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Chen HT, Zhang XY, Wu QB, Zhao QW, Chen XA, Li YQ. Production improvement of FK506 in Streptomyces tsukubaensis by metabolic engineering strategy. J Appl Microbiol 2023; 134:lxad142. [PMID: 37429605 DOI: 10.1093/jambio/lxad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/28/2023] [Accepted: 07/09/2023] [Indexed: 07/12/2023]
Abstract
AIMS Study of the effect of isoleucine on the biosynthesis of FK506 and modification of its producing strain to improve the production of FK506. METHODS AND RESULTS Metabolomics analysis was conducted to explore key changes in the metabolic processes of Streptomyces tsukubaensis Δ68 in medium with and without isoleucine. In-depth analysis revealed that the shikimate pathway, methylmalonyl-CoA, and pyruvate might be the rate-limiting factors in FK506 biosynthesis. Overexpression of involved gene PCCB1 in S. tsukubaensis Δ68, a high-yielding strain Δ68-PCCB1 was generated. Additionally, the amino acids supplement was further optimized to improve FK506 biosynthesis. Finally, FK506 production was increased to 929.6 mg L-1, which was 56.6% higher than that in the starter strain, when supplemented isoleucine and valine at 9 and 4 g L-1, respectively. CONCLUSIONS Methylmalonyl-CoA might be the key rate-limiting factors in FK506 biosynthesis and overexpression of the gene PCCB1 and further addition of isoleucine and valine could increase the yield of FK506 by 56.6%.
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Affiliation(s)
- Hai-Tao Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Xiao-Ying Zhang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Bin Wu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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2
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Al-Rooqi MM, Ullah Mughal E, Raja QA, Obaid RJ, Sadiq A, Naeem N, Qurban J, Asghar BH, Moussa Z, Ahmed SA. Recent advancements on the synthesis and biological significance of pipecolic acid and its derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Poshekhontseva VY, Fokina VV, Tarlachkov SV, Machulin AV, Shutov AA, Donova MV. Streptomyces tsukubensis VKM Aс-2618D-an Effective Producer of Tacrolimus. APPL BIOCHEM MICRO+ 2021; 57:939-948. [PMID: 34924587 PMCID: PMC8670718 DOI: 10.1134/s0003683821090064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/02/2020] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
The Streptomyces sp. VKM Ac-2618D strain has been identified, and its morphological and physiological features have been studied in relation to the production of the immunosuppressant tacrolimus. The phenotypic variability of the strain was analyzed, and a dissociant with a high level of tacrolimus production was selected. Based on a comprehensive study of morphological, physiological, and chemotaxonomic properties and on phylogenetic analysis, the strain was named Streptomyces tsukubensis VKM Ac-2618D. The strain genome contains the full version of the tacrolimus biosynthetic gene cluster. The advantages of fed-batch cultivation mode for tacrolimus biosynthesis are shown. The results broaden the understanding of the characteristics of polyketide biosynthesis and can be used in the development of technology for tacrolimus production.
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Affiliation(s)
- V Yu Poshekhontseva
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia.,Pharmins, Ltd, 142290 Pushchino, Moscow oblast Russia
| | - V V Fokina
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia.,Pharmins, Ltd, 142290 Pushchino, Moscow oblast Russia
| | - S V Tarlachkov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia.,Branch of the Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia
| | - A V Machulin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia
| | - A A Shutov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia.,Pharmins, Ltd, 142290 Pushchino, Moscow oblast Russia
| | - M V Donova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia.,Pharmins, Ltd, 142290 Pushchino, Moscow oblast Russia
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4
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Zhang X, Wu Q, Zhang X, Lv Z, Mo X, Li Y, Chen XA. Elevation of FK506 production by regulatory pathway engineering and medium optimization in Streptomyces tsukubaensis. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Wu QB, Zhang XY, Chen XA, Li YQ. Improvement of FK506 production via metabolic engineering-guided combinational strategies in Streptomyces tsukubaensis. Microb Cell Fact 2021; 20:166. [PMID: 34425854 PMCID: PMC8383387 DOI: 10.1186/s12934-021-01660-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background FK506, a macrolide mainly with immunosuppressive activity, can be produced by various Streptomyces strains. However, one of the major challenges in the fermentation of FK506 is its insufficient production, resulting in high fermentation costs and environmental burdens. Herein, we tried to improve its production via metabolic engineering-guided combinational strategies in Streptomyces tsukubaensis. Results First, basing on the genome sequencing and analysis, putative competitive pathways were deleted. A better parental strain L19-2 with increased FK506 production from 140.3 to 170.3 mg/L and a cleaner metabolic background was constructed. Subsequently, the FK506 biosynthetic gene cluster was refactored by in-situ promoter-substitution strategy basing on the regulatory circuits. This strategy enhanced transcription levels of the entire FK506 biosynthetic gene cluster in a fine-tuning manner and dramatically increased the FK506 production to 410.3 mg/mL, 1.41-fold higher than the parental strain L19-2 (170.3 mg/L). Finally, the FK506 production was further increased from 410.3 to 603 mg/L in shake-flask culture by adding L-isoleucine at a final concentration of 6 g/L. Moreover, the potential of FK506 production capacity was also evaluated in a 15-L fermenter, resulting in the FK506 production of 830.3 mg/L. Conclusion From the aspects of competitive pathways, refactoring of the FK506 biosynthetic gene cluster and nutrients-addition, a strategy for hyper-production and potentially industrial application of FK506 was developed and a hyper-production strain L19-9 was constructed. The strategy presented here can be generally applicable to other Streptomyces for improvement of FK506 production and streamline hyper-production of other valuable secondary metabolites. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01660-w.
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Affiliation(s)
- Qing-Bin Wu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine , Hangzhou, 310058, China.,Zhejiang Provincial Key Lab for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xiao-Ying Zhang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine , Hangzhou, 310058, China.,Zhejiang Provincial Key Lab for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine , Hangzhou, 310058, China.,Zhejiang Provincial Key Lab for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine , Hangzhou, 310058, China. .,Zhejiang Provincial Key Lab for Microbial Biochemistry and Metabolic Engineering, Hangzhou, 310058, China.
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6
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Cibichakravarthy B, Jose PA. Biosynthetic Potential of Streptomyces Rationalizes Genome-Based Bioprospecting. Antibiotics (Basel) 2021; 10:antibiotics10070873. [PMID: 34356794 PMCID: PMC8300671 DOI: 10.3390/antibiotics10070873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Streptomyces are the most prolific source of structurally diverse microbial natural products. Advancing genome-based analysis reveals the previously unseen potential of Streptomyces to produce numerous novel secondary metabolites, which allows us to take natural product discovery to the next phase. However, at present there is a huge disproportion between the rate of genome reports and discovery of new compounds. From this perspective of harnessing the enduring importance of Streptomyces, we discuss the recent genome-directed advancements inspired by hidden biosynthetic wealth that provide hope for future antibiotics.
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Affiliation(s)
- Balasubramanian Cibichakravarthy
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761000, Israel;
| | - Polapass Arul Jose
- Department of Entomology and Plant Pathology & Microbiology, The Hebrew University of Jerusalem, POB 12, Rehovot 761000, Israel
- Correspondence:
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7
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Combination of atmospheric and room temperature plasma (ARTP) mutagenesis, genome shuffling and dimethyl sulfoxide (DMSO) feeding to improve FK506 production in Streptomyces tsukubaensis. Biotechnol Lett 2021; 43:1809-1820. [PMID: 34160747 DOI: 10.1007/s10529-021-03154-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
FK506 is a clinically important macrocyclic polyketide with immunosuppressive activity produced by Streptomyces tsukubaensis. However, the production capacity of the strain is very low. To improve production, atmospheric and room temperature plasma (ARTP) mutagenesis was adopted to get the initial strains used in genome shuffling (GS). After three rounds of GS, S. tsukubaensis R3-C4 was the most productive strain, resulting in a FK506 concentration of 335 μg/mL, 2.6 times than that of the original wild-type strain. Moreover, exogenous DMSO 4% (v/v) addition could induce efflux of FK506 and increased FK506 production by 27.9% to 429 μg/mL. Finally, analyses of the differences in morphology, fermentation characteristics and specific gene expression levels between S. tsukubaensis R3-C4 and the wild-type strain revealed that R3-C4 strain: has hampered spore differentiation, thicker mycelia and more red pigment, which are likely related to the downregulation of bldD and cdgB expression. In addition, the expression levels of fkbO, fkbP, dahp, pccB and prpE all showed up-regulation at diverse degrees compared to the wild-type S. tsukubaensis. Overall, these results show that a combined approach involving classical random mutation and exogenous feeding can be applied to increase FK506 biosynthesis and may be applied also to the improvement of other important secondary metabolites.
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8
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Yan L, Zhang Z, Zhang Y, Yang H, Qiu G, Wang D, Lian Y. Improvement of tacrolimus production in Streptomyces tsukubaensis by mutagenesis and optimization of fermentation medium using Plackett-Burman design combined with response surface methodology. Biotechnol Lett 2021; 43:1765-1778. [PMID: 34021830 DOI: 10.1007/s10529-021-03144-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 04/30/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE This study was conducted to enhance the production of tacrolimus in Streptomyces tsukubaensis by strain mutagenesis and optimization of the fermentation medium. RESULTS A high tacrolimus producing strain S. tsukubaensis FIM-16-06 was obtained by ultraviolet mutagenesis coupled with atmospheric and room temperature plasma mutagenesis.Then, nine variables were screened using Plackett-Burman experimental design, in which soluble starch, peptone and Tween 80 showed significantly affected tacrolimus production. Further studies were carried out employing central composite design to elucidate the mutual interaction between the variables and to work out optimal fermentation medium composition for tacrolimus production. The optimum fermentation medium was found to contain 61.61 g/L of soluble starch, 20.61 g/L of peptone and 30.79 g/L of Tween 80. In the optimized medium, the production of tacrolimus reached 1293 mg/L in shake-flask culture, and reached 1522 mg/L while the scaled-up fermentation was conducted in a 1000 L fermenter, which was about 3.7 times higher than that in the original medium. CONCLUSIONS Combining compound mutation with rational medium optimization is an effective approach for improving tacrolimus production, and the optimized fermentation medium could be efficiently used for industrial production.
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Affiliation(s)
- Lingbin Yan
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China
| | - Zhulan Zhang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China.
| | - Yin Zhang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China
| | - Huangjian Yang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China
| | - Guanrong Qiu
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China
| | - Desen Wang
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China
| | - Yunyang Lian
- Fujian Provincial Key Laboratory of Screening for Novel Microbial Products, Fujian Institute of Microbiology, Fuzhou, 350007, China.
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9
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Chen G, Wang M, Ni X, Xia H. Optimization of tetramycin production in Streptomyces ahygroscopicus S91. J Biol Eng 2021; 15:16. [PMID: 34022922 PMCID: PMC8141235 DOI: 10.1186/s13036-021-00267-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tetramycin is a 26-member tetraene antibiotic used in agriculture. It has two components, tetramycin A and tetramycin B. Tetramycin B is obtained by the hydroxylation of tetramycin A on C4. This reaction is catalyzed by the cytochrome P450 monooxygenase TtmD. The two components of tetramycin have different antifungal activities against different pathogenic fungi. Therefore, the respective construction of high-yield strains of tetramycin A and tetramycin B is conducive to more targeted action on pathomycete and has a certain practical value. RESULTS Streptomyces ahygroscopicus S91 was used as the original strain to construct tetramycin A high-yield strains by blocking the precursor competitive biosynthetic gene cluster, disrupting tetramycin B biosynthesis, and overexpressing the tetramycin pathway regulator. Eventually, the yield of tetramycin A in the final strain was up to 1090.49 ± 136.65 mg·L- 1. Subsequently, TtmD, which catalyzes the conversion from tetramycin A to tetramycin B, was overexpressed. Strains with 2, 3, and 4 copies of ttmD were constructed. The three strains had different drops in tetramycin A yield, with increases in tetramycin B. The strain with three copies of ttmD showed the most significant change in the ratio of the two components. CONCLUSIONS A tetramycin A single-component producing strain was obtained, and the production of tetramycin A increased 236.84% ± 38.96% compared with the original strain. In addition, the content of tetramycin B in a high-yield strain with three copies of ttmD increased from 26.64% ± 1.97 to 51.63% ± 2.06%.
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Affiliation(s)
- Guang Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Mengqiu Wang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, No.103 Wenhua Road, Shenyang, Liaoning, China.
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Wang P, Yin Y, Wang X, Wen J. Enhanced ascomycin production in Streptomyces hygroscopicus var. ascomyceticus by employing polyhydroxybutyrate as an intracellular carbon reservoir and optimizing carbon addition. Microb Cell Fact 2021; 20:70. [PMID: 33731113 PMCID: PMC7968196 DOI: 10.1186/s12934-021-01561-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Ascomycin is a multifunctional antibiotic produced by Streptomyces hygroscopicus var. ascomyceticus. As a secondary metabolite, the production of ascomycin is often limited by the shortage of precursors during the late fermentation phase. Polyhydroxybutyrate is an intracellular polymer accumulated by prokaryotic microorganisms. Developing polyhydroxybutyrate as an intracellular carbon reservoir for precursor synthesis is of great significance to improve the yield of ascomycin. RESULTS The fermentation characteristics of the parent strain S. hygroscopicus var. ascomyceticus FS35 showed that the accumulation and decomposition of polyhydroxybutyrate was respectively correlated with cell growth and ascomycin production. The co-overexpression of the exogenous polyhydroxybutyrate synthesis gene phaC and native polyhydroxybutyrate decomposition gene fkbU increased both the biomass and ascomycin yield. Comparative transcriptional analysis showed that the storage of polyhydroxybutyrate during the exponential phase accelerated biosynthesis processes by stimulating the utilization of carbon sources, while the decomposition of polyhydroxybutyrate during the stationary phase increased the biosynthesis of ascomycin precursors by enhancing the metabolic flux through primary pathways. The comparative analysis of cofactor concentrations confirmed that the biosynthesis of polyhydroxybutyrate depended on the supply of NADH. At low sugar concentrations found in the late exponential phase, the optimization of carbon source addition further strengthened the polyhydroxybutyrate metabolism by increasing the total concentration of cofactors. Finally, in the fermentation medium with 22 g/L starch and 52 g/L dextrin, the ascomycin yield of the co-overexpression strain was increased to 626.30 mg/L, which was 2.11-fold higher than that of the parent strain in the initial medium (296.29 mg/L). CONCLUSIONS Here we report for the first time that polyhydroxybutyrate metabolism is beneficial for cell growth and ascomycin production by acting as an intracellular carbon reservoir, stored as polymers when carbon sources are abundant and depolymerized into monomers for the biosynthesis of precursors when carbon sources are insufficient. The successful application of polyhydroxybutyrate in increasing the output of ascomycin provides a new strategy for improving the yields of other secondary metabolites.
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Affiliation(s)
- Pan Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xin Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
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11
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Zhang B, Chen Y, Jiang SX, Cai X, Huang K, Liu ZQ, Zheng YG. Comparative metabolomics analysis of amphotericin B high-yield mechanism for metabolic engineering. Microb Cell Fact 2021; 20:66. [PMID: 33750383 PMCID: PMC7945361 DOI: 10.1186/s12934-021-01552-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The polyene macrocyclic compound amphotericin B (AmB) is an important antifungal antibiotic for the clinical treatment of invasive fungal infections. To rationally guide the improvement of AmB production in the main producing strain Streptomyces nodosus, comparative metabolomics analysis was performed to investigate the intracellular metabolic changes in wild-type S. nodosus ZJB20140315 with low-yield AmB production and mutant S. nodosus ZJB2016050 with high-yield AmB production, the latter of which reached industrial criteria on a pilot scale. RESULTS To investigate the relationship of intracellular metabolites, 7758 metabolites were identified in mutant S. nodosus and wildtype S. nodosus via LC-MS. Through analysis of metabolism, the level of 26 key metabolites that involved in carbon metabolism, fatty acids metabolism, amino acids metabolism, purine metabolism, folate biosynthesis and one carbon pool by folate were much higher in mutant S. nodosus. The enrichment of relevant metabolic pathways by gene overexpression strategy confirmed that one carbon pool by folate was the key metabolic pathway. Meanwhile, a recombinant strain with gene metH (methionine synthase) overexpressed showed 5.03 g/L AmB production within 120 h fermentation, which is 26.4% higher than that of the mutant strain. CONCLUSIONS These results demonstrated that comparative metabolomics analysis was an effective approach for the improvement of AmB production and could be applied for other industrially or clinically important compounds as well.
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Affiliation(s)
- Bo Zhang
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu Chen
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Sheng-Xian Jiang
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Xue Cai
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Kai Huang
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Zhi-Qiang Liu
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
| | - Yu-Guo Zheng
- Department, Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
- Engineering Research Center of Bioconversion and Bio-Purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 People’s Republic of China
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Abstract
Inflammatory processes occur as a generic response of the immune system and can be triggered by various factors, such as infection with pathogenic microorganisms or damaged tissue. Due to the complexity of the inflammation process and its role in common diseases like asthma, cancer, skin disorders or Alzheimer's disease, anti-inflammatory drugs are of high pharmaceutical interest. Nature is a rich source for compounds with anti-inflammatory properties. Several studies have focused on the structural optimization of natural products to improve their pharmacological properties. As derivatization through total synthesis is often laborious with low yields and limited stereoselectivity, the use of biosynthetic, enzyme-driven reactions is an attractive alternative for synthesizing and modifying complex bioactive molecules. In this minireview, we present an outline of the biotechnological methods used to derivatize anti-inflammatory natural products, including precursor-directed biosynthesis, mutasynthesis, combinatorial biosynthesis, as well as whole-cell and in vitro biotransformation.
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Affiliation(s)
- Lea Winand
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
| | - Angela Sester
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
- Current address: Chair of Technical BiochemistryTechnical University of DresdenBergstrasse 6601069DresdenGermany
| | - Markus Nett
- Department of Biochemical and Chemical EngineeringLaboratory of Technical BiologyTU Dortmund UniversityEmil-Figge-Strasse 6644227DortmundGermany
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Characterization and directed evolution of propionyl-CoA carboxylase and its application in succinate biosynthetic pathway with two CO2 fixation reactions. Metab Eng 2020; 62:42-50. [DOI: 10.1016/j.ymben.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/18/2020] [Accepted: 08/24/2020] [Indexed: 11/20/2022]
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14
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The Onset of Tacrolimus Biosynthesis in Streptomyces tsukubaensis Is Dependent on the Intracellular Redox Status. Antibiotics (Basel) 2020; 9:antibiotics9100703. [PMID: 33076498 PMCID: PMC7602649 DOI: 10.3390/antibiotics9100703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/02/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022] Open
Abstract
The oxidative stress response is a key mechanism that microorganisms have to adapt to changeling environmental conditions. Adaptation is achieved by a fine-tuned molecular response that extends its influence to primary and secondary metabolism. In the past, the role of the intracellular redox status in the biosynthesis of tacrolimus in Streptomyces tsukubaensis has been briefly acknowledged. Here, we investigate the impact of the oxidative stress response on tacrolimus biosynthesis in S. tsukubaensis. Physiological characterization of S. tsukubaensis showed that the onset of tacrolimus biosynthesis coincided with the induction of catalase activity. In addition, tacrolimus displays antioxidant properties and thus a controlled redox environment would be beneficial for its biosynthesis. In addition, S. tsukubaensis ∆ahpC strain, a strain defective in the H2O2-scavenging enzyme AhpC, showed increased production of tacrolimus. Proteomic and transcriptomic studies revealed that the tacrolimus over-production phenotype was correlated with a metabolic rewiring leading to increased availability of tacrolimus biosynthetic precursors. Altogether, our results suggest that the carbon source, mainly used for cell growth, can trigger the production of tacrolimus by modulating the oxidative metabolism to favour a low oxidizing intracellular environment and redirecting the metabolic flux towards the increase availability of biosynthetic precursors.
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Moreira JV, Silva SCM, Cremasco MA. Evaluation of carbon:nitrogen ratio in semi-defined culture medium to tacrolimus biosynthesis by Streptomyces tsukubaensis and the effect on bacterial growth. BIOTECHNOLOGY REPORTS 2020; 26:e00440. [PMID: 32190550 PMCID: PMC7068638 DOI: 10.1016/j.btre.2020.e00440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 11/29/2022]
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Zhang B, Zhou YT, Jiang SX, Zhang YH, Huang K, Liu ZQ, Zheng YG. Amphotericin B biosynthesis in Streptomyces nodosus: quantitative analysis of metabolism via LC-MS/MS based metabolomics for rational design. Microb Cell Fact 2020; 19:18. [PMID: 32005241 PMCID: PMC6995120 DOI: 10.1186/s12934-020-1290-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 01/21/2020] [Indexed: 01/19/2023] Open
Abstract
Background Amphotericin B (AmB) is widely used against fungal infection and produced mainly by Streptomyces nodosus. Various intracellular metabolites of S. nodosus were identified during AmB fermentation, and the key compounds that related to the cell growth and biosynthesis of AmB were analyzed by principal component analysis (PCA) and partial least squares (PLS). Results Rational design that based on the results of metabolomics was employed to improve the AmB productivity of Streptomyces nodosus, including the overexpression of genes involved in oxygen-taking, precursor-acquiring and product-exporting. The AmB yield of modified strain S. nodosus VMR4A was 6.58 g/L, which was increased significantly in comparison with that of strain S. nodosus ZJB2016050 (5.16 g/L). This was the highest yield of AmB reported so far, and meanwhile, the amount of by-product amphotericin A (AmA) was decreased by 45%. Moreover, the fermentation time of strain S. nodosus VMR4A was shortened by 24 h compared with that of strain. The results indicated that strain S. nodosus VMR4A was an excellent candidate for the industrial production of AmB because of its high production yield, low by-product content and the fast cell growth. Conclusions This study would lay the foundation for improving the AmB productivity through metabolomics analysis and overexpression of key enzymes.![]()
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yi-Teng Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Sheng-Xian Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yu-Han Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Kai Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Bio-purification, Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Mojicevic M, D'Agostino PM, Pavic A, Vojnovic S, Senthamaraikannan R, Vasiljevic B, Gulder TAM, Nikodinovic-Runic J. Streptomyces sp. BV410 isolate from chamomile rhizosphere soil efficiently produces staurosporine with antifungal and antiangiogenic properties. Microbiologyopen 2020; 9:e986. [PMID: 31989798 PMCID: PMC7066459 DOI: 10.1002/mbo3.986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/20/2022] Open
Abstract
Applying a bioactivity‐guided isolation approach, staurosporine was separated and identified as the active principle in the culture extract of the new isolate Streptomyces sp. BV410 collected from the chamomile rhizosphere. The biotechnological production of staurosporine by strain BV410 was optimized to yield 56 mg/L after 14 days of incubation in soy flour–glucose–starch–mannitol‐based fermentation medium (JS). The addition of FeSO4 significantly improved the staurosporine yield by 30%, while the addition of ZnSO4 significantly reduced staurosporine yield by 62% in comparison with the starting conditions. Although staurosporine was first isolated in 1977 from Lentzea albida (now Streptomyces staurosporeus) and its potent kinase inhibitory effect has been established, here, the biological activity of this natural product was assessed in depth in vivo using a selection of transgenic zebrafish (Danio rerio) models, including Tg(fli1:EGFP) with green fluorescent protein‐labeled endothelial cells allowing visualization and monitoring of blood vessels. This confirmed a remarkable antiangiogenic activity of the compound at doses of 1 ng/ml (2.14 nmol/L) which is below doses inducing toxic effects (45 ng/ml; 75 nmol/L). A new, efficient producing strain of commercially significant staurosporine has been described along with optimized fermentation conditions, which may lead to optimization of the staurosporine scaffold and its wider applicability.
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Affiliation(s)
- Marija Mojicevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Department of Biotechnology and Pharmaceutical Engineering, Faculty of Technology, University of Novi Sad, Novi Sad, Serbia
| | - Paul M D'Agostino
- Chair of Technical Biochemistry, Technische Universität Dresden, Dresden, Germany.,Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching bei München, Germany
| | - Aleksandar Pavic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sandra Vojnovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Branka Vasiljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technische Universität Dresden, Dresden, Germany.,Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Technische Universität München, Garching bei München, Germany
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Xu J, Yue T, Yu X, Zhao P, Li T, Li N. Enhanced production of individual ganoderic acids by integrating Vitreoscilla haemoglobin expression and calcium ion induction in liquid static cultures of Ganoderma lingzhi. Microb Biotechnol 2019; 12:1180-1187. [PMID: 30821132 PMCID: PMC6801144 DOI: 10.1111/1751-7915.13381] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/18/2019] [Accepted: 02/04/2019] [Indexed: 11/30/2022] Open
Abstract
Ganoderic acids produced by Ganoderma exhibit anticancer and antimetastatic activities. A novel approach by combining Vitreoscilla haemoglobin (VHb) expression and calcium ion induction was developed to enhance ganoderic acid (GA) production in liquid static cultures of G. lingzhi. The maximum contents of GA-O, GA-S and GA-Me were 1451.33 ± 67.50, 1431.23 ± 79.74 and 1283.81 ± 85.13 μg per 100 mg cell weight, respectively under the integrated approach, which are the highest contents as ever reported in Ganoderma. The contents of squalene and lanosterol were increased by 2.0- and 3.0-fold in this case compared with those in the control. The transcription levels of 3-hydroxy-3-methylglutaryl coenzyme A reductase, farnesyl-diphosphate synthase, squalene synthase and cytochrome P450 CYP5150L8 were upregulated by 2.56-, 3.31-, 2.59- and 6.12-fold respectively. Additionally, the expression of VHb improved the ratio of type I to type II GA in liquid static cultivation of G. lingzhi. The transcription levels of cyp512a2, cyp512v2 and cyp512a13, candidate cytochrome P450 genes involved in oxidative modification of the lanostane skeleton in GA biosynthesis, were also increased by 2.28-, 2.65- and 3.54-fold in the VHb-expressing strain respectively. Our results illustrated that the approach described here efficiently improved GA production in G. lingzhi fermentation.
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Affiliation(s)
- Jun‐Wei Xu
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunming650500China
| | - Tong‐Hui Yue
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunming650500China
| | - Xuya Yu
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunming650500China
| | - Peng Zhao
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunming650500China
| | - Tao Li
- Faculty of Life Science and TechnologyKunming University of Science and TechnologyKunming650500China
| | - Na Li
- Faculty of ScienceKunming University of Science and TechnologyKunming650500China
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Zhang Y, Chen H, Wang P, Wen J. Identification of the regulon FkbN for ascomycin biosynthesis and its interspecies conservation analysis as LAL family regulator. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Li Y, Liang S, Wang J, Ma D, Wen J. Enhancing the production of tacrolimus by engineering target genes identified in important primary and secondary metabolic pathways and feeding exogenous precursors. Bioprocess Biosyst Eng 2019; 42:1081-1098. [PMID: 30887101 DOI: 10.1007/s00449-019-02106-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/12/2019] [Indexed: 12/29/2022]
Abstract
Tacrolimus has been widely used as a powerful novel immunosuppressant. The objective of this study was to improve the production of tacrolimus by engineering the target genes of important primary and secondary metabolic pathways and feeding exogenous precursors. Based on the metabonomics analysis, the shikimic acid pathway is an important primary metabolic pathway for the producing tacrolimus. Combined overexpression of shikimate kinase and dehydroquinic acid synthetase genes led to a 33.1% enhancement of tacrolimus production compared to parent strain. To predict the most efficient targets in secondary metabolic pathways for improving the production of tacrolimus, a genome-scale dynamic metabolic network model was used. A knockout of the D-lactate dehydrogenase gene, combined with the overexpression of tryptophane synthase and aspartate 1-decarboxylase genes, led to a 29.8% enhancement of tacrolimus production compared to the parent strain. Finally, we investigated the impact of the genetic manipulations on transcription levels, cell growth, cell morphology and production of tacrolimus by qRT-PCR and scanning electron microscopy to reveal the relationship between the growth of strains, the effects of engineering and fermentation. As the efficient synthesis of tacrolimus requires a rich supply of external substrates, the efficiency of the metabolic pathways that convert these substances is extremely important. The combined addition of three external substrates such as shikimic acid, alanine and the n-dodecane increased tacrolimus production by 49.5%. The insights obtained in this study will help further elucidate the mechanisms by which the identified target genes promote the activity of important primary and secondary metabolic pathways for tacrolimus biosynthesis and provide a new feeding strategy to improve tacrolimus production.
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Affiliation(s)
- Yang Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Shaoxiong Liang
- College Laboratory of Chemical Engineering, Huaqiao University, Xiamen, 361021, People's Republic of China
| | - Junhua Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Dongxu Ma
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
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Zhang Y, Zhang H, Zheng Q. How Chorismatases Regulate Distinct Reaction Channels in a Single Conserved Active Pocket: Mechanistic Analysis with QM/MM (ONIOM) Investigations. Chemistry 2019; 25:1326-1336. [PMID: 30395358 DOI: 10.1002/chem.201804622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Indexed: 01/12/2023]
Abstract
The FkbO and Hyg5 subfamilies of chorismatases share the same active-site architectures, but perform distinct reaction mechanisms, that is, FkbO employs a hydrolysis reaction whereas Hyg5 proceeds through an intramolecular mechanism. Despite extensive research efforts, the detailed mechanism of the product selectivity in chorismatases need to be further unmasked. In this study, the effects of the A/G residue group (A244FkbO /G240Hyg5 ) and the V/Q residue group (V209FkbO /Q201Hyg5 ) on the catalytic mechanisms are investigated by employing molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of the two wild-type models (FkbO/CHO and Hyg5/CHO; CHO=chorismate) and four mutants models (A244G-FkbO/CHO and G240A-Hyg5/CHO; V209Q-FkbO/CHO and Q201V-Hyg5/CHO). Our results showed that the A/G residue group mentioned by previous works would cause changes in the binding states of the substrate and the orientation of the catalytic glutamate, but only these changes affect the product selectivity in chorismatases limitedly. Interestingly, the distal V/Q residue group, which determines the internal water self-regulating ability at the active site, has significant impact on the selectivity of the catalytic mechanisms. The V/Q residue group is suggested to be an important factor to control the catalytic activities in chorismatases. The results are consistent with biochemical and structural experiments, providing novel insight into the mechanism of product selectivity in chorismatases.
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Affiliation(s)
- Yulai Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China
| | - Hongxing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry, of Education, Jilin University, Changchun, 130023, P.R. China
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22
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Mohite OS, Weber T, Kim HU, Lee SY. Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production. Biotechnol J 2018; 14:e1800377. [DOI: 10.1002/biot.201800377] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/11/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Omkar S. Mohite
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 kongens Lyngby Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 kongens Lyngby Denmark
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; 2800 kongens Lyngby Denmark
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Korea Advanced Institute of Science and Technology (KAIST); 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
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Wang C, Huang D, Liang S. Identification and metabolomic analysis of chemical elicitors for tacrolimus accumulation in Streptomyces tsukubaensis. Appl Microbiol Biotechnol 2018; 102:7541-7553. [DOI: 10.1007/s00253-018-9177-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/24/2022]
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Analysis and validation of the pho regulon in the tacrolimus-producer strain Streptomyces tsukubaensis: differences with the model organism Streptomyces coelicolor. Appl Microbiol Biotechnol 2018; 102:7029-7045. [PMID: 29948118 DOI: 10.1007/s00253-018-9140-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/20/2018] [Accepted: 05/23/2018] [Indexed: 10/14/2022]
Abstract
Inorganic and organic phosphate controls both primary and secondary metabolism in Streptomyces genus. Metabolism regulation by phosphate in Streptomyces species is mediated by the PhoR-PhoP two-component system. Response regulator PhoP binds to conserved sequences of 11 nucleotides called direct repeat units (DRus), whose organization and conservation determine the binding of PhoP to distinct promoters. Streptomyces tsukubaensis is the industrial producer of the clinical immunosuppressant tacrolimus (FK506). A bioinformatic genome analysis detected several genes with conserved PHO boxes involved in phosphate scavenging and transport, nitrogen regulation, and secondary metabolite production. In this article, the PhoP regulation has been confirmed by electrophoretic mobility shift assays (EMSA) of the most relevant members of the traditional pho regulon such as the two-component system PhoR-P or genes involved in high-affinity phosphate transport (pstSCAB) and low-affinity phosphate transport (pit). However, the PhoP control over phosphatase genes in S. tsukubaensis is significantly different from the pattern reported in the model bacteria Streptomyces coelicolor. Thus, neither the alkaline phosphatase PhoA nor PhoD is regulated by PhoP. On the contrary, the binding of PhoP to the promoter of a novel putative phosphatase PhoX was confirmed. A crosstalk of the PhoP and GlnR regulators, which balances phosphate and nitrogen utilization, also occurs in S. tsukubaensis but slightly modified. Finally, PhoP regulates genes, like afsS, that link phosphate control and secondary metabolite production in S. tsukubaensis. In summary, there are notable differences between the regulation of specific genes of the pho regulon in S. tsukubaensis and the model organism S. coelicolor.
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Ordóñez-Robles M, Santos-Beneit F, Martín JF. Unraveling Nutritional Regulation of Tacrolimus Biosynthesis in Streptomyces tsukubaensis through omic Approaches. Antibiotics (Basel) 2018; 7:antibiotics7020039. [PMID: 29724001 PMCID: PMC6022917 DOI: 10.3390/antibiotics7020039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022] Open
Abstract
Streptomyces tsukubaensis stands out among actinomycetes by its ability to produce the immunosuppressant tacrolimus. Discovered about 30 years ago, this macrolide is widely used as immunosuppressant in current clinics. Other potential applications for the treatment of cancer and as neuroprotective agent have been proposed in the last years. In this review we introduce the discovery of S. tsukubaensis and tacrolimus, its biosynthetic pathway and gene cluster (fkb) regulation. We have focused this work on the omic studies performed in this species in order to understand tacrolimus production. Transcriptomics, proteomics and metabolomics have improved our knowledge about the fkb transcriptional regulation and have given important clues about nutritional regulation of tacrolimus production that can be applied to improve production yields. Finally, we address some points of S. tsukubaensis biology that deserve more attention.
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Affiliation(s)
- María Ordóñez-Robles
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León 24071, Spain.
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, León 24006, Spain.
| | - Fernando Santos-Beneit
- Instituto de Biotecnología de León, INBIOTEC, Avda. Real no. 1, León 24006, Spain.
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo 33006, Spain.
| | - Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León 24071, Spain.
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Ma D, Wang C, Chen H, Wen J. Manipulating the expression of SARP family regulator BulZ and its target gene product to increase tacrolimus production. Appl Microbiol Biotechnol 2018; 102:4887-4900. [PMID: 29666890 DOI: 10.1007/s00253-018-8979-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/27/2018] [Accepted: 04/02/2018] [Indexed: 11/27/2022]
Abstract
Tacrolimus (FK506), an effective immunosuppressant, is widely used in the treatment of autoimmune diseases. In this study, we identified that BulZ, a Streptomyces antibiotic regulatory protein (SARP) family regulator, acted as a positive regulator for spore differentiation and tacrolimus production. A knockout of bulZ resulted in a 47.5% decrease of tacrolimus production and a delay of spore differentiation. Using quantitative real-time PCR (qRT-PCR) analysis and electrophoretic mobility shift assays (EMSAs), it was found that BulZ directly activated the transcriptions of bulZ and bulS2, a putative γ-butyrolactone (GBL) synthetase, and bulS2 was shown to play a positive role in tacrolimus biosynthesis. Meanwhile, BulZ was able to indirectly regulate the transcriptions of the cluster-linked activator genes tcs7 and fkbN, as well as the GBL receptor gene bulR1. STSU_RS22595, which encoded a WhiB family transcriptional regulator, was found to be a previously unknown potential target gene of BulZ based on a whole-genome search of the conserved sequence (5'-TSVAVVVNVNBTSRAGNN-3') of the SARP-binding motifs. Although overexpression of STSU_RS22595 did not result in an obvious enhancement of tacrolimus yield, STSU_RS22595 might have important effects on the spore differentiation process. Finally, co-overexpression of bulZ and its target gene bulS2 improved tacrolimus production by 36% compared to the control strain, reaching 324 mg/L. The insights obtained in this study will help further elucidate the regulatory mechanism of tacrolimus biosynthesis and provide new avenues for further improvement of tacrolimus production.
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Affiliation(s)
- Dongxu Ma
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- 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
| | - Cheng Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- 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
| | - Hong Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China
- 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
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, People's Republic of China.
- 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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Combining metabolomics and network analysis to improve tacrolimus production in Streptomyces tsukubaensis using different exogenous feedings. ACTA ACUST UNITED AC 2017; 44:1527-1540. [DOI: 10.1007/s10295-017-1974-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/31/2017] [Indexed: 02/07/2023]
Abstract
Abstract
Tacrolimus is widely used as an immunosuppressant in the treatment of various autoimmune diseases. However, the low fermentation yield of tacrolimus has thus far restricted its industrial applications. To solve this problem, the time-series response mechanisms of the intracellular metabolism that were highly correlated with tacrolimus biosynthesis were investigated using different exogenous feeding strategies in S. tsukubaensis. The metabolomic datasets, which contained 93 metabolites, were subjected to weighted correlation network analysis (WGCNA), and eight distinct metabolic modules and seven hub metabolites were identified to be specifically associated with tacrolimus biosynthesis. The analysis of metabolites within each metabolic module suggested that the pentose phosphate pathway (PPP), shikimate and aspartate pathway might be the main limiting factors in the rapid synthesis phase of tacrolimus accumulation. Subsequently, all possible key-limiting steps in the above metabolic pathways were further screened using a genome-scale metabolic network model (GSMM) of S. tsukubaensis. Based on the prediction results, two newly identified targets (aroC and dapA) were overexpressed experimentally, and both of the engineered strains showed higher tacrolimus production. Moreover, the best strain, HT-aroC/dapA, that was engineered to simultaneously enhanced chorismate and lysine biosynthesis was able to produce 128.19 mg/L tacrolimus, 1.64-fold higher than control (78.26 mg/L). These findings represent a valuable addition to our understanding of tacrolimus accumulation in S. tsukubaensis, and pave the way to further production improvements.
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Wang J, Wang C, Song K, Wen J. Metabolic network model guided engineering ethylmalonyl-CoA pathway to improve ascomycin production in Streptomyces hygroscopicus var. ascomyceticus. Microb Cell Fact 2017; 16:169. [PMID: 28974216 PMCID: PMC5627430 DOI: 10.1186/s12934-017-0787-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/26/2017] [Indexed: 12/22/2022] Open
Abstract
Background Ascomycin is a 23-membered polyketide macrolide with high immunosuppressant and antifungal activity. As the lower production in bio-fermentation, global metabolic analysis is required to further explore its biosynthetic network and determine the key limiting steps for rationally engineering. To achieve this goal, an engineering approach guided by a metabolic network model was implemented to better understand ascomycin biosynthesis and improve its production. Results The metabolic conservation of Streptomyces species was first investigated by comparing the metabolic enzymes of Streptomyces coelicolor A3(2) with those of 31 Streptomyces strains, the results showed that more than 72% of the examined proteins had high sequence similarity with counterparts in every surveyed strain. And it was found that metabolic reactions are more highly conserved than the enzymes themselves because of its lower diversity of metabolic functions than that of genes. The main source of the observed metabolic differences was from the diversity of secondary metabolism. According to the high conservation of primary metabolic reactions in Streptomyces species, the metabolic network model of Streptomyces hygroscopicus var. ascomyceticus was constructed based on the latest reported metabolic model of S. coelicolor A3(2) and validated experimentally. By coupling with flux balance analysis and using minimization of metabolic adjustment algorithm, potential targets for ascomycin overproduction were predicted. Since several of the preferred targets were highly associated with ethylmalonyl-CoA biosynthesis, two target genes hcd (encoding 3-hydroxybutyryl-CoA dehydrogenase) and ccr (encoding crotonyl-CoA carboxylase/reductase) were selected for overexpression in S. hygroscopicus var. ascomyceticus FS35. Both the mutants HA-Hcd and HA-Ccr showed higher ascomycin titer, which was consistent with the model predictions. Furthermore, the combined effects of the two genes were evaluated and the strain HA-Hcd-Ccr with hcd and ccr overexpression exhibited the highest ascomycin production (up to 438.95 mg/L), 1.43-folds improvement than that of the parent strain FS35 (305.56 mg/L). Conclusions The successful constructing and experimental validation of the metabolic model of S. hygroscopicus var. ascomyceticus showed that the general metabolic network model of Streptomyces species could be used to analyze the intracellular metabolism and predict the potential key limiting steps for target metabolites overproduction. The corresponding overexpression strains of the two identified genes (hcd and ccr) using the constructed model all displayed higher ascomycin titer. The strategy for yield improvement developed here could also be extended to the improvement of other secondary metabolites in Streptomyces species. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0787-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junhua Wang
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Cheng Wang
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Kejing Song
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Jianping Wen
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China. .,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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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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Bauer JS, Fillinger S, Förstner K, Herbig A, Jones AC, Flinspach K, Sharma C, Gross H, Nieselt K, Apel AK. dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome. RNA Biol 2017; 14:1617-1626. [PMID: 28665778 DOI: 10.1080/15476286.2017.1341020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
FK506 (tacrolimus) is a valuable immunosuppressant produced by several Streptomyces strains. In the genome of the wild type producer Streptomyces tsukubaensis NRRL18488, FK506 biosynthesis is encoded by a gene cluster that spans 83.5 (kb). A whole transcriptome differential shotgun sequencing (dRNA-seq) of S. tsukubaensis was performed to analyze transcription at 2 different time points; before and during active FK506 production. In total, 8,914 transcription start sites were identified in either condition, which enabled precise determination of the 5'-UTR length of the corresponding transcripts as well as the identification of 2 consensus sequence motifs in the promoter regions. The transcription start sites of all gene operons within the FK506 cluster were identified, including 3 examples of leaderless RNA transcripts. These data provide detailed insight into the transcription of the FK506 biosynthetic gene cluster to support future regulatory studies, genetic manipulation, and industrial production.
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Affiliation(s)
- Judith S Bauer
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany.,b German Centre for Infection Research (DZIF), Partner Site Tübingen , Tübingen , Germany
| | - Sven Fillinger
- c Integrative Transcriptomics, Center for Bioinformatics Tübingen, University of Tübingen , Germany
| | - Konrad Förstner
- e Research Center for Infectious Diseases , University of Würzburg , Würzburg , Germany , Core Unit Systems Medicine , Institute for Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Alexander Herbig
- d Max Planck Institute for the Science of Human History , Jena , Germany
| | - Adam C Jones
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany
| | - Katrin Flinspach
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany
| | - Cynthia Sharma
- e Research Center for Infectious Diseases , University of Würzburg , Würzburg , Germany , Core Unit Systems Medicine , Institute for Molecular Infection Biology, University of Würzburg , Würzburg , Germany
| | - Harald Gross
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany.,b German Centre for Infection Research (DZIF), Partner Site Tübingen , Tübingen , Germany
| | - Kay Nieselt
- c Integrative Transcriptomics, Center for Bioinformatics Tübingen, University of Tübingen , Germany
| | - Alexander K Apel
- a Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , Tübingen , Germany.,b German Centre for Infection Research (DZIF), Partner Site Tübingen , Tübingen , Germany
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Liu H, Huang D, Jin L, Wang C, Liang S, Wen J. Integrating multi-omics analyses of Nonomuraea dietziae to reveal the role of soybean oil in [(4'-OH)MeLeu] 4-CsA overproduction. Microb Cell Fact 2017; 16:120. [PMID: 28709434 PMCID: PMC5512743 DOI: 10.1186/s12934-017-0739-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 12/29/2022] Open
Abstract
Background Nonomuraea dietziae is a promising microorganism to mediate the region-specific monooxygenation reaction of cyclosporine A (CsA). The main product [(4′-OH)MeLeu]4-CsA possesses high anti-HIV/HCV and hair growth-stimulating activities while avoiding the immunosuppressive effect of CsA. However, the low conversion efficiency restricts the clinical application. In this study, the production of [(4′-OH)MeLeu]4-CsA was greatly improved by 55.6% from 182.8 to 284.4 mg/L when supplementing soybean oil into the production medium, which represented the highest production of [(4′-OH)MeLeu]4-CsA so far. Results To investigate the effect of soybean oil on CsA conversion, some other plant oils (corn oil and peanut oil) and the major hydrolysates of soybean oil were fed into the production medium, respectively. The results demonstrated that the plant oils, rather than the hydrolysates, could significantly improve the [(4′-OH)MeLeu]4-CsA production, suggesting that soybean oil might not play its role in the lipid metabolic pathway. To further unveil the mechanism of [(4′-OH)MeLeu]4-CsA overproduction under the soybean oil condition, a proteomic analysis based on the two-dimensional gel electrophoresis coupled with MALDI TOF/TOF mass spectrometry was implemented. The results showed that central carbon metabolism, genetic information processing and energy metabolism were significantly up-regulated under the soybean oil condition. Moreover, the gas chromatography-mass spectrometry-based metabolomic analysis indicated that soybean oil had a great effect on amino acid metabolism and tricarboxylic acid cycle. In addition, the transcription levels of cytochrome P450 hydroxylase (CYP) genes for CsA conversion were determined by RT-qPCR and the results showed that most of the CYP genes were up-regulated under the soybean oil condition. Conclusions These findings indicate that soybean oil could strengthen the primary metabolism and the CYP system to enhance the mycelium growth and the monooxygenation reaction, respectively, and it will be a guidance for the further metabolic engineering of this strain. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0739-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huanhuan Liu
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Di Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, People's Republic of China
| | - Lina Jin
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Cheng Wang
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Shaoxiong Liang
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China.,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
| | - Jianping Wen
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, 300072, People's Republic of China. .,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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A genome-scale dynamic flux balance analysis model of Streptomyces tsukubaensis NRRL18488 to predict the targets for increasing FK506 production. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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33
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Insights into the metabolic mechanism of rapamycin overproduction in the shikimate-resistant Streptomyces hygroscopicus strain UV-II using comparative metabolomics. World J Microbiol Biotechnol 2017; 33:101. [DOI: 10.1007/s11274-017-2266-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/12/2017] [Indexed: 01/27/2023]
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34
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Wang J, Liu H, Huang D, Jin L, Wang C, Wen J. Comparative proteomic and metabolomic analysis of Streptomyces tsukubaensis reveals the metabolic mechanism of FK506 overproduction by feeding soybean oil. Appl Microbiol Biotechnol 2017; 101:2447-2465. [DOI: 10.1007/s00253-017-8136-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/11/2017] [Accepted: 01/16/2017] [Indexed: 11/29/2022]
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35
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Dang L, Liu J, Wang C, Liu H, Wen J. Enhancement of rapamycin production by metabolic engineering in Streptomyces hygroscopicus based on genome-scale metabolic model. ACTA ACUST UNITED AC 2017; 44:259-270. [DOI: 10.1007/s10295-016-1880-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/26/2016] [Indexed: 12/18/2022]
Abstract
Abstract
Rapamycin, as a macrocyclic polyketide with immunosuppressive, antifungal, and anti-tumor activity produced by Streptomyces hygroscopicus, is receiving considerable attention for its significant contribution in medical field. However, the production capacity of the wild strain is very low. Hereby, a computational guided engineering approach was proposed to improve the capability of rapamycin production. First, a genome-scale metabolic model of Streptomyces hygroscopicus ATCC 29253 was constructed based on its annotated genome and biochemical information. The model consists of 1003 reactions, 711 metabolites after manual refinement. Subsequently, several potential genetic targets that likely guaranteed an improved yield of rapamycin were identified by flux balance analysis and minimization of metabolic adjustment algorithm. Furthermore, according to the results of model prediction, target gene pfk (encoding 6-phosphofructokinase) was knocked out, and target genes dahP (encoding 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase) and rapK (encoding chorismatase) were overexpressed in the parent strain ATCC 29253. The yield of rapamycin increased by 30.8% by knocking out gene pfk and increased by 36.2 and 44.8% by overexpression of rapK and dahP, respectively, compared with parent strain. Finally, the combined effect of the genetic modifications was evaluated. The titer of rapamycin reached 250.8 mg/l by knockout of pfk and co-expression of genes dahP and rapK, corresponding to a 142.3% increase relative to that of the parent strain. The relationship between model prediction and experimental results demonstrates the validity and rationality of this approach for target identification and rapamycin production improvement.
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Affiliation(s)
- Lanqing Dang
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Jiao Liu
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Cheng Wang
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Huanhuan Liu
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
| | - Jianping Wen
- grid.419897.a 0000 0004 0369 313X Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 School of Chemical Engineering and Technology Tianjin University 300072 Tianjin People’s Republic of China
- grid.33763.32 0000000417612484 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) 300072 Tianjin People’s Republic of China
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Bilyk O, Luzhetskyy A. Metabolic engineering of natural product biosynthesis in actinobacteria. Curr Opin Biotechnol 2016; 42:98-107. [DOI: 10.1016/j.copbio.2016.03.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/03/2016] [Accepted: 03/11/2016] [Indexed: 11/25/2022]
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FkbN and Tcs7 are pathway-specific regulators of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis L19. J Ind Microbiol Biotechnol 2016; 43:1693-1703. [PMID: 27757551 DOI: 10.1007/s10295-016-1849-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
FK506 (tacrolimus), which is produced by many Streptomyces strains, is clinically used as an immunosuppressive agent and for treatment of inflammatory skin diseases. Here, we identified that the FK506 biosynthetic gene cluster in an industrial FK506-producing strain Streptomyces tsukubaensis L19 is organized as eight transcription units. Two pathway-specific regulators, FkbN and Tcs7, involved in FK506 biosynthesis from S. tsukubaensis L19 were characterized in vivo and in vitro. FkbN activates the transcription of six transcription units in FK506 biosynthetic gene cluster, and Tcs7 activates the transcription of fkbN. In addition, the DNA-binding specificity of FkbN was determined. Finally, a high FK506-producing strain was constructed by overexpression of both fkbN and tcs7 in S. tsukubaensis L19, which improved FK506 production by 89 % compared to the parental strain.
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Improvement of FK506 production by synthetic biology approaches. Biotechnol Lett 2016; 38:2015-2021. [DOI: 10.1007/s10529-016-2202-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 08/23/2016] [Indexed: 12/25/2022]
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Ferguson NL, Peña-Castillo L, Moore MA, Bignell DRD, Tahlan K. Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus. ACTA ACUST UNITED AC 2016; 43:537-55. [DOI: 10.1007/s10295-016-1733-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/02/2016] [Indexed: 12/11/2022]
Abstract
Abstract
The genus Streptomyces comprises bacteria that undergo a complex developmental life cycle and produce many metabolites of importance to industry and medicine. Streptomyces clavuligerus produces the β-lactamase inhibitor clavulanic acid, which is used in combination with β-lactam antibiotics to treat certain β-lactam resistant bacterial infections. Many aspects of how clavulanic acid production is globally regulated in S. clavuligerus still remains unknown. We conducted comparative proteomics analysis using the wild type strain of S. clavuligerus and two mutants (ΔbldA and ΔbldG), which are defective in global regulators and vary in their ability to produce clavulanic acid. Approximately 33.5 % of the predicted S. clavuligerus proteome was detected and 192 known or putative regulatory proteins showed statistically differential expression levels in pairwise comparisons. Interestingly, the expression of many proteins whose corresponding genes contain TTA codons (predicted to require the bldA tRNA for translation) was unaffected in the bldA mutant.
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Affiliation(s)
- Nicole L Ferguson
- grid.25055.37 0000000091306822 Department of Biology Memorial University of Newfoundland A1B 3X9 St. John’s NL Canada
| | - Lourdes Peña-Castillo
- grid.25055.37 0000000091306822 Department of Biology Memorial University of Newfoundland A1B 3X9 St. John’s NL Canada
- grid.25055.37 0000000091306822 Department of Computer Science Memorial University of Newfoundland A1B 3X5 St. John’s NL Canada
| | - Marcus A Moore
- grid.25055.37 0000000091306822 Department of Biology Memorial University of Newfoundland A1B 3X9 St. John’s NL Canada
| | - Dawn R D Bignell
- grid.25055.37 0000000091306822 Department of Biology Memorial University of Newfoundland A1B 3X9 St. John’s NL Canada
| | - Kapil Tahlan
- grid.25055.37 0000000091306822 Department of Biology Memorial University of Newfoundland A1B 3X9 St. John’s NL Canada
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40
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Metabolic Engineering for Production of Small Molecule Drugs: Challenges and Solutions. FERMENTATION-BASEL 2016. [DOI: 10.3390/fermentation2010004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Lee DW, Ng BG, Kim BS. Increased valinomycin production in mutants of Streptomyces sp. M10 defective in bafilomycin biosynthesis and branched-chain α-keto acid dehydrogenase complex expression. ACTA ACUST UNITED AC 2015; 42:1507-17. [DOI: 10.1007/s10295-015-1679-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/24/2015] [Indexed: 01/24/2023]
Abstract
Abstract
Streptomyces sp. M10 is a valinomycin-producing bacterial strain that shows potent bioactivity against Botrytis blight of cucumber plants. During studies to increase the yield of valinomycin (a cyclododecadepsipeptide) in strain M10, additional antifungal metabolites, including bafilomycin derivatives (macrolide antibiotics), were identified. To examine the effect of bafilomycin biosynthesis on valinomycin production, the bafilomycin biosynthetic gene cluster was cloned from the genome of strain M10, as were two branched-chain α-keto acid dehydrogenase (BCDH) gene clusters related to precursor supply for bafilomycin biosynthesis. A null mutant (M10bafm) of one bafilomycin biosynthetic gene (bafV) failed to produce bafilomycin, but resulted in a 1.2- to 1.5-fold increase in the amount of valinomycin produced. In another null mutant (M10bkdFm) of a gene encoding a subunit of the BCDH complex (bkdF), bafilomycin production was completely abolished and valinomycin production increased fourfold relative to that in the wild-type M10 strain. The higher valinomycin yield was likely the result of redistribution of the metabolic flux from bafilomycin to valinomycin biosynthesis, because the two antibiotics share a common precursor, 2-ketoisovaleric acid, a deamination product of valine. The results show that directing precursor flux toward active ingredient biosynthesis could be used as a prospective tool to increase the competence of biofungicides.
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Affiliation(s)
- Dong Wan Lee
- grid.222754.4 0000000108402678 Plant Pharmacology Laboratory, Department of Biosystems and Biotechnology Korea University Graduate School 136-713 Seoul Republic of Korea
| | - Bee Gek Ng
- grid.222754.4 0000000108402678 Division of Biotechnology, College of Life Sciences and Biotechnology Korea University 136-713 Seoul Republic of Korea
| | - Beom Seok Kim
- grid.222754.4 0000000108402678 Plant Pharmacology Laboratory, Department of Biosystems and Biotechnology Korea University Graduate School 136-713 Seoul Republic of Korea
- grid.222754.4 0000000108402678 Division of Biotechnology, College of Life Sciences and Biotechnology Korea University 136-713 Seoul Republic of Korea
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Ban YH, Park SR, Yoon YJ. The biosynthetic pathway of FK506 and its engineering: from past achievements to future prospects. J Ind Microbiol Biotechnol 2015; 43:389-400. [PMID: 26342319 DOI: 10.1007/s10295-015-1677-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/19/2015] [Indexed: 11/28/2022]
Abstract
FK506, a 23-membered macrolide produced by several Streptomyces species, is an immunosuppressant widely used to prevent the rejection of transplanted organs. In addition, FK506 and its analogs possess numerous promising therapeutic potentials including antifungal, neuroprotective, and neuroregenerative activities. Herein, we introduce the biological activities and mechanisms of action of FK506 and discuss recent progress made in understanding its biosynthetic pathway, improving production, and in the mutasynthesis of diverse analogs. Perspectives highlighting further strain improvement and structural diversification aimed at generating more analogs with improved pharmaceutical properties will be emphasized.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Sung Ryeol Park
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yeo Joon Yoon
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 120-750, Republic of Korea.
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Zhang C, Sheng C, Wang W, Hu H, Peng H, Zhang X. Identification of the Lomofungin Biosynthesis Gene Cluster and Associated Flavin-Dependent Monooxygenase Gene in Streptomyces lomondensis S015. PLoS One 2015; 10:e0136228. [PMID: 26305803 PMCID: PMC4549113 DOI: 10.1371/journal.pone.0136228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
Streptomyces lomondensis S015 synthesizes the broad-spectrum phenazine antibiotic lomofungin. Whole genome sequencing of this strain revealed a genomic locus consisting of 23 open reading frames that includes the core phenazine biosynthesis gene cluster lphzGFEDCB. lomo10, encoding a putative flavin-dependent monooxygenase, was also identified in this locus. Inactivation of lomo10 by in-frame partial deletion resulted in the biosynthesis of a new phenazine metabolite, 1-carbomethoxy-6-formyl-4,9-dihydroxy-phenazine, along with the absence of lomofungin. This result suggests that lomo10 is responsible for the hydroxylation of lomofungin at its C-7 position. This is the first description of a phenazine hydroxylation gene in Streptomyces, and the results of this study lay the foundation for further investigation of phenazine metabolite biosynthesis in Streptomyces.
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Affiliation(s)
- Chunxiao Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chaolan Sheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- * E-mail:
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huasong Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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Gajzlerska W, Kurkowiak J, Turło J. Use of three-carbon chain compounds as biosynthesis precursors to enhance tacrolimus production in Streptomyces tsukubaensis. N Biotechnol 2015; 32:32-9. [DOI: 10.1016/j.nbt.2014.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 07/06/2014] [Accepted: 07/17/2014] [Indexed: 01/11/2023]
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45
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Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU, Lee SY. Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends Biotechnol 2014; 33:15-26. [PMID: 25497361 DOI: 10.1016/j.tibtech.2014.10.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/21/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022]
Abstract
Actinomycetes are excellent sources for novel bioactive compounds, which serve as potential drug candidates for antibiotics development. While industrial efforts to find and develop novel antimicrobials have been severely reduced during the past two decades, the increasing threat of multidrug-resistant pathogens and the development of new technologies to find and produce such compounds have again attracted interest in this field. Based on improvements in whole-genome sequencing, novel methods have been developed to identify the secondary metabolite biosynthetic gene clusters by genome mining, to clone them, and to express them in heterologous hosts in much higher throughput than before. These technologies now enable metabolic engineering approaches to optimize production yields and to directly manipulate the pathways to generate modified products.
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Affiliation(s)
- Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ewa Maria Musiol-Kroll
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Hyun Uk Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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Fernández J, Marín L, Alvarez-Alonso R, Redondo S, Carvajal J, Villamizar G, Villar CJ, Lombó F. Biosynthetic modularity rules in the bisintercalator family of antitumor compounds. Mar Drugs 2014; 12:2668-99. [PMID: 24821625 PMCID: PMC4052310 DOI: 10.3390/md12052668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/05/2022] Open
Abstract
Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development.
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Affiliation(s)
- Javier Fernández
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Laura Marín
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Raquel Alvarez-Alonso
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Saúl Redondo
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Juan Carvajal
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Germán Villamizar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Claudio J Villar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Felipe Lombó
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
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Du W, Huang D, Xia M, Wen J, Huang M. Improved FK506 production by the precursors and product-tolerant mutant of Streptomyces tsukubaensis based on genome shuffling and dynamic fed-batch strategies. J Ind Microbiol Biotechnol 2014; 41:1131-43. [PMID: 24788378 DOI: 10.1007/s10295-014-1450-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/18/2014] [Indexed: 01/09/2023]
Abstract
FK506, a secondary metabolite produced by Streptomyces tsukubaensis, is well known for its immunosuppressant properties to prevent rejection of transplanted organs and treat autoimmune diseases. However, the low titer of FK506 in the original producer strain limits the further industrialization efforts and restricts its clinical applications. To address this issue, a highly efficient method combined genome shuffling and dynamic fed-batch strategies was systematically performed in this work. Firstly, after five rounds of genome shuffling based on precursors and product resistances, a higher yielding strain TJ-P325 was successfully acquired, whose production reached 365.6 mg/L, 11-fold increase compared with the original strain. Then, the possible mechanism of different production capabilities between TJ-P325 and the wild type was explored through comparative gene expression analysis of key genes. Results showed that the transcription level of key genes was altered significantly in the mutant. Moreover, precursors addition enhanced the FK506 production by 28 %, as well as reduced the by-products biosynthesis. Finally, the disodium malonate and disodium methylmalonate dynamic fed-batch strategies dramatically led to the production of 514.5 mg/L in a 7.5-L bioreactor. These results demonstrated that genome shuffling and dynamic fed-batch strategies could be successfully applied to generate high-yield strains with value-added natural products during industrial microbial fermentation.
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Affiliation(s)
- Wenjie Du
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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Trends in the biosynthesis and production of the immunosuppressant tacrolimus (FK506). Appl Microbiol Biotechnol 2013; 98:497-507. [PMID: 24272367 DOI: 10.1007/s00253-013-5362-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 01/03/2023]
Abstract
The current off-patent state of tacrolimus (FK506) has opened the hunting season for new generic pharmaceutical formulations of this immunosuppressant. This fact has boosted the scientific and industrial research on tacrolimus for the last 5 years in order to improve its production. The fast discovery of tacrolimus producer strains has generated a huge number of producers, which presents the biosynthetic cluster of FK506 as a high promiscuous genetic region. For the first time, the current state-of-the-art on the tacrolimus biosynthesis, production improvements and drug purification is reviewed. On one hand, all the genes involved in the tacrolimus biosynthesis, in addition to the traditional PKS/NRPS, as well as their regulation are analysed. On the other hand, tacrolimus direct and indirect precursors are reviewed as a straight manner to improve the final yield, which is a current trend in the field. Twenty years of industrial and scientific improvements on tacrolimus production are summarised, whereas future trends are also drafted.
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