TABLE 1.

Bacterial strains and plasmids used in this study

Strain or plasmidGenotype and/or descriptionReference or source
E. coli K-12 strains
    DH5αFΔlacU169 φ80 dlacZΔM15 hsdR17 recA1 endA1 gyrA96 thi-1 relA1 supE4477
    JM109F′ traD36 proA+ proB+ lacIq lacZΔMI5/recA1 endA1 gyrA96 (Nalr) thi hsdR17 supE44 relA1 Δ(lac-proAB)79
    HB101F Δ(gpt-proA) 62 leuB6 supE44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Smr) xyl-5 mtl-1 recA133
    CC118 λpirΔ(ara-leu) araD ΔlacX74 galE galK phoA20 thi-I rps-1 rpoB argE(Amp) recA thi pro hsdRM+ RP4-2-Tc34
    S17-1 λpirλpir recA thi pro hsdR M+, RP4:2-Tc::Mu::Km Tn7Tpr Smr67
E. coli W strains
    AF141E. colipaa lacZ Rif+ derivative25
    BMRAF141 with chromosomal insertion of mini-Tn5Km2 Phmg-lacZThis study
P. putida strains
    UWild type8
    U-7P. putida U hmgA due to a Tn5 insertionThis study
    U-95P. putida U hmgA due to a Tn5 insertionThis study
    U-SG6P. putida U hmgA due to a Tn5 insertionThis study
    U-111P. putida U hpd due to a Tn5 insertionThis study
    U-215P. putida U phhA due to a Tn5 insertionThis study
    U-A2P. putida U hpaB due to a Tn5 insertionUnpublished data
    U-dhmgAP. putida U hmgA::pK18mobThis study
    U-dhmgBP. putida U hmgB::pK18mobThis study
    U-dhmgCP. putida U hmgC::pK18mobThis study
    U-dhpdP. putida U hpd::pK18mobThis study
    U-ΔhmgP. putida U with hmgABC operon deleted from the genomeThis study
    U-ΔhpdP. putida U lacking the hpd geneThis study
    U-dphhAP. putida U phhA::pK18mobThis study
    U-A2dhpdP. putida U hpaB due to a Tn5 insertion and disrupted in the hpd gene with the pJQhpd constructionThis study
    KT2440hsdMR2
    KT2440Rif+Spontaneous KT2440 rifampin-resistant mutantThis study
    KT2440-dhmgAKT2440Rif+ hmgA::pK18mobThis study
    KT2440-dhpdKT2440Rif+ hpd::pK18mobThis study
    KT2440-dphhAKT2440Rif+ phhA::pK18mobThis study
    KT2440-dhmgRKT2440Rif+ hmgR::pK18mobThis study
Plasmidsa
    pUC18Apr oriColE1 lacZα+ lac promoter79
    pGEM-T easyApr oriColE1 lacZα+ SP6 T7 lac promoters, direct cloning of PCR productsPromega
    pK18mobKmr oriColE1 Mob+ lacZα+, used for directed insertional disruption62
    pRK600Cmr oriColE1 oriV Mob+, helper plasmid in triparental matings37
    pBBR1MCS-2Kmr oripBBR1 Mob+ lac promoter lacZα+, broad-host-range cloning and expression vector38
    pBBR1MCS-3Tcr oripBBR1 Mob+ lac promoter lacZα+, broad-host-range cloning and expression vector38
    pJQ200KSGmr orip15A Mob+ lacZα+ sacB, used to generate deletions by double-recombination events56
    pQE32Apr oriColE1 T5 promoterllac operator, lambda t0/E. coli rrnB T1 terminators, N-terminal 6-HisQIAGEN
    pSJ3Apr oriColE1r, lacZ promoter-probe vector25
    pUTminiTn5Km2Apr Kmr oriR6K Mob+, mini-Tn5Km2 transposon delivery plasmid11
    pUT-Phmg-lacZpUTminiTn5Km2 derivative carrying the Phmg-lacZ translational fusionThis study
    pU-HHpUC18 derivative expressing the hmgABC and hpd genesThis study
    pU-HHPpUC18 derivative containing the Tyr catabolic cassette (hmgABC hpd tyrB1)This study
    pM2-HHPpBBR1MCS-2 derivative harboring the SacI/HindIII Tyr catabolic cassette from pU-HHPThis study
    pGS9Conjugative plasmid containing the Tn5 transposon65
  • a For plasmids obtained by cloning of a PCR-generated fragment see Table 2.