Journal Article

The human gut bacterial genotoxin colibactin alkylates DNA

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

2019

Overview

The bacterial toxin colibactin causes double-stranded DNA breaks and is associated with the occurrence of bacterially induced colorectal cancer in humans. However, isolation of colibactin is difficult, and its mode of action is poorly understood. Wilson et al. studied Escherichia coli that contain the biosynthetic gene island called pks , which is associated with colibactin production (see the Perspective by Bleich and Arthur). They identified the DNA adducts that resulted from incubating pks + E. coli in human cells. To overcome the lack of colibactin for direct analysis, mimics of the pks product were synthesized. From the resulting synthetic adenine-colibactin adducts, it became evident that alkylation via a cyclopropane “warhead” breaks the DNA strands. Similar DNA adducts were then identified in the gut epithelia of mice infected with pks + E. coli. Science , this issue p. eaar7785 ; see also p. 689 DNA adducts in cells and animals exposed to colibactin-producing gut microbes shed light on the mode of action of a cancer-linked genotoxin. 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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Adducts / Adenine / Alkylates / Alkylating Agents / Alkylation / Animal models / Animals / Astrochemistry / Bacteria / Biomarkers / Biotechnology / Cancer / Carcinogenesis / Carcinogenesis - genetics / Carcinogenesis - metabolism / Carcinogens / Cell cycle / Chemical reactions / Chemical synthesis / Chemistry / Colitis / Colorectal cancer / Colorectal Neoplasms - genetics / Colorectal Neoplasms - microbiology / Crosslinking / Cyclopropane / Cyclopropanes - chemistry / Cyclopropanes - metabolism / Cytotoxicity / Deoxyribonucleic acid / DNA / DNA adducts / DNA Adducts - metabolism / DNA biosynthesis / DNA Damage / E coli / Epithelial cells / Escherichia coli / Escherichia coli - metabolism / Escherichia coli - pathogenicity / Exposure / Familial adenomatous polyposis / Gastrointestinal Microbiome / Genetic disorders / Genomic instability / Genomic islands / Genotoxicity / Germ-Free Life / HeLa Cells / HT29 Cells / Humans / Intestinal microflora / Liquid chromatography / Literary Devices / Mammalian cells / Mammals / Mass spectrometry / Mass spectroscopy / Metabolites / Mice / Mice, Inbred C57BL / Microorganisms / Mode of action / Molecular structure / Mutagens - metabolism / Mutagens - toxicity / Natural products / Organic chemistry / Pathogenesis / Peptides - chemistry / Peptides - metabolism / Peptides - toxicity / Polyketides - chemistry / Polyketides - metabolism / Polyketides - toxicity / Polyps / RESEARCH ARTICLE SUMMARY / Senescence / Structural analysis / Toxins