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Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains

Streptomyces venezuelae is well known to produce various secondary metabolites, including chloramphenicol, jadomycin, and pikromycin. Although many strains have been classified as S. venezuelae species, only a limited number of strains have been explored extensively for their genomic contents. Moreo...

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Autores principales: Kim, Woori, Lee, Namil, Hwang, Soonkyu, Lee, Yongjae, Kim, Jihun, Cho, Suhyung, Palsson, Bernhard, Cho, Byung-Kwan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357120/
https://www.ncbi.nlm.nih.gov/pubmed/32516997
http://dx.doi.org/10.3390/biom10060864
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author Kim, Woori
Lee, Namil
Hwang, Soonkyu
Lee, Yongjae
Kim, Jihun
Cho, Suhyung
Palsson, Bernhard
Cho, Byung-Kwan
author_facet Kim, Woori
Lee, Namil
Hwang, Soonkyu
Lee, Yongjae
Kim, Jihun
Cho, Suhyung
Palsson, Bernhard
Cho, Byung-Kwan
author_sort Kim, Woori
collection PubMed
description Streptomyces venezuelae is well known to produce various secondary metabolites, including chloramphenicol, jadomycin, and pikromycin. Although many strains have been classified as S. venezuelae species, only a limited number of strains have been explored extensively for their genomic contents. Moreover, genomic differences and diversity in secondary metabolite production between the strains have never been compared. Here, we report complete genome sequences of three S. venezuelae strains (ATCC 10712, ATCC 10595, and ATCC 21113) harboring chloramphenicol and jadomycin biosynthetic gene clusters (BGC). With these high-quality genome sequences, we revealed that the three strains share more than 85% of total genes and most of the secondary metabolite biosynthetic gene clusters (smBGC). Despite such conservation, the strains produced different amounts of chloramphenicol and jadomycin, indicating differential regulation of secondary metabolite production at the strain level. Interestingly, antagonistic production of chloramphenicol and jadomycin was observed in these strains. Through comparison of the chloramphenicol and jadomycin BGCs among the three strains, we found sequence variations in many genes, the non-coding RNA coding regions, and binding sites of regulators, which affect the production of the secondary metabolites. We anticipate that these genome sequences of closely related strains would serve as useful resources for understanding the complex secondary metabolism and for designing an optimal production process using Streptomyces strains.
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spelling pubmed-73571202020-07-23 Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains Kim, Woori Lee, Namil Hwang, Soonkyu Lee, Yongjae Kim, Jihun Cho, Suhyung Palsson, Bernhard Cho, Byung-Kwan Biomolecules Article Streptomyces venezuelae is well known to produce various secondary metabolites, including chloramphenicol, jadomycin, and pikromycin. Although many strains have been classified as S. venezuelae species, only a limited number of strains have been explored extensively for their genomic contents. Moreover, genomic differences and diversity in secondary metabolite production between the strains have never been compared. Here, we report complete genome sequences of three S. venezuelae strains (ATCC 10712, ATCC 10595, and ATCC 21113) harboring chloramphenicol and jadomycin biosynthetic gene clusters (BGC). With these high-quality genome sequences, we revealed that the three strains share more than 85% of total genes and most of the secondary metabolite biosynthetic gene clusters (smBGC). Despite such conservation, the strains produced different amounts of chloramphenicol and jadomycin, indicating differential regulation of secondary metabolite production at the strain level. Interestingly, antagonistic production of chloramphenicol and jadomycin was observed in these strains. Through comparison of the chloramphenicol and jadomycin BGCs among the three strains, we found sequence variations in many genes, the non-coding RNA coding regions, and binding sites of regulators, which affect the production of the secondary metabolites. We anticipate that these genome sequences of closely related strains would serve as useful resources for understanding the complex secondary metabolism and for designing an optimal production process using Streptomyces strains. MDPI 2020-06-05 /pmc/articles/PMC7357120/ /pubmed/32516997 http://dx.doi.org/10.3390/biom10060864 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Kim, Woori
Lee, Namil
Hwang, Soonkyu
Lee, Yongjae
Kim, Jihun
Cho, Suhyung
Palsson, Bernhard
Cho, Byung-Kwan
Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
title Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
title_full Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
title_fullStr Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
title_full_unstemmed Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
title_short Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains
title_sort comparative genomics determines strain-dependent secondary metabolite production in streptomyces venezuelae strains
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357120/
https://www.ncbi.nlm.nih.gov/pubmed/32516997
http://dx.doi.org/10.3390/biom10060864
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