TABLE 1.
Bacterial strains and plasmids
| Strain or plasmid | Genotype and/or phenotype | Reference or source |
|---|---|---|
| Strains | ||
| Ralstonia sp. strain U2 | Wild-type naphthalene degrader containing plasmid pWWU2 | 7 |
| P. putida PaW340 | Trp− Strr plasmid-free derivative of P. putida mt-2 | 11 |
| Plasmids | ||
| pUC19 | Vector; Apr; multiple cloning site in lacZα | 27 |
| pKOK6.1 | Apr; promoterless lacZ | 15 |
| pRK415 | Tcr; mobilizable broad-host-range vector; origin of replication (oriV) and origin of transfer (oriT) of RK2 | 14 |
| pRK415-ZP | pRK415 with lacZ-Km cassette from pKOK6.1 inserted into PstI site, with the start of lacZ adjacent to the SalI site of pRK415 | This study |
| pWWF24 | 8.3-kb XhoI fragment from strain U2 carrying the naphthalene dioxygenase region cloned in the XhoI site of pBluescript II SK(+) | 8 |
| pWWF116 | pWWF24 with a 4-bp deletion at the NsiI site within nagR | This study |
| pWWF119 | pGEM-T Easy with RACE fragment created by using Pnag as the template | This study |
| pWWF120F | 1.6-kb wild-type fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites | This study |
| pWWF120R | Like pWWF120F, but with restriction sites reversed, creating a 1.6-kb fragment in the opposite direction | This study |
| pWWF121 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having bases −68 to −70 of Pnag deleted | This study |
| pWWF122 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having bases −60 to −62 of Pnag deleted | This study |
| pWWF123 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having bases −64 to −66 of Pnag deleted | This study |
| pWWF124 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having bases −60 to −71 of Pnag deleted | This study |
| pWWF125 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having a C-to-T substitution at base −70 of Pnag | This study |
| pWWF126 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having a G-to-A substitution at base −61 of Pnag | This study |
| pWWF128 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having C-to-T and G-to-A substitutions at bases −51 to −53 of Pnag | This study |
| pWWF129 | 1.6-kb fragment in pUC18 containing nagR and 347 bp of nagAa PCR amplified at designed XbaI and KpnI restriction sites and having C-to-T and G-to-A substitutions at bases −77 to −79 of Pnag | This study |
| pWWF120F-Z | 1.6-kb XbaI/KpnI fragment from pWWF120 inserted into pRK415-ZP | This study |
| pWWF120R-Z | 1.6-kb KpnI/XbaI fragment from pWWF120 inserted into pRK415-ZP | This study |
| pWWF121-Z | 1.6-kb XbaI/KpnI fragment from pWWF121 inserted into pRK415-ZP | This study |
| pWWF122-Z | 1.6-kb XbaI/KpnI fragment from pWWF122 inserted into pRK415-ZP | This study |
| pWWF123-Z | 1.6-kb XbaI/KpnI fragment from pWWF123 inserted into pRK415-ZP | This study |
| pWWF124-Z | 1.6-kb XbaI/KpnI fragment from pWWF124 inserted into pRK415-ZP | This study |
| pWWF125-Z | 1.6-kb XbaI/KpnI fragment from pWWF125 inserted into pRK415-ZP | This study |
| pWWF126-Z | 1.6-kb XbaI/KpnI fragment from pWWF126 inserted into pRK415-ZP | This study |
| pWWF128-Z | 1.6-kb XbaI/KpnI fragment from pWWF128 inserted into pRK415-ZP | This study |
| pWWF129-Z | 1.6-kb XbaI/KpnI fragment from pWWF129 inserted into pRK415-ZP | This study |