Table 4.
Differentially expressed genes and proteins connected to p-hydroxybenzoate production in P. putida S12palB1
| Protein description (gene) | KT2440 locus tag | Transcriptome fold changes | Proteome fold changes | ||
|---|---|---|---|---|---|
| Glycerola | Glucoseb | Glycerola | Glucoseb | ||
| Aromatic amino acid biosynthesis | |||||
| Tryptophan synthase, alpha subunit (trpA) | PP0082 | 1.6 | |||
| Anthranilate synthase, component I (trpE) | PP0417 | 6.5 | 9.2 | 2.7 ± 0.1c | 13.1 ± 4.2c |
| Anthranilate synthase, component II (trpG) | PP0420 | 4.2 | 10.3 | 2.9 | 2.7 |
| Anthranilate phosphoribosyltransferase (trpD) | PP0421 | 4.4 | 7.8 | ||
| Indole-3-glycerol phosphate synthase (trpC) | PP0422 | 2.6 | 5.6 | 4.0 | |
| DAHP synthase, class I (aroF1) | PP2324 | 2.5 | 2.6 | ||
| DAHP synthase, class I (aroF2) | PP3080 | 3.1 | 9.3 | ||
| Quinate dehydrogenase (pyrroloquinoline-quinone), putative | PP3569 | 1.4d | 2.8 | ||
| Phenylalanine-4-hydroxylase (phhA) | PP4490 | 3.3 | 107.0 | ||
| Pterin-4-alpha-carbinolamine dehydratase (phhB) | PP4491 | 3.5 | 76.3 | ||
| p-Coumarate catabolism | |||||
| Acyl-CoA dehydrogenase, ferrulic acid biotransformation protein, putative (acd) | PP3354 | 2.5 | 28.2 | ||
| β-ketothiolase (aat) | PP3355 | 1.8d | 11.9 | ||
| Feruloyl-CoA-synthetase (fcs) | PP3356 | 3.6 | 72.8 | ||
| Vanillin dehydrogenase (vdh) | PP3357 | 3.0 | 37.7 | ||
| Enoyl-CoA hydratase aldolase (ech) | PP3358 | 2.5 | 12.2 | ||
| Hydroxycinnamic acid degradation regulator, putative | PP3359 | 1.9d | 2.9 | ||
| Aromatic catabolism | |||||
| Tyrosine decarboxylase, putative | PP2552 | 0.92d | 48.0 | ||
| 4-hydroxyphenylpyruvate dioxygenase (hpd) | PP3433 | 1.5d | 2.8 | ||
| Transport systems | |||||
| Amino acid ABC transporter, periplasmic amino acid-binding protein | PP0282 | 1.6 | |||
| Aromatic amino acid transporter (aroP2) | PP0927 | 3.0 | 9.0 | ||
| Amino acid ABC transporter ATP-binding protein | PP1068 | 2.5 | |||
| Amino acid ABC transporter, periplasmic amino acid-binding protein | PP1071 | 0.64 ± 0.01c | |||
| Branched-chain amino acid ABC transporter, ATP-binding protein (braG) | PP1137 | 2.0 | |||
| Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein (braC) | PP1141 | 2.1 ± 0.1c | |||
| Multidrug efflux MFS transporter, putative | PP1271 | 3.8 | 7.6 | ||
| Multidrug efflux MFS membrane fusion protein | PP1272 | 13.7 | 17.4 | ||
| Multidrug efflux MFS outer membrane protein | PP1273 | 4.8 | 10.1 | ||
| General amino acid ABC transporter, periplasmic binding protein (aapJ) | PP1297 | 0.48d | 3.4 | 0.57 ± 0.06c | 5.1 ± 0.6c |
| General amino acid ABC transporter, permease protein (aapQ) | PP1298 | 0.51d | 4.6 | ||
| General amino acid ABC transporter, permease protein (aapM) | PP1299 | 0.70d | 2.9 | ||
| General amino acid ABC transporter, ATP-binding protein (aapP) | PP1300 | 0.56d | 3.0 | 0.61 | 2.6 |
| Amino acid transporter, AAT family | PP3727 | 2.5 | 4.2 | ||
| Aromatic amino acid transporter (aroP1) | PP4495 | 4.0 | 14.1 | ||
| Branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein | PP4867 | 0.65 | 2.4 ± 0.1c | ||
aFold change in expression level of P. putida S12palB1 compared to P. putida S12 pJTTpal on glycerol as substrate; values below 1 represent down regulation and values above 1 represent upregulation in P. putida S12palB1
bFold change in expression level of P. putida S12palB1 compared to P. putida S12 pJNNmcs(t) on glucose as substrate; values below 1 represent down regulation and values above 1 represent upregulation in P. putida S12palB1
cAverage of all spots per protein, errors represent the maximum deviation from the mean. See supplemental data for values per spot
dBelow threshold