Table 1.
Genes identified by RNA-seq analysis that were dysregulated in both lysogenic strains (RN450-ϕ11 and RN450-ϕ80α) compared to prophage-free strain RN450 and overlaps with sigma B- and CcpA-regulated genes.
| Genea | Gene name | ϕ11b | ϕ80αb | SigB regulonc | CcpA regulonc |
|---|---|---|---|---|---|
| SAOUHSC_00061 | 2.35 | 4.97 | Up | ||
| SAOUHSC_00069* | spa | 3.70 | 5.40 | Up | |
| SAOUHSC_00070 | sarS | 3.26 | 4.73 | Up | |
| SAOUHSC_00156 | 2.47 | 3.18 | Up | ||
| SAOUHSC_00157 | murQ | 3.13 | 4.18 | Up | |
| SAOUHSC_00158 | 3.39 | 4.35 | Up | ||
| SAOUHSC_00160 | 2.31 | 3.46 | Up | ||
| SAOUHSC_00183 | uhpT | 3.72 | 7.31 | Up | |
| SAOUHSC_00196 | fadB | 2.82 | 4.12 | Up | |
| SAOUHSC_00257 | 0.48 | 0.28 | |||
| SAOUHSC_00291 | 2.32 | 2.18 | Up | ||
| SAOUHSC_00317 | 2.81 | 3.78 | Up | ||
| SAOUHSC_00356 | 3.96 | 11.49 | Up | ||
| SAOUHSC_00358 | 4.67 | 12.22 | Up | ||
| SAOUHSC_00401 | 0.33 | 0.16 | |||
| SAOUHSC_00619 | 5.66 | 21.10 | Up | ||
| SAOUHSC_00624 | 2.72 | 7.23 | Up | ||
| SAOUHSC_00625 | mnhA2 | 2.10 | 4.29 | Up | |
| SAOUHSC_00626 | mnhB2 | 2.14 | 3.70 | Up | |
| SAOUHSC_00627 | mnhC2 | 2.13 | 3.97 | Up | |
| SAOUHSC_00628 | mnhD2 | 2.14 | 3.75 | Up | |
| SAOUHSC_00629 | mnhE2 | 2.08 | 3.58 | Up | |
| SAOUHSC_00630 | 2.05 | 3.51 | |||
| SAOUHSC_00632 | mnhG2 | 2.04 | 3.42 | Up | |
| SAOUHSC_00655 | 2.07 | 2.76 | Up | ||
| SAOUHSC_00831 | 3.48 | 9.45 | Up | ||
| SAOUHSC_00845 | 8.90 | 31.38 | Up | ||
| SAOUHSC_00846 | 2.97 | 8.59 | |||
| SAOUHSC_00988* | sspA | 0.49 | 0.32 | Down | |
| SAOUHSC_01017 | purH | 2.17 | 2.57 | ||
| SAOUHSC_01018 | purD | 2.00 | 2.43 | ||
| SAOUHSC_01135 | 0.40 | 0.06 | |||
| SAOUHSC_01136 | 0.44 | 0.06 | |||
| SAOUHSC_01318 | 2.18 | 2.48 | Up | ||
| SAOUHSC_01513 | 0.49 | 0.26 | |||
| SAOUHSC_01601 | 2.70 | 4.10 | |||
| SAOUHSC_01602 | 2.67 | 3.98 | |||
| SAOUHSC_01603 | 2.21 | 2.89 | |||
| SAOUHSC_01729 | 7.55 | 18.24 | Up | ||
| SAOUHSC_01730 | 6.31 | 19.71 | Up | ||
| SAOUHSC_01794 | 3.77 | 5.80 | |||
| SAOUHSC_01910 | pckA | 3.14 | 4.92 | Up | |
| SAOUHSC_01918 | 2.01 | 2.89 | |||
| SAOUHSC_01920 | 2.35 | 3.23 | |||
| SAOUHSC_01921 | 2.21 | 2.74 | |||
| SAOUHSC_01935 | splF | 0.46 | 0.47 | ||
| SAOUHSC_01939 | splC | 0.47 | 0.47 | Down | |
| SAOUHSC_01941 | splB | 0.40 | 0.32 | Down | |
| SAOUHSC_01942 | splA | 0.36 | 0.26 | Down | |
| SAOUHSC_01945 | 0.46 | 0.41 | |||
| SAOUHSC_01949 | 0.48 | 0.36 | |||
| SAOUHSC_01950 | 0.46 | 0.32 | |||
| SAOUHSC_01951 | 0.48 | 0.31 | |||
| SAOUHSC_01952 | 0.48 | 0.30 | |||
| SAOUHSC_02137 | sdcS | 2.15 | 3.17 | Up | |
| SAOUHSC_02163 | 0.19 | 0.08 | |||
| SAOUHSC_02240 | 0.31 | 0.11 | |||
| SAOUHSC_02260* | hld | 0.40 | 0.04 | ||
| SAOUHSC_02261* | agrB | 0.50 | 0.17 | ||
| SAOUHSC_02265 | 0.50 | 0.20 | |||
| SAOUHSC_02266 | 0.45 | 0.24 | |||
| SAOUHSC_02387 | 3.30 | 11.15 | Up | ||
| SAOUHSC_02400 | 3.31 | 8.23 | |||
| SAOUHSC_02401 | 3.63 | 9.77 | Up | ||
| SAOUHSC_02402 | 4.08 | 11.06 | Up | ||
| SAOUHSC_02403 | mtlD | 3.27 | 8.74 | Up | |
| SAOUHSC_02425 | 2.39 | 3.26 | Up | ||
| SAOUHSC_02441 | asp23 | 9.56 | 28.18 | Up | |
| SAOUHSC_02442 | 7.60 | 27.27 | Up | ||
| SAOUHSC_02443 | 8.17 | 29.88 | Up | ||
| SAOUHSC_02444 | 4.99 | 19.92 | Up | ||
| SAOUHSC_02451 | 0.44 | 0.49 | |||
| SAOUHSC_02452 | lacD | 0.38 | 0.45 | ||
| SAOUHSC_02453 | lacC | 0.39 | 0.49 | ||
| SAOUHSC_02597 | 2.12 | 2.90 | Up | ||
| SAOUHSC_02620 | 0.45 | 0.24 | Down | ||
| SAOUHSC_02729 | 2.20 | 3.14 | Up | ||
| SAOUHSC_02771 | 2.96 | 5.46 | Up | ||
| SAOUHSC_02772 | 2.32 | 6.49 | Up | ||
| SAOUHSC_02812 | 3.00 | 7.98 | Up | ||
| SAOUHSC_02815 | 2.63 | 4.38 | Up | ||
| SAOUHSC_02822 | fbp | 2.31 | 3.17 | Up | |
| SAOUHSC_02848 | glcB | 2.07 | 2.90 | ||
| SAOUHSC_02862 | clpL | 5.24 | 16.79 | Up | |
| SAOUHSC_02877 | crtN | 2.14 | 5.93 | Up | |
| SAOUHSC_02879 | crtM | 3.46 | 10.17 | Up | |
| SAOUHSC_02880 | crtQ | 3.88 | 13.11 | Up | |
| SAOUHSC_02881* | crtP | 3.08 | 10.10 | Up | |
| SAOUHSC_02882 | crtO | 2.93 | 8.93 | Up | |
| SAOUHSC_02905 | 0.35 | 0.15 | |||
| SAOUHSC_02906 | 0.31 | 0.14 | |||
| SAOUHSC_02907 | 0.35 | 0.14 | |||
| SAOUHSC_02908 | 2.49 | 5.89 | Up | ||
| SAOUHSC_02964 | arcR | 0.42 | 0.24 | Down | |
| SAOUHSC_02965 | arcC2 | 0.34 | 0.24 | Down | |
| SAOUHSC_02967 | 0.33 | 0.22 | Down | ||
| SAOUHSC_02968 | argF | 0.38 | 0.22 | Down | |
| SAOUHSC_02969 | arcA | 0.34 | 0.22 | Down | |
| SAOUHSC_02970 | 0.48 | 0.19 | |||
| SAOUHSC_02971 | 0.45 | 0.30 | Down | ||
| SAOUHSC_03028 | 2.34 | 6.42 | Up | ||
| SAOUHSC_03032 | 2.09 | 4.46 | Up | ||
| SAOUHSC_A00354 | 5.17 | 13.93 |
aGenes marked with an asterisk (*) were confirmed by RT-qPCR; the reference gene used to calculate the fold-change was rplD.
bChanges in gene expression below 1 (<1) indicate downregulation in the lysogen, whereas changes above 1 (>1) indicate upregulation in the lysogenic strain.
cGenes under SigB and CcpA control.