The human gut bacterial genotoxin colibactin alkylates DNA

Matthew R. Wilson, Yindi Jiang, Peter W. Villalta, Alessia Stornetta, Paul D. Boudreau, Andrea Carrá, Caitlin A. Brennan, Eunyoung Chun, Lizzie Ngo, Leona D. Samson, Bevin P. Engelward, Wendy S. Garrett, Silvia Balbo, Emily P. Balskus

Research output: Contribution to journalArticlepeer-review

245 Scopus citations


Certain Escherichia coli strains residing in the human gut produce colibactin, a small-molecule genotoxin implicated in colorectal cancer pathogenesis. However, colibactin’s chemical structure and the molecular mechanism underlying its genotoxic effects have remained unknown for more than a decade. Here we combine an untargeted DNA adductomics approach with chemical synthesis to identify and characterize a covalent DNA modification from human cell lines treated with colibactin-producing E. coli. Our data establish that colibactin alkylates DNA with an unusual electrophilic cyclopropane. We show that this metabolite is formed in mice colonized by colibactin-producing E. coli and is likely derived from an initially formed, unstable colibactin-DNA adduct. Our findings reveal a potential biomarker for colibactin exposure and provide mechanistic insights into how a gut microbe may contribute to colorectal carcinogenesis.

Original languageEnglish (US)
Article numbereaar7785
Issue number6428
StatePublished - Feb 15 2019

Bibliographical note

Funding Information:
We thank G. Heffron and C. Sheehan (Harvard Medical School, Boston, MA) for help with NMR experiments; M. Volpe and N. Braffman (Balskus lab, Harvard University) for assistance with DP4 computational analysis; L. Zhang (Balskus lab, Harvard University) for helping with Sephadex LH-20 chromatography; and L. Zha, V. M. Rekdal, A. Waldman, T. Ng, and N. Koppel (Harvard University) for helpful discussions. We thank W. G. Tilly (MIT) for providing the TK6 cell line and C. Woo (Harvard University) for providing the HT29 cell line. Funding: Financial support was provided by the Packard Fellowship for Science and Engineering (E.P.B.), the Damon Runyon-Rachleff Innovation Award (E.P.B.), and National Institutes of Health grants R01 CA208834 (E.P.B.), R01 CA154426 (W.S.G.), and R01 ES022872 (L.D.S.). This work was also supported by National Institute of Environmental Health Sciences grant R44 ES024698 (B.P.E.) and Center for Environmental Health Sciences grant P30 ES002109 (B.P.E.). Salary support for P.W.V. was provided by the U.S. National Institutes of Health and National Cancer Institute (grant R50-CA211256). Mass spectrometry was carried out in the Analytical Biochemistry Shared Resource of the Masonic Cancer Center, supported in part by the U.S. National Institutes of Health and National Cancer Institute (Cancer Center Support Grant CA-77598). M.R.W. acknowledges support from the American Cancer Society–New England Division Postdoctoral Fellowship PF-16-122-01-CDD. C.A.B. is the Dennis and Marsha Dammerman fellow of the Damon Runyon Cancer Research Foundation (DRG-2205-14). Mention of commercial products does not constitute endorsement.

Publisher Copyright:
© The Authors, some rights reserved.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't


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