Table 1. Bacterial strains and plasmids used in this study.
| Strain or plasmid | Relevant genotype | Source or reference |
|---|---|---|
| Bacterial strains | ||
| Escherichia coli | ||
| DH5α λpir | Φ80dlacZΔM15 Δ(lacZYA-argF) U196 recA1 hsdR17 deoR thi-l supE44 gyrA96 relA1/ëpir | Miller and Mekalanos (1988) |
| WM3064 | ThrB1004 pro thi rpsL hsdS lacZΔM15 RP4-1360 Δ(araBAD)567 ΔdapA1341::[erm pir(wt)] | W Metacalf, University of Illinois, Urbana |
| Shewanella oneidensis | ||
| MR-1 | Shewanella oneidensis MR-1 wild type | Venkateswaran et al. (1999) |
| S198 | MR-1, tagged with eGfp in a mini-Tn7 construct, Cmr | This work |
| S176 | MR-1, tagged with Cfp in a mini-Tn7 construct, Cmr | This work |
| S199 | MR-1, tagged with Yfp in a mini-Tn7 construct, Cmr | This work |
| S1407 | MR-1 ΔMuSo1, deletion of gene cluster SO0641–SO0685 | This work |
| S1412 | MR-1 ΔMuSo1, tagged with eGfp in a mini-Tn7 construct, Cmr | This work |
| S1381 | MR-1 ΔMuSo2, deletion of gene cluster SO2651–SO2704 | This work |
| S1392 | MR-1 ΔMuSo2, tagged with eGfp in a mini-Tn7 construct, Cmr | This work |
| S1387 | MR-1 ΔLambdaSo, deletion of gene cluster SO2939–SO3013 | This work |
| S1393 | MR-1 ΔLambdaSo, tagged with eGfp in a mini-Tn7 construct, Cmr | This work |
| S1421 | MR-1 ΔLambdaSo ΔMuSo1 | This work |
| S1426 | MR-1 ΔLambdaSo ΔMuSo2 | This work |
| S1422 | MR-1 ΔMuSo1 ΔMuSo2 | This work |
| S1419 | MR-1 ΔLambdaSo ΔMuSo2 ΔMuSo1 | This work |
| S1461 | MR-1 ΔlambdaSo ΔMuSo2 ΔMuSo1, tagged with eGfp in a mini-Tn7 construct, Cmr | This work |
| Plasmids | ||
| pNTPS-138-R6K | Ori-R6K sacB, suicide plasmid for generating in-frame deletions, Kmr | Lassak et al. (2010) |
| pNTPS-R6K-dMu1 | Fragment for in-frame deletion of the gene region SO0641–SO0685 in pNTPS-R6K | This work |
| pNTPS-R6K-dMu2 | Fragment for in-frame deletion of the gene region SO2651–SO2704 in pNTPS-R6K | This work |
| pNTPS-R6K-dlambda | Fragment for in-frame deletion of the gene region SO2939–SO3013 in pNTPS-R6K | This work |
| pME6031 | repA oriVpVS1 oriVp15A oriT, Tcr, broad-host-range plasmid | Heeb et al. (2000) |
| pME6031-Pmot-lacZ | motAB promoter fused to lacZ, Tcr | This work |
| pUC18-R6KT-miniTn7T | ori-R6K, Tn7 recognition sites, Apr | Choi et al. (2005) |
| pTNS2 | ori-R6K; encodes the TnsABC+D specific transposition pathway, Apr | Choi et al. (2005) |
| pBK-miniTn7-gfp3 | ori-ColE1, gfp3, Apr, Cmr, Gmr | Lambertsen et al. (2005) |
| miniTn7(Gm)PA1/04//03-eyfp-a | ori-ColE1, eyfp, Apr, Cmr, Gmr | Lambertsen et al. (2005) |
| miniTn7(Gm)PA1/04//03-ecfp-a | ori-ColE1, ecfp, Apr, Cmr, Gmr | Lambertsen et al. (2005) |
| pUC18-R6KT-miniTn7T-egfp | NotI-egfp-Cmr-NotI fragment from pBK-miniTn7-gfp3 in pUC18-R6KT-miniTn7T | This work |
| pUC18-R6KT-miniTn7T-ecfp | NotI-ecfp-Cmr-NotI fragment from miniTn7(Gm)PA1/04//03-ecfp-a in pUC18-R6KT-miniTn7T | This work |
| pUC18-R6KT-miniTn7T-eyfp | NotI-eyfp-Cmr-NotI fragment from miniTn7(Gm)PA1/04//03-eyfp-a in pUC18-R6KT-miniTn7T | This work |
| pASK-IBA3plus | expression vector, Apr, Strep-TagII epitope | IBA GmbH, Göttingen, Germany |
| pASK-SO_2963 | SO_2963 in pASK-IBA3plus | This work |
| pASK-SO_2685 | SO_2685 in pASK-IBA3plus | This work |
Apr, ampicillin resistance; Cmr, chloramphenicol resistance; Gmr, gentamicin resistance; Tcr, tetracyclin resistance.