TABLE 3.
Deregulated proteins identified by proteomic analysis
| Band or spot | Designation (gene) | Protein | Predicted function | Mol wt | Relative change in Δhfq mutant (fold)a |
|---|---|---|---|---|---|
| Downregulated proteins | |||||
| C1 | NMB0758 (pnp) | Polyribonucleotide nucleotidyltransferase | RNA metabolism | 76,374 | −3.0 |
| C2 2D12 | NMB1938 (atpA) | ATP synthase F1, alpha subunit | Energy metabolism: ATP-proton motive force interconversion | 55,257 | −2.4 |
| C3 | NMB1936 (atpB) | ATP synthase F1, beta subunit | Energy metabolism: ATP-proton motive force interconversion | 50,360 | −2.1 |
| T1 C4 | NMB0763 (cysK) | Cysteine synthase | Amino acid biosynthesis: serine family | 32,800 | −2.4 |
| 2D13 | NMB0335 (dapD) | 2,3,4,5-Tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | Amino acid biosynthesis: aspartate family | 29,391 | −2.3 |
| 2D6 | NMB0138 (fusA) | Elongation factor G | Protein synthesis | 77,408 | −1.3 |
| 2D7 | NMB0618 (ppsA) | Phosphoenolpyruvate synthase | Energy metabolism: glycolysis/gluconeogenesis, carbohydrate transport, and metabolism | 87,115 | −2 |
| Upregulated proteins | |||||
| T2 E6 E17 2D1 | NMB1572 (acnB) | Aconitase hydratase 2 | Energy metabolism: tricarboxylic acid cycle | 92,657 | 2.3 |
| T3 2D2 | NMB0920 (icd) | Isocitrate dehydrogenase | Energy metabolism: tricarboxylic acid cycle | 80,113 | 1.4 |
| 2D3 | NMB0954 (gltA) | Citrate synthase | Energy metabolism: tricarboxylic acid cycle | 48,587 | 2 |
| C9 | NMB431 (pprC) | Methylcitrate synthase | Energy metabolism: propionate metabolism | 42,792 | 1.6 |
| 2D4 | NMB0435 (ackA-1) | Acetate kinase | Energy metabolism: fermentation | 43,336 | 2 |
| E2 | NMB1388 (pgi-2) | Glucose-6-phosphate isomerase | Energy metabolism: carbohydrate transport and metabolism | 62,044 | 1.3 |
| 2D10 2D11 | NMB1796 | Conserved hypothetical protein, oxidoreductase | Energy metabolism: electron transport | 20,989 | 2.9 |
| 2D8 | NMB1584 | 3-Hydroxyacid dehydrogenase | Central intermediary metabolism: other | 30,359 | 1.9 |
| E1 E16 2D5 | NMB1055 (glyA) | Serine hydroxymethyltransferase | Amino acid biosynthesis: serine family | 45,243 | 3 |
| E5 | NMB0944 (metH) | 5-Methyltetrahydropteroyltriglutamate-homocysteine methyltransferase | Amino acid biosynthesis: aspartate family | 85,024 | 1.3 |
| T5, E3 | NMB1972 (groEL) | Chaperonin, GroEL (60 kDa) | Protein fate: protein folding and stabilization | 57,387 | 1.4 |
| T7 | NMB0946 (prx) | Peroxiredoxin 2 family protein/glutaredoxin | Detoxification: oxidative stress response | 26,894 | 1.4 |
| C5 | NMB0884 (sodB) | Superoxide dismutase | Detoxification: oxidative stress response | 21,879 | 1.7 |
| C7 | NMB1590 | Conserved hypothetical protein: putative peroxidase | Unknown function: oxidative stress response | 11,526 | 1.6 |
| E4, E10 | NMB0182 (omp85) | OMP Omp85 | Outer membrane lipid biogenesis | 88,382 | 1.2b |
| E15 | NMB1053 (opc) | Class 5 OMP | Pathogenesis: adhesion | 29,973 | 1.3 |
| S10 | NMB1053 (opc) | Class 5 OMP | Pathogenesis: adhesion | 29,973 | 2.3 |
| NMB1636 | Opacity protein | 30,161 | 2.3 | ||
| S7 | NMB1541 (lbpB) | Lactoferrin binding protein B | Transport of iron cations | 81,082 | 1.8 |
| S11 | NMB0634 (fbpA) | Iron ABC transporter, periplasmic binding protein | Transport of iron cations | 35,806 | 1.5 |
| 2D9 | NMB0018 | Pilin PilE | Pathogenesis: cell motility and adhesion | 18,202 | 1.6 |
a
Relative abundance of protein in the Δhfq mutant compared with the wild type. The differentially regulated bands and spots were quantified using ImageQuant software, the values were normalized with respect to an unchanged internal protein control, and the relative quantities are expressed as changes compared with the wild type.
b
Deregulation of this band was not seen in all of the biological replicates tested.