Table 3 Plasmids and strains used in this study
Strains and plasmids | Description | References |
|---|---|---|
Plasmids | Â | Â |
pSEVA211 | KmR, ori R6K, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA221 | KmR, ori RK2, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA231 | KmR, ori pBBR1, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA241 | KmR, ori pRO1600/ColE1, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA251 | KmR, ori RFS1010, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA261 | KmR, ori p15A, standard multiple cloning site | |
pSEVA271 | KmR, ori pSC101, standard multiple cloning site | |
pSEVA281 | KmR, ori pUC, standard multiple cloning site | |
pSEVA291 | KmR, ori pBR322/ROP, standard multiple cloning site | |
pSEVA121 | Apr, ori RK2, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA321 | CmR, ori RK2, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA421 | Sm/SpR, ori RK2, standard multiple cloning site | Lorenzo et al. [26] |
pSEVA521 | TcR, ori RK2, standard multiple cloning site | Lorenzo et al. [26] |
pRK600 | CmR, ori ColE1, tra + mob + of RK2 | Boyer et al. [77] |
pEMG | KmR, oriR6K, lacZα with two flanking I-SceI sites | Lorenzo et al. [56] |
pSW2 | GmR, oriRK2, xylS, Pm → I sceI (transcriptional fusion of I-sceI to Pm) | Yang et al. [78] |
pBG14b FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14b, msfGFP | Zobel et al. [51] |
pBG14b FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14c, msfGFP | Zobel et al. [51] |
pBG14c FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14d, msfGFP | Zobel et al. [51] |
pBG14d FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14d, msfGFP | Zobel et al. [51] |
pBG14e FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14e, msfGFP | Zobel et al. [51] |
pBG14f FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14g, msfGFP | Zobel et al. [51] |
pBG14g FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter 14g, msfGFP | Zobel et al. [51] |
pBG13 FRT Kan | KmR, GmR, oriR6K, pBG-derived, promoter Pem7, msfGFP | Zobel et al. [51] |
pBG_pcaRtphA2A3BA1pcaK | KmR, oriR6K, pBG-derived, tph operon | Nugraha et al. [58] |
p∆PHB | KmR, oriR6K, carrying TS1 and TS2 elements each 1000 bp upstream and downstream respectively of PHB cassette in P. pantotrophus DSM 2944 | This study |
Strains | Â | Â |
Escherichia coli | Â | Â |
DH5α | supE44, 1lacU169 (Φ80lacZ1M15), hsdR17 (rK − mK +), recA1, endA1, thi-1, gyrA96, relA1 | Hanahan et al. [79] |
Top10 | mcrA, Δ(mrr-hsdRMS-mcrBC), Phi80lacZ(del)M15, ΔlacX74, deoR, recA1, araD139, Δ(ara-leu)7697, galU, galK, rpsL(SmR), endA1, nupG | Invitrogen |
CC118 | F- LAM- araD139 DE(ara leu)7697 DE(lacX74) phoA20(del) galE galK thi rpsE rpoB argE(Am) recA1 | Invitrogen |
DH5αλpir | endA1 hsdR17 glnV44 (supE44) thi-1 recA1 gyrA96 relA1 φ80dlacΔ(lacZ)M15 Δ(lacZYA-argF)U169 zdg-232::Tn10 uidA::pir +  | Platt et al. [80] |
HB101 | F − mcrB mrr hsdS20(rB − mB −) recA13 leuB6 ara-14 proA2 lacY1 galK2 xyl-5 mtl-1 rpsL20(SmR) gln V44 λ −  | Hanahan et al. [79] |
pTnS-1 | ApR, ori R6K, TnSABC + D operon | Choi et al. [81] |
PIR2 | F- Δlac169 rpoS (Am) robA1 creC510 hsdR514 endA reacA1 uidA (ΔMLui)::pir | Choi et al. [81] |
pSW1 | psw-1: ApR, oriRK2, xylS, Pm → I-sceI (transcriptional fusion of I-sceI to Pm) | Life Technologies |
Pseudomonas putida KT2440 | Â | Â |
WT | Wild type | Nelson et al. [82] |
BG14b FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG14b FRT Kan | Köbbing et al. [48] |
BG14c FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG14c FRT Kan | Köbbing et al. [48] |
BG14d FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG14d FRT Kan | Köbbing et al. [48] |
BG14e FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG14e FRT Kan | Köbbing et al. [48] |
BG14f FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG14f FRT Kan | Köbbing et al. [48] |
BG14g FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG14g FRT Kan | Köbbing et al. [48] |
BG13 FRT Kan | KmR with FRT flanking sequences, P. putida KT2440 with genomic insertion of pBG13 FRT Kan | Köbbing et al. [48] |
Paracoccus pantotrophus DSM 2944 | Â | Â |
WT | Wild type | Bockwoldt et al. [24] |
∆PHB | P. pantotrophus strain with the entire polyhydroxyalkanoate cassette deleted, unable to produce PHB | This study |
tph | P. pantotrophus strain with the tph operon integrated at the attn7 site | This study |
TA static tph | P. pantotrophus strain with the tph operon evolved in terephthalic acid | This study |
dynamic tph | P. pantotrophus strain with the tph operon evolved in alternating carbon sources of ethylene glycol and terephthalic acid | This study |
tph EG static | P. pantotrophus strain with the tph operon evolved in ethylene glycol | This study |