TABLE 1.
Bacterial strains, plasmids, and primers used in this study
| Strain, plasmid, or oligonucleotide | Relevant features or sequence | Source or reference |
|---|---|---|
| Strains | ||
| E. coli | ||
| EPI300-T1R | F−mcrA Δ(mrr-hsdRMS-mcrBC) φ80dlacZΔM15 ΔlacX74 recA1 endA1 araD139 Δ(ara, leu)7697 galU galK λ−rpsL nupG trfA dhfr | Epicentre |
| EC100 pir+ | F−mcrA Δ(mrr-hsdRMS-mcrBC) φ80dlacZΔM15 ΔlacX74 recA1 endA1 araD139 Δ(ara, leu)7697 galU galK λ−rpsL nupG trfA dhfr | Epicentre |
| DH5α | F− φ80dlacZΔM15 endA41 recAl hsdR17(rK− mK−) supE44 thi-1 gyrA96 | BRL |
| BL21 | hsdS gal (λcIts857 ind1 Sam7 nin5 lacUV-T7 gene 1) | Novagen |
| P. carotovorum subsp. carotovorum | ||
| Pcc3 | Carocin D−, sensitive to carocin D, Rifr | 17 |
| Pcc21 | Carocin D+, Rifr | 17 |
| Pcc21DK1,2,6,7,9 | Pcc21; caroDK::Tn5, carocin D−, Rifr Kanr | This study |
| Plasmids | ||
| pBluescript II KS(+) | AmprlacZ, cloning vector | Stratagene |
| pGEM-T Easy | TA-cloning vector; Ampr | Promega |
| pLUG-multi | TA-cloning vector; Ampr | Intron |
| pGFPuv | Ampr, lac promoter | Clontech |
| pDSK519 | Cloning vector; Kanr | 8 |
| pCC1FOS | Fosmid vector; Chlr | Epicentre |
| pRF6-A4 | Fosmid library, pCC1FOS with 35-kb genomic DNA fragment | This study |
| pRB41 | pBluescript II KS(+) with ClaI/BamHI 4.1-kb fragment | This study |
| pRG3431 | pGEM-T Easy with 221 to ∼3,651 bp of ClaI/BamHI 4.1-kb fragment | This study |
| pRG2878 | pGEM-T Easy with 385 to ∼3,263 bp of ClaI/BamHI 4.1-kb fragment | This study |
| pRG2808 | pGEM-T Easy with 221 to ∼3,028 bp of ClaI/BamHI 4.1-kb fragment | This study |
| pRL1208 | pLUG-multi with 1,821 to ∼3,028 bp of ClaI/BamHI 4.1-kb fragment | This study |
| pRG369 | pGEM-T Easy with 2,895 to ∼3,262 bp of ClaI/BamHI 4.1-kb fragment | This study |
| pRP369 | pGFPuv with HindIII/EcoRI 0.4-kb fragment of pRG369 | This study |
| pRD2808 | pDSK519 with SalI/BamHI 2.9-kb fragment of pRG2808 | This study |
| Oligonucleotides | ||
| caro-F-1762 | 5′-GAA AAC GCA GGC GGA AAC AGG TC-3′ | This study |
| caro-F-1926 | 5′-TTT AGC CAG ATC AGA GAA GTC-3′ | This study |
| caro-F-3362 | 5′-TTG CCG AAG AAA AAG AGA TAA-3′ | This study |
| caro-F-4436 | 5′-AAC CGT TGT ACA CTG ATG CT-3′ | This study |
| caro-R-3263 | 5′-AGC GCG TAT TAA TTA AGA ACA CA-3′ | This study |
| caro-R-4569 | 5′-GCA AAA ACG GTA AGC ACA TCT-3′ | This study |
| caro-R-4803 | 5′-GCG CGT ATT AAT TAA GAA CAC A-3′ | This study |
| caro-R-5192 | 5′-CGG CGT CAG CGT GGT GGT ATC-3′ | This study |
| DK3751 | 5′-GTA GCG GGC AGT TAT GAC AAA AAT-3′ | This study |
| DK4121 | 5′-ATC GGA CCG CCT GCC TTA TC-3′ | This study |
| DI4578 | 5′-CAG ATT ATA AAC AAT TGG ATA GAC-3′ | This study |
| DI4723 | 5′-CAC CCA ATT AGT CCC TTT TAC-3′ | This study |
| DKI3744 | 5′-CAG AGG TGT AGC GGG CAG TTA TGA-3′ | This study |
| DKI4730 | 5′-GCC ACC CAA TTA GTC CCT TTT ACA-3′ | This study |