Modulating complex secondary metabolism in Streptomyces rimosus by targeted genome engineering

Avbelj, Martina (author), Slemc, Lucija (author), Pšeničnik, Alen (author), Zver, Špela (author), Lazova, Anastasija (author), Mervič, Kristina (author), Sarim, Khan Mohammad (author), Paš, Maja (author), Starčević, Antonio (author), Šala, Martin (author), Tome, Miha (author), Vujaklija, Dušica (author), Petković, Hrvoje (author)

Research background. Numerous biosynthetic gene clusters (BGCs) encoding unknown structures have been uncovered in the genomes of diverse microorganisms, representing a potentially rich source of novel natural products. However, the majority of the BGCs identified do not seem to be active, since we cannot detect any corresponding metabolites. Therefore, a better understanding of the regulation and biosynthesis of secondary metabolites encoded by these so-called “silent” BGCs is of great importance. Experimental approach. We conducted bioinformatic analysis of the Streptomyces rimosus ATCC 10970 strain, producer of the antibiotic oxytetracycline, while focusing on the expression of identified BGCs. We then reviewed experimentally identified compounds and putative structures, which were predicted based on genome data and similarity to known metabolites. We analysed available data on the regulation of two major metabolites - oxytetracycline and rimocidin, and experimentally evaluated the effect of the deletion of two oxytetracycline-competing pathways. Finally, we evaluated the effect of overexpressing BGC encoding the biosynthesis of the carotenoid isorenieratene, which cannot be detected in the culture of the native strain. Results and conclusions. We identified 48 BGCs in the genome of Streptomyces rimosus ATCC 10970. However, only around 15 structures were predicted or identified in the culture of this strain. Transcriptional analysis of identified BGCs demonstrated a very high variability in expression strength. Interestingly around 30 % of BGCs were “silent”. In trans overexpression of one such silent BGC, encoding the biosynthesis of the carotenoid isorenieratene, resulted in strong production of this metabolite, suggesting that silent BGCs are likely to be still functional. Interestingly, we have demonstrated that BGCs encoding two major metabolites, oxytetracycline and rimocidin, both made of malonyl-CoA, are not competitive pathways. Surprisingly, deletion of one silent BGC, also made of malonyl-CoA, does show a very strong effect on the biosynthesis of oxytetracycline. Novelty and scientific contribution. We observed that the expression strength of genes from BGCs identified in Streptomyces rimosus does not correspond to the experimental data gathered by the engineered strains, suggesting much more complex regulatory mechanisms than previously thought. Engineered Streptomyces rimosus host strains thus represent a very good model system to study the expression of “silent” BGCs.

• Language: English
• Keywords: biosynthetic gene cluster, oxytetracycline, rimocidin, gene regulation, genome reduction
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Publication date: 01.01.2026
• Year: 2026
• Number of pages: Str. 97-112
• Numbering: Vol. 64, no. 1
• PID: 20.500.12556/RUL-185646
• UDC: 604.4:615.33:577.21
• ISSN on article: 1330-9862
• DOI: 10.17113/ftb.64.01.26.9441
• COBISS.SI-ID: 271539971
• Publication date in RUL: 14.08.2026

Record is a part of a journal

• Title: Food technology and biotechnology : journal of the Faculty of Food Technology and Biotechnology University of Zagreb
• Shortened title: Food technol. biotechnol.
• Publisher: Faculty of Food Technology and Biotechnology
• ISSN: 1330-9862
• COBISS.SI-ID: 40116737

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: antibiotiki, oksitetraciklin, Streptomyces rimosus, biosinteza, gruča biosinteznih genov, sekundarni metaboliti