TABLE 4.
Selected categories of genes were differentially expressed under swarming conditions in PA14 ntrB and/or ntrC mutant strains.
| PAO1 locus | Name | Annotation | FC ΔntrB | FC ΔntrC |
| A. Metabolic genes involved in nitrogen metabolism (KEGG) | ||||
| PA0296 | spuI | Glutamylpolyamine synthetase | −2.57 | −2.56 |
| PA0298 | spuB | Glutamylpolyamine synthetase | −1.87 | −1.73 |
| PA3356 | pauA5 | Glutamine synthetase | −1.51 | −1.47 |
| PA1783 | nasA | Nitrate transporter | −16 | −650 |
| PA1781 | nirB | Assimilatory nitrite reductase large | −50 | −137 |
| PA1780 | nirD | Assimilatory nitrite reductase small | −64.2 | −340 |
| PA1779 | – | ASSIMILATORY nitrate reductase | −39.9 | −90.0 |
| PA1566 | pauA3 | Glutamylpolyamine synthetase | −42.6 | −42.0 |
| PA1172 | napC | Cytochrome c-type protein NapC | −1.08 | −1.59 |
| PA1174 | napA | Nitrate reductase catalytic subunit | −1.29 | −1.60 |
| PA1175 | napD | NapD protein of periplasmic nitrate reductase | −1.13 | −1.64 |
| PA1176 | napF | Ferredoxin component of nitrate reductase | −2.29 | −2.22 |
| PA1177 | napE | Periplasmic nitrate reductase NapE | −1.62 | −2.27 |
| PA1785 | nasT | Regulation of nitrate assimilation | −92.8 | −83.4 |
| PA1786 | nasS | Nitrate binding ABC transport protein | −121 | −91.2 |
| PA4588 | gdhA | Glutamate dehydrogenase | 17.2 | 16.5 |
| PA4864 | ureD | Urease accessory protein | −3.91 | −4.13 |
| PA4865 | ureA | Urease gamma subunit | −3.37 | −3.72 |
| PA4867 | ureB | Urease beta subunit | −3.80 | −4.46 |
| PA4868 | ureC | Urease alpha subunit | −3.60 | −3.80 |
| PA4891 | ureE | Urease accessory protein UreE | −7.86 | −5.75 |
| PA4892 | ureF | Urease accessory protein UreF | −6.70 | −7.79 |
| PA4893 | ureG | Urease accessory protein UreG | −5.89 | −5.97 |
| PA5119 | glnA | Glutamine synthetase | −1.92 | −1.98 |
| PA5173 | arcC | Carbamate kinase | −1.25 | −1.58 |
| PA5287 | amtB | Ammonium transporter AmtB | −19.2 | −15.7 |
| PA5288 | glnK | Nitrogen regulatory protein P-II | −2.51 | −2.68 |
| PA5530 | – | C5−dicarboxylate transporter | 13.3 | 12.4 |
| B. Metabolic genes involved in central carbon metabolism (KEGG) | ||||
| PA0130 | bauC | Aldehyde dehydrogenase | −2.67 | −2.45 |
| PA0552 | pgk | Phosphoglycerate kinase | 1.57 | 2.19 |
| PA0555 | fda | Fructose-1,6-bisphosphate aldolase | 2.02 | 2.43 |
| PA0851 | – | Hypothetical protein | −1.54 | −1.56 |
| PA0854 | fumC2 | Fumarate hydratase | 1.52 | 1.85 |
| PA1326 | ilvA2 | Threonine dehydratase | −3.84 | −3.45 |
| PA1562 | acnA | Aconitate hydratase | 1.39 | 2.07 |
| PA1581 | sdhC | Succinate dehydrogenase, cytochrome b556 subunit | 2.71 | 1.91 |
| PA1582 | sdhD | Succinate dehydrogenase (D subunit) | 2.20 | 2.23 |
| PA1583 | sdhA | Succinate dehydrogenase flavoprotein subunit | 1.70 | 2.00 |
| PA1584 | sdhB | Succinate dehydrogenase iron−sulfur subunit | 1.55 | 1.68 |
| PA1585 | sucA | 2-oxoglutarate dehydrogenase E1 | 1.93 | 2.06 |
| PA1787 | acnB | Bifunctional aconitate hydratase | 1.60 | 1.77 |
| PA2147 | katE | Hydroperoxidase II | 6.56 | 16.2 |
| PA2250 | lpdV | Lipoamide dehydrogenase-Val | −1.62 | −1.31 |
| PA2442 | gcvT2 | Glycine cleavage system protein T2 | −1.62 | −1.47 |
| PA2443 | sdaA | L−serine dehydratase | −1.64 | −1.52 |
| PA2553 | – | Acyl−CoA thiolase | −1.34 | −1.53 |
| PA2634 | aceA | Isocitrate lyase | 2.00 | 2.10 |
| PA3001 | gapA | Glyceraldehyde-3-phosphate dehydrogenase | 1.75 | 1.96 |
| PA3014 | faoA | Multifunctional fatty acid oxidation complex subunit α | 1.74 | 1.75 |
| PA3182 | pgl | 6-phosphogluconolactonase | −1.80 | −1.63 |
| PA3183 | zwf | Glucose-6-phosphate 1-dehydrogenase | −1.55 | −1.52 |
| PA3415 | – | Probable dihydrolipoamide acetyltransferase | −2.61 | −2.80 |
| PA3416 | pdhB | Prob. pyruvate dehydrogenase E1 component, β chain | −2.28 | −2.55 |
| PA3417 | – | Pyruvate dehydrogenase E1 component subunit alpha | −2.39 | −2.53 |
| PA3570 | mmsA | Methylmalonate-semialdehyde dehydrogenase | −1.92 | −2.44 |
| PA3635 | eno | Phosphopyruvate hydratase | 1.61 | 1.61 |
| PA4152 | – | Branched-chain α-keto acid dehydrogenase subunit E2 | −3.96 | −1.81 |
| PA4333 | fumA | Fumarase | 2.00 | 2.13 |
| PA4470 | fumC1 | Fumarate hydratase | −2.84 | −2.31 |
| PA4640 | mqoB | Malate:quinone oxidoreductase | 1.57 | 1.87 |
| PA4670 | prs | Ribose-phosphate pyrophosphokinase | 1.62 | 1.57 |
| PA4785 | yfcY | Acetyl-CoA acetyltransferase | 1.26 | 2.10 |
| PA5110 | fbp | Fructose-1,6-bisphosphatase | 1.36 | 1.83 |
| PA5131 | pgm | Phosphoglyceromutase | 1.75 | 2.31 |
| PA5173 | arcC | Carbamate kinase | 1.75 | −1.58 |
| PA5192 | pckA | Phosphoenolpyruvate carboxykinase | 1.26 | 1.35 |
| PA5213 | gcvP1 | Glycine dehydrogenase | −1.48 | −1.61 |
| PA5322 | algC | Phosphomannomutase | 1.58 | 1.90 |
| PA5353 | glcF | Glycolate oxidase subunit GlcF | −15.6 | −20.0 |
| PA5354 | glcE | Glycolate oxidase subunit GlcE | −25.5 | −16.5 |
| PA5355 | glcD | Glycolate oxidase subunit GlcD | −9.09 | −8.42 |
| PA5415 | glyA1 | serine hydroxymethyltransferase | −4.76 | −4.96 |
| PA5421 | fdhA | Glutathione-independent formaldehyde dehydrogenase | −1.45 | −1.79 |
| PA5445 | – | Coenzyme A transferase | 1.87 | 3.38 |
| C. Pathogenicity genes required for PA14 virulence in rat chronic lung infection | ||||
| PA0098 | – | 3−oxoacyl−ACP synthase | −112 | −153 |
| PA0158 | triC | RND efflux transporter | 1.51 | 2.22 |
| PA0287 | gpuP | Sodium:solute symporter | −2.41 | −4.01 |
| PA0298 | spuB | Glutamine synthetase | −1.87 | −1.73 |
| PA0441 | dht | Phenylhydantoinase | −38.2 | −48.4 |
| PA0454 | – | Hypothetical protein | −1.83 | −1.8 |
| PA0552 | pgk | Phosphoglycerate kinase | 1.57 | 2.19 |
| PA0762 | algU | RNA polymerase sigma factor AlgU | 1.45 | 2.78 |
| PA0765 | mucC | Positive regulator for alginate biosynthesis MucC | 1.76 | 2.47 |
| PA1174 | napA | Nitrate reductase catalytic subunit napA | −1.28 | −1.60 |
| PA1596 | htpG | Heat shock protein 90 | 3.14 | 4.47 |
| PA1874 | – | Hypothetical protein | −1.75 | −1.89 |
| PA2408 | fpvD | ABC transporter ATP-binding protein | −4.64 | −6.59 |
| PA2704 | – | AraC family transcriptional regulator | −3.85 | −3.15 |
| PA2895 | sbrR | SbrR | −1.08 | 1.76 |
| PA2972 | – | Maf−like protein | 1.53 | 1.75 |
| PA3001 | – | Glyceraldehyde-3-phosphate dehydrogenase | 1.75 | 1.96 |
| PA3173 | – | Short chain dehydrogenase | 1.65 | 1.34 |
| PA3284 | – | Hypothetical protein | −2.26 | −2.27 |
| PA3598 | – | Hypothetical protein | 1.44 | 2.98 |
| PA3611 | – | Hypothetical protein | 2.17 | 2.93 |
| PA3620 | mutS | DNA mismatch repair protein MutS | 1.50 | 1.39 |
| PA3659 | – | Succinyldiaminopimelate transaminase | −1.41 | −1.61 |
| PA3922 | – | Hypothetical protein | −2.53 | −2.75 |
| PA4024 | eutB | Ethanolamine ammonia-lyase large subunit | −4.66 | −5.59 |
| PA4172 | – | Hypothetical protein | −1.58 | 8.93 |
| PA4308 | – | Exonuclease III | −1.03 | 1.04 |
| PA4338 | – | Hypothetical protein | 1.49 | 2.26 |
| PA4659 | – | MerR family transcriptional regulator | 2.72 | 1.96 |
| PA4915 | – | Methyl−accepting chemotaxis protein | −1.72 | −2.04 |
| PA4929 | – | Hypothetical protein | −2.56 | −2.77 |
| PA5075 | – | ABC transporter permease | −2.21 | −2.18 |
| PA5078 | opgG | Glucan biosynthesis protein G | 1.94 | 2.57 |
| PA5112 | estA | Esterase EstA | −1.7 | −1.88 |
| PA5131 | pgm | Phosphoglyceromutase | 1.75 | 2.31 |
| D. Pathogenicity genes required for lesb58 virulence in rat chronic lung infection | ||||
| PA1695 | pscP | Translocation protein in type III secretion | 6.67 | 10.7 |
| PA2399 | pvdD | Pyoverdine synthetase D | −2.09 | −2.00 |
| PA2525 | opmB | Outer membrane protein | 1.49 | 2.32 |
| PA2526 | muxC | Efflux transporter | 1.26 | 1.78 |
| PA2527 | muxB | RND efflux transporter | 1.41 | 1.95 |
| PA0325 | – | ABC transporter permease | −36.4 | −31.0 |
| PA2705 | – | Hypothetical protein | 1.20 | 1.62 |
| PA2023 | galU | UTP-glucose-1-phosphate uridylyltransferase | 2.36 | 3.86 |
| PA1897 | – | Hypothetical protein | −6.91 | −7.42 |
| PA1721 | pscH | Type III export protein PscH | 3.24 | 4.79 |
| PA1181 | – | Sensor protein | −1.62 | −1.68 |
| PA0766 | mucD | Serine protease MucD | 1.75 | 2.40 |
| PA4710 | phuR | Heme/hemoglobin uptake outer membrane receptor | 1.60 | 2.16 |
| PA5111 | hsiC3 | Lactoylglutathione lyase | 2.15 | −2.71 |
| PA5271 | – | Hypothetical protein | −1.04 | −1.59 |
Genes in four categories that were differentially expressed according to RNA−Seq in PA14 mutant strains. Gene expression for mutants is reported as fold-change (FC) relative to PA14 wild-type (WT). Briefly, swarm plates were inoculated with 5 μl of planktonic cells suspended at an OD600 = 0.4–0.6 in basal medium (BM2) supplemented with 0.1% casamino acids and 0.4% glucose, then incubated for 18–24 h at 37°C. Swarming cells were harvested from the tip of the swarm tendrils and RNA was isolated using Qiagen RNEasy MiniPrep kit.