TABLE 2.
Genes/proteins found to be significantly upregulated upon iberin treatmenta
| Strain no. | Gene | QSb | Description of productc | RNA-seq (500 μM) |
iTRAQ proteomics (500 μM) |
||
|---|---|---|---|---|---|---|---|
| Fold changed | P value | Fold changed | P value | ||||
| PA0140 | ahpF | Alkyl hydroperoxide reductase subunit F | 4.85 | <0.01 | |||
| PA0182 | Probable short-chain dehydrogenase | 7.6 | 0.04 | ||||
| PA0185 | Probable permease of ABC transporter | 8.9 | 0.04 | ||||
| PA0201 | Hypothetical protein | 25.9 | 0.01 | ||||
| PA0202 | Probable amidase | 20.7 | 0.03 | ||||
| PA0283 | sbp | Sulfate-binding protein precursor | 26.0 | 0.01 | |||
| PA0284 | Hypothetical protein | 32.9 | 0.04 | ||||
| PA0565 | Conserved hypothetical protein | 2.91 | <0.01 | ||||
| PA0849 | trxB2 | Thioredoxin reductase 2 | 2.94 | 0.01 | |||
| PA0865 | hpd | 4-Hydroxyphenylpyruvate dioxygenase | 42.2 | 0.04 | 2.75 | <0.01 | |
| PA0878 | Hypothetical protein | 7.9 | 0.04 | ||||
| PA1240 | Probable enoyl-CoA hydratase/isomerase | 3.45 | <0.01 | ||||
| PA1260 | Amino acid ABC transporter periplasmic-binding protein | 4.49 | <0.01 | ||||
| PA1285 | Probable transcriptional regulator | 5.2 | 0.05 | ||||
| PA1310 | phnW | 2-Aminoethylphosphonate–pyruvate aminotransferase | 19.3 | 0.05 | |||
| PA1332 | Hypothetical protein | 17.7 | 0.05 | ||||
| PA1334 | Probable oxidoreductase | 74.7 | 0.04 | 5.74 | <0.01 | ||
| PA1493 | cysP | Sulfate-binding protein of ABC transporter | 8.2 | <0.01 | |||
| PA1999 | dhcA | DhcA, dehydrocarnitine CoA transferase, subunit A | 9.1 | 0.01 | |||
| PA2000 | dhcB | DhcB, dehydrocarnitine CoA transferase, subunit B | 9.5 | <0.01 | |||
| PA2008 | fahA | Fumarylacetoacetase | 54.8 | 0.03 | |||
| PA2009 | hmgA | Homogentisate 1,2-dioxygenase | 62.0 | 0.02 | |||
| PA2197 | Conserved hypothetical protein | 2.07 | <0.01 | ||||
| PA2247 | bkdA1 | 2-Oxoisovalerate dehydrogenase (alpha subunit) | 2.71 | <0.01 | |||
| PA2248 | bkdA2 | 2-Oxoisovalerate dehydrogenase (beta subunit) | 2.98 | <0.01 | |||
| PA2249 | bkdB | Branched-chain alpha-keto acid dehydrogenase (lipoamide component) | 2.64 | <0.01 | |||
| PA2277 | arsR | ArsR protein | 15.3 | 0.05 | |||
| PA2278 | arsB | ArsB protein | 9.6 | 0.02 | |||
| PA2310 | Hypothetical protein | 20.5 | 0.03 | ||||
| PA2311 | Hypothetical protein | 51.8 | 0.05 | ||||
| PA2312 | Probable transcriptional regulator | 29.6 | <0.01 | ||||
| PA2327 | X | Probable permease of ABC transporter | 6.6 | 0.05 | |||
| PA2359 | Probable transcriptional regulator | 34.5 | 0.03 | ||||
| PA2444 | glyA2 | Serine hydroxymethyltransferase | 37.4 | 0.05 | |||
| PA2445 | gcvP2 | Glycine cleavage system protein P2 | 3.67 | <0.01 | |||
| PA2483 | Conserved hypothetical protein | 3.30 | <0.01 | ||||
| PA2490 | Conserved hypothetical protein | 16.4 | 0.05 | ||||
| PA2491 | mexS | MexS | 34.1 | 0.03 | 5.08 | 0.01 | |
| PA2493 | mexE | RND multidrug efflux membrane fusion protein MexE precursor | 5.69 | <0.01 | |||
| PA2494 | mexF | RND multidrug efflux transporter MexF | 129.4 | 0.04 | 5.69 | <0.01 | |
| PA2495 | oprN | Multidrug efflux outer membrane protein OprN precursor | 102.3 | 0.03 | 5.34 | <0.01 | |
| PA2535 | Probable oxidoreductase | 3.02 | <0.01 | ||||
| PA2575 | Hypothetical protein | 28.5 | 0.02 | 4.01 | <0.01 | ||
| PA2579 | kynA | l-Tryptophan:oxygen 2,3-oxidoreductase (decyclizing) KynA | 5.3 | 0.05 | |||
| PA2580 | Conserved hypothetical protein | 26.1 | 0.01 | 4.58 | 0.01 | ||
| PA2594 | X | Conserved hypothetical protein | 9.0 | 0.02 | |||
| PA2599 | Conserved hypothetical protein | 12.1 | 0.05 | ||||
| PA2600 | Hypothetical protein | 21.0 | <0.01 | ||||
| PA2610 | Conserved hypothetical protein | 5.2 | 0.03 | ||||
| PA2758 | Probable transcriptional regulator | 63.7 | 0.02 | ||||
| PA2759 | Hypothetical protein | 179.3 | 0.01 | ||||
| PA2767 | Probable enoyl-CoA hydratase/isomerase | 5.8 | 0.03 | ||||
| PA2786 | Hypothetical protein | 8.6 | 0.05 | ||||
| PA2812 | Probable ATP-binding component of ABC transporter | 20.4 | 0.03 | ||||
| PA2813 | Probable glutathione S-transferase | 32.7 | 0.04 | ||||
| PA2844 | Conserved hypothetical protein | 8.3 | 0.04 | ||||
| PA2845 | Hypothetical protein | 91.2 | 0.04 | ||||
| PA2931 | cifR | CifR | 10.4 | 0.03 | |||
| PA2932 | morB | Morphinone reductase | 45.7 | 0.03 | |||
| PA3035 | Probable glutathione S-transferase | 8.0 | <0.01 | ||||
| PA3126 | ibpA | Heat shock protein IbpA | 4.37 | <0.01 | |||
| PA3222 | Hypothetical protein | 5.4 | 0.04 | ||||
| PA3229 | Hypothetical protein | 311.5 | 0.04 | ||||
| PA3230 | Conserved hypothetical protein | 69.5 | 0.01 | ||||
| PA3938 | Probable periplasmic taurine-binding protein precursor | 24.5 | 0.05 | ||||
| PA3446 | Conserved hypothetical protein | 63.5 | 0.05 | ||||
| PA3450 | Probable antioxidant protein | 39.4 | 0.01 | ||||
| PA3931 | Conserved hypothetical protein | 44.7 | 0.05 | ||||
| PA4166 | Probable acetyltransferase | 77.6 | 0.02 | ||||
| PA4167 | dkgB | Probable oxidoreductase | 112.0 | <0.01 | 4.93 | <0.01 | |
| PA4173 | Conserved hypothetical protein | 12.4 | 0.01 | ||||
| PA4236 | katA | Catalase | 4.01 | <0.01 | |||
| PA4354 | Conserved hypothetical protein | ||||||
| PA4355 | pyeM | PyeM | 37.3 | <0.01 | |||
| PA4356 | xenB | Xenobiotic reductase | 4.28 | <0.01 | |||
| PA4385 | groEL | GroEL protein | 6.4 | 0.04 | 2.48 | <0.01 | |
| PA4386 | groES | GroES protein | 6.4 | 0.03 | |||
| PA4387 | Conserved hypothetical protein | 8.0 | 0.05 | ||||
| PA4613 | katB | Catalase | 5.10 | <0.01 | |||
| PA4623 | Hypothetical protein | 727.4 | 0.01 | ||||
| PA4973 | thiC | Thiamine biosynthesis protein ThiC | 2.58 | <0.01 | |||
a
Upregulation was defined as a >5-fold increase in the RNA-Seq result and a >2-fold increase in the iTRAQ proteomics result. Only genes/proteins showing a significant difference in expression from the control (i.e., P value < 0.05) were selected.
b
An “X” indicates that the gene/protein is regulated by quorum sensing (4), in reference to the QS-regulated genes/proteins, as determined previously.
c
CoA, coenzyme A; RND, resistance-nodulation-cell division.
d
Empty lines indicate no significant change in expression levels.