Table 1. Genes with a shared PhoP-dependent differential expression pattern in more than one environmental condition.
Criteria for significance: ≥ 2-fold difference, P ≤ 0.05 or ≥ 1.5-fold difference, P ≤ 0.001. Fold-change values in parentheses not significant based on P value. Genes in bold type are associated with an upstream consensus PhoP-binding site and are predicted or have been shown to be directly regulated by PhoP (Harari et al., 2010; Li et al., 2008; Perez et al., 2009).
| Relative expression (fold-change; WT versus ΔphoP) during growth in |
||||||
| Gene ID | Gene name | Predicted function of gene product | Flea | LB (flow cell) |
LB (exponential) |
LB (stationary) |
| Significantly higher expression in WT Y. pestis in all conditions | ||||||
| y1795 | – | Predicted outer membrane protein; next to phoP | 7.2 | 20.7 | 57.5 | 18.5 |
| y1877 | – | Predicted N-acetylmuramoyl-l-alanine amidase | 2.5 | 7.2 | 13.8 | 4.7 |
| y1917 * | pgbP (pmrH) | Lipid A modification; aminoarabinose synthesis | 2.8 | 16.2 | 18.2 | 8.6 |
| y1918 * | pmrF | Lipid A modification; UDP-aminoarabinose transferase | 5.2 | 11.6 | 16.7 | 7.4 |
| y1919 * | pmrI | Lipid A modification; UDP-glucuronic acid decarboxylase/ UDP-aminoarabinose formyltransferase |
3.0 | 10.7 | 17.1 | 8.8 |
| y1920 * | pmrJ | Lipid A modification; UDP-aminoarabinose deformylase | 3.0 | 13.3 | 14.9 | 6.7 |
| y1921 * | pmrK (arnT) | Lipid A modification; aminoarabinose transfer | 1.9 | 7.8 | 13.9 | 4.7 |
| y1922 * | pmrL | Lipid A modification; aminoarabinose phospho-UDP flippase subunit | 1.6 | 6.6 | 8.8 | 3.1 |
| y1923 * | pmrM | Lipid A modification; aminoarabinose phospho-UDP flippase subunit | 2.2 | 11.5 | 12.8 | 4.1 |
| y2124 | – | Putative inner membrane protein | 5.1 | 16.0 | 31.7 | 11.2 |
| y2147 | ugd | Lipid A modification; aminoarabinose synthesis | 4.5 | 7.6 | 15.1 | 4.7 |
| y2608 | – | Predicted nucleoside-diphosphate sugar epimerase | 3.3 | 15.4 | 24.0 | 15.2 |
| y2859 | – | Undecaprenyl-pyrophosphate phosphatase; ybjG homologue | 3.2 | 6.8 | 9.5 | 4.6 |
| y3968 | – | Putative glycosyltransferase | 2.8 | 3.1 | 3.5 | 3.1 |
| YPO1659+ PhoP binding† | – | Hypothetical protein; next to mgtC | 3.6 | 17.4 | 27.7 | 15.9 |
| Significantly higher expression in ΔphoPY. pestis in all conditions | ||||||
| y2882 | psaA | pH 6 antigen fimbrial subunit | − 81.7 | − 26.3 | − 61.0 | − 130.4 |
| Significantly higher expression in WTY. pestis in biofilm conditions (flea and flow cell) only | ||||||
| y1741 | rcsA | Transcriptional regulator RcsA; Rcs regulatory system (pseudogene) | 4.9 | 2.8 | (2.2) | (2.0) |
| y1792 | – | Hypothetical protein; next to phoQ | 2.1 | 2.0 | (1.7) | 1.1 |
| Significantly higher expression in WTY. pestis during in vitro growth only | ||||||
| y0447 | – | Membrane-associated alkaline phosphatase | (1.5) | 4.0 | 4.0 | 4.0 |
| y1820 | mgtC | Mg2+ transport ATPase protein C | 1.3 | 12.5 | 19.4 | 6.1 |
| y2563 | pagP | Lipid A acylation; palmitoyltransferase | 1.1 | 20.4 | 46.6 | 9.9 |
| y2816 | – | virK-like virulence factor | (1.5) | 17.4 | 28.5 | 24.9 |
| y2858 | – | Membrane protein | (1.9) | 5.4 | 7.0 | 2.9 |
* Linked genes.
† Gene not annotated in Y. pestis KIM (YPO number indicates Y. pestis CO92 homologue).