Table 1.
Differentially expressed genes identified in the T1 wild-type and Cp13 mutant strain of C. pseudotuberculosis
| Gene/Locus ID | Product | LI vs HI Log(2)Fold-change | LI vs HI Fold-change | p-value* | |||
|---|---|---|---|---|---|---|---|
| T1 | Cp13 | T1 | Cp13 | T1 | Cp13 | ||
| Cp1002B_95 | Hypothetical protein | −0.7619 (DOWN) | −0.5325 (UNC.) | 0.59 | 0.69 | 0.000814 | 0.019094 |
| sdcS | Sodium-dependent dicarboxylate transporter | −1.2318 (DOWN) | −0.5604 (UNC.) | 0.43 | 0.68 | 6.21E-16 | 0.011373 |
| Cp1002B_1235 | Hypothetical protein | −1.1201 (DOWN) | −0.9908 (DOWN) | 0.46 | 0.50 | 0.002796 | 0.000258 |
| ccsA | Cytochrome c biogenesis protein ccsa | 0.6175 (UP) | 0.9430 (UP) | 1.53 | 1.92 | 0.022829 | 0.002895 |
| htaA | Cell-surface hemin receptor | 0.9624 (UP) | 1.4327 (UP) | 1.95 | 2.70 | 2.66E-12 | 0.000128 |
| hmuT | ABC transporter substrate-binding protein | 0.8922 (UP) | 1.6025 (UP) | 1.86 | 3.04 | 1.19E-11 | 5.47E-05 |
| hmuU | Hemin import atp-binding protein | 0.5849 (UP) | 1.0666 (UP) | 1.50 | 2.09 | 3.31E-05 | 0.005646 |
| htaC | Hypothetical protein | 2.7936 (UP) | 2.8902 (UP) | 6.93 | 7.41 | 9.8E-66 | 3.33E-11 |
| Cp1002B_2935 | Transglycosylase associated protein | −1.3034 (DOWN) | −0.8085 (DOWN) | 0.41 | 0.57 | 6.46E-15 | 3.39E-05 |
| hrrA | DNA-binding response regulator | 0.7473 (UP) | 1.9853 (UP) | 1.68 | 3.96 | 3.02E-06 | 4.02E-05 |
| Cp1002B_3070 | Hypothetical protein | 3.0864 (UP) | 4.5174 (UP) | 8.49 | 22.90 | 1.74E-34 | 3.62E-26 |
| Cp1002B_3075 | Hypothetical protein | 3.3487 (UP) | 4.8177 (UP) | 10.19 | 28.20 | 1.71E-47 | 2.43E-32 |
| Cp1002B_3725 | FUSC family protein | 0.4215 (UNC.) | 0.5911 (UP) | 1.34 | 1.51 | 0.004667 | 2.37E-05 |
| Cp1002B_4550 | Antimicrobial peptide ABC transporter | −0.6302 (DOWN) | −0.4877 (UNC.) | 0.65 | 0.71 | 0.003592 | 0.003453 |
| htaF | Cell-surface hemin receptor | 1.7558 (UP) | 2.8668 (UP) | 3.38 | 7.29 | 4.16E-27 | 2.69E-14 |
| htaG | Uncharacterized protein htac | 1.4734 (UP) | 2.5507 (UP) | 2.78 | 5.86 | 3.62E-24 | 0.002598 |
| ctaC | Cytochrome c oxidase subunit II | −1.3075 (DOWN) | −1.0670 (DOWN) | 0.40 | 0.48 | 5.17E-13 | 1.06E-06 |
| ctaF | Cytochrome c oxidase polypeptide 4 | −1.1573 (DOWN) | −1.0888 (DOWN) | 0.45 | 0.47 | 7.95E-11 | 1.08E-07 |
| ctaE | Cytochrome c oxidase subunit III | −1.2057 (DOWN) | −1.3813 (DOWN) | 0.43 | 0.38 | 9.09E-10 | 7.24E-11 |
| qcrC | Ubiquinol-cytochrome C reductase cytochrome C | −1.5080 (DOWN) | −1.3603 (DOWN) | 0.35 | 0.39 | 1.19E-14 | 1.02E-09 |
| qcrA | Ubiquinol-cytochrome c reductase iron-sulfur | −1.2355 (DOWN) | −1.1237 (DOWN) | 0.42 | 0.46 | 7.6E-05 | 0.000568 |
| qcrB | Ubiquinol-cytochrome C reductase cytochrome B | −1.2774 (DOWN) | −1.2865 (DOWN) | 0.41 | 0.41 | 4.7E-13 | 6.48E-07 |
| Cp1002B_5915 | Hypothetical protein | 0.5118 (UNC.) | 1.0689 (UP) | 1.43 | 2.10 | 0.006998 | 1.59E-11 |
| rbfA | Ribosome-binding factor A | −0.6969 (DOWN) | −0.6192 (DOWN) | 0.62 | 0.65 | 0.00192 | 0.002598 |
| Cp1002B_8515 | Hypothetical protein | 0.4077 (UNC.) | 0.6311 (UP) | 1.33 | 1.55 | 0.039677 | 0.01409 |
| ywlC | Trna threonylcarbamoyladenosine biosynthesis protein ywlc | 0.6784 (UP) | 0.6002 (UP) | 1.60 | 1.52 | 0.016627 | 3.39E-05 |
| ripA | HTH-type transcriptional repressor of iron protein A | 1.0919 (UP) | 1.2883 (UP) | 2.13 | 2.44 | 1.193E-12 | 6.07E-13 |
| rpfB | Resuscitation-promoting factor rpfb | 0.3968 (UNC.) | 0.7641 (UP) | 1.32 | 1.70 | 0.039677 | 1.58E-07 |
| fkbP | Peptidyl-prolyl cis-trans isomerase, FKBP-type | −0.9806 (DOWN) | −0.6872 (DOWN) | 0.51 | 0.62 | 0.000242 | 0.013233 |
| Cp1002B_10210 | Substrate-binding protein | −2.4417 (DOWN) | −1.2848 (DOWN) | 0.18 | 0.41 | 2.89E-17 | 1.28E-07 |
| Cp1002B_10495 | Hypothetical protein | 2.3140 (UP) | 2.6553 (UP) | 4.97 | 6.30 | 3.14E-62 | 2.66E-14 |
| Cp1002B_10785 | Hypothetical protein | 1.8433 (UP) | 2.5687 (UP) | 3.59 | 5.93 | 2.63E-17 | 3.23E-32 |
Log (2) Fold- change values correspond to the average normalized count ratio between LI (low iron) media and HI (high iron) media for each individual strain. *p-values were adjusted using the Benjamin and Hochberg false discovery rate (FDR) approach. Genes with p-values < 0.05 and a base-2 log-ratio ≥ 0.5849 (i.e., ≥ 1.5-fold) or ≤ −0.5848 (i.e., ≤ 0.66-fold) in relation to the HI media were considered as differentially expressed. Gene regulation is based on the LI:HI ratio expression value: UP, up-regulated (log (2) fold-change ≥0.5849); UNC. unchanged (− 0.5849 < log (2) fold-change < 0.5849); DOWN, down-regulated (log (2) fold-change ≤ − 0.5849)