Table 1.
Plasmids, bacteriophage and strains
| Strain or Plasmid | Relevant genotype | Use | Source or reference |
|---|---|---|---|
| E. coli | |||
| DBH13 | HB101 [F− leu − pro −]; StrR | ‘Mating out’ recipient | [36] |
| ER2507 | zjc::Tn5; KanR | Source of zjc::Tn5 | NEB |
| DBH179 | NK5830 [recA − arg −/F’ lacpro +] zjc::Tn5; KanR | ‘Mating out’ donor | This study |
| DBH184 | DBH179 hfq-1::Ωcat; KanRCmR | ‘Mating out’ donor | This study |
| DBH228 | RZ211/pOX38Gen | Source of pOX38Gen | [37] |
| DBH233 | HW-5 [phoA4(Am) his-45 recA1 rpsL99 met-54 F−]; StrR | Parent strain | [38] |
| DBH259 | DBH233/pOX38Gen; StrRGenR | Parent strain | This study |
| DBH261 | DBH259 zjc::Tn5; StrRGenRKanR | ‘Mating out’ donor | This study |
| DBH271 | DBH261 hfq-1::Ωcat; StrRGenRKanRCmR | ‘Mating out’ donor | This study |
| DBH272 | DBH261 dam::Tn9cat; StrRGenRKanRCmR | ‘Mating out’ donor | This study |
| DBH107 | MC4100 [F− Δ(argF-lac)169* rpsL150]; StrR | Parent strain | [39] |
| DBH265 | DBH107/λDBH849; StrRKanR | Miller Assay | This study |
| DBH267 | DBH265 hfq-1::Ωcat; StrRCmRKanR | Miller Assay | This study |
| DBH268 | DBH265 dam::Tn9cat; StrRCmRKanR | Miller Assay | This study |
| DBH281 | DBH107/λDBH812; StrRKanR | Miller Assay | This study |
| DBH283 | DBH281 hfq-1::Ωcat; StrRCmRKanR | Miller Assay | This study |
| DBH285 | DBH281 dam::Tn9cat; StrRCmRKanR | Miller Assay | This study |
| DBH303 | DBH107/λDBH888; StrRCmR | Miller Assay | This study |
| DBH306 | DBH303 Δhfq722::kan; StrRCmRKanR | Miller Assay | This study |
| DBH307 | DBH303 Δcrp765::kan; StrRCmRKanR | Miller Assay | This study |
| DBH315 | DBH303 Δlrp787::kan; StrRCmRKanR | Miller Assay | This study |
| DBH33 | NK5830 [recA − arg −/F’ lacpro +] | Parent strain | [40] |
| DBH16 | DBH33 hfq-1::Ωcat; CmR | Parent strain | [7] |
| DBH241 | DBH33 dam::Tn9cat; CmR | Parent strain | This study |
| DBH238 | DBH33/λDBH849; KanR | Miller Assay | This study |
| DBH239 | DBH238 hfq-1::Ωcat; KanRCmR | Miller Assay | This study |
| DBH240 | DBH238 dam::Tn9cat; KanRCmR | Miller Assay | This study |
| DBH208 | DBH33/λDBH812; KanR | Miller Assay | This study |
| DBH210 | DBH208 hfq-1::Ωcat; KanRCmR | Miller Assay | This study |
| DBH237 | DBH208 dam::Tn9cat; KanRCmR | Miller Assay | This study |
| DBH323 | DBH107 recA −; StrR | Miller Assay | This study |
| DBH326 | DBH107 recA − hfq-1::Ωcat; StrRCmR | Miller Assay | This study |
| DBH242 | DBH33 Δcrp765::kan | Parent strain | This study |
| DBH344 | DBH242 Δcrp765; KanS | Parent strain | This study |
| DBH345 | DBH344 zjc::Tn5; Kan R | ‘Mating out’ donor | This study |
| TM338 | W3110mlc rne-Flag-cat; rifSCmR | RNA half-life measurements | [41] |
| TM618 | W3110mlc rne-Flag-cat Δhfq; rifSCmR | RNA half-life measurements | [42] |
| DH5α | recA − | Plasmid propagation | Invitrogen |
| Plasmids | |||
| pWKS30 | pSC101-derived; low copy-number ori ; ApR | ‘Empty vector’ for Hfq expression | [35] |
| pDH700 | pWKS30-P3-hfq WT; ApR | HfqWT expression | [7] |
| pDH701 | pWKS30-P3-hfq K56A; ApR | HfqK56A expression | [7] |
| pDH713 | pWKS30-P3-hfq Y25A; ApR | HfqY25A expression | [8] |
| pDH533 | pUC18-derivative; Tn5 t’ase M56A; ApRCmR | Source of Tn5 transposase (No Inh.) | [43] |
| pDH752 | pDH533 with t’ase mutated to G53A,C61A; ApRCmR | DAM-insensitive t’ase | This study |
| pDH828 | pDH533 with t’ase mutated to D97A; ApRCmR | Catalytic− t’ase | This study |
| pNK81 | pBR333-derivative; encodes his operon; ApR | Lambda crosses | [44] |
| pDH682 | pUC18-derivative; IS50-lacZ TCF; ApR | Source of TCF | This study |
| pDH838 | pDH682-derivative; TCF ‘marked’ with kanR | Parent of pDH849 | This study |
| pDH883 | pDH682-derivative; TCF ‘marked’ with cmR | Parent of pDH888 | This study |
| pDH849 | TCF-kanR from pDH682 cloned into BclI-cut pNK81; ApRKanR | For crossing TCF onto λ | This study |
| pDH888 | TCF-cmR cloned onto BclI-cut pNK81; ApRCmR | For crossing TCF onto λ | This study |
| pDH658 | pRZ9905-derivative; full-length IS50-lacZ TLF; ApR | Parent of pDH795 | This study |
| pDH795 | pDH658-derivative; ‘deletion’ TLF used in this study; ApR | Parent of pDH804 | This study |
| pDH804 | pDH795-derivative; TLF ‘marked’ with kanR | Parent of pDH812 | This study |
| pDH812 | TLF-kanR cloned into BclI-cut pNK81; ApRKanR | For crossing TLF onto λ | This study |
| pDH753 | pWKS30-derivative; contains IS50-lacZ TLF from pDH658; ApR | Parent of pDH798 | This study |
| pDH798 | pDH753-derivative; ApSKanR | Miller Assay | This study |
| pDH763 | pBR-plac; ApR | Vector for sRNA-induction | [45] |
| pDH764 | pBR-plac-sgrS; ApR | SgrS-induction | [46] |
| pDH895 | pBR-plac-sgrS1; ApR | SgrS1-induction | [47] |
| pDH766 | pBR-plac-rybB; ApR | RybB-induction | [48] |
| pDH768 | pBR-plac-micC; ApR | MicC-induction | [48] |
| pDH772 | pBR-plac-ryeB; ApR | RyeB-induction | [48] |
| pDH908 | pDH795-derivative; Lpp-TLF | Miller Assay | This study |
| Phage | |||
| λNK1039 | Encodes his operon | Parent phage | [49] |
| λDBH812 | IS50-lacZ translational fusion (TLF) from pDH812 marked with kanR | Chromosomal TLF construction | This study |
| λDBH849 | IS50-lacZ transcriptional fusion (TCF) marked with kanR | Chromosomal TCF construction | This study |
| λDBH888 | IS50-lacZ transcriptional fusion (TCF) marked with cmR | Chromosomal TCF construction | This study |