Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches
Abstract Background Streptomyces chattanoogensis L10 is the industrial producer of natamycin and has been proved a highly efficient host for diverse natural products. It has an enormous potential to be developed as a versatile cell factory for production of heterologous secondary metabolites. Here w...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | Microbial Cell Factories |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12934-019-1055-7 |
| _version_ | 1819036648135983104 |
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| author | Qing-Ting Bu Pin Yu Jue Wang Zi-Yue Li Xin-Ai Chen Xu-Ming Mao Yong-Quan Li |
| author_facet | Qing-Ting Bu Pin Yu Jue Wang Zi-Yue Li Xin-Ai Chen Xu-Ming Mao Yong-Quan Li |
| author_sort | Qing-Ting Bu |
| collection | DOAJ |
| description | Abstract Background Streptomyces chattanoogensis L10 is the industrial producer of natamycin and has been proved a highly efficient host for diverse natural products. It has an enormous potential to be developed as a versatile cell factory for production of heterologous secondary metabolites. Here we developed a genome-reduced industrial Streptomyces chassis by rational ‘design-build-test’ pipeline. Results To identify candidate large non-essential genomic regions accurately and design large deletion rationally, we performed genome analyses of S. chattanoogensis L10 by multiple computational approaches, optimized Cre/loxP recombination system for high-efficient large deletion and constructed a series of universal suicide plasmids for rapid loxP or loxP mutant sites inserting into genome. Subsequently, two genome-streamlined mutants, designated S. chattanoogensis L320 and L321, were rationally constructed by depletion of 1.3 Mb and 0.7 Mb non-essential genomic regions, respectively. Furthermore, several biological performances like growth cycle, secondary metabolite profile, hyphae morphological engineering, intracellular energy (ATP) and reducing power (NADPH/NADP+) levels, transformation efficiency, genetic stability, productivity of heterologous proteins and secondary metabolite were systematically evaluated. Finally, our results revealed that L321 could serve as an efficient chassis for the production of polyketides. Conclusions Here we developed the combined strategy of multiple computational approaches and site-specific recombination system to rationally construct genome-reduced Streptomyces hosts with high efficiency. Moreover, a genome-reduced industrial Streptomyces chassis S. chattanoogensis L321 was rationally constructed by the strategy, and the chassis exhibited several emergent and excellent performances for heterologous expression of secondary metabolite. The strategy could be widely applied in other Streptomyces to generate miscellaneous and versatile chassis with minimized genome. These chassis can not only serve as cell factories for high-efficient production of valuable polyketides, but also will provide great support for the upgrade of microbial pharmaceutical industry and drug discovery. |
| first_indexed | 2024-12-21T08:08:51Z |
| format | Article |
| id | doaj.art-311ab6f767094f7db4f34649928c05d7 |
| institution | Directory Open Access Journal |
| issn | 1475-2859 |
| language | English |
| last_indexed | 2024-12-21T08:08:51Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbial Cell Factories |
| spelling | doaj.art-311ab6f767094f7db4f34649928c05d72022-12-21T19:10:43ZengBMCMicrobial Cell Factories1475-28592019-01-0118111710.1186/s12934-019-1055-7Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approachesQing-Ting Bu0Pin Yu1Jue Wang2Zi-Yue Li3Xin-Ai Chen4Xu-Ming Mao5Yong-Quan Li6Institute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Pharmaceutical Biotechnology & First Affiliated Hospital, Zhejiang University School of MedicineAbstract Background Streptomyces chattanoogensis L10 is the industrial producer of natamycin and has been proved a highly efficient host for diverse natural products. It has an enormous potential to be developed as a versatile cell factory for production of heterologous secondary metabolites. Here we developed a genome-reduced industrial Streptomyces chassis by rational ‘design-build-test’ pipeline. Results To identify candidate large non-essential genomic regions accurately and design large deletion rationally, we performed genome analyses of S. chattanoogensis L10 by multiple computational approaches, optimized Cre/loxP recombination system for high-efficient large deletion and constructed a series of universal suicide plasmids for rapid loxP or loxP mutant sites inserting into genome. Subsequently, two genome-streamlined mutants, designated S. chattanoogensis L320 and L321, were rationally constructed by depletion of 1.3 Mb and 0.7 Mb non-essential genomic regions, respectively. Furthermore, several biological performances like growth cycle, secondary metabolite profile, hyphae morphological engineering, intracellular energy (ATP) and reducing power (NADPH/NADP+) levels, transformation efficiency, genetic stability, productivity of heterologous proteins and secondary metabolite were systematically evaluated. Finally, our results revealed that L321 could serve as an efficient chassis for the production of polyketides. Conclusions Here we developed the combined strategy of multiple computational approaches and site-specific recombination system to rationally construct genome-reduced Streptomyces hosts with high efficiency. Moreover, a genome-reduced industrial Streptomyces chassis S. chattanoogensis L321 was rationally constructed by the strategy, and the chassis exhibited several emergent and excellent performances for heterologous expression of secondary metabolite. The strategy could be widely applied in other Streptomyces to generate miscellaneous and versatile chassis with minimized genome. These chassis can not only serve as cell factories for high-efficient production of valuable polyketides, but also will provide great support for the upgrade of microbial pharmaceutical industry and drug discovery.http://link.springer.com/article/10.1186/s12934-019-1055-7Streptomyces chattanoogensisCell factoryComputational approachesCre/loxP recombination systemBiological performancesGenome-reduced chassis |
| spellingShingle | Qing-Ting Bu Pin Yu Jue Wang Zi-Yue Li Xin-Ai Chen Xu-Ming Mao Yong-Quan Li Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches Microbial Cell Factories Streptomyces chattanoogensis Cell factory Computational approaches Cre/loxP recombination system Biological performances Genome-reduced chassis |
| title | Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches |
| title_full | Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches |
| title_fullStr | Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches |
| title_full_unstemmed | Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches |
| title_short | Rational construction of genome-reduced and high-efficient industrial Streptomyces chassis based on multiple comparative genomic approaches |
| title_sort | rational construction of genome reduced and high efficient industrial streptomyces chassis based on multiple comparative genomic approaches |
| topic | Streptomyces chattanoogensis Cell factory Computational approaches Cre/loxP recombination system Biological performances Genome-reduced chassis |
| url | http://link.springer.com/article/10.1186/s12934-019-1055-7 |
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