TABLE 1.
Bacterial strains and plasmids
| Strain or plasmid | Relevant characteristics | Genotype | Reference or source |
|---|---|---|---|
| E. coli DH5α | F−φ80dlacZΔM15 Δ(lacZYA-argF)U169 deoR recA1 endA1 hsdR17 (rK− mK−) supE44 λ−thi-1 gyrA96 relA1 | Invitrogen | |
| Acinetobacter sp. strains | |||
| ADP1 | Wild-type strain (also known as BD413) | 29 | |
| ADP992 | 90-bp deletion in pobA; block in p-hydroxybenzoate hydroxylase | ΔpobA992 | D. A. D'Argenio, unpublished data |
| ADP1027 | 100-bp deletion in hcaC; block in hydroxycinnamate: CoASH ligase | ΔhcaC1 | 55 |
| ADP8010 | 25.8-kb NdeI deletion from pZR8033 with endpoints in a dca intergenic region (between dcaECHF and dcaAKIJPQ) and the pobS gene; genes deleted include those required for dicarboxylate, protocatechuate, and quinate catabolism | Δ(dca-quiA)1 | This study |
| ADP8078 | Kmr; Δ (hcaR orf1)::sacB-Kmr from pZR8231 introduced into the ADP1 chromosome | Δ(hcaR-orf1)::sacB-Kmr | This study |
| ADP8079 | Kmr; Δ(hcaKAB)::sacB-Kmr from pZR8227 introduced into the ADP1 chromosome | Δ(hcaKAB)1::sacB-Kmr | This study |
| ADP8081 | Kmr; ΔhcaB1::lacZ-Kmr from pZR8238 in the chromosome of ADP1 | ΔhcaB1::lacZ-Kmr | This study |
| ADP8083 | 217-bp HincII deletion in hcaR from pZR8233 in the ADP8078 chromosome | ΔhcaR1 | This study |
| ADP8084 | 600-bp EcoRI deletion in hcaB from pZR8215 in the chromosome of ADP8079 | ΔhcaB3 | This study |
| ADP8085 | 163-bp HpaI deletion in hcaA from pZR8216 in the chromosome of ADP8079 | ΔhcaA1 | This study |
| ADP8088 | Kmr; Δ(hcaR-orf1)::sacB-Kmr from pZR8231 in the chromosome of ADP8083 | ΔhcaR1 ΔhcaB1::lacZ-Kmr | This study |
| ADP8101 | Kmr; Δ(hcaRorf1)::sacB-Kmr from pZR8246 in the chromosome of ADP1027 | ΔhcaC1 Δ(hcaR-orf1)::sacB-Kmr | This study |
| ADP8102 | Kmr; hcaK::sacB-Kmr from pZR8246 in ADPI background | hcaK1::sac-Kmr | This study |
| ADP8110 | Kmr; hcaE::lacZ-Kmr from pZR8264 in the chromosome of ADP1 | hcaE1::lacZ-Kmr | This study |
| ADP8113 | Kmr; hcaE::lacZ-Kmr from pZR8264 in the chromosome of ADP1027 | ΔhcaC1 hcaE1::lacZ-Kmr | This study |
| ADP8114 | Kmr; hcaE::lacZ-Kmr from pZR8264 in the chromosome of ADP8085 | ΔhcaA1 hcaE1::lacZ-Kmr | This study |
| ADP8116 | Kmr; hcaE::lacZ-Kmr from pZR8264 in the chromosome of ADP8084 | ΔhcaB3 hcaE1::lacZ-Kmr | This study |
| ADP8117 | Kmr; hcaE::lacZ-Kmr from pZR8264 in the chromosome of ADP8083 | ΔhcaR1 hcaE1::lacZ-Kmr | This study |
| ADP8119 | Kmr; ΔhcaK from pZR8271 in the chromosome of ADP8102 | ΔhcaK3 | This study |
| ADP8121 | ΔhcaR1 from pZR8233 in the chromosome of ADP8101 | ΔhcaC1 ΔhcaR1 | This study |
| ADP8135 | Δ(hcaRKABCDEFG) from pZR8207 in the chromosome of ADP8102; hydroxycinnamate negative | Δ(hcaRKABCDEFG)1 | This study |
| ADP8136 | Kmr; hcaE::lacZ-Kmr from pZR8264 in the chromosome of ADP8121 | ΔhcaC1 ΔhcaR1 hcaE1::lacZ-Kmr | This study |
| Plasmids | |||
| pBKS | Apr; narrow host range cloning vector | Stratagene | |
| pBKSΔ1 | Ap; pBKS which is ΔSmaI-HincII | This study | |
| pKOK6 | Apr Kmr Tcr; contains 4.6-kb promoterless lacZ-Kmr cassette for constructing operon fusions | 31 | |
| pRMJ1 | Apr Kmr; contains sacB-Kmr cassette for genetic replacement by positive selection | 27 | |
| pRK415 | Tcr; broad-host-range vector | 30 | |
| pUC4K | Apr Kmr; contains antibiotic resistance cassette | Amersham Pharmacia Biotech | |
| pUC18 and pUC19 | Apr; narrow-host-range cloning vectors | 61 | |
| pZR8000 | Chlr; 34.8-kb Acinetobacter sp. strain ADP1 SacI insert in pBBR1MCS containing dca, pca, qui, and pob genes | 45 | |
| pZR8033 | Chlr; 25.8-kb NdeI deletion in pZR8000 | This study | |
| pZR8038 | Apr; 8.9-kb HindIII-SacII insert of dca genes from pZR8000 in pUC19 | 45 | |
| pZR8200 | Apr; 16.5-kb HindIII-XbaI insert of DNA from strain ADP8010::pZR8038, which encompasses 1-kb of dca DNA, the pob and hca genes; in pUC19 | This study | |
| pZR8203 | Apr; pZR8203 with a mutation introduced at the unique XcmI site in hcaB | This study | |
| pZR8207 | ΔhcaRKABCDEFG of pZR8200 created by exonuclease activity of Klenow fragment | This study | |
| pZR8210 | Apr; 6.5-kb SacI insert with hca genes from pZR8200 in pBKSΔ1 | This study | |
| pZR8215 | Apr; 600-bp EcoRI deletion of hcaB in pZR8210 | This study | |
| pZR8216 | Apr; 163-bp HpaI deletion of hcaA in pZR8210 | This study | |
| pZR8219 | Apr; 1.66-kb SacI subclone of pZR8200 in pBKSΔ1 | This study/PICK> | |
| pZR8220 | Apr; 2.4-kb PstI deletion from hcaB to hcaK in pZR8210 | This study | |
| pZR8224 | Apr; 1.6-kb SacI subclone of pZR8200 containing hcaR and ORF1 in pBKSΔ1 | This study | |
| pZR8227 | Apr; Kmr; sacB-Kmr cassette of pRMJ1 inserted at the site of the PstI deletion in pZR8220 | This study | |
| pZR8231 | Apr; sacB-Kmr cassette of pRMJ1 inserted at the site of a 0.63-kb BglII deletion in pZR8224 | This study | |
| pZR8233 | Apr; 217-bp HincII deletion within hcaR in pZR8224 | This study | |
| pZR8238 | TcrKmr; lacZ-Kmr cassette from pKOK6 in the ΔBglII site of hcaB in pZR8223; lacZ expression is in the same direction as that of hcaB | This study | |
| pZR8239 | Tcr; 1.2-kb HindIII-SacI insert of hcaK′ in pRK415 | This study | |
| pZR8240 | Tcr; 3.3-kb SacI-BglII insert of hcaC plus the 3′ part of hcaB | This study | |
| pZR8246 | Tcr Kmr; pRMJ1 sacB-Kmr cassette in PstI site of hcaK in pZR8239 | This study | |
| pZR8247 | Apr; 2.1-kb KpnI-BglII subclone of pZR8240 in pUC18 | This study | |
| pZR8248 | Apr; 0.95-kb HindIII-BglII subclone of pZR8240 which includes 268 bp of hcaC and part of hcaB in pUC18 | This study | |
| pZR8264 | Apr Kmr; lacZ-Kmr cassette from pKOK6 in the SalI site of hcaE in pZR8219; lacZ expression is in the same direction as that of hcaE | This study | |
| pZR8265 | Apr; 1.2-kb HindIII-SacI insert of pZR8239 in pUC18 | This study | |
| pZR8271 | Apr; 775-bp BsrGI deletion within hcaK in pZR8265 | This study |