Skip to main content

Table 1 Plasmids, bacteriophage and strains

From: Tn5 transposition in Escherichia coli is repressed by Hfq and activated by over-expression of the small non-coding RNA SgrS

Strain or Plasmid Relevant genotype Use Source or reference
E. coli    
DBH13 HB101 [Fleupro]; StrR ‘Mating out’ recipient [36]
ER2507 zjc::Tn5; KanR Source of zjc::Tn5 NEB
DBH179 NK5830 [recAarg/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 Δhfq 722::kan; StrRCmRKanR Miller Assay This study
DBH307 DBH303 Δcrp 765::kan; StrRCmRKanR Miller Assay This study
DBH315 DBH303 Δlrp 787::kan; StrRCmRKanR Miller Assay This study
DBH33 NK5830 [recAarg/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 recAhfq-1::Ωcat; StrRCmR Miller Assay This study
DBH242 DBH33 Δcrp 765::kan Parent strain This study
DBH344 DBH242 Δcrp 765; KanS Parent strain This study
DBH345 DBH344 zjc::Tn5; KanR ‘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