TABLE 2.

Changes in relative transcript amounts in the Pc-pcsB+ ΔvicR mutant compared to its Pc-pcsB+ vicR+ parent grown in BHI and CDMa

R6 database no.GeneBHICDM
Average fold changeBayesian PAverage fold changeBayesian P
Changed in ΔvicR mutant and when VicR was depleted (42)
    spr2021b,cpcsB1.13.79E-11.15.29E-1
    spr0121cpspA−2.84.32E-7−2.41.64E-4
    spr0096cspr0096−16.43.63E-9−51.31.99E-10
    spr0709spr0709−3.01.70E-5−10.12.15E-9
    spr1875cspr1875−3.71.09E-8−28.01.53E-11
    spr1874spr1874−2.06.11E-6−3.83.26E-6
Changed in ΔvicR mutant, but not when VicR was depleted (42)
    spr0446hsdS−2.02.44E-5−2.81.78E-5
    spr0448hsdS3.01.39E-73.51.98E-7
    spr1108mutY2.25.76E-64.12.33E-7
Changed when VicR was depleted (42), but not in ΔvicR mutant
    spr1684cpiuB−1.22.45E-22.62.37E-2
    spr1685cpiuC−1.34.84E-31.53.05E-2
    spr1686cpiuD−1.22.76E-23.21.66E-4
    spr1687cpiuA−1.06.68E-11.34.98E-2
    spr1834ptcC−2.81.02E-61.27.60E-2
    spr1835ptcB−1.65.62E-41.14.36E-1
    spr1836ptcA−1.84.20E-41.26.42E-2
    spr1895pstS1.58.51E-3−1.21.91E-1
    spr1896pstC1.65.01E-31.23.13E-1
    spr1897pstA1.63.50E-31.18.12E-1
    spr1898pstB1.53.58E-31.31.72E-1
    spr1899phoU1.39.34E-31.37.72E-2
    spr0307clpL−1.13.17E-12.01.19E-3
    spr0453chrcA1.19.29E-11.51.54E-2
    spr0454cgrpE1.18.00E-11.15.77E-1
    spr0455cdnaK1.27.26E-11.31.18E-1
    spr0456dnaJ1.23.10E-11.37.17E-2
Other genes of interest discussed in the text
    spr0867clytB−1.43.12E-3−3.01.9E-6
    spr1106cvicK1.32.16E-21.54.62E-3
    spr1105vicX1.22.72E-21.57.88E-3
Genes that mediate fatty acid biosynthesis (see text)
    spr0376cfabR−1.42.47E-2−1.13.92E-1
    spr0377cfabH−1.07.99E-1−1.15.55E-1
    spr0378cacp−1.09.69E-1−1.09.09E-1
    spr0379cfabK−1.21.00E-1−1.46.11E-2
    spr0380cfabD−1.21.51E-1−1.51.77E-2
    spr0381cfabG−1.21.52E-1−1.46.84E-2
    spr0382cfabF−1.42.45E-2−1.51.09E-2
    spr0383caccB1.16.61E-1−1.71.30E-3
    spr0384cfabZ−1.13.03E-1−2.09.92E-4
    spr0385caccC−1.15.46E-1−1.41.29E-2
    spr0386caccD−1.29.97E-2−2.04.12E-4
    spr0387caccA1.12.36E-1−1.12.56E-1
  • a Growth of bacteria, preparation of RNA, microarray analyses, calculation of signal ratios and fold changes, and statistical analyses are described in Materials and Methods. Positive and negative fold changes correspond to increased and decreased transcript amounts, respectively, in the Pc-pcsB+ ΔvicR mutant compared to the Pc-pcsB+vicR+ parent (see Materials and Methods). Significant changes in relative transcript amounts were considered positive or negative 1.8-fold with Bayesian P of <0.001. Entries that do not meet these criteria are shown for genes of interest based on previous microarray analyses (39, 42) (see text). A several fold change of −1.0 means that there was a very slight decrease in relative transcript amount before rounding and is equivalent to no change (1.0).

  • b No change was expected, because pcsB+ expression was uncoupled from VicR regulation by fusion to the artificial Pc promoter.

  • c Genes that showed significant changes in relative transcript amounts when VicR was overexpressed as reported by Mohedano et al (39).