The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links
Creators
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1.
California Institute of Technology
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2.
Yale University
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3.
Harvard University
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4.
University of Copenhagen
Abstract
Colibactin is a secondary metabolite produced by bacteria present in the human gut and is implicated in the development of colorectal cancer. This genotoxin alkylates deoxyadenosines on opposite strands of host cell DNA to produce DNA interstrand cross-links. While cells have evolved multiple mechanisms to resolve ("unhook") interstrand cross-links, little is known about which of these pathways promote resistance to colibactin. Here, we use Xenopus egg extracts to investigate replication-coupled repair of colibactin-induced interstrand cross-links. We show that replication fork stalling at a colibactin-induced interstrand cross-link activates the Fanconi anemia interstrand cross-link repair pathway, which unhooks the interstrand cross-link through nucleolytic incisions. These incisions generate a DNA double-strand break intermediate in one sister chromatid, which can be repaired by homologous recombination, and a monoadduct ("interstrand cross-link remnant") in the other. Translesion synthesis past the colibactin-induced interstrand cross-link remnant depends on Pol η and the Pol κ-REV1-Pol ζ polymerase complex and introduces predominantly T>A point mutations at the sites of colibactin alkylation. Taken together, our work provides a molecular framework for understanding how cells tolerate a naturally occurring and clinically relevant interstrand cross-link.
Copyright and License
© 2025, The Author(s). Open Access. This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
Acknowledgement
The authors thank J. Campbell and members of the Semlow, Balskus, Herzon, and Duxin labs for comments on the manuscript. The authors thank P. Knipscheer for advice on rFANCI-D2 purification and the Tijsterman lab for assistance with implementation of the SIQ software package for NGS data analysis. REV1 and FANCD2 antibodies were gifts from J. Walter and P. Knipscheer, respectively. FLAG-xlFANCI, Strep-xlFANCD2, and Strep-xlFANCD2K562R expression plasmids were also a gift from J. Walter. D.R.S. is supported by NIH grant no. R01GM151410 and a Shurl and Kay Curci Foundation Research Grant, and is a Ronald and JoAnne Willens Scholar. S.B.H. is supported by NIH grant no. R01CA215553. E.P.B. is supported by NIH grant no. R01CA208834 and is a Howard Hughes Medical Institute Investigator. J.P.D. is supported by Novo Nordisk Foundation Grants no. NNF14CC0001 and no. NNF220C0074140. J.W.H.W. was supported by the A*STAR NSS (PhD) predoctoral fellowship.
Conflict of Interest
E.P.B. is an inventor on the following patents related to detection and inhibition of colibactin biosynthesis: U.S. Patent 11,617,759, U.S. Patent 12,115,176, and U.S. Patent 11,040,951. All other authors have no competing interests to declare.
Data Availability
Supplemental Material
Supplementary Information: https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-025-65606-1/MediaObjects/41467_2025_65606_MOESM1_ESM.pdf
Files
s41467-025-65606-1.pdf
Additional details
Identifiers
- PMCID
- PMC12657977
- PMID
- 41298418
Related works
- Describes
- Journal Article: https://rdcu.be/eS16b (URL)
Funding
- National Institutes of Health
- R01GM151410
- National Institutes of Health
- R01CA208834
- Novo Nordisk Foundation
- NNF14CC0001
- Novo Nordisk Foundation
- NNF220C0074140
Dates
- Accepted
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2025-10-25Accepted