Table 2.
Selected genes with significant expression level changes in crp/fnr knockout mutants
| Regulator and category | Gene name | Annotation | Log2R (mutant/wild type)a |
|||
|---|---|---|---|---|---|---|
| JW9007 | JW9009 | JW9011 | JW9013 | |||
| Amino acid transport and metabolism | ||||||
| DVU0465 | trpE | Anthranilate synthase, component I | 1.33 (1.78) | 0.23 (0.32) | N/A | N/A |
| DVU0466 | trpG | Anthranilate synthase, glutamine amidotransferase | 1.52 (2.35) | 0.08 (0.12) | −1.33 (−1.66) | −0.81 (−0.60) |
| DVU0467 | trpD | Anthranilate phosphoribosyltransferase | 1.44 (2.24) | −0.17 (−0.18) | −0.32 (−0.49) | −0.08 (−0.12) |
| DVU0468 | trpC | Indole-3-glycerol phosphate synthase | 1.23 (2.08) | 0.12 (0.21) | −0.90 (−1.41) | −0.19 (−0.28) |
| DVU0469 | trpF-1 | N-(5-phosphoribosyl)anthranilate isomerase | 0.88 (1.30) | −0.17 (−0.24) | −1.00 (−1.45) | −0.13 (−0.16) |
| DVU0470 | trpB-2 | Tryptophan synthase, beta subunit | 1.43 (2.52) | 0.34 (0.56) | −0.56 (−0.95) | 0.15 (0.25) |
| DVU0471 | trpA | Tryptophan synthase, alpha subunit | 1.48 (2.66) | 0.42 (0.70) | −0.44 (−0.74) | 0.32 (0.54) |
| DVU0386 | glnH | Amino acid ABC transporter, periplasmic amino acid binding protein | 0.55 (1.01) | 1.83 (3.32) | 1.64 (2.89) | 1.51 (2.76) |
| Inorganic ion transport and metabolism | ||||||
| DVU2571 | feoB | Ferrous iron transport protein B | −2.11 (−2.53) | −1.81 (−2.16) | −1.32 (−2.14) | −1.78 (−1.96) |
| DVU2572 | feoA | Ferrous iron transport protein A | −1.69 (−2.51) | −1.73 (−2.17) | −1.50 (−2.25) | −1.75 (−1.97) |
| DVU2573 | N/A | Hypothetical protein | −0.62 (−0.96) | −0.52 (−0.85) | −0.64 (−1.13) | −0.46 (−0.62) |
| DVU2574 | feoA | Ferrous iron transporter component feoA | −2.17 (−2.79) | −1.34 (−1.30) | −1.70 (−2.51) | −2.00 (−2.98) |
| Energy production and conversion | ||||||
| DVU3171 | N/A | Cytochrome c3 | 0.63 (0.64) | 1.26 (1.30) | 0.88 (0.93) | 1.45 (1.52) |
| DVU2784 | lldD | Dehydrogenase, flavin mononucleotide -dependent family | 0.63 (0.97) | 1.36 (2.32) | 1.07 (1.90) | 1.51 (2.15) |
| DVU3143 | N/A | Iron-sulfur cluster-binding protein | 1.30 (1.68) | 0.97 (1.32) | 1.21 (1.72) | 1.74 (2.08) |
| DVU1165 | ndh | NADH respiratory dehydrogenase | −0.54 (−0.55) | −0.80 (−0.66) | −0.75 (−1.06) | −1.42 (−2.27) |
| DVU2543 | b0873 | Hybrid cluster protein | −0.72 (−1.07) | −1.22 (−1.81) | −2.79 (−3.61) | −1.46 (−1.96) |
| DVU2544 | N/A | Iron-sulfur cluster binding protein | −0.45 (−0.59) | −0.82 (−0.95) | −1.26 (−1.32) | −1.06 (−1.33) |
| DVU2680 | fld | Flavodoxin, iron repressed | −2.66 (−2.64) | −2.64 (−2.44) | −2.91 (−3.67) | −2.78 (−3.26) |
| DVU2247 | ahpC | Alkyl hydroperoxide reductase C | −1.41 (−2.47) | −0.29 (−0.47) | −0.34 (−0.61) | −0.74 (−1.33) |
| Transcription | ||||||
| DVU2577 | N/A | DNA-binding response regulator, LuxR family | 1.60 (2.53) | 1.15 (1.76) | 0.71 (1.09) | 1.01 (1.57) |
| DVU2785 | pdhR | Transcriptional regulator, GntR family | 1.28 (2.00) | 1.46 (2.14) | 1.16 (1.82) | 1.94 (2.15) |
| DVU2827 | N/A | Sigma-54 dependent transcriptional regulator | −0.76 (−0.91) | −2.20 (−1.75) | −0.63 (−1.12) | −1.24 (−1.64) |
| Signal transduction mechanisms | ||||||
| DVU0878 | N/A | dnaK suppressor protein, putative | 2.13 (3.75) | 0.68 (1.13) | 0.19 (0.31) | 1.00 (1.83) |
| DVU0888 | N/A | Response regulator | 0.62 (0.67) | 0.72 (0.82) | 0.21 (0.24) | 1.81 (1.57) |
| DVU1169 | N/A | Methyl-accepting chemotaxis protein | 0.72 (0.77) | 1.57 (2.01) | 1.97 (2.83) | 1.94 (2.86) |
| DVU1594 | cheA-1 | Chemotaxis protein CheA | −0.98 (−1.33) | −1.07 (−1.27) | −1.40 (−2.25) | −1.71 (−2.56) |
| DVU1595 | cheR-1 | Chemotaxis protein methyltransferase | −0.54 (−0.66) | −1.33 (−1.04) | −1.55 (−2.03) | −1.76 (−2.47) |
| DVU3182 | dcrA | Methyl-accepting chemotaxis protein DcrA | −0.38 (−0.49) | −1.15 (−0.75) | −0.21 (−0.35) | −1.69 (−2.14) |
| DVU3155 | dcrH | Methyl-accepting chemotaxis protein DcrH | −1.28 (−1.36) | −1.83 (−1.62) | −1.29 (−1.53) | −1.75 (−2.20) |
| DVU2577 | N/A | DNA-binding response regulator, LuxR family | 1.60 (2.53) | 1.15 (1.76) | 0.71 (1.09) | 1.01 (1.57) |
| DVU0039 | N/A | C4-type zinc finger protein, DksA/TraR family | 0.58 (0.62) | 0.78 (0.77) | 0.82 (0.92) | 2.14 (1.80) |
| DVU0598 | N/A | Carbon starvation protein A, putative | −2.76 (−2.15) | −1.79 (−2.04) | −1.69 (−2.91) | −3.07 (−4.02) |
| DVU0599 | N/A | Carbon starvation protein A, putative | −1.38 (−1.23) | −1.44 (−1.32) | −1.05 (−1.09) | −1.69 (−1.87) |
| DVU3023 | atoC | Sigma-54-dependent DNA-binding response | −1.49 (−1.33) | −1.50 (−1.02) | −0.08 (−0.11) | −2.01 (−1.65) |
a
N/A, no gene name has been assigned to the locus yet or no data for the gene. Z scores are shown in parentheses.