Polyketides are structurally diverse bioactive secondary metabolites with high biomedical relevance. The carbon skeleton of these natural products is synthesized by an invariable core machinery of type II polyketide synthases (PKS). This so-called Minimal PKS System consists of an acyl carrier protein (ACP), an α/β heterodimeric ketosynthase (KSα-KSβ), and a malonyl-transacylase (MCAT). The ACP mediates specific protein-protein interactions that shuttle acyl substrates to the distinct components of the Minimal PKS System. However, due to the transient nature of the enzyme interactions and the chemical instability of the poly-β-keto intermediates, no MCAT:ACP or KSα-KSβ-ketosynthase:ACP complex structures have been reported for type II PKSs so far.
The present study provides detailed molecular insights into the Minimal PKS System of anthraquinone biosynthesis from Photorhabdus luminescens (Pl), which produces an ACP-bound octaketide using malonyl-CoA as the sole substrate. High resolution structures reveal interactions of the acyl carrier protein AntF with each component of the core machinery. Interestingly, the function of PlMCAT can be replaced by an orthologous transacylase from E. coli during heterologous expression of AntFholo. This promiscuity of MCAT is surprising considering the unique protein sequences of ACPs. The resolved PlMCAT:AntFholo complex structure discloses predominant interaction of AntFholo with PlMCAT via a phosphopantetheinyl arm (PPant), and illustrates why chimeric Minimal PKS Systems are active. In addition, the crystallographic studies of the ternary AntDE:Fholo complex identified a small but contact-rich motif between the ACP and its KSα-KSβ-ketosynthase by interaction sites that are conserved. Interestingly, the heterologous expression of AntDE from P. luminescens in E. coli was found to result in the formation of a premature hexaketide covalently bound to the active site of the ketosynthase, but although the endogenous ACP of the host system is able to adapt the function of AntFholo, chain elongation to the octaketide has to overcome high energetic barriers that requires a genuine shuttle machinery. The ACPs involved in polyketide chain elongation are therefore only partially interchangeable, at least during anthraquinone biosynthesis, illustrating how organisms with multiple Minimal PKS Systems could coordinate the production of diverse polyketides.
In summary, the ternary complexes of an acyl-carrier protein with its malonyl-transacylase and its α/β heterodimeric ketosynthase provide a major contribution to natural product research. The discovered molecular principles of polyketide biosynthesis could inspire future engineering of these pharmaceutically important compounds.