Table 3. Real time RT-PCR analyses predominantly confirm RNA-seq data.
| Genes tested | Annotation | Median Q-value (Genecounter) | Putative hrp-box | pBAD system* # | Fold induction in pBAD system | Native system* ∧ | % expression in ΔhrpL vs. WT |
| PSPTO_4332 | hypothetical protein | 4.66E-13 | − | + | 15.3 | + | 3.8 |
| PSPTO_2130 | LuxR family DNA-binding response regulator | 3.45E-10 | + | + | 5.2 | + | 19.0 |
| PSPTO_3086 | transcriptional regulator | 3.75E-10 | − | + | 24.0 | + | 4.1 |
| PSPTO_2129 | sensory box histidine kinase/response regulator | 4.86E-05 | − | + | 3.4 | + | 21.3 |
| PSPTO_2208 | htpG heat shock protein 90 | 9.82E-05 | − | + | 2.7 | + | 53.6 |
| PSPTO_0871 | macrolide efflux protein | 1.51E-04 | + | + | 2.8 | ND | ND |
| PSPTO_1843 | aspartate kinase | 1.48E-03 | − | − | 0.9 | ND | ND |
| PSPTO_4716 | hypothetical protein | 1.89E-02 | − | − | 1.5 | ND | ND |
| PSPPH_A0112 | phosphoglycerate mutase family protein | 3.11E-11 | − | + | 4.8 | + | 20.5 |
| PSPPH_A0110 | hypothetical protein | 3.94E-10 | − | ND | ND | + | 53.6 |
| PSPPH_A0109 | sulfotransferase, putative | 7.96E-08 | − | + | 4.3 | + | 51.6 |
| PSPPH_1906 | LuxR family DNA-binding response regulator | 5.51E-07 | + | + | 4.9 | + | 4.1 |
| PSPPH_0762 | hypothetical protein | 4.45E-03 | − | + | 4.4 | + | 9.9 |
| PSPPH_A0106 | hypothetical protein | 7.49E-03 | − | ND | ND | + | 46.4 |
| PSPPH_A0108 | adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 1.27E-02 | − | ND | ND | + | 36.7 |
| Psyr_0737 | putative transmembrane protein | 1.00E-46 | + | + | 23.3 | + | 8.0 |
| Psyr_0027 | hypothetical protein | 1.64E-14 | − | + | 4.3 | − | 84.5 |
| PORcurated_00518 | hypothetical protein | 2.49E-54 | + | + | 84.3 | + | 2.0 |
| PORcurated_04644 | Methyltransferase small domain | 1.16E-37 | + | + | 48.4 | + | 3.5 |
| PORcurated_03530 | hypothetical protein | 3.03E-30 | + | + | 19.5 | + | 34.2 |
| PORcurated_04640 | hypothetical protein | 1.72E-27 | + | + | 19.8 | + | 42.3 |
| PORcurated_04022 | Alkylated DNA repair protein | 4.24E-24 | − | +/− | 1.7 | ND | ND |
| PORcurated_04648 | hypothetical protein | 2.35E-14 | − | + | 4.1 | + | 41.7 |
| PORcurated_04371 | hypothetical protein | 3.39E-24 | + | + | 5.2 | + | 30.2 |
| PORcurated_04025 | hypothetical protein | 1.99E-11 | − | + | 3.4 | ND | ND |
| PORcurated_04024 | Domain of unknown function (DUF1883) | 1.06E-04 | − | − | 0.6 | ND | ND |
*
+ found up-regulated by qRT-PCR; − no up-regulation. ND, not determined. See Figure S2 and S3 for detailed qRT-PCR results.
#
expression compared between Ps (pBAD::EV) strain and Ps (pBAD::hrpL) strain grown in media containing arabinose.
∧
expression compared between a wild type strain and an isogenic clean hrpL deletion mutant grown in MM media.