Table 2.
Repressed genes with ≤ 0.5 fold change in expression level FDR (p-value ≤ 0.05)
| Fold change extract/control | ||||
|---|---|---|---|---|
| Gene | Gene product | L | A | P |
| Cluster VII Iron uptake and metabolism | ||||
| pvdS | RNA polymerase sigma-70 factor, ECF subfamily | 0.01 | 0.09 | |
| fpvA | outer membrane ferripyoverdine receptor | 0.47 | ||
| PSPPH_4765 | RNA polymerase sigma-70 family protein | 0.26 | 0.55 | |
| PSPPH_1911 | pyoverdine chromophore precursor synthetase | 0.04 | 0.14 | |
| PSPPH_1912 | diaminobutyrate--2-oxoglutarate transaminase | 0.26 | 0.53 | |
| PSPPH_1923 | pyoverdine sidechain peptide synthetase I, epsilon-Lys module | 0.03 | 0.25 | |
| PSPPH_1924 | pyoverdine sidechain peptide synthetase II, D-Asp-L-Thr component | 0.03 | 0.09 | |
| PSPPH_1925 | pyoverdine sidechain peptide synthetase III, L-Thr-L-Ser component | 0.02 | 0.10 | |
| PSPPH_1926 | pyoverdine sidechain peptide synthetase IV, D-Asp-L-Ser component | 0.08 | 0.27 | |
| PSPPH_1929 | pyoverdine ABC transporter, ATP-binding/permease protein | 0.26 | 0.40 | |
| PSPPH_1930 | conserved hypothetical protein | 0.11 | ||
| PSPPH_1933 | Tat (twin-arginine translocation) pathway signal sequence domain protein | 0.05 | 0.28 | |
| PSPPH_1934 | outer membrane efflux lipoprotein, NodT family | 0.14 | ||
| PSPPH_2751 | achromobactin biosynthetic protein AcsD | 0.26 | ||
| pchA | isochorismate synthase | 0.18 | 0.25 | |
| PSPPH_2895 | ABC transporter, ATP-binding/permease protein | 0.07 | ||
| PSPPH_2896 | ABC transporter, ATP-binding/permease protein | 0.14 | 0.18 | |
| PSPPH_2897 | yersiniabactin non-ribosomal peptide synthetase | 0.15 | 0.13 | |
| exbD1 | TonB system transport protein ExbD1 | 0.16 | 0.30 | |
| PSPPH_3266 | TonB-dependent siderophore receptor, putative | 0.48 | ||
| PSPPH_2117 | FecR protein superfamily | 0.15 | 0.41 | 0.61 |
| PSPPH_5185 | iron compound ABC transporter, iron compound-binding protein | 0.13 | 0.19 | |
| PSPPH_2957 | Mn2+/Fe2+ transporter, NRAMP family | 0.20 | 0.08 | 0.07 |
| PSPPH_3288 | Predicted periplasmic lipoprotein involved in iron transport | 0.17 | ||
| Cluster VIII Unknown function | ||||
| PSPPH_4882 | conserved hypothetical protein | 0.11 | 0.06 | 0.05 |
| PSPPH_2116 | conserved hypothetical protein | 0.12 | 0.32 | 0.65 |
| PSPPH_1082 | conserved hypothetical protein | 0.14 | 0.28 | 0.63 |
| PSPPH_5155 | conserved hypothetical protein | 0.37 | 0.20 | 0.31 |
| PSPPH_1173 | conserved hypothetical protein | 0.46 | 0.66 | |
| PSPPH_1243 | conserved hypothetical protein | 0.18 | ||
| PSPPH_2103 | conserved hypothetical protein | 0.20 | ||
| PSPPH_5180 | conserved hypothetical protein | 0.50 | ||
| Cluster IX None particular cluster | ||||
| PSPPH_2486 | acetyltransferase, GNAT family | 0.37 | 0.45 | 0.58 |
| PSPPH_2918 | membrane protein, putative | 0.37 | 0.13 | 0.12 |
| PSPPH_2919 | carbonic anhydrase, putative | 0.27 | 0.18 | 0.19 |
| osmC | hydroperoxide resistance protein OsmC | 0.22 | 0.45 | 0.63 |
| PSPPH_4984 | prophage PSPPH06, site-specific recombinase, phage integrase family | 0.11 | 0.25 | 0.62 |
| PSPPH_2219 | transcriptional regulator, AsnC family | 0.09 | 0.15 | 0.59 |
| PSPPH_3916 | membrane protein, putative | 0.07 | 0.01 | 0.02 |
| PSPPH_2216 | zinc carboxypeptidase domain protein | 0.04 | 0.20 | 0.54 |
| PSPPH_2747 | transcriptional regulator, Cro/CI family | 0.49 | 0.59 | |
| PSPPH_B0005 | transcriptional regulator, Cro/CI family | 0.46 | 0.45 | |
| PSPPH_3928 | ABC transporter, binding protein | 0.34 | 0.63 | |
| PSPPH_0189 | ATP-dependent DNA helicase RecG | 0.34 | 0.42 | |
| PSPPH_4962 | prophage PSPPH06, C4-type zinc finger protein, DksA/TraR family | 0.24 | 0.16 | |
| PSPPH_0194 | ActC family protein | 0.24 | 0.56 | |
| PSPPH_2746 | dipeptide ABC transporter, ATP binding protein | 0.14 | 0.33 | |
| PSPPH_0970 | O-methyltransferase I | 0.12 | 0.24 | |
| PSPPH_0592 | high-affinity branched-chain amino acid ABC transporter, permease protein BraE | 0.08 | 0.30 | |
| eda2 | 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase | 0.43 | ||
| PSPPH_4761 | glutathione S-transferase family protein | 0.43 | ||
| PSPPH_1737 | transcriptional regulator, LysR family | 0.42 | ||
| PSPPH_4723 | molybdate transport regulator ModE, putative | 0.41 | ||
| PSPPH_3100 | isocitrate dehydrogenase, NADP-dependent | 0.40 | ||
| PSPPH_3284 | beta-lactamase | 0.34 | ||
| PSPPH_1244 | transcriptional regulator, AsnC family | 0.30 | ||
| PSPPH_3265 | acetyltransferase, GNAT family | 0.27 | ||
| pilo | type IV pilus biogenesis protein PilO | 0.16 | ||
| PSPPH_5152 | pyridoxal kinase | 0.43 | ||
The table includes genes that shown ≤ 0.5 fold change in expression level. L Bean leaf extract, A apoplastic fluid and P Bean pod extract. ORF nomenclature corresponding to 1448A reference sequenced strain. For a complete list of all statistically repressed genes please consult Additional File 1.