Bacterial strains and plasmids E. coli strain K12 isolate MG1655 (gift from Dr. Sydney Kustu, University of California) was used as the parental strain in all analyses described in this report. Mutagenesis was carried out using the one-step
mutagenesis method by Datsenko and Wanner . Mutant bacterial strains and sequences of oligonucleotides used for mutagenesis are listed in Table 1. In the ΔarcA mutant, the wild type arcA allele was replaced by a kanamycin-resistance cassette (Kanr). In the ΔarcB mutant, the wild type arcB allele was replaced by a chloramphenicol-resistance cassette (Cmr). Each mutation was transduced into fresh E. YAP-TEAD Inhibitor 1 cell line coli by general transduction with phage P1 before further analysis. In the ΔfliC mutant, the wild type fliC allele was replaced by Cmr, which was subsequently removed to generate a non-polar mutant . The ΔarcA/ΔfliC mutant was prepared by transducing arcA::kan from the ΔarcA mutant into the ΔfliC non-polar mutant E. coli. A revertant of ΔarcB mutant E. coli was generated through a two-step process. First, a mutant, arcB(Kanr), was generated in which Kanr was inserted downstream to the arcB buy VX-689 coding sequence without affecting the arcB open reading frame. Subsequently, phage P1 was prepared
from arcB(Kanr) and used to transduce the ΔarcB mutant E. coli. Kanamycin-resistant and chloramphenicol-sensitive colonies were selected, in which the deletion mutant arcB allele learn more in the ΔarcB mutant E. coli was replaced by a wild type allele from arcB(Kanr). The genome structure surrounding the arcB allele was determined to verify that wild type arcB allele was restored. The resultant bacterial strain was referred to as ΔarcB-rev. Plasmid pRB3-arcA
used to complement the ΔarcA mutant E. coli was described previously . Plasmid pRB3-arcD2A was constructed using megaprimer method as described (-)-p-Bromotetramisole Oxalate . Briefly, a 260-bp section of the arcA gene that included the Asp54 was amplified using mutagenesis primer 5′-CAACCTGGTGATCATGGCGATCAATCTGCC-3′ and an arcA primer 5′-CAACGCTACGACGCTCTTC-3′. Sequence in bold in the mutagenesis primer introduced an aspartate to alanine mutation (Asp → Ala) at amino acid 54 in ArcA. The PCR product was used as a megaprimer to amplify plasmid pRB3-arcA together with a vector primer 5′-GTTTTCCCAGTCACGAC-3′. The PCR product was subsequently digested with KpnI and cloned into KpnI-digested plasmid pRB3-arcA to replace the wild type arcA gene with the corresponding sequence that introduced an Asp54 → Ala mutation. The resulting plasmid pRB3-arcD2A contained the same sequence as the original plasmid pRB3-arcA except that GAT which codes for Asp54 of ArcA was mutated to GCG which codes for Ala. Survival assays of bacteria after exposure to oxidative and other stresses Survival of E. coli after H2O2 and other stress conditions was assayed as described previously [38, 52]. E. coli was cultured in 2 ml of Luria Bertani (LB) broth at 37°C overnight with shaking at 225 rpm.