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Mu X, Lei R, Yan S, Deng Z, Liu R, Liu T. The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa. Synth Syst Biotechnol 2024; 9:609-617. [PMID: 38784197 PMCID: PMC11108826 DOI: 10.1016/j.synbio.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
Spinosad, a potent broad-spectrum bioinsecticide produced by Saccharopolyspora spinosa, has significant market potential. Despite its effectiveness, the regulatory mechanisms of spinosad biosynthesis remain unclear. Our investigation identified the crucial role of the LysR family transcriptional regulator ORF-L16, located upstream of spinosad biosynthetic genes, in spinosad biosynthesis. Through reverse transcription PCR (RT-PCR) and 5'-rapid amplification of cDNA ends (5'-Race), we unveiled that the spinosad biosynthetic gene cluster (BGC) contains six transcription units and seven promoters. Electrophoretic mobility shift assays (EMSAs) demonstrated that ORF-L16 bound to seven promoters within the spinosad BGC, indicating its involvement in regulating spinosad biosynthesis. Notably, deletion of ORF-L16 led to a drastic reduction in spinosad production from 1818.73 mg/L to 1.69 mg/L, accompanied by decreased transcription levels of spinosad biosynthetic genes, confirming its positive regulatory function. Additionally, isothermal titration calorimetry (ITC) and EMSA confirmed that spinosyn A, the main product of the spinosad BGC, served as an effector of ORF-L16. Specifically, it decreased the binding affinity between ORF-L16 and spinosad BGC promoters, thus exerting negative feedback regulation on spinosad biosynthesis. This research enhances our comprehension of spinosad biosynthesis regulation and lays the groundwork for future investigations on transcriptional regulators in S. spinosa.
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Affiliation(s)
- Xin Mu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Ru Lei
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Shuqing Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ran Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430072, Hubei Province, China
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
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Xie H, Su YT, Bu QT, Li YP, Zhao QW, Du YL, Li YQ. Stepwise increase of fidaxomicin in an engineered heterologous host Streptomyces albus through multi-level metabolic engineering. Synth Syst Biotechnol 2024; 9:766-774. [PMID: 39021363 PMCID: PMC11253128 DOI: 10.1016/j.synbio.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/28/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The anti-Clostridium difficile infection (CDI) drug fidaxomicin is a natural polyketide metabolite mainly produced by Micromonosporaceae, such as Actinoplanes deccanensis, Dactylosporangium aurantiacum, and Micromonospora echinospora. In the present study, we employed a stepwise strategy by combining heterologous expression, chassis construction, promoter engineering, activator and transporters overexpression, and optimization of fermentation media for high-level production of fidaxomicin. The maximum yield of 384 mg/L fidaxomicin was achieved with engineered Streptomyces albus D7-VHb in 5 L-tank bioreactor, and it was approximately 15-fold higher than the native strain Actinoplanes deccanensis YP-1 with higher strain stability and growth rate. This study developed an enhanced chassis strain, and for the first time, achieved the heterologous synthesis of fidaxomicin through a combinatorial metabolic engineering strategy.
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Affiliation(s)
- Huang Xie
- 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
| | - Yi-Ting Su
- 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-Ting Bu
- 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
| | - Yue-Ping 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
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi-Ling Du
- 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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Dai P, Qin Y, Li L, Li H, Lv L, Xu D, Song Y, Huang T, Lin S, Deng Z, Tao M. Enhancing tylosin production by combinatorial overexpression of efflux, SAM biosynthesis, and regulatory genes in hyperproducing Streptomyces xinghaiensis strain. Synth Syst Biotechnol 2023; 8:486-497. [PMID: 37519989 PMCID: PMC10372049 DOI: 10.1016/j.synbio.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Tylosin is a 16-membered macrolide antibiotic widely used in veterinary medicine to control infections caused by Gram-positive pathogens and mycoplasmas. To improve the fermentation titer of tylosin in the hyperproducing Streptomyces xinghaiensis strain TL01, we sequenced its whole genome and identified the biosynthetic gene cluster therein. Overexpression of the tylosin efflux gene tlrC, the cluster-situated S-adenosyl methionine (SAM) synthetase gene metKcs, the SAM biosynthetic genes adoKcs-metFcs, or the pathway-specific activator gene tylR enhanced tylosin production by 18%, 12%, 11%, and 11% in the respective engineered strains TLPH08-2, TLPH09, TLPH10, and TLPH12. Co-overexpression of metKcs and adoKcs-metFcs as two transcripts increased tylosin production by 22% in the resultant strain TLPH11 compared to that in TL01. Furthermore, combinational overexpression of tlrC, metKcs, adoKcs-metFcs, and tylR as four transcripts increased tylosin production by 23% (10.93g/L) in the resultant strain TLPH17 compared to that in TL01. However, a negligible additive effect was displayed upon combinational overexpression in TLPH17 as suggested by the limited increment of fermentation titer compared to that in TLPH08-2. Transcription analyses indicated that the expression of tlrC and three SAM biosynthetic genes in TLPH17 was considerably lower than that of TLPH08-2 and TLPH11. Based on this observation, the five genes were rearranged into one or two operons to coordinate their overexpression, yielding two engineered strains TLPH23 and TLPH24, and leading to further enhancement of tylosin production over TLPH17. In particular, the production of TLPH23 reached 11.35 g/L. These findings indicated that the combinatorial strategy is a promising approach for enhancing tylosin production in high-yielding industrial strains.
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Affiliation(s)
- Penghui Dai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuyao Qin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Luyuan Li
- Zhejiang Apeloa Biotechnology Co., Ltd., Jinhua, 322109, China
| | - Haidi Li
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Lihuo Lv
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Danying Xu
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Yuqing Song
- Zhejiang Apeloa Jiayuan Pharmaceutical Co., Ltd., Jinhua, 322118, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
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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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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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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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7
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Wu QB, Chen XA, Lv ZY, Zhang XY, Liu Y, Li YQ. Activation and discovery of tsukubarubicin from Streptomyces tsukubaensis through overexpressing SARPs. Appl Microbiol Biotechnol 2021; 105:4731-4741. [PMID: 34021812 DOI: 10.1007/s00253-021-11344-5] [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: 02/04/2021] [Revised: 04/23/2021] [Accepted: 05/09/2021] [Indexed: 12/11/2022]
Abstract
Genome sequencing has revealed that each Streptomyces contains a wide range of biosynthetic gene clusters (BGCs) and has the capability to produce more novel natural products than what is expected. However, most gene clusters for secondary metabolite biosynthesis are cryptic under normal growth conditions. In Streptomyces tsukubaensis, combining overexpression of the putative SARPs (Streptomyces antibiotic regulatory proteins) and bioactivity-guided screening, the silent gene cluster (tsu) was successfully activated and a novel bioactive anthracycline tsukubarubicin was further isolated and identified. Biological activity assays demonstrated that tsukubarubicin possessed much better antitumor bioactivities against various human cancer cell lines (especially the breast cancer cell lines) than clinically used doxorubicin. Moreover, the previously unreported gene cluster (tsu) for biosynthesis of tsukubarubicin was first characterized and detailed annotations of this gene cluster were also conducted. Our strategy presented in this work is broadly applicable in other Streptomyces and will assist in enriching the natural products for potential drug leads. KEY POINTS: • Generally scalable strategy to activate silent gene clusters by manipulating SARPs. • The novel anthracycline tsukubarubicin with potent antitumor bioactivities. • Identification and annotation of the previously uncharacterized tsu gene cluster.
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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
| | - Xin-Ai Chen
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Zhong-Yuan Lv
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xiao-Ying Zhang
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yu Liu
- Zhejiang University College of Life Sciences, Hangzhou, 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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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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Crotonylation of key metabolic enzymes regulates carbon catabolite repression in Streptomyces roseosporus. Commun Biol 2020; 3:192. [PMID: 32332843 PMCID: PMC7181814 DOI: 10.1038/s42003-020-0924-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/31/2020] [Indexed: 12/22/2022] Open
Abstract
Due to the plethora natural products made by Streptomyces, the regulation of its metabolism are of great interest, whereas there is a lack of detailed understanding of the role of posttranslational modifications (PTM) beyond traditional transcriptional regulation. Herein with Streptomyces roseosporus as a model, we showed that crotonylation is widespread on key enzymes for various metabolic pathways, and sufficient crotonylation in primary metabolism and timely elimination in secondary metabolism are required for proper Streptomyces metabolism. Particularly, the glucose kinase Glk, a keyplayer of carbon catabolite repression (CCR) regulating bacterial metabolism, is identified reversibly crotonylated by the decrotonylase CobB and the crotonyl-transferase Kct1 to negatively control its activity. Furthermore, crotonylation positively regulates CCR for Streptomyces metabolism through modulation of the ratio of glucose uptake/Glk activity and utilization of carbon sources. Thus, our results revealed a regulatory mechanism that crotonylation globally regulates Streptomyces metabolism at least through positive modulation of CCR. Chen-Fan Sun et al. show that key enzymes in several metabolic pathways are crotonylated in Streptomyces roseosporus. This study suggests that crotonylation increases carbon catabolite repression by increasing glucose uptake while reducing the activity of glucose kinase.
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Xia H, Li X, Li Z, Zhan X, Mao X, Li Y. The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining. Front Microbiol 2020; 11:406. [PMID: 32265866 PMCID: PMC7105598 DOI: 10.3389/fmicb.2020.00406] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xuming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongquan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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Guan H, Li Y, Zheng J, Liu N, Zhang J, Tan H. Important role of a LAL regulator StaR in the staurosporine biosynthesis and high-production of Streptomyces fradiae CGMCC 4.576. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1638-1654. [PMID: 31820200 DOI: 10.1007/s11427-019-1597-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 01/27/2023]
Abstract
Staurosporine, belonging to indolocarbazole compounds, is regarded as an excellent lead compound for synthesizing antitumor agents as a potent inhibitor against various protein kinases. In this study, two separate clusters (cluster A and cluster B), corresponding to biosyntheses of K-252c (staurosporine aglycone) and sugar moiety, were identified in Streptomyces fradiae CGMCC 4.576 and heterologously expressed in Streptomyces coelicolor M1146 separately or together. StaR, a cluster-situated LAL family regulator, activates staurosporine biosynthesis by binding to the promoter regions of staO-staC and staG-staN. The conserved sequences GGGGG and GCGCG were found through gradually truncating promoters of staO and staG, and further determined by mutational experiments. Overexpression of staR with the supplementation of 0.01 g L-1 FeSO4 increased staurosporine production to 5.2-fold compared with that of the parental strain Streptomyces fradiae CGMCC 4.576 in GYM medium. Our results provided an approach for improvement of staurosporine production mediated by a positive regulator and established the basis for dissecting the regulatory mechanisms of other indolocarbazole compounds with clinical application value.
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Affiliation(s)
- Hanye Guan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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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 YP, Yu P, Li JF, Tang YL, Bu QT, Mao XM, Li YQ. FadR1, a pathway-specific activator of fidaxomicin biosynthesis in Actinoplanes deccanensis Yp-1. Appl Microbiol Biotechnol 2019; 103:7583-7596. [DOI: 10.1007/s00253-019-09949-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 12/18/2022]
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Yu Z, Shen X, Wu Y, Yang S, Ju D, Chen S. Enhancement of ascomycin production via a combination of atmospheric and room temperature plasma mutagenesis in Streptomyces hygroscopicus and medium optimization. AMB Express 2019; 9:25. [PMID: 30778695 PMCID: PMC6379505 DOI: 10.1186/s13568-019-0749-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/07/2019] [Indexed: 12/16/2022] Open
Abstract
Ascomycin, a key intermediate for chemical synthesis of immunosuppressive drug pimecrolimus, is produced by Streptomyces hygroscopicus var. ascomyceticus. In order to improve the strain production, the original S. hygroscopicus ATCC 14891 strain was treated here with atmospheric and room temperature plasma to obtain a stable high-producing S. hygroscopicus SFK-36 strain which produced 495.3 mg/L ascomycin, a 32.5% increase in ascomycin compared to the ATCC 14891. Then, fermentation medium was optimized using response surface methodology to further enhance ascomycin production. In the optimized medium containing 81.0 g/L soluble starch, 57.4 g/L peanut meal, and 15.8 g/L soybean oil, the ascomycin yield reached 1466.3 mg/L in flask culture. Furthermore, the fermentation process was carried out in a 5 L fermenter, and the ascomycin yield reached 1476.9 mg/L, which is the highest ascomycin yield reported so far. Therefore, traditional mutagenesis breeding combined with medium optimization is an effective approach for the enhancement of ascomycin production.
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Karadeniz E, Ozbilgin M, Egeli T, Agalar C, Cevlik AD, Aysal A, Ellidokuz H, Unek T, Astarcioglu I. Assessment of Effect of Intraperitoneal Tacrolimus on Liver Regeneration in Major (70%) Hepatectomy Model After Experimental Pringle Maneuver in Rats. Transplant Proc 2019; 51:1172-1179. [PMID: 31101194 DOI: 10.1016/j.transproceed.2019.01.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 01/21/2019] [Indexed: 12/12/2022]
Abstract
AIM Small-for-size grafts have become more important, especially in living donor liver transplants. The Pringle maneuver, used to reduce blood loss, and the immunosuppressive medications used to prevent graft rejection in liver transplants have different side effects on liver regeneration. We researched the effect of situations where tacrolimus and the Pringle maneuver were applied or not on liver regeneration in rats with partial hepatectomy. MATERIAL AND METHODS This study was completed with 35 Wistar Albino rats. The subjects were randomly divided into 5 groups: Group 1 had the abdomen opened and no other procedure was performed; Group 2 underwent a 70% hepatectomy; Group 3 underwent a 15-minute Pringle maneuver + 70% hepatectomy; Group 4 underwent a 70% hepatectomy + 5 days of 1 mg/kg/day intraperitoneal tacrolimus; and Group 5 underwent a 150 minute Pringle maneuver + 0% hepatectomy + 5 days of 1 mg/kg/day intraperitoneal tacrolimus. All rats were sacrificed on the seventh postoperative day, remaining liver tissue was weighed, and weight indices created. The remaining liver tissue was stained with phosphohistone H3 and the mitotic index calculated. RESULTS The groups that underwent the Pringle maneuver, 70% hepatectomy, and tacrolimus administration were compared with the control group in terms of mitotic index and weight index, but no statistically significant differences were identified. CONCLUSION Suppression of regeneration forms a risk after liver transplantation with small-volume grafts. As a result, research on the effect of tacrolimus combined with the Pringle maneuver is important, especially for transplantations using segmented liver grafts. In our study, we showed that the use of tacrolimus had no negative effect on liver regeneration.
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Affiliation(s)
- E Karadeniz
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - M Ozbilgin
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey.
| | - T Egeli
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - C Agalar
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - A D Cevlik
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - A Aysal
- Department of Pathology, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - H Ellidokuz
- Department of Preventive Oncology, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - T Unek
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - I Astarcioglu
- Department of General Surgery, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
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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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17
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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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Engineering of the LysR family transcriptional regulator FkbR1 and its target gene to improve ascomycin production. Appl Microbiol Biotechnol 2017; 101:4581-4592. [DOI: 10.1007/s00253-017-8242-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/01/2017] [Accepted: 03/10/2017] [Indexed: 01/07/2023]
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