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

Abstract

Over the past decade, the One Strain Many Compounds (OSMAC) approach has been established for silent gene cluster activation and elicitation of secondary metabolite production, but so far the full secondary metabolome of a biosynthetically promising bacterium has not been elucidated yet. Here, we investigate the ability of seven categories of OSMAC conditions to enhance the diversity of new mass features from bacterial strains with little literature coverage but high biosynthetic potential. The strains Bacillus. amyloliquefaciens DSM7, Corallococcus. coralloides DSM2259, Pyxidicoccus. fallax HKI727, Rhodococcus. jostii DSM44719, and Streptomyces. griseochromogenes DSM40499 were selected after genome mining with antiSMASH. After cultivation under OSMAC conditions, the generated extracts were subjected to LC-MS and MZmine analysis to determine new mass features and evaluate the tested culture conditions. 4 predicted compounds, bacillibactin, desferrioxamine B, myxochelin A, and surfactin, were identified and up to 147 new mass features were detected in the generated extracts, which greatly surpasses the number of predicted gene clusters. Among the new mass features are bioactive compounds that were so far unreported for the strains such as cyclo-(Tyr-Pro) from DSM7 and nocardamin from DSM2259. Furthermore, the tested culture conditions were evaluated regarding their suitability for the generation of new mass features from the selected strains and promising new starting points for further screenings are postulated. Especially culture conditions with little prior literature coverage are responsible for the activation of predicted gene clusters

Streptomyces cell-free systems for natural product discovery and engineering

“…This is because conditions that imitate environmental factors can serendipitously activate "silent" BGCs through unknown gene expression regulators. 16 Other OSMAC approaches included small molecule elicitor library screening 17 and co-culturing, 18 which can simulate complex microbiome interactions in native microenvironments to trigger BGC gene expression and natural product biosynthesis. 18 However, the OSMAC approach is best applied to novel strains, since key limitations include rediscoveries due to screening bias towards common targets (i.e., antimicrobials), while many BGCs will remain switched-off in terms of gene expression.…”

Training old dogs to do new tricks: A general multi-pronged activation approach for natural product discovery in Actinomycetes

“…Despite these advantages, most current native strain activation strategies have only been demonstrated on limited or speci c strains genus. [16][17][18][19][20][21][22] Here, we describe a highly robust, exible, and e cient approach featuring one-step integrase mediated genetic activation with "one strain many compounds" OSMAC requirements 10,23,24 to perturb and upregulate silent and/or low yielding secondary metabolites (Fig. 1) across a range of 54 actinobacterial strains.…”

“…To unlock the chemical repertoire of Nature's biodiversity and tap into this vast hidden resource represented by silent or poorly expressing BGCs, a variety of genetic and non-genetic based strategies have been developed to activate and upregulate NP biosyntheses in native and heterologous microbial strains. [10][11][12][13] While advances in heterologous-based technologies and synthetic biology have enabled examination of a large number of BGCs, 14,15 native strain activation technologies can circumvent the intrinsic limitations of heterologous expression by leveraging on fundamental regulatory and metabolic requirements for NP biosynthesis. Despite these advantages, most current native strain activation strategies have only been demonstrated on limited or speci c strains genus.…”

Detection of Antimicrobial Compounds From Thermophilic Actinomycetes Using One Strain Many Compounds (Osmac) Approach

“…Aspergillus ochraceus was able to produce 15 additional metabolites, while previously only known to produce a metabolite called aspinonene (Bode et al, 2002;Romano et al, 2018). The OSMAC approach is carried out under certain growth conditions so that one microorganism strain has the potential to produce several compounds and increase the possibility of discovering new metabolites (Schwarz et al, 2021). Several studies have been carried out using the OSMAC approach to discover new metabolites and assays for the antimicrobial activity from the fungal group (Li et al, 2019;Meng et al, 2017;Ozkaya et al, 2018).…”