1
|
Duan Y, Fang F, Mu X, Wang H, Shen Z, Deng Z, Liu T, Wang Z, Liu R. Exploration of Streptomyces fradiae J1-021 as a Potential Host for the Heterologous Production of Spinosad. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38597928 DOI: 10.1021/acs.jafc.3c08884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Spinosad is a potent insecticide produced by Saccharopolyspora spinosa. However, it harbors certain limitations of a low growing rate and unfeasible genetic manipulation that can be overcome by adopting a superior platform, such as Streptomyces. Herein, we exploited the industrial tylosin-producing Streptomyces fradiae J1-021 for the heterologous production of spinosad. An engineered strain (HW01) with deletion of the tylosin biosynthetic gene cluster (BGC) was constructed and then transformed with the natural spinosad BGC. The distribution and expression levels of the tylosin BGC operons were assessed to construct a natural promoter library. The rate-limiting steps of spinosad biosynthesis were identified by analyzing the transcriptional expression of the spinosad biosynthetic genes. The stepwise engineering work involved the overexpression of the biosynthetic genes participating in rate-limiting pathways using strong promoters, affording an increase in spinosad production to 112.4 μg/L. These results demonstrate that strain HW01 has the potential to be used as a chassis for the heterologous production of polyketides.
Collapse
Affiliation(s)
- Yuhua Duan
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fang Fang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin Mu
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Hui Wang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiyong Shen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tiangang Liu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhangqian Wang
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Ran Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
2
|
An Z, Tao H, Wang Y, Xia B, Zou Y, Fu S, Fang F, Sun X, Huang R, Xia Y, Deng Z, Liu R, Liu T. Increasing the heterologous production of spinosad in Streptomyces albus J1074 by regulating biosynthesis of its polyketide skeleton. Synth Syst Biotechnol 2021; 6:292-301. [PMID: 34584996 PMCID: PMC8453208 DOI: 10.1016/j.synbio.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Spinosyns are natural broad-spectrum biological insecticides with a double glycosylated polyketide structure that are produced by aerobic fermentation of the actinomycete, Saccharopolyspora spinosa. However, their large-scale overproduction is hindered by poorly understood bottlenecks in optimizing the original strain, and poor adaptability of the heterologous strain to the production of spinosyn. In this study, we genetically engineered heterologous spinosyn-producer Streptomyces albus J1074 and optimized the fermentation to improve the production of spinosad (spinosyn A and spinosyn D) based on our previous work. We systematically investigated the result of overexpressing polyketide synthase genes (spnA, B, C, D, E) using a constitutive promoter on the spinosad titer in S. albus J1074. The supply of polyketide synthase precursors was then increased to further improve spinosad production. Finally, increasing or replacing the carbon source of the culture medium resulted in a final spinosad titer of ∼70 mg/L, which is the highest titer of spinosad achieved in heterologous Streptomyces species. This research provides useful strategies for efficient heterologous production of natural products.
Collapse
Key Words
- 2-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl)amino]ethanesulfonic acid, (TES)
- HPLC-high resolution mass spectrometer, (HPLC-HRMS)
- Heterologous production
- Luria−Bertani, (LB)
- Polyketide
- Polyketide synthase
- Spinosad
- Spinosyn
- Streptomyces
- acetyl-CoA carboxylase, (ACC)
- acetyl-CoA synthetase, (AcsA)
- biosynthetic gene cluster, (BGC)
- high-performance liquid chromatography, (HPLC)
- limit of detection, (LoD)
- overlap extension-polymerase chain reaction, (OE-PCR)
- polyketide synthase, (PKS)
- propionyl-CoA carboxylase, (PCC)
- soya flour mannitol, (SFM)
- β and ε subunits of Acc, (AccBE)
- β and ε subunits of PCC, (PccBE)
Collapse
Affiliation(s)
- Ziheng An
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Bingqing Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yang Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Shuai Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Fang Fang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Xiao Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Renqiong Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Yao Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
| | - Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, PR China
- Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, 430075, PR China
| |
Collapse
|
3
|
He H, Tang J, Chen J, Hu J, Zhu Z, Liu Y, Shuai L, Cao L, Liu Z, Xia Z, Ding X, Hu S, Zhang Y, Rang J, Xia L. Flaviolin-Like Gene Cluster Deletion Optimized the Butenyl-Spinosyn Biosynthesis Route in Saccharopolyspora pogona. ACS Synth Biol 2021; 10:2740-2752. [PMID: 34601869 DOI: 10.1021/acssynbio.1c00344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reduction and optimization of the microbial genome is an important strategy for constructing synthetic biological chassis cells and overcoming obstacles in natural product discovery and production. However, it is of great challenge to discover target genes that can be deleted and optimized due to the complicated genome of actinomycetes. Saccharopolyspora pogona can produce butenyl-spinosyn during aerobic fermentation, and its genome contains 32 different gene clusters. This suggests that there is a large amount of potential competitive metabolism in S. pogona, which affects the biosynthesis of butenyl-spinosyn. By analyzing the genome of S. pogona, six polyketide gene clusters were identified. From those, the complete deletion of clu13, a flaviolin-like gene cluster, generated a high butenyl-spinosyn-producing strain. Production of this strain was 4.06-fold higher than that of the wildtype strain. Transcriptome profiling revealed that butenyl-spinosyn biosynthesis was not primarily induced by the polyketide synthase RppA-like but was related to hypothetical protein Sp1764. However, the repression of sp1764 was not enough to explain the enormous enhancement of butenyl-spinosyn yields in S. pogona-Δclu13. After the comparative proteomic analysis of S. pogona-Δclu13 and S. pogona, two proteins, biotin carboxyl carrier protein (BccA) and response regulator (Reg), were investigated, whose overexpression led to great advantages of butenyl-spinosyn biosynthesis. In this way, we successfully discovered three key genes that obviously optimize the biosynthesis of butenyl-spinosyn. Gene cluster simplification performed in conjunction with multiomics analysis is of great practical significance for screening dominant chassis strains and optimizing secondary metabolism. This work provided an idea about screening key factors and efficient construction of production strains.
Collapse
Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Zirong Zhu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Yang Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Ling Shuai
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Li Cao
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Youming Zhang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410083, China
| |
Collapse
|
4
|
Comparative transcriptomic analysis of two Saccharopolyspora spinosa strains reveals the relationships between primary metabolism and spinosad production. Sci Rep 2021; 11:14779. [PMID: 34285307 PMCID: PMC8292330 DOI: 10.1038/s41598-021-94251-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/06/2021] [Indexed: 11/23/2022] Open
Abstract
Saccharopolyspora spinosa is a well-known actinomycete for producing the secondary metabolites, spinosad, which is a potent insecticides possessing both efficiency and safety. In the previous researches, great efforts, including physical mutagenesis, fermentation optimization, genetic manipulation and other methods, have been employed to increase the yield of spinosad to hundreds of folds from the low-yield strain. However, the metabolic network in S. spinosa still remained un-revealed. In this study, two S. spinosa strains with different spinosad production capability were fermented and sampled at three fermentation periods. Then the total RNA of these samples was isolated and sequenced to construct the transcriptome libraries. Through transcriptomic analysis, large numbers of differentially expressed genes were identified and classified according to their different functions. According to the results, spnI and spnP were suggested as the bottleneck during spinosad biosynthesis. Primary metabolic pathways such as carbon metabolic pathways exhibited close relationship with spinosad formation, as pyruvate and phosphoenolpyruvic acid were suggested to accumulate in spinosad high-yield strain during fermentation. The addition of soybean oil in the fermentation medium activated the lipid metabolism pathway, enhancing spinosad production. Glutamic acid and aspartic acid were suggested to be the most important amino acids and might participate in spinosad biosynthesis.
Collapse
|
5
|
Li S, Yang B, Tan GY, Ouyang LM, Qiu S, Wang W, Xiang W, Zhang L. Polyketide pesticides from actinomycetes. Curr Opin Biotechnol 2021; 69:299-307. [PMID: 34102376 DOI: 10.1016/j.copbio.2021.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/19/2021] [Accepted: 05/22/2021] [Indexed: 12/18/2022]
Abstract
Natural product derived pesticides have increased in popularity worldwide because of their high efficacy, eco-friendly nature and favorable safety profile. The development of polyketide pesticides from actinomycetes reflects this increase in popularity in the past decades. These pesticides, which include avermectins, spinosyns, polynactins, tetramycin and their analogues, have been successfully applied in crop protection. Moreover, the advance of biotechnology has led to continuous improvement in the discovery and production processes. In this review, we summarize these polyketide pesticides, their activities and provide insight into their development. We also discuss engineering strategies and the current status of industrial production for these pesticides. Given that actinomycetes are known to produce a wide range of bioactive secondary metabolites, the description of pesticide development and high yield strain improvement presented herein will facilitate further development of these valuable polyketide pesticides from actinomycetes.
Collapse
Affiliation(s)
- Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bowen Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Li-Ming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shiwen Qiu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Weishan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; School of Life Sciences, Northeast Agricultural University, Harbin 150030, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| |
Collapse
|
6
|
Liu X, Zhang Y, Huang K, Yin T, Li Q, Zou Q, Guo D, Zhang X. rpoB and efp are stable candidate reference genes for quantitative real-time PCR analysis in Saccharopolyspora spinosa. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1899852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Xiaomeng Liu
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Nutrition and Health Research Institute, COFCO, Beijing, PR China
| | - Yunpeng Zhang
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Nutrition and Health Research Institute, COFCO, Beijing, PR China
| | - Kexue Huang
- Qilu Pharmaceutical (Inner Mongolia) Co., Ltd, Hohhot, Inner Mongolia, PR China
| | - Tie Yin
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Nutrition and Health Research Institute, COFCO, Beijing, PR China
| | - Qi Li
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Nutrition and Health Research Institute, COFCO, Beijing, PR China
| | - Qiulong Zou
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Nutrition and Health Research Institute, COFCO, Beijing, PR China
| | - Dongsheng Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu Province, PR China
| | - Xiaolin Zhang
- Beijing Key Laboratory of Nutrition & Health and Food Safety, Nutrition and Health Research Institute, COFCO, Beijing, PR China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu Province, PR China
| |
Collapse
|
7
|
Lü J, Long Q, Zhao Z, Chen L, He W, Hong J, Liu K, Wang Y, Pang X, Deng Z, Tao M. Engineering the Erythromycin-Producing Strain Saccharopolyspora erythraea HOE107 for the Heterologous Production of Polyketide Antibiotics. Front Microbiol 2020; 11:593217. [PMID: 33363524 PMCID: PMC7752772 DOI: 10.3389/fmicb.2020.593217] [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: 08/10/2020] [Accepted: 11/10/2020] [Indexed: 11/17/2022] Open
Abstract
Bacteria of the genus Saccharopolyspora produce important polyketide antibiotics, including erythromycin A (Sac. erythraea) and spinosad (Sac. spinosa). We herein report the development of an industrial erythromycin-producing strain, Sac. erythraea HOE107, into a host for the heterologous expression of polyketide biosynthetic gene clusters (BGCs) from other Saccharopolyspora species and related actinomycetes. To facilitate the integration of natural product BGCs and auxiliary genes beneficial for the production of natural products, the erythromycin polyketide synthase (ery) genes were replaced with two bacterial attB genomic integration sites associated with bacteriophages ϕC31 and ϕBT1. We also established a highly efficient conjugation protocol for the introduction of large bacterial artificial chromosome (BAC) clones into Sac. erythraea strains. Based on this optimized protocol, an arrayed BAC library was effectively transferred into Sac. erythraea. The large spinosad gene cluster from Sac. spinosa and the actinorhodin gene cluster from Streptomyces coelicolor were successfully expressed in the ery deletion mutant. Deletion of the endogenous giant polyketide synthase genes pkeA1-pkeA4, the product of which is not known, and the flaviolin gene cluster (rpp) from the bacterium increased the heterologous production of spinosad and actinorhodin. Furthermore, integration of pJTU6728 carrying additional beneficial genes dramatically improved the yield of actinorhodin in the engineered Sac. erythraea strains. Our study demonstrated that the engineered Sac. erythraea strains SLQ185, LJ161, and LJ162 are good hosts for the expression of heterologous antibiotics and should aid in expression-based genome-mining approaches for the discovery of new and cryptic antibiotics from Streptomyces and rare actinomycetes.
Collapse
Affiliation(s)
- Jin Lü
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingshan Long
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhilong Zhao
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Lu Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weijun He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiali Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yemin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuhua Pang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meifeng Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, School of Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
8
|
Liu Z, Zhu Z, Tang J, He H, Wan Q, Luo Y, Huang W, Yu Z, Hu Y, Ding X, Xia L. RNA-Seq-Based Transcriptomic Analysis of Saccharopolyspora spinosa Revealed the Critical Function of PEP Phosphonomutase in the Replenishment Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14660-14669. [PMID: 33258371 DOI: 10.1021/acs.jafc.0c04443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spinosyns, the secondary metabolites produced by Saccharopolyspora spinosa, are the active ingredients in a family of novel biological insecticides. Although the complete genome sequence of S. spinosa has been published, the transcriptome of S. spinosa remains poorly characterized. In this study, high-throughput RNA sequencing (RNA-seq) technology was applied to dissect the transcriptome of S. spinosa. Through transcriptomic analysis of different periods of S. spinosa growth, we found large numbers of differentially expressed genes and classified them according to their different functions. Based on the RNA-seq data, the CRISPR-Cas9 method was used to knock out the PEP phosphonomutase gene (orf 06952-4171). The yield of spinosyns A and D in S. spinosa-ΔPEP was 178.91 mg/L and 42.72 mg/L, which was 2.14-fold and 1.76-fold higher than that in the wild type (83.51 and 24.34 mg/L), respectively. The analysis of the mutant strains also verified the validity of the transcriptome data. The deletion of the PEP phosphonomutase gene leads to an increase in pyruvate content and affects the biosynthesis of spinosad. The replenishment of phosphoenol pyruvate in S. spinosa provides the substrate for the production of spinosad. We envision that these transcriptomic analysis results will contribute to the further study of secondary metabolites in actinomycetes.
Collapse
Affiliation(s)
- Zhudong Liu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Zirong Zhu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Jianli Tang
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Haocheng He
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Qianqian Wan
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yuewen Luo
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Weitao Huang
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Ziquan Yu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Yibo Hu
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Xuezhi Ding
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Liqiu Xia
- State Key Laboratory of Development Biology of Freshwater Fish, Hunan Provincial Key Laboratory for Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha 410081, China
| |
Collapse
|
9
|
He H, Peng S, Yuan S, Tang J, Liu Z, Rang J, Xia Z, Hu J, Chen J, Ding X, Hu S, Sun Y, Xia L. Effects of lytS-L on the primary metabolism and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona. Gene 2020; 766:145130. [PMID: 32911030 DOI: 10.1016/j.gene.2020.145130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 07/31/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
The LytTR family two-component system widely exists in bacterial cells and plays an important role in metabolic regulation. The lytS-L gene that encodes for a LytTR family sensor kinase was knocked out to study its influence on the growth, phenotype, and the biosynthesis of the insecticidal polyketide butenyl-spinosyn in Saccharopolyspora pogona NRRL 30141 (S. pogona). High performance liquid chromatography (HPLC) results showed that the butenyl-spinosyn yield of the lytS-L knockout mutant decreased by 58.9% compared with that of the parental strain. This is manifested by a weak toxicity of the mutant against the insect Helicoverpa assulta (H. armigera). Comparative proteomic analysis revealed the expression characteristics of the proteins in S. pogona and S. pogona-ΔlytS-L: a total of 14 proteins involved in energy metabolism were down-regulated, 9 proteins related to carbon metabolism such as glycolysis, and tricarboxylic acid cycle (TCA) were up-regulated, while 13 proteins involved in the biosynthesis of butenyl-spinosyn were down-regulated (fold change >1.2 or< 0.83). The qRT-PCR (Quantitative Real-time PCR) analysis illustrated that the changes in the expression levels of transcription and translation of the identified genes were consistent. This study explores the function of the two-component system of the LytTR family in S. pogona and shows that the lytS-L gene has an important influence on regulating primary metabolism and butenyl-spinosyn biosynthesis of S. pogona.
Collapse
Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengnan Peng
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shuangqin Yuan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yunjun Sun
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| |
Collapse
|
10
|
Abstract
Abstract
Purpose
This study aimed to analyze the complete genome sequence of the butenyl-spinosyn-producing strain Saccharopolyspora sp. ASAGF58, isolated from Zhejiang province.
Methods
PacBio RS II sequencing platform with single-molecule real-time technology was used to obtain the complete genome sequence of Saccharopolyspora sp. ASAGF58. Gene prediction and annotation analysis were carried out through several software and databases. The antiSMASH online server was used to evaluate the secondary metabolite potential of strain ASAGF58.
Results
The whole genome of Saccharopolyspora sp. ASAGF58 is 8,190,340 bp divided into one chromosome of 8,044,361 bp with a GC content of 68.1% and a plasmid of 145,979 bp with a GC content of 64.6%. A total of 7486 coding sequences, 15 rRNA genes, 61 tRNA genes, 41 miscRNA genes, and 1 tmRNA gene were predicted. The domains encoded by one of the type I polyketide synthase (T1PKS) gene clusters have 91% similarity with those encoded by a spinosad biosynthetic gene cluster from Saccharopolyspora spinosa. In addition, antiSMASH results predicted that the strain also contains the biosynthetic gene clusters for the synthesis of ectoine, geosmin, and erythreapeptin.
Conclusions
Our data revealed the complete genome sequence of a new isolated butenyl-spinosyn-producing strain. This work will provide some methods, from genetics to biotechnology and biochemistry, aimed at the production improvement of butenyl-spinosyns.
Collapse
|
11
|
He H, Yuan S, Hu J, Chen J, Rang J, Tang J, Liu Z, Xia Z, Ding X, Hu S, Xia L. Effect of the TetR family transcriptional regulator Sp1418 on the global metabolic network of Saccharopolyspora pogona. Microb Cell Fact 2020; 19:27. [PMID: 32046731 PMCID: PMC7011500 DOI: 10.1186/s12934-020-01299-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Background Saccharopolyspora pogona is a prominent industrial strain due to its production of butenyl-spinosyn, a high-quality insecticide against a broad spectrum of insect pests. TetR family proteins are diverse in a tremendous number of microorganisms and some are been researched to have a key role in metabolic regulation. However, specific functions of TetR family proteins in S. pogona are yet to characterize. Results In the present study, the overexpression of the tetR-like gene sp1418 in S. pogona resulted in marked effects on vegetative growth, sporulation, butenyl-spinosyn biosynthesis, and oxidative stress. By using qRT-PCR analysis, mass spectrometry, enzyme activity detection, and sp1418 knockout verification, we showed that most of these effects could be attributed to the overexpression of Sp1418, which modulated enzymes related to the primary metabolism, oxidative stress and secondary metabolism, and thereby resulted in distinct growth characteristics and an unbalanced supply of precursor monomers for butenyl-spinosyn biosynthesis. Conclusion This study revealed the function of Sp1418 and enhanced the understanding of the metabolic network in S. pogona, and provided insights into the improvement of secondary metabolite production.
Collapse
Affiliation(s)
- Haocheng He
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shuangqin Yuan
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jinjuan Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianming Chen
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianli Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Zhudong Liu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Ziyuan Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Shengbiao Hu
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China.
| |
Collapse
|
12
|
Li L, Rang J, He H, He S, Liu Z, Tang J, Xiao J, He L, Hu S, Yu Z, Ding X, Xia L. Impact on strain growth and butenyl-spinosyn biosynthesis by overexpression of polynucleotide phosphorylase gene in Saccharopolyspora pogona. Appl Microbiol Biotechnol 2018; 102:8011-8021. [DOI: 10.1007/s00253-018-9178-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 01/15/2023]
|
13
|
Tao H, Zhang Y, Deng Z, Liu T. Strategies for Enhancing the Yield of the Potent Insecticide Spinosad in Actinomycetes. Biotechnol J 2018; 14:e1700769. [DOI: 10.1002/biot.201700769] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/19/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Hui Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic Microbiology; Wuhan Institute of Biotechnology; Wuhan 430075 P. R. China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education and Wuhan University School of Pharmaceutical Sciences; Wuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic Microbiology; Wuhan Institute of Biotechnology; Wuhan 430075 P. R. China
| |
Collapse
|