TABLE 1

Bacterial strains, plasmids, and primers used in this study

Strain, plasmid, or primerGenotype or relevant characteristics, relevant properties and cloning strategies, or sequence (5′–3′)aReference or source
Strains
    Rhodococcus rhodochrous PY112HP-degrading bacterium14
    R. erythropolis SQ1Mutant of Rhodococcus erythropolis strain ATCC 4277-1 with increased transformability15
    E. coli BL21(DE3)F ompT hsdSB(rB mB) gal dcm (DE3), strain for protein overexpressionNovagen, Germany
    E. coli DH5αF ϕ80dlacZΔM15 Δ(lacZYA-argF)U169 recA1 endA1 hsdR17(rK mK+) phoA supE44 λ thi-1 gyrA96 relA1Fermentas, Lithuania
Plasmids
    pUC19Apr ori ColE1 lacZα, high copy-no. cloning vector18
    pTZ57R/TApr ori ColE1 lacZα, high copy-no. cloning vectorThermo Fisher Scientific, Lithuania
    pET-21bpBR322-derived ColE1, T7 lac promoter, AprNovagen, Germany
    pET-28bpBR322-derived ColE1, T7 lac promoter, KmrNovagen, Germany
    pETDuet-1pBR322-derived ColE1, T7 lac promoter, two MCSs,a AprNovagen, Germany
    pCDFDuet-1CloDF13 replicon, T7 lac promoter, two MCSs, SmrNovagen, Germany
    pART2E. coli-A. nicotinovorans shuttle plasmid for hdnOp-driven constitutive expression, MCS, Kmr16
    pNitQC1E. coli-Rhodococcus shuttle vector for constitutive expression, Chlr repAB17
    pETDuet-hpoBThe hpoB gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoBF and hpoBR, digested with NdeI and XhoI, and cloned into the corresponding sites of the pETDuet-1 vectorThis study
    pCDFDuet-hpoCThe hpoC gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoCF and hpoCR, digested with NcoI and HindIII, and cloned into the pCDFDuet-1 vector cut with NcoI and HindIIIThis study
    pET21-hpoDThe hpoD gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoDF2 and hpoDR, digested with NdeI and HindIII, and cloned into the corresponding sites of the pET21b vectorThis study
    pCDFDuet-hpoFThe hpoF gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoFF and hpoFR, digested with BglII and KpnI, and cloned into the corresponding sites of the pCDFDuet-1 vectorThis study
    pB/DThe hpoD gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoDF1 and hpoDR, digested with EcoRI and HindIII, and cloned into the corresponding sites of the pETDuet-hpoB plasmidThis study
    pF/CThe hpoC gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoCF and hpoCR, digested with NcoI and HindIII, and cloned into the corresponding sites of the pCDFDuet-hpoF plasmidThis study
    pET28-hpoIThe hpoI gene was amplified by PCR using genomic DNA of Rhodococcus rhodochrous PY11 and primers hpoIF and hpoIR, digested with NdeI and XhoI, and cloned into the corresponding sites of the pET28b vectorThis study
    pART2HpoEThe hpoE gene was amplified by PCR using plasmid pHpoBCDEFG and primers hpoEF and hpoER, digested with KpnI and XbaI, and cloned into the corresponding sites of the pART2 vectorThis study
    pNitHpoBCDThe hpoBCD genes were amplified by PCR using plasmid pHpoBCDEFG and primers hpoBF and hpoDR, digested with NdeI and HindIII, and cloned into the corresponding sites of the pNitQC1 vectorThis study
    pHpoBCDEFGA 5.2-kb Bsp1407I genomic DNA fragment containing the hpoB, hpoC, hpoD, hpoE, hpoF, and hpoG genes from Rhodococcus rhodochrous PY11 was inserted into the pART2 vector cut with Acc65IThis study
    pNitHpoHThe hpoH gene was amplified by PCR using genomic DNA of Rhodococcus rhodochrous PY11 and primers hpoHF and hpoHR, digested with NcoI and HindIII, and cloned into the corresponding sites of the pNitQC1 vectorThis study
Primers
    hpoBFGCACATATGAGCACATACGTCTGCAACThis study
    hpoBRCAGCTCGAGCTATGGCTGCGTGTTGThis study
    hpoCFCTACCATGGTGACCGCCACAGTGGATCThis study
    hpoCRCTAAAGCTTGGCATTGTTGGCTCGATTCThis study
    hpoDF1CTAGAATTCGATGCCTAAGCAGCTGThis study
    hpoDF2GCACATATGCCTAAGCAGCTGCThis study
    hpoDRCAGAAGCTTTCAGACATGAGCGGGAThis study
    hpoFFGACAGATCTCATGAGCACGATCGATGThis study
    hpoFRGACGGTACCTCAGATGTCGAGGATCAGThis study
    hpoIFCCTAGATCTCCATATGAGTAACCGGCTCGThis study
    hpoIRCATCTCGAGTCAGGCGACGCCGATCGThis study
    hpoEFCTCGGTACCCATGTCTGACGGCAAGGTCThis study
    hpoERGAGTCTAGATGTCACGAAGCCTCCGTCThis study
    hpoHFGTACCATGGGAACGGACCTGATCACCTCThis study
    hpoFRGATAAGCTTCCGATCACCGGTCCTCAGThis study
Primers for mRNA differential display
    RAN1CGGAGCAGAAGACATGAThis study
    RAN2CGGAGCAGAAGACATGCThis study
    RAN3CGGAGCAGAAGACATGGThis study
    RAN4CGGAGCAGAAGACATGTThis study
    RAN5CGGAGCAGAAGACAATGThis study
  • a MCSs, multiple-cloning sites.