TABLE 3.
A subset of genes whose expression is dependent on PecS in E. chrysanthemi that have been selected for their potential link with plant interaction
| Gene product category and gene name | GeneID no. | Gene product description | Fold changeb | FDR-adjusted P value |
|---|---|---|---|---|
| Secreted proteins and secretion systems | ||||
| avrL | 19143 | Avirulence protein L | 2.65 | 3.33E-06 |
| avrM | 15381 | Avirulence protein M | 2.36 | 8.21E-06 |
| celZa | 18772 | Endo-1,4-β-glucanase | 4.04 | 2.04E-07 |
| hcpA | 17270 | Haemolysin-coregulated protein | 1.36 | 1.82E-03 |
| hcpB | 15893 | Haemolysin-coregulated protein | 1.33 | 5.31E-03 |
| hrpBa | 19592 | HrpB, type III protein secretion system | 1.48 | 5.38E-05 |
| nipE | 15387 | Similar to necrosis-inducing protein | 2.38 | 2.95E-06 |
| outDa | 18230 | Type II secretory pathway component, OutD | 1.40 | 2.72E-03 |
| pelAa | 19643 | Pectate lyase PelA | 1.40 | 1.03E-03 |
| pelCa | 20837 | Pectate lyase PelC | 1.98 | 7.88E-06 |
| pelDa | 19648 | Pectate lyase PelD | 1.36 | 9.01E-03 |
| pelEa | 19646 | Pectate lyase PelE | 2.95 | 1.83E-06 |
| pelL | 18773 | Pectate lyase PelL | 2.99 | 1.15E-06 |
| pelN | 19391 | Pectate lyase PelN | 2.43 | 1.15E-06 |
| prtA | 20373 | Secreted metalloprotease A | 2.80 | 3.42E-06 |
| prtB | 47107 | Secreted metalloprotease B | 3.13 | 2.51E-07 |
| prtC | 20371 | Secreted metalloprotease C | 3.41 | 2.51E-07 |
| prtG | 17123 | Secreted metalloprotease G | 2.33 | 6.62E-06 |
| virK | 20481 | Similar to VirK of A. tumefaciens | 3.39 | 3.48E-07 |
| xynA | 19026 | Xylanase | 1.83 | 1.12E-03 |
| yoaJ | 14642 | Endoglucanase | 1.46 | 9.78E-03 |
| 19566 | Unknown exported protein | 2.04 | 1.37E-04 | |
| 15573 | Unknown exported protein | 2.01 | 8.70E-04 | |
| Oxidative stress response proteins | ||||
| acsA | 18857 | Achromobactin biosynthetic protein AcsA | 1.46 | 1.12E-03 |
| acsC | 18859 | Achromobactin biosynthetic protein AcsC | 1.36 | 1.03E-03 |
| acsF | 18866 | Diaminobutyrate-2-oxoglutarate transaminase | 1.33 | 4.13E-03 |
| ahpC | 18570 | Alkyl hydroperoxide reductase small subunit | 2.70 | 1.43E-05 |
| asnB | 46967 | Asparagine synthase B | 1.71 | 1.52E-02 |
| atpA | 14787 | Membrane-bound ATP synthase, F1 sector, alpha-subunit | 1.49 | 3.61E-04 |
| atpB | 14794 | F0F1-type ATP synthase, subunit a | 1.39 | 1.40E-03 |
| atpC | 14784 | F0F1-type ATP synthase, epsilon subunit | 1.39 | 7.71E-04 |
| atpD | 14785 | F0F1-type ATP synthase, beta subunit | 1.33 | 1.59E-04 |
| atpE | 14792 | F0F1-type ATP synthase, subunit c | 1.39 | 1.67E-04 |
| atpF | 14791 | F0F1-type ATP synthase, subunit b | 1.40 | 1.43E-04 |
| atpG | 14786 | F0F1-type ATP synthase, gamma subunit | 1.40 | 1.37E-04 |
| atpH | 14789 | F0F1-type ATP synthase, delta subunit | 1.49 | 2.97E-04 |
| atpI | 14795 | F0F1-type ATP synthase, subunit I | 1.33 | 8.40E-04 |
| grxC | 20419 | Lipid hydroperoxide reductase | 1.40 | 4.90E-04 |
| indAa | 16084 | Indigoidine biosynthesis | 8.18 | 3.26E-08 |
| indBa | 16083 | Indigoidine biosynthesis | 12.24 | 4.16E-09 |
| indCa | 16081 | Indigoidine synthase | 12.94 | 3.26E-08 |
| groL/mopA | 18669 | Chaperonin GroEL | 1.35 | 1.94E-02 |
| tsaA | 17551 | Peroxiredoxin | 1.73 | 4.28E-03 |
| yfeH | 15572 | Similar to putative cytochrome oxidase from E. coli/Shigella | 1.51 | 9.18E-04 |
| Motility proteins | ||||
| flgE | 17935 | Flagellar biosynthesis, hook protein | 1.51 | 1.27E-02 |
| flgF | 17936 | Flagellar biosynthesis, cell-proximal portion of basal-body rod | 1.39 | 3.72E-02 |
| fliA | 19722 | Alternative sigma factor F | 1.50 | 6.53E-03 |
| fliC | 19735 | Flagellin, filament structural protein | 1.38 | 9.13E-03 |
| fliD | 17963 | Flagellar biosynthesis; filament capping protein; enables filament assembly | 1.34 | 2.26E-03 |
| fliY | 17013 | Amino acid ABC transporter, periplasmic amino acid-binding protein | −1.45 | 6.03E-05 |
| fliZ | 19721 | Regulatory protein | 2.14 | 2.40E-03 |
| rhlA | 19839 | Acyltransferase | 10.87 | 3.43E-07 |
| 14536 | Methyl-accepting chemotaxis protein | 2.04 | 8.21E-06 | |
| 18765 | Methyl-accepting chemotaxis protein | −1.43 | 2.19E-03 | |
| Regulatory proteins | ||||
| fadR | 18979 | Negative regulator for fad regulon and positive activator of fabA | 2.13 | 6.29E-06 |
| hha | 19540 | Hemolysin expression modulating protein | −1.34 | 1.51E-03 |
| hns | 20646 | H-NS protein; DNA-binding protein HLP-II (HU, BH2, HD, NS); pleiotropic regulator | −1.34 | 5.83E-04 |
| rsmA | 19320 | Posttranscriptional RNA-binding regulatory protein RsmA | −1.39 | 8.65E-03 |
| vfmE | 16073 | DNA-binding transcriptional regulatory protein VfmE | 2.06 | 3.48E-07 |
a
Previously shown as regulated by PecS.
b
Positive values represent genes upregulated in the pecS mutant, whereas negative values represent genes downregulated in the pecS mutant compared to the wild-type strain.