The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin

Carlson, E. S.; Haslecker, R.; Lecchi, C.; Ramos, M. A.; Vennelakanti, V.; Honaker, L.; Stornetta, A.; Millan, E. S.; Johnson, B. A.; Kulik, H. J.; Balbo, S.; Villalta, P. W.; D'Souza, V.; Balskus, E. P.

doi:10.1101/2025.05.26.655968

bioRxiv · 10.1101/2025.05.26.655968

The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin

Carlson, E. S.·Haslecker, R.·Lecchi, C.·Ramos, M. A.·Vennelakanti, V.·Honaker, L.·Stornetta, A.·Millan, E. S.·Johnson, B. A.·Kulik, H. J.·Balbo, S.·Villalta, P. W.·D'Souza, V.·Balskus, E. P.

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Abstract

Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are thought to arise from colibactin-DNA interstrand crosslinks (ICLs). However, we currently lack direct information regarding the structure of this lesion. Here, we combine mass spectrometry and nuclear magnetic resonance spectroscopy to elucidate the specificity and structure of the colibactin-DNA ICL. We find that colibactin alkylates within the minor groove of AT-rich DNA, explaining the origins of mutational signatures. Unexpectedly, we discover that the chemically unstable central motif of colibactin mediates the sequence specificity of crosslinking. By directly elucidating colibactins interactions with DNA, this work enhances our understanding of the structure and genotoxic mechanisms of this cancer-linked gut bacterial natural product.

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Carlson, E. S., Haslecker, R., Lecchi, C., Ramos, M. A., Vennelakanti, V., Honaker, L., Stornetta, A., Millan, E. S., Johnson, B. A., Kulik, H. J., Balbo, S., Villalta, P. W., D'Souza, V., Balskus, E. P.. 2025-05-27. The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin. https://doi.org/10.1101/2025.05.26.655968

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