Table 1.
Bacterial strains and plasmids.
| Bacterial strains or plasmids | Descriptiona | Reference/origin |
|---|---|---|
| Bacteria: S. Typhimurium | ||
| D23580 derivatives | ||
| JH3621 | D23580 WT | Kingsley et al., 2009 |
| JH3874 | ΔGifsy-1 | This study |
| JH3875 | ΔGifsy-2 | This study |
| JH3877 | ΔBTP1 | This study |
| JH3878 | ΔBTP5 | This study |
| JH3881 | ΔBTP1 ΔBTP5 | This study |
| JH3940 | ΔBTP1 ΔBTP5 ΔGifsy-1 | This study |
| JH3942 | ΔBTP1 ΔBTP5 ΔGifsy-1 ΔGifsy-2 | This study |
| JH3949 | ΔΦ (ΔBTP1 ΔBTP5 ΔGifsy-1 ΔGifsy-2 ΔST64B) | This study |
| JH3983 | ΔGifsy-1, aph-galE496; KmR | This study |
| JH3984 | ΔGifsy-2, aph-galE496; KmR | This study |
| JH3986 | ΔST64B | This study |
| JH3987 | PdinI-gfoA from 14028s (C→T substitution, position 2,790,162 in D23580 chromosome) | This study |
| D23580 ΔrecA | D23580 with recA gene replaced with nptII from pKD13 and subsequently flipped out using Flp recombinase encoding pCP20 plasmid | This study |
| 14028s derivatives | ||
| MA5958 | 14028s, WT | L. Bossi |
| MA6684 | ΔGifsy-1 ΔGifsy-2 bio-106::Tn10 galE496; TcR | L. Bossi, Campoy et al., 2006 |
| LT2 derivatives | ||
| LT2 | LT2, WT | Zinder and Lederberg, 1952 |
| MA8508 | Gifsy-1[-] Gifsy-2[-] Fels-2[-] Fels-1[Δ(int-attR)104::cat] | L. Bossi, Lemire et al., 2011 |
| LT2 [BTP1] | LT2 derivative MA8508 lysogenised with phage BTP1 | This study |
| LT2 [P22] | LT2 derivative MA8508 lysogenised with phage P22 (wildtype) | This study |
| LT2 Δrec | LT2 derivative MA8508 with recA gene replaced with nptII from pKD13 and subsequently flipped out using Flp recombinase encoding pCP20 plasmid | This study |
| 4/74 derivative | ||
| 4/74 | 4/74, WT | Rankin and Taylor, 1966 |
| E. coli | ||
| S17-1 λpir | pro thi hsdR recA chromosome::RP4-2 Tc::Mu Km::Tn7/λpir; TpR, SmR | Simon et al., 1983 |
| Plasmids: | ||
| pEMG | Suicide plasmid; KmR | Martínez-García and de Lorenzo, 2011 |
| pKD13 | nptII-cassette template plasmid; KmR | Datsenko and Wanner, 2000 |
| pKD4 | aph-cassette template plasmid; KmR | Datsenko and Wanner, 2000 |
| pKD4-I-SceI | pKD4 derivative with an I-SceI site cloned upstream of aph; KmR | This study |
| pKD46 | λ Red recombination plasmid, arabinose-inducible; ApR | Datsenko and Wanner, 2000 |
| pKD46 bla::Tn10 | pKD46 derivative; OxyTcR | Passaris et al., 2014 |
| pCP20 | Plasmid carrying the Flp recombinase to remove kanamycin resistance from pKD13 derived resistance cassette insertions; ApR | Cherepanov and Wackernagel, 1995 |
| pCP20-TcR | Derivative of plasmid carrying the Flp recombinase to remove kanamycin resistance from pKD4 derived resistance cassette insertions; TcR | Kintz et al., 2015 |
| pNAW15 | Suicide plasmid pEMG::attBGifsy-1; KmR | This study |
| pNAW16 | Suicide plasmid pEMG::attBGifsy-2; KmR | This study |
| pNAW17 | Suicide plasmid pEMG::attBBTP1; KmR | This study |
| pNAW18 | Suicide plasmid pEMG::attBBTP5; KmR | This study |
| pNAW42 | Suicide plasmid pEMG::attBST64B; KmR | This study |
| pSIM5-tet | λ Red recombination plasmid, temperature-inducible; TcR | Koskiniemi et al., 2011 |
| pSW-2 | Plasmid for m-toluate-inducible expression of the I-SceI enzyme; GmR | Martínez-García and de Lorenzo, 2011 |
aRelevant antibiotic resistances are indicated by R: Ap, ampicillin; Gm, gentamicin; Km, kanamycin, OxyTc, oxytetracycline; Sm, streptomycin; Tc, tetracycline; Tp, trimethoprim. For the purpose of clarity the natural resistances of D23580 and its derivatives are not indicated.