthesis became a bottleneck for improvement of PQQ-dependent D-sorbitol dehydrogenase (mSLDH) activity. Five expression plasmids were constructed for the co-expression of the pqqABCDE gene cluster and the tldD gene on the basis of pBBR1-gHp0169-sldAB in G. oxydans to increase the biosynthesis of PQQ. The G. oxydans/pGA004, in which pqqABCDE and tldD were expressed as a cluster under the control of gHp0169 promoter, showed the optimal performance. The intracellular PQQ concentration and specific activity of mSLDH in cells increased by 79.3 % and 53.7 %, respectively, compared to that in G. oxydans/pBBR-sldAB. Then, the repeated batch biotransformation of NHEG to 6NSL by G. oxydans/pGA004 was carried out. Up to 75.0 ± 3.0 g/L of 6NSL production with 94.5 ± 3.6 % of average conversion rate of NHEG to 6NSL was achieved after four cycles of run. These results indicated that G. oxydans/pGA004 with high productivity had great potential for 6NSL production in industrial bioprocess.
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Affiliation(s)
- Dong Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Xia Ke
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Zhong-Ce Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
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12
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Breeding of Gluconobacter oxydans with high PQQ-dependent D-sorbitol dehydrogenase for improvement of 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose production. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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Fang J, Wan H, Zeng W, Li J, Chen J, Zhou J. Transcriptome Analysis of Gluconobacter oxydans WSH-003 Exposed to Elevated 2-Keto-L-Gulonic Acid Reveals the Responses to Osmotic and Oxidative Stress. Appl Biochem Biotechnol 2020; 193:128-141. [PMID: 32827065 DOI: 10.1007/s12010-020-03405-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/12/2020] [Indexed: 11/24/2022]
Abstract
Industrial production of 2-keto-L-gulonic acid (2-KLG), the precursor of vitamin C, is mainly achieved by a two-step fermentation process carried out by Gluconobacter oxydans, Bacillus, and Ketogulonicigenium. One of the most promising innovations that could replace this complicated two-step fermentation process is the integration of the essential genes for synthesis of 2-KLG into G. oxydans and use of it as the producer. Therefore, determining the tolerance and response of G. oxydans to 2-KLG is a priority for improving the direct production of 2-KLG in this bacterium. In this study, a global view of the gene expression of G. oxydans WSH-003 in response to 2-KLG challenge was investigated by RNA sequencing. A total of 363 genes of G. oxydans that were differentially expressed in response to 2-KLG were uncovered. The results showed that 2-KLG could lead to oxidative stress, osmotic stress, and DNA damage in G. oxydans.
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Affiliation(s)
- Jun Fang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Hui Wan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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14
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Repeated production of 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose by immobilized Gluconobacter oxydans cells with a strategy of in situ exhaustive cell regeneration. Bioprocess Biosyst Eng 2020; 43:1781-1789. [PMID: 32399751 DOI: 10.1007/s00449-020-02368-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 04/26/2020] [Indexed: 01/04/2023]
Abstract
The major troubles in 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose (6NSL) production from N-2-hydroxyethyl glucamine (NHEG) by Gluconobacter oxydans were low cell yield during cell preparation and loss of cells' biocatalytic ability during biotransformation, resulting in high production cost and low 6NSL production. The target of this work was to enhance 6NSL production by reusing cells and improving the cells biocatalytic ability. First, inhibitory effects of substrate and product on 6NSL production, and optimization of cell regeneration condition were investigated, respectively. Then repeated production of 6NSL by immobilized cell using a strategy of in situ exhaustive cell regeneration in a bubble column bioreactor was developed. As a result, the bioprocess underwent nine cycles, the average 6NSL production and conversion rate of NHEG to 6NSL reached 42.6 g L-1 and 83.1% in each batch was achieved, respectively.
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15
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Gao L, Wu X, Zhu C, Jin Z, Wang W, Xia X. Metabolic engineering to improve the biomanufacturing efficiency of acetic acid bacteria: advances and prospects. Crit Rev Biotechnol 2020; 40:522-538. [DOI: 10.1080/07388551.2020.1743231] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ling Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology Shandong Academy of Sciences, Jinan, PR China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Cailin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Wu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
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16
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Shan X, Liu L, Zeng W, Chen J, Zhou J. High Throughput Screening Platform for a FAD-Dependent L-Sorbose Dehydrogenase. Front Bioeng Biotechnol 2020; 8:194. [PMID: 32258011 PMCID: PMC7092628 DOI: 10.3389/fbioe.2020.00194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
2-Keto-L-gulonic acid (2-KLG) is the direct precursor for the production of L-ascorbic acid (L-Asc) on industrial scale. Currently, the production of L-Asc in the industry is a two-step fermentation process. Owing to many unstable factors in the fermentation process, the conversion rate of L-sorbose to 2-KLG has remained at about 90% for many years. In order to further improve the production efficiency of 2-KLG, a FAD-dependent sorbose dehydrogenase (SDH) has been obtained in our previous research. The SDH can directly convert L-sorbose to 2-KLG at a very high efficiency. However, the enzyme activity of the SDH is relatively low. In order to further improve the enzyme activity of the SDH, a high throughput screening platform the dehydrogenase is essential. By optimizing the promoter, host and sorbosone dehydrogenase (SNDH), knockout of the aldosterone reductases and PTS related genes, a reliable platform for high-throughput screening of more efficient FAD-dependent SDH has been established. By using the high-throughput screening platform, the titer of the 2-KLG has been improved by 14.1%. The method established here could be useful for further enhancing the FAD-dependent SDH, which is important to achieve the efficient one-strain-single-step fermentation production of 2-KLG.
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Affiliation(s)
- Xiaoyu Shan
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Li Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Weizhu Zeng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jian Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
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17
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Mi Z, Cheng J, Zhao P, Tian P, Tan T. Improved Production of Pyrroloquinoline Quinone by Simultaneous Augmentation of Its Synthesis Gene Expression and Glucose Metabolism in Klebsiella pneumoniae. Curr Microbiol 2020; 77:1174-1183. [PMID: 32080751 DOI: 10.1007/s00284-020-01918-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/10/2020] [Indexed: 10/25/2022]
Abstract
Klebsiella pneumoniae can naturally synthesize pyrroloquinoline quinone (PQQ), but current low yield restricts its commercialization. Here, we reported that PQQ production can be improved by simultaneously intensifying PQQ gene expression and glucose metabolism. Firstly, tandem repetitive tac promoters were constructed to overexpress PQQ synthesis genes. Results showed that when three repeats of tac promoter were recruited to overexpress PQQ synthesis genes, the recombinant strain generated 1.5-fold PQQ relative to the strain recruiting only one tac promoter. Quantitative real-time PCR (qRT-PCR) revealed the increased transcription levels of PQQ synthesis genes. Next, fermentation parameters were optimized to augment the glucose direct oxidation pathway (GDOP) mediated by PQQ-dependent glucose dehydrogenase (PQQ-GDH). Results demonstrated that the cultivation conditions of sufficient glucose (≥ 32 g/L), low pH (5.8), and limited potassium (0.7 nmol/L) significantly promoted the biosynthesis of gluconic acid, 2-ketogluconic acid, and PQQ. In optimum shake flask fermentation conditions, the K. pneumoniae strain overexpressing PQQ synthesis genes under three repeats of tac promoter generated 363.3 nmol/L of PQQ, which was 2.6-fold of that in original culture conditions. In bioreactor cultivation, this strain produced 2371.7 nmol/L of PQQ. To our knowledge, this is the highest PQQ titer reported so far using K. pneumoniae as a host strain. Overall, simultaneous intensification of pqq gene expression and glucose metabolism is effective to improve PQQ production.
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Affiliation(s)
- Zhiwei Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Jingchao Cheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Peng Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Pingfang Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
| | - Tianwei Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
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18
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Chen Y, Liu L, Shan X, Du G, Zhou J, Chen J. High-Throughput Screening of a 2-Keto-L-Gulonic Acid-Producing Gluconobacter oxydans Strain Based on Related Dehydrogenases. Front Bioeng Biotechnol 2019; 7:385. [PMID: 31921801 PMCID: PMC6923176 DOI: 10.3389/fbioe.2019.00385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/18/2019] [Indexed: 01/31/2023] Open
Abstract
High-throughput screening is a powerful tool for discovering strains in the natural environment that may be suitable for target production. Herein, a novel enzyme-based high-throughput screening method was developed for rapid screening of strains overproducing 2-keto-L-gulonic acid (2-KLG). The screening method detects changes in the fluorescence of reduced nicotinamide adenine dinucleotide (NADH) at 340 nm using a microplate reader when 2-KLG is degraded by 2-KLG reductase. In this research, three different 2-KLG reductases were expressed, purified, and studied. The 2-KLG reductase from Aspergillus niger were selected as the best appropriate reductase to establishment the method for its high activity below pH 7. Using the established method, and coupled with fluorescence-activated cell sorting, we achieved a high 2-KLG-producing strain of Gluconobacter oxydans WSH-004 from soil. When cultured with D-sorbitol as the substrate, the 2-KLG yield was 2.5 g/L from 50 g/L D-sorbitol without any side products. Compared with other reported screening methods, our enzyme-based method is more efficient and accurate for obtaining high-producing 2-KLG strains, and it is also convenient and cost-effective. The method is broadly applicable for screening keto acids and other products that can be oxidized via nicotinamide adenine dinucleotide (NAD+) or nicotinamide adenine dinucleotide phosphate (NADP+).
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Affiliation(s)
- Yue Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Li Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiaoyu Shan
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
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19
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Glutamate addition improves the activity of membrane-bound sorbitol dehydrogenase in a pyrroloquinoline quinone-dependent manner: A feasible strategy for the cost-effective fermentation of Gluconobacter oxydans. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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Systematic characterization of sorbose/sorbosone dehydrogenases and sorbosone dehydrogenases from Ketogulonicigenium vulgare WSH-001. J Biotechnol 2019; 301:24-34. [DOI: 10.1016/j.jbiotec.2019.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/05/2019] [Accepted: 05/23/2019] [Indexed: 11/22/2022]
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21
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Liu C, Qi L, Yang S, He Y, Jia X. Increased sedimentation of a Pseudomonas–Saccharomyces microbial consortium producing medium chain length polyhydroxyalkanoates. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2018.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Ke X, Pan-Hong Y, Hu ZC, Chen L, Sun XQ, Zheng YG. Synergistic improvement of PQQ-dependent D-sorbitol dehydrogenase activity from Gluconobacter oxydans for the biosynthesis of miglitol precursor 6-(N-hydroxyethyl)-amino-6-deoxy-α-L-sorbofuranose. J Biotechnol 2019; 300:55-62. [PMID: 31100333 DOI: 10.1016/j.jbiotec.2019.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 01/24/2023]
Abstract
6-(N-hydroxyethyl) amino-6-deoxy-l-sorbofuranose (6NSL) is the direct precursor of miglitol for diabetes therapy. The regio- and stereo-selective dehydrogenation offered by the membrane-bound d-sorbitol dehydrogenase (mSLDH) from Gluconobacter oxydans provides an elegant enzymatic method for 6NSL production. In this study, two subunits sldA and sldB of mSLDH were introduced into G. oxydans ZJB-605, and the specific enzyme activity of mSLDH towards NHEG was enhanced by 2.15-fold. However, the endogenous PQQ level was dramatically reduced in the recombinant strain and became a bottleneck to support the holo-enzyme activity. A combined supplementation of four amino acids (Glu, Ile, Ser, Arg) involved in biosynthesis of PQQ in conventional media effectively increased extracellular accumulation of PQQ by 1.49-fold, which further enhanced mSLDH activity by 1.33-fold. The synergic improvement of mSLDH activity provided in this study supports the superior high dehydrogenate activity towards substrate N-2-hydroxyethyl-glucamine, 184.28 g·L-1 of 6NSL was produced after a repeated bioconversion process catalyzed by the resting cells of G. oxydans/pBB-sldAB, all of which presenting a great potential of their industrial application in 6NSL biosynthesis.
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Affiliation(s)
- Xia Ke
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Yu Pan-Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Zhong-Ce Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China
| | - Liang Chen
- Zhejiang Medicine CO., LTD. Xinchang Pharmaceutical Factory, Shaoxing, Zhejiang 312500, PR China
| | - Xin-Qiang Sun
- Zhejiang Medicine CO., LTD. Xinchang Pharmaceutical Factory, Shaoxing, Zhejiang 312500, PR China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China.
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23
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Ding M, Chen B, Ji X, Zhou J, Wang H, Tian X, Feng X, Yue H, Zhou Y, Wang H, Wu J, Yang P, Jiang Y, Mao X, Xiao G, Zhong C, Xiao W, Li B, Qin L, Cheng J, Yao M, Wang Y, Liu H, Zhang L, Yu L, Chen T, Dong X, Jia X, Zhang S, Liu Y, Chen Y, Chen K, Wu J, Zhu C, Zhuang W, Xu S, Jiao P, Zhang L, Song H, Yang S, Xiong Y, Li Y, Zhang Y, Zhuang Y, Su H, Fu W, Huang Y, Li C, Zhao ZK, Sun Y, Chen GQ, Zhao X, Huang H, Zheng Y, Yang L, Su Z, Ma G, Ying H, Chen J, Tan T, Yuan Y. Biochemical engineering in China. REV CHEM ENG 2019. [DOI: 10.1515/revce-2017-0035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abstract
Chinese biochemical engineering is committed to supporting the chemical and food industries, to advance science and technology frontiers, and to meet major demands of Chinese society and national economic development. This paper reviews the development of biochemical engineering, strategic deployment of these technologies by the government, industrial demand, research progress, and breakthroughs in key technologies in China. Furthermore, the outlook for future developments in biochemical engineering in China is also discussed.
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Affiliation(s)
- Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Biqiang Chen
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Xiaojun Ji
- College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 211816 , China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University , Nanjing 210009 , China
| | - Jingwen Zhou
- School of Biotechnology, Jiangnan University , Wuxi 214122 , China
| | - Huiyuan Wang
- Shanghai Information Center of Life Sciences (SICLS), Shanghai Institute of Biology Sciences (SIBS), Chinese Academy of Sciences , Shanghai 200031 , China
| | - Xiwei Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai 200237 , China
| | - Xudong Feng
- School of Life Science, Beijing Institute of Technology , Beijing 100081 , China
| | - Hua Yue
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yongjin Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Hailong Wang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Jinan 250100 , China
| | - Jianping Wu
- Institute of Biology Engineering, College of Chemical and Biological Engineering, Zhejiang University , Hangzhou 310027 , China
| | - Pengpeng Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Yu Jiang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Xuming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University , Hangzhou 310058 , China
| | - Gang Xiao
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Cheng Zhong
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology , Tianjin 300457 , China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Bingzhi Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Lei Qin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Jingsheng Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Hong Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Linling Yu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Tao Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Xiaoyan Dong
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yanfeng Liu
- School of Biotechnology, Jiangnan University , Wuxi 214122 , China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Jinglan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Chenjie Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Wei Zhuang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Pengfei Jiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Lei Zhang
- Tianjin Ltd. of BoyaLife Inc. , Tianjin 300457 , China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
| | - Sheng Yang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China
| | - Yan Xiong
- Shanghai Information Center of Life Sciences (SICLS), Shanghai Institute of Biology Sciences (SIBS), Chinese Academy of Sciences , Shanghai 200031 , China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University , Hangzhou 310058 , China
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Jinan 250100 , China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Shanghai 200237 , China
| | - Haijia Su
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Weiping Fu
- China National Center of Biotechnology Development , Beijing , China
| | - Yingming Huang
- China National Center of Biotechnology Development , Beijing , China
| | - Chun Li
- School of Life Science, Beijing Institute of Technology , Beijing 100081 , China
| | - Zongbao K. Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
| | - Yan Sun
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - Guo-Qiang Chen
- Center of Synthetic and Systems Biology, School of Life Sciences, Tsinghua University , Beijing 100084 , China
| | - Xueming Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
| | - He Huang
- College of Pharmaceutical Sciences, Nanjing Tech University , Nanjing 211816 , China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University , Nanjing 210009 , China
| | - Yuguo Zheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology , Hangzhou 310014 , China
| | - Lirong Yang
- Institute of Biology Engineering, College of Chemical and Biological Engineering, Zhejiang University , Hangzhou 310027 , China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190 , China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , Nanjing 210009 , China
- National Engineering Technique Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University , Nanjing 210009 , China
| | - Jian Chen
- School of Biotechnology, Jiangnan University , Wuxi 214122 , China
| | - Tianwei Tan
- Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072 , China
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24
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Ma Q, Bi YH, Wang EX, Zhai BB, Dong XT, Qiao B, Ding MZ, Yuan YJ. Integrated proteomic and metabolomic analysis of a reconstructed three-species microbial consortium for one-step fermentation of 2-keto-l-gulonic acid, the precursor of vitamin C. ACTA ACUST UNITED AC 2019; 46:21-31. [DOI: 10.1007/s10295-018-2096-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/21/2018] [Indexed: 01/04/2023]
Abstract
Abstract
Microbial consortia, with the merits of strong stability, robustness, and multi-function, played critical roles in human health, bioenergy, and food manufacture, etc. On the basis of ‘build a consortium to understand it’, a novel microbial consortium consisted of Gluconobacter oxydans, Ketogulonicigenium vulgare and Bacillus endophyticus was reconstructed to produce 2-keto-l-gulonic acid (2-KGA), the precursor of vitamin C. With this synthetic consortium, 73.7 g/L 2-KGA was obtained within 30 h, which is comparable to the conventional industrial method. A combined time-series proteomic and metabolomic analysis of the fermentation process was conducted to further investigate the cell–cell interaction. The results suggested that the existence of B. endophyticus and G. oxydans together promoted the growth of K. vulgare by supplying additional nutrients, and promoted the 2-KGA production by supplying more substrate. Meanwhile, the growth of B. endophyticus and G. oxydans was compromised from the competition of the nutrients by K. vulgare, enabling the efficient production of 2-KGA. This study provides valuable guidance for further study of synthetic microbial consortia.
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Affiliation(s)
- Qian Ma
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0000 9735 6249 grid.413109.e College of Biotechnology Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Yan-Hui Bi
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - En-Xu Wang
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Bing-Bing Zhai
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Xiu-Tao Dong
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Bin Qiao
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Ming-Zhu Ding
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Ying-Jin Yuan
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
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25
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Wang CY, Li Y, Gao ZW, Liu LC, Wu YC, Zhang MY, Zhang TY, Zhang YX. Reconstruction and analysis of carbon metabolic pathway of Ketogulonicigenium vulgare SPU B805 by genome and transcriptome. Sci Rep 2018; 8:17838. [PMID: 30546118 PMCID: PMC6293013 DOI: 10.1038/s41598-018-36038-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/09/2018] [Indexed: 11/23/2022] Open
Abstract
Ketogulonicigenium vulgare has been widely used in vitamin C two-step fermentation. Four K. vulgare strains (WSH-001, Y25, Hbe602 and SKV) have been completely genome-sequenced, however, less attention was paid to elucidate the reason for the differences in 2-KGA yield on genetic level. Here, a novel K. vulgare SPU B805 with higher 2-keto-L-gulonic acid (2-KGA) yield, was genome-sequenced to confirm harboring one circular chromosome with plasmid free. Comparative genome analyses showed that the absence of plasmid 2 was an important factor for its high 2-KGA productivity. The amino acid biosynthetic pathways in strain SPU B805 are much more complete than those in other K. vulgare strains. Meanwhile, strain SPU B805 harbored a complete PPP and TCA route, as well as a disabled EMP and ED pathway, same as to strain SKV, whereas strain WSH-001, Y25 and Hbe602 harbored complete PPP, ED, TCA pathway and a nonfunctional EMP pathway. The transcriptome of strain SPU B805 validated the carbon metabolism in cytoplasm mainly through the PPP pathway due to its higher transcriptional levels. This is the first time to elucidate the underlying mechanism for the difference in 2-KGA yield, and it is of great significance for strain improvement in the industrial fermentation.
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Affiliation(s)
- Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Ye Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.,Northeast Pharmaceutical Group Co., Ltd, Shenyang, 110026, People's Republic of China
| | - Zi-Wei Gao
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Li-Cheng Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Ying-Cai Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Tian-Yuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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26
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Current challenges facing one-step production of l-ascorbic acid. Biotechnol Adv 2018; 36:1882-1899. [DOI: 10.1016/j.biotechadv.2018.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/20/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
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27
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Wang CY, Li Y, Gao ZW, Liu LC, Zhang MY, Zhang TY, Wu CF, Zhang YX. Establishing an innovative carbohydrate metabolic pathway for efficient production of 2-keto-L-gulonic acid in Ketogulonicigenium robustum initiated by intronic promoters. Microb Cell Fact 2018; 17:81. [PMID: 29778095 PMCID: PMC5960096 DOI: 10.1186/s12934-018-0932-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Background 2-Keto-l-gulonic acid (2-KGA), the precursor of vitamin C, is currently produced by two-step fermentation. In the second step, l-sorbose is transformed into 2-KGA by the symbiosis system composed of Ketogulonicigenium vulgare and Bacillus megaterium. Due to the different nutrient requirements and the uncertain ratio of the two strains, the symbiosis system significantly limits strain improvement and fermentation optimization. Results In this study, Ketogulonicigenium robustum SPU_B003 was reported for its capability to grow well independently and to produce more 2-KGA than that of K. vulgare in a mono-culture system. The complete genome of K. robustum SPU_B003 was sequenced, and the metabolic characteristics were analyzed. Compared to the four reported K. vulgare genomes, K. robustum SPU_B003 contained more tRNAs, rRNAs, NAD and NADP biosynthetic genes, as well as regulation- and cell signaling-related genes. Moreover, the amino acid biosynthesis pathways were more complete. Two species-specific internal promoters, P1 (orf_01408 promoter) and P2 (orf_02221 promoter), were predicted and validated by detecting their initiation activity. To efficiently produce 2-KGA with decreased CO2 release, an innovative acetyl-CoA biosynthetic pathway (XFP-PTA pathway) was introduced into K. robustum SPU_B003 by expressing heterologous phosphoketolase (xfp) and phosphotransacetylase (pta) initiated by internal promoters. After gene optimization, the recombinant strain K. robustum/pBBR-P1_xfp2502-P2_pta2145 enhanced acetyl-CoA approximately 2.4-fold and increased 2-KGA production by 22.27% compared to the control strain K. robustum/pBBR1MCS-2. Accordingly, the transcriptional level of the 6-phosphogluconate dehydrogenase (pgd) and pyruvate dehydrogenase genes (pdh) decreased by 24.33 ± 6.67 and 8.67 ± 5.51%, respectively. The key genes responsible for 2-KGA biosynthesis, sorbose dehydrogenase gene (sdh) and sorbosone dehydrogenase gene (sndh), were up-regulated to different degrees in the recombinant strain. Conclusions The genome-based functional analysis of K. robustum SPU_B003 provided a new understanding of the specific metabolic characteristics. The new XFP-PTA pathway was an efficient route to enhance acetyl-CoA levels and to therefore promote 2-KGA production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0932-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cai-Yun Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Ye Li
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China.,Northeast Pharmaceutical Group Co., Ltd, Shenyang, 110026, People's Republic of China
| | - Zi-Wei Gao
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Li-Cheng Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Tian-Yuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Chun-Fu Wu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, Liaoning, People's Republic of China.
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28
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Reconstruction of amino acid biosynthetic pathways increases the productivity of 2-keto-l-gulonic acid in Ketogulonicigenium vulgare-Bacillus endophyticus consortium via genes screening. ACTA ACUST UNITED AC 2017; 44:1031-1040. [DOI: 10.1007/s10295-017-1928-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/22/2017] [Indexed: 01/26/2023]
Abstract
Abstract
Defect in the amino acid biosynthetic pathways of Ketogulonicigenium vulgare, the producing strain for 2-keto-l-gulonic acid (2-KGA), is the key reason for its poor growth and low productivity. In this study, five different strains were firstly reconstructed by expressing absent genes in threonine, proline and histidine biosynthetic pathways for better 2-KGA productivity. When mono-cultured in the shake flasks, the strain SyBE_Kv02080002 expressing hsk from Gluconobacter oxydans in threonine biosynthetic pathway achieved the highest biomass and the titer increased by 25.13%. When co-cultured with Bacillus endophyticus, the fermentation cycle decreased by 28.57% than that of the original consortium in 5-L fermenter. Furthermore, reconstruction of threonine biosynthetic pathway resulted in up-regulation of genes encoding sorbosone dehydrogenase and idonate-dehydrogenase, which increased the 2-KGA productivity in SyBE_Kv02080002. This study shows that reconstruction of absent biosynthetic pathways in bacteria is an effective way to enhance the productivity of target products.
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29
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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Comparative genomics and metabolomics analyses of the adaptation mechanism in Ketogulonicigenium vulgare-Bacillus thuringiensis consortium. Sci Rep 2017; 7:46759. [PMID: 28440340 PMCID: PMC5404267 DOI: 10.1038/srep46759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Adaptive evolution by serial subcultivation of co-cultured Bacillus thuringiensis and Ketogulonicigenium vulgare significantly enhanced the productivity of 2-keto-L-gulonic acid in two-step vitamin C production. The adaptation mechanism in K. vulgare-B. thuringiensis consortium was investigated in this study based on comparative genomics and metabolomics studies. It was found that the growth, anti-oxidation, transcription and regulation were significantly enhanced in the adapted consortium. The mutation of the genes, which encode amidohydrolase in adapted K. vulgare (K150) and amino acid permease in adapted B. thuringiensis (B150), resulted in the increase of some amino acids levels in each species, and further enhanced the metabolic exchange and growth ability of the two species. Besides, the mutation of the gene encoding spore germination protein enhanced the metabolic levels of tricarboxylic acid cycle, and decreased the sporulation in B150, which induced its growth. The mutation of the genes, which encode NADPH nitroreductase in K150 and NADPH-dependent FMN reductase in B150, may enhance the ability of anti-oxidation. Overall, the long-term adaptation of K. vulgare and B. thuringiensis influenced the global regulation and made them more inseparable in metabolite exchange. Our work will provide ideas for the molecular design and optimization in microbial consortium.
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Complete Genome Sequence of the Industrial Bacterium Ketogulonicigenium vulgare SKV. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01426-16. [PMID: 28007860 PMCID: PMC5180388 DOI: 10.1128/genomea.01426-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Ketogulonicigenium vulgare has been widely used in vitamin C two-step fermentation, which converts l-sorbose to 2-keto-l-gluonic acid. Here, the complete genome of K. vulgare SKV, which performs better fermentation production than K. vulgare Hbe602, is deciphered to understand the key differences in metabolism between K. vulgare strains SKV and Hbe602.
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Guleria S, Zhou J, Koffas MA. Nutraceuticals (Vitamin C, Carotenoids, Resveratrol). Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Sanjay Guleria
- Sher-e-Kashmir University of Agricultural Sciences and Technology; Division of Biochemistry, Faculty of Basic Sciences; Main Campus Chatha Jammu 180 009 India
| | - Jingwen Zhou
- Jiangnan University; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology; 1800 Lihu Road Wuxi Jiangsu 214122 China
| | - Mattheos A.G. Koffas
- Rensselaer Polytechnic Institute; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Center for Biotechnology and Interdisciplinary Studies; 110 8th Street Troy NY 12180 USA
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Chen S, Jia N, Ding MZ, Yuan YJ. Comparative analysis of L-sorbose dehydrogenase by docking strategy for 2-keto-L-gulonic acid production in Ketogulonicigenium vulgare and Bacillus endophyticus consortium. J Ind Microbiol Biotechnol 2016; 43:1507-1516. [PMID: 27565673 DOI: 10.1007/s10295-016-1829-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/28/2016] [Indexed: 12/11/2022]
Abstract
Improving the yield of 2-keto-L-gulonic acid (2-KGA), the direct precursor of vitamin C, draws more and more attention in industrial production. In this study, we try to increase the 2-KGA productivity by computer-aided selection of genes encoding L-sorbose dehydrogenases (SDH) of Ketogulonicigenium vulgare. First, six SDHs were modeled by docking strategy to predict the binding mode with co-factor PQQ. The binding energy between SSDA1-H/SSDA1-L and PQQ was the highest, followed by SSDA3/SSDA2. The binding energy between SSDA1-P/SSDB and PQQ was the lowest. Then, these genes were overexpressed, respectively, in an industrial strain K. vulgare HKv604. Overexpression of ssda1-l and ssda1-h enhanced the 2-KGA production by 7.89 and 12.56 % in mono-cultured K. vulgare, and by 13.21 and 16.86 % when K. vulgare was co-cultured with Bacillus endophyticus. When the engineered K. vulgare SyBE_Kv000116013 (overexpression of ssda1-p) or SyBE_Kv000116016 (overexpression of ssdb) was co-cultured with B. endophyticus, the 2-KGA production decreased significantly. The docking results were in accordance with the experimental data, which indicated that computer-aided modeling is an efficient strategy for screening more efficient enzymes.
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Affiliation(s)
- Si Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Nan Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
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Overexpression of pyrroloquinoline quinone biosynthetic genes affects l -sorbose production in Gluconobacter oxydans WSH-003. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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35
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Novel and efficient screening of PQQ high-yielding strains and subsequent cultivation optimization. Appl Microbiol Biotechnol 2016; 100:10321-10330. [PMID: 27464830 DOI: 10.1007/s00253-016-7739-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
A novel and efficient screening method for pyrroloquinoline quinone (PQQ) high-yielding methylotrophic strains was developed by using glucose dehydrogenase apoenzyme (GDHA) which depended on PQQ as the cofactor. Using this high-throughput method, PQQ high-yielding strains were rapidly screened out from thousands of methylotrophic colonies at a time. The comprehensive phylogenetic analysis revealed that the highest PQQ-producing strain zju323 (CCTCC M 2016079) could be assigned to a novel species in the genus Methylobacillus of the Betaproteobacteria. After systematic optimization of different medium components and cultivation conditions, about 33.4 mg/L of PQQ was obtained after 48 h of cultivation with Methylobacillus sp. zju323 at the shake flask scale. Further cultivations of Methylobacillus sp. zju323 were carried out to investigate the biosynthesis of PQQ in 10-L bench-top fermenters. In the batch operation, the PQQ accumulation reached 78 mg/L in the broth after 53 h of cultivation. By adopting methanol feeding strategy, the highest PQQ concentration was improved up to 162.2 mg/L after 75 h of cultivation. This work developed a high-throughput strategy of screening PQQ-producing strains from soil samples and also demonstrated one potential bioprocess for large-scale PQQ production with the isolated PQQ strain.
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Yuan J, Wu M, Lin J, Yang L. Combinatorial metabolic engineering of industrial Gluconobacter oxydans DSM2343 for boosting 5-keto-D-gluconic acid accumulation. BMC Biotechnol 2016; 16:42. [PMID: 27189063 PMCID: PMC4869267 DOI: 10.1186/s12896-016-0272-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/10/2016] [Indexed: 11/10/2022] Open
Abstract
Background L-(+)-tartaric acid (L-TA) is an important organic acid, which is produced from the cream of tartar or stereospecific hydrolysis of the cis-epoxysuccinate. The former method is limited by the availability of raw material and the latter is dependent on the petrochemical material. Thus, new processes for the economical preparation of L-TA from carbohydrate or renewable resource would be much more attractive. Production of 5-keto-D-gluconate (5-KGA) from glucose by Gluconobacter oxydans is the first step to produce L-TA. The aim of this work is to enhance 5-KGA accumulation using combinatorial metabolic engineering strategies in G. oxydans. The sldAB gene, encoding sorbitol dehydrogenase, was overexpressed in an industrial strain G. oxydans ZJU2 under a carefully selected promoter, P0169. To enhance the efficiency of the oxidation by sldAB, the coenzyme pyrroloquinoline quinone (PQQ) and respiratory chain were engineered. Besides, the role in sldAB overexpression, coenzyme and respiratory chain engineering and their subsequent effects on 5-KGA production were investigated. Results An efficient, stable recombinant strain was constructed, whereas the 5-KGA production could be enhanced. By self-overexpressing the sldAB gene in G. oxydans ZJU2 under the constitutive promoter P0169, the resulting strain, G. oxydans ZJU3, produced 122.48 ± 0.41 g/L of 5-KGA. Furthermore, through the coenzyme and respiratory chain engineering, the titer and productivity of 5-KGA reached 144.52 ± 2.94 g/L and 2.26 g/(L · h), respectively, in a 15 L fermenter. It could be further improved the 5-KGA titer by 12.10 % through the fed-batch fermentation under the pH shift and dissolved oxygen tension (DOT) control condition, obtained 162 ± 2.12 g/L with the productivity of 2.53 g/(L · h) within 64 h. Conclusions The 5-KGA production could be significantly enhanced with the combinatorial metabolic engineering strategy in Gluconobacter strain, including sldAB overexpression, coenzyme and respiratory chain engineering. Fed-batch fermentation could further enlarge the positive effect and increase the 5-KGA production. All of these demonstrated that the robust recombinant strain can efficiently produce 5-KGA in larger scale to fulfill the industrial production of L-TA from 5-KGA.
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Affiliation(s)
- Jianfeng Yuan
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
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Jia X, Liu C, Song H, Ding M, Du J, Ma Q, Yuan Y. Design, analysis and application of synthetic microbial consortia. Synth Syst Biotechnol 2016; 1:109-117. [PMID: 29062933 PMCID: PMC5640696 DOI: 10.1016/j.synbio.2016.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 01/28/2016] [Accepted: 02/12/2016] [Indexed: 12/17/2022] Open
Abstract
The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.
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Affiliation(s)
- Xiaoqiang Jia
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Chang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jin Du
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Qian Ma
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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Jia N, Ding MZ, Du J, Pan CH, Tian G, Lang JD, Fang JH, Gao F, Yuan YJ. Insights into mutualism mechanism and versatile metabolism of Ketogulonicigenium vulgare Hbe602 based on comparative genomics and metabolomics studies. Sci Rep 2016; 6:23068. [PMID: 26979567 PMCID: PMC4793288 DOI: 10.1038/srep23068] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/29/2016] [Indexed: 02/02/2023] Open
Abstract
Ketogulonicigenium vulgare has been widely used in vitamin C two steps fermentation and requires companion strain for optimal growth. However, the understanding of K. vulgare as well as its companion strain is still preliminary. Here, the complete genome of K. vulgare Hbe602 was deciphered to provide insight into the symbiosis mechanism and the versatile metabolism. K. vulgare contains the LuxR family proteins, chemokine proteins, flagellar structure proteins, peptides and transporters for symbiosis consortium. Besides, the growth state and metabolite variation of K. vulgare were observed when five carbohydrates (D-sorbitol, L-sorbose, D-glucose, D-fructose and D-mannitol) were used as carbon source. The growth increased by 40.72% and 62.97% respectively when K. vulgare was cultured on D-mannitol/D-sorbitol than on L-sorbose. The insufficient metabolism of carbohydrates, amino acids and vitamins is the main reason for the slow growth of K. vulgare. The combined analysis of genomics and metabolomics indicated that TCA cycle, amino acid and nucleotide metabolism were significantly up-regulated when K. vulgare was cultured on the D-mannitol/D-sorbitol, which facilitated the better growth. The present study would be helpful to further understand its metabolic structure and guide the engineering transformation.
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Affiliation(s)
- Nan Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Jin Du
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Cai-Hui Pan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
| | - Geng Tian
- Sequencing platform of Tsinghua University, Beijing, 100084, PR China
| | - Ji-Dong Lang
- Sequencing platform of Tsinghua University, Beijing, 100084, PR China
| | - Jian-Huo Fang
- Sequencing platform of Tsinghua University, Beijing, 100084, PR China
| | - Feng Gao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- Department of Physics, Tianjin University, Tianjin, 300072, PR China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China
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Martínez I, Mohamed MES, Rozas D, García JL, Díaz E. Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metab Eng 2016; 35:46-54. [PMID: 26802977 DOI: 10.1016/j.ymben.2016.01.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/27/2015] [Accepted: 01/11/2016] [Indexed: 01/04/2023]
Abstract
The 4S pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. It consists of three sequential functional units, encoded by the dszABCD genes, through which the model compound dibenzothiophene (DBT) is transformed into the sulfur-free 2-hydroxybiphenyl (2HBP) molecule. In this work, a set of synthetic dsz cassettes were implanted in Pseudomonas putida KT2440, a model bacterial "chassis" for metabolic engineering studies. The complete dszB1A1C1-D1 cassette behaved as an attractive alternative - to the previously constructed recombinant dsz cassettes - for the conversion of DBT into 2HBP. Refactoring the 4S pathway by the use of synthetic dsz modules encoding individual 4S pathway reactions revealed unanticipated traits, e.g., the 4S intermediate 2HBP-sulfinate (HBPS) behaves as an inhibitor of the Dsz monooxygenases, and once secreted from the cells it cannot be further taken up. That issue should be addressed for the rational design of more efficient biocatalysts for DBT bioconversions. In this sense, the construction of synthetic bacterial consortia to compartmentalize the 4S pathway into different cell factories for individual optimization was shown to enhance the conversion of DBT into 2HBP, overcome the inhibition of the Dsz enzymes by the 4S intermediates, and enable efficient production of unattainable high added value intermediates, e.g., HBPS, that are difficult to obtain using the current monocultures.
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Affiliation(s)
- Igor Martínez
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | | | - Daniel Rozas
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - José Luis García
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
| | - Eduardo Díaz
- Environmental Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
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Qi H, Li BZ, Zhang WQ, Liu D, Yuan YJ. Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnol Adv 2015; 33:1412-9. [DOI: 10.1016/j.biotechadv.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/12/2015] [Accepted: 04/05/2015] [Indexed: 01/24/2023]
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41
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Influence of Altered NADH Metabolic Pathway on the Respiratory-deficient Mutant of Rhizopus oryzae and its L-lactate Production. Appl Biochem Biotechnol 2015; 176:2053-64. [PMID: 26047930 DOI: 10.1007/s12010-015-1700-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/28/2015] [Indexed: 02/07/2023]
Abstract
Respiratory-deficient mutants of Rhizopus oryzae (R. oryzae) AS 3.3461 were acquired by ultraviolet (UV) irradiation to investigate changes in intracellular NADH metabolic pathway and its influence on the fermentation characteristics of the strain. Compared with R. oryzae AS 3.3461, the intracellular ATP level of the respiratory-deficient strain UV-1 decreased by 52.7 % and the glucose utilization rate rose by 8.9 %; When incubated for 36 h, the activities of phosphofructokinase (PFK), hexokinase (HK), and pyruvate kinase (PK) in the mutant rose by 74.2, 7.2, and 12.0 %, respectively; when incubated for 48 h, the intracellular NADH/NAD(+) ratio of the mutant rose by 14.6 %; when a mixed carbon source with a glucose/gluconic acid ratio of 1:1 was substituted to culture the mutant, the NADH/NAD(+) ratio decreased by 4.6 %; the ATP content dropped by 27.6 %; the lactate dehydrogenase (LDH) activity rose by 22.7 %; and the lactate yield rose by 11.6 %. These results indicated that changes to the NADH metabolic pathway under a low-energy charge level can effectively increase the glycolytic rate and further improve the yield of L-lactate of R. oryzae.
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42
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Unraveling interactions in microbial communities - from co-cultures to microbiomes. J Microbiol 2015; 53:295-305. [PMID: 25935300 DOI: 10.1007/s12275-015-5060-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/02/2014] [Accepted: 04/09/2014] [Indexed: 12/15/2022]
Abstract
Microorganisms do not exist in isolation in the environment. Instead, they form complex communities among themselves as well as with their hosts. Different forms of interactions not only shape the composition of these communities but also define how these communities are established and maintained. The kinds of interaction a bacterium can employ are largely encoded in its genome. This allows us to deploy a genomescale modeling approach to understand, and ultimately predict, the complex and intertwined relationships in which microorganisms engage. So far, most studies on microbial communities have been focused on synthetic co-cultures and simple communities. However, recent advances in molecular and computational biology now enable bottom up methods to be deployed for complex microbial communities from the environment to provide insight into the intricate and dynamic interactions in which microorganisms are engaged. These methods will be applicable for a wide range of microbial communities involved in industrial processes, as well as understanding, preserving and reconditioning natural microbial communities present in soil, water, and the human microbiome.
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43
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Song H, Ding MZ, Jia XQ, Ma Q, Yuan YJ. Synthetic microbial consortia: from systematic analysis to construction and applications. Chem Soc Rev 2014; 43:6954-81. [PMID: 25017039 DOI: 10.1039/c4cs00114a] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.
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Affiliation(s)
- Hao Song
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, and Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China.
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Gao L, Hu Y, Liu J, Du G, Zhou J, Chen J. Stepwise metabolic engineering of Gluconobacter oxydans WSH-003 for the direct production of 2-keto-l-gulonic acid from d-sorbitol. Metab Eng 2014; 24:30-7. [DOI: 10.1016/j.ymben.2014.04.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/18/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
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45
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Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Mol Syst Biol 2014; 10:731. [PMID: 24952589 PMCID: PMC4265053 DOI: 10.15252/msb.20134955] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Developing predictive models of multi-protein genetic systems to understand and optimize their behavior remains a combinatorial challenge, particularly when measurement throughput is limited. We developed a computational approach to build predictive models and identify optimal sequences and expression levels, while circumventing combinatorial explosion. Maximally informative genetic system variants were first designed by the RBS Library Calculator, an algorithm to design sequences for efficiently searching a multi-protein expression space across a > 10,000-fold range with tailored search parameters and well-predicted translation rates. We validated the algorithm's predictions by characterizing 646 genetic system variants, encoded in plasmids and genomes, expressed in six gram-positive and gram-negative bacterial hosts. We then combined the search algorithm with system-level kinetic modeling, requiring the construction and characterization of 73 variants to build a sequence-expression-activity map (SEAMAP) for a biosynthesis pathway. Using model predictions, we designed and characterized 47 additional pathway variants to navigate its activity space, find optimal expression regions with desired activity response curves, and relieve rate-limiting steps in metabolism. Creating sequence-expression-activity maps accelerates the optimization of many protein systems and allows previous measurements to quantitatively inform future designs.
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Affiliation(s)
- Iman Farasat
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Jason Collens
- Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
| | - Michael Easterbrook
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Matthew Guido
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Howard M Salis
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA Department of Biological Engineering, Pennsylvania State University, University Park, PA, USA
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