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Fu B, Chen M, Bao X, Lu J, Zhu Z, Guan F, Yan C, Wang P, Fu L, Yu P. Site-directed mutagenesis of bifunctional riboflavin kinase/FMN adenylyltransferase via CRISPR/Cas9 to enhance riboflavin production. Synth Syst Biotechnol 2024; 9:503-512. [PMID: 38680946 PMCID: PMC11047187 DOI: 10.1016/j.synbio.2024.04.011] [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: 11/19/2023] [Revised: 03/20/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
Vitamin B2 is an essential water-soluble vitamin. For most prokaryotes, a bifunctional enzyme called FAD synthase catalyzes the successive conversion of riboflavin to FMN and FAD. In this study, the plasmid pNEW-AZ containing six key genes for the riboflavin synthesis was transformed into strain R2 with the deleted FMN riboswitch, yielding strain R5. The R5 strain could produce 540.23 ± 5.40 mg/L riboflavin, which was 10.61 % higher than the R4 strain containing plasmids pET-AE and pAC-Z harboring six key genes. To further enhance the production of riboflavin, homology matching and molecular docking were performed to identify key amino acid residues of FAD synthase. Nine point mutation sites were identified. By comparing riboflavin kinase activity, mutations of T203D and N210D, which respectively decreased by 29.90 % and 89.32 % compared to wild-type FAD synthase, were selected for CRISPR/Cas9 gene editing of the genome, generating engineered strains R203 and R210. pNEW-AZ was transformed into R203, generating R6. R6 produced 657.38 ± 47.48 mg/L riboflavin, a 21.69 % increase compared to R5. This study contributes to the high production of riboflavin in recombinant E. coli BL21.
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Affiliation(s)
- Bing Fu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
- College of Forestry Science and Technology, Lishui Vocational and Technical College, 357 Zhongshan Street North, Lishui, Zhejiang Province, 323000, People's Republic of China
| | - Meng Chen
- Lishui Institute for Quality Inspection and Testing, 395 Zhongshan Street, Lishui, Zhejiang Province, 323000, People's Republic of China
| | - Xianfeng Bao
- College of Forestry Science and Technology, Lishui Vocational and Technical College, 357 Zhongshan Street North, Lishui, Zhejiang Province, 323000, People's Republic of China
| | - Jiajie Lu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Zhiwen Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Fuyao Guan
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Chuyang Yan
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Peize Wang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Linglin Fu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
| | - Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, 149 Jiaogong Road, Hangzhou, Zhejiang Province, 310035, People's Republic of China
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Pérez-García F, Brito LF, Bakken TI, Brautaset T. Riboflavin overproduction from diverse feedstocks with engineered Corynebacterium glutamicum. Biofabrication 2024; 16:045012. [PMID: 38996414 DOI: 10.1088/1758-5090/ad628e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/12/2024] [Indexed: 07/14/2024]
Abstract
Riboflavin overproduction byCorynebacterium glutamicumwas achieved by screening synthetic operons, enabling fine-tuned expression of the riboflavin biosynthetic genesribGCAH.The synthetic operons were designed by means of predicted translational initiation rates of each open reading frame, with the best-performing selection enabling riboflavin overproduction without negatively affecting cell growth. Overexpression of the fructose-1,6-bisphosphatase (fbp) and 5-phosphoribosyl 1-pyrophosphate aminotransferase (purF) encoding genes was then done to redirect the metabolic flux towards the riboflavin precursors. The resulting strain produced 8.3 g l-1of riboflavin in glucose-based fed-batch fermentations, which is the highest reported riboflavin titer withC. glutamicum. Further genetic engineering enabled both xylose and mannitol utilization byC. glutamicum, and we demonstrated riboflavin overproduction with the xylose-rich feedstocks rice husk hydrolysate and spent sulfite liquor, and the mannitol-rich feedstock brown seaweed hydrolysate. Remarkably, rice husk hydrolysate provided 30% higher riboflavin yields compared to glucose in the bioreactors.
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Affiliation(s)
- Fernando Pérez-García
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luciana Fernandes Brito
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Thea Isabel Bakken
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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3
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Qian J, Wang Y, Hu Z, Shi T, Wang Y, Ye C, Huang H. Bacillus sp. as a microbial cell factory: Advancements and future prospects. Biotechnol Adv 2023; 69:108278. [PMID: 37898328 DOI: 10.1016/j.biotechadv.2023.108278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/27/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.
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Affiliation(s)
- Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Zijian Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China.
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4
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Klein VJ, Brito LF, Perez-Garcia F, Brautaset T, Irla M. Metabolic engineering of thermophilic Bacillus methanolicus for riboflavin overproduction from methanol. Microb Biotechnol 2023; 16:1011-1026. [PMID: 36965151 PMCID: PMC10128131 DOI: 10.1111/1751-7915.14239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 03/27/2023] Open
Abstract
The growing need of next generation feedstocks for biotechnology spurs an intensification of research on the utilization of methanol as carbon and energy source for biotechnological processes. In this paper, we introduced the methanol-based overproduction of riboflavin into metabolically engineered Bacillus methanolicus MGA3. First, we showed that B. methanolicus naturally produces small amounts of riboflavin. Then, we created B. methanolicus strains overexpressing either homologous or heterologous gene clusters encoding the riboflavin biosynthesis pathway, resulting in riboflavin overproduction. Our results revealed that the supplementation of growth media with sublethal levels of chloramphenicol contributes to a higher plasmid-based riboflavin production titre, presumably due to an increase in plasmid copy number and thus biosynthetic gene dosage. Based on this, we proved that riboflavin production can be increased by exchanging a low copy number plasmid with a high copy number plasmid leading to a final riboflavin titre of about 523 mg L-1 in methanol fed-batch fermentation. The findings of this study showcase the potential of B. methanolicus as a promising host for methanol-based overproduction of extracellular riboflavin and serve as basis for metabolic engineering of next generations of riboflavin overproducing strains.
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Affiliation(s)
- Vivien Jessica Klein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luciana Fernandes Brito
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Fernando Perez-Garcia
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marta Irla
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
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5
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Fu B, Ying J, Chen Q, Zhang Q, Lu J, Zhu Z, Yu P. Enhancing the biosynthesis of riboflavin in the recombinant Escherichia coli BL21 strain by metabolic engineering. Front Microbiol 2023; 13:1111790. [PMID: 36726568 PMCID: PMC9885008 DOI: 10.3389/fmicb.2022.1111790] [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: 11/30/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
In this study, to construct the riboflavin-producing strain R1, five key genes, ribA, ribB, ribC, ribD, and ribE, were cloned and ligated to generate the plasmid pET-AE, which was overexpressed in Escherichia coli BL21. The R1 strain accumulated 182.65 ± 9.04 mg/l riboflavin. Subsequently, the R2 strain was constructed by the overexpression of zwf harboring the constructed plasmid pAC-Z in the R1 strain. Thus, the level of riboflavin in the R2 strain increased to 319.01 ± 20.65 mg/l (74.66% increase). To further enhance ribB transcript levels and riboflavin production, the FMN riboswitch was deleted from E. coli BL21 with CRISPR/Cas9 to generate the R3 strain. The R4 strain was constructed by cotransforming pET-AE and pAC-Z into the R3 strain. Compared to those of E. coli BL21, the ribB transcript levels of R2 and R4 improved 2.78 and 3.05-fold, respectively. The R4 strain accumulated 437.58 ± 14.36 mg/l riboflavin, increasing by 37.17% compared to the R2 strain. These results suggest that the deletion of the FMN riboswitch can improve the transcript level of ribB and facilitate riboflavin production. A riboflavin titer of 611.22 ± 11.25 mg/l was achieved under the optimal fermentation conditions. Ultimately, 1574.60 ± 109.32 mg/l riboflavin was produced through fed-batch fermentation with 40 g/l glucose. This study contributes to the industrial production of riboflavin by the recombinant E. coli BL21.
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Affiliation(s)
- Bing Fu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China,College of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, Zhejiang, China
| | - Junhui Ying
- College of Forestry Science and Technology, Lishui Vocational and Technical College, Lishui, Zhejiang, China
| | - Qingwei Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Qili Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Jiajie Lu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Zhiwen Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China
| | - Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, China,*Correspondence: Ping Yu,
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6
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Liu Y, Zhang Q, Qi X, Gao H, Wang M, Guan H, Yu B. Metabolic Engineering of Bacillus subtilis for Riboflavin Production: A Review. Microorganisms 2023; 11:microorganisms11010164. [PMID: 36677456 PMCID: PMC9863419 DOI: 10.3390/microorganisms11010164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
Riboflavin (vitamin B2) is one of the essential vitamins that the human body needs to maintain normal metabolism. Its biosynthesis has become one of the successful models for gradual replacement of traditional chemical production routes. B. subtilis is characterized by its short fermentation time and high yield, which shows a huge competitive advantage in microbial fermentation for production of riboflavin. This review summarized the advancements of regulation on riboflavin production as well as the synthesis of two precursors of ribulose-5-phosphate riboflavin (Ru5P) and guanosine 5'-triphosphate (GTP) in B. subtilis. The different strategies to improve production of riboflavin by metabolic engineering were also reviewed.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Zhang
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
- Correspondence: (Q.Z.); (B.Y.)
| | - Xiaoxiao Qi
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huipeng Gao
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
| | - Meng Wang
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
| | - Hao Guan
- Key Laboratory of Biofuels and Biochemical Engineering, SINOPEC (Dalian) Research Institute of Petroleum and Petro-Chemicals Co., Ltd., Dalian 116045, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Q.Z.); (B.Y.)
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7
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Li Y, Li Y, Chen Y, Cheng M, Yu H, Song H, Cao Y. Coupling riboflavin de novo biosynthesis and cytochrome expression for improving extracellular electron transfer efficiency in Shewanella oneidensis. Biotechnol Bioeng 2022; 119:2806-2818. [PMID: 35798677 DOI: 10.1002/bit.28172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/06/2022]
Abstract
Shewanella oneidensis MR-1, as a model exoelectrogen with divergent extracellular electron transfer (EET) pathways, has been widely used in microbial fuel cells (MFCs). The electron transfer rate is largely determined by riboflavin (RF) and c-type cytochromes (c-Cyts). However, relatively low RF production and inappropriate amount of c-Cyts substantially impedes the capacity of improving the EET rate. In this work, coupling of riboflavin de novo biosynthesis and c-Cyts expression was implemented to enhance the efficiency of EET in S. oneidensis. Firstly, the upstream pathway of RF de novo biosynthesis was divided into four modules, and the expression level of 22 genes in above four modules was fine-tuned by employing promoters with different strength. Among them, genes zwf*, glyA, ybjU which exhibited the optimal RF production were combinatorially overexpressed, leading to enhancement of maximum output power density by 166%. Secondly, the diverse c-Cyts genes were overexpressed to match high RF production, and omcA was selected for further combination. Thirdly, RF de novo biosynthesis and c-Cyts expression were combined, resulting in 2.34-fold higher power output than the parent strain. This modular and combinatorial manipulation strategy provides a generalized reference to advance versatile practical applications of electroactive microorganisms. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yan Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yuanyuan Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yaru Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Meijie Cheng
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
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Wang J, Li Z, Wang W, Pang S, Yao Y, Yuan F, Wang H, Xu Z, Pan G, Liu Z, Chen Y, Fan K. Dynamic Control Strategy to Produce Riboflavin with Lignocellulose Hydrolysate in the Thermophile Geobacillus thermoglucosidasius. ACS Synth Biol 2022; 11:2163-2174. [PMID: 35677969 DOI: 10.1021/acssynbio.2c00087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient utilization of both glucose and xylose, the two most abundant sugars in biomass hydrolysates, is one of the main objectives of biofermentation with lignocellulosic materials. The utilization of xylose is commonly inhibited by glucose, which is known as glucose catabolite repression (GCR). Here, we report a GCR-based dynamic control (GCR-DC) strategy aiming at better co-utilization of glucose and xylose, by decoupling the cell growth and biosynthesis of riboflavin as a product. Using the thermophilic strain Geobacillus thermoglucosidasius DSM 2542 as a host, we constructed additional riboflavin biosynthetic pathways that were activated by xylose but not glucose. The engineered strains showed a two-stage fermentation process. In the first stage, glucose was preferentially used for cell growth and no production of riboflavin was observed, while in the second stage where glucose was nearly depleted, xylose was effectively utilized for riboflavin biosynthesis. Using corn cob hydrolysate as a carbon source, the optimized riboflavin yields of strains DSM2542-DCall-MSS (full pathway dynamic control strategy) and DSM2542-DCrib (single-module dynamic control strategy) were 5.3- and 2.3-fold higher than that of the control strain DSM 2542 Rib-Gtg constitutively producing riboflavin, respectively. This GCR-DC strategy should also be applicable to the construction of cell factories that can efficiently use natural carbon sources with multiple sugar components for the production of high-value chemicals in future.
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Affiliation(s)
- Junyang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Pang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fang Yuan
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Huizhuan Wang
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Zhen Xu
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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9
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You J, Du Y, Pan X, Zhang X, Yang T, Rao Z. Increased Production of Riboflavin by Coordinated Expression of Multiple Genes in Operons in Bacillus subtilis. ACS Synth Biol 2022; 11:1801-1810. [PMID: 35467340 DOI: 10.1021/acssynbio.1c00640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboflavin is an essential vitamin widely used in the food, pharmaceutical, and feed industries. However, the insufficient supply of precursors caused by the imbalance of intracellular metabolic flow limits the riboflavin synthesis by industrial strains. Here, we increase riboflavin production by tuning multiple gene expression to balance intracellular metabolic flow. First, we tuned the expression of mCherry and egfp genes within operons by generating libraries of tunable intergenic regions (TIGRs) and confirmed the relative expression of the two reporter genes. The TIGR library can coordinate the expression ratio of reporter genes more than 180 times in Escherichia coli and more than 70 times in Bacillus subtilis. Next, we used this strategy to tune the expression of zwf, ribBA, and ywlf genes within operons through the TIGR library to increase the intracellular precursor pool for riboflavin biosynthesis. Based on the fluorescence characteristics of riboflavin, 96-well plates were used to screen the optimal combination mutants quickly. The best-engineered strain was selected from the library, which produced 2.7 g/L riboflavin, increasing by 64.35% in the shake flask. Finally, the riboflavin titer increased by 59.27% to 11.77 g/L in fed-batch fermentation. The strategy described here will contribute to the industrial production of riboflavin and related products by B. subtilis.
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Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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10
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Zhang M, Zhao X, Chen X, Li M, Wang X. Enhancement of riboflavin production in Bacillus subtilis via in vitro and in vivo metabolic engineering of pentose phosphate pathway. Biotechnol Lett 2021; 43:2209-2216. [PMID: 34606014 DOI: 10.1007/s10529-021-03190-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES The production of riboflavin with Bacillus subtilis, is an established process, however it is yet to be fully optimized. The aim of this study was to explore how riboflavin yields can be improved via in vitro and in vivo metabolic engineering modification of the pentose phosphate pathway (PPP). RESULTS In vitro, glucose was replaced with sodium gluconate to enhance PPP. Flask tests showed that the riboflavin titer increased from 0.64 to 0.87 g/L. The results revealed that the direct use of sodium gluconate could benefit riboflavin production. In vivo, gntP (encoding gluconate permease) was overexpressed to improve sodium gluconate uptake. The riboflavin titer reached 1.00 g/L with the mutant B. subtilis RF01. Ultimately, the fermentation verification of the engineered strain was carried out in a 7-L fermenter, with the increased riboflavin titer validating this approach. CONCLUSIONS The combination of metabolic engineering modifications in vitro and in vivo was confirmed to promote riboflavin production efficiently by increasing PPP and has great potential for industrial application. This work is aimed to explore how to improve the riboflavin yield by the rational renovation of the pentose phosphate pathway (PPP). In vitro, metabolic engineering mainly uses sodium gluconate as a carbon source instead of glucose, and in vivo, metabolic engineering mainly includes the overexpression of sodium gluconate utility-related genes. The effect of sodium gluconate on cell growth, riboflavin production was investigated in the flasks and fermenter scale.
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Affiliation(s)
- Mengxue Zhang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xingcong Zhao
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xi Chen
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Mingyue Li
- College of Biological Science, University of California, Davis, USA
| | - Xuedong Wang
- State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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11
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Liu S, Hu W, Wang Z, Chen T. Rational Engineering of Escherichia coli for High-Level Production of Riboflavin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12241-12249. [PMID: 34623820 DOI: 10.1021/acs.jafc.1c04471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Riboflavin is widely used as a food additive. Here, multiple strategies were used to increase riboflavin production in Escherichia coli LS31T. First, purR deletion and co-overexpression of fbp, purF, prs, gmk, and ndk genes resulted in an increase of 18.6% in riboflavin titer (reaching 729.7 mg/L). Second, optimization of reduced nicotinamide adenine dinucleotide phosphate/nicotinamide adenine dinucleotide ratio and respiratory chain activity in LS31T increased the titer up to 1020.2 mg/L. Third, the expression level of the guaC gene in LS31T was downregulated by ribosome binding site replacement, and the riboflavin production was increased by 10.6% to 658.5 mg/L. Then, all the favorable modifications were integrated together, and the resulting strain LS72T produced 1339 mg/L of riboflavin. Moreover, the riboflavin titer of LS72T reached 21 g/L in fed-batch cultivation, with a yield of 110 mg riboflavin/g glucose. To our knowledge, both the riboflavin titer and yield obtained in fed-batch fermentation are the highest ones among all the rationally engineered strains.
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Affiliation(s)
- Shuang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Wenya Hu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Zhiwen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
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12
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You J, Pan X, Yang C, Du Y, Osire T, Yang T, Zhang X, Xu M, Xu G, Rao Z. Microbial production of riboflavin: Biotechnological advances and perspectives. Metab Eng 2021; 68:46-58. [PMID: 34481976 DOI: 10.1016/j.ymben.2021.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/19/2021] [Accepted: 08/31/2021] [Indexed: 10/24/2022]
Abstract
Riboflavin is an essential nutrient for humans and animals, and its derivatives flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are cofactors in the cells. Therefore, riboflavin and its derivatives are widely used in the food, pharmaceutical, nutraceutical and cosmetic industries. Advances in biotechnology have led to a complete shift in the commercial production of riboflavin from chemical synthesis to microbial fermentation. In this review, we provide a comprehensive review of biotechnologies that enhance riboflavin production in microorganisms, as well as representative examples. Firstly, the synthesis pathways and metabolic regulatory processes of riboflavin in microorganisms; and the current strategies and methods of metabolic engineering for riboflavin production are systematically summarized and compared. Secondly, the using of systematic metabolic engineering strategies to enhance riboflavin production is discussed, including laboratory evolution, histological analysis and high-throughput screening. Finally, the challenges for efficient microbial production of riboflavin and the strategies to overcome these challenges are prospected.
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Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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13
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You J, Yang C, Pan X, Hu M, Du Y, Osire T, Yang T, Rao Z. Metabolic engineering of Bacillus subtilis for enhancing riboflavin production by alleviating dissolved oxygen limitation. BIORESOURCE TECHNOLOGY 2021; 333:125228. [PMID: 33957462 DOI: 10.1016/j.biortech.2021.125228] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Riboflavin, an essential vitamin for animals, is used widely in the pharmaceutical industry and as a food and feed additive. The microbial synthesis of riboflavin requires a large amount of oxygen, which limits the industrial-scale production of the vitamin. In this study, a metabolic engineering strategy based on transcriptome analysis was identified as effective in increasing riboflavin production. First, transcriptional profiling revealed that hypoxia affects purine, and nitrogen metabolism. Next, the precursor supply pool was increased by purR knockout and tnrA and glnR knockdown to balance intracellular nitrogen metabolism. Finally, increased oxygen utilization was achieved by dynamically regulating vgb. Fed-batch fermentation of the engineered strain in a 5-liter bioreactor produced 10.71 g/l riboflavin, a 45.51% higher yield than that obtained with Bacillus subtilis RF1. The metabolic engineering strategy described herein is useful for alleviating the oxygen limitation of bacterial strains used for the industrial production of riboflavin and related products.
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Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mengkai Hu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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14
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Fedorovych DV, Dmytruk KV, Sibirny AA. Recent Advances in Construction of the Efficient Producers of Riboflavin and Flavin Nucleotides (FMN, FAD) in the Yeast Candida famata. Methods Mol Biol 2021; 2280:15-30. [PMID: 33751426 DOI: 10.1007/978-1-0716-1286-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The approaches used by the authors to design the Candida famata strains capable to overproduce riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) are described. The metabolic engineering approaches include overexpression of SEF1 gene encoding positive regulator of riboflavin biosynthesis, IMH3 (coding for IMP dehydrogenase) orthologs from another species of flavinogenic yeast Debaryomyces hansenii, and the homologous genes RIB1 and RIB7 encoding GTP cyclohydrolase II and riboflavin synthase, the first and the last enzymes of riboflavin biosynthesis pathway, respectively. Overexpression of the above mentioned genes in the genetically stable riboflavin overproducer AF-4 obtained by classical selection resulted in fourfold increase of riboflavin production in shake flask experiments.Overexpression of engineered enzymes phosphoribosyl pyrophosphate synthetase and phosphoribosyl pyrophosphate amidotransferase catalyzing the initial steps of purine nucleotide biosynthesis enhances riboflavin synthesis in the flavinogenic yeast C. famata even more.Recombinant strains of C. famata containing FMN1 gene from D. hansenii encoding riboflavin kinase under control of the strong constitutive TEF1 promoter were constructed. Overexpression of the FMN1 gene in the riboflavin-producing mutant led to the 30-fold increase of the riboflavin kinase activity and 400-fold increase of FMN production in the resulting recombinant strains which reached maximally 318.2 mg/L.FAD overproducing strains of C. famata were also constructed. This was achieved by overexpression of FAD1 gene from D. hansenii in C. famata FMN overproducing strain. The 7- to 15-fold increase in FAD synthetase activity as compared to the wild-type strain and FAD accumulation into cultural medium were observed. The maximal FAD titer 451.5 mg/L was achieved.
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Affiliation(s)
- Dariya V Fedorovych
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
| | - Andriy A Sibirny
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine.
- Department of Microbiology and Biotechnology, University of Rzeszow, Rzeszow, Poland.
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15
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Yang H, Zhang X, Liu Y, Liu L, Li J, Du G, Chen J. Synthetic biology-driven microbial production of folates: Advances and perspectives. BIORESOURCE TECHNOLOGY 2021; 324:124624. [PMID: 33434873 DOI: 10.1016/j.biortech.2020.124624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
With the development and application of synthetic biology, significant progress has been made in the production of folate by microbial fermentation using cell factories, especially for using generally regarded as safe (GRAS) microorganism as production host. In this review, the physiological functions and applications of folates were firstly discussed. Second, the current advances of folate-producing GRAS strains development were summarized. Third, the applications of synthetic biology-based metabolic regulatory tools in GRAS strains were introduced, and the progress in the application of these tools for folate production were summarized. Finally, the challenges to folates efficient production and corresponding emerging strategies to overcome them by synthetic biology were discussed, including the construction of biosensors using tetrahydrofolate riboswitches to regulate metabolic pathways, adaptive evolution to overcome the flux limitations of the folate pathway. The combination of new strategies and tools of synthetic biology is expected to further improve the efficiency of microbial folate synthesis.
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Affiliation(s)
- Han Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiaolong Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China; Qingdao Special Food Research Institute, Qingdao 266109, China.
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16
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Hoff B, Plassmeier J, Blankschien M, Letzel AC, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power-Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2021; 60:2258-2278. [PMID: 33026132 DOI: 10.1002/anie.202004248] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Fermentation as a production method for chemicals is especially attractive, as it is based on cheap renewable raw materials and often exhibits advantages in terms of costs and sustainability. The tremendous development of technology in bioscience has resulted in an exponentially increasing knowledge about biological systems and has become the main driver for innovations in the field of metabolic engineering. Progress in recombinant DNA technology, genomics, and computational methods open new, cheaper, and faster ways to metabolically engineer microorganisms. Existing biosynthetic pathways for natural products, such as vitamins, organic acids, amino acids, or secondary metabolites, can be discovered and optimized efficiently, thereby enabling competitive commercial production processes. Novel biosynthetic routes can now be designed by the rearrangement of nature's unlimited number of enzymes and metabolic pathways in microbial strains. This expands the range of chemicals accessible by biotechnology and has yielded the first commercial products, while new fermentation technologies targeting novel active ingredients, commodity chemicals, and CO2 -fixation methods are on the horizon.
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Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Jens Plassmeier
- Biomaterials, Conagen, Inc., 15 DeAngelo Drive, 01730, Bedford, MA, USA
| | - Matthew Blankschien
- James R. Randall Research Center, ADM, 1001 North Brush College Road, 62521, Decatur, Il, USA
| | - Anne-Catrin Letzel
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Lauralynn Kourtz
- R&D, Allied Microbiota, 1345 Ave of Americas, 10105, New York, NY, USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Walter Koch
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
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17
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Yang BT, Wen B, Ji Y, Wang Q, Zhang HR, Zhang Y, Gao JZ, Chen ZZ. Comparative metabolomics analysis of pigmentary and structural coloration in discus fish (Symphysodon haraldi). J Proteomics 2020; 233:104085. [PMID: 33378721 DOI: 10.1016/j.jprot.2020.104085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 12/15/2022]
Abstract
Discus fish have a variety of body colors including pigmentary and structural colors, studies on specific substances and related metabolic pathways associated with body coloration, however, are scarce to the present. Here, we used single-color (blue, yellow and white) of discus for comparative metabolomics analysis of pigmentary and structural coloration. Statistical model showed significant separations between three colors of discus, suggesting the distinct metabolite profiles of discus pigmentary and structural colors. More astaxanthin was found in yellow discus, which might be the cause of yellow pigmentary color. Moreover, docosahexaenoic acid, arachidonic acid, linoleic acid, eicosapentaenoic acid, 1-stearoyl-2-oleoyl-sn-glycerol 3-phosphocholine, dodecanoic acid and myristic acid related to lipid metabolism and pathways of ABC transporters and biosynthesis of unsaturated fatty acids were more enriched in yellow discus. More adenine, xanthine and hypoxanthine were enriched in blue discus, which might account for the blue structural color. Moreover, amino acids associated with purine biosynthesis, e.g., L-alanine and L-isoleucine, were reduced but pathways of protein digestion and absorption, aminoacyl-tRNA biosynthesis, purine metabolism and glycine, serine and threonine metabolism were enriched in blue discus. Overall, these results reveal specific chromophores and related metabolic pathways involved in pigmentary and structural coloration of discus fish. SIGNIFICANCE: We detected specific chromophores present in skin of pigmentary and structural colors of discus and revealed potential metabolic pathways associated with body coloration. These results contribute to our understanding of the mechanism of body color formation in discus fish.
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Affiliation(s)
- Bo-Tian Yang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Bin Wen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
| | - Yu Ji
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Qin Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Hao-Ran Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Yuan Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jian-Zhong Gao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Zai-Zhong Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China.
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18
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Sun Y, Liu C, Tang W, Zhang D. Manipulation of Purine Metabolic Networks for Riboflavin Production in Bacillus subtilis. ACS OMEGA 2020; 5:29140-29146. [PMID: 33225145 PMCID: PMC7675574 DOI: 10.1021/acsomega.0c03867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Guanosine monophosphate, the precursor for riboflavin biosynthesis, can be converted to or generated from other purine compounds in purine metabolic networks. In this study, genes in these networks were manipulated in a riboflavin producer, Bacillus subtilis R, to test their contribution to riboflavin biosynthesis. Knocking out adenine phosphoribosyltransferase (apt), xanthine phosphoribosyltransferase (xpt), and adenine deaminase (adeC) increased the riboflavin production by 14.02, 6.78, and 41.50%, respectively, while other deletions in the salvage pathway, interconversion pathway, and nucleoside decomposition genes have no positive effects. The enhancement of riboflavin production in apt and adeC deletion mutants is dependent on the purine biosynthesis regulator PurR. Repression of ribonucleotide reductases (RNRs) led to a 13.12% increase of riboflavin production, which also increased in two RNR regulator mutants PerR and NrdR by 37.52 and 8.09%, respectively. The generation of deoxyribonucleoside competed for precursors with riboflavin biosynthesis, while other pathways do not contribute to the supply of precursors; nevertheless, they have regulatory effects.
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Affiliation(s)
- Yiwen Sun
- Department
of Biological Sciences, School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, People’s Republic of China
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, People’s Republic
of China
| | - Chuan Liu
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, People’s Republic
of China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic
of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
| | - Wenzhu Tang
- Department
of Biological Sciences, School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, People’s Republic of China
| | - Dawei Zhang
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, People’s Republic
of China
- Key
Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic
of China
- University
of Chinese Academy of Sciences, Beijing 100049, People’s
Republic of China
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19
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Hoff B, Plassmeier J, Blankschien M, Letzel A, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power—Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Jens Plassmeier
- Biomaterials Conagen, Inc. 15 DeAngelo Drive 01730 Bedford, MA USA
| | - Matthew Blankschien
- James R. Randall Research Center ADM 1001 North Brush College Road 62521 Decatur, Il USA
| | - Anne‐Catrin Letzel
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Lauralynn Kourtz
- R&D Allied Microbiota 1345 Ave of Americas 10105 New York, NY USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Walter Koch
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
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20
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Dmytruk KV, Ruchala J, Fedorovych DV, Ostapiv RD, Sibirny AA. Modulation of the Purine Pathway for Riboflavin Production in Flavinogenic Recombinant Strain of the Yeast Candida famata. Biotechnol J 2020; 15:e1900468. [PMID: 32087089 DOI: 10.1002/biot.201900468] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 02/10/2020] [Indexed: 11/10/2022]
Abstract
Riboflavin (vitamin B2 ) is an indispensable nutrient for humans and animals, since it is the precursor of the essential coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), involved in variety of metabolic reactions. Riboflavin is produced on commercial scale and is used for feed and food fortification purposes, and in medicine. Until recently, the mutant strains of the flavinogenic yeast Candida famata were used in industry for riboflavin production. Guanosine triphosphate is the immediate precursor of riboflavin synthesis. Therefore, the activation of metabolic flux toward purine nucleotide biosynthesis is a promising approach to improve riboflavin production. The phosphoribosyl pyrophosphate synthetase and phosphoribosyl pyrophosphate amidotransferase are the rate limiting enzymes in purine biosynthesis. Corresponding genes PRS3 and ADE4 from yeast Debaryomyces hansenii are modified to avoid feedback inhibition and cooverexpressed on the background of a previously constructed riboflavin overproducing strain of C. famata. Constructed strain accumulates twofold more riboflavin when compared to the parental strain.
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Affiliation(s)
- Kostyantyn V Dmytruk
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza, 4, Rzeszow, 35-601, Poland
| | - Daria V Fedorovych
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Roman D Ostapiv
- Laboratory of high-performance liquid chromatography, State Scientific-Research Control Institute of Veterinary Medicinal Products and Feed Additives, Donetska Street, 11, Lviv, 79019, Ukraine
| | - Andriy A Sibirny
- Department of Molecular Biology and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine.,Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza, 4, Rzeszow, 35-601, Poland
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Liu S, Hu W, Wang Z, Chen T. Production of riboflavin and related cofactors by biotechnological processes. Microb Cell Fact 2020; 19:31. [PMID: 32054466 PMCID: PMC7017516 DOI: 10.1186/s12934-020-01302-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Riboflavin (RF) and its active forms, the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), have been extensively used in the food, feed and pharmaceutical industries. Modern commercial production of riboflavin is based on microbial fermentation, but the established genetically engineered production strains are facing new challenges due to safety concerns in the food and feed additives industry. High yields of flavin mononucleotide and flavin adenine dinucleotide have been obtained using whole-cell biocatalysis processes. However, the necessity of adding expensive precursors results in high production costs. Consequently, developing microbial cell factories that are capable of efficiently producing flavin nucleotides at low cost is an increasingly attractive approach. The biotechnological processes for the production of RF and its cognate cofactors are reviewed in this article.
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Affiliation(s)
- Shuang Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Wenya Hu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
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Wang J, Guo R, Wang W, Ma G, Li S. Insight into the surfactin production of Bacillus velezensis B006 through metabolomics analysis. ACTA ACUST UNITED AC 2018; 45:1033-1044. [PMID: 30203399 DOI: 10.1007/s10295-018-2076-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/30/2018] [Indexed: 11/25/2022]
Abstract
Abstract
Bacillus velezensis B006 is a biocontrol agent which functions through effective colonization and surfactin production. To reveal the surfactin-producing mechanism, gas chromatography–mass spectrometry based untargeted metabolomics was performed to compare the metabolite profiles of strain B006 grown in industrial media M3 and M4. Based on the statistical and pathway topology analyses, a total of 31 metabolites with a fold change of less than − 1.0 were screened as the significantly altered metabolites, which distributed in 15 metabolic pathways. Fourteen amino acids involving in the metabolisms of alanine/aspartate/glutamate, glycine/serine/threonine, arginine/proline, glutathione/cysteine/methionine and valine/leucine/isoleucine as well as succinic acid in TCA cycle were identified to be the hub metabolites. Aminoacyl-tRNA biosynthesis, glycerolipid metabolism, and pantothenate/CoA biosynthesis also contributed to surfactin production. To the best of our knowledge, this study is the first to investigate the metabolic pathways of B. velezensis on surfactin production, and will benefit the optimization of commercial fermentation for higher surfactin yield.
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Affiliation(s)
- Junqiang Wang
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
- Jiangsu Frey Agrochemicals Co. Ltd 222005 Lianyungang Jiangsu China
| | - Rongjun Guo
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
| | - Wenchao Wang
- Shanghai ProfLeader Biotech Co. Ltd 200231 Shanghai China
| | - Guizhen Ma
- 0000 0004 1800 0658 grid.443480.f School of Chemical Engineering Huaihai Institute of Technology 222005 Lianyungang Jiangsu China
| | - Shidong Li
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
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Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications. Metab Eng 2018; 50:109-121. [DOI: 10.1016/j.ymben.2018.05.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 01/29/2023]
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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Bioproduction of riboflavin: a bright yellow history. J Ind Microbiol Biotechnol 2016; 44:659-665. [PMID: 27696023 DOI: 10.1007/s10295-016-1842-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Riboflavin (vitamin B2) is an essential nutrient for humans and animals that must be obtained from the diet. To ensure an optimal supply, riboflavin is used on a large scale as additive in the food and feed industries. Here, we describe a historical overview of the industrial process of riboflavin production starting from its discovery and the need to produce the vitamin in bulk at prices that would allow for their use in human and animal nutrition. Riboflavin was produced industrially by chemical synthesis for many decades. At present, the development of economical and eco-efficient fermentation processes, which are mainly based on Bacillus subtilis and Ashbya gossypii strains, has replaced the synthetic process at industrial scale. A detailed account is given of the development of the riboflavin overproducer strains as well as future prospects for its improvement.
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Liu S, Kang P, Cui Z, Wang Z, Chen T. Increased riboflavin production by knockout of 6-phosphofructokinase I and blocking the Entner-Doudoroff pathway in Escherichia coli. Biotechnol Lett 2016; 38:1307-14. [PMID: 27071937 DOI: 10.1007/s10529-016-2104-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/06/2016] [Indexed: 01/30/2023]
Abstract
OBJECTIVES To construct an Escherichia coli strain capable of producing riboflavin with high titer and yield. RESULTS A low copy number plasmid pLS01 containing a riboflavin operon under the control of a constitutive promoter was constructed and introduced into Escherichia coli MG1655. Subsequently, the pfkA, edd and ead genes were disrupted, and the resulting strain LS02T produced 667 mg riboflavin/l in MSY medium supplied with 10 g glucose/l in flask cultivation. In a fed-batch process, riboflavin production of the strain reached 10.4 g/l with a yield of 56.8 mg riboflavin/g glucose. CONCLUSION To our knowledge, this is the first report of engineered E. coli strains that can produce more than 10 g riboflavin/l in fed-batch cultivation, indicating that E. coli has potential for riboflavin production.
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Affiliation(s)
- Shuang Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Pei Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Zhenzhen Cui
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, People's Republic of China.
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Biotechnology of riboflavin. Appl Microbiol Biotechnol 2016; 100:2107-19. [DOI: 10.1007/s00253-015-7256-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
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Thakur K, Tomar SK, De S. Lactic acid bacteria as a cell factory for riboflavin production. Microb Biotechnol 2015; 9:441-51. [PMID: 26686515 PMCID: PMC4919986 DOI: 10.1111/1751-7915.12335] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 11/30/2022] Open
Abstract
Consumers are increasingly becoming aware of their health and nutritional requirements, and in this context, vitamins produced in situ by microbes may suit their needs and expectations. B groups vitamins are essential components of cellular metabolism and among them riboflavin is one of the vital vitamins required by bacteria, plants, animals and humans. Here, we focus on the importance of microbial production of riboflavin over chemical synthesis. In addition, genetic abilities for riboflavin biosynthesis by lactic acid bacteria are discussed. Genetically modified strains by employing genetic engineering and chemical analogues have been developed to enhance riboflavin production. The present review attempts to collect the currently available information on riboflavin production by microbes in general, while placing greater emphasis on food grade lactic acid bacteria and human gut commensals. For designing riboflavin‐enriched functional foods, proper selection and exploitation of riboflavin‐producing lactic acid bacteria is essential. Moreover, eliminating the in situ vitamin fortification step will decrease the cost of food production.
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Affiliation(s)
- Kiran Thakur
- Division of Dairy Microbiology, National Dairy Research Institute, Karnal, Haryana, India
| | - Sudhir Kumar Tomar
- Division of Dairy Microbiology, National Dairy Research Institute, Karnal, Haryana, India
| | - Sachinandan De
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
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Xu Z, Lin Z, Wang Z, Chen T. Improvement of the riboflavin production by engineering the precursor biosynthesis pathways in Escherichia coli. Chin J Chem Eng 2015. [DOI: 10.1016/j.cjche.2015.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zhai Y, Han D, Pan Y, Wang S, Fang J, Wang P, Liu XW. Enhancing GDP-fucose production in recombinant Escherichia coli by metabolic pathway engineering. Enzyme Microb Technol 2014; 69:38-45. [PMID: 25640723 DOI: 10.1016/j.enzmictec.2014.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/10/2014] [Accepted: 12/01/2014] [Indexed: 01/22/2023]
Abstract
Guanosine 5'-diphosphate (GDP)-fucose is the indispensible donor substrate for fucosyltransferase-catalyzed synthesis of fucose-containing biomolecules, which have been found involving in various biological functions. In this work, the salvage pathway for GDP-fucose biosynthesis from Bacterioides fragilis was introduced into Escherichia coli. Besides, the biosynthesis of guanosine 5'-triphosphate (GTP), an essential substrate for GDP-fucose biosynthesis, was enhanced via overexpression of enzymes involved in the salvage pathway of GTP biosynthesis. The production capacities of metabolically engineered strains bearing different combinations of recombinant enzymes were compared. The shake flask fermentation of the strain expressing Fkp, Gpt, Gmk and Ndk obtained the maximum GDP-fucose content of 4.6 ± 0.22 μmol/g (dry cell mass), which is 4.2 fold that of the strain only expressing Fkp. Through fed-batch fermentation, the GDP-fucose content further rose to 6.6 ± 0.14 μmol/g (dry cell mass). In addition to a better productivity than previous fermentation processes based on the de novo pathway for GDP-fucose biosynthesis, the established schemes in this work also have the advantage to be a potential avenue to GDP-fucose analogs encompassing chemical modification on the fucose residue.
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Affiliation(s)
- Yafei Zhai
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China; The State Key Laboratory of Microbial Technology and School of Life Science, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Donglei Han
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China; The State Key Laboratory of Microbial Technology and School of Life Science, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Ying Pan
- The State Key Laboratory of Microbial Technology and School of Life Science, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Shuaishuai Wang
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China; The State Key Laboratory of Microbial Technology and School of Life Science, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Junqiang Fang
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Peng Wang
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China
| | - Xian-wei Liu
- National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250100, People's Republic of China.
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Lin Z, Xu Z, Li Y, Wang Z, Chen T, Zhao X. Metabolic engineering of Escherichia coli for the production of riboflavin. Microb Cell Fact 2014; 13:104. [PMID: 25027702 PMCID: PMC4223517 DOI: 10.1186/s12934-014-0104-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/09/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Riboflavin (vitamin B2), the precursor of the flavin cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), is used commercially as an animal feed supplement and food colorant. E. coli is a robust host for various genetic manipulations and has been employed for efficient production of biofuels, polymers, amino acids, and bulk chemicals. Thus, the aim of this study was to understand the metabolic capacity of E. coli for the riboflavin production by modification of central metabolism, riboflavin biosynthesis pathway and optimization of the fermentation conditions. RESULTS The basic producer RF01S, in which the riboflavin biosynthesis genes ribABDEC from E. coli were overexpressed under the control of the inducible trc promoter, could accumulate 229.1 mg/L of riboflavin. Further engineering was performed by examining the impact of expression of zwf (encodes glucose 6-phosphate dehydrogenase) and gnd (encodes 6-phosphogluconate dehydrogenase) from Corynebacterium glutamicum and pgl (encodes 6-phosphogluconolactonase) from E. coli on riboflavin production. Deleting pgi (encodes glucose-6-phosphate isomerase) and genes of Entner-Doudoroff (ED) pathway successfully redirected the carbon flux into the oxidative pentose phosphate pathway, and overexpressing the acs (encodes acetyl-CoA synthetase) reduced the acetate accumulation. These modifications increased riboflavin production to 585.2 mg/L. By further modulating the expression of ribF (encodes riboflavin kinase) for reducing the conversion of riboflavin to FMN in RF05S, the final engineering strain RF05S-M40 could produce 1036.1 mg/L riboflavin in LB medium at 37°C. After optimizing the fermentation conditions, strain RF05S-M40 produced 2702.8 mg/L riboflavin in the optimized semi-defined medium, which was a value nearly 12-fold higher than that of RF01S, with a yield of 137.5 mg riboflavin/g glucose. CONCLUSIONS The engineered strain RF05S-M40 has the highest yield among all reported riboflavin production strains in shake flask culture. This work collectively demonstrates that E. coli has a potential to be a microbial cell factory for riboflavin bioproduction.
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Affiliation(s)
- Zhenquan Lin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Zhibo Xu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Yifan Li
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xueming Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People’s Republic of China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, People’s Republic of China
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Shi T, Wang Y, Wang Z, Wang G, Liu D, Fu J, Chen T, Zhao X. Deregulation of purine pathway in Bacillus subtilis and its use in riboflavin biosynthesis. Microb Cell Fact 2014; 13:101. [PMID: 25023436 PMCID: PMC4223553 DOI: 10.1186/s12934-014-0101-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/06/2014] [Indexed: 11/15/2022] Open
Abstract
Background Purine nucleotides are essential metabolites for living organisms because they are involved in many important processes, such as nucleic acid synthesis, energy supply, and biosynthesis of several amino acids and riboflavin. Owing to the pivotal roles of purines in cell physiology, the pool of intracellular purine nucleotides must be maintained under strict control, and hence the de novo purine biosynthetic pathway is tightly regulated by transcription repression and inhibition mechanism. Deregulation of purine pathway is essential for this pathway engineering in Bacillus subtilis. Results Deregulation of purine pathway was attempted to improve purine nucleotides supply, based on a riboflavin producer B. subtilis strain with modification of its rib operon. To eliminate transcription repression, the pur operon repressor PurR and the 5’-UTR of pur operon containing a guanine-sensing riboswitch were disrupted. Quantitative RT-PCR analysis revealed that the relative transcription levels of purine genes were up-regulated about 380 times. Furthermore, site-directed mutagenesis was successfully introduced into PRPP amidotransferase (encoded by purF) to remove feedback inhibition by homologous alignment and analysis. Overexpression of the novel mutant PurF (D293V, K316Q and S400W) significantly increased PRPP amidotransferase activity and triggered a strong refractory effect on purine nucleotides mediated inhibition. Intracellular metabolite target analysis indicated that the purine nucleotides supply in engineered strains was facilitated by a stepwise gene-targeted deregulation. With these genetic manipulations, we managed to enhance the metabolic flow through purine pathway and consequently increased riboflavin production 3-fold (826.52 mg/L) in the purF-VQW mutant strain. Conclusions A sequential optimization strategy was applied to deregulate the rib operon and purine pathway of B. subtilis to create genetic diversities and to improve riboflavin production. Based on the deregulation of purine pathway at transcription and metabolic levels, an extended application is recommended for the yield of products, like inosine, guanosine, adenosine and folate which are directly stemming from purine pathway in B. subtilis.
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Enhancement of riboflavin production by deregulating gluconeogenesis in Bacillus subtilis. World J Microbiol Biotechnol 2014; 30:1893-900. [DOI: 10.1007/s11274-014-1611-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 01/19/2014] [Indexed: 10/25/2022]
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Birkenmeier M, Neumann S, Röder T. Kinetic modeling of riboflavin biosynthesis in Bacillus subtilis under production conditions. Biotechnol Lett 2014; 36:919-28. [PMID: 24442413 DOI: 10.1007/s10529-013-1435-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 12/12/2013] [Indexed: 11/29/2022]
Abstract
To study the network dynamics of the riboflavin biosynthesis pathway and to identify potential bottlenecks in the system, an ordinary differential equation-based model was constructed using available literature data for production strains. The results confirmed that the RibA protein is rate limiting in the pathway. Under the conditions investigated, we determined a potential limiting order of the remaining enzymes under increased RibA concentration (>0.102 mM) and therefore higher riboflavin production (>0.045 mmol g(CDW)(-1) h(-1) and 0.0035 mM s(-1), respectively). The reductase activity of RibG and lumazine synthase (RibH) might be the next most limiting steps. The computational minimization of the enzyme concentrations of the pathway suggested the need for a greater RibH concentration (0.251 mM) compared with the other enzymes (RibG: 0.188 mM, RibB: 0.023 mM).
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Affiliation(s)
- Markus Birkenmeier
- Institute of Chemical Process Engineering, Mannheim University of Applied Sciences, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany,
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Abstract
Transcriptome profiling allows massively parallel analysis of the dynamic expression of all genes and captures the cell physiology and regulatory mechanism in a holistic manner. Compared to other "omic" techniques, transcriptome is more tractable and sensitive. Transcriptomics has profoundly promoted development and applications of metabolic engineering by analysis of cell metabolism at a system level. Our recent effort was performed on a comparative transcriptome profiling between a riboflavin-producing Bacillus subtilis strain RH33 and the wild-type strain B. subtilis 168 to rationally identify new targets for improving riboflavin production. This transcriptome analysis-guided method improved the riboflavin titer by 32 ± 3 %. Herein, we describe the detailed experimental protocols for predicting new engineering targets using comparative transcriptome analysis.
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Liu L, Liu Y, Shin HD, Chen RR, Wang NS, Li J, Du G, Chen J. Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology. Appl Microbiol Biotechnol 2013; 97:6113-27. [DOI: 10.1007/s00253-013-4960-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/25/2013] [Accepted: 04/27/2013] [Indexed: 01/29/2023]
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Hao T, Han B, Ma H, Fu J, Wang H, Wang Z, Tang B, Chen T, Zhao X. In silico metabolic engineering of Bacillus subtilis for improved production of riboflavin, Egl-237, (R,R)-2,3-butanediol and isobutanol. MOLECULAR BIOSYSTEMS 2013; 9:2034-44. [DOI: 10.1039/c3mb25568a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Jayashree S, Rajendhran J, Jayaraman K, Kalaichelvan G, Gunasekaran P. Improvement of Riboflavin Production byLactobacillus fermentumIsolated from Yogurt. FOOD BIOTECHNOL 2011. [DOI: 10.1080/08905436.2011.590769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wang Z, Chen T, Ma X, Shen Z, Zhao X. Enhancement of riboflavin production with Bacillus subtilis by expression and site-directed mutagenesis of zwf and gnd gene from Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2011; 102:3934-40. [PMID: 21194928 DOI: 10.1016/j.biortech.2010.11.120] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/23/2010] [Accepted: 11/25/2010] [Indexed: 05/03/2023]
Abstract
Zwf (code for glucose-6-phosphate dehydrogenase) and gnd (code for 6-phosphogluconate dehydrogenase) genes from Corynebacterium glutamicum were firstly cloned, and then site-directed mutagenesis was successfully introduced to remove allosteric inhibition by intracellular metabolites. Expression of the mutant zwf and gnd in Bacillus subtilis RH33 resulted in significant enhancement of riboflavin productivity, while the specific growth rate decreased slightly and the specific glucose uptake rate was unchanged. Introduction of the mutant zwf and gnd led to approximately 18% and 22% increased riboflavin production, respectively. An improvement by 31% and 39% of the riboflavin production was obtained by co-expression of the mutated dehydrogenases in shaker flask and fed-batch cultivation. Intracellular metabolites analysis indicated that metabolites detected in pentose phosphate pathway or riboflavin synthesis pathway of engineered strains showed higher concentration, while TCA cycle and glycolysis metabolites detected were lower abundance than that of parent strain.
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Affiliation(s)
- Zhiwen Wang
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, People's Republic of China
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