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Liu C, Xia M, Fang H, Xu F, Wang S, Zhang D. De novo engineering riboflavin production Bacillus subtilis by overexpressing the downstream genes in the purine biosynthesis pathway. Microb Cell Fact 2024; 23:159. [PMID: 38822377 PMCID: PMC11141002 DOI: 10.1186/s12934-024-02426-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 05/16/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Bacillus subtilis is widely used in industrial-scale riboflavin production. Previous studies have shown that targeted mutagenesis of the ribulose 5-phosphate 3-epimerase in B. subtilis can significantly enhance riboflavin production. This modification also leads to an increase in purine intermediate concentrations in the medium. Interestingly, B. subtilis exhibits remarkable efficiency in purine nucleoside synthesis, often exceeding riboflavin yields. These observations highlight the importance of the conversion steps from inosine-5'-monophosphate (IMP) to 2,5-diamino-6-ribosylamino-4(3 H)-pyrimidinone-5'-phosphate (DARPP) in riboflavin production by B. subtilis. However, research elucidating the specific impact of these reactions on riboflavin production remains limited. RESULT We expressed the genes encoding enzymes involved in these reactions (guaB, guaA, gmk, ndk, ribA) using a synthetic operon. Introduction of the plasmid carrying this synthetic operon led to a 3.09-fold increase in riboflavin production compared to the control strain. Exclusion of gmk from the synthetic operon resulted in a 36% decrease in riboflavin production, which was further reduced when guaB and guaA were not co-expressed. By integrating the synthetic operon into the genome and employing additional engineering strategies, we achieved riboflavin production levels of 2702 mg/L. Medium optimization further increased production to 3477 mg/L, with a yield of 0.0869 g riboflavin per g of sucrose. CONCLUSION The conversion steps from IMP to DARPP play a critical role in riboflavin production by B. subtilis. Our overexpression strategies have demonstrated their effectiveness in overcoming these limiting factors and enhancing riboflavin production.
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Affiliation(s)
- Chuan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Miaomiao Xia
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Xu
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- School of Chemical Engineering, Hebei University of Technology, Tianjin, 300131, China
| | - Sijia Wang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Mrudulakumari Vasudevan U, Mai DHA, Krishna S, Lee EY. Methanotrophs as a reservoir for bioactive secondary metabolites: Pitfalls, insights and promises. Biotechnol Adv 2023; 63:108097. [PMID: 36634856 DOI: 10.1016/j.biotechadv.2023.108097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/10/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023]
Abstract
Methanotrophs are potent natural producers of several bioactive secondary metabolites (SMs) including isoprenoids, polymers, peptides, and vitamins. Cryptic biosynthetic gene clusters identified from these microbes via genome mining hinted at the vast and hidden SM biosynthetic potential of these microbes. Central carbon metabolism in methanotrophs offers rare pathway intermediate pools that could be further diversified using advanced synthetic biology tools to produce valuable SMs; for example, plant polyketides, rare carotenoids, and fatty acid-derived SMs. Recent advances in pathway reconstruction and production of isoprenoids, squalene, ectoine, polyhydroxyalkanoate copolymer, cadaverine, indigo, and shinorine serve as proof-of-concept. This review provides theoretical guidance for developing methanotrophs as microbial chassis for high-value SMs. We summarize the distinct secondary metabolic potentials of type I and type II methanotrophs, with specific attention to products relevant to biomedical applications. This review also includes native and non-native SMs from methanotrophs, their therapeutic potential, strategies to induce silent biosynthetic gene clusters, and challenges.
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Affiliation(s)
- Ushasree Mrudulakumari Vasudevan
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Dung Hoang Anh Mai
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Shyam Krishna
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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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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Guo J, Xie Z, Jiang H, Xu H, Liu B, Meng Q, Peng Q, Tang Y, Duan Y. The Molecular Mechanism of Yellow Mushroom (Floccularia luteovirens) Response to Strong Ultraviolet Radiation on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:918491. [PMID: 35794915 PMCID: PMC9251379 DOI: 10.3389/fmicb.2022.918491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) is the highest plateau in the world, and its ultraviolet (UV) radiation is much greater than that of other regions in the world. Yellow mushroom (Floccularia luteovirens) is a unique and widely distributed edible fungus on the QTP. However, the molecular mechanism of F. luteovirens’s response to strong UV radiation remains unclear. Herein, we reported the 205 environmental adaptation and information processing genes from genome of F. luteovirens. In addition, we assembled the RNA sequence of UV-affected F. luteovirens at different growth stages. The results showed that in response to strong UV radiation, a total of 11,871 significantly different genes were identified, of which 4,444 genes in the vegetative mycelium (VM) stage were significantly different from the young fruiting bodies (YFB) stage, and only 2,431 genes in the YFB stage were significantly different from fruiting bodies (FB) stage. A total of 225 differentially expressed genes (DEGs) were found to be involved in environmental signal transduction, biochemical reaction preparation and stress response pathway, pigment metabolism pathway, and growth cycle regulation, so as to sense UV radiation, promote repair damage, regulate intracellular homeostasis, and reduce oxidative damage of UV radiation. On the basis of these results, a molecular regulation model was proposed for the response of F. luteovirens to strong UV radiation. These results revealed the molecular mechanism of adaptation of F. luteovirens adapting to strong UV radiation, and provided novel insights into mechanisms of fungi adapting to extreme environmental conditions on the QTP; the production the riboflavin pigment of the endemic fungi (Yellow mushroom) in the QTP was one of the response to extreme environment of the strong UV radiation.
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Affiliation(s)
- Jing Guo
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Zhanling Xie
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
- *Correspondence: Zhanling Xie,
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Qinghai Provincial Key Laboratory of Geology and Environment of Salt Lakes, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining, China
| | - Hongyan Xu
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Baolong Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Qing Meng
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | - Qingqing Peng
- College of Ecological and Environment Engineering, Qinghai University, Xining, China
- State Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Qinghai University, Xining, China
| | | | - Yingzhu Duan
- Test Station for Grassland Improvement, Xining, China
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