TABLE 1.
Bacterial strains and plasmids
| Bacterial strain or plasmid | Relevant characteristic(s) | Source or reference(s) |
|---|---|---|
| Bacterial strains | ||
| E. coli K-12 DH5α | F− ϕ80dlacZΔM15 Δ(lacZYA-argF)U169 endA1 recA1 hsdR17(rK− mK+) deoR thi-1 supE44 gyrA96 relA1 λ− phoA | Toyobo |
| E. coli K-12 S17-1λpir | recA thi pro hsdR; RP4-2 integrated into the chromosome (kan::Tn7 ter::Mu) λpir | 44 |
| P. putida KT2440 | Naturally Cmr | 45 |
| P. putida KT2440KR | Derivative strain of KT2440, spontaneously Rifr, with introduced Kmr gene | This study |
| P. putida KT2440(pCAR1) | KT2440 harboring pCAR1 | 35 |
| P. putida KT2440(pCAR1pmrHis::Gmr) | KT2440(pCAR1pmrHis) harboring Gmr gene cassette and FRT sites | 23 |
| P. putida KT2440(pCAR1Δpmr::Gmr) | KT2440 harboring pCAR1 carrying disrupted pmr gene by Gmr gene cassette and FRT sites | This study |
| P. putida KT2440(pCAR1Δpmr)a | KT2440(pCAR1) single-deletion mutant lacking pmr gene | This study |
| P. putida KT2440(pCAR1Δpnd::Gmr) | KT2440 harboring pCAR1 carrying disrupted pnd gene by Gmr gene cassette and FRT sites | This study |
| P. putida KT2440(pCAR1Δpnd) | KT2440(pCAR1) single-deletion mutant lacking pnd gene | This study |
| P. putida KT2440(pCAR1Δphu::Gmr) | KT2440 harboring pCAR1 carrying disrupted phu gene by Gmr gene cassette and FRT sites | This study |
| P. putida KT2440(pCAR1Δphu) | KT2440(pCAR1) single-deletion mutant lacking phu gene | This study |
| P. putida KT2440(pCAR1ΔpmrΔpnd::Gmr) | KT2440(pCAR1Δpmr) in which pnd gene is disrupted by Gmr gene cassette and FRT sites | This study |
| P. putida KT2440(pCAR1ΔpmrΔpnd) | KT2440(pCAR1) double-deletion mutant lacking pmr and pnd genes | This study |
| P. putida KT2440(pCAR1ΔpmrΔphu::Gmr) | KT2440(pCAR1Δpmr) in which phu gene is disrupted by Gmr gene cassette and FRT sites | This study |
| P. putida KT2440(pCAR1ΔpmrΔphu) | KT2440(pCAR1) double-deletion mutant lacking pmr and phu genes | This study |
| P. putida KT2440(pCAR1ΔpndΔphu::Gmr) | KT2440(pCAR1Δpnd) in which phu gene is disrupted by Gmr gene cassette and FRT sites | This study |
| P. putida KT2440(pCAR1ΔpndΔphu) | KT2440(pCAR1) double-deletion mutant lacking pnd and phu genes | This study |
| P. putida KT2440(pCAR1PMGΔpmrΔpnd) | KT2440(pCAR1ΔpmrΔpnd) containing Gmr gene cassette with FRT sites and 0.57-kb pmr cassette inserted into 101,000–101,001 region of pCAR1 | This study |
| P. putida KT2440(pCAR1PMΔpmrΔpnd) | KT2440(pCAR1ΔpmrΔpnd) containing 0.57-kb pmr cassette inserted into 101,000–101,001 region of pCAR1 | This study |
| P. putida KT2440(pCAR1PMGΔpmrΔphu) | KT2440(pCAR1ΔpmrΔphu) containing Gmr gene cassette with FRT sites and 0.57-kb pmr cassette inserted into 101,000–101,001 region of pCAR1 | This study |
| P. putida KT2440(pCAR1PMΔpmrΔphu) | KT2440(pCAR1ΔpmrΔphu) containing 0.57-kb pmr cassette inserted into 101,000–101,001 region of pCAR1 | This study |
| Plasmids | ||
| pBBad18K | Kmr, l-arabinose-inducible vector based on the pBBR1MCS-4 replicon | 33 |
| pBBad18K-recT | pBBad18K, BamHI-XbaI fragment containing recT | This study |
| pBSLKmr | Mini-Tn5, R6K ori, Apr, Kmr | 34 |
| pFLP2Km | pFLP2, Kmr gene cassette inserted into its ScaI site | 23 |
| pK19mobsacB | Kmr, oriT (RP4), sacB, lacZα, pMB1 replicon | 32 |
| pK19mobsacBΔpmr | pK19mobsacB containing 5′- and 3′-flanking regions of pmr and Gmr gene cassette, which is flanked by FRT sites | This study |
| pK19mobsacBΔpnd | pK19mobsacB containing 5′- and 3′-flanking regions of pnd and Gmr gene cassette, which is flanked by FRT sites | This study |
| pK19mobsacBΔphu | pK19mobsacB containing 5′- and 3′-flanking regions of phu and Gmr gene cassette, which is flanked by FRT sites | This study |
| pK19mobsacBpmr | pK19mobsacB containing 100,550–101,000 and 101,001–101,382 regions of pCAR1, pmr, and Gmr gene cassette | This study |
| pPS856 | Apr, Kmr, FRT sites | 31 |
| pT7Blue T-vector | Apr, lacZα, T7 promoter, f1 origin, pUC/M13 priming sites | Novagen |
| pTpmr | pT7Blue T-vector with PCR fragment amplified from total DNA of KT2440(pCAR1) with primer set pmr_qRT_F and pmr_qRT_R | 35 |
| pTpnd | pT7Blue T-vector with PCR fragment amplified from total DNA of KT2440(pCAR1) with primer set pnd_qRT_F and pnd_qRT_R | This study |
| pTphu | pT7Blue T-vector with PCR fragment amplified from total DNA of KT2440(pCAR1) with primer set phu_qRT_F and phu_qRT_R | This study |
| pTuniv16S | pT7Blue T-vector with PCR fragment amplified from total DNA of P. resinovorans CA10 with primer set univ16S-F and univ16S-R | 35 |
| pZErO-2 | Kmr, T7 promoter, ColE1 and f1 origin, ccdB lethal gene, M13 priming sites | Invitrogen |
a
KT2440(pCAR1Δpmr), which was used in our previous study (23), was reconstructed in this study as described in Materials and Methods.