TABLE 1.
Bacterial strains, phage, and plasmids used in this study
| Strain, phage, or plasmid | Relevant characteristicsa | Reference(s) or source |
|---|---|---|
| Strains | ||
| M. vanbaalenii PYR-1 | Mineralizes PAHs, such as fluoranthene, pyrene, and phenanthrene | 21, 29 |
| E. coli XL1-Blue MRF′ | Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 endA1 supE44 thi-1 recA1 gyrA96 relA1 lac [F′ proAB lacIqZΔM15 Tn10 (Tetr)] | Stratagene |
| E. coli XLOLR | Δ(mcrA)183 Δ(mcrCB-hsdSMR-mrr)173 endA1 thi-1 recA1 gyrA96 lac [F′ proAB lacIqZΔM15 Tn10 (Tetr)] Su (nonsuppressing) λR | Stratagene |
| E. coli DH5α | F− Φ80dlacZΔM15 Δ(lacZYA-argF) U169 deoR recA1 endA1 hsdR17 (rK− mK+) phoA supE44 λ−thi-1 gyrA96 relA1 | 17 |
| E. coli TOP10 | F−mcrA Δ(mrr-hsdRMS-mcrBC) υ80lacZΔM15 ΔlacX74 recA1 araD139 galU galK Δ(ara-leu)7697 rpsL (StrR) endA1 nupG | Invitrogen |
| E. coli BL21(DE3) | F−ompT hsdSB (rB− mB−) gal dcm (DE3) | Novagen |
| ExAssist helper phage | For in vivo excision of the pBK-CMV phagemid from ZAP Express vector with E. coli XLOLR | Stratagene |
| Plasmids | ||
| pGEM-T Easy | Apr, TA cloning vector | Promega |
| pCR2.1-TOPO | Apr, TA cloning vector | Invitrogen |
| pET-17b | Expression vector; Apr T7 promoter | 38 |
| pBRCD | Gmr, pBBR1MCS-5 containing phdCD | 60 |
| pNCK30 | pGEM-T Easy with a 109-bp PCR fragment | This study |
| pNCK31 | 3.7-kb BamHI fragment including nidA3B3 genes of M. vanbaalenii PYR-1 cloned into pBK-CMV phagemid | This study |
| pNCK32 | 1.87-kb PCR fragment including nidA3B3 genes from pNCK31 cloned into pCR2.1-TOPO | This study |
| pNCK33 | 1.87-kb NdeI-HindIII fragment from pNCK32 cloned into NdeI-HindIII of pET-17b | This study |
a
Apr, ampicillin resistance; Gmr, gentamicin resistance.