Genomic scale analysis of assembly-line polyketide synthase diversity and evolution

Abstract

Covering: up to 2026

Assembly-line polyketide synthases (PKSs) are among the most sophisticated catalysts in nature, responsible for the biosynthesis of many medicinally important natural products including antibiotics, anticancer agents, immunosuppressants and veterinary agents. While conventional methods for polyketide natural product discovery have fallen out of favor, the rapid expansion of microbial genome sequencing has revealed a vast untapped diversity of assembly-line PKSs, most of which can be regarded as “orphans” in that their product identity is unknown. A clear picture of how this sequence diversity reflects the evolutionary history of assembly-line PKSs could enable judicious prioritization of experimental efforts aimed at decoding these orphans. To this end we have used a scalable curation workflow to hand-curate an updated catalogue, PKSClusterDB, that includes 16 633 non-redundant assembly-line PKSs. We have also formulated an automatable “anchor-window” framework based on conserved multimodular segments of assembly-line PKSs to identify and interrogate PKS families of interest. Application of this framework to three different PKS families extracted from PKSClusterDB revealed lineage-dependent patterns of diversification, ranging from broadly diversified families to more compact or sharply bounded lineages. PKSClusterDB has also proven useful in exploring other aspects of PKS diversity, including scaffold architecture, extender-unit specificity, reductive-state programming, stereochemical control and modular organization. In closing, we consider how advances in machine learning could be harnessed to accelerate our understanding of assembly-line PKS evolution, diversity and biosynthetic mechanisms.