TABLE 1.

Strains and plasmids used in this study

Strain or plasmidRelevant characteristic(s)aSource or reference
Comamonas sp.
    E6Wild type, TPA+ 30
    EME009E6 derivative, ΔtphRItphCIThis study
    EME010EME009 derivative, ΔtphRIIThis study
    EME011EME009 derivative, ΔtphA2IA3IBIA1ItphA2IIThis study
E. coli
    DH5α supE44 ΔlacU169 (φ80 lacZΔM15) hsdR17 recA1 endA1 gyrA96 thi-1 relA1 12
    XL2-Blue recA1 endA1 gyrA96 thi-1 hsdR17 supE44 relA1 lac [F′ proAB lacIqZΔM15 Tn10 (Tcr) Amy Cmr]Stratagene
    BL21(DE3)FompT hsdSB(rB mB) gal dcm (DE3), T7 RNA polymerase gene under control of the lacUV promoter 35
Plasmids
    pBluescript II SK(+)Cloning vector, Apr 34
    pT7BlueCloning vector, Apr T7 promoterNovagen
    pK19mobsacB oriT sacB Kmr 31
    pKT230MCIncQ broad-host-range cloning vector, Kmr 25
    pJB866RK2 broad-host-range expression vector, Tcr PmxylS 2
    pET16bExpression vector, N-terminal His10 tag, Apr T7 promoterNovagen
    pPR9TZBroad-host-range promoter probe vector, RK2 ori Apr Cmr 17
    pSS92RpBluescript II SK(+) with a 4.0-kb SalI fragment carrying tphRI and tphCIThis study
    pK19RCIpK19mobsacB with a 2.5-kb EcoRV-HindIII fragment of pSS92RThis study
    pDTRCIpK19RCI with a deletion of a 0.5-kb XbaI-SmaI fragment carrying the tphRI-tphCI intergenic regionThis study
    pEJ89pJB866 with a 8.9-kb EcoRI fragment carrying tphRIICIIA2IIA3IIBIIA1II 30
    pEJ84pEJ89 with a deletion of a 0.6-kb MunI-Tth111I fragment carrying part of tphRII 30
    pDTRIIpK19mobsacB with a 2.3-kb EcoRI-HindIII fragment of pEJ84This study
    pK19A2IIpK19mobsacB with a 2.0-kb HindIII-XhoI fragment carrying tphA2IIThis study
    pDTA2IIpK19A2II with a deletion of a 0.5-kb SphI-PstI fragment carrying part of tphA2IIThis study
    pK19ABIFpK19mobsacB with a 4.3-kb HindIII fragment carrying tphA2IA3IBIA1IThis study
    pDTABIpK19ABIF with a deletion of a 1.9-kb PstI fragment carrying tphA2IA3IBIA1IThis study
    pKTRIIpKT230MC with a 1.8-kb KpnI fragment carrying tphRIIThis study
    pKTtphIIpKT230MC with a 8.9-kb EcoRI fragment carrying tphRIICIIA2IIA3IIBIIA1IIThis study
    pTRIIpT7Blue with a 779-bp PCR fragment generated by the TphRII-F and TphRII-R primer pairThis study
    pETtprIIpET16b with a 772-bp NdeI-XhoI fragment of pTRIIThis study
    pTTCpT7Blue with a 393-bp PCR fragment carrying the tphRII-tphCII intergenic regionThis study
    pZTCpPR9TZ with a 381-bp HindIII-KpnI fragment of pTTCThis study
    pTTRpT7Blue with a 500-bp PCR fragment carrying the tphRII-tphCII intergenic regionThis study
    pZTRpPR9TZ with a 379-bp HindIII-KpnI fragment of pTTRThis study
    pTTCT5CSite-directed mutant of pTTC generated by the SMT5C-F and SMT5C-R primer pairThis study
    pTTCG6ASite-directed mutant of pTTC generated by the RM315-F and RM315-R primer pairThis study
    pTTCC7TSite-directed mutant of pTTC generated by the SMC7T-F and SMC7T-R primer pairThis study
    pTTCG8ASite-directed mutant of pTTC generated by the SMG8A-F and SMG8A-R primer pairThis study
    pT5CpPR9TZ with a 381-bp HindIII-KpnI fragment of pTTCT5CThis study
    pG6ApPR9TZ with a 381-bp HindIII-KpnI fragment of pTTCG6AThis study
    pC7TpPR9TZ with a 381-bp HindIII-KpnI fragment of pTTCC7TThis study
    pG8ApPR9TZ with a 381-bp HindIII-KpnI fragment of pTTCG8AThis study
  • a Abbreviations: TPA+, able to grow on TPA as the sole carbon source; Apr, Kmr, Tcr, and Cmr, resistance to ampicillin, kanamycin, tetracycline, and chloramphenicol, respectively.