Prediction of gene cluster function based on transcriptional regulatory networks uncovers a novel locus required for desferrioxamine B biosynthesis

Augustijn, H.E.; Reitz, Z.L.; Zhang, L.; Boot, J.A.; Elsayed, S.S.M.A.; Challis, G.L.; Medema, M.H.; Wezel, G.P., van

doi:doi:10.1101/2024.06.10.598258

Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining revealed millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, and the major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Studying the regulon of iron master regulator DmdR1 in Streptomyces coelicolor combined with co-expression data and large-scale comparative genome analysis identified the novel desJGH gene cluster. Mutational and metabolomics analysis showed that desJGH is required for biosynthesis of the clinical drug desferrioxamine B. DesJGH thereby dictate the balance between the structurally distinct desferrioxamines B and E....Show more Bacteria produce a plethora of natural products that are in clinical, agricultural and biotechnological use. Genome mining revealed millions of biosynthetic gene clusters (BGCs) that encode their biosynthesis, and the major challenge is to predict the bioactivities of the molecules these BGCs specify, and how to elicit their expression. Here, we present an innovative strategy whereby we harness the power of regulatory networks combined with global gene expression patterns to predict BGC functions. Studying the regulon of iron master regulator DmdR1 in Streptomyces coelicolor combined with co-expression data and large-scale comparative genome analysis identified the novel desJGH gene cluster. Mutational and metabolomics analysis showed that desJGH is required for biosynthesis of the clinical drug desferrioxamine B. DesJGH thereby dictate the balance between the structurally distinct desferrioxamines B and E. We propose regulation-based genome mining as a promising approach to functionally prioritize BGCs to accelerate the discovery of novel bioactive molecules.
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Prediction of gene cluster function based on transcriptional regulatory networks uncovers a novel locus required for desferrioxamine B biosynthesis