TABLE 1.
Proteins of the aromatic and C1 metabolic pathways identified by MASCOT-based analysis of MALDI-TOF-generated mass spectra
| Protein | MASCOT scorea | No. of peptides matched | Sequence coverage (%) | Normalized volumeb
|
||||
|---|---|---|---|---|---|---|---|---|
| Succ-ML | Benz-ML | Benz-TP | Biph-ML | Biph-TP | ||||
| BphA | 115 | 10 | 23 | 1.2 | 2.1 | 2.1 | 15c | 11c |
| BphE | 162 | 10 | 69 | 0.71 | 1.1 | 1.1 | 7.6 | 7.4 |
| BphG | 83 | 13 | 43 | 0.08 | 0.03 | 0.11 | 0.26 | 0.59 |
| BphB | 125 | 10 | 49 | 0.13 | 0.15 | 0.39 | 0.77 | 1.2 |
| BphC | 103 | 15 | 62 | 0.12 | 0.31 | 0.35 | 1.9 | 1.9 |
| BphD | 120 | 8 | 30 | 0.16 | 0.31 | 0.35 | 1.5 | 2.5 |
| BphH | 58 | 5 | 31 | 0.02 | 0.02 | 0.03 | 0.25 | 0.28 |
| BphI | 60 | 8 | 40 | 0.10 | 0.03 | 0.10 | 0.29 | 0.68 |
| BphJ | 101 | 10 | 46 | 0.07 | 0.02 | 0.03 | 0.14 | 0.61 |
| BenA | 172 | 9 | 29 | ND | 1.8 | 1.6 | LRc | LRc |
| BenB | 60 | 6 | 45 | ND | 0.55 | 1.1 | 0.12 | 0.02 |
| BenC | 102 | 9 | 32 | ND | 0.26 | 0.34 | 0.05 | 0.01 |
| BenD | 68 | 9 | 38 | ND | 0.29 | 1.2 | 0.08 | 0.05 |
| CatA | 62 | 7 | 29 | ND | 0.24 | 2.5 | 0.25 | 0.33 |
| CatB | 90 | 10 | 28 | ND | 0.59 | 1.1 | 0.29 | 0.12 |
| PcaF | 105 | 16 | 45 | ND | 0.57 | LR | 0.14 | 0.08 |
| PcaJ | 55 | 5 | 28 | ND | 0.26 | 0.61 | 0.07 | 0.04 |
| Benzoate-CoA ligaseC | 90 | 9 | 24 | ND | ND | ND | 0.51 | 0.61 |
| BoxBC | 225 | 22 | 54 | ND | ND | 0.03 | 0.20 | 0.22 |
| BoxCC | 247 | 19 | 51 | ND | ND | 0.13 | 0.71 | 0.63 |
| Aldehyde dehydrogenaseC | 121 | 19 | 39 | ND | ND | ND | 0.13 | 0.35 |
| Benzoate-CoA ligaseM | 71 | 12 | 22 | ND | ND | 0.07 | ND | ND |
| BoxBM | 162 | 18 | 37 | ND | ND | 0.47 | ND | ND |
| BoxCM | 188 | 25 | 61 | ND | ND | 0.78 | ND | ND |
| Aldehyde dehydrogenaseM | 100 | 14 | 33 | ND | ND | 0.12 | ND | ND |
| ClcA | 56 | 6 | 29 | ND | 0.05 | 0.21 | 0.01 | 0.01 |
| AmnC | 78 | 11 | 26 | ND | 0.68 | 0.47 | 0.11 | 0.12 |
| AmnD | 57 | 5 | 29 | ND | 0.41 | 0.26 | ND | ND |
| AmnH | 55 | 8 | 35 | ND | 0.05 | 0.03 | ND | 0.01 |
| XoxF | 157 | 19 | 40 | ND | ND | ND | ND | 0.71 |
| Fae | 90 | 5 | 49 | ND | ND | ND | 0.01 | 0.65 |
| PqqC | 65 | 7 | 30 | ND | ND | ND | ND | 0.51 |
MASCOT-generated probability-based Mowse score. In the LB400 protein database scores greater than 52 are significant (P < 0.05).
Average normalized volumes over the three biological replicates under each of the tested growth conditions. LR, low resolution in area where spot was expected. ND, not detected.
Because of their almost identical pI and mass, BenA (pH 5.99 and 52.6 kDa) and BphA (pH 5.99 and 51.9 kDa) were not well resolved on the 2D gel. Due to their relative abundance, separate spots were resolved on gels of the benzoate-grown samples but not on gels of the biphenyl-grown samples. However, levels of BenB in biphenyl-grown samples together with relative levels of BenA and BenB in benzoate-grown samples indicate that BenA constituted less that 5% of the signal of the BphA spot in biphenyl-grown samples.