Table 1.
Indole and 7HI regulate quorum‐sensing genes in P. aeruginosa PAO1.
| PA# | Gene | Fold changea | Description | ||
|---|---|---|---|---|---|
| Indole versus no indole | 7HI versus no 7HI | IAA versus no IAA | |||
| Multidrug efflux transporter | |||||
| PA4205 | mexG | −13.0 | −7.0 | −1.1 | Hypothetical protein, part of the mexGHI‐opmD cluster |
| PA4206 | mexH | −11.3 | −5.7 | −1.3 | Efflux membrane fusion protein precursor |
| PA4207 | mexI | −6.1 | −4.0 | −1.3 | Efflux transporter |
| PA4208 | opmD | −7.5 | −4.6 | −1.1 | Probable outer membrane efflux protein |
| Phenazine (pyocyanin) synthesis | |||||
| PA1901 | phzC2 | −2.5 | −2.1 | −1.2 | Phenazine biosynthesis protein PhzC |
| PA1902 | phzD2 | −3.2 | −3.0 | −1.1 | Phenazine biosynthesis protein PhzD |
| PA1903 | phzE2 | −3.5 | −2.6 | −1.2 | Phenazine biosynthesis protein PhzE |
| PA1904 | phzF2 | −4.0 | −4.3 | −1.1 | Phenazine biosynthesis protein |
| PA1905 | phzG2 | −3.2 | −3.2 | −1.2 | Pyridoxamine 5′‐phosphate oxidase |
| PA2274 | −4.9 | −3.2 | −1.1 | Possible monooxygenase, involved in phenazine biosynthesis | |
| PA4210 | phzA1 | −2.5 | −3.7 | −1.1 | Phenazine biosynthesis protein |
| PA4211 | phzB1 | −2.3 | −2.3 | −1.3 | Phenazine biosynthesis protein |
| PA4217 | phzS | −2.8 | −2.8 | −1.1 | Flavin‐containing monooxygenase |
| PQS synthesis | |||||
| PA0996 | pqsA | −1.9 | −2.0 | −1.1 | PqsA, probable coenzyme A ligase |
| PA0997 | pqsB | −2.3 | −2.5 | −1.1 | PqsB, homologous to beta‐keto‐acyl‐acyl‐carrier protein synthase |
| PA0998 | pqsC | −1.7 | −1.9 | −1.1 | PqsC, homologous to beta‐keto‐acyl‐acyl‐carrier protein synthase |
| PA0999 | pqsD | −1.3 | −1.9 | −1.1 | PqsD, 3‐oxoacyl‐[acyl‐carrier‐protein] synthase III |
| PA1000 | pqsE | −2.0 | −2.1 | −1.1 | PqsE, quinolone signal response protein |
| PA1003 | mvfR | 1.3 | −1.1 | −1.1 | MvfR (PqsR), PQS transcriptional regulator |
| Pyochelin synthesis | |||||
| PA4225 | pchF | −2.0 | −1.1 | 1.3 | Pyochelin synthetase |
| PA4226 | pchE | −2.8 | −1.3 | 1.2 | Dihydroaeruginoic acid synthetase |
| PA4227 | pchR | −1.5 | −1.2 | 1.1 | Transcriptional regulator PchR |
| PA4228 | pchD | −3.2 | −1.3 | 1.2 | Pyochelin biosynthesis protein PchD |
| PA4229 | pchC | −2.3 | −1.1 | 1.2 | Pyochelin biosynthetic protein PchC |
| PA4230 | pchB | −2.0 | −1.2 | 1.2 | Salicylate biosynthesis protein PchB |
| PA4231 | pchA | −2.1 | −1.3 | 1.2 | Salicylate biosynthesis isochorismate synthase |
| Pyoverdine synthesis | |||||
| PA2385 | pvdQ | −2.1 | −1.6 | 1.1 | pyoverdine biosynthesis protein PvdQ |
| PA2393 | pvdM | −2.5 | −1.1 | 2.1 | pyoverdine biosynthesis protein PvdM |
| PA2394 | pvdN | −2.5 | −1.2 | 1.3 | pyoverdine biosynthesis protein PvdN |
| PA2395 | pvdO | −2.0 | −1.1 | 1.5 | pyoverdine biosynthesis protein PvdO |
| PA2397 | pvdE | −2.0 | −1.4 | 1.1 | pyoverdine biosynthesis protein PvdE |
| PA2424 | pvdL | −2.3 | −1.3 | 1.9 | pyoverdine biosynthesis protein PvdV |
| PA2426 | pvdS | −6.1 | −2.6 | 2.0 | Sigma factor PvdS, transcriptional regulator |
| Metabolism | |||||
| PA0283 | sbp | −8.6 | −1.7 | 1.3 | Sulfate‐binding protein precursor |
| PA1838 | cysI | −6.1 | −2.1 | 1.2 | Sulfite reductase |
| PA3441 | ssuF | −7.5 | −5.7 | 1.2 | SsuF, part of the ssu locus |
| PA3442 | ssuB | −4.6 | −2.6 | 1.3 | SsuB, part of the ssu locus |
| PA3443 | ssuC | −3.2 | −2.6 | 1.3 | SsuC, part of the ssu locus |
| PA3444 | ssuD | −6.1 | −2.1 | 1.1 | SsuD, part of the ssu locus |
| PA3445 | ssuA | −6.5 | −2.8 | 2.8 | SsuA, part of the ssu locus |
| PA3446 | ssuE | −6.5 | −1.6 | 1.5 | SsuE, part of the ssu locus |
| PA4442 | cysN | −4.6 | −2.0 | −1.1 | ATP sulfurylase GTP‐binding subunit |
| PA4443 | cysD | −4.9 | −1.7 | 1.2 | ATP sulfurylase small subunit |
| PA5025 | metY | −2.6 | −1.3 | −1.1 | Homocysteine synthase |
| PA5427 | adhA | 2.1 | 2.6 | −1.1 | Alcohol dehydrogenase |
| Fimbriae and pili | |||||
| PA2131 | −1.9 | −2.6 | 1.0 | Probable pili assembly chaperone | |
| PA2570 | pa1L | 1.6 | −2.8 | 1.1 | PA‐I galactophilic lectin |
| PA4084 | cupB3 | −2.8 | −4.0 | 1.5 | Probable fimbrial biogenesis usher protein |
| PA4085 | cupB2 | −3.0 | −2.1 | 1.1 | Probable pili assembly chaperone |
| PA4297 | tadG | 2.3 | 3.5 | 1.7 | TadG |
| PA4298 | 1.6 | −3.2 | 1.2 | Hypothetical protein | |
| PA4299 | tadD | 1.7 | −2.6 | 1.1 | Flp pilus assembly protein TadD |
| PA4300 | tadC | 1.7 | −2.3 | 1.3 | Flp pilus assembly protein TadC |
| PA4301 | tadB | 1.6 | −3.0 | 1.5 | Flp pilus assembly protein TadB |
| PA4302 | tadA | 1.9 | −2.5 | 1.2 | Flp pilus assembly protein, ATPase CpaF |
| PA4303 | tadZ | 1.7 | −2.3 | 1.2 | Flp pilus assembly protein, ATPase CpaE |
| PA4304 | rcpA | 2.0 | −1.9 | 1.0 | Flp pilus assembly protein, secretin CpaC |
| PA4305 | rcpC | 1.6 | −2.5 | 1.1 | Flp pilus assembly protein CpaB |
| PA4306 | flp | 1.5 | −2.8 | 1.1 | Flp pilus assembly protein, pilin Flp |
| PA4651 | 2.0 | −3.5 | 1.3 | Probable pili assembly chaperone | |
| Transport of small molecules | |||||
| PA1108 | −1.9 | −5.7 | 1.5 | Probable MFS transporter | |
| PA2092 | −2.6 | −4.0 | 1.4 | Probable MFS transporter | |
| PA2204 | −9.8 | −1.9 | 1.1 | Binding protein component of ABC transporter | |
| PA2328 | −6.1 | −5.3 | 1.1 | Hypothetical protein in the cluster of ABC transporter | |
| PA2329 | −5.7 | −5.7 | 1.0 | Probable ATP‐binding component of ABC transporter | |
| PA2330 | −4.9 | −4.3 | 1.1 | Hypothetical protein in the cluster of ABC transporter | |
| PA2331 | −5.7 | −4.0 | −1.1 | Hypothetical protein in the cluster of ABC transporter | |
| PA3531 | bfrB | 3.2 | 2.3 | −1.2 | Bacterioferritin, transport of small molecules |
| PA3926 | −1.7 | −2.0 | 1.3 | Probable MFS transporter | |
| PA4514 | piuA | −4.3 | −2.5 | 1.1 | Probable outer membrane receptor for iron transport |
| Oxygenases | |||||
| PA2512 | antA | 5.3 | −2.0 | 9.2 | Anthranilate dioxygenase large subunit |
| PA2513 | antB | 6.1 | −2.6 | 1.6 | Anthranilate dioxygenase small subunit |
| PA2514 | antC | 3.0 | −2.8 | 1.6 | Anthranilate dioxygenase reductase |
| PA0106 | coxA | 3.2 | 1.4 | 1.0 | Cytochrome c oxidase, subunit I |
| PA0107 | 2.8 | 1.3 | −1.1 | Predicted cytochrome oxidase assembly factor | |
| PA0108 | coIII | 3.2 | 1.2 | −1.1 | Cytochrome c oxidase, subunit III |
| PA0109 | 2.0 | −1.1 | 1.1 | Hypothetical protein in the cluster of oxidase | |
| PA0110 | 2.6 | 1.4 | 1.1 | Hypothetical protein in the cluster of oxidase | |
| PA0111 | 3.0 | 1.3 | 1.1 | Hypothetical protein in the cluster of oxidase | |
| PA0112 | 3.0 | 1.1 | 1.1 | Hypothetical protein in the cluster of oxidase | |
| PA0113 | 3.0 | 1.4 | −1.3 | Probable cytochrome c oxidase assembly | |
| Others | |||||
| PA0715 | 3.7 | 1.4 | −2.0 | Probable bacteriophage protein | |
| PA0716 | 5.7 | 7.0 | −1.3 | Probable bacteriophage protein | |
| PA0740 | sdsA1 | −8.6 | −3.0 | 1.1 | Probable beta‐lactamase |
| PA1109 | −2.6 | −5.7 | 2.5 | Transcriptional regulator | |
| PA2258 | ptxR | −1.6 | −3.2 | 1.9 | Transcriptional regulator PtxR |
| PA3153 | wzx | 2.6 | 1.0 | −1.4 | O‐antigen translocase |
| PA3154 | wzy | 3.5 | 1.0 | −1.3 | B‐band O‐antigen polymerase |
| PA3155 | wbpE | 2.8 | 1.5 | −1.2 | Probable aminotransferase WbpE |
| PA3156 | wbpD | 2.3 | 1.4 | −1.1 | Probable acetyltransferase |
| PA3234 | yjcG | 4.3 | 2.0 | −1.1 | Probable sodium:solute symporter |
| PA3337 | rfaD | 2.0 | 2.5 | 1.1 | ADP‐l‐glycero‐d‐mannoheptose 6‐epimerase |
| PA3450 | lsfA | −6.1 | −1.4 | 1.1 | Probable antioxidant protein |
| PA3721 | nalC | 3.0 | −1.1 | 1.6 | Transcriptional regulator NalC, induced by MvfR |
| PA4563 | rpsT | 2.8 | 2.8 | −1.1 | 30S ribosomal protein S20 |
| Hypothetical proteins | |||||
| PA0284 | −13.9 | −1.6 | 1.2 | Hypothetical protein, induced by MvfR | |
| PA0492 | −4.3 | −3.5 | 1.9 | Hypothetical protein | |
| PA0696 | −4.3 | −2.5 | 1.3 | Hypothetical protein | |
| PA0939 | −1.1 | −5.3 | 1.6 | Hypothetical protein | |
| PA1190 | 5.7 | 1.6 | 1.2 | Hypothetical protein | |
| PA1837 | −4.6 | −2.1 | 1.1 | Hypothetical protein | |
| PA1914 | 1.1 | −6.1 | 1.1 | Hypothetical protein | |
| PA1953 | −3.2 | −6.1 | 1.5 | Hypothetical protein | |
| PA2036 | −2.0 | −7.0 | 1.1 | Hypothetical protein | |
| PA2078 | −3.0 | −5.7 | 1.6 | Hypothetical protein | |
| PA2419 | −1.6 | 6.1 | 1.5 | Hypothetical protein | |
| PA2805 | 2.3 | 2.1 | 1.1 | Hypothetical protein | |
| PA3080 | 3.2 | 1.1 | −1.1 | Hypothetical protein | |
| PA3235 | 4.0 | 2.5 | 1.1 | Hypothetical protein | |
| PA3237 | −1.9 | −6.1 | 1.9 | Hypothetical protein | |
| PA3572 | 2.0 | 2.5 | 1.1 | Hypothetical protein | |
| PA3719 | 4.6 | 1.3 | 1.3 | Hypothetical protein | |
| PA3720 | 2.6 | 1.2 | 1.6 | Hypothetical protein | |
| PA3931 | −5.3 | −1.7 | 1.0 | Hypothetical protein | |
| PA4087 | −2.5 | −3.5 | 1.0 | Hypothetical protein | |
| PA4359 | −4.0 | −1.1 | 1.3 | Hypothetical protein | |
| PA4377 | 3.7 | 1.7 | 1.4 | Hypothetical protein | |
| PA4614 | 3.5 | 1.4 | 1.1 | Hypothetical protein | |
| PA4638 | 6.5 | −1.6 | −1.2 | Hypothetical protein | |
| PA4683 | −2.8 | −1.3 | 1.1 | Hypothetical protein | |
a.
Partial list of differentially expressed genes in LB medium after 7 h for (i) biofilm cells grown with 1.0 mM indole versus no indole, (ii) biofilm cells grown with 0.5 mM 7‐hydroxyindole (7HI) versus no 7HI and (iii) biofilm cells grown with 1.0 mM indole‐3‐acetic acid (IAA, control compound) versus no IAA. Most significant changes are shown in bold.