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Open AccessArticle

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

1
Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
2
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
3
Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
4
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
5
Intelligent Synthetic Biology Center, Daejeon 34141, Korea
*
Author to whom correspondence should be addressed.
Biomolecules 2020, 10(6), 864; https://doi.org/10.3390/biom10060864
Received: 15 April 2020 / Revised: 30 May 2020 / Accepted: 1 June 2020 / Published: 5 June 2020
(This article belongs to the Special Issue Recent Advance of Actinomycetes)
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. View Full-Text
Keywords: comparative genomics; Streptomyces venezuelae; chloramphenicol; jadomycin; biosynthetic gene cluster comparative genomics; Streptomyces venezuelae; chloramphenicol; jadomycin; biosynthetic gene cluster
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Kim, W.; Lee, N.; Hwang, S.; Lee, Y.; Kim, J.; Cho, S.; Palsson, B.; Cho, B.-K. Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains. Biomolecules 2020, 10, 864.

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