TABLE 1.
Strains and plasmids used in this study
| Strain or plasmid | Relevant characteristic(s) | Source or reference |
|---|---|---|
| Strains | ||
| Agrobacterium tumefaciens C58 | Free of IS1071 | 35 |
| Comamonas testosteroni JCM5832 | Free of IS1071; type strain | JCMa |
| Delftia acidovorans B | Harboring pUO1 | 14 |
| D. acidovorans B123 | pUO1-cured derivative of strain B, more than one copy of IS1071 in the chromosome | 14 |
| Escherichia coli DH5α | recA lacZΔM15; free of IS1071 | 1 |
| E. coli HB101 | recA; free of IS1071 | 1 |
| E. coli JM109 | NalrrecA hsdR17; free of IS1071 | 1 |
| Pseudomonas alcaligenes JCM5967 | Free of IS1071; type strain | JCMa |
| P. putida PpN1 | Free of IS1071 | 4 |
| Plasmids | ||
| pUO1 | Hgr, haloacetate degradation, TnHad1, TnHad2 (Fig. 1A) | 14 |
| pBBR1MCS | Cmr, broad-host-range cloning vector | 16 |
| pBBR1MCS-3 | Tcr, broad-host-range cloning vector | 15 |
| pCB182 | Apr, promoter-probe vector, lacZ gene without its promoter sequence (Fig. 2B) | 22 |
| pME6012 | Tcr, broad-host-range vector, pVS1 and p15A replicons | 8 |
| pNIT6012 | Tcr, pME6012 derivative carrying the oriT sequence of RP4 at BamHI site | Laboratory collection |
| pMS0252 | Tcr, pBBR1MCS-3 derivative carrying IS1071 (Fig. 1C) | This study |
| pMS0310 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative with 110-bp IRs (Fig. 1B and C) | This study |
| pMS0311 | Cmr, pBBR1MCS derivative carrying an IS1071 derivative that lacked the outermost 83-bp sequence in both IRs (Fig. 1B and C) | This study |
| pMS0321 | Apr, pCB182 derivative carrying the 145-bp sequence upstream of the tnpA gene in IS1071 between BglII and SalI sites (Fig. 2A and B) | This study |
| pMS0324 | Cmr, pBBR1MCS derivative carrying the BamHI-PstI fragment of pMS0321 (Fig. 2B) | This study |
| pMS0326 | Cmr, pBBR1MCS derivative carrying the BglII-PstI fragment of pCB182 (Fig. 2B) | This study |
| pMS0361 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative with the outermost 38-bp sequences of the IRs (Fig. 1B and C) | This study |
| pMS0362 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative with the outermost 48-bp sequences of the IRs (Fig. 1B and C) | This study |
| pMS0363 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative with the outermost 70-bp sequences of the IRs (Fig. 1B and C) | This study |
| pMS0364 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative with the outermost 90-bp sequences of the IRs (Fig. 1B and C) | This study |
| pMS0366 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative with the outermost 100-bp sequences of the IRs (Fig. 1B and C) | This study |
| pMS0368 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative whose IRs have a 20-bp deletion at positions 51 to 70 (Fig. 1B and C) | This study |
| pMS0369 | Tcr Kmr, pNIT6012 derivative carrying a Kmr-IS1071 derivative whose IRs have a 20-bp deletion at positions 71 to 90 (Fig. 1B and C) | This study |
| pUC4K | Apr Kmr, cloning vector, Kmr gene is flanked by the EcoRI, BamHI, SalI, and PstI sites | 26 |
| R388 | Tpr Sur, conjugal plasmid free of transposons, IncW replicon | 32 |
a
JCM, Japan Collection of Microorganisms.