Characterizing Colibactin Toxicity and the Resulting Cellular Response to DNA Damage in Mammalian and Bacterial Systems

Abstract

The bacterial toxin colibactin, produced primarily by the B2 phylogroup of Escherichia coli, crosslinks DNA and can promote colon cancer in human hosts, where it has been extensively studied. A systematic approach to identify the DNA damage response to colibactin-induced toxicity has yet to be applied and colibactin toxicity in bacteria remains underexplored. Using a genome-wide CRISPR screen in colon cancer cells, I found that colibactin activates most DNA repair pathways with key roles for Fanconi anemia/interstrand crosslink repair and fork quality control pathways. I also conducted a genome-wide loss-of-function screen in E. coli that identified a key role for homologous recombination in repairing colibactin-induced damage. I determined that colibactin induces a mutational pattern in E. coli in A/T rich regions, as it does in colon cells, but that the resulting mutational signature differs in E. coli. I then predicted that long- term colibactin exposure will culminate in a genomic bias based on this mutational signature, which may be detected in colibactin-producing bacteria. I tested this prediction by analyzing thousands of E. coli genomes andfound that colibactin-producing strains show skewness in trinucleotide composition. Finally, I used a sensitive DNA damage reporter assay to find that cell-cell contact is not required in bacteria as was previously suggested for both bacteria and mammalian cells, and that this needs to be reevaluated in mammalian cells. Taken together, this work revealed the DNA damage response to colibactin-induced damage in both colon and bacteria cells, a bacteria-specific mutation pattern, and that cell-cell contact is not required in bacteria.