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Mao J, Zhang M, Dai W, Fu C, Wang Z, Wang X, Yao Q, Kong L, Qin J. Metabolic perturbation of Streptomyces albulus by introducing NADP-dependent glyceraldehyde 3-phosphate dehydrogenase. Front Microbiol 2024; 15:1328321. [PMID: 38328422 PMCID: PMC10847347 DOI: 10.3389/fmicb.2024.1328321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
The available resources of Streptomyces represent a valuable repository of bioactive natural products that warrant exploration. Streptomyces albulus is primarily utilized in the industrial synthesis of ε-poly-L-lysine (ε-PL). In this study, the NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (GapN) from Streptococcus mutans was heterologously expressed in S. albulus CICC11022, leading to elevated intracellular NADPH levels and reduced NADH and ATP concentrations. The resulting perturbation of S. albulus metabolism was comprehensively analyzed using transcriptomic and metabolomic methodologies. A decrease in production of ε-PL was observed. The expression of gapN significantly impacted on 23 gene clusters responsible for the biosynthesis of secondary metabolites. A comprehensive analysis revealed a total of 21 metabolites exhibiting elevated levels both intracellularly and extracellularly in the gapN expressing strain compared to those in the control strain. These findings underscore the potential of S. albulus to generate diverse bioactive natural products, thus offering valuable insights for the utilization of known Streptomyces resources through genetic manipulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Linghui Kong
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Jiayang Qin
- School of Pharmacy, Binzhou Medical University, Yantai, 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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CRISPR/Cas9-Mediated Multi-Locus Promoter Engineering in ery Cluster to Improve Erythromycin Production in Saccharopolyspora erythraea. Microorganisms 2023; 11:microorganisms11030623. [PMID: 36985197 PMCID: PMC10059589 DOI: 10.3390/microorganisms11030623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Erythromycins are a group of macrolide antibiotics produced by Saccharopolyspora erythraea. Erythromycin biosynthesis, which is a long pathway composed of a series of biochemical reactions, is precisely controlled by the type I polyketide synthases and accessary tailoring enzymes encoded by ery cluster. In the previous work, we have characterized that six genes representing extremely low transcription levels, SACE_0716-SACE_0720 and SACE_0731, played important roles in limiting erythromycin biosynthesis in the wild-type strain S. erythraea NRRL 23338. In this study, to relieve the potential bottlenecks of erythromycin biosynthesis, we fine-tuned the expression of each key limiting ery gene by CRISPR/Cas9-mediated multi-locus promoter engineering. The native promoters were replaced with different heterologous ones of various strengths, generating ten engineered strains, whose erythromycin productions were 2.8- to 6.0-fold improved compared with that of the wild-type strain. Additionally, the optimal expression pattern of multiple rate-limiting genes and preferred engineering strategies of each locus for maximizing erythromycin yield were also summarized. Collectively, our work lays a foundation for the overall engineering of ery cluster to further improve erythromycin production. The experience of balancing multiple rate-limiting factors within a cluster is also promising to be applied in other actinomycetes to efficiently produce value-added natural products.
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Del Carratore F, Hanko EK, Breitling R, Takano E. Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules. Curr Opin Biotechnol 2022; 77:102762. [PMID: 35908316 DOI: 10.1016/j.copbio.2022.102762] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/30/2022]
Abstract
Streptomyces is one of the most relevant genera in biotechnology, and its rich secondary metabolism is responsible for the biosynthesis of a plethora of bioactive compounds, including several clinically relevant drugs. The use of Streptomyces species for the manufacture of natural products has been established for more than half a century; however, the tremendous advances observed in recent years in genetic engineering and molecular biology have revolutionised the optimisation of Streptomyces as cell factories and drastically expanded the biotechnological potential of these bacteria. Here, we illustrate the most exciting advances reported in the past few years, with a particular focus on the approaches significantly improving the biotechnological capacity of Streptomyces to produce clinical drugs and other valuable secondary metabolites.
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Affiliation(s)
- Francesco Del Carratore
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Erik Kr Hanko
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, Faculty of Science and Engineering, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Deep-Sea Hydrothermal Vent-Derived Streptomyces sp. SCSIO ZS0520. Mar Drugs 2022; 20:md20060393. [PMID: 35736196 PMCID: PMC9228677 DOI: 10.3390/md20060393] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 01/27/2023] Open
Abstract
Streptomyces sp. SCSIO ZS0520 is a deep-sea hydrothermal vent-derived actinomycete. Our previous metabolism investigation showed that Streptomyces sp. SCSIO ZS0520 is a producer of cytotoxic actinopyrones. Here, another four types of secondary metabolites were identified, including six salinomycin isomers (2–7), the macrolide elaiophylin (8), the triterpene N-acetyl-aminobacteriohopanetriol (9), and the pyrone minipyrone (10). Among them, compounds 2–6 and 10 are new compounds. To understand the biosynthetic pathway of these compounds, a bioinformatic analysis of the whole genome was carried out, which identified 34 secondary metabolite biosynthetic gene clusters. Next, the biosynthetic pathways responsive to four types of products were deduced on the basis of gene function predictions and structure information. Taken together, these findings prove the metabolite potential of ZS0520 and lay the foundations to solve the remaining biosynthetic issues in four types of marine natural products.
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León-Buitimea A, Balderas-Cisneros FDJ, Garza-Cárdenas CR, Garza-Cervantes JA, Morones-Ramírez JR. Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs. Front Bioeng Biotechnol 2022; 10:869206. [PMID: 35600895 PMCID: PMC9114757 DOI: 10.3389/fbioe.2022.869206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.
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Affiliation(s)
- Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Francisco de Jesús Balderas-Cisneros
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - César Rodolfo Garza-Cárdenas
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Javier Alberto Garza-Cervantes
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
- *Correspondence: José Rubén Morones-Ramírez,
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Rational engineering strategies for achieving high-yield, high-quality and high-stability of natural product production in actinomycetes. Metab Eng 2021; 67:198-215. [PMID: 34166765 DOI: 10.1016/j.ymben.2021.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 12/11/2022]
Abstract
Actinomycetes are recognized as excellent producers of microbial natural products, which have a wide range of applications, especially in medicine, agriculture and stockbreeding. The three main indexes of industrialization (titer, purity and stability) must be taken into overall consideration in the manufacturing process of natural products. Over the past decades, synthetic biology techniques have expedited the development of industrially competitive strains with excellent performances. Here, we summarize various rational engineering strategies for upgrading the performance of industrial actinomycetes, which include enhancing the yield of natural products, eliminating the by-products and improving the genetic stability of engineered strains. Furthermore, the current challenges and future perspectives for optimizing the industrial strains more systematically through combinatorial engineering strategies are also discussed.
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