TABLE 2.
Regulation of the Rcs regulon by anti-sense fliPQR RNAa
| Name b | Ratio c | SD | Ratio | SD | |
|---|---|---|---|---|---|
| Virulence genes negatively regulated | Others positively regulated (cont’nd) | ||||
| avrA | 2.6 | 0.5 | melA | 3.0 | 0.9 |
| hilC | 122 | 95 | narV (narZ) | 3.1 | 0.7 |
| hilD | 2.3 | 0.3 | nirB (nirB) | 2.2 | 0.6 |
| invC,F,G,J,spaO,S (invF) | 1.4–2.8 | 0.1–0.7 | ompF | 24 | 11.8 |
| prgH,I,K,orgA,STM2868 (prgH) | 2.0–4.9 | 0.3–1.1 | osmE | 2.5 | 0.4 |
| sicA,P,sipA~D,iacP,sptP (sicA) | 1.7–2.3 | 0.1–1.0 | ptsG | 3.1 | 1.1 |
| sopA | 2.4 | 0.2 | rmf | 4.3 | 1.6 |
| sopB (sopB) | 4.8 | 1.4 | rpsP,rimM,trmD,rplS (rpsP) | 2.2–3.0 | 0.3–0.5 |
| ssaC (ssaB) | 1.6 | 0.1 | sodC | 2.0 | 0.7 |
| ssaJ,L (ssaG) | 2.5–4.3 | 0.2–0.9 | spvA | 4.5 | 1.7 |
| sseA,B,sscA (sseA) | 1.7–2.1 | 0.1 | spvB | 2.6 | 0.8 |
| sseF,G (sscB) | 1.9–2.1 | 0.3–0.4 | spy | 2.2 | 0.4 |
| sseJ | 9.8 | 2.1 | STM0950 (STM0951) | 2.7 | 0.9 |
| ssrA,B (ssrA) | 1.6–2.6 | 0.2–0.6 | STM1273 | 3.4 | 0.2 |
| Others negatively regulated | STM1561 | 2.4 | 0.5 | ||
| cadB | 36.5 | 7.0 | STM1633 (STM1633) | 2.3 | 0.4 |
| cdd | 8.4 | 1.5 | STM1638 | 7.3 | 2.0 |
| fabB | 2.5 | 0.1 | STM4071 | 5.3 | 0.8 |
| ppk (ppk) | 2.4 | 0.3 | STM4239,yjbJ (dinF) | 3.2–5.3 | 0.7–1.6 |
| sfbA (sfbA) | 2.3 | 0.5 | STM4242 | 3.6 | 0.6 |
| STM1328 | 6.6 | 0.4 | STM4510 | 5.6 | 1.5 |
| STM2287 | 4.9 | 0.4 | STM4519 | 5.4 | 2.4 |
| tdcE (tdcD) | 3.2 | 0.7 | yahoo | 5.6 | 1.7 |
| Others positively regulated | yaiA (aroL) | 2.8 | 1.0 | ||
| aceA~B (aceB) | 103–143 | 43–46 | yciE,STM1731 (yciE) | 3.5–3.9 | 1.6–1.9 |
| bax | 3.0 | 0.5 | yciF | 2.6 | 1.2 |
| chaB | 2.5 | 0.8 | ydeV | 5.6 | 0.8 |
| dniR | 3.6 | 2.2 | ydeW | 7.0 | 2.0 |
| ecnB | 2.5 | 0.6 | yeaG | 2.6 | 0.9 |
| ego, ydeY,Z, yneA~C, STM4080 (ego) | 2.5–20 | 0.1–4.6 | yebF | 2.2 | 0.5 |
| fbaB | 4.1 | 1.4 | yehZ (yehZ) | 2.1 | 0.7 |
| galP | 2.2 | 0.6 | ygiM | 2.3 | 0.8 |
| ggt | 5.6 | 5.0 | yhbO | 2.0 | 0.9 |
| katE | 2.0 | 0.6 | yibD | 2.8 | 0.9 |
| malE | 2.3 | 0.5 | yieF (yieE) | 2.5 | 0.8 |
| manX~Z (manX) | 7.3–13 | 1.5–4.9 | yncB | 2.7 | 1.1 |
The microarray data are for RNA harvested from cells at stationary phase.
Genes and open reading frames from the same operon are listed together. The first gene of the operon is indicated in parenthesis. ~ indicates intervening genes in the operon.
Transcription ratios are expressed such that the numbers are >1 for both positively and negatively regulated genes, because it is easier to compare fold regulation using whole numbers rather than fractions. Positive ratios were derived by dividing QW119 (igaA*) values by either QW422 ( fliR::kan, igaA*), QW471 ( fliQR, igaA*) or QW556 (ΔRA 1–48, igaA*); negative ratios were reverse of these. The differentially regulated Rcs regulon genes common to all three pairs of strains are shown. The range indicates low and high values for individual genes within the operon. The ratios represent an average of 4 independent repeats. SD, standard deviation.