TABLE 3.
Summary of differential expression, expressed as ratios relative to succinate expression, for transport and regulation specific to biphenyl or benzoate (annotation manually verified by using BLAST)
| ORF | Annotation | Function | Regulation of expression | Expression ratioa
|
||
|---|---|---|---|---|---|---|
| Benzo | BiphML | BiphES | ||||
| 1980 | Extracellular ligand-binding receptor (livK) | Transport | Down | 0.56 (0.25) | 0.38 (0.23) | 0.20 (0.04) |
| 2329 | Porin, gram-negative type (ompC) | Transport | Down | 0.62 (0.22) | 0.06 (0.13) | 0.05 (0.13) |
| 10345 | Probable amino acid-binding periplasmic (pbp) ABC transporter protein (livK) | Transport | Down | 1.11 (0.45) | 0.29 (0.25) | 0.37 (0.12) |
| 13513 | MFS transporter (partial) | Transport | Down | 0.78 (0.22) | 0.15 (0.12) | 0.09 (0.04) |
| 13514 | MFS transporter (partial) | Transport | Down | 0.78 (0.22) | 0.15 (0.12) | 0.09 (0.04) |
| 12907 | Bacterial regulatory protein (lysR) | Regulator | Down | 0.81 (0.32) | 0.47 (0.39) | 0.41 (0.24) |
| 7315 | Carbohydrate-selective porin (oprB) | Transport | Down | 1.10 (0.38) | 0.34 (0.22) | 0.87 (0.36) |
| 9981 | Membrane protein involved in aromatic hydrocarbon degradation (todX) | Transport | Down | 0.84 (0.20) | 0.43 (0.34) | 0.86 (0.29) |
| 12874 | Bacterial regulatory protein (gntR/fadR) | Regulator | Down | 0.80 (0.43) | 0.35 (0.24) | 0.83 (0.47) |
| 7135 | Porin, gram-negative type (ompC) | Transport | Down | 0.50 (0.21) | 1.01 (0.07) | 1.38 (0.62) |
| 13094 | ABC transporter, iron transport (fepC) | Transport | Down | 0.49 (0.09) | 0.71 (0.32) | 0.52 (0.11) |
| 1226 | Putative porin signal peptide protein (ompC) | Transport | Up | 0.84 (0.45) | 2.85 (0.81) | 5.83 (1.42) |
| 1937 | Putative substrate-binding periplasmic (pbp) ABC transporter protein (livK) | Transport | Up | 1.10 (0.13) | 3.59 (0.57) | 4.92 (1.22) |
| 7737 | Conserved hypothetical protein (orf1, downstream of bphE) | Transport | Up | 1.69 (0.57) | 5.89 (1.26) | 15.82 (3.03) |
| 10382 | Extracellular ligand-binding receptor (livK) | Transport | Up | 1.00 (0.10) | 3.11 (0.46) | 3.29 (1.25) |
| 13684 | Possible porin signal peptide protein (ompC, partial) | Transport | Up | 1.14 (0.38) | 2.53 (0.83) | 4.66 (1.23) |
| 10103 | Bacterial regulatory protein (lysR) | Regulator | Up | 0.97 (0.06) | 2.38 (0.42) | 12.02 (1.91) |
| 668 | Lipoprotein, involved in inorganic ion transport (nlpA) | Transport | Up | 1.04 (0.55) | 2.76 (0.66) | 1.93 (0.63) |
| 14292 | ABC transporter (uup) | Transport | Up | 0.83 (0.34) | 2.59 (0.30) | 1.25 (0.85) |
| 5285 | RNA polymerase σ24 (rpoE) | Regulator | Up | 1.03 (0.06) | 2.17 (0.52) | 1.28 (0.63) |
| 6767 | Bacterial regulatory protein (lysR) | Regulator | Up | 1.46 (0.14) | 2.12 (0.24) | 1.25 (0.06) |
| 12574 | Bacterial regulatory proteins, IclR family (pcaR) | Regulator | Up | 0.94 (0.27) | 2.03 (0.21) | 1.13 (0.33) |
| 4744 | Putative porin signal peptide protein (ompC, partial) | Transport | Up | 2.94 (0.61) | 0.53 (0.33) | 1.10 (0.48) |
| 4746 | Putative porin signal peptide protein (ompC, partial) | Transport | Up | 2.00 (0.53) | 0.70 (0.50) | 1.19 (0.63) |
| 12426 | Bacterial regulatory protein (arsR) | Regulator | Up | 2.15 (0.20) | 1.11 (0.06) | 1.07 (0.18) |
a
Values in parentheses are standard errors for biological replicates. Boldface type indicates values for genes that are significantly differentially expressed (P < 0.05). Benzo, benzoate-grown cells; BiphML, mid-log-phase biphenyl-grown cells; BiphES, early-stationary-phase biphenyl-grown cells.