TABLE 4.

Transcriptome analysis of V. fischeri quorum-sensing mutants

Category and ORFbAnnotation (putative function)Ratioa
Wild type/ainScluxO/LuxO(D47E)d
Motility
    VF0777Methyl-accepting chemotaxis protein−3.0 (0.6)−2.9 (6.5)
    VF1836Flagellar biosynthesis protein, FlhF−2.3 (0.9)−3.3 (0.7)
    VF1846eFlagellar protein, FliL−1.8 (6)−3.1 (0.3)
    VF1853eFlagellar hook-basal body protein, FliE−1.9 (0.4)−4.2 (0.9)
    VF1862Flagellin, FlaE−5.0 (0.4)−15.5 (0.2)
    VF1863Flagellin, FlaD−4.0 (0.3)−8.3 (0.7)
    VF1864eFlagellin, FlaC−1.7 (18)−4.2 (0.1)
    VF1865eFlagellin, FlaB−1.6 (12)−3.0 (6.4)
    VF1866eFlagellin, FlaA−1.8 (7)−7.2 (4.1)
    VF1874eFlagellar hook protein, FlgE−1.4 (28)−3.8 (0.9)
    VF1875Basal-body rod modification protein, FlgD−5.6 (0.2)−5.1 (0.1)
    VF1876Flagellar basal-body rod protein, FlgC−11.8 (0.1)−11.1 (0.1)
    VF1877Flagellar basal-body rod protein, FlgB−3.3 (0.3)−8.6 (0.7)
    VF1881Negative regulator of flagellin synthesis, FlgM−3.7 (0.7)−7.2 (32.3)
    VF2079Flagellin, FlaF−7.1 (0.1)−8.0 (0.1)
Transcriptional regulators
    VF1573DNA-binding protein−3.1 (0.1)−2.7 (2.5)
    VF2177Transcriptional regulator, LitR10.3 (4.2)5.9 (<0.1)
    VFA1014Hypothetical protein (sensory transduction)2.5 (10.6)2.2 (17.5)
    VFA1015Sigma factor, RpoS like5.5 (0.1)2.3 (2.9)
    VFA1017Possible response regulator7.0 (4.0)4.9 (0.3)
Metabolism
    VF0008Cystine-binding protein transporter−3.8 (<0.1)−2.5 (25)
    VF0316Drug/metabolite exporter−3.2 (3.8)−5.2 (5.5)
    VF2247Dihydroneopterin aldolase (folate biosynthesis)−2.5 (19)−3.1 (2.0)
    VFA0452Formiminoglutamase (histidine metabolism)2.3 (0.8)2.6 (0.5)
    VFA0806Glucose-1-phosphate adenylyltransferase (polysaccharide biosynthesis)3.9 (0.4)3.1 (1.6)
    VFA0995High-affinity ferrous iron permease−5.6 (0.3)−2.3 (0.6)
EPS biosynthesis
    VF0171Hypothetical protein4.2 (0.4)2.4 (17.5)
    VF0172O-Acetyltransferase3.6 (0.1)3.8 (0.5)
Hypothetical proteins
    VF1355Hypothetical protein2.0 (3.5)2.8 (1.1)
    VF2255Hypothetical protein2.3 (0.3)3.2 (0.2)
  • a The V. fischeri microarray includes 95% of the ORFs present in the genome, arrayed in three replicates. Negative values represent repression by ain quorum sensing. Indicated in parentheses are the results of a two-tailed, paired Student t-test, expressed as percent probability that the data sets are identical.

  • b ORF designations are those found at http://www.ergo-light.com/ERGO/.

  • c Average ratios of six values for each ORF (two microarrays, with three replicates on each array).

  • d Average ratios of three values for each ORF (one microarray, with three replicates on each array).

  • e Regulation of the ORFs was selected with less stringent criteria (see Results).