## 3 Results
### FQ Persisters Depend on Similar DNA Repair Systems When Deprived of Different Nutrients  
Previous studies have demonstrated the importance of different DNA repair enzymes to FQ persistence in non-growing cultures [23; 24; 34; 35; 37]. Given that the abundances of FQ persisters varied as a function of deprived nutrient and drug used, we assessed to what extent the DNA repair systems used by persisters in the different cultures were shared or distinct. Over the eight different combinations of starvation and FQ, we observed a similar ranking of importance of DNA repair systems for FQ persistence (Figures 3 and 4, Supplementary Figures S4 and S5). Consistently, the mutants \(\Delta\)_recA_, \(\Delta\)_recB_, _lexA3_, \(\Delta\)_uvrD_, \(\Delta\)_ruvA_, and \(\Delta\)_recN_ were significantly lower than wild-type (WT), whereas \(\Delta\)_recF_ for some samples was significantly higher. We note that \(\Delta\)_recF_ has been shown before to increase persister  
Figure 2: Fluoroquinoline (FQ) persistence levels depend on the type of nutrient starvation and antibiotic used. _E. coli_ cultures that underwent 16 h of starvation for C, N, P, or Mg\({}^{2+}\) and an exponentially-growing control in complete media (M9) were treated with 5 ug/mL levofloxacin (LEVO) (**A**) or 5 ug/mL movifloxacin (MOXI) (**B**) for 5 h and survival was monitored. Before antibiotic treatment (at 0 h) and at 1, 3 and 5 h after antibiotic treatment, samples were obtained, washed in phosphate buffered saline (PBS) three times, and plated on LB-agar to enumerate colony forming units per milliliter (CFUs/mL). Data points indicate the means of five biological replicates, whereas error bars indicate the standard errors of those means. One-way ANOVA with post-hoc Tukey tests were conducted for each drug treatment to assess significance. (**A**) Complete media samples exhibited a significant difference with starvation samples at 1, 3, and 5 h time points. N-starved samples exhibited a significantly higher rate of survival from C-, P-, and Mg\({}^{2+}\)-starved samples at 3 and 5 h. (**B**) Complete media samples exhibited a significant difference with all starvation samples at 1, 3 and 5 h time points. P-starved samples exhibited a significantly higher rate of survival from C-, N-, and Mg\({}^{2+}\)-starved samples at 1, 3, and 5 h. N-starved samples exhibited a significantly higher rate of survival from C- and Mg\({}^{2+}\)-starved samples at 3 and 5 h time points. * Indicates a significance of \(p<0.05\). levels in some conditions and that the effect depended on RecA, which suggested that the ability of RecF to load RecA onto ssDNA could be detrimental to survival following FQ treatment [37]. Deletions of _recA_ and _recB_ resulted in the largest declines in persister levels (typically \(\sim\)1,000-fold reduction), followed by \(\Delta uvrD\) mutants and an uncleavable _lexA_ mutant (_lexA3_) (typically \(\sim\)100-fold reduction), though for some scenarios these four mutants were indistinguishable (Figure 4C). Deletions of _ruvA_ and _recN_ constituted the next grouping, which yielded \(\sim\)10-fold fewer persisters than WT; however, in environments devoid of Mg\({}^{2+}\) their impacts were negligible (Figures 3D and 4D). Interestingly, even for nutrient-deprived cultures with extremely high survival (N- and LEVO, P- and MOXI), DNA repair systems remained important, which suggested that even under conditions where FQs appear to largely lose their bactericidal activities, DNA damage occurs from treatment. Figure 3: Importance of DNA repair machinery to LEVO persistence is largely invariant in non-growing populations starved for different nutrients. Persister levels in populations of _ArccA_, _ArccB_, _lexA3_, _AuvrD_, _ArnvA_, _ArecF_, _ArecN_ and WT under the indicated starvation conditions were assessed with LEVO. Data points indicate the means of three biological replicates, whereas the error bars indicate the standard errors of those means. One-way ANOVA with post-hoc Tukey test were conducted for each starvation condition to assess significance.