This PDF file includes:Supplementary Methods Figs. S1 to S5 Tables S1 to S3
Supplementary Information Text
Bacterial strains, plasmids, routine growth condition, and compound susceptibility testBacterial strains and plasmids used in this study are listed in Table S1. Miller's lysogeny broth (LB) 1 and LB-agar were used for routine growth and bacterial selection during plasmid construction. To maintain plasmids, 100 µg/mL ampicillin (Ap), 10 µg/mL chloramphenicol (Cm), and 50 µg/mL kanamycin (Km) were added to the media as needed. Compound susceptibility testing to determine MICs was performed in cation adjusted Mueller-Hinton II broth (CAMHB) according to CLSI protocols, as described previously 2 . To induce genes under the control of a lac promoter, 100 µM isopropyl β-D-1-thiogalactopyranoside (IPTG) was added to the media used in susceptibility testing. Compounds were synthesized at Novartis as described below. CHIR-090 was purchased from ChemScene (CS-0973).
Spontaneous mutant selectionFor mutant selection with compound 1, cells in overnight culture of MG1655 ΔtolC were spread on LB agar containing 0.5 µg/mL compound 1. For mutant selection with compound 14, overnight culture of CDY0154 was used and the cells were spread on L-agar containing 16 and 32 µg/mL compound 14. Serial dilutions of the overnight culture were spread on LB agar to determine the number of cells (approximately 10 8 and 10 9 cells) used for selection. The LB agar plates were incubated overnight at 37 °C. Colonies arose and were streaked on fresh LB agar. After incubation overnight at 37 °C, a single colony of each mutant was grown in LB and stored in 15% glycerol at -80 °C for genome sequencing and susceptibility tests. The fabZ mutants were isolated from selection with inhibitors of LpxA and LpxD.
Genome sequencing and mutation confirmationGenomic DNA for whole genome sequencing was isolated from E. coli strains using the Qiagen DNeasy Blood and Tissue kit with following the instruction for Gram-negative bacterial DNA. To sequence the genomes of isolated mutants, library preparation and sequencing reaction for next generation sequencing, and data analysis were performed using the Illumina Sample Preparation kits and Illumina Sequencer as described previously 2 . Sequencing reads were aligned to the reference E. coli MG1655 genome (Genbank ID: NC_000913.3) using bwa for determining single nucleotide polymorphisms and short insertion/deletions (indels, typically <10 bp). Mutations identified by genomics were confirmed by targeted PCR and Sanger sequencing. The primers were used to amplify the gene of interest with Phusion High-Fidelity PCR Master Mix with GC Buffer according to established protocols. Sequencing was performed by Elim BioPharma (Hayward, CA). The primers used for PCR and sequencing were TU117, TU243, TU276, TU332, TU475, TU503, TU504, TU512, and TU513.
Construction of CDY0154The acrAB locus was replaced with the kanamycin resistant cassette (Km r ) using the λRED recombination system as described previously 3 . The DNA fragmen...