Table 1.
Bacterial strains and plasmids used in this work
| Strain or plasmid | Genotype or relevant characteristicsa | Source or referenceb |
|---|---|---|
| Strains | ||
| MG1655 | F− λ− ilvG rph-1 | CGSC 7740 |
| BW25141 | F− λ− Δ(araB-araD)567 ΔlacZ4787(::rrnB3) Δ(phoB-phoR)580 galU95 ΔuidA3::pir+ recA1 ΔendA9::FRT rph-1 Δ(rhaB-rhaD)568 hsdR514 | CGSC 7635 |
| BL21(DE3) | F− ompT gal dcm lon hsdSB(rb− rm−) λ(DE3 [lacI lacUV5-T7 gene1 ind1 sam7 nin5]) | G. W. Ordal |
| JW5249 | F− λ− rph-1 Δ(araB-araD)567 ΔlacZ4787(::rrnB3) Δ(rhaB-rhaD)568 hsdR514 ΔmarA752::kan | CGSC 11269 |
| JW4023 | F− λ− rph-1 Δ(araB-araD)567 ΔlacZ4787(::rrnB3) Δ(rhaB-rhaD)568 hsdR514 ΔsoxS756::kan | CGSC 10891 |
| JTG1078 | F− λ− rph-1 rfb-50 INV(rrnD-rrnE)1 rpsL179 soxR105 zjc-2206::Tn10dKan | CGSC 7594 |
| CR700 | attλ::[kan marR′-yfp oriR6K] | 10 |
| CR715 | attλ::[kan micF′-yfp oriR6K] | 11 |
| CR719 | ΔmarRAB::FRTc | 11 |
| CR720 | ΔsoxRS::FRT | 11 |
| CR721 | Δrob::FRT | 11 |
| CR723 | ΔmarRAB::FRT ΔsoxRS::FRT | 11 |
| CR724 | ΔmarRAB::FRT Δrob::FRT | 11 |
| CR725 | ΔsoxRS::FRT Δrob::FRT | 11 |
| CR726 | ΔmarRAB::FRT ΔsoxRS::FRT Δrob::FRT | 11 |
| CR765 | ΔmarRAB::FRT attλ::[kan micF′-yfp oriR6K] | 11 |
| CR766 | ΔsoxRS::FRT attλ::[kan micF′-yfp oriR6K] | 11 |
| CR777 | Δrob::FRT attλ::[kan micF′-yfp oriR6K] | 11 |
| CR779 | ΔmarRAB::FRT ΔsoxRS::FRT attλ::[kan micF′-yfp oriR6K] | 11 |
| CR782 | ΔmarRAB::FRT ΔsoxRS::FRT Δrob::FRT attλ::[kan micF′-yfp oriR6K] | 11 |
| CR903 | JTG1078 ΔsoxS::cat (4275086–4275406) | |
| CR904 | ΔsoxS::cat soxR105 (Kans) | |
| CR905 | ΔmarRAB::FRT ΔsoxS::cat soxR105 | |
| CR906 | Δrob::FRT ΔsoxS::cat soxR105 | |
| CR907 | ΔmarRAB::FRT Δrob::FRT ΔsoxS::cat soxR105 | |
| CR908 | ΔmarA752::kan | |
| CR909 | ΔsoxS756::kan | |
| CR910 | ΔmarA752::FRT ΔsoxS756::FRT | |
| CR911 | ΔmarA752::FRT Δrob::FRT | |
| CR912 | ΔsoxS756::FRT Δrob::FRT | |
| CR913 | ΔmarA752::FRT ΔsoxS756::FRT Δrob::FRT | |
| CR914 | attλ::[kan soxS′-yfp oriR6K] | |
| CR915 | attλ::[kan rob′-yfp oriR6K] | |
| CR916 | attλ::[kan inaA′-yfp oriR6K] | |
| CR917 | ΔmarRAB::FRT Δrob::FRT ΔsoxS::cat soxR105 attλ::[kan marR′-yfp oriR6K] | |
| CR918 | ΔmarRAB::FRT Δrob::FRT ΔsoxS::cat soxR105 attλ::[kan soxS′-yfp oriR6K] | |
| CR919 | ΔmarRAB::FRT Δrob::FRT ΔsoxS::cat soxR105 attλ::[kan rob′-yfp oriR6K] | |
| CR920 | ΔmarRAB::FRT Δrob::FRT ΔsoxS::cat soxR105 attλ::[kan inaA′-yfp oriR6K] | |
| CR921 | ΔmarRAB::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR922 | ΔmarRAB::FRT ΔsoxRS::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR923 | ΔmarRAB::FRT Δrob::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR924 | ΔmarRAB::FRT ΔsoxRS::FRT Δrob::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR925 | ΔsoxS::cat soxR105 attλ::[kan soxS′-yfp oriR6K] | |
| CR926 | ΔmarRAB::FRT ΔsoxS::cat soxR105 attλ::[kan soxS′-yfp oriR6K] | |
| CR927 | Δrob::FRT ΔsoxS::cat soxR105 attλ::[kan soxS′-yfp oriR6K] | |
| CR928 | ΔmarRAB::FRT Δrob::FRT ΔsoxS::cat soxR105 attλ::[kan soxS′-yfp oriR6K] | |
| CR929 | Δrob::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR930 | ΔmarRAB::FRT Δrob::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR931 | ΔsoxRS::FRT Δrob::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR932 | ΔmarRAB::FRT ΔsoxRS::FRT Δrob::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR933 | ΔsoxS756::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR934 | Δrob::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR935 | ΔsoxS756::FRT Δrob::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR936 | ΔmarA752::FRT ΔsoxS756::FRT Δrob::FRT attλ::[kan marR′-yfp oriR6K] | |
| CR937 | ΔmarA752::FRT attλ::[kan soxS′-yfp oriR6K] | |
| CR938 | Δrob::FRT attλ::[kan soxS′-yfp oriR6K] | |
| CR939 | ΔmarA752::FRT Δrob::FRT attλ::[kan soxS′-yfp oriR6K] | |
| CR940 | ΔmarA752::FRT ΔsoxS756::FRT Δrob::FRT attλ::[kan soxS′-yfp oriR6K] | |
| CR941 | ΔmarA752::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR942 | ΔsoxS756::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR943 | ΔmarA752::FRT ΔsoxS756::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR944 | ΔmarA752::FRT ΔsoxS756::FRT Δrob::FRT attλ::[kan rob′-yfp oriR6K] | |
| CR945 | ΔsoxRS::FRT Δrob::FRT attλ::[kan inaA′-yfp oriR6K] | |
| CR946 | ΔmarRAB::FRT Δrob::FRT attλ::[kan inaA′-yfp oriR6K] | |
| CR947 | ΔmarRAB::FRT ΔsoxRS::FRT attλ::[kan inaA′-yfp oriR6K] | |
| CR948 | ΔmarRAB::FRT ΔsoxRS::FRT Δrob::FRT attλ::[kan inaA′-yfp oriR6K] | |
| CR949 | ΔsoxRS::FRT Δrob::FRT attλ::[kan micF′-yfp oriR6K] | |
| CR950 | ΔmarRAB::FRT Δrob::FRT attλ::[kan micF′-yfp oriR6K] | |
| CR951 | ΔmarRAB::FRT ΔsoxRS::FRT attλ::[kan micF′-yfp oriR6K] | |
| CR952 | ΔmarRAB::FRT ΔsoxRS::FRT Δrob::FRT attλ::[kan micF′-yfp oriR6K] | |
| Plasmids | ||
| pKD46 | bla PBAD gam bet exo pSC101 ori(Ts) | 14 |
| pCP20 | bla cat cI857 λPR′-flp pSC101 ori(Ts) | 9 |
| pKD3 | bla rgnB FRT cat FRT oriR6K | 14 |
| pET28a | kan PT7/lacO-6 × His-MCS lacIq ColE1 | Novagen |
| pBAD30 | bla araC PBADp15A ori | 17 |
| pMarA | pBAD30::RBS-marA | 11 |
| pRob | pBAD30::RBS-rob | 11 |
| pSoxS | pBAD30::RBS-soxS | |
| pVenus | kan MCS yfp(venus) t0 attλ oriR6K | 53 |
| pVenus-soxS | kan MCS soxS′-yfp t0 attλ oriR6K | |
| pVenus-rob | kan MCS rob′-yfp t0 attλ oriR6K | |
| pVenus-inaA | kan MCS inaA′-yfp t0 attλ oriR6K | |
| pET28a-rob | kan PT7/lacO-6×His-rob lacIq ColE1 |
a
Except for BL21(DE3), all strains are isogenic derivatives of E. coli K-12 strain MG1655. Numbers in parentheses indicate deletion endpoints determined using the MG1655 genome sequence.
b
All strains and plasmids are from this work unless otherwise noted. CGSC, E. coli Genetic Stock Center, Yale University.
c
FRT, FLP recombination target.