Nature Genetics: doi: /ng Supplementary Figure 1. Susceptibility of MTase-deficient E. coli K12 to sublethal ampicillin treatment.

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1 Supplementary Figure 1 Susceptibility of MTase-deficient E. coli K12 to sublethal ampicillin treatment. (a,b) Wild-type (wt) or MTase-deficient E. coli BW25113 (a) or MG1655 (b) were grown in LB to an OD of 0.3 and then treated with ampicillin (2.5 μg/ml) or left untreated. CFUs and/or OD were monitored hourly. (c) Determination of ampicillin MIC (left) and MBC 90 (right) for E. coli BW25113 by broth microdilution in LB. Wild-type and dam MIC values were 6 g/ml and 4 g/ml, respectively; wildtype and dam MBC 90 values were 2.7 g/ml and 1.5 g/ml, respectively. Dotted lines indicate cutoff values for MIC (OD < 0.1) or MBC 90 (10% survival). MBC 90 values were interpolated using a sigmoidal curve fit model as shown. In a c, data are shown as means ± s.e.m. of n = 2 3 independent experiments.

2 Supplementary Figure 2 Complementation of dam E. coli ampicillin sensitivity with wild-type or catalytically inactive mutant Dam. Wild-type or dam E. coli BW25113 were transformed with the indicated Cm r plasmid expressing gfp, dam or mutant dam in which the catalytic DPPY motif is disrupted by a single amino acid change (D181S, D181N or P183R). Plasmid-bearing strains were grown in LB supplemented with chloramphenicol (15 g/ml). (a) Genomic DNA extracted from the indicated strains at stationary phase was either digested with DpnII, which cleaves at GATC sites only in the absence of methylation, or left undigested. Digests were run on a 0.8% agarose gel containing ethidium bromide. (b) OD kinetics of wild-type or dam E. coli BW25113 harboring the indicated Cm r plasmids cultured in LB supplemented with chloramphenicol (15 g/ml) with or without ampicillin (2.5 g/ml) at log phase. (c) The indicated E. coli BW25113 strains were grown in LB to an OD of 0.2 and then treated with 2 g/ml ampicillin or left untreated. In b and c, CFUs and/or OD were monitored hourly to assess survival. Data are shown as means ± s.e.m. of n = 3 independent experiments.

3 Supplementary Figure 3 Stability of GATC methylome kinetics during growth in the presence or absence of ampicillin. Genome-wide GATC methylation kinetics displayed as in Figure 2d during growth in LB (top) or in LB supplemented with 2.5 g/ml ampicillin (bottom). The top panel is the same as the plot displayed in Figure 2d. The empty green arrowhead highlights the only GATC site displaying statistically significant differential methylation between untreated and ampicillin-treated samples (Supplementary Table 2 and Supplementary Data Set 1).

4 Supplementary Figure 4 dinb, muts and muth dependence of dam E. coli sensitivity to ampicillin. The indicated E. coli BW25113 strains were grown in LB to an OD of 0.3 and then treated with 2.5 g/ml of ampicillin or left untreated. OD was monitored hourly to assess survival. Data are shown as means ± s.e.m. of n = 2 independent experiments.

5 Supplementary Figure 5 dinb, muts and muth dependence of dam sensitivity to ofloxacin. The indicated E. coli BW25113 strains were grown in LB to an OD of 0.3 and then treated with ofloxacin (50 ng/ml) or left untreated. CFUs in bacterial cultures were monitored hourly to assess survival. Data are shown as mean percent survival ± s.e.m. of n = 2 independent experiments.

6 Supplementary information Supplementary table 1: GATC sites partially or fully non-methylated during log-tostationary phase transition in LB or over the course of ampicillin treatment. Methylation pattern over time Methylation increases Methylation decreases Non-methylated Hemimethylated Other Genetic arrangement Site Position Coverage b Inter- Upstream Downstream /intragenic gene gene (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) 104 ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± 21 Overlapping protein binding site intergenic sert (-) hyaa (+) - - intergenic ycgg (+) ymgf (+) - - intergenic ydcd (+) ynci (+) - - intergenic yiaj (-) yiak(+) R- Pol* - intergenic dgor (+) yidx (+) - - intergenic ycdy (+) ycdz (+) CRP intergenic comr (-) bhsa (+) CRP - intergenic yohk (+) cdd (+) CRP intergenic ppia (-) tgsa (+) CRP - intergenic yibl (-) mlta (+) CRP - intergenic comr (-) bhsa (+) ComR* intergenic rpsa (+) ynfa (+) Yhdf* intergenic mltb (+) guta (+) CRP; GutR* intergenic soda (+) kdgt (+) - - intergenic -- (+) -nr (+) Fis intergenic insg (+) yjhb (+) -nr* - intergenic -nc (-) fimb (+) -nr* - intergenic fepd (-) ents (+) Fur - intragenic gdha (+) gdha(+) - - a Base pairs and strand; b average sequencing coverage ± SD, n = 2 3 replicates; *protein binding sites is within 10 bp of methylation site. Sites are grouped based on methylation pattern over time in untreated E. coli. Ref ,2,4 1,2,4 -

7 Supplementary table 2: Statistical analysis of differential methylation in LB versus ampicillin treatment at selected GATC sites from Fig. 2d. P-values (undjusted) b P-values (multiplicity adjusted) c Site Position a 1h 2h 3h 4h 1h 2h 3h 4h (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) (+) (-) a Base pairs and strand; b p-value determined using a two-tailed heteroskedastic (unequal variances) t-test; c p-value adjusted for multiple hypothesis testing on the whole dataset using Benjamini-Hochberg false discovery rate correction; for sites with no change in frac between LB and ampicillin treatment the t-test cannot be performed and the adjusted p-value is 1 (non-significant); cells in red, p<0.05.

8 Supplementary table 3: Quinolone-resistance conferring mutations in Cipro R UPEC clinical isolate Gene Function Mutation Ref. gyra D- gyrase subunit A S83L 5 D87N parc D- topoisomerase IV, subunit A S80I pare D- topoisomerase IV, subunit B S458A marr Activator of multidrug efflux system 6 G103S Y137H Supplementary references 1. Tavazoie, S. & Church, G.M. Quantitative whole-genome analysis of Dam protein interactions by in vivo methylase protection in E. coli. Nat Biotechnol 16, (1998). 2. Wang, M.X. & Church, G.M. A whole genome approach to in vivo Dam protein interactions in E. coli. Nature 360, (1992). 3. Holst, B., Sogaard-Andersen, L., Pedersen, H. & Valentin-Hansen, P. The camp- CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the camp-crp activator complex are involved in combinatorial regulation of the cdd promoter. EMBO J 11, (1992). 4. Hale, W.B., van der Woude, M.W. & Low, D.A. Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli. J Bacteriol 176, (1994). 5. Mavroidi, A. et al. Ciprofloxacin-resistant Escherichia coli in Central Greece: mechanisms of resistance and molecular identification. BMC Infect Dis 12, 371 (2012). 6. Zayed, A.A., Essam, T.M., Hashem, A.G. & El-Tayeb, O.M. 'Supermutators' found amongst highly levofloxacin-resistant E. coli isolates: a rapid protocol for the detection of mutation sites. Emerg. Microbes Infect. Dis. 4(2015).