Table 1 Plasmids, bacteriophage and strains

E. coli

DBH13

HB101 [F⁻leu⁻pro⁻]; Str^R

‘Mating out’ recipient

[36]

ER2507

zjc::Tn5; Kan^R

Source of zjc::Tn5

NEB

DBH179

NK5830 [recA⁻arg⁻/F’ lacpro⁺] zjc::Tn5; Kan^R

‘Mating out’ donor

This study

DBH184

DBH179 hfq-1::Ωcat; Kan^RCm^R

‘Mating out’ donor

This study

DBH228

RZ211/pOX38Gen

Source of pOX38Gen

[37]

DBH233

HW-5 [phoA4(Am) his-45 recA1 rpsL99 met-54 F⁻]; Str^R

Parent strain

[38]

DBH259

DBH233/pOX38Gen; Str^RGen^R

Parent strain

This study

DBH261

DBH259 zjc::Tn5; Str^RGen^RKan^R

‘Mating out’ donor

This study

DBH271

DBH261 hfq-1::Ωcat; Str^RGen^RKan^RCm^R

‘Mating out’ donor

This study

DBH272

DBH261 dam::Tn9cat; Str^RGen^RKan^RCm^R

‘Mating out’ donor

This study

DBH107

MC4100 [F⁻ Δ(argF-lac)169* rpsL150]; Str^R

Parent strain

[39]

DBH265

DBH107/λDBH849; Str^RKan^R

Miller Assay

This study

DBH267

DBH265 hfq-1::Ωcat; Str^RCm^RKan^R

Miller Assay

This study

DBH268

DBH265 dam::Tn9cat; Str^RCm^RKan^R

Miller Assay

This study

DBH281

DBH107/λDBH812; Str^RKan^R

Miller Assay

This study

DBH283

DBH281 hfq-1::Ωcat; Str^RCm^RKan^R

Miller Assay

This study

DBH285

DBH281 dam::Tn9cat; Str^RCm^RKan^R

Miller Assay

This study

DBH303

DBH107/λDBH888; Str^RCm^R

Miller Assay

This study

DBH306

DBH303 Δhfq 722::kan; Str^RCm^RKan^R

Miller Assay

This study

DBH307

DBH303 Δcrp 765::kan; Str^RCm^RKan^R

Miller Assay

This study

DBH315

DBH303 Δlrp 787::kan; Str^RCm^RKan^R

Miller Assay

This study

DBH33

NK5830 [recA⁻arg⁻/F’ lacpro⁺]

Parent strain

[40]

DBH16

DBH33 hfq-1::Ωcat; Cm^R

Parent strain

[7]

DBH241

DBH33 dam::Tn9cat; Cm^R

Parent strain

This study

DBH238

DBH33/λDBH849; Kan^R

Miller Assay

This study

DBH239

DBH238 hfq-1::Ωcat; Kan^RCm^R

Miller Assay

This study

DBH240

DBH238 dam::Tn9cat; Kan^RCm^R

Miller Assay

This study

DBH208

DBH33/λDBH812; Kan^R

Miller Assay

This study

DBH210

DBH208 hfq-1::Ωcat; Kan^RCm^R

Miller Assay

This study

DBH237

DBH208 dam::Tn9cat; Kan^RCm^R

Miller Assay

This study

DBH323

DBH107 recA⁻; Str^R

Miller Assay

This study

DBH326

DBH107 recA⁻hfq-1::Ωcat; Str^RCm^R

Miller Assay

This study

DBH242

DBH33 Δcrp 765::kan

Parent strain

This study

DBH344

DBH242 Δcrp 765; Kan^S

Parent strain

This study

DBH345

DBH344 zjc::Tn5; Kan^R

‘Mating out’ donor

This study

TM338

W3110mlc rne-Flag-cat; rif^SCm^R

RNA half-life measurements

[41]

TM618

W3110mlc rne-Flag-cat Δhfq; rif^SCm^R

RNA half-life measurements

[42]

DH5α

recA ⁻

Plasmid propagation

Invitrogen

Plasmids

pWKS30

pSC101-derived; low copy-number ori ; Ap^R

‘Empty vector’ for Hfq expression

[35]

pDH700

pWKS30-P3-hfq _WT ; Ap^R

Hfq_WT expression

[7]

pDH701

pWKS30-P3-hfq _K56A ; Ap^R

Hfq_K56A expression

[7]

pDH713

pWKS30-P3-hfq _Y25A ; Ap^R

Hfq_Y25A expression

[8]

pDH533

pUC18-derivative; Tn5 t’ase M56A; Ap^RCm^R

Source of Tn5 transposase (No Inh.)

[43]

pDH752

pDH533 with t’ase mutated to G53A,C61A; Ap^RCm^R

DAM-insensitive t’ase

This study

pDH828

pDH533 with t’ase mutated to D97A; Ap^RCm^R

Catalytic⁻ t’ase

This study

pNK81

pBR333-derivative; encodes his operon; Ap^R

Lambda crosses

[44]

pDH682

pUC18-derivative; IS50-lacZ TCF; Ap^R

Source of TCF

This study

pDH838

pDH682-derivative; TCF ‘marked’ with kan^R

Parent of pDH849

This study

pDH883

pDH682-derivative; TCF ‘marked’ with cm^R

Parent of pDH888

This study

pDH849

TCF-kan^R from pDH682 cloned into BclI-cut pNK81; Ap^RKan^R

For crossing TCF onto λ

This study

pDH888

TCF-cm^R cloned onto BclI-cut pNK81; Ap^RCm^R

For crossing TCF onto λ

This study

pDH658

pRZ9905-derivative; full-length IS50-lacZ TLF; Ap^R

Parent of pDH795

This study

pDH795

pDH658-derivative; ‘deletion’ TLF used in this study; Ap^R

Parent of pDH804

This study

pDH804

pDH795-derivative; TLF ‘marked’ with kan^R

Parent of pDH812

This study

pDH812

TLF-kan^R cloned into BclI-cut pNK81; Ap^RKan^R

For crossing TLF onto λ

This study

pDH753

pWKS30-derivative; contains IS50-lacZ TLF from pDH658; Ap^R

Parent of pDH798

This study

pDH798

pDH753-derivative; Ap^SKan^R

Miller Assay

This study

pDH763

pBR-plac; Ap^R

Vector for sRNA-induction

[45]

pDH764

pBR-plac-sgrS; Ap^R

SgrS-induction

[46]

pDH895

pBR-plac-sgrS1; Ap^R

SgrS1-induction

[47]

pDH766

pBR-plac-rybB; Ap^R

RybB-induction

[48]

pDH768

pBR-plac-micC; Ap^R

MicC-induction

[48]

pDH772

pBR-plac-ryeB; Ap^R

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 kan^R

Chromosomal TLF construction

This study

λDBH849

IS50-lacZ transcriptional fusion (TCF) marked with kan^R

Chromosomal TCF construction

This study

λDBH888

IS50-lacZ transcriptional fusion (TCF) marked with cm^R

Chromosomal TCF construction

This study