Table 3.
Differentially expressed genes related with OMVs of genes in E. coli BW25113, rfaC knockout (ΔrfaC), rfaG knockout (ΔrfaG), and rfaL knockout (ΔrfaL) strains.
| Gene | Log2 Ratio | ΔrfaC/BW25113 | ΔrfaG/BW25113 | ΔrfaL/BW25113 | |||||
|---|---|---|---|---|---|---|---|---|---|
| ΔrfaC/BW25113 | ΔrfaG/BW25113 | ΔrfaL/BW25113 | Normalized Ratio | Trend | Normalized Ratio | Trend | Normalized Ratio | Trend | |
| ygdI | 2.634 | 2.419 | −0.748 | 6.205 | upregulated | 5.347 | upregulated | 0.595 | - |
| htpG | 2.330 | 0.647 | −0.231 | 5.028 | upregulated | 1.566 | - | 0.852 | - |
| fepA | 2.203 | 1.322 | 0.651 | 4.604 | upregulated | 2.501 | - | 1.571 | - |
| galF | 1.792 | 1.588 | 1.317 | 3.463 | upregulated | 3.006 | upregulated | 2.492 | upregulated |
| clpX | 1.788 | 1.270 | 1.543 | 3.453 | upregulated | 2.412 | - | 2.914 | upregulated |
| tufA | 1.761 | 1.305 | 0.702 | 3.388 | upregulated | 2.472 | - | 1.627 | - |
| tig | 1.690 | 2.258 | 0.461 | 3.226 | upregulated | 4.785 | upregulated | 1.376 | - |
| rplC | 1.676 | 1.312 | −0.172 | 3.196 | upregulated | 2.484 | - | 0.887 | - |
| pflB | 1.672 | 0.310 | 0.040 | 3.187 | upregulated | 1.240 | - | 1.028 | - |
| yedD | 1.582 | 1.015 | −0.271 | 2.995 | upregulated | 2.021 | - | 0.829 | - |
| rpsH | 1.539 | 1.921 | 0.136 | 2.905 | upregulated | 3.787 | upregulated | 1.099 | - |
| rpmA | 1.534 | 2.610 | 0.165 | 2.897 | upregulated | 6.104 | upregulated | 1.121 | - |
| lepA | 1.534 | 2.212 | 0.645 | 2.896 | upregulated | 4.634 | upregulated | 1.563 | - |
| accA | 1.413 | 1.829 | 0.910 | 2.663 | - | 3.552 | upregulated | 1.878 | - |
| rplK | 1.399 | 1.600 | 0.279 | 2.638 | - | 3.031 | upregulated | 1.213 | - |
| fabB | 1.146 | 1.377 | 1.164 | 2.214 | - | 2.597 | - | 2.241 | upregulated |
| grpE | 1.049 | 1.572 | 1.461 | 2.069 | - | 2.973 | upregulated | 2.754 | upregulated |
| mlaC | 0.950 | −2.114 | −0.324 | 1.932 | - | 0.231 | downregulated | 0.799 | - |
| fimH | 0.944 | −1.798 | −0.016 | 1.924 | - | 0.288 | downregulated | 0.989 | - |
| tnaA | 0.879 | 1.925 | 1.418 | 1.839 | - | 3.798 | upregulated | 2.672 | upregulated |
| rplI | 0.737 | 1.633 | −0.251 | 1.666 | - | 3.101 | upregulated | 0.840 | - |
| cra | 0.544 | 1.199 | 1.457 | 1.458 | - | 2.296 | - | 2.745 | upregulated |
| gapA | 0.454 | −0.106 | 1.372 | 1.370 | - | 0.929 | - | 2.589 | upregulated |
| potD | 0.390 | −3.029 | −0.621 | 1.311 | - | 0.123 | downregulated | 0.650 | - |
| rpsF | 0.386 | 1.523 | −0.258 | 1.307 | - | 2.874 | upregulated | 0.836 | - |
| pfkA | 0.258 | 0.773 | 1.444 | 1.196 | - | 1.709 | - | 2.721 | upregulated |
| gatY | −0.020 | −1.517 | 1.487 | 0.986 | - | 0.349 | - | 2.803 | upregulated |
| crp | −0.090 | −0.112 | 1.310 | 0.940 | - | 0.925 | - | 2.479 | upregulated |
| yajG | −0.140 | −2.288 | −0.815 | 0.907 | - | 0.205 | downregulated | 0.569 | - |
| aceA | −0.146 | 0.561 | 1.231 | 0.904 | - | 1.476 | - | 2.347 | upregulated |
| fliD | −0.148 | 0.238 | 2.531 | 0.902 | - | 1.180 | - | 5.778 | upregulated |
| lpp | −0.150 | 1.700 | −0.410 | 0.901 | - | 3.249 | upregulated | 0.753 | - |
| fliC | −0.239 | 0.138 | 2.108 | 0.848 | - | 1.100 | - | 4.311 | upregulated |
| feoB | −0.347 | 0.505 | 1.262 | 0.786 | - | 1.419 | - | 2.398 | upregulated |
| rplP | −0.421 | −1.032 | −1.515 | 0.747 | - | 0.489 | - | 0.350 | downregulated |
| rplV | −0.452 | 0.958 | −1.197 | 0.731 | - | 1.942 | - | 0.436 | downregulated |
| flgL | −0.502 | 0.170 | 1.231 | 0.706 | - | 1.125 | - | 2.346 | upregulated |
| pykA | −0.538 | 0.937 | 1.210 | 0.689 | - | 1.914 | - | 2.313 | upregulated |
| rplM | −0.711 | −0.484 | −1.197 | 0.611 | - | 0.715 | - | 0.436 | downregulated |
| lpdA | −1.115 | −1.944 | −0.019 | 0.462 | - | 0.260 | downregulated | 0.987 | - |
| pspA | −1.453 | −1.747 | −1.043 | 0.365 | - | 0.298 | downregulated | 0.485 | downregulated |
| cpoB | −1.649 | −1.615 | −0.779 | 0.319 | downregulated | 0.326 | downregulated | 0.583 | - |
| agp | −1.651 | −1.890 | −0.814 | 0.319 | downregulated | 0.270 | downregulated | 0.569 | - |
| rplB | −1.695 | −1.150 | −0.257 | 0.309 | downregulated | 0.451 | - | 0.837 | - |
| rpsD | −1.711 | −1.532 | −0.254 | 0.305 | downregulated | 0.346 | - | 0.838 | - |
| lptD | −1.805 | −1.331 | −0.213 | 0.286 | downregulated | 0.398 | - | 0.863 | - |
| ydiY | −1.835 | −1.552 | −1.103 | 0.280 | downregulated | 0.341 | - | 0.466 | downregulated |
| yfaZ | −1.859 | −0.389 | −0.687 | 0.276 | downregulated | 0.764 | - | 0.621 | - |
| rpoC | −1.863 | −0.736 | 0.656 | 0.275 | downregulated | 0.601 | - | 1.576 | - |
| rpmC | −1.905 | −0.869 | −1.082 | 0.267 | downregulated | 0.548 | - | 0.472 | downregulated |
| rplT | −1.922 | −1.968 | 0.377 | 0.264 | downregulated | 0.256 | downregulated | 1.299 | - |
| glnA | −1.976 | −0.772 | 0.150 | 0.254 | downregulated | 0.586 | - | 1.110 | - |
| rpsM | −1.999 | −2.230 | −0.284 | 0.250 | downregulated | 0.213 | downregulated | 0.822 | - |
| fecA | −2.064 | −1.346 | 0.818 | 0.239 | downregulated | 0.393 | - | 1.763 | - |
| rpsT | −2.124 | −1.986 | −1.968 | 0.229 | downregulated | 0.253 | downregulated | 0.256 | downregulated |
| rpmB | −2.181 | −3.315 | −2.844 | 0.220 | downregulated | 0.100 | downregulated | 0.139 | downregulated |
| aceF | −2.289 | −2.137 | −0.014 | 0.205 | downregulated | 0.227 | downregulated | 0.991 | - |
| ompF | −2.563 | −1.045 | −0.419 | 0.169 | downregulated | 0.485 | - | 0.748 | - |
| adhE | −2.721 | −2.274 | −0.703 | 0.152 | downregulated | 0.207 | downregulated | 0.614 | - |
| ftnA | −2.772 | −1.436 | −0.106 | 0.146 | downregulated | 0.370 | - | 0.929 | - |
| groL | −3.092 | −2.541 | −0.119 | 0.117 | downregulated | 0.172 | downregulated | 0.921 | - |