TABLE 6.
Bacterial strains and plasmids used in this study
| Strains or plasmids | Relevant characteristics | Reference |
|---|---|---|
| Bacterial strains | ||
| Escherichia coli | ||
| DH5α | F−, endA1, hsdR17(rk−, mk−), phoA, supE44, thi-1, λ−, recA1, gyrA96, relA1, Δ(lacZYA- argF)U169, ψ80dlacZΔM15 | RBCBioscience |
| JM109 | F' [traD36, proAB, lacIq, lacZΔM15], recA1, endA1, gyrA96, thi-1, hsdR17(rK− mK+), e14− (mcrA−), supE44, relA1, Δ(lac-proAB) | RBCBioscience |
| MG1655 | F−, λ−, rph-1 | 58, 59 |
| MG1655R | Spontaneous Rifr strain of MG1655 | This study |
| MG1655RG | MG1655, Rifr, mini-Tn5-Gmr gene was inserted in the chromosome | This study |
| MG1655RK | MG1655, Rifr, mini-Tn10-Kmr gene was inserted in the chromosome | This study |
| MG1655RT | MG1655, Rifr, mini-Tn10-Tcr gene was inserted in the chromosome | This study |
| MG1655RGFP | MG1655, Rifr, mini-Tn5-Km-PA1/O4/O3-RBSII-gfpmut3*-T0-Cmr-T1 was inserted in 578584 nt in the chromosome (accession no. NC_000913) | This study |
| S17-1λpir | Tmr, Smr, recA, thi, pro, hsdR−M+, RP4: 2-Tc:Mu: Km Tn7, λpir | 55 |
| Pseudomonas putida | ||
| KT2440 | pWW0-free Pseudomonas putida mt-2 | 60 |
| KT2440G | Derivative strain of KT2440, Gmr gene is inserted into PP_4780 (NC_021505, see Supplemental text S1) | This study |
| SMDBS | A dapB-deleted strain of SM1443, Rifr of KT2440 (KT2442) with mini-Tn5-lacIq cassette inserted into the chromosome | 25 |
| SMDBS(pSN1104-11gfpTc) | SMDBS harboring pSN1104-11gfpTc | This study |
| SMDBS(pSN0729-62::gfp) | SMDBS harboring pSN0729-62::gfp | This study |
| P. resinovorans CA10dm4R | Derivative strain of CA10dm4 spontaneously Rifr. | 61 |
| P. resinovorans CA10dm4RGFP | CA10dm4R, miniTn7(Gm) PA1/O4/O3 gfp-a was inserted into chromosome, just downstream of glmS gene (6265580 nt, NC_021499) (Gmr, Cmr). | 5 |
| Plasmids | ||
| mini-pBP136_Km | Kmr, DNA region containing ssb, trfA, oriV of pBP136 | This study |
| mini-pBP136_Tc | Tcr, DNA region containing ssb, trfA, oriV of pBP136 | This study |
| mini-pYKCG107_Tc | Tcr, DNA region containing ssb, trfA, oriV of pYKCG107 | This study |
| mini-pMHAD031_Km | Kmr, DNA region containing ssb, trfA, oriV of pMHAD031 | This study |
| mini-pMHAD031_Tc | Tcr, DNA region containing ssb, trfA, oriV of pMHAD031 | This study |
| mini-pYKCS045_Km | Kmr, DNA region containing ssb, trfA, oriV of pYKCS045 | This study |
| mini-pYKCS045_Tc | Tcr, DNA region containing ssb, trfA, oriV of pYKCS045 | This study |
| mini-pMNBM077_Km | Kmr, DNA region containing ssb, trfA, oriV of pMNBM077 | This study |
| mini-pMNBM077_Tc | Tcr, DNA region containing ssb, trfA, oriV of pMNBM077 | This study |
| mini-pYKBG036_Km | Kmr, DNA region containing trfA, oriV of pYKBG036 | This study |
| mini-pYKBG036_Tc | Tcr, DNA region containing trfA, oriV of pYKBG036 | This study |
| mini-pYKAM101_Km | Kmr, DNA region containing trfA, oriV of pYKAM101 | This study |
| mini- pYKAM101_Tc | Tcr, DNA region containing trfA, oriV of pYKAM101 | This study |
| mini-pDS1_Km | Kmr, DNA region containing ssb, trfA, oriV of pDS1 | This study |
| mini-pDS1_Tc | Tcr, DNA region containing ssb, trfA, oriV of pDS1 | This study |
| mini-pMNCG080-1_Km | Kmr, DNA region containing ssb, trfA, oriV of pMNCG080-1 | This study |
| mini-pMNCG080-1_Tc | Tcr, DNA region containing ssb, trfA, oriV of pMNCG080-1 | This study |
| mini-pMNCG082-1_Km | Kmr, DNA region containing ssb, trfA, oriV of pMNCG082-1 | This study |
| mini-pMNCG082-1_Tc | Tcr, DNA region containing ssb, trfA, oriV of pMNCG082-1 | This study |
| mini-pMH0613-68_Tc | Tcr, DNA region containing repA, oriV of pMH0613-68 | This study |
| mini-pSN0729-62_Tc | Tcr, DNA region containing repA, oriV of pSN0729-62 | This study |
| mini-pSN1104-11_Tc | Tcr, DNA region containing repA, oriV of pSN1104-11 | This study |
| mini-pYK0414-12_Tc | Tcr, DNA region containing repA, oriV of pYK0414-12 | This study |
| pBBR1MCS-2 | Kmr, lacZα mob; compatible with IncP, IncQ, and IncW plasmids | 7 |
| pBBR1MCS-3 | Tcr, lacZα mob; compatible with IncP, IncQ, and IncW plasmids | 7 |
| pBBR1MCS-5 | Gmr, lacZα mob; compatible with IncP, IncQ, and IncW plasmids | 7 |
| pBSL202 | Apr, Gmr mini-Tn5 | 62 |
| pJBA28 | Apr, Kmr, delivery plasmid for mini-Tn5-Km-PA1/O4/O3-RBSII-gfpmut3*-T0- Cmr-T1 | 54 |
| pK18_1104-11 | pK18mobsacB with homologous DNA region with pSN1104-11 (1-kb DNA regions upstream and downstream of the target site) and Tcr and PA1/O4/O3-RBSII-gfpmut3* cassette | This study |
| pK18mobsacB | pMB1, lacZα, mob, kan, sacB | 63 |
| pRK2013 | ColEI replicon, a helper plasmid for RP4/RK2 oriT-mediated conjugative transfer; Kmr | 64 |
| pSN0729-62 | PromAδ plasmid | 5 |
| pSN0729-62::gfp | Mini-Tn5-Km-PA1/O4/O3-RBSII-gfpmut3*-T0-Cmr-T1 cassette in 35612 nt of pSN0729-62 (AP018705) | This study |
| pSN1104-11 | PromAγ plasmid | 5 |
| pSN1104-11gfpTc | Tcr and PA1/O4/O3-RBSII-gfpmut3* cassette in 37978 nt of pSN1104-11 (AP018707) | This study |