Table 1.
Bacterial strains and plasmids used in this studya.
| Strain | Characteristics | References |
|---|---|---|
| E. coli | ||
| DH5α | supE44 Δ(lacZYA-argF)U169 ϕ80 lacZΔM15 hsdR17 ( ) recA1 endA1 gyrA96 thi1 relA1; NalR | Hanahan, 1983 |
| TOP10F′ | F′[lacIq, Tn10 (TetR)] mcrA Δ(mrr-hsdRMS-mcrBC) Φ80lacZΔM15 ΔlacX74 recA1 araD139 Δ(ara leu) 7697 galU galK rpsL (StrR) endA1 nupG; TcR | Invitrogen |
| P. putida | ||
| KT2440 | hsdR1, wild-type strain; RifR | Franklin et al., 1981 |
| ΔiutY | Markerless KT2440 null mutant in the iutY (PP2192) gene; RifR | Bastiaansen et al., 2014 |
| Δprc | Markerless KT2440 null mutant in the prc (PP1719) gene; RifR | Bastiaansen et al., 2014 |
| ΔrseP | Markerless KT2440 null mutant in the rseP (PP1598) gene; RifR | Bastiaansen et al., 2014 |
| ΔiutA | Markerless KT2440 null mutant in the iutA (PP2193) gene; RifR | This study |
| ΔiutY Δprc | ΔiutY carrying an additional markerless null mutation in prc (PP1719) gene; RifR | This study |
| ΔiutY ΔrseP | ΔiutY carrying an additional markerless null mutation in rseP (PP1598) gene; RifR | This study |
| ΔiutY ΔiutA | ΔiutY carrying an additional markerless null mutation in iutA (PP2193) gene; RifR | This study |
| P. aeruginosa | ||
| PAO1 pvdF ΔfoxR | PAO1 pvdF with a deletion of amino acids 12–295 of the FoxR (PA2467) protein; KmR | Mettrick and Lamont, 2009 |
| PAO1 pvdF ΔfiuR | PAO1 pvdF with a deletion of amino acids 12–319 of the FiuR (PA0471) protein; KmR | Mettrick and Lamont, 2009 |
| PLASMID | ||
| pKNG101 | Gene replacement suicide vector, oriR6K, oriTRK2, sacB; SmR | Kaniga et al., 1991 |
| pKΔprc | pKNG101 carrying the P. putida prc (PP1719) deletion construct; SmR | Bastiaansen et al., 2014 |
| pKΔrseP | pKNG101 carrying the P. putida rseP (PP1598) deletion construct; SmR | Bastiaansen et al., 2014 |
| pKΔiutA | pKNG101 carrying in XbaI-BamHI a 2.8-Kb PCR fragment containing the regions up- and downstream the P. putida iutA (PP2193) gene; SmR | This study |
| pMMB67EH | IncQ broad-host range plasmid, lacIq; ApR | Fürste et al., 1986 |
| pMMBK1-HA | pMMB67EH carrying an N-terminally HA-tagged P. putida iutY gene (PP2192); ApR | Bastiaansen et al., 2014 |
| pMMBK1-HA-168 | pMMBK1-HA in which a premature stop codon was inserted after residue 168 (from the random mutagenesis screen); ApR | This study |
| pMMBK1-HA-201 | pMMBK1-HA in which a premature stop codon was inserted after residue 201 (from the random mutagenesis screen); ApR | This study |
| pMMBK1-HA-260 | pMMBK1-HA in which a premature stop codon was inserted after residue 260 (from the random mutagenesis screen); ApR | This study |
| pMMBK1-HA-318 | pMMBK1-HA in which a premature stop codon was inserted after residue 318 (from the random mutagenesis screen); ApR | This study |
| pMMBK1-HA-365 | pMMBK1-HA in which a premature stop codon was inserted after residue 365 (from the random mutagenesis screen); ApR | This study |
| pMMBK1-HA-225 | pMMB67EH carrying in EcoRI-HindIII a 6.75-Kb PCR fragment encoding the first 225 amino acids of the P. putida IutY protein with an N-terminal HA-tag; ApR | This study |
| pMMBK1-HA-236 | pMMB67EH carrying in EcoRI-HindIII a 7.08-Kb PCR fragment encoding the first 236 amino acids of the P. putida IutY protein with an N-terminal HA-tag; ApR | This study |
| pMMBK1-HA-293 | pMMB67EH carrying in EcoRI-HindIII a 8.79-Kb PCR fragment encoding the first 293 amino acids of the P. putida IutY protein with an N-terminal HA-tag; ApR | This study |
| pMMBK1-HA-338 | pMMB67EH carrying in EcoRI-HindIII a 1.01-Kb PCR fragment encoding the first 338 amino acids of the P. putida IutY protein with an N-terminal HA-tag; ApR | This study |
| pMMBK1-HA-G201C | pMMBK1-HA in which glycine-201 has been mutated to a cysteine; ApR | This study |
| pMMBK1-HA-D210A | pMMBK1-HA in which aspartic acid-210 has been mutated to an alanine; ApR | This study |
| pMMBK1-HA-F226L | pMMBK1-HA in which phenylalanine-226 has been mutated to a leucine; ApR | This study |
| pMMBK1-HA-E230K | pMMBK1-HA in which glutamic acid-230 has been mutated to a lysine; ApR | This study |
| pMMBK1-HA-R231Q | pMMBK1-HA in which arginine-231 has been mutated to a glutamine; ApR | This study |
| pMMBK1-HA-A240E | pMMBK1-HA in which alanine-240 has been mutated to a glutamic acid; ApR | This study |
| pMMBK1-HA-F251S | pMMBK1-HA in which phenylalanine-251 has been mutated to a serine; ApR | This study |
| pMMBK1-HA-V253D | pMMBK1-HA in which valine-253 has been mutated to an aspartic acid; ApR | This study |
| pMMBK1-HA-R271C | pMMBK1-HA in which arginine-271 has been mutated to a cysteine; ApR | This study |
| pMMBK1-HA-W301G | pMMBK1-HA in which tryptophan-301 has been mutated to a glycine; ApR | This study |
| pMMBK1-HA-G304D | pMMBK1-HA in which glycine-304 has been mutated to an aspartic acid; ApR | This study |
| pMMBK1-HA-T365I | pMMBK1-HA in which threonine-365 has been mutated to an isoleucine; ApR | This study |
| pMMBK1-HA-LtoP | pMMBK1-HA in which leucine-313, leucine-317 and leucine-320 have been mutated to prolines; ApR | This study |
| pMMB/HA-FoxR | pMMB67EH carrying the P. aeruginosa foxR gene (PA2467) which has been N-terminally HA-tagged; ApR | Bastiaansen et al., 2015a |
| pMMB/HA-FoxR-D132A | pMMB/HA-FoxR in which aspartic acid-132 has been mutated to an alanine; ApR | This study |
| pMMB/HA-FoxR-R153Q | pMMB/HA-FoxR in which asparagine-153 has been mutated to a glutamine; ApR | This study |
| pMMB/HA-FoxR-V180D | pMMB/HA-FoxR in which valine-180 has been mutated to an aspartic acid; ApR | This study |
| pMMB/HA-FiuR | pMMB67EH carrying in EcoRI-XbaI a 0.97-Kb PCR fragment containing a N-terminally HA-tagged P. aeruginosa fiuR gene; ApR | Bastiaansen et al., 2015a |
| pMMB/HA-FiuR-D133A | pMMB/HA-FiuR in which aspartic acid-133 has been mutated to an alanine; ApR | This study |
| pMMB/HA-FiuR-R154Q | pMMB/HA-FiuR in which asparagine-154 has been mutated to a glutamine; ApR | This study |
| pMMB/HA-FiuR-V177D | pMMB/HA-FiuR in which valine-177 has been mutated to an aspartic acid; ApR | This study |
| pMP220 | IncP broad-host-range lacZ fusion vector; TcR | Spaink et al., 1987 |
| pMPK4 | pMP220 carrying the P. putida iutA (PP2193) promoter region cloned upstream the lacZ gene; TcR | Bastiaansen et al., 2014 |
| pMPR8b | pMP220 carrying the P. aeruginosa foxA (PA2466) promoter region cloned upstream the lacZ gene; TcR | Llamas et al., 2006 |
| pMPFiuA | pMP220 carrying the P. aeruginosa fiuA (PA0470) promoter region cloned upstream the lacZ gene; TcR | Llamas et al., 2006 |
a
ApR, KmR, NalR, RifR, SmR, and TcR, resistance to ampicillin, kanamycin, nalidixic acid, rifampicin, streptomycin, and tetracycline, respectively.