TABLE 2.
Dual regulation of virulence and other genes by the Rcs systema
| Gene/open reading frame and functional categoryb | WT/ΔrcsBc | WT/RcsB++d | Function/descriptione |
|---|---|---|---|
| Pathogenicity (47) | |||
| mig-14 | 4.0 | 2.4 | Put. transcription activator |
| pagC | 13 | 35 | PhoP regulated; reduced macrophage survival |
| pagD | 13 | 9.5 | PhoP regulated |
| pagK | 3.6 | 5.5 | PhoPQ-activated gene |
| pgtE | 3.4 | 2.9 | Phosphoglycerate transport; outer membrane protein E |
| pipB | 7.5 | 59 | Pathogenicity island-encoded protein; SPI-3 |
| sifA | 16 | 38 | Replication in macrophages |
| sifB | 8.8 | 26 | Translocated effector; translocated by SPI-2 |
| spvA | 2.0 | 4.4 | Salmonella plasmid virulence; outer membrane protein |
| spvC | 1.9 | 12 | Salmonella plasmid virulence; hydrophilic protein |
| spvD | 1.9 | 5.5 | Salmonella plasmid virulence; hydrophilic protein |
| ssaB, ssaC, ssaD, ssaE (ssaB) | 7.3-26 | 8.0-89 | Secretion system apparatus |
| ssaG∼L, STM1410 (ssaG) | 12-30 | 17-150 | Secretion system apparatus |
| ssaM∼Q, ssaV (ssaM) | 4.0-34 | 4.4-33 | Secretion system apparatus |
| sscB, sseF, sseG | 3.4-13 | 4.9-35 | Secretion system chaperone |
| sseA∼E, sscA (sseA) | 13-19 | 42-58 | Secretion system effector |
| sseJ | 42 | 48 | Salmonella translocated effector; regulated by SPI-2 |
| ssrA, ssrB (ssrA) | 3.6-5.4 | 9.7-11 | Secretion system regulator; sensor component |
| STM0972 | 11 | 22 | Homologous to secreted protein SopD |
| ugtL (ugtL) | 13 | 16 | Put. membrane protein; homology with chitinase |
| virK | 7.3 | 6.4 | Virulence gene; homologous to virK in Shigella |
| yscR, ssaS, ssaT, ssaU (yscR) | 2.8-16 | 3.6-56 | Homology with YscR of Yersinia secretion system |
| Fimbriae (8) | |||
| fimA | 74.3 | 37.2 | Major type 1 subunit fimbrin (pilin) |
| fimI, fimC, fimD, fimF (fimI) | 1.8-14 | 2.1-15 | Fimbrial protein internal segment |
| fimW | 9.8 | 8.5 | Put. fimbrial protein |
| fimZ | 15 | 15 | Fimbrial protein Z; Put. transcriptional regulator |
| stdA | 12 | 14 | Put. fimbria-like protein |
| Membrane and periplasm (11) | |||
| cvpA, purF (cvpA) | 2.3-2.4 | 3.4 | Membrane protein required for colicin V production |
| STM1689 (STM1689) | 23 | 78 | Put. inner membrane protein |
| STM2139 | 8.3 | 18 | Put. inner membrane protein |
| STM2245 | 8.0 | 10 | Put. outer membrane protein |
| STM4257∼4262 (STM4257) | 2.6-8.1 | 20-40 | Put. inner membrane or exported |
| Others (14) | |||
| carA, carB (carA) | 3.0-3.4 | 8.2-13 | Carbamoyl-phosphate synthetase |
| ilvB, ilvN (ilvB) | 2.7 | 2.4-3.0 | Acetolactate synthase I; large subunit, valine sensitive |
| STM1055 (STM1055) | 2.4 | 2.3 | Gifsy-2 prophage |
| STM1548 | 2.7 | 4.9 | S-adenosylmethionine/tRNA-ribosyltransferase-isomerase |
| STM2137 | 4.1 | 4.7 | Put. cytoplasmic protein |
| STM2138 | 9.5 | 28 | Put. cytoplasmic protein |
| STM2287 | 17 | 38 | Put. cytoplasmic protein |
| STM2585 | 4.3 | 7.3 | Gifsy-1 prophage; similar to transposase |
| STM2778 | 7.6 | 25 | Pseudogene; frameshift |
| STM2780 | 9.8 | 33 | Homologue of pipB; Put. pentapeptide repeats |
| STM3133, STM3132 (STM3133) | 2.1-3.6 | 3.7 | Put. amidohydrolase |
The microarray data are for RNA prepared from cells harvested at stationary phase. Indicated transcription ratios are averages from two to five independent experiments. These 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. The range indicates low and high values for individual genes within the operon.
Genes and open reading frames from the same operon are listed together; the first gene of the operon is indicated in parentheses. ∼ indicates intervening genes in the operon. Operon prediction was based on data from reference 47 and from http://biocyc.org/STYP99287/NEW-IMAGE?object=Transcription-Units. Only genes significantly differentially expressed in an operon are listed. The genes are grouped under broad functional categories, and the total number in each category is indicated in parentheses.
ΔrcsB refers to strain QW434, which contains a deletion of rcsB. Genes in this column are positively regulated by RcsB.
RcsB++ refers to the igaA mutant strain QW119 with elevated RcsB levels and activity. Genes in this column are negatively regulated by RcsB.
Functions and descriptions are based on data from reference 45; when several genes in an operon are listed, only the first one is described. Put., putative.