Bacterial Strains, Plasmids and Growth Media
Genotypes of the bacterial strains, plasmid descriptions, and sequences of primers used in this study are listed in Tables S2-S3. Bacteria were grown in DifcoTM LB Broth (BD brand #240230 consisting of Tryptone 10 g/L, Yeast Extract 5 g/L, Sodium Chloride 5 g/L). LB agar plates were prepared from DifcoTM LB Agar (BD brand #240110). The growth media was supplemented with an appropriate amount of antibiotics (100 μg/mL ampicillin, 25 μg/mL chloramphenicol, 50 μg/mL kanamycin, 12.5 μg/mL tetracycline) when necessary for the selection of strains and maintenance of plasmids.
Keio collection deletion strains, including ∆ybeX , ∆ybeY , and ∆ybeZ , and Escherichia coli wild-type BW25113 strains were used in this study (Baba et al. , 2006). We also reconstructed the ybeX single deletion strain using E. coli MG1655 and BW25113 via lambda red recombination (Datsenko and Wanner, 2000). The kanamycin resistance gene (kan) was removed from the bacterial chromosome using the pCP20 plasmid.
E. coli DH5α strain was used for plasmid cloning and propagation. In addition, the TransBac library, a new E. coli overexpression library based on a single-copy vector, was obtained from Dr Hirotada Mori (Nara Institute of Science and Technology, Japan) as a stab stock (Otsuka et al. , 2015).