TABLE 1.
Proteins quantified by label-free proteomic analysis that showed a significant increase in abundance in response to vanillin treatmenta
| Protein name |
Protein description | Fold increase in abundance |
P value |
|---|---|---|---|
| Oxidative stress defense | |||
| AhpC | Alkyl hydroperoxide reductase subunit C | 4.1 | 1.86E−05 |
| AhpF | Alkyl hydroperoxide reductase subunit F | 2.6 | 1.30E−04 |
| KatE | Catalase HPII | 4.8 | 4.65E−02 |
| MarR | Multiple antibiotic resistance protein | 9.4 | 3.89E−03 |
| OsmC | Peroxiredoxin | 4.4 | 2.74E−03 |
| SodA | Superoxide dismutase (Mn) | 5.0 | 3.58E−02 |
| Glutathione | |||
| GrxB | Glutaredoxin-2 | 7.5 | 4.94E−04 |
| GshB | Glutathione synthetase | 8.4 | 1.44E−02 |
| Gss | Glutathionylspermidine synthetase/amidase | 3.4 | 5.99E−04 |
| GstA | Glutathione S-transferase | 4.2 | 1.14E−02 |
| YghU | Disulfide-bond oxidoreductase | 6.5 | 1.01E−03 |
| YqjG | Glutathionyl-hydroquinone reductase | 3.7 | 5.01E−04 |
| Low-MW compound accumulation | |||
| GadC | Glutamate/γ-aminobutyrate antiporter | 5.5 | 4.87E−03 |
| GltB | Glutamate synthase (NADPH) large chain | 2.8 | 9.58E−02 |
| OtsA | α,α-Trehalose-phosphate synthase (UDP forming) | 4.6 | 1.48E−03 |
| Chaperones and proteases | |||
| CbpA | Curved DNA-binding protein | 3.4 | 3.89E−03 |
| ClpB | Chaperone protein | 2.8 | 3.78E−05 |
| Dcp | Periplasmic serine endoprotease | 3.1 | 1.44E−05 |
| DegP | Periplasmic serine endoprotease | 5.7 | 1.08E−05 |
| HchA | Molecular chaperone Hsp31 and glyoxalase 3 | 9.6 | 2.72E−03 |
| HslO | 33-kDa chaperonin | 4.3 | 2.23E−02 |
| PepB | Peptidase B | 5.2 | 2.45E−05 |
| Metal homeostasis | |||
| EntB | Enterobactin synthase component B | 37.2 | 1.17E−05 |
| EntE | Enterobactin synthase component E | 8.5 | 1.19E−03 |
| EntF | Enterobactin synthase component F | 23.1 | 6.64E−03 |
| MoaB | Molybdenum cofactor biosynthesis protein B | 9.2 | 1.40E−06 |
| SufB | FeS cluster assembly protein | 5.9 | 4.04E−04 |
| SufD | FeS cluster assembly protein | 5.2 | 6.42E−03 |
| SufS | Cysteine desulfurase | 5.6 | 1.86E−03 |
| Aldehyde detoxification | |||
| Ahr | Aldehyde reductase | 8.5 | 1.82E−03 |
| AldB | Aldehyde dehydrogenase B | 7.9 | 6.58E−04 |
| DkgA | 2,5-Diketo-d-gluconic acid reductase A | 41.1 | 6.46E−04 |
| YahK | Aldehyde reductase | 3.6 | 3.90E−02 |
| YghA | Uncharacterized oxidoreductase | 4.3 | 1.87E−02 |
| YqhD | Alcohol dehydrogenase | 34.8 | 6.11E−04 |
| Central carbon metabolism and energy production | |||
| AceA | Isocitrate lyase | 5.1 | 3.15E−02 |
| AceB | Malate synthase A | 6.4 | 6.52E−03 |
| AcnA | Aconitate hydratase 1 | 8.0 | 7.53E−03 |
| Acs | Acetyl-coenzyme A synthetase | 5.6 | 2.60E−02 |
| FbaB | Fructose-bisphosphate aldolase class 1 | 6.9 | 2.82E−03 |
| FumC | Fumarate hydratase class II | 38.4 | 1.49E−05 |
| GltA | Citrate synthase | 3.3 | 1.51E−02 |
| Mdh | Malate dehydrogenase | 4.0 | 3.12E−04 |
| MtlA | PTS mannitol-specific EIICBA component | 4.1 | 4.68E−04 |
| PfkB | ATP-dependent 6-phosphofructokinase isozyme 2 | 3.6 | 2.00E−02 |
| Ppk | Polyphosphate kinase | 3.5 | 6.31E−04 |
| PoxB | Pyruvate oxidase (ubiquinone reducing) | 10.9 | 1.24E−02 |
| Sad | Succinate semialdehyde dehydrogenase | 6.8 | 1.02E−02 |
| TalA | Transaldolase A | 4.7 | 1.06E−02 |
| TktB | Transketolase 2 | 5.3 | 2.03E−02 |
| Zwf | Glucose-6-phosphate 1-dehydrogenase | 3.6 | 4.46E−04 |
| Nitrocompound detoxification | |||
| NfsA | Oxygen-insensitive NADPH nitroreductase | 12.8 | 5.64E−06 |
| NfnB | Oxygen-insensitive NAD(P)H nitroreductase | 14.8 | 7.03E−06 |
| Amino acid biosynthesis | |||
| AstC | Succinylornithine transaminase | 4.1 | 4.80E−02 |
| HisB | Histidine biosynthesis bifunctional protein | 5.5 | 4.59E−03 |
| HisC | Histidinol-phosphate aminotransferase | 5.2 | 2.21E−02 |
| HisD | Histidinol dehydrogenase | 3.8 | 2.90E−03 |
| HisG | ATP phosphoribosyltransferase | 8.0 | 9.55E−05 |
| IlvB | Acetolactate synthase isozyme 1 large subunit | 3.9 | 3.32E−02 |
| LysC | Lysine-sensitive aspartokinase 3 | 3.0 | 4.23E−04 |
| PheA | P-protein | 3.4 | 1.13E−02 |
| TrpB | Tryptophan synthase beta chain | 2.7 | 6.73E−04 |
| YecD | Isochorismatase family protein | 7.2 | 5.35E−04 |
| Folate metabolism | |||
| FolE | GTP cyclohydrolase 1 | 3.1 | 1.31E−04 |
| PanB | 3-Methyl-2-oxobutanoate hydroxymethyltransferase | 3.5 | 8.48E−03 |
| YbgI | Putative GTP cyclohydrolase 1 type 2 | 3.1 | 7.58E−03 |
| YgfZ | tRNA-modifying protein | 4.9 | 2.44E−03 |
| β-d-Glucuronide and d-glucuronate degradation | |||
| UidA | Beta-glucuronidase | 5.6 | 1.78E−03 |
| UxaC | Uronate isomerase | 12.8 | 8.36E−05 |
| UxuA | Mannonate dehydratase | 4.1 | 1.00E−02 |
| Uncharacterized | |||
| YbjP | Uncharacterized lipoprotein | 4.0 | 4.46E−02 |
| YdhJ | Uncharacterized protein | 3.5 | 1.06E−02 |
| YeiR | Uncharacterized protein | 6.4 | 1.90E−02 |
| YhbW | Uncharacterized protein | 77.1 | 4.18E−08 |
| YjhC | Uncharacterized oxidoreductase | 23.8 | 4.43E−03 |
| YncE | Uncharacterized protein | 9.5 | 1.31E−02 |
| Others | |||
| Add | Adenosine deaminase | 3.5 | 2.75E−04 |
| Amn | AMP nucleosidase | 5.5 | 6.10E−06 |
| AnmK | Anhydro-N-acetylmuramic acid kinase | 3.2 | 2.39E−04 |
| Cfa | Cyclopropane-fatty-acyl-phospholipid synthase | 4.2 | 4.81E−04 |
| CodA | Cytosine deaminase | 3.2 | 2.99E−02 |
| CurA | NADPH-dependent curcumin reductase | 4.1 | 3.97E−03 |
| DcyD | d-Cysteine desulfhydrase | 4.4 | 3.35E−03 |
| EmrA | Multidrug export protein | 4.5 | 1.26E−02 |
| GhrA | Glyoxylate/hydroxypyruvate reductase A | 4.8 | 5.56E−04 |
| HdhA | 7-Alpha-hydroxysteroid dehydrogenase | 10.4 | 3.08E−04 |
| HemB | Delta-aminolevulinic acid dehydratase | 9.0 | 3.32E−03 |
| LysU | Lysine-tRNA ligase, heat inducible | 3.8 | 1.18E−05 |
| MdaB | Modulator of drug activity B | 8.4 | 1.93E−05 |
| MetG | Methionine-tRNA ligase | 2.7 | 4.19E−05 |
| MnmA | tRNA-specific 2-thiouridylase | 2.8 | 1.60E−02 |
| TorA | Trimethylamine-N-oxide reductase 1 | 8.1 | 5.48E−03 |
| YadG | Uncharacterized ABC transporter ATP-binding protein | 8.9 | 3.26E−04 |
a
Fold increase data were calculated from the average abundances of four independent vanillin-treated replicates relative to those of the four independent untreated replicates. PTS, phosphotransferase system.