Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation

Abstract

Actinomycetes and filamentous fungi produce a wide range of bioactive compounds, with applications as antimicrobials, anticancer agents or agrochemicals. Their genomes contain a far larger number of gene clusters for natural products than originally anticipated, and novel approaches are required to exploit this potential reservoir of new drugs. Here, we show that co-cultivation of the filamentous model microbes Streptomyces coelicolor and Aspergillus niger has a major impact on their secondary metabolism. NMR-based metabolomics combined with multivariate data analysis revealed several compounds that correlated specifically to co-cultures, including the cyclic dipeptide cyclo(Phe-Phe) and 2-hydroxyphenylacetic acid, both of which were produced by A. niger in response to S. coelicolor. Furthermore, biotransformation studies with o-coumaric acid and caffeic acid resulted in the production of the novel compounds (E)-2-(3-hydroxyprop-1-en-1-yl)-phenol and (2E,4E)-3-(2-carboxy-1-hydroxyethyl)-2,4-hexadienedioxic acid, respectively. This highlights the utility of microbial co-cultivation combined with NMR-based metabolomics as an efficient pipeline for the discovery of novel natural products.

Taxonomy, Physiology, and Natural Products of Actinobacteria

“…Information on the interactions between microbes is not just of ecological and evolutionary importance, since it could also be useful in drug discovery efforts. Indeed, data on the interactions between microbes could provide key clues concerning the activation of cryptic biosynthetic pathways (372)(373)(374)(375)(376).…”

Aromatic Polyketide GTRI‐02 is a Previously Unidentified Product of theactGene Cluster inStreptomyces coelicolor A3(2)

“…The poor reproducibility of the co‐culture experiments might have been caused by major variations in the metabolome of A. niger between the different experiments. For instance, the major metabolite produced in previous A. niger monoculture was carbonarone A, but here it predominantly synthesized TAN‐1612, a premithramycinone‐type polyketide, under the same culture conditions (Figures S7, S8).…”

“…An NMR‐based metabolomics study performed in our laboratory demonstrated that co‐cultivation of the filamentous model microbes S. coelicolor A3(2) and Aspergillus niger N402 has a substantial impact on their mutual metabolism . In response to challenge with S. coelicolor , A. niger shut down the production of the γ‐pyrone derivatives carbonarone A and aurasperone B, but instead switched on phenylalanine metabolism, resulting in the production of cyclo(Phe‐Phe), hydroxyacetic acid, and phenylacetic acid …”

“…To test this, additional Aspergillus / Streptomyces co‐cultivations were performed. S. coelicolor M145 was inoculated into submerged Minimal Medium (NMMP) cultures at pH 5 . After 72 h growth, spores from A. niger N402 were added, and co‐cultivation was allowed to proceed for 72 h. The control experiments were M145 and N402 monocultures, corresponding to the cultivation time of each strain in the co‐culture.…”

Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture

“…The central issue they discuss is the possibility that toxic secondary metabolites can be produced by the newly formed microbial communities. The basis of this assumption is the fact that gene clusters encoding secondary metabolites may be expressed in coculture with other microorganisms (Abrudan et al 2015;Brakhage 2013;Wu et al 2015), while they are not expressed when microbes are cultured alone. Deising et al argue that because applied biocontrol microbes will become part of the plant's microbiome, interaction with the resident microbiome may lead to the production of novel perhaps toxic and even carcinogenic metabolites.…”