TABLE 2.
Genes with an apparent link to phenol production that are differentially expressed in P. putida S12TPL3 compared to control strain P. putida S12JNNmcs(t)
| Functional group | Protein description (gene) | KT2440 locus tag | Fold changea |
|---|---|---|---|
| Tyrosine biosynthesis | DAHP synthase, class I (aroF-1) | PP2324 | 2.2 |
| Shikimate 5-dehydrogenase/quinate 5-dehydrogenase family protein | PP2406 | 2.7b | |
| 3-Dehydroquinate dehydratase, type II | PP2407 | 6.3b | |
| Shikimate dehydrogenase family protein | PP2608 | 5.1b | |
| DAHP synthase, class I (aroF-2) | PP3080 | 21.1 | |
| Quinate dehydrogenase (pyrroloquinoline quinone dependent), putative | PP3569 | 7.8 | |
| Phenylalanine-4-hydroxylase (phhA) | PP4490 | 87.6 | |
| Pterin-4-alpha-carbinolamine dehydratase (phhB) | PP4491 | 57.0 | |
| Tryptophan biosynthesis | Anthranilate synthase, component I (trpE) | PP0417 | 8.6 |
| Anthranilate synthase, component II (trpG) | PP0420 | 6.8 | |
| Anthranilate phosphoribosyltransferase (trpD) | PP0421 | 6.3 | |
| Indole-3-glycerol phosphate synthase (trpC) | PP0422 | 5.9 | |
| Aromatic degradation | 4-Hydroxybenzoate transporter (pcaK) | PP1376 | 3.4b |
| Beta-ketoadipyl coenzyme A thiolase (pcaF) | PP1377 | 7.1b | |
| 3-Oxoadipate enol-lactone hydrolase (pcaD) | PP1380 | 2.1b | |
| 4-Carboxymuconolactone decarboxylase (pcaC) | PP1381 | 1.9 | |
| BenF-like protein | PP1383 | 25.1 | |
| Tyrosine decarboxylase, putative | PP2552 | 3.7 | |
| 4-Hydroxyphenylpyruvate dioxygenase, putative | PP2554 | 3.8b | |
| Fumarylacetoacetate hydrolase family protein | PP2836 | 29.3 | |
| 4-Hydroxyphenylpyruvate dioxygenase (hpd) | PP3433 | 2.8 | |
| 4-Hydroxybenzoate hydroxylase (pobA) | PP3537 | 2.4b | |
| 3-Oxoadipate coenzyme A transferase, subunit A (pcaI) | PP3951 | 5.0b | |
| 3-Oxoadipate coenzyme A transferase, subunit B (pcaJ) | PP3952 | 3.2 | |
| Protocatechuate 3,4-dioxygenase, alpha subunit (pcaG) | PP4655 | 2.9 | |
| Protocatechuate 3,4-dioxygenase, beta subunit (pcaH) | PP4656 | 4.9b | |
| Amino acid transport | Transporter, LysE family | PP0198 | 2.1 |
| Branched-chain amino acid ABC transporter, ATP-binding protein | PP0615 | 0.6 | |
| Branched-chain amino acid ABC transporter, permease protein | PP0618 | 0.4 | |
| Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein | PP0619 | 0.5 | |
| Aromatic amino acid transporter (aroP2) | PP0927 | 10.7 | |
| Amino acid ABC transporter, permease protein | PP1070 | 0.5 | |
| Amino acid efflux protein, putative | PP3023 | 2.1 | |
| Aromatic amino acid transporter (aroP1) | PP4495 | 10.5 | |
| TCA cycle | Fumarate hydratase, class I | PP0897 | 0.5 |
| Oxidoreductase, Ldh family | PP2835 | 111.5 | |
| Isocitrate dehydrogenase, NADP dependent, prokaryotic type | PP4011 | 1.9 | |
| Malic enzyme | PP5085 | 2.2 |
a
Fold change in expression level in P. putida S12TPL3 compared to P. putida S12JNNmcs(t).
b
There was a large variation of expression levels between duplicates of P. putida S12TPL3. The average fold changes shown were confirmed by RT-qPCR.