Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage

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Colibactin is an assumed human gut bacterial genotoxin, whose biosynthesis is linked to the clb genomic island that has a widespread distribution in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumour formation and enhance the progression of colorectal cancer via cellular senescence and death induced by DNA double-strand breaks (DSBs); however, the chemical basis that contributes to the pathogenesis at the molecular level has not been fully characterized. Here, we report the discovery of colibactin-645, a macrocyclic colibactin metabolite that recapitulates the previously assumed genotoxicity and cytotoxicity. Colibactin-645 shows strong DNA DSB activity in vitro and in human cell cultures via a unique copper-mediated oxidative mechanism. We also delineate a complete biosynthetic model for colibactin-645, which highlights a unique fate of the aminomalonate-building monomer in forming the C-terminal 5-hydroxy-4-oxazolecarboxylic acid moiety through the activities of both the polyketide synthase ClbO and the amidase ClbL. This work thus provides a molecular basis for colibactin’s DNA DSB activity and facilitates further mechanistic study of colibactin-related colorectal cancer incidence and prevention.

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Fig. 1: Structures and proposed biosynthesis of precolibactins.
Fig. 2: Genes and proposed mechanisms of aminomalonate-utilizing PKSs in the biosynthesis of precolibactins.
Fig. 3: Maturation of colibactin.
Fig. 4: Analysis of DNA damage by colibactin cleavage in vitro.
Fig. 5: Colibactin-induced DNA damage in cell cultures.

Data availability

The authors declare that all the data supporting the findings of this study are available within the paper and the Supplementary Information, and/or from the corresponding authors upon reasonable request.


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This work was supported by an NSFC grant (no. 41576140), a China Ocean Mineral Resources Research and Development Association grant (COMRRDA17SC01) a grant from National Key R&D Programmes of China and a grant from the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) to P.-Y.Q., grants from the National Institutes of Health (DP2AT009148), the Alfred P. Sloan Foundation and the Chan Zuckerberg Biohub Investigator Program to W.Z. and a grant from the National Institutes of Health (R01-GM85770) to B.S.M. We thank D. Lin and L. Feng for NMR measurements, Y. K. Tam and N. Harris for assistance with mass spectrometry experiments, Y. Huang and S. Jia for helpful discussions and A. Cheung for manuscript proofreading. Z.-R.L. acknowledges support from the International House at UC Berkeley, Chevron Corporation and UC Berkeley as the fellow of Chevron-Xenel PhD Gateway Fellowship. S.M.K.M. acknowledges the NSERC-PDF fellowship.

Author information

Z.-R.L. performed the experiments, J.Y.H.L. conducted some of the fermentation work, Z.-R.L., J.L., W.C. and S.M.K.M. analysed NMR data, Z.-R.L. and W.-P.Z. performed the gene analysis, Z.-R.L., W.Z. and P.-Y.Q. designed the study and wrote the manuscript, with input from J.L. and B.S.M.

Correspondence to Wenjun Zhang or Pei-Yuan Qian.

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Materials and Methods, Supplementary text, Supplementary Figs. 1–27, Supplementary Tables 1–7 and Supplementary references 1–28.

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Li, Z., Li, J., Cai, W. et al. Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage. Nat. Chem. 11, 880–889 (2019) doi:10.1038/s41557-019-0317-7

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