Table 1.
Induced genes with ≥ 2.0 fold change in expression level FDR (p-value ≤ 0.05)
| Fold change extract/control | ||||
|---|---|---|---|---|
| Gene/ORF | Gene product | L | A | P |
| Cluster I Plant-bacteria interaction | ||||
| pnlA | pectin lyase | 3.0 | ||
| PSPPH_A0072 | Polygalacturonase | 2.0 | 1.8 | 1.9 |
| hopAK1 | type III effector HopAK1 | 2.9 | ||
| hopAT1 | type III effector HopAT1 | 2.5 | 1.6 | |
| PSPPH_3107 | type II and III secretion system family protein | 3.7 | 2.6 | 1.8 |
| PSPPH_2990 | phytase domain protein | 3.2 | ||
| Cluster II Phaseolotoxin synthesis (Cluster Pht) | ||||
| phtM | hypothetical protein | 2.3 | 2.3 | |
| phtM-phtN | hypothetical protein (control) | 2.1 | 2.1 | |
| phtO | hypothetical protein | 2.1 | 2.1 | |
| amtA | L-arginine:lysine amidinotransferase, putative | 2.9 | 2.5 | |
| phtQ | conserved hypothetical protein | 2.7 | 2.1 | |
| phtS | adenylylsulfate kinase | 2.7 | 3.2 | |
| phtT | membrane protein, putative | 3.3 | 2.8 | |
| phtU | hypothetical protein | 3.5 | 2.9 | |
| phtL | pyruvate phosphate dikinase, PEP/pyruvate binding domain protein | 2.1 | 2.0 | |
| phtL | pyruvate phosphate dikinase, PEP/pyruvate binding domain protein(control) | 2.6 | 2.3 | |
| Cluster III Bacterial metabolism | ||||
| Ppc | phosphoenolpyruvate carboxylase | 2.2 | ||
| acsA | acetate-CoA ligase | 3.0 | ||
| PSPPH_1186 | aldose 1-epimerase family protein | 2.8 | ||
| PSPPH_1256 | transketolase, N-terminal subunit, putative | 6.0 | ||
| PSPPH_2070 | nitrate reductase | 2.2 | ||
| PSPPH_3291 | oxidoreductase, molybdopterin-binding | 2.0 | ||
| hutH2 | histidine ammonia-lyase | 2.0 | 1.5 | |
| nuoE | NADH-quinone oxidoreductase, E subunit | 5.0 | ||
| nuoF | NADH-quinone oxidoreductase, F subunit | 2.4 | ||
| nuoG | NADH-quinone oxidoreductase, G subunit | 6.6 | 2.4 | |
| nuoH | NADH-quinone oxidoreductase, H subunit | 4.3 | 1.7 | |
| PSPPH_2973 | monooxygenase, NtaA/SnaA/SoxA family | 2.3 | ||
| PSPPH_2357 | xylose operon regulatory protein | 2.1 | 1.8 | |
| PSPPH_0756 | glycosyl hydrolase, family 3 | 2.1 | ||
| Cluster IV Adaptation responses | ||||
| clpB2 | clpB protein | 2.2 | 1.5 | |
| groEL | chaperonin, 60 kDa | 4.3 | ||
| dnaK | dnaK protein | 2.8 | ||
| hslU | heat shock protein HslVU, ATPase subunit HslU | 2.1 | ||
| bfr2 | Bacterioferritin | 3.1 | 1.8 | |
| Cluster V Unknown function | ||||
| PSPPH_3261 | conserved hypothetical protein | 4.4 | ||
| PSPPH_3262 | conserved hypothetical protein | 4.4 | ||
| PSPPH_1192 | conserved hypothetical protein | 2.8 | ||
| PSPPH_2708 | conserved hypothetical protein | 2.5 | ||
| PSPPH_1613 | conserved hypothetical protein | 2.3 | ||
| PSPPH_1422 | conserved hypothetical protein | 2.2 | ||
| PSPPH_4323 | conserved hypothetical protein | 2.0 | ||
| PSPPH_3212 | conserved hypothetical protein | 4.9 | 2.3 | |
| PSPPH_3852 | conserved hypothetical protein | 2.5 | 1.6 | |
| PSPPH_3020 | conserved hypothetical protein | 2.1 | ||
| PSPPH_1470 | conserved hypothetical protein | 2.2 | 1.9 | |
| Cluster VI None particular group | ||||
| PSPPH_0804 | methyl-accepting chemotaxis protein | 3.2 | ||
| PSPPH_2971 | methyl-accepting chemotaxis transducer/sensory box protein | 2.2 | ||
| PSPPH_2994 | transcriptional regulator, AraC family | 2.3 | ||
| PSPPH_1595 | transcriptional regulator, GntR family | 2.1 | ||
| pbpC | penicillin-binding protein 1C | 2.3 | ||
| PSPPH_2053 | membrane protein, putative | 2.2 | ||
| PSPPH_3868 | ompA family protein | 2.6 | 2.1 | |
| PSPPH_3993 | acetyltransferase, GNAT family | 3.0 | ||
| PSPPH_0740 | Ribosomal large subunit pseudouridine synthase D(Pseudouridine synthase) (Uracil hydrolyase) | 2.6 | 1.6 | |
| PSPPH_2812 | PAP2 superfamily protein | 2.3 | 2.1 | |
| PSPPH_0920 | S-type pyocin family protein | 2.3 | ||
| fadB | fatty oxidation complex, alpha subunit FadB | 2.3 | ||
| iucD | siderophore biosynthesis protein | 2.0 | ||
| PSPPH_2652 | ABC transporter, ATP-binding protein | 8.7 | ||
| PSPPH_2653 | lipopolysaccharide core biosynthesis domain protein | 10.5 | ||
| PSPPH_2654 | lipoprotein, putative | 6.4 | ||
The table comprises all the genes that shown ≥ 2.0 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 induced genes please consult Additional File 1.