A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis

Abstract

Polyketide synthases assemble diverse natural products with numerous important applications. The thioester intermediates in polyketide assembly are covalently tethered to acyl carrier protein domains of the synthase. Several mechanisms for polyketide chain release are known, contributing to natural product structural diversification. Here, we report a dual transacylation mechanism for chain release from the enacyloxin polyketide synthase, which assembles an antibiotic with promising activity against Acinetobacter baumannii. A non-elongating ketosynthase domain transfers the polyketide chain from the final acyl carrier protein domain of the synthase to a separate carrier protein, and a non-ribosomal peptide synthetase condensation domain condenses it with (1S,3R,4S)-3,4-dihydroxycyclohexane carboxylic acid. Molecular dissection of this process reveals that non-elongating ketosynthase domain-mediated transacylation circumvents the inability of the condensation domain to recognize the acyl carrier protein domain. Several 3,4-dihydroxycyclohexane carboxylic acid analogues can be employed for chain release, suggesting a promising strategy for producing enacyloxin analogues.

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Fig. 1: Proposed mechanism for chain release from the enacyloxin PKS and confirmation that Bamb_5915 and Bamb_5917 are involved in enacyloxin biosynthesis.
Fig. 2: Acyl transfer and active site acylation assays reveal that the KS0 domain of Bamb_5919 functions as a transacylase.
Fig. 3: Functional characterization of Bamb_5915.
Fig. 4: In vitro reconstitution of chain release from the enacyloxin PKS.
Fig. 5: Bamb_5915 tolerates a wide range of acyl acceptors.
Fig. 6: Examples of trans-AT PKS architectures containing KS0 domains.

Data availability

The genome sequence of B. ambifaria BCC0203 has been deposited in the European Nucleotide Archive (accession no. ERS782625). All other data are available from the authors upon request.

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Acknowledgements

This research was supported by grants from the BBSRC (BB/L021692/1 to G.L.C., E.M. and J.P. and BB/K002341/1 to G.L.C.), the European Commission (through a Marie Sklodowska-Curie Fellowship to J.M., contract no. 656067) and the Research Foundation Flanders (to J.M.). Support from the University of Warwick through a fellowship from the Institute of Advanced Study (to P.K.S.) and a PhD studentship (to C.H.) is acknowledged. The Bruker maXis Impact and maXis II UHPLC-ESI-Q-TOF-MS systems used in this research were funded by the BBSRC (BB/K002341/1 and BB/M017982/1, respectively). G.L.C. is the recipient of a Wolfson Research Merit Award from the Royal Society (WM130033). Z.L.Y. was funded by a Cardiff University Undergraduate Research Opportunities Programme (CUROP) award to C.J. and E.M. The authors thank M. Tosin for providing the Sfp, PanK, PPAT and DPCK expression vectors. Correspondence and requests for materials should be addressed to G.L.C.

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J.M., P.K.S. and G.L.C. designed the experiments. P.K.S. cloned the B. ambifaria genes into pET151 and created the site-directed mutants. J.M., P.K.S. and C.H. carried out the in vitro biochemical experiments. C.J., Z.L.Y. and E.M. identified strain BCC0203 as being amenable to genetic manipulation, established selection conditions and constructed and complemented the B. ambifaria gene deletion mutants. J.P. supervised sequencing and assembly of the B. ambifaria BCC0203 genome. C.J. analysed the genome sequence of strain BCC0203 and made the initial comparisons to the genome of the AMMD strain. C.H., R.H., D.M.R., P.K.S. and J.M. synthesized substrates. J.M. and G.L.C. wrote the manuscript with input from the other authors.

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Correspondence to Gregory L. Challis.

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Competing interests

The broad substrate specificity of Bamb_5915, exploited for the production of enacyloxin analogues, is the subject of International (PCT) Patent Application no. PCT/GB2018/051058 (applicant, University of Warwick; inventors, G.L.C., J.M., C.H., X. Jian; status of application, filed 23 April 2018).

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The Supplementary Information file contains details of the methods used, and Supplementary Figs. 1–15 and Supplementary Tables 1–2

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Masschelein, J., Sydor, P.K., Hobson, C. et al. A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis. Nat. Chem. 11, 906–912 (2019). https://doi.org/10.1038/s41557-019-0309-7

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