TABLE 1.
Bacterial strains and plasmids used in this study
| Strain or plasmid | Relevant characteristic(s) and/or plasmid constructiona | Source or reference |
|---|---|---|
| Strains | ||
| E. coli | ||
| DH5α | endA1 hsdR17 supE44 thi-1 recA1 gyrA96 (Nalr) relA1Δ(lacIZYA-argF)U169 deoR(φ80dlacZΔM15) | Clontech |
| S17-1 | hsdR17(rK− mK−) recA RP4-2 (Tcr::Mu-Kmr::Tn7 Strr) | 42 |
| JM109 | F′ [traD36 proAB+lacIqlacZΔM15]/recA1 supE44 endA1 hsdR17 gyrA96 relA1 thi-1 mcrA Δ(lac-proAB) | Promega |
| F. hibernum | ||
| W22 | Wild type | This study |
| W22 R1 | Rifampin-resistant mutant | This study |
| F. johnsoniae UW101 | ATCC 17061 | 1 |
| Plasmids | ||
| pGEM-T easy vector | Cloning vector, Apr | Promega |
| pKEN2 | gfpmut3, Apr | 11 |
| pMMB66EH | IncQ RSF1010Δ(PstI-PvuII, 2.87 kb) Ω [lacIqtacP rrnB] Apr | 13 |
| pMMB207 | IncQ RSF1010 derived, Cmr | 33 |
| pMMB503 | IncQ RSF1010 derived, Smr | 32 |
| pCP23 | ColE1 ori (pCP1 ori), E. coli-Flavobacterium shuttle plasmid, Apr (Tcr) | 1 |
| pCP29 | ColE1 ori, (pCP1 ori), E. coli-Flavobacterium shuttle plasmid, Apr (Cfxr, Emr) | 21 |
| pNJR5 | IncQ, E. coli-Bacteroides shuttle vector, Kmr (Emr) | 41 |
| pSCH01 | gfpmut3 gene inserted in BamHI and PstI sites in pMMB603EH, Apr | This study |
| pSCH02F | Expression cassettes including lacIq, ptac, and gfpmut3 fragment in pCP23 (ORF1, forward), Apr (Tcr) | This study |
| pSCH02R | Expression cassettes in pCP23 (ORF1, reverse), Apr (Tcr) | This study |
| pSCH03 | Promoterless gfpmut3 including E. coli RBS in pCP23, Apr (Tcr) | This study |
| pSCH41 | HU fragment trapped in pSCH03, Apr (Tcr) | This study |
| pSCH41.−210 | D1, 375-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| pSCH41.−100 | D2, 300-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| pSCH41.−52 | D3, 275-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| pSCH41.−23 | D4, 217-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| pSCH41.34 | D5, 98-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| pSCH41.67 | D6, 68-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| pSCH41.97 | D7, 36-bp fragment of HU fused to gfpmut3, Apr (Tcr) | This study |
| WT RBS | Wild-type RBS, Apr (Tcr) | This study |
| M1 | RBS mutant, TAATA→TCGTT, Apr (Tcr) | This study |
| M2 | RBS mutant, TAATA→TTGTT, Apr (Tcr) | This study |
| M3 | RBS mutant, TAATA→TATTA, Apr (Tcr) | This study |
| M4 | RBS mutant, TAATA→TTTTA, Apr (Tcr) | This study |
| M5 | RBS mutant, TAATA→TTTTT, Apr (Tcr) | This study |
| M6 | RBS mutant, TAATA→TGATA, Apr (Tcr) | This study |
| M7 | RBS mutant, TAATA→TAATG, Apr (Tcr) | This study |
| M8 | RBS mutant, TAATA→TAAAA, Apr (Tcr) | This study |
| M9 | RBS mutant, TAATA→TAGTA, Apr (Tcr) | This study |
a
Antibiotic resistance phenotype: Apr, ampicillin; Tcr, tetracycline; Emr, erythromycin; Cfxr, cefoxitin; Cmr, chloramphenicol; Kmr, kanamycin; and Smr, streptomycin. Unless indicated otherwise, antibiotic resistance phenotypes are those expressed in E. coli. Antibiotic resistance phenotypes listed in parentheses are those expressed in Flavobacterium strains but not in E. coli.