Table 3.
Genes regulated by the EanI/R quorum sensing system in P. ananatis LMG 2665T. Genes were identified by pairwise comparison between wild-type at OD600 = 0.2 (no QS) and wild type at OD600 = 0.5 (during QS) (W2 versus W5) and pairwise comparison of the wild-type at OD600 = 0.5 and QS mutant at OD600 = 0.5 (M5 versus W5).
| Functional Category | Gene or Protein Encoded | Log2 Ratio | |
|---|---|---|---|
| W2 vs. W5 | M5 vs. W5 | ||
| Genes up regulated between the wild-type strain LMG 2665T in the presence of AHLs (at OD600 = 0.5) versus the same strain in the absence if AHLs (OD600 = 0.2) | |||
| Redox sensing | 3-oxoacyl-ACP reductase | 1.833 | 1.638 |
| Oxidoreductase | 2.115 | 1.93 | |
| Metabolism | pyruvate oxidase | 1.156 | 1.217 |
| malate:quinone oxidoreductase | 1.42 | 0.561 | |
| transketolase/WP_014593932.1 | 1.401 | 1.588 | |
| lysine 6-monooxygenase | 1.351 | 0.966 | |
| ketol-acid reductoisomerase | 1.187 | 0.888 | |
| alcA | 1.532 | 0.869 | |
| IucA | 2.106 | 1.444 | |
| siderophore-interacting protein (WP_014606889.1) | 1.686 | 1.014 | |
| pyridine nucleotide-disulphide oxidoreductase | 0.845 | −0.738 | |
| Wza | 0.971 | −0.984 | |
| Flagella formation and flagella mediated Motility | fliA | 2.837 | 0.848 |
| flgK | 2.447 | 0.795 | |
| flagellin/WP_014593940.1 | 3.053 | 0.952 | |
| fliZ | 2.607 | 1.012 | |
| fliL | 2.336 | 0.797 | |
| fligL | 2.2 | 0.881 | |
| fliM | 2.032 | 0.699 | |
| flhA | 2.086 | 1.488 | |
| flgG | 2.39 | 1.855 | |
| flagellar basal body P-ring protein | 2.104 | 1.542 | |
| fliS | 2.681 | 1.161 | |
| fliE | 2.293 | 1.921 | |
| flgN | 1.325 | 0.468 | |
| flgA | 2.279 | 1.357 | |
| flagellin/WP_013027859.1 | 1.6 | 4.051 | |
| flagellar basal body rod modification protein | 2.779 | 1.991 | |
| motB | 1.728 | 0.595 | |
| flit | 2.475 | 1.313 | |
| flgF | 2.508 | 1.697 | |
| flgJ | 1.934 | 1.267 | |
| flhB | 2.199 | 1.559 | |
| flgE | 2.392 | 1.892 | |
| flgC | 2.743 | 2.05 | |
| flgL | 2.201 | 0.881 | |
| flagellar basal body L-ring protein | 2.487 | 1.699 | |
| flgB | 2.875 | 1.96 | |
| flip | 1.89 | 0.595 | |
| Cell adhesion and biofilm formation | fliD/WP_014593941.1 | 2.93 | 1.104 |
| bcsO | 1.136 | 0.699 | |
| yhjQ | 0.942 | 0.717 | |
| Gene regulators | luxR | 0.816 | 1.276 |
| Fis family transcriptional regulator | 0.874 | 0.961 | |
| transcriptional regulator/WP_028714798.1 | 1.669 | 0.877 | |
| transcriptional regulator/WP_013027687.1 | 0.589 | 0.639 | |
| proQ | 2.497 | 0.534 | |
| luxI | 0.734 | 6.21 | |
| dgdR | 1.747 | −0.55 | |
| Methyl accepting proteins and Chemotaxis | WP_019105711.1 | 2.45 | 1.955 |
| WP_028714945.1 | 0.994 | 0.683 | |
| WP_050442519.1 | 1.888 | 0.734 | |
| WP_014605659.1 | 3.141 | 0.869 | |
| exbD | 2.259 | 1.512 | |
| chemotaxis protein-glutamate O-methyltransferase | 2.259 | 0.761 | |
| WP_014605660.1 | 2.716 | 0.882 | |
| chemotaxis response regulator (cheZ) | 2.194 | 0.717 | |
| Regulator of chemotaxis (cheA) | 1.888 | 0.743 | |
| chemotaxis response regulator (cheY) | 2.497 | 0.777 | |
| Outer membrane proteins | ligand-gated channel protein | 1.061 | 1.621 |
| lpoA | 1.102 | 0.431 | |
| Outer Membrane protein/ WP_026020991.1 | 1.806 | −0.929 | |
| Cell wall synthesis | endopeptidase | 2.145 | 0.907 |
| D-alanyl-D-alanine carboxypeptidase | 1.618 | 0.953 | |
| Stress response | hslV | 1.741 | 1.539 |
| carbamoyl phosphate synthase large subunit | 1.053 | 1.514 | |
| universal stress protein B | 1.457 | −0.751 | |
| Transport | magnesium-translocating P-type ATPase | 2.884 | 1.793 |
| MFS transporter/WP_028715176.1 | 2.149 | 1.176 | |
| pyridine nucleotide-disulphide oxidoreductase | 2.32 | 1.387 | |
| anion permease | 2.394 | 1.498 | |
| ligand-gated channel protein/WP_014595119.1 | 1.491 | 0.954 | |
| MFS transporter/WP_028715950.1 | 1.363 | 0.958 | |
| NCS2 family permease | 0.687 | 0.836 | |
| pyridine nucleotide-disulphide oxidoreductase | 2.32 | 1.387 | |
| glucose dehydrogenase | 0.732 | 0.544 | |
| WP_014593931.1/Transketolase | 1.267 | 1.129 | |
| sugar ABC transporter substrate-binding protein | 1.686 | 0.847 | |
| ferrous iron transporter A | 0.928 | −2.909 | |
| Hypothetical proteins | WP_013026151.1 | 2.51 | 2.214 |
| WP_019106310.1 | 1.013 | 0.601 | |
| WP_014593929.1 | 1.724 | 1.689 | |
| WP_014333251.1 | 1.197 | 0.612 | |
| WP_014604614.1 | 1.65 | 1.154 | |
| WP_028715174.1 | 1.039 | 0.632 | |
| WP_013027988.1 | 0.902 | 0.654 | |
| WP_013026097.1 | 1.84 | 1.293 | |
| WP_013024239.1 | 0.998 | 0.882 | |
| WP_014593930.1 | 0.902 | 0.847 | |
| WP_028715108.1 | 0.703 | 0.814 | |
| WP_050442523.1 | 0.955 | 1.876 | |
| WP_013025497.1 | 0.671 | 0.711 | |
| WP_014332946.1(putative motility protein) | 3.038 | 0.542 | |
| WP_013025421.1 | 3.227 | 0.923 | |
| WP_033765947.1 | 2.576 | 1.051 | |
| WP_028715248.1 | 1.979 | 1.442 | |
| WP_028715109.1 | 1.95 | 1.442 | |
| WP_014593989.1 | 1.376 | 0.594 | |
| WP_013024991.1 | 1.996 | −0.63 | |
| WP_014604946.1 | 0.597 | −0.777 | |
| WP_028715989.1 | 0.77 | −0.76 | |
| WP_050442541.1 | 1.443 | −2.11 | |
| WP_013025383.1 | 1.579 | −0.98 | |
| WP_028716027.1 | 1.033 | −0.715 | |
| Other | srfB (virulence factor) | 1.681 | 1.21 |
| Maa | 2.816 | 2.347 | |
| N6-hydroxylysine O-acetyltransferase | 1.74 | 0.936 | |
| Aminotransferase | 1.281 | 1.153 | |
| acyl—CoA ligase | 1.049 | 1.111 | |
| dTDP-4-dehydrorhamnose 3,5-epimerase | 1.467 | 1.13 | |
| traF | 1.88 | 0.524 | |
| peptidase C39 | 0.831 | 1.103 | |
| dusB | 0.983 | 0.713 | |
| cytochrome ubiquinol oxidase subunit II | 0.698 | 1.17 | |
| 2,5-didehydrogluconate reductase A | 1.438 | −0.598 | |
| aspartyl β-hydroxylase | 1.016 | −1.295 | |
| DNA polymerase III subunit ε | 1.574 | −0.854 | |
| Genes down regulated between the wild-type strain LMG 2665T in the presence of AHLs (at OD600 = 0.5) versus the same strain in the absence of AHLs (OD600 = 0.2). | |||
| Metabolism | erythrose-4-phosphate dehydrogenase | −0.977 | −0.762 |
| apbE | −0.62 | −1.113 | |
| nicotinate-nucleotide diphosphorylase | −1.559 | −0.78 | |
| dGTPase | −0.498 | −0.44 | |
| suhB | −0.649 | −0.472 | |
| L-aspartate oxidase | −1.706 | −0.601 | |
| Protease | −1.64 | −0.711 | |
| cystathionine β-lyase | −0.789 | −0.575 | |
| peptidylprolyl isomerase | −0.722 | 0.624 | |
| betaine-aldehyde dehydrogenase | −2.498 | 0.571 | |
| choline dehydrogenase | −2.154 | 0.674 | |
| 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase | −0.837 | 2.096 | |
| Outer membrane proteins | ompC/WP_013026835.1 | −1.236 | −2.393 |
| Stress response | FAD/NAD(P) binding domain-containing protein | −0.93 | −1.039 |
| GNAT family N-acetyltransferase | −0.751 | −0.596 | |
| class C β-lactamase | −0.953 | −0.743 | |
| exodeoxyribonuclease I | −0.533 | −0.487 | |
| NUDIX hydrolase | −0.751 | −0.759 | |
| htpG | −1.09 | 0.877 | |
| groEL | −0.921 | 0.814 | |
| dnaJ | −0.84 | 0.742 | |
| sulfurtransferase | −0.733 | 0.971 | |
| hslU | −0.619 | 0.473 | |
| Transport | MFS transporter/WP_033765526.1 | −2.103 | −0.716 |
| sulfate transporter subunit | −1.613 | −0.567 | |
| C4-dicarboxylate ABC transporter | −1.445 | −0.993 | |
| MATE family efflux transporter | −1.266 | −0.806 | |
| tcyP | −0.908 | −1.025 | |
| MFS transporter/WP_028714804.1 | −0.957 | −0.716 | |
| ABC transporter permease | −0.712 | −0.522 | |
| flavocytochrome c | −0.712 | −0.934 | |
| microcin B17 transporter | −0.954 | 1.872 | |
| MFS transporter/WP_014598266.1 | −1.048 | 1.327 | |
| MFS transporter/WP_013024876.1 | −0.701 | 1.31 | |
| nickel transporter | −0.58 | 1.433 | |
| Gene regulators | DNA-binding response regulator | −0.6 | −0.603 |
| lysR/WP_028714815.1 | −1.675 | −0.718 | |
| draR | −0.974 | −1.295 | |
| lclR | −0.862 | −1.004 | |
| pbsX | −0.863 | −0.758 | |
| DNA-binding response regulator | −0.734 | 1.974 | |
| yqeI | −0.747 | 1.789 | |
| cdaR | −1.262 | 0.891 | |
| ompR | −0.734 | 1.974 | |
| Hypothetical proteins | WP_028715941.1 | −1.129 | −1.493 |
| WP_014593863.1 | −1.269 | −0.683 | |
| WP_028715707.1 | −1.481 | −1.226 | |
| WP_026021031.1 | −1.69 | −1.957 | |
| WP_028715464.1 | −0.864 | −1.032 | |
| WP_014594750.1 | −0.711 | −0.535 | |
| WP_028714922.1 | −1.067 | −1.138 | |
| WP_014605434.1 | −1.964 | −1.308 | |
| WP_014606741.1 | −1.173 | −0.939 | |
| WP_028715967.1 | −0.788 | −0.779 | |
| WP_028715704.1 | −0.939 | −0.922 | |
| WP_013024364.1 | −0.83 | −0.595 | |
| WP_028715521.1 | −0.742 | −0.578 | |
| WP_028715342.1 | −0.874 | −1.013 | |
| WP_050442548.1 | −1.663 | −1.265 | |
| WP_026021018.1 | −1.426 | −0.732 | |
| WP_014593149.1 | −1.931 | −1.472 | |
| WP_013026749.1 | −0.722 | 1.177 | |
| WP_022622675.1 | −0.63 | 1.053 | |
| WP_013024276.1 | −1.146 | 0.744 | |
| Cell wall synthesis | penicillin-binding protein 2 | −0.598 | 1.418 |
| ftsI | −0.726 | 1.406 | |
| murJ | −0.562 | 0.549 | |
| D-alanyl-D-alanine carboxypeptidase/WP_013026332.1 | −1.335 | 3.127 | |
| N-acetylmuramoyl-L-alanine amidase | −1.08 | 1.914 | |
| murein transglycosylase B | −1.155 | 0.608 | |
| Other | FUSC family protein | −0.918 | −0.704 |
| quinolinate synthetase | −1.122 | −0.863 | |
| dGTPase | −0.498 | −0.44 | |
| diaA | −0.658 | 0.527 | |
| U32 family peptidase | −0.641 | 0.884 | |
| peptidylprolyl isomerase | −0.722 | 0.624 | |
| K+/H+ antiporter | −0.727 | 0.879 | |