Table 1.

Bacterial strains and plasmids used in this study

Strain or plasmidDescriptionReference(s) or source
A. keyseri12BGrows with o-phthalate and dibutylphthalate24, 43, 45
A. keyseri 12B-C14Derivative of A. keyseri 12B containing pRE1 (cured of pRE2 and pRE3)This study
E. coli JM109recA endA1 gyrA96 thi hsdR17 supE44 relA1Δ(lac-proAB) (F′ traD36 proAB lacIqM15)91
E. coliBL21(DE3)(pLysS)FompT hsdSB(rB mB)gal dcm (DE3) pLysS. λDE3 prophage carries T7 RNA polymerase under lacUV5 control; Cmr; obtained from Novagen82
pBBR1MCS2Kmr, multiple cloning site in lacZα48
pBluescriptII KSApr, multiple cloning site in lacZα, between lac and T7 promoters; obtained from Stratagene Cloning Systems1
pBluescriptII SKApr, multiple cloning site in lacZα, between lac and T7 promoters; obtained from Stratagene Cloning Systems1
pLV59Encodes EcoRI restriction endonuclease and temperature-sensitive EcoRI methylase, Cmr, positive-selection cloning vector68
pUCBM21Apr, derived from pUC18 with additional cloning sites inserted intolacZα; obtained from Boehringer Mannheim91
pRE1130-kbp plasmid from A. keyseri 12B and 12B-C14, encodes phthalate catabolismThis study
pRE75214.1-kbpBglII fragment from pRE1 (map coordinates 19.4 to 33.5) inserted into pLV59This study
pRE7547.79-kbpBglII fragment from pRE1 (map coordinates 10.5 to 18.3) inserted into pLV59This study
pRE7558.07-kbpBglII fragment from pRE1 (map coordinates 2.4 to 10.5) inserted into pLV59, hybridized to pRE920This study
pRE7611.15-kbp BglII fragment from pRE1 (map coordinates 18.3 to 19.4) inserted into pLV59This study
pRE7902.4-kbp BglII fragment from pRE1 (map coordinates 0 to 2.4) inserted into pLV59, hybridized to pRE920This study
pRE8248.14-kbp PstI fragment from pRE1 (from a mixture of plasmids from strain 12B) (map coordinates 17.2 to 25.4) inserted into pLV59, clone identified by screening on 2-trifluoromethylbenzoate-containing mediumThis study
pRE8268.14-kbp PstI fragment from pRE824 inserted into pUCBM21This study
pRE8429.1-kbp HindIII fragment from pRE1 (from a mixture of plasmids from strain 12B) (map coordinates 16.3 to 25.8) inserted into pLV59; identified by hybridization to the PstI fragment of pRE824This study
pRE8611.97-kbp HindIII-BglII fragment from pRE754 (map coordinates 16.3 to 18.3) inserted intoHindIII-BamHI-digested pBluescriptII KS; carries pehA, lac orientationThis study
pRE8719.1-kbp HindIII fragment from pRE842 inserted into pBluescriptII KS; lac orientationThis study
pRE899pRE871 with ClaI fragment (map coordinates 17.0 to 18.8) deleted; lacks phtBThis study
pRE92016.5-kbp HindIII fragment from pRE1 (map coordinates-0.2 to 16.3) inserted into pLV59; identified by hybridization to a SmaI fragment (map coordinates 13.1 to 14.4) from pRE754This study
pRE9955.4 kbp-ClaI-BglII fragment (map coordinates 5.1 to 10.5) from pRE755 inserted intoClaI-BamHI-digested pBluescriptII KS; carries most of the pcm operon, T7 orientationThis study
pRE1026966-bp BspEI-XmaI fragment (map coordinates 23.0 to 24.0) from pRE824 inserted intoXmaI-digested pBluescriptII SK; carries phtC, lacorientationThis study
pRE10431.86 kbpXhoI-BamHI fragment (map coordinates 6.1 to 8.0) from pRE920 inserted into pBluescriptII KS; carries pcmA, T7 orientationThis study
pRE10561.16-kbp PstI fragment (map coordinates 4.3 to 5.5) from pRE920 inserted into pBluescriptII SK; carries pcmF, possible dehydrogenase gene; T7 orientationThis study
pRE10581.19-kbp BssHI fragment (map coordinates 5.3 to 6.5) inserted into pBluescriptII SK; carries pcmB, lac orientationThis study
pRE10625.24-kbp SalI fragment (map coordinates 16.3 to 17.0 + 18.8 to 23.4) from pRE899 inserted into pBBR1MCS2; Kmr; carries phtAaAbAcAd downstream fromlac promoterThis study
pRE10651.66-kbpNgoMIV fragment (map coordinates 7.4 to 9.0) from pRE920 inserted into XmaI-digested pBluescriptII SK; carriespcmC, T7 orientationThis study
pRE10669.1-kbpHindIII fragment from pRE842 inserted into pBBR1MCS2; Kmr; carries pht operon downstream fromlac promoterThis study
pRE1089XbaI-digested 723-bp PCR product (map coordinates 16.4 to 17.1), made using Taq polymerase and primers ACG GTC TAG AAA GGA GGA AAG CAT GTC CGC G and TGC GTC TAG AGC GCT GGC ATG with pRE754 as template inserted into pBluescriptII SK; carries pehA, lac orientationThis study
pRE1096BspEI-XbaI-digested 3.8-kbp PCR product (map coordinates 13.2 to 17.1), made using Taqpolymerase and primers TCA TTC CGG AGG AGA AGG GTA TGG ACG TAA and TGC GTC TAG AGC GCT GGC ATG with pRE754 as template, inserted intoXmaI-XbaI-digested pBluescript II SK; carriesptrDABC pehA, T7 orientationThis study