Deconvolution of functions of a model DNA damage-control network.

Mutations that drive evolution and cancer often result from spontaneous DNA damage, yet the origins of DNA damage in living cells remain unclear. We discovered large, diverse, conserved networks of cancer-associated “DNA damage-control” (DDC) genes, and, here, report the kinds and causes of DNA damage instigated by overproduction of proteins in a 208-gene Escherichia coli model DDC network. Using massive, quantitative live-cell assays with synthetic proteins that label specific DNA-damage intermediates, and other indicators, we sorted E. coli DDC proteins into those that provoke DNA breaks, replication stalling, reactive oxygen, specific DNA-repair depletion, and failed chromosome segregation. Cluster analysis reveals six function clusters, indicating at least six molecular mechanisms of DNA-damage promotion, three of which we identified. The results reveal that dysregulation of fundamental conserved cellular processes creates DNA damage by diverse mechanisms that feedback to genomes to drive mutation rate, evolution, and, potentially, functions of many cancer-driving genes.