TABLE 1.
Bacterial strains and plasmids used for this study
| Strain or plasmid | Genotype or construction | Source or reference |
|---|---|---|
| E. coli | ||
| TG1 | supE hsd Δ5 thi Δ(lac-proAB) F′ (traD36 proAB+lacIqlacZΔM15) | 18 |
| DH5α | supE44 ΔlacU169 (Φ80 lacZΔM15) recA1 endA1 hsdR17 thi-1 gyrA96 relA1 | Invitrogen |
| HB101 | subE44 subF58 hsdS3 (rB− mB−) recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1 | 12 |
| CC118 λpir | Δ(ara-leu) araD ΔlacX74 galE galK phoA20 thi-1 rpsE rpoB argE (Am) recA1 λpir phage lysogen | 32 |
| P. putida | ||
| PaW85 | Wild type | 6 |
| PaWRulAB | PaW85, carrying the rulAB genes from pWW0 in chromosome in attTn7 site | This study |
| PaWMutY | PaW85, mutY::tet | This study |
| PaWMutM | PaW85, ΔmutM::km | This study |
| PaWMutT | PaW85, ΔmutT::km | This study |
| PaWDps | PaW85, Δdps::km | This study |
| PaWMutYRulAB | PaWRulAB, mutY::tet | This study |
| PaWMutMRulAB | PaWRulAB, ΔmutM::km | This study |
| PaWMutTRulAB | PaWRulAB, ΔmutT::km | This study |
| Plasmids | ||
| pBluescript KS(+) | Cloning vector (Apr) | Stratagene |
| pUTmini-Tn5 Km2 | Delivery plasmid for mini-Tn5 Km2 (Apr Kmr) | 19 |
| pGP704 L | Delivery plasmid for homologous recombination (Apr) | 62 |
| pRK2013 | Helper plasmid for conjugal transfer of pGP704 L (Kmr) | 21 |
| pBK-miniTn7-ΩSm1 | pUC19-based delivery plasmid for miniTn7-ΩSm1 (Smr, Apr) | 42 |
| pUX-BF13 | R6K replicon-based helper plasmid, providing the Tn7 transposase proteins (Apr, mob+) | 4 |
| pGP704mutY::tet | mutY::tet-sequence-containing SacI-KpnI fragment from pB1scrMutY-Tet cloned into pGP704L | 67 |
| pKSmutM | pBluescript KS(+) containing the PCR-amplified mutM gene region inserted in EcoRV-opened vector plasmid | This study |
| pKSΔmutM::km | mutM in pKSmutM is interrupted with the Kmr gene from pUTmini-Tn5 Km2 by replacing PaeI- and Van9II-generated fragment from mutM by Kmr gene | This study |
| pGP704ΔmutM::km | pGP704 L with Acc65I-XbaI fragment of ΔmutM::km from pKSΔmutM::km in vector plasmid opened with the same restrictases | This study |
| pKSmutT | pBluescript KS(+) containing the PCR-amplified mutT gene region inserted into EcoRV-opened vector plasmid | This study |
| pKSΔmutT::km | mutT in pKSmutT is interrupted with Kmr gene from pUTmini-Tn5 Km2 by replacing Bpu1102I-Van91I-generated fragment in mutT with Kmr gene | This study |
| pGP704ΔmutT::km | pGP704 L with Acc65I-XbaI fragment of ΔmutT::km from pKSΔmutT::km in vector plasmid opened with the same restrictases | This study |
| pKSdps | pBluescript KS(+) containing the PCR-amplified dps gene region inserted into EcoRV-opened vector plasmid | This study |
| pKSΔdps::km | dps in pKSdps is interrupted with Kmr gene from pUTmini-Tn5 Km2 by replacing Eco130I-EcoRV-generated fragment in dps with Kmr gene | This study |
| pGP704Δdps::km | pGP704 L with Acc65I-XbaI fragment of Δdps::km from pKSΔdps::km in vector plasmid opened with the same restrictases | This study |
| pUCNotrulAB | pUC18Not containing rulAB genes | 74 |
| pBK-miniTn7-ΩSm1rulAB | rulAB genes from pUC18NotrulAB in NotI site of pBK-miniTn7-ΩSmI | This study |
| pKTpheA56+A | Test system for detection of Phe+ revertants occurring due to 1-bp deletions | 76 |
| pKTpheA22TAG | Test system for detection of Phe+ revertants occurring due to base substitutions | 75 |
| pKT240 | Medium-copy broad-host-range cloning vector (Apr Kmr) | 3 |