Table 2.
Strains, plasmids, and primers
| Escherichia coli | Relevant characteristics | Source or reference |
|---|---|---|
| LSBJ | fadB::Cm, ΔfadJ, atoC512 (Const), fadR601 | Tappel et al. (2012a) |
| RSC02 | ΔarcA LSBJ | This study |
| RSC04 | ΔompR LSBJ | This study |
| RSC06 | ΔarcA, ΔompR LSBJ | This study |
| Plasmids | ||
| pKD46 | λ Red recombinase expression plasmid; expresses exo, β, and γ genes from λ phage; P-araB promoter; araC; AmpR; temperature sensitive replicon | Datsenko and Wanner (2000) |
| pKD13 | Neomycin phosphotransferase flanked by FLP recombinase recognition targets, AmpR, KmR | Datsenko and Wanner (2000) |
| pCP20 | FLP recombinase expression plasmid, AmpR, temperature sensitive replicon | Datsenko and Wanner ( 2000) |
| pBBR-C1J4SII | pBBR1MCS-2 derivative ΔphaAB, phaJ4, phaC1 (STQK) | Tappel et al. (2012b) |
| Primers a,b | Sequence (5′ to 3′) | |
| pKD13.F.arcA | ATGCAGACCCCGCACATTCTTATCGTTGAAGACGAGTTGGTAACACGCAAGTGTAGGCTGGAGCTGCTTC | |
| pKD13.R.arcA | TTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGATTCCGTGGATCCGTCGACC | |
| pKD13.F.ompR | ATGCAAGAGAACTACAAGATTCTGGTGGTCGATGACGACATGCGCCTGCGGTGTAGGCTGGAGCTGCTTC | |
| pKD13.R.ompR | TTAGAACATTACCTTATGACCGTACTGCTCAAGAATGCCTTTCACGCGTTATTCCGTGGATCCGTCGACC | |
| arcA.check.F/R | GTTAATTTGCAGCATGCATCAGG/GACGATGAGTTACGTATCTGG | |
| ompR.check.F/R | AAATTGTTGCGAACCTTTGG/GCAATAACGTACGGGCAAAT | |
| qAtoA.F/R | GGTGCAGCCATGTTTGATAG/CGCGAGGTTTGCTTCTTC | |
| qAtoD.F/R | ACTTGGCAACCTGACCTATC/GACCAGTTCATCTGGCTCTAC | |
| qAtoE.F/R | ACTCGGTATCGCTTACCTTG/GCAGACCCGCAATCATAAAC | |
| qFadD.F/R | TCTCCAGTCTGCATCTTTCC/CCATAGCCTTCCAGCAGATAC | |
| qFadE.F/R | TTACCCGTCTGGATGAACTG/GACGGCTTTCTTCAGCTTTC | |
| qFadL.F/R | GGGCGCTTCTATTACCTCTAA/TTTCAAGGTCGGTTGTACCC | |
| qRpoD.F/R | GAGCAAGGCTATCTGACCTATG/GCCCATGTCGTTGATCATTTG | |
aUnderlined sequences are homologous to the gene to be deleted
bForward and reverse primers are denoted with an F or R, respectively, and primers used for qPCR are denoted with a q