Table 1

Allele designations of chromosomal gene disruptions

Mutation*Template(s)Homology extensionsPriming sites
DE(lacZYA)514pKD3, pKD436 nt; H1: 365662C; H2: 360842P0; P2
DE(ompR-envZ)516pKD1350 nt; H1: 3534269C; H2: 3532141P1; P4
DE(torSTRCAD)517pKD1350 nt; H1: 1052654; H2: 1061625CP1; P4
ΔarcB40 pKD350 nt; H1: 3350706C; H2: 3348269P1; P2
ΔcyaA1403 pKD1338 nt; H1: 3988674; H2: 3991330CP1; P4
ΔphnR171 pKD436 nt; H1: 2242; H2: 3016CP3; P2
ΔpstB608 pKD444 nt; H1: 3906010C; H2: 3905260P1; P2
ΔpstCA607 pKD444 nt; H1: 3908039C; H2: 3905991P1; P2
ΔpstS605 pKD3, pKD436 nt; H1: 3909143C; H2: 3908059P3; P2
ΔpstSCAB-phoU606 pKD1336 nt; H1: 3909339C; H2: 3904418P1; P4
ΔrecA635 pKD1350 nt; H1: 2821868C; H2: 2820743P1; P4
  • * All except two were made in pKD20 transformants of BW25113. DE(lacZYA)514 mutants were made in the isogenic Lac+ strain BW25993; phnR was disrupted in three similar strains carrying the Salmonella typhimurium LT2 phosphonatase gene cluster (32) on the chromosome. Some were also made in MG1655 transformants. 

  • Extension lengths are given first. Numerals identify the 3′ nucleotide of the extension in the E. coli genome sequence [(ref. 33; GenBank accession no. U00096) or the S. typhimurium phnR entry (GenBank accession no. U69493)]. C, complement; H1, homology 1; H2, homology 2. 

  • One primer had the H1 extension and the 3′ sequence for priming site 0 (P0), 1 (P1), or 3 (P3). The other had the H2 extension and the 3′ sequence for the complement of priming site 2 (P2) or 4 (P4).