Table 2.
Strains, plasmids, and primers used in this study.
| Strain, plasmid or primer | Relevant characteristics | Source or reference |
|---|---|---|
| Strains | ||
| E. coli | ||
| Trans1 T1 | F−, φ80 (lacZ), ΔM15, ΔlacX74, hsdR (rK −, mK +), ΔrecA1398, endA1, tonA | Transgen |
| P. putida | ||
| KT2440 | Wild type | ATCC 47054 |
| KTU | upp-deficient KT2440 | This study |
| KTU-T1 | KT2440 mutant (Δupp, ΔalgA, dhaA90R +) | This study |
| KTU-T2 | KT2440 mutant (Δupp, ΔalgF&algJ, hheC +) | This study |
| KTU-T3 | KT2440 mutant (Δupp, ΔalgI, echA +) | This study |
| KTU-T12 | KT2440 mutant (Δupp, ΔalgA, ΔalgF&algJ, dhaA90R +, hheC +) | This study |
| KTU-T123 | KT2440 mutant (Δupp, ΔalgA, ΔalgF&algJ, ΔalgI, dhaA90R +, hheC +, echA +) | This study |
| KTU-TG | KT2440 mutant (Δupp, ΔalgA, ΔalgF&algJ, ΔalgI, ΔglpR, dhaA90R +, hheC +, echA +) | This study |
| KTU-TGV | KT2440 mutant (Δupp, ΔalgA, ΔalgF&algJ, ΔalgI, ΔglpR, Δfcs, dhaA90R +, hheC +, echA +, vgb +) | This study |
| KTU-TGF | KT2440 mutant (Δupp, ΔalgA, ΔalgF&algJ, ΔalgI, ΔglpR, Δflagellar operon, dhaA90R + , hheC + , echA +) | This study |
| KTU-TGVF | KT2440 mutant (Δupp, ΔalgA, ΔalgF&algJ, ΔalgI, ΔglpR, Δfcs, Δflagellar operon, dhaA90R + , hheC + , echA + , vgb +) | This study |
| Plasmids | ||
| pK18mobsacB | Kanr, suicide plasmid for gene knockout | 33 |
| pKU | Kanr, pK18mobsacB containing upp gene | This study |
| pKU-T1 | Kanr, pK18mobsacB containing upp and dhaA90R | This study |
| pKU-T2 | Kanr, pK18mobsacB containing upp and hheC | This study |
| pKU-T3 | Kanr, pK18mobsacB containing upp and echA | This study |
| pKU-G | Kanr, pK18mobsacB containing upp and ΔglpR | This study |
| pKU-V | Kanr, pK18mobsacB containing upp and vgb | This study |
| pKU-F | Kanr, pK18mobsacB containing upp and Δflagellar operon | This study |
| Primers | ||
| T1-1 | 5′-TTCTGGTGGTAGCGGTTCCCGTCTG-3' | This study |
| T1-2 | 5′-CTGCGCGATGGTCTTCACCGAAACG-3' | This study |
| T2-1 | 5′-GATGACCCTGCTCAACGGCAAGCTG-3' | This study |
| T2-2 | 5′-GGTCAGTTGCTGGTCGCTCAGGTTC-3' | This study |
| T3-1 | 5′-CCTGTTCCTGTTCTTGCCGATCTTC-3' | This study |
| T3-2 | 5′-CTGGAAGTAAAGGAACGGCGAGTAG-3' | This study |
| G-1 | 5′-CCCGAATTCCGAGTATTTCGCCAGCAAGG-3' | This study |
| G-2 | 5′-GCGGCATGCATGCCGGACAAATTCTGCAAT-3' | This study |
| G-3 | 5′-TTGTCCGGCATGCATGCCGCCAGACTTTTG-3' | This study |
| G-4 | 5′-CCCGAATTCAGGTGGTCGTAGAGGAACAG-3' | This study |
| V-1 | 5′-GCCCGGACACCACTTTCATC-3' | This study |
| V-2 | 5′-CTTGGGCATCGCGGTTCAAG-3' | This study |
| F-1 | 5′-AGACTTCCATTGCCAAAGCCCTCAC-3' | This study |
| F-2 | 5′-ACTGCGCGATGGTCTTCACCGAAAC-3' | This study |
| F-3 | 5′-AGACTTCCATTGCCAAAGCCCTCAC-3' | This study |
| F-4 | 5′-ACTGCGCGATGGTCTTCACCGAAAC-3' | This study |
| T1-F | 5′-CAGCTACCTGTGGCGCAACATCATC-3' | This study |
| T1-R | 5′-GTGCAGCCAGTTCATGTAGGCTTCC-3' | This study |
| T2-F | 5′-CACGACGAGAGCTTCAAGCAGAAGG-3' | This study |
| T2-R | 5′-AGAAGTACGGGCTGTCTTCGCTGTG-3' | This study |
| T3-F | 5′-CCTGAGCAAGTACAGCCTGGACAAG-3' | This study |
| T3-R | 5′-GTACTTCGGCACGAACTCGATCAGC-3' | This study |
| V-F | 5′-ATGTTAGACCAGCAAACCATTAACA-3' | This study |
| V-R | 5′-TTATTCAACCGCTTGAGCGTACAAA-3' | This study |