TABLE 3.

Changes in relative transcript amounts caused by PcsB underexpression in strain IU1979 compared to isogenic strain IU1533 growing exponentially in BHI broth at 37°Ca

Effect on expression and gene tagFunctionbFold changecBayesian P valuec
Decreased relative expression
    spr0088Hypothetical protein−1.95.6E-04
    spr0128Hypothetical protein−1.91.6E-04
    spr0446hsdS; type I restriction enzyme EcoKI specificity protein (S protein)−2.42.9E-05
    spr0504licT; transcriptional anti-terminator (BglG family)−1.92.1E-04
    spr0505pts-eii; phosphotransferase system sugar-specific EII component−2.01.4E-04
    spr0506bglH; 6-phospho-beta-glucosidase−1.91.9E-04
    spr0778fruR; transcriptional repressor of the fructose operon−1.95.3E-03
    spr0779fruB; fructose-1-phosphate kinase−2.11.5E-03
    spr0780fruA; fructose specific-phosphotransferase system IIBC component−2.21.4E-03
Increased relative expression
    spr0096Hypothetical protein4.11.2E-06
    spr0307clpL; ATP-dependent protease ATP-binding subunit2.63.5E-07
    spr0445hsdS; type I restriction enzyme3.49.0E-07
    spr0565bgaA; β-galactosidase precursor2.44.1E-05
    spr0867lytB; Endo-β-N-acetylglucosaminidase2.76.6E-07
    spr1016Hypothetical protein2.07.5E-05
    spr1601Hypothetical protein1.91.6E-05
    spr1722groEL; chaperonin GroEL2.33.7E-05
    spr1723groES; co-chaperonin GroES2.31.4E-06
    spr1872pcp-truncation; pyrrolidone carboxyl peptidase, truncation1.94.8E-05
    spr1873Conserved hypothetical protein2.43.3E-06
    spr1874marR; transcriptional regulator, MarR family3.31.2E-06
    spr1875Conserved hypothetical protein7.93.9E-09
  • a IU1533 (R6 pcsB+ ΔbgaA′::Pc-pcsB+) was used as the parent strain instead of R6 to control for insertion into the bgaA locus required to construct PcsB-underexpressing strain IU1979 (ΔpcsB<>ermAM ΔbgaA′::Pc-pcsB+). Representative growth curves from these experiments are shown in Fig. S2 of the supplemental material.

  • b Members of the VicRK regulon are shown in bold type.

  • c Microarray analyses were performed as described in Materials and Methods. The data set includes four biological replicates, including two dye swaps, with final cutoff values of <1.8 for fold changes and P < 0.005.