TABLE 1.

ΔciaRH downregulated and upregulated ORFs

ORF type and ΔciaRH/wt ratioaPbSpecificcTIRG4 ORFdTIRG4 annotatione
Downregulated ORFs
    0.04 (−1.43)1.3 × 10−2YSP2239Serine protease (htrAf)
    0.09 (−1.06)3.6 × 10−2YSP2240SpoJ proteing (spoJf)
    0.11 (−0.94)5.2 × 10−3YSP0798DNA-binding response regulator CiaR (ciaR)
    0.20 (−0.70)5.5 × 10−3NSP1468Pyridoxine biosynthesis protein
    0.25 (−0.61)2.7 × 10−3NSP1467Conserved hypothetical protein
    0.30 (−0.53)3.3 × 10−3NSP1742Conserved hypothetical protein
    0.31 (−0.51)2.7 × 10−2NSP1771Glycosyltransferase, family 2/glycosyltransferase family 8
    0.32 (−0.49)3.0 × 10−2NSP1546Conserved domain protein
    0.34 (−0.46)3.8 × 10−2NSP1027Conserved hypothetical protein
    0.34 (−0.46)4.5 × 10−2YSP0799Sensor histidine kinase CiaH (ciaH)
    0.35 (−0.46)2.1 × 10−3NSP2106Glycogen phosphorylase family protein
    0.35 (−0.46)1.4 × 10−2NSP0463Cell wall surface anchor family protein
    0.35 (−0.45)2.6 × 10−2YSP1268Choline transporter (licB)
    0.35 (−0.45)1.9 × 10−2YSP0797Aminopeptidase N (pepN)h
    0.36 (−0.44)6.2 × 10−3YSP1744Iojap-related protein
    0.37 (−0.44)7.0 × 10−3NSP1790ATPase, AAA family
    0.40 (−0.40)4.9 × 10−2YSP1567Endoribonuclease L-PSP
    0.40 (−0.40)4.5 × 10−2NSP1555Dihydrodipicolinate reductase (dapB)
    0.41 (−0.39)7.6 × 10−3NSP0105 l-Serine dehydratase, iron-sulfur-dependent, alpha subunit (sdhA)
    0.43 (−0.37)3.1 × 10−2YSP0081Glycosyl transferase, family 2, authentic point mutation
    0.43 (−0.37)3.3 × 10−2YSP1357ABC transporter, ATP-binding/permease protein
    0.46 (−0.34)3.5 × 10−2YSP0855Topoisomerase IV, subunit A (parC)
    0.46 (−0.33)4.1 × 10−2YSP0479Potassium uptake protein, Trk family
    0.50 (−0.30)1.5 × 10−2NSP1212tRNA pseudouridine synthase B (truB)
Upregulated ORFs
    39.6 (1.60)1.5 × 10−4NSP0955Competence protein CelB (celB)
    33.0 (1.52)3.7 × 10−2NSP2047Conserved domain protein
    33.0 (1.52)6.0 × 10−3NSP2051Competence protein CglC (cglC)
    24.5 (1.39)3.6 × 10−2NSP2053Competence protein CglA (cglA)
    23.7 (1.38)4.3 × 10−3YSP1266DNA processing protein DprA, putative
    19.9 (1.30)4.1 × 10−2NSP2052Competence protein CglB (cglB)
    19.4 (1.29)8.7 × 10−3NSP2048Conserved hypothetical protein
    19.4 (1.29)5.7 × 10−5YSP2208Helicase, putative
    19.3 (1.29)1.8 × 10−2YSP0954Competence protein CelA (celA)
    18.2 (1.26)2.3 × 10−2YSP1908Single-stranded DNA-binding protein, authentic point mutation (ssbB)
    10.7 (1.03)2.9 × 10−2YSP1088DNA repair protein RadC (radC)
    10.4 (1.02)1.0 × 10−2YSP2201Choline-binding protein D (cbpD)
    4.6 (0.66)3.3 × 10−2YSP1810Hypothetical protein
    3.9 (0.59)4.6 × 10−2NSP1941Competence/damage-inducible protein CinA
    3.3 (0.52)2.1 × 10−2YSP0791Oxidoreductase, aldo/keto-reductase family
    3.3 (0.52)3.0 × 10−2NSP2206Ribosomal subunit interface protein (yfiA)
    3.3 (0.51)4.5 × 10−3NSP0143Conserved domain protein
    2.6 (0.41)1.1 × 10−3YSP1937Autolysin (lytA)i
    2.5 (0.40)5.0 × 10−2YSP0577PTS system, beta-glucoside-specific IIABC components
    2.4 (0.39)4.4 × 10−2YSP1051Conserved hypothetical protein
    2.2 (0.34)2.8 × 10−2NSP2156SPFH domain/band 7 family
    2.0 (0.31)2.5 × 10−2YSP2013Conserved hypothetical protein
  • a ΔciaRH/0100993 wild-type (wt) gene expression ratios as determined by microarray hybridization. The log10ciaRH/wild-type) gene expression ratios are given in parentheses to facilitate comparison with Fig. 2.

  • b P values from individual t tests that reflect the confidence assigned to measured differences in gene expression between the ΔciaRH mutant and the wild-type strain 0100993 are given.

  • c Indicates whether the altered expression of the specified gene in the ΔciaRH mutant was considered to be specific to the ΔciaRH strain as determined by comparison to the expression profiles of the Δ478HK, Δ486HK, Δ486RR, Δ492HK, Δ539HK, and Δ539RR strains as detailed in the text.

  • d Designations of the ORFs in the TIGR4 sequence (28) matching the microarray probes showing differences in expression between ΔciaRH and 0100993.

  • e Published annotations of the TIGR4 ORFs.

  • f Gene designations htrA and spoJ used in this article.

  • g Annotated in TIGR4 sequence as “spspoJ protein.”

  • h This ORF terminates 111 nucleotides upstream of ciaRH and is transcribed in the same direction in the TIGR4 sequence (28). Its decreased expression in the ΔciaRH strain raises the possibility that CiaR controls expression of an extended operon containing both pepN and the ciaRH locus itself.

  • i Increased lytA expression was seen with two independent probes for this gene present on the microarray. The expression ratio presented is the geometric mean of the two observations (3.1 and 2.2) while the P value shown is the product of the two independent P values (2.9×10−2 and 3.7×10−2).