Table 1.
Selected genes whose expression was altered in the prdR mutant and/or in excess of proline.
| Class a | Gene number | Gene Name | Putative Product | prdR/WTb | TYP/TYb |
|---|---|---|---|---|---|
| Cell Wall | CD1413 | Putative membrane protein | 6.11 | ||
| Cell Wall | CD0830 | Putative membrane protein | 0.17 | ||
| Fermentation | CD1054–1059 | bcd2, etfB, etfA, crt2, hdb, thlA1 | Butyrate production | 5.92–9.26 | 0.03–0.05 |
| Fermentation | CD2338–2344 | 4hbD*,cat2*, abfD*, sucD, cat1 | Succinate utilization | 3.33 – 10.44 | 0.04.0.17 |
| Fermentation | CD2966 | adhE | Aldehyde-alcohol dehydrogenase | 12.77 | 0.05 |
| Membrane Transport | CD0324–0327 | cbiM, cbiN, cbiQ, cbiO | Cobalamin biosynthesis protein, cobalt ABC-type transport system | 8.04–12.07 | 0.25–0.27 |
| Membrane Transport | CD2666–2667 | ptsG-A, ptsG-BC | PTS system, glucose-specific transporter | 0.04 | |
| Membrane Transport | CD3136–3138 | bglA, bglF, bglG | PTS system, b-glucoside transporter | 0.11 – 0.29 | |
| Membrane Transport | CD2954–2961 | atpDBAFCEKI | ATP synthase | 2.90–3.49 | 0.13–0.19 |
| Membrane Transport | CD3036 | Transporter, Major Facilitator Superfamily | 6.03 | ||
| Metabolism-Amino Acid | CD2348–2358 | grdDCBAE, trxA2, trxB3, grdX | Glycine reductase | 6.61 – 64.16 | 0.04–0.1 |
| Metabolism-Amino Acid | CD3236–3247 | prdC, prdR, prdABDEE2F | Proline reductase | 0.03–0.05 | 3.44–64.29 |
| Metabolism-Amino Acid | CD0994–0996 | ser | Serine biosynthesis | 0.19–0.21 | |
| Metabolism-Carbon | CD1767 | gapB | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) | 0.07 | |
| Metabolism-Carbon | CD3248 | Polysaccharide deacetylase | 0.17 | 7 | |
| Metabolism-Lipids | CD1906–1925 | eutG, eutS, eutPVWABCLMEKTDNHQ | Ethanolamine utilization | 5.55 – 61.95 | |
| Regulation | CD1811 | Putative two-component sensor histidine kinase (N-terminal region) | 5.25 | ||
| Regulation | CD2668 | Transcription antiterminator, LicT family | 0.19 |
a
A selection of genes whose expression was affected more than 5-fold by a prdR mutation or by growth in excess proline. Not all genes that were affected >2-fold by the prdR mutation were affected >2-fold by the presence of proline and vice versa. (All genes whose expression was affected ≥2-fold by a prdR mutation or by proline excess are listed in Tables S1 and S2.)
b
The cutoff for significant change was set at 5-fold. Three genes, indicated by asterisks (*), had a fold-change less than 5-fold but were included because they are apparently in the same transcription unit as genes regulated ≥5-fold.