Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria.

Jenny Schwarz,Stephan Lütz,Katrin Rosenthal,Georg Hubmann

doi:10.3390/biom11020193

Abstract

Over the past decade, the one strain many compounds (OSMAC) approach has been established for the activation of biosynthetic gene clusters (BGCs), which mainly encode the enzymes of secondary metabolite (SM) biosynthesis pathways. These BGCs were successfully activated by altering various culture conditions, such as aeration rate, temperature, and nutrient composition. Here, we determined the biosynthetic potential of 43 bacteria using the genome mining tool antiSMASH. Based on the number of BGCs, biological safety, availability of deposited cultures, and literature coverage, we selected five promising candidates: Bacillus amyloliquefaciens DSM7, Corallococcus coralloides DSM2259, Pyxidicoccus fallax HKI727, Rhodococcus jostii DSM44719, and Streptomyces griseochromogenes DSM40499. The bacteria were cultivated under a broad range of OSMAC conditions (nutrient-rich media, minimal media, nutrient-limited media, addition of organic solvents, addition of biotic additives, and type of culture vessel) to fully assess the biosynthetic potential. In particular, we investigated so far scarcely applied OSMAC conditions to enhance the diversity of SMs. We detected the four predicted compounds bacillibactin, desferrioxamine B, myxochelin A, and surfactin. In total, 590 novel mass features were detected in a broad range of investigated OSMAC conditions, which outnumber the predicted gene clusters for all investigated bacteria by far. Interestingly, we detected mass features of the bioactive compounds cyclo-(Tyr-Pro) and nocardamin in extracts of DSM7 and DSM2259. Both compounds were so far not reported for these strains, indicating that our broad OSMAC screening approach was successful. Remarkably, the infrequently applied OSMAC conditions in defined medium with and without nutrient limitation were demonstrated to be very effective for BGC activation and for SM discovery.

Highlights

For an initial bioinformatics evaluation, 43 bacteria were considered with regard to biological safety, availability of deposited cultures, genome sequences, and literature coverage
The genome analysis showed that the percentage of the bacterial genome encoding putative secondary metabolite (SM) gene clusters varies greatly among the examined bacteria
The results showed that a high number of predicted biosynthetic gene clusters (BGCs) does not necessarily correspond to high biosynthetic potential in terms of a high number of new mass features, as evident when comparing, e.g., B. amyloliquefaciens and C. coralloides (Table 6)

Summary

Introduction

The one strain many compounds (OSMAC) approach has been established for the activation of biosynthetic gene clusters (BGCs), which mainly encode the enzymes of secondary metabolite (SM) biosynthesis pathways. These BGCs were successfully activated by altering various culture conditions, such as aeration rate, temperature, and nutrient composition. We detected mass features of the bioactive compounds cyclo-(Tyr-Pro) and nocardamin in extracts of DSM7 and DSM2259 Both compounds were so far not reported for these strains, indicating that our broad OSMAC screening approach was successful.

Objectives

Methods

Results

Conclusion