| Strains |
|
|
|
E. coli
|
|
|
| DH5α |
supE44 ΔlacU169 (Φ80 lacZΔM15) recA1 endA1 hsdR17 thi-1 gyrA96 relA1
|
Invitrogen |
| HB101 |
subE44 subF58 hsdS3 (rB- mB-) recA13 ara-14 proA2 lacY1 galK2 rpsL20
|
[53] |
|
xyl-5 mtl-1
|
|
| CC118 λpir |
Δ(ara-leu) araD ΔlacX74 galE galK phoA20 thi-1 rpsE rpoB argE (Am)
|
[52] |
|
recA1 λpir phage lysogen
|
|
| BL21(DE3)pLysS |
F- ompT gal dcm lon hsdSB(rB- mB-) λ(DE3) pLysS(cmR)
|
Invitrogen |
| AB1157 |
thr-1, araC14, leuB6(Am), Δ(gpt-proA)62, lacY1, tsx-33, qsr’-0, glnV44(AS)
|
[71] |
|
galK2(Oc), LAM-, Rac-0, hisG4(Oc), rfbC1, mgl-51, rpoS396(Am) rpsL31(strR),
|
|
|
kdgK51, xylA5, mtl-1, argE3(Oc), thi-1
|
|
| AB1157alkA |
As AB1157 but ∆alkA::km
|
This study |
| DM12 |
As AB1157 but ∆alkB::km
|
[23] |
| AB1157ada |
As AB1157 but ada10::Tn10 ; constructed by P1 phage transduction |
This study |
| BS87 |
As AB1157 but ∆alkB::ap
|
[72] |
| BS87alkA |
BS87 but ∆alkA::km; constructed by P1 phage transduction |
This study |
| AB1157alkAada |
As AB1157 but ∆alkA::km; ada10::Tn10
|
This study |
| AB1157alkBada |
As AB1157 but ∆alkB::km; ada10::Tn10
|
This study |
| BS87alkAada |
As BS87 but ∆alkA::km; ada10::Tn10
|
This study |
| UC978 |
araD8l Δ(uvrB-bio) ∆ogt1::km ada10::Tn10; used as a donor of ada10::Tn10
|
[73] |
|
P. putida
|
|
|
| PaW85 |
Wild-type, isogenic to KT2440 |
[55,56] |
| PaWAlkB |
PaW85, ∆alkB::gm
|
This study |
| PaWAda |
PaW85, Δada::km
|
This study |
| PaWAlkA |
PaW85, ∆alkA
|
This study |
| PaWAdaAlkB |
PaW85, Δada::km; ΔalkB::gm
|
This study |
| PaWAlkAAlkB |
PaW85, ∆alkA; ΔalkB::gm
|
This study |
| PaWAlkAAda |
PaW85, ∆alkA; ∆ada::km
|
This study |
| PaWAlkAAdaAlkB |
PaW85, ΔalkA; ∆ada::km; ΔalkB::gm
|
This study |
| Plasmids |
|
|
| pBluescript KS (+) |
Cloning vector (Apr) |
Stratagene |
| pUTmini-Tn5 Km2 |
Delivery plasmid for mini-Tn5 Km2 (Apr Kmr) |
[59] |
| pBK-miniTn7-ΩGm |
pUC19-based delivery plasmid for miniTn7-ΩGm (Gmr, Apr) |
[58] |
| pGP704 L |
Delivery plasmid for homologous recombination (Apr) |
[57] |
| pRK2013 |
Helper plasmid for conjugal transfer of pGP704 L (Kmr) |
[54] |
| pEMG |
Cloning vector (Kmr), oriR6K, lacZα with two flanking I-SceI sites |
[61] |
| pSW (I-SceI) |
The I-SceI-expression plasmid (Apr) |
[62] |
| pKSalkB |
pBluescript KS (+) containing the PCR-amplified sequence of the alkB gene |
This study |
|
in SacI and Acc65I restriction sites |
|
| pKSΔalkB::gm |
alkB in pKSalkB is interrupted with the Gmr gene from pBK-miniTn7-ΩGm |
This study |
|
by replacing SacII and HindIII-generated fragment from alkB by the Gmr gene |
|
| pGP704ΔalkB::gm |
pGP704 L with SacI-Acc65I fragment of ΔalkB::gm from pKS∆alkB::gm |
This study |
|
in vector plasmid opened with the same restrictases |
|
| pKSada |
pBluescript KS(+) containing the PCR-amplified sequence of the ada gene in SacI |
This study |
|
and XbaI restriction sites |
|
| pKSΔada::km |
ada in pKSada is interrupted with the Kmr gene from pUTmini-Tn5 Km2 by |
This study |
|
replacing Cfr42I and NcoI-generated fragment from ada by the Kmr gene |
|
| pGP704Δada::km |
pGP704 L with SacI-XbaI fragment of Δada::km from pKSΔada::km in vector |
This study |
|
plasmid opened with the same restrictases |
|
| pEMGalkA |
pEMG containing PCR-amplified sequence of alkA in SacI and XbaI sites |
This study |
| pVB1x |
A low copy number vector (~6 copies/cell) with a toluic acid inducible |
Vectron Biosolutions |
|
promoter (Apr) |
|
| pVB1x:EcalkB
|
As pVB1x but expressing EcalkB |
This study |
| pVB1x:PpalkB
|
As pVB1x but expressing PpalkB |
This study |
| pET28a(+) |
Expression vector (Kmr) |
Invitrogen |
| pET28a::PpalkB
|
As pET28a(+) but expressing PpalkB |
This study |
| pPROBE-NT |
Promoterless vector with gfp reporter (Kmr) |
[63] |
| pPROBE-AT |
Promoterless vector with gfp reporter (Apr) |
[63] |
| pPROBE-NT:alkAp
|
As pPROBE-NT with P. putida alkA promoter (-100, -1) |
This study |
| pPROBE-NT:alkBp
|
As pPROBE-NT with P. putida alkB promoter (-100, -1) |
This study |
| pPROBE-NT:alkBpΔ(-68,-18) |
As pPROBE-NT with P. putida alkB promoter (-100, -1) |
This study |
|
with deletion of (-68,-18) nucleotides |
|
| pPROBE-NT:adap
|
As pPROBE-NT with P. putida ada promoter (-100, -1) |
This study |
| pPROBE-NT:Ecadap
|
As pPROBE-NT with E. coli ada promoter (-100, -1) |
This study |
| pPROBE-AT:alkAp
|
As pPROBE-AT with P. putida alkA promoter (-100, -1) |
This study |
| pPROBE-AT:alkBp
|
As pPROBE-AT with P. putida alkB promoter (-100, -1) |
This study |
| pPROBE-KT:kanp |
As pPROBE-KT but with kanamycin resistance gene promoter |
Prof. S. E. Lindow |
|
|
Berkeley, California |
