Table 1. Strains and plasmids.
| No. | Strains or plasmids | Genotype or description | Source |
|---|---|---|---|
| Strains | |||
| Escherichia coli MG1656 | MG1655 (K-12F– λ– ilvG– rfb-50 rph-1) ΔlacMluI | Espéli et al. (2001) | |
| Escherichia coli MG1656 λatt::gfp | MG1656 strain containing the gfpmut3 gene at the λatt site | This study | |
| Escherichia coli MG1656 Δcpxl::km-frt | cpxl gene replaced by the km-frt cassette in strain MG1656 | Beloin et al. (2004) | |
| Plasmids | |||
| pKOBEGA | λ red recombination system expression plasmid | Chaveroche et al. (2000) | |
| pCP20 | FLP flippase expression plasmid | Cherepanov and Wackernagel (1995) | |
| pZE1-gfpmut3 | gfpmut3 gene under the control of the constitutive pλR promoter | Gift from C Guet | |
| pZE-km-frt-gfpmut3 | km-frt cassette amplified from MG1656Δcpxl::km-frt using primers 7-8 (Supplementary Table S1) and cloned into pZE1R-gfpmut3 (SacI–XhoI). | This study | |
| p1W | integron intI1-aac(6′)-Ib-dfrA15-aadA1-catB9 with PcW promoter cloned into pSU38ΔtotlacZ | Barraud and Ploy (2015) | |
| p1S | integron intI1-aac(6′)-Ib-dfrA15-aadA1-catB9 with PcS promoter cloned into pSU38ΔtotlacZ | Barraud and Ploy (2015) | |
| p1WTGN-10 | integron intI1-aac(6′)-Ib-dfrA15-aadA1-catB9 with PcWTGN-10 promoter cloned into pSU38ΔtotlacZ | Barraud and Ploy (2015) | |
| p16Sa | integron intI1-aac(6′)-Ib-dfrA15-aadA1-catB9-aac(6′)-Ib-dfrA15-aadA1-catB9 cloned into pSU38ΔtotlacZ | Barraud and Ploy (2015) | |
| p8741 | pBAD::intI1Y312F | Loot et al. (2014) | |
| pZA2 and derivatives | |||
| 1 | pZA2 | pZA2 plasmid, Kmr | Lutz and Bujard (1997) |
| 2 | pW-4GC | integron intI1-aadA1-catB9-aac(6′)-Ib-dfrA15 with PcW promoter cloned into pZA2 | This study |
| 3 | pH1-4GC | integron intI1-aadA1-catB9-aac(6′)-Ib-dfrA15 with PcH1 promoter cloned into pZA2 | This study |
| 4 | pWTGN-10-4GC | integron intI1-aadA1-catB9-aac(6′)-Ib-dfrA15 with PcWTGN-10 promoter cloned into pZA2 | This study |
| 5 | pS-4GC | integron intI1-aadA1-catB9-aac(6′)-Ib-dfrA15 with PcS promoter cloned into pZA2 | This study |
| 6 | pW PintI*-4GC | pW-4GC with inactivated PintI promoter (no intI1 expression) | This study |
| 7 | pH1 PintI*-4GC | pH1-4GC with inactivated PintI promoter (no intI1 expression) | This study |
| 8 | pWTGN-10 PintI*-4GC | pWTGN-10-4GC with inactivated PintI promoter (no intI1 expression) | This study |
| 9 | pS PintI*-4GC | pS-4GC with inactivated PintI promoter (no intI1 expression) | This study |
| 10 | pW*PintI*-4GC | pW-4GC with inactivated Pc promoter and inactivated PintI promoter (no intI1 expression nor cassette expression) | This study |
| 11 | pW*-4GC | pW-4GC with inactivated PcW promoter (silent mutation, IntI1R32-H39 integrase variant, no cassette expression) | This study |
| 12 | pWTGN-10*-4GC | pWTGN-10-4GC with inactivated PcWTGN-10 promoter (silent mutation, IntI1P32-H39 integrase variant, no cassette expression) | This study |
| 13 | pS*-4GC | pS-4GC with inactivated PcS promoter (silent mutation, IntI1R32-N39 integrase variant, no cassette expression) | This study |
| 14 | pW*lexA*-4GC | pW-4GC with inactivated PcW promoter (no cassette expression) and IntI1R32-H39 constitutive expression (mutated LexA box) | This study |
| 15 | pWTGN-10*lexA*-4GC | pWTGN-10-4GC with inactivated PcWTGN-10 promoter (no cassette expression) and IntI1P32-H39 constitutive expression (mutated LexA box) | This study |
| 16 | pS*lexA*-4GC | pS-4GC with inactivated PcS promoter (no cassette expression) and IntI1R32-N39 constitutive expression (mutated LexA box) | This study |
| 17 | pWY312F*lexA*-4GC | pW* lexA*-4GC encoding an inactive integrase (catalytic amino acid Y312 mutated) | This study |
| 18 | pS-2GC | integron intI1-aadA1-catB9 with PcS promoter cloned into pZA2 | This study |
| 19 | pW*PintI*-2GC | pS-2GC with inactivated Pc promoter and inactivated PintI promoter (no intI1 expression nor GCs expression) | This study |
| 20 | pS-aadA1 | integron intI1-aadA1 with PcS promoter cloned into pZA2 | This study |
| 21 | pS-catB9 | integron intI1- catB9 with PcS promoter cloned into pZA2 | This study |
| 22 | pS-aac(6′)-Ib | integron intI1- aac(6′)-Ib with PcS promoter cloned into pZA2 | This study |
| 23 | pS-dfrA15 | integron intI1- dfrA15 with PcS promoter cloned into pZA2 | This study |
| 24 | pW*PintI*-aadA1 | pW-aad with inactivated Pc promoter and inactivated PintI promoter (no intI1 expression nor GCs expression) | This study |
| 25 | pW-aac(6′)-Ib | integron intI1- aac(6′)-Ib with PcW promoter cloned into pZA2 | This study |
Abbreviation: GC, gene cassette. Bold was used to highlight the change of Pc variant between constructions.