TABLE 1.
DsrA functional genomics in E. coli K-12
| Category and genes | Location (min)a | Function | Fold change
|
|
|---|---|---|---|---|
| Filter arrayb | Primer extensionc | |||
| Acid resistance | ||||
| 1 hdeA | 78.76 | Acid resistance | 10-26 | 26 |
| 2 hdeB | 78.75 | Acid resistance | 12-43 | — |
| 3 hdeD | 78.78 | Acid resistance | 2.2-3.4 | — |
| 4 gadA | 78.98 | Acid resistance | 2.3-3.0 | 3.5 |
| 5 gadX (alias yhiX) | 78.95 | Acid resistance-virulence regulator | 2.3-3.2 | 2.6 |
| 6 gadB | 33.81 | Acid resistance | 1 | 3.5 |
| 7 adiY | 93.44 | Acid resistance regulator | 3.7-5.7 | NS |
| 8 adiA | 93.46 | Acid resistance | 1 | NS |
| Membrane or transport | ||||
| 9 proX | 60.47 | Osmotic shock | 3.3-3.9 | — |
| 10 ompX | 18.32 | Outer membrane protein | 2.3-4.5 | — |
| 11 ompA | 21.95 | Outer membrane protein | 2-2.6 | — |
| 12 ompF | 21.23 | Outer membrane protein | 2-2.5 | — |
| 13 ompT | 12.59 | Outer membrane protein | 1.9-3.1 | — |
| 14 rbsB | 84.80 | Periplasmic ribose-binding proteind | −2.6-3.4 | — |
| Regulatory | ||||
| 15 malT | 76.54 | Activator-maltose regulon | −2.3-2.5 | — |
| 16 rpoE | 58.36 | Activator-sigma factor | −2-2.5 | — |
| 17 hns | 27.84 | Repressor-nucleoid | 1 | 1.3e |
| 18 stpA | 60.27 | Repressor-nucleoid-RNA chaperone | 1.2-2.3 | 3.1 |
| 19 rcsA | 43.58 | Activator-capsule synthesis | 1.3-1.4 | ∼10f |
| 20 dps | 18.27 | DNA protection | 1.9-3.4 | — |
| Motility | ||||
| 21 fimA | 97.88 | Fimbriae | 2.2-3.5 | — |
| 22 fliA | 43.09 | Flagella | −2.1 | — |
| 23 fliC | 43.11 | Flagella | −2.6-7.3 | — |
| Other | ||||
| 24 ftn | 42.83 | Ferritin (iron storage) | 2.8-3.6 | — |
| 25 xylA | 80.34 | d-Xylose isomerase | 2.5-2.9 | — |
| 26 sucA | 16.34 | 2-Ketoglutarate dehydrogenase | −2-2.3 | — |
| 27 groS (alias mopB) | 94.16 | Chaperonin | −2.6-2.9 | — |
| 28 garR (alias yhaE) | 70.48 | Tartronate semialdehyde reductase | −2.3-3.2 | — |
| 29 sgbU (alias yiaR) | 80.77 | Hexulose 6-phosphate isomerase (putative) | −2.4-3.4 | — |
| 30 hchA (alias yedU) | 43.84 | Heat-inducible chaperone | 4.7-5.9 | — |
| 31 rihC (alias yaaF) | 0.59 | Ribonucleoside hydrolase | −2-2.2 | — |
| 32 nfnBg | 13.02 | Nitroreductase (control)g | 1 | 1.2g |
| Hypothetical protein | ||||
| 33 yagU | 6.51 | Alias b0287 | 2.6-2.8 | — |
| 34 yncC | 32.73 | Alias b1450 | 2.1-4.4 | — |
| 35 yeaK | 40.34 | Alias b1787 | 2-2.9 | — |
| 36 yeaP | 40.43 | Alias b1794 | 2-2.2 | — |
| 37 yeaQ | 40.46 | Alias b1795 | 2.9-3.3 | — |
| 38 yedW | 43.89 | Alias b1969 | 2.3-4 | — |
| 39 ybfE | 15.32 | Alias b2253 | 2.1-3.2 | — |
Sigma-Genosys nylon membrane gene array. Fold changes for each experiment (n = 2) are given as ranges. All values that decrease are so indicated by minus signs.
Average fold effect (n = 3 or 4). NS, no extension product seen. —, primer extension not performed.
DsrA also contains an antisense sequence complementary to rbsD in the rbsDACBK operon (19).
The hns mRNA levels do not change, because of H-NS autoregulation, while H-NS protein levels decrease. Values shown here are comparable to those seen previously for primer extension quantitation (19). RpoS mRNA is stabilized, and levels slightly increased (18).
The rcsA transcript levels were determined previously (34). Visual estimate of primer extension was ∼10-fold. Activity of a reporter gene fusion was elevated 13-fold.
The nfnB gene was unaffected by DsrA overproduction and was used as a control.