TABLE 1.
E. coli K-12 strains
| Strain | Description or genotypea | Reference or construction (reference[s])b |
|---|---|---|
| C41(DE3) | BL21(DE3) derivate for toxic protein expression | 55 |
| Donor strains for transduction | ||
| JW1183-1 | BW25113 ΔycgR784Kan (KEIO collection) | 56 |
| JW1880-1 | BW25113 ΔflhC744Kan (KEIO collection) | 56 |
| M182 stpA::tet | ΔlacIZYA-74 galU galK strA stpA::tet | 57 |
| U171 | U65 ΔpdeHKan | U65 (27)/pKD46 × OA603/OA604 (pKD4) |
| S3754 | MG1655 ΔhnsKan | 58 |
| MG1655 | Wild-type E. coli K-12 flhDC+; motile (no IS1 or IS5 insertion at flhDC) (laboratory storage no. S3837) | CGSC 6300 |
| T2517 | MG1655 flgET224C flhDC+; motile (T224C is an ACA-to-TGC exchange) | No-SCAR recombineering using pKDsgRNA-flgE-T224 (pKES337) and oligonucleotide OA553 |
| T2599 | MG1655 flgET224C IG(flgL-rne)Cm | T2517/pKD46 × OA785/OA786 (pKD3) |
| BW30270 and derivatives | ||
| BW30270 | MG1655 rph+ flhDC(IS1); motile (IS1 insertion upstream of the flhDC promoter) (laboratory storage no. S3839) | CGSC 7925 |
| T2055 | BW30270 ΔpdeLKan | BW30270 × T4GT7[U99 ΔpdeLKan] |
| T2057 | BW30270 ΔpdeLFRT | T2055 × pCP20 |
| T2604 | BW30270 flgE+ IG(flgL-rne)Cm | BW30270 × P1vir[IG(flgL-rne)Cm] |
| T2607 | BW30270 flgET224C IG(flgL-rne)Cm | S3839 × P1vir[T2599; cotransduction of flgET224C and IG(flgL-rne)Cm] |
| T2611 | BW30270 flgE+ IG(flgL-rne)FRT | T2604 × pCP20 |
| T2614 | BW30270 flgET224C IG(flgL-rne)FRT | T2607 × pCP20 |
| T1241 and derivatives | ||
| T1241 | BW30270 ilvG+ flhDC(IS1); motile | 59 |
| U98 | T1241 ΔpdeLCm | T1241/pKD46 × OA112/OA115 (pKD3) |
| U99 | T1241 ΔpdeLKan | T1241/pKD46 × OA112/OA115 (pKD4) |
| U102 | T1241 ΔpdeLKan | T1241 × T4GT7[U99 ΔpdeLKan] |
| U106 | T1241 ΔpdeLFRT | U102 × pCP20 |
| U114 | T1241 pdeL3×FLAGKan | T1241/pKD46 × OA274/OA275 (pSUB11) |
| U286 | T1241 pdeL3×FLAG-FRT | U114 × pCP20 |
| U287 | T1241 pdeL3×FLAG-FRT ΔpdeHKan | U286 × P1vir[ΔpdeHKan] |
| U291 | T1241 pdeL3×FLAG-FRT ΔpdeHFRT | U287 × pCP20 |
| Strains for construction of U281 and derivatives | ||
| U53 | T1241 Δ(araC-BAD) Δlac(I-ZYA)FRT Pcp8 araE | 27 |
| U279 | U53 ΔaraFGHCm | U53/pKD46 × OA908/OA909 (pKD3) |
| U281 | U53 ΔaraFGHFRT | U279 × pCP20 |
| U283 | U281 ΔpdeHKan | U281 × P1vir[ΔpdeHKan] |
| U288 | U281 ΔpdeHFRT | U283 × pCP20 |
| U284 | U281 ΔycgRKan | U281 × P1vir[JW1183-1 ΔycgRKan] |
| U289 | U281 ΔycgRFRT | U284 × pCP20 |
| U285 | U281 ΔpdeLKan | U281 × P1vir[U99 ΔpdeLKan] |
| U290 | U281 ΔpdeLFRT | U285 × pCP20 |
| U296 | U281 ΔpdeHFRT ΔpdeLKan | U288 × P1vir[U99 ΔpdeLKan] |
| U303 | U281 ΔpdeHFRT ΔpdeLFRT | U296 × pCP20 |
| U293 | U281 ΔycgRFRT ΔpdeLKan | U289 × P1vir[U99 ΔpdeLKan] |
| U294 | U281 ΔpdeHFRT ΔycgRKan | U288 × P1vir[JW1183-1 ΔycgRKan] |
| U301 | U281 ΔpdeHFRT ΔycgRFRT | U294 × pCP20 |
| U300 | U281 ΔycgRFRT ΔpdeLFRT | U293 × pCP20 |
| U307 | U281 ΔpdeHFRT ΔpdeLFRT ΔycgRKan | U303 × P1vir[JW1183-1 ΔycgRKan] |
| U309 | U281 ΔpdeHFRT ΔpdeLFRT ΔycgRFRT | U307 × pCP20 |
| U298 | U281 IG(fliE-fliF)::[PL fliE FRT-Kan-FRT Ptac fliF] | U281/pKD46 × OA914/OA915 (pKES263) |
| lacZ reporter strains | ||
| U4 | T1241 ΔlacZ | Scarless lacZ deletion constructed using pFDY217 (60, 61) |
| U264 | U4 ΔpdeLCm | U4 × P1vir[U98 ΔpdeLCm] |
| U266 | U4 ΔpdeLFRT | U264 × pCP20 |
| U423 | U4 ΔpdeLFRT ΔflhCKan | U266 × P1vir[T2779 ΔflhCKan] |
| U427 | U4 ΔpdeLFRT ΔflhCFRT | U423 × pCP20 |
| U31 | U4 attB::(Specr PpdeL lacZ) | U4/pLDR8 × pKESL161 |
| U32 | U4 attB::(Specr PpdeL lacZ) ΔhnsKan | U31 × T4GT7[S3754 hnsKan] |
| U33 | U4 attB::(Specr PpdeL lacZ) ΔstpA::tet | U31 × T4GT7[M182 stpA::tet] |
| U34 | U4 attB::(Specr PpdeL lacZ) ΔstpA::tet ΔhnsKan | U33 × T4GT7[S3754 hnsKan] |
| U113 | U4 attB::(Specr PpdeL lacZ) ΔhnsFRT | U32 × pCP20 |
| U226 | U4 attB::(Specr PpdeL lacZ) ΔpdeLCm | U31 × P1vir[U98 ΔpdeLCm] |
| U230 | U4 attB::(Specr PpdeL lacZ) ΔpdeLFRT | U226 × pCP20 |
| U277 | U4 attB::(Specr PpdeL lacZ) (translational fusion) | U4/pLDR8 × pKECY51 |
| U278 | U4 attB::(Specr PpdeL lacZ) (translational fusion) ΔpdeLFRT | U266/pLDR8 × pKECY51 |
a
IG(flgL-rne)Cm describes the insertion of an FRT-flanked chloramphenicol resistance gene in the intergenic region between flgL and rne. IG(fliE-fliF)::[PL fliE FRT-Kan-FRT Ptac fliF] describes the insertion of a PL-FRT-Kanr-FRT-Ptac cassette in the intergenic region of fliE and fliF, exchanging the native sequence between positions 2013034 and 2013209 (E. coli K-12 MG1655 genome [GenBank accession number U00096.3]).
b
Strains were constructed by transduction, which is stated as “× phage[donor strain]”; λ Red recombineering, stated as “× PCR primer pair (template),” followed by Flp recombinase-catalyzed deletion of the resistance marker, “× pCP20”; and integration of a PpdeL lacZ fusion at attB, indicated as “× pKESL161” (62).