TABLE 1.
Bacterial strains, plasmids, and oligonucleotides used in this study
| Strain, plasmid, or oligonucleotide | Relevant phenotype or genotypea | Source or reference |
|---|---|---|
| Strains | ||
| Rhodococcus erythropolis | ||
| MI2 | Wild type, DTDB degrading | 17 |
| HK1 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK2 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK3 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK4 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK5 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK6 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK7 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| HK8 | Transposon-induced mutant of R. erythropolis MI2; no growth with DTDB as the sole carbon source | This study |
| MI2::noxΩtsr | No growth with DTDB as the sole carbon source | This study |
| PR4 | Wild type; degradation of polychlorinated biphenyls | NBRC100887 |
| IGTS8 | Wild type; desulfurization of fossil fuel and DBT | ATCC 53968 |
| Rhodococcus ruber | Wild type; PHA producer | NCIMB 20146 |
| Escherichia coli | ||
| TOP10 | F− mcrA Δ(mrr-hsdRMS-mcrBC) rpsL nupG ϕ80lacZΔM15 ΔlacX74 deoR recA1 araD139 Δ(ara-leu)7697 galU galK endA1 | Invitrogen, Carlsbad, CA |
| XL1-Blue | recA1 endA1 gyrA96 thi-1 hsdR17 (rK− mK+) supE44 relA1 λ− lac [F′ proAB lacIq lacZΔM15 Tn10 (Tcr)] | Stratagene, San Diego, CA |
| BL21(DE3)pLysS | F− ompT hsdSB(rB− mB−) gal dcm λ(DE3) pLysS(Cmr) | Novagen, Madison, WI |
| Plasmids | ||
| pTNR-TA | Apr Tsr | 9 |
| pJQ200mp18 | sacB oriV oriT traJ; Gmr | 77 |
| pJQ200mp18::noxΩtsr | pJQ200mp18 harboring the interrupted oxidoreductase gene | This study |
| pET23a(+) | pBR322 ori, f1 ori His6; Apr T7lac | Novagen, Madison, WI |
| pET23a(+)::nox | pET23a(+) harboring the oxidoreductase gene | This study |
| Primers | ||
| Walking IS1 | GGAAAAGGACTGCTGTCGCTGCC | MWG-Biotech AG |
| Sequencing IS1 | GCCGTAGACCTCGATGAACTCCAC | MWG-Biotech AG |
| Forward-nox-XbaI | AAAATCTAGAATGACCACAGCGCCCACAC | MWG-Biotech AG |
| Reverse-nox-XhoI | AAAACTCGAGTCACTGGCCGAGGCGC | MWG-Biotech AG |
| Forward-nox-NdeI | AAAACATATGACCACAGCGCCCACACC | MWG-Biotech AG |
| Forward-thio-BamHI | AAAAGGATCCATGAATGACTGAGTTGGAC | MWG-Biotech AG |
| Reverse-thio-BamHI | AAAAGGATCCTTATCGGTTGGCCGCGAG | MWG-Biotech AG |
a
Underlined letters in primer sequences indicate restriction sites.