Semi-rational mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity

The biosynthesis of the valuable antibiotic enduracidin by Streptomyces fungicidicus TXX3120 is a complex multistep process. To identify the rate-limiting step of the entire biosynthetic process, we carried out a deep RNA sequencing towards the mycelia of TXX3120 at different fermentation stages. Co...

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Veröffentlicht in:Applied microbiology and biotechnology 2020-04, Vol.104 (8), p.3459-3471
Hauptverfasser: Zhang, Jing, He, Zilong, Xu, JinTian, Song, Shuting, Zhu, Qianhui, Wu, Guoguo, Guan, Ying, Wu, Xiaonong, Yue, Rong, Wang, Yue, Yu, Tao, Hu, Songnian, Lu, Fuping, Zhang, Huitu
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container_issue 8
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container_title Applied microbiology and biotechnology
container_volume 104
creator Zhang, Jing
He, Zilong
Xu, JinTian
Song, Shuting
Zhu, Qianhui
Wu, Guoguo
Guan, Ying
Wu, Xiaonong
Yue, Rong
Wang, Yue
Yu, Tao
Hu, Songnian
Lu, Fuping
Zhang, Huitu
description The biosynthesis of the valuable antibiotic enduracidin by Streptomyces fungicidicus TXX3120 is a complex multistep process. To identify the rate-limiting step of the entire biosynthetic process, we carried out a deep RNA sequencing towards the mycelia of TXX3120 at different fermentation stages. Comparative RNA-seq analysis indicated that the expression level of the endC gene during the enduracidin production phase was evidently lower than that of the other relevant genes to enduracidin biosynthesis. This result was further confirmed by quantitative RT-PCR, and the giant non-ribosomal peptide synthase (NRPS) encoded by endC was predicated to be the rate-limiting enzyme in enduracidin biosynthesis. To increase the expression of endC during the enduracidin production phase, a reporter-based selection system was developed by genetically replacing the initial part of the endC gene with a thiostrepton resistance gene ( tsr ), which will then act as a selectable marker to report the expression level of the rate-limiting gene endC , thereby facilitating the selection of enduracidin-overproducing mutants following random mutagenesis. After one round of mutagenesis, thiostrepton resistance selection, and restoration of the endC gene, three mutant strains with improved endC expression levels were obtained. Their highest enduracidin titers reached 9780.54, 9272.46, and 8849.06 U/mL, respectively representing 2.31-, 2.19-, and 2.09-fold of the initial industrial strain TXX3120. Our research provides a useful strategy for the rational breeding of industrial strains that synthesize complex natural products. Key Points • Dynamic analysis of the expression profiles of enduracidin gene cluster revealed the rate-limiting step for enduracidin biosynthesis. • Construction of a transcriptionally linked selection marker system for directional breeding of an industrially used enduracidin-producing strain. • An efficient method for selecting mutants with improved end-product titers, which overcomes uncertainty of random selection and the blindness.
doi_str_mv 10.1007/s00253-020-10488-0
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To identify the rate-limiting step of the entire biosynthetic process, we carried out a deep RNA sequencing towards the mycelia of TXX3120 at different fermentation stages. Comparative RNA-seq analysis indicated that the expression level of the endC gene during the enduracidin production phase was evidently lower than that of the other relevant genes to enduracidin biosynthesis. This result was further confirmed by quantitative RT-PCR, and the giant non-ribosomal peptide synthase (NRPS) encoded by endC was predicated to be the rate-limiting enzyme in enduracidin biosynthesis. To increase the expression of endC during the enduracidin production phase, a reporter-based selection system was developed by genetically replacing the initial part of the endC gene with a thiostrepton resistance gene ( tsr ), which will then act as a selectable marker to report the expression level of the rate-limiting gene endC , thereby facilitating the selection of enduracidin-overproducing mutants following random mutagenesis. After one round of mutagenesis, thiostrepton resistance selection, and restoration of the endC gene, three mutant strains with improved endC expression levels were obtained. Their highest enduracidin titers reached 9780.54, 9272.46, and 8849.06 U/mL, respectively representing 2.31-, 2.19-, and 2.09-fold of the initial industrial strain TXX3120. Our research provides a useful strategy for the rational breeding of industrial strains that synthesize complex natural products. Key Points • Dynamic analysis of the expression profiles of enduracidin gene cluster revealed the rate-limiting step for enduracidin biosynthesis. • Construction of a transcriptionally linked selection marker system for directional breeding of an industrially used enduracidin-producing strain. • An efficient method for selecting mutants with improved end-product titers, which overcomes uncertainty of random selection and the blindness.</description><identifier>ISSN: 0175-7598</identifier><identifier>EISSN: 1432-0614</identifier><identifier>DOI: 10.1007/s00253-020-10488-0</identifier><identifier>PMID: 32095861</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Analysis ; Anti-Bacterial Agents - biosynthesis ; Antibiotics ; Applied Genetics and Molecular Biotechnology ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biomarkers ; Biomedical and Life Sciences ; Biosynthesis ; Biosynthetic Pathways - genetics ; Biotechnology ; Blindness ; Breeding ; Constraining ; Enduracidin ; Enzymes ; Fatigue limit ; Fermentation ; Gene expression ; Gene sequencing ; Industrial strains ; Life Sciences ; Methicillin ; Microbial Genetics and Genomics ; Microbiology ; Multigene Family ; Mutagenesis ; Mutants ; Mycelia ; Natural products ; Niacin - biosynthesis ; Non-ribosomal peptide synthase ; Peptide synthase ; Peptide Synthases - genetics ; Peptide Synthases - metabolism ; Polymerase chain reaction ; Random mutagenesis ; Restoration ; Ribonucleic acid ; RNA ; RNA sequencing ; RNA-Seq ; Streptomyces ; Streptomyces - enzymology ; Streptomyces - genetics ; Thiostrepton ; Thiostrepton - pharmacology ; Transcription</subject><ispartof>Applied microbiology and biotechnology, 2020-04, Vol.104 (8), p.3459-3471</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2020</rights><rights>COPYRIGHT 2020 Springer</rights><rights>Applied Microbiology and Biotechnology is a copyright of Springer, (2020). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c513t-31220faf2bc41f67c990494f9fe3ed9bc16a0edccec8c837a8f8c874129c923f3</citedby><cites>FETCH-LOGICAL-c513t-31220faf2bc41f67c990494f9fe3ed9bc16a0edccec8c837a8f8c874129c923f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00253-020-10488-0$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00253-020-10488-0$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32095861$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhang, Jing</creatorcontrib><creatorcontrib>He, Zilong</creatorcontrib><creatorcontrib>Xu, JinTian</creatorcontrib><creatorcontrib>Song, Shuting</creatorcontrib><creatorcontrib>Zhu, Qianhui</creatorcontrib><creatorcontrib>Wu, Guoguo</creatorcontrib><creatorcontrib>Guan, Ying</creatorcontrib><creatorcontrib>Wu, Xiaonong</creatorcontrib><creatorcontrib>Yue, Rong</creatorcontrib><creatorcontrib>Wang, Yue</creatorcontrib><creatorcontrib>Yu, Tao</creatorcontrib><creatorcontrib>Hu, Songnian</creatorcontrib><creatorcontrib>Lu, Fuping</creatorcontrib><creatorcontrib>Zhang, Huitu</creatorcontrib><title>Semi-rational mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity</title><title>Applied microbiology and biotechnology</title><addtitle>Appl Microbiol Biotechnol</addtitle><addtitle>Appl Microbiol Biotechnol</addtitle><description>The biosynthesis of the valuable antibiotic enduracidin by Streptomyces fungicidicus TXX3120 is a complex multistep process. To identify the rate-limiting step of the entire biosynthetic process, we carried out a deep RNA sequencing towards the mycelia of TXX3120 at different fermentation stages. Comparative RNA-seq analysis indicated that the expression level of the endC gene during the enduracidin production phase was evidently lower than that of the other relevant genes to enduracidin biosynthesis. This result was further confirmed by quantitative RT-PCR, and the giant non-ribosomal peptide synthase (NRPS) encoded by endC was predicated to be the rate-limiting enzyme in enduracidin biosynthesis. To increase the expression of endC during the enduracidin production phase, a reporter-based selection system was developed by genetically replacing the initial part of the endC gene with a thiostrepton resistance gene ( tsr ), which will then act as a selectable marker to report the expression level of the rate-limiting gene endC , thereby facilitating the selection of enduracidin-overproducing mutants following random mutagenesis. After one round of mutagenesis, thiostrepton resistance selection, and restoration of the endC gene, three mutant strains with improved endC expression levels were obtained. Their highest enduracidin titers reached 9780.54, 9272.46, and 8849.06 U/mL, respectively representing 2.31-, 2.19-, and 2.09-fold of the initial industrial strain TXX3120. Our research provides a useful strategy for the rational breeding of industrial strains that synthesize complex natural products. Key Points • Dynamic analysis of the expression profiles of enduracidin gene cluster revealed the rate-limiting step for enduracidin biosynthesis. • Construction of a transcriptionally linked selection marker system for directional breeding of an industrially used enduracidin-producing strain. • An efficient method for selecting mutants with improved end-product titers, which overcomes uncertainty of random selection and the blindness.</description><subject>Analysis</subject><subject>Anti-Bacterial Agents - biosynthesis</subject><subject>Antibiotics</subject><subject>Applied Genetics and Molecular Biotechnology</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biomarkers</subject><subject>Biomedical and Life Sciences</subject><subject>Biosynthesis</subject><subject>Biosynthetic Pathways - genetics</subject><subject>Biotechnology</subject><subject>Blindness</subject><subject>Breeding</subject><subject>Constraining</subject><subject>Enduracidin</subject><subject>Enzymes</subject><subject>Fatigue limit</subject><subject>Fermentation</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Industrial strains</subject><subject>Life Sciences</subject><subject>Methicillin</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Multigene Family</subject><subject>Mutagenesis</subject><subject>Mutants</subject><subject>Mycelia</subject><subject>Natural products</subject><subject>Niacin - biosynthesis</subject><subject>Non-ribosomal peptide synthase</subject><subject>Peptide synthase</subject><subject>Peptide Synthases - genetics</subject><subject>Peptide Synthases - metabolism</subject><subject>Polymerase chain reaction</subject><subject>Random mutagenesis</subject><subject>Restoration</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>RNA-Seq</subject><subject>Streptomyces</subject><subject>Streptomyces - enzymology</subject><subject>Streptomyces - genetics</subject><subject>Thiostrepton</subject><subject>Thiostrepton - 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mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity</title><author>Zhang, Jing ; He, Zilong ; Xu, JinTian ; Song, Shuting ; Zhu, Qianhui ; Wu, Guoguo ; Guan, Ying ; Wu, Xiaonong ; Yue, Rong ; Wang, Yue ; Yu, Tao ; Hu, Songnian ; Lu, Fuping ; Zhang, Huitu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c513t-31220faf2bc41f67c990494f9fe3ed9bc16a0edccec8c837a8f8c874129c923f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Analysis</topic><topic>Anti-Bacterial Agents - biosynthesis</topic><topic>Antibiotics</topic><topic>Applied Genetics and Molecular Biotechnology</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biomarkers</topic><topic>Biomedical and Life Sciences</topic><topic>Biosynthesis</topic><topic>Biosynthetic Pathways - genetics</topic><topic>Biotechnology</topic><topic>Blindness</topic><topic>Breeding</topic><topic>Constraining</topic><topic>Enduracidin</topic><topic>Enzymes</topic><topic>Fatigue limit</topic><topic>Fermentation</topic><topic>Gene expression</topic><topic>Gene sequencing</topic><topic>Industrial strains</topic><topic>Life Sciences</topic><topic>Methicillin</topic><topic>Microbial Genetics and Genomics</topic><topic>Microbiology</topic><topic>Multigene Family</topic><topic>Mutagenesis</topic><topic>Mutants</topic><topic>Mycelia</topic><topic>Natural products</topic><topic>Niacin - biosynthesis</topic><topic>Non-ribosomal peptide synthase</topic><topic>Peptide synthase</topic><topic>Peptide Synthases - genetics</topic><topic>Peptide Synthases - metabolism</topic><topic>Polymerase chain reaction</topic><topic>Random mutagenesis</topic><topic>Restoration</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA 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mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity</atitle><jtitle>Applied microbiology and biotechnology</jtitle><stitle>Appl Microbiol Biotechnol</stitle><addtitle>Appl Microbiol Biotechnol</addtitle><date>2020-04-01</date><risdate>2020</risdate><volume>104</volume><issue>8</issue><spage>3459</spage><epage>3471</epage><pages>3459-3471</pages><issn>0175-7598</issn><eissn>1432-0614</eissn><abstract>The biosynthesis of the valuable antibiotic enduracidin by Streptomyces fungicidicus TXX3120 is a complex multistep process. To identify the rate-limiting step of the entire biosynthetic process, we carried out a deep RNA sequencing towards the mycelia of TXX3120 at different fermentation stages. Comparative RNA-seq analysis indicated that the expression level of the endC gene during the enduracidin production phase was evidently lower than that of the other relevant genes to enduracidin biosynthesis. This result was further confirmed by quantitative RT-PCR, and the giant non-ribosomal peptide synthase (NRPS) encoded by endC was predicated to be the rate-limiting enzyme in enduracidin biosynthesis. To increase the expression of endC during the enduracidin production phase, a reporter-based selection system was developed by genetically replacing the initial part of the endC gene with a thiostrepton resistance gene ( tsr ), which will then act as a selectable marker to report the expression level of the rate-limiting gene endC , thereby facilitating the selection of enduracidin-overproducing mutants following random mutagenesis. After one round of mutagenesis, thiostrepton resistance selection, and restoration of the endC gene, three mutant strains with improved endC expression levels were obtained. Their highest enduracidin titers reached 9780.54, 9272.46, and 8849.06 U/mL, respectively representing 2.31-, 2.19-, and 2.09-fold of the initial industrial strain TXX3120. Our research provides a useful strategy for the rational breeding of industrial strains that synthesize complex natural products. Key Points • Dynamic analysis of the expression profiles of enduracidin gene cluster revealed the rate-limiting step for enduracidin biosynthesis. • Construction of a transcriptionally linked selection marker system for directional breeding of an industrially used enduracidin-producing strain. • An efficient method for selecting mutants with improved end-product titers, which overcomes uncertainty of random selection and the blindness.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>32095861</pmid><doi>10.1007/s00253-020-10488-0</doi><tpages>13</tpages></addata></record>
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1432-0614
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subjects Analysis
Anti-Bacterial Agents - biosynthesis
Antibiotics
Applied Genetics and Molecular Biotechnology
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biomarkers
Biomedical and Life Sciences
Biosynthesis
Biosynthetic Pathways - genetics
Biotechnology
Blindness
Breeding
Constraining
Enduracidin
Enzymes
Fatigue limit
Fermentation
Gene expression
Gene sequencing
Industrial strains
Life Sciences
Methicillin
Microbial Genetics and Genomics
Microbiology
Multigene Family
Mutagenesis
Mutants
Mycelia
Natural products
Niacin - biosynthesis
Non-ribosomal peptide synthase
Peptide synthase
Peptide Synthases - genetics
Peptide Synthases - metabolism
Polymerase chain reaction
Random mutagenesis
Restoration
Ribonucleic acid
RNA
RNA sequencing
RNA-Seq
Streptomyces
Streptomyces - enzymology
Streptomyces - genetics
Thiostrepton
Thiostrepton - pharmacology
Transcription
title Semi-rational mutagenesis of an industrial Streptomyces fungicidicus strain for improved enduracidin productivity
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-20T13%3A10%3A14IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_proqu&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Semi-rational%20mutagenesis%20of%20an%20industrial%20Streptomyces%20fungicidicus%20strain%20for%20improved%20enduracidin%20productivity&rft.jtitle=Applied%20microbiology%20and%20biotechnology&rft.au=Zhang,%20Jing&rft.date=2020-04-01&rft.volume=104&rft.issue=8&rft.spage=3459&rft.epage=3471&rft.pages=3459-3471&rft.issn=0175-7598&rft.eissn=1432-0614&rft_id=info:doi/10.1007/s00253-020-10488-0&rft_dat=%3Cgale_proqu%3EA618388665%3C/gale_proqu%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2381960349&rft_id=info:pmid/32095861&rft_galeid=A618388665&rfr_iscdi=true