The SOS response acts as a regulatory switch that balances helicase anti-recombination with transcription-replication conflict resolution activities in Escherichia coli.

Transcription-replication conflicts are a major source of genome instability, particularly at highly transcribed ribosomal RNA genes, where RNA polymerase stalling can trigger replication fork collapse and double-strand breaks. We investigated how the SOS DNA damage response regulates the activities of the UvrD, DinG, RecQ, and Rep helicases in Escherichia coli, focusing on their roles in resolving transcription-replication conflicts and repairing double-strand breaks at ribosomal RNA loci. We systematically assessed the contribution of each helicase to cell growth, DNA break formation, SOS induction, and survival. Our results show that SOS induction functions as a regulatory switch, modulating UvrD and DinG activities between protective transcription-replication conflict resolution and detrimental anti-recombination. RecA abundance emerges as the key determinant of this switch. While RecQ consistently promotes genome stability by facilitating timely SOS activation and recombinational repair, Rep primarily supports replisome progression, functioning independently of SOS response status. Under nalidixic acid treatment, where survival relies mainly on double-strand break repair, we observed a similar SOS-dependent modulation of helicase activity, reinforcing this regulatory model. Together, these findings uncover a dynamic regulatory mechanism that fine-tunes helicase activities to resolve transcription-replication conflicts while limiting deleterious anti-recombination, thereby preserving chromosome integrity under transcriptional or antibiotic-induced stress.