Bacterial Strains and Culture Conditions

All wild-type and mutant bacterial strains used in this study are listed in Supplementary Table S2 and plasmids used are listed in Supplementary Table S3. Mutant strains TUV93-0 ΔyhiF, CFT073 ΔdsdA and CFT073 ΔdsdXΔcycA as well as complementation constructs (pyhiF, pdsdA and pdsdX) were generated as described elsewhere and generously supplied as gifts for use in this study (Anfora and Welch, 2006 (link); Tree et al., 2011 (link)). Single colonies of bacteria were inoculated into 5 ml LB broth containing the appropriate antibiotics where specified (ampicillin 100 μg ml⁻¹; kanamycin 50 μg ml⁻¹; chloramphenicol 25 μg ml⁻¹) and cultured overnight at 37 °C, 200 r.p.m. Overnight cultures were used to inoculate pre-warmed MEM-HEPES (Sigma-Aldrich, St Louis, MO, USA; cat # m7278) at an OD⁶⁰⁰ of 0.05 and samples were cultured subsequently at 37 °C, 200 r.p.m. D-AAs for screening were purchased from Sigma-Aldrich and supplemented into MEM-HEPES at a concentration of 1 mM unless otherwise stated. Mitomycin C was used as a positive control for inducing the SOS response at a concentration of 5 μM.