Table 1

Plasmids, primers, and probes used in this study

Plasmid, primer, or probeDescription or sequence (5′–3′)Source or reference
Plasmids
    pBBR1MCS-1Cmr; broad-host-range cloning vector18
    pBC SK(−)Cmr; ori pBBR322Stratagene
    pCSI1Apr Cmr; source of the Cmr gene used in this study19
    pCSI2Apr Kmr; source of the Kmr gene used in this study19
    pGP704Apr; ori R6K, mob RP44
    pGP704KmApr Kmr; pGP704-derivative containing the Kmr gene at the EcoRI site of its MCSThis study
    pKNG101Smr; ori R6K, mob RK220
    pJOC21Apr; pGP704-derivative containing miniUIB (IRL-MCS-IRR of ISPst9)This study
    pJOC22KmApr Kmr; pJOC21-derivative containing miniUIB-Km (1.6 kb, IRL-Kmr-IRR)This study
    pJOC22CmApr Cmr; pJOC21-derivative containing miniUIB-Cm (2.1 kb, IRL-Cmr-IRR)This study
    pJOC22BCApr Cmr; pJOC21-derivative containing miniUIB-BC (3.6 kb, IRL-pBC SK-IRR)This study
    pJOC22KmBCApr Cmr Kmr; pJOC21-derivative containing miniUIB-KmBC (5.0 kb, IRL-Kmr-pBC SK-IRR)This study
    pJOC22KNGApr Smr; pJOC21-derivative containing miniUIB-KNG (7.0 kb, IRL-pKNG101-IRR)This study
    pJOC22KmKNGApr Kmr Smr; pJOC21-derivative containing miniUIB-KmKNG (8.4 kb, IRL-Kmr-pKNG101-IRR)This study
    pJOC22BCKmKNGApr Kmr Smr; pJOC21-derivative containing miniUIB-BCKmKNG (11.8 kb, IRL-pBC SK-Kmr-pKNG101-IRR)This study
    pALKBApr; pJOC21-derivative containing miniUIB-ALKB (8.5 kb, IRL-alkBFGHJKL-IRR)This study
    pALKApr; pJOC21-derivative containing miniUIB-ALK (12.8 kb, IRL-alkST-alkBFGHJKL-IRR)This study
    pJOC100Apr; pJOC21-derivative containing miniUIB100 (IRL-MCS-IRR-ISPpu12 without IRs)This study
    pJOC100KmApr Kmr; pJOC100-derivative containing miniUIB100-Km (IRL-Kmr-IRR-ISPpu12 without IRs)This study
    pJOC100ALKApr; pJOC100-derivative containing miniUIB100-ALK (IRL-alkST-alkBFGHJKL-IRR-ISPpu12 without IRs)This study
Primers
    KM-FAAA CGT CTT GCT CGA GGC CThis study
    KM-RGGA GAA AAC TCA CCG AGG CThis study
    PCR3-FGAG ATC TTC GGG TAT GCG GAT TTA ATGThis study
    PCR3-RGAT CTA GAC CCG GGC TAT TGT CAA GAC AGThis study
    PCR1-FCAG GTA CCG CAT GAC CGA AAT GCC CGAThis study
    PCR1-RGGA ATT CGT GGG TAT GCG GAT TTA ATG GThis study
    ALK1-FAAT CTA GAT TTC CAG CAG ACG ACG GAG CThis study
    ALK1-RCGC GCC GAG CTC CAG CGT TGT CCThis study
    ALK2-FGGC GAG TAC CAG GAC GGC GTA GGGThis study
    ALK2-RTTG AGC TCT TAG AAA ACA TAT GAC GCA CCThis study
    ALKRsma-FAAC CCG GGG CAC GTA CGG AGT GCG GGThis study
    ALKRsma-RAAC CCG GGG GCG AAG GCC GAA GTC GGCThis study
    ISPPU25Eco-FTTG AAT TCT TAC CTT TGC ATG AGA GTG AGThis study
    ISPPU3348Eco-RTTG AAT TCG GGG CAC CTT CAC CCC ATCThis study
Probes
    TNPAtnpA of ISPst9 and ISPpu1213
    TNPRtnpR of ISPpu1212
    KMKmr gene of pCSI2, PCR using KM-F and KM-R primersThis study
    ALKalkBFGH genes of P. putida TF4-1L (GPo1), PCR using ALK1-F and ALK1-R primersThis study
    PGPEntire EcoRI-digested pGP704 plasmidThis study
  • a Cmr, chloramphenicol resistance; Apr, ampicillin resistance; Smr, streptomycin resistance; Kmr, kanamycin resistance.