TABLE 2.
Proteins quantified by label-free proteomic analysis that showed a significant decrease in abundance in response to vanillin treatmenta
| Protein name |
Protein description | Fold decrease |
P value |
|---|---|---|---|
| Anaerobic response and FeS-cluster-containing proteins | |||
| DmsA | Dimethyl sulfoxide reductase | 21.5 | 1.90E−03 |
| FrdA | Fumarate reductase flavoprotein subunit | 4.3 | 9.34E−05 |
| FrdB | Fumarate reductase iron-sulfur subunit | 6.5 | 2.09E−05 |
| FumB | Fumarate hydratase class I, anaerobic | 4.8 | 2.79E−03 |
| GlpA | Anaerobic glycerol-3-phosphate dehydrogenase subunit A | 24.7 | 6.51E−04 |
| GlpB | Anaerobic glycerol-3-phosphate dehydrogenase subunit B | 4.6 | 3.39E−03 |
| MiaB | tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase | 9.1 | 1.56E−02 |
| NarG | Respiratory nitrate reductase 1 alpha chain | 6.2 | 9.52E−02 |
| NarH | Respiratory nitrate reductase 1 beta chain | 11.4 | 1.09E−02 |
| NirB | Nitrite reductase (NADH) large subunit | 37.4 | 2.96E−04 |
| PreT | NAD-dependent dihydropyrimidine dehydrogenase subunit | 15.4 | 1.46E−06 |
| SdaB | l-Serine dehydratase 2 | 31.1 | 1.13E−01 |
| TdcG | l-Serine/threonine dehydratase | 12.3 | 3.04E−05 |
| Glycyl radical proteins | |||
| GrcA | Autonomous glycyl radical cofactor | 5.2 | 1.88E−03 |
| TdcE | PFL-like enzyme (ketobutyrate formate lyase) | 60.6 | 2.89E−04 |
| Maltose and trehalose | |||
| LamB | Maltoporin | 16.5 | 8.15E−03 |
| MalE | Maltose-binding periplasmic protein | 15.0 | 1.34E−03 |
| MalP | Maltodextrin phosphorylase | 4.5 | 3.21E−05 |
| MalQ | 4-Alpha-glucanotransferase | 5.5 | 1.44E−03 |
| TreB | PTS trehalose-specific EIIBC component | 36.2 | 4.38E−03 |
| TreC | Trehalose-6-phosphate hydrolase | 9.5 | 1.53E−04 |
| Porins | |||
| FadL | Long-chain fatty acid transport protein | 10.4 | 7.97E−03 |
| OmpF | Outer membrane protein F | 11.5 | 2.18E−02 |
| Tsx | Nucleoside-specific channel-forming protein | 5.3 | 2.82E−03 |
| Replication and cell division | |||
| DeaD | ATP-dependent RNA helicase | 13.9 | 1.40E−02 |
| MnmG | tRNA uridine 5-carboxymethylaminomethyl modification | 7.6 | 2.89E−02 |
| MurA | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | 3.6 | 2.89E−03 |
| ParE | DNA topoisomerase 4 subunit B | 6.1 | 2.10E−02 |
| RimO | Ribosomal protein S12 methylthiotransferase | 3.1 | 1.52E−02 |
| RplD | 50S ribosomal protein L4 | 3.2 | 1.78E−02 |
| RplP | 50S ribosomal protein L16 | 4.3 | 2.28E−02 |
| RplT | 50S ribosomal protein L20 | 3.4 | 2.78E−02 |
| RplU | 50S ribosomal protein L21 | 3.3 | 4.12E−03 |
| RplY | 50S ribosomal protein L25 | 4.0 | 3.47E−02 |
| RpmB | 50S ribosomal protein L28 | 3.2 | 1.86E−02 |
| TtcA | tRNA 2-thiocytidine biosynthesis protein | 8.7 | 2.84E−02 |
| LPS biosynthesis | |||
| rfbB | dTDP-glucose 4,6-dehydratase 1 | 3.8 | 3.06E−05 |
| RfbD | dTDP-4-dehydrorhamnose reductase | 4.3 | 1.17E−02 |
| Aspartate/asparagine catabolism | |||
| AnsB | l-Asparaginase 2 | 7.8 | 1.19E−02 |
| AsnA | Aspartate-ammonia ligase | 7.1 | 3.30E−03 |
| AspA | Aspartate ammonia-lyase | 5.7 | 1.09E−05 |
| Glyoxylate degradation | |||
| GarD | d-Galactarate dehydratase | 3.8 | 3.55E−03 |
| GarR | 2-Hydroxy-3-oxopropionate reductase | 8.7 | 2.70E−03 |
| Uncharacterized | |||
| YdhQ | Uncharacterized protein YdhQ | 5.5 | 9.51E−04 |
| YgeV | Uncharacterized σ54-dependent transcriptional regulator | 3.4 | 2.01E−03 |
| YjjI | Uncharacterized protein YjjI | 6.2 | 3.36E−03 |
| Others | |||
| FtnA | Bacterial nonheme ferritin | 5.2 | 1.83E−02 |
| GatZ | d-Tagatose-1,6-bisphosphate aldolase subunit | 4.1 | 2.37E−03 |
| GuaC | GMP reductase | 4.7 | 1.72E−03 |
| HupA | DNA-binding protein HU-alpha | 4.1 | 4.90E−03 |
| HypB | Hydrogenase isoenzymes nickel incorporation protein | 7.1 | 5.01E−02 |
| NanA | N-Acetylneuraminate lyase | 3.4 | 3.08E−03 |
| PepE | Peptidase E | 3.9 | 5.16E−04 |
| RpoS | RNA polymerase sigma factor | 4.9 | 3.77E−04 |
a
Fold decrease was calculated from the average abundance of four independent vanillin-treated replicates relative to that of the four independent untreated replicates. LPS, lipopolysaccharide; PFL, pyruvate formate lyase.