TABLE 2.

Dual regulation of virulence and other genes by the Rcs systema

Gene/open reading frame and functional categorybWT/ΔrcsBcWT/RcsB++dFunction/descriptione
Pathogenicity (47)
    mig-144.02.4Put. transcription activator
    pagC1335PhoP regulated; reduced macrophage survival
    pagD139.5PhoP regulated
    pagK3.65.5PhoPQ-activated gene
    pgtE3.42.9Phosphoglycerate transport; outer membrane protein E
    pipB7.559Pathogenicity island-encoded protein; SPI-3
    sifA1638Replication in macrophages
    sifB8.826Translocated effector; translocated by SPI-2
    spvA2.04.4Salmonella plasmid virulence; outer membrane protein
    spvC1.912Salmonella plasmid virulence; hydrophilic protein
    spvD1.95.5Salmonella plasmid virulence; hydrophilic protein
    ssaB, ssaC, ssaD, ssaE (ssaB)7.3-268.0-89Secretion system apparatus
    ssaG∼L, STM1410 (ssaG)12-3017-150Secretion system apparatus
    ssaM∼Q, ssaV (ssaM)4.0-344.4-33Secretion system apparatus
    sscB, sseF, sseG3.4-134.9-35Secretion system chaperone
    sseA∼E, sscA (sseA)13-1942-58Secretion system effector
    sseJ4248Salmonella translocated effector; regulated by SPI-2
    ssrA, ssrB (ssrA)3.6-5.49.7-11Secretion system regulator; sensor component
    STM09721122Homologous to secreted protein SopD
    ugtL (ugtL)1316Put. membrane protein; homology with chitinase
    virK7.36.4Virulence gene; homologous to virK in Shigella
    yscR, ssaS, ssaT, ssaU (yscR)2.8-163.6-56Homology with YscR of Yersinia secretion system
Fimbriae (8)
    fimA74.337.2Major type 1 subunit fimbrin (pilin)
    fimI, fimC, fimD, fimF (fimI)1.8-142.1-15Fimbrial protein internal segment
    fimW9.88.5Put. fimbrial protein
    fimZ1515Fimbrial protein Z; Put. transcriptional regulator
    stdA1214Put. fimbria-like protein
Membrane and periplasm (11)
    cvpA, purF (cvpA)2.3-2.43.4Membrane protein required for colicin V production
    STM1689 (STM1689)2378Put. inner membrane protein
    STM21398.318Put. inner membrane protein
    STM22458.010Put. outer membrane protein
    STM4257∼4262 (STM4257)2.6-8.120-40Put. inner membrane or exported
Others (14)
    carA, carB (carA)3.0-3.48.2-13Carbamoyl-phosphate synthetase
    ilvB, ilvN (ilvB)2.72.4-3.0Acetolactate synthase I; large subunit, valine sensitive
    STM1055 (STM1055)2.42.3Gifsy-2 prophage
    STM15482.74.9S-adenosylmethionine/tRNA-ribosyltransferase-isomerase
    STM21374.14.7Put. cytoplasmic protein
    STM21389.528Put. cytoplasmic protein
    STM22871738Put. cytoplasmic protein
    STM25854.37.3Gifsy-1 prophage; similar to transposase
    STM27787.625Pseudogene; frameshift
    STM27809.833Homologue of pipB; Put. pentapeptide repeats
    STM3133, STM3132 (STM3133)2.1-3.63.7Put. amidohydrolase
  • a 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.

  • b 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.

  • c ΔrcsB refers to strain QW434, which contains a deletion of rcsB. Genes in this column are positively regulated by RcsB.

  • d RcsB++ refers to the igaA mutant strain QW119 with elevated RcsB levels and activity. Genes in this column are negatively regulated by RcsB.

  • e 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.