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Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides

Nature Chemistry volume 16, pages 1320–1329 (2024) Cite this article

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Abstract

Recent efforts in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs) have expanded the diversity of post-translational modification chemistries. However, RiPPs are rarely reported as hybrid molecules incorporating biosynthetic machinery from other natural product families. Here we report lipoavitides, a class of RiPP/fatty-acid hybrid lipopeptides that display a unique, putatively membrane-targeting 4-hydroxy-2,4-dimethylpentanoyl (HMP)-modified N terminus. The HMP is formed via condensation of isobutyryl-coenzyme A (isobutyryl-CoA) and methylmalonyl-CoA catalysed by a 3-ketoacyl-(acyl carrier protein) synthase III enzyme, followed by successive tailoring reactions in the fatty acid biosynthetic pathway. The HMP and RiPP substructures are then connected by an acyltransferase exhibiting promiscuous activity towards the fatty acyl and RiPP substrates. Overall, the discovery of lipoavitides contributes a prototype of RiPP/fatty-acid hybrids and provides possible enzymatic tools for lipopeptide bioengineering.

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Fig. 1: Representative RiPPs produced by RiPP/non-RiPP hybrid BGCs.
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Fig. 2: Representative BGCs identified in bioinformatics study.
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Fig. 3: Heterologous expression and product characterization of lpv.
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Fig. 4: Proposed biosynthetic pathway for the HMP moiety.
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Fig. 5: Biosynthesis of the HMP moiety.
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Fig. 6: Characterization of the acyltransferase LpvE.
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Data availability

We declare that all data supporting the findings of this study are presented in the main text and Supplementary Information. NCBI (https://www.ncbi.nlm.nih.gov/), Protein Data Bank (PDB; https://www.rcsb.org/) and Uniprot (https://www.uniprot.org/) accessions are referenced in Supplementary Information, and these accessions are publicly accessible on the respective NCBI, RCSB PDB and Uniprot websites. Source data are provided with this paper.

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Acknowledgements

We thank J. Arrington from the Roy J. Carver Biotechnology Center for HR-MS/MS assistance. This work was supported by a grant from the National Institutes of Health (AI144967 to D.A.M. and H.Z.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the paper.

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Author notes

  1. These authors contributed equally: Hengqian Ren, Chunshuai Huang.

Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Hengqian Ren & Huimin Zhao

  2. Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Hengqian Ren, Chunshuai Huang, Shravan R. Dommaraju, Haiyang Cui, Maolin Li, Mayuresh G. Gadgil, Douglas A. Mitchell & Huimin Zhao

  3. Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Yuwei Pan

  4. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Shravan R. Dommaraju, Mayuresh G. Gadgil, Douglas A. Mitchell & Huimin Zhao

  5. Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Douglas A. Mitchell

  6. Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA

    Huimin Zhao

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Contributions

H.R. performed bioinformatics analysis, direct cloning, heterologous expression, HR-MS/MS analysis, stereochemistry determination, bioactivity assays, mutational analysis and enzymatic reactions. C.H. performed compound purification, the isotopic feeding study and intermediate characterization. C.H. also designed, performed and analysed NMR experiments. Y.P. assisted in compound purification and genetic manipulation. H.C. performed the AlphaFold2 and AutoDock analysis. D.A.M. contributed to the bioinformatics analysis of lpv genes. S.R.D. performed Marfey’s analysis, reductive desulfurization and interpretation of NMR data to assign stereochemistry with oversight from D.A.M.; M.L. designed and assisted in synthesizing the racemic and (S)-DPD standards. M.G.G. performed and analysed 1H–1H ROESY NMR experiments with oversight from D.A.M.; H.R. and C.H. wrote the paper with editorial oversight from H.Z., along with input from all other authors. H.Z. conceived of and supervised the overall project.

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Correspondence to Huimin Zhao.

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Ren, H., Huang, C., Pan, Y. et al. Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides. Nat. Chem. 16, 1320–1329 (2024). https://doi.org/10.1038/s41557-024-01491-3

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