TABLE 3.

Microarray analysis of transcripts strongly regulated by the WalRKSpn, CiaRHSpn, or LiaSRSpn TCS in SpxB-Pta-AckA pathway mutants, compared to the D39 spxB+ pta+ ackA+ parent strain

Regulon and gene tag (spd no./ spr no.)aMetabolite or gene descriptionRelative metabolite or transcript fold changeb in strain (genotype)
IU2687 (Δpta)IU2173 (ΔspxB)IU3590 (ΔspxB ΔackA)IU2689 (ΔspxB Δpta)IU2837 (ΔspxB ΔackA Δpta)IU1885 (ΔwalKSpn)IU4319 (ΔspxB ΔackA ΔwalKSpn)IU3107 (ΔspxB Δpta ΔackA ΔwalKSpn)
ATP1.1 ± 0.11.0 ± 0.10.53 ± 0.040.50 ± 0.050.54 ± 0.09NDNDND
AcP1.0 ± 0.10.18 ± 0.021.9 ± 0.20.08 ± 0.040.07 ± 0.01NDNDND
WalRKSpn regulonc
    0104/0096LysM domain protein1.01.21.1−2.2 ± 0.5−2.5 ± 0.2−3.2 ± 0.1−2.0−4.4 ± 0.9
    1874/1875LysM domain protein (putative lysozyme)−1.1−1.21.1−3.4 ± 0.7−2.9 ± 0.3−7.8 ± 1.5−7.2−10.0 ± 1.4
    2043/2021pcsB; cell division protein1.01.11.1−1.3−1.9 ± 0.1−4.1 ± 0.7−2.1−3.9 ± 0.7
CiaRHSpn regulonc
    0775/0782Conserved hypothetical protein−1.2−1.9 ± 0.4−2.2 ± 0.8−2.0 ± 0.7−4.8 ± 0.41.7−1.1−1.6
    0913/0931Conserved hypothetical protein−1.0−2.0 ± 0.4−3.7 ± 1.2−3.1 ± 0.1−7.8 ± 1.51.4−1.1−2.0 ± 0.8
    2068/2045htrA; serine protease−1.0−2.2 ± 0.5−3.5 ± 1.6−3.1 ± 0.6−9.4 ± 1.9−1.0−1.5−2.5 ± 0.5
LiaSRSpn regulonc
    0178/0173Conserved hypothetical protein1.21.1−1.1−1.2−1.61.11.21.1
    0351/0343liaS; sensor histidine kinase−1.0−1.4−1.2−1.2−2.2 ± 0.3−1.2−1.1−1.1
    0803/0810Conserved hypothetical protein1.1−1.2−1.3−1.6−2.5 ± 0.31.21.01.0
  • a Gene tags are shown for both the D39 serovar 2 strain (spd no.) used in the study and laboratory strain R6 (spr no.) used in previous studies by various laboratories.

  • b All amounts are relative to those in parent strain IU1781 (D39 cps+ rpsL1). ATP and AcP values are restated from Table 2 for ease of comparison. ND, not determined.

  • c Microarray analyses were performed as described in Materials and Methods. At least three biological replicates were performed for IU2687 (Δpta) and IU2837 (ΔspxB ΔackA Δpta). Two biological replicates were performed for the other strains, except IU4319 (ΔspxB ΔackA ΔwalKSpn), which was evaluated once for comparison. Standard errors are indicated for fold changes above ±1.8, which was used as the cutoff. Relative transcript amounts of other WalRKSpn, CiaRHSpn, and LiaSRSpn regulon members also changed significantly but are not shown here for the sake of simplicity. Lists of all significant changes in relative transcript amounts are provided in the supplemental material and in the GEO database (accession number GSE23404).