TABLE 3.
Selected upregulated genes upon TRQ treatment.
| Sampling timec |
|||||
| ORFa | Geneb | EXP | STA | QSd | Protein descriptione |
| Amino acid biosynthesis and metabolism | |||||
| PA0025 | aroE | 1.3 | Shikimate dehydrogenase | ||
| PA0245 | aroQ2 | 3.6 | 3-Dehydroquinate dehydratase | ||
| PA0331 | ilvA1 | 1.2 | Threonine dehydratase, biosynthetic | ||
| PA0390 | metX | 1.7 | Homoserine O-acetyltransferase | ||
| PA0782 | putA | 1.8 | Proline dehydrogenase PutA | ||
| PA0895 | aruC | 1.4 | N2-succinylornithine 5-aminotransferase (SOAT) | ||
| PA0896 | aruF | 1.2 | Subunit I of arginine N2-succinyltransferase | ||
| PA0897 | aruG | 1.2 | Subunit II of arginine N2-succinyltransferase | ||
| PA1818 | cadA | 1.2 | Lysine decarboxylase | ||
| PA3082 | gbt | 1.2 | Glycine betaine transmethylase | ||
| PA4731 | panD | 1.4 | 1.2 | Aspartate 1-decarboxylase precursor | |
| Carbon compound catabolism | |||||
| PA0153 | pcaH | 3.9 | Protocatechuate 3,4-dioxygenase, beta subunit | ||
| PA0154 | pcaG | 4.1 | Protocatechuate 3,4-dioxygenase, alpha subunit | ||
| PA0226 | 3.5 | 1.6 | Probable CoA transferase, subunit A | ||
| PA0227 | 3.3 | Probable CoA transferase, subunit B | |||
| PA0232 | pcaC | 1.4 | 1.3 | Gamma-carboxymuconolactone decarboxylase | |
| PA0247 | pobA | 1.7 | P-Hydroxybenzoate hydroxylase | ||
| PA2261 | 2.5 | + | Probable 2-ketogluconate kinase | ||
| PA2323 | gapN | 2.7 | GapN | ||
| PA2507 | catA | 2.1 | 3.4 | Catechol 1,2-dioxygenase | |
| PA2508 | catC | 2.0 | 3.3 | Muconolactone delta-isomerase | |
| PA2509 | catB | 1.5 | 1.4 | Muconate cycloisomerase I | |
| PA2515 | xylL | 3.2 | Cis-1,2- dihydroxycyclohexa3-,4-diene carboxylate dehydrogenase | ||
| PA2517 | xylY | 4.1 | 2.8 | Toluate 1,2-dioxygenase beta subunit | |
| PA2518 | xylX | 4.5 | 2.7 | Toluate 1,2-dioxygenase alpha subunit | |
| PA4091 | hpaA | 4.7 | 4-Hydroxyphenylacetate 3-monooxygenase large chain | ||
| PA4092 | hpaC | 4.5 | 4-Hydroxyphenylacetate 3-monooxygenase small chain | ||
| PA4123 | hpcC | 4.2 | 5-Carboxy-2-hydroxymuconate semialdehyde dehydrogenase | ||
| PA4124 | hpcB | 4.0 | Homoprotocatechuate 2,3-dioxygenase | ||
| PA4125 | hpcD | 4.0 | 5-Carboxymethyl-2-hydroxymuconate isomerase | ||
| PA4127 | hpcG | 3.8 | 2-Oxo-hept3–ene-1,7-dioate hydratase | ||
| PA5351 | rubA1 | 1.4 | Rubredoxin 1 | ||
| PA4670 | prs | 1.6 | 2.0 | Ribose-phosphate pyrophosphokinase | |
| PA2862 | lipA | 1.8 | 2.7 | Lactonizing lipase precursor | |
| PA3363 | amiR | 1.5 | 1.0 | Aliphatic amidase regulator | |
| Central intermediary metabolism | |||||
| PA0654 | speD | 1.5 | S-Adenosylmethionine decarboxylase proenzyme | ||
| PA2393 | 1.6 | Putative dipeptidase | |||
| PA3182 | pgl | 1.8 | + | 6-Phosphogluconolactonase | |
| PA3582 | glpK | 1.5 | 2.2 | Glycerol kinase | |
| PA4100 | 1.3 | Probable dehydrogenase | |||
| PA4956 | rhdA | 1.3 | Thiosulfate:cyanide sulfurtransferase | ||
| PA5435 | 2.3 | 1.3 | Probable transcarboxylase subunit | ||
| PA5436 | 2.7 | 1.1 | Probable biotin carboxylase subunit of a transcarboxylase | ||
| PA4442 | cysN | 1.7 | −1.9 | + | ATP sulfurylase GTP-binding subunit/APS kinase |
| PA4443 | cysD | 2.1 | −1.1 | + | ATP sulfurylase small subunit |
| PA3181 | 1.6 | + | 2-Keto3–deoxy-6-phosphogluconate aldolase | ||
| PA4748 | tpiA | 1.2 | Triosephosphate isomerase | ||
| PA3562 | fruI | 1.3 | Phosphotransferase system transporter enzyme I, FruI | ||
| Energy metabolism | |||||
| PA0519 | nirS | 1.7 | 1.9 | Nitrite reductase precursor | |
| PA0521 | 2.0 | Probable cytochrome c oxidase subunit | |||
| PA0523 | norC | 4.8 | Nitric-oxide reductase subunit C | ||
| PA0524 | norB | 4.3 | Nitric-oxide reductase subunit B | ||
| PA0525 | 3.1 | Probable denitrification protein NorD | |||
| PA1317 | cyoA | 1.5 | −1.3 | + | Cytochrome o ubiquinol oxidase subunit II |
| PA2382 | lldA | 2.1 | L-Lactate dehydrogenase | ||
| PA2664 | fhp | 3.0 | Flavohemoprotein | ||
| PA3392 | nosZ | 2.9 | + | Nitrous-oxide reductase precursor | |
| PA3393 | nosD | 1.9 | + | NosD protein | |
| PA3872 | narI | 2.0 | + | Respiratory nitrate reductase gamma chain | |
| PA3873 | narJ | 1.8 | + | Respiratory nitrate reductase delta chain | |
| PA3874 | narH | 1.8 | + | Respiratory nitrate reductase beta chain | |
| PA3875 | narG | 2.2 | + | Respiratory nitrate reductase alpha chain | |
| PA2321 | gntK | 3.1 | + | GntK | |
| PA2516 | xylZ | 4.1 | 1.7 | Toluate 1,2-dioxygenase electron transfer component | |
| PA3183 | zwf | 2.1 | + | Glucose-6-phosphate 1-dehydrogenase | |
| PA3194 | edd | 1.5 | + | Phosphogluconate dehydratase | |
| PA3195 | gapA | 2.5 | + | Glyceraldehyde 3-phosphate dehydrogenase | |
| PA3394 | nosF | 1.6 | + | NosF protein | |
aPA numbers are from http://www.pseudomonas.com; ORF, open reading frame. bGenes are obtained from http://www.pseudomonas.com. cThe ratios (log2 ratio) represent expression levels in PAO1 cultures supplemented with 1/4 TRQ relative to that of the control at exponential phase (EXP) and stationary phase (STA). dThese genes were identified as QS regulated in previous transcriptome studies. eProteins are described from http://www.pseudomonas.com.