TABLE 3.

Hierarchical clusters of genes showing significant differences in gene expression after ANOVA statistical analysis in the lamA mutant versus wild-type strain during early, mid-, and late logarithmic growth

Cluster and ORFaGenebDescriptionNo. of clonesChange (fold)c
EMdL
Cluster 1
    lp_0184sacK1Fructokinase21.10.0−12.1
    lp_0185pts1BCASucrose PTS, EIIBCAe31.0−0.2−13.6
    lp_0187sacAβ-Fructofuranosidase11.1−0.3−18.5
    lp_0188sacRSucrose operon repressor10.31.6−14.6
    lp_0189agl2α-Glucosidase10.31.6−14.6
    lp_0263treAα,α-Phosphotrehalase1−2.20.4−15.3
    lp_0264pts4ABCPTS, trehalose-specific IIBC component2−1.90.4−13.9
    lp_0435Transcription regulator, GntR family11.80.4−8.2
    lp_0436pts7CCellobiose PTS, EIIC11.80.4−8.2
    lp_3480galTUTP-hexose-1-phosphate uridylyltransferase11.11.4−10.6
    lp_3481galE4UDP-glucose 4-epimerase11.11.4−10.6
    lp_3482galKGalactokinase11.4−0.2−21.9
Cluster 2
    lp_0525kup1Potassium uptake protein1−2.8−3.9−2.7
    lp_0526carBCarbamoyl-phosphate synthase, large subunit1−2.8−3.9−2.7
    lp_0683Prophage P1 protein 6010.5−4.5−3.7
    lp_0684Prophage P1 protein 6110.5−4.5−3.7
    lp_0925Acyltransferase1−0.7−4−5.7
    lp_0926Integral membrane protein1−8.8−11−6.1
    lp_0927Hypothetical protein2−8.0−10.4−6.7
    lp_0928Hypothetical protein2−8.0−10.4−6.7
    lp_0929asp1Alkaline shock protein2−8.0−10.4−6.7
    lp_0930asp2Alkaline shock protein2−8.0−10.4−6.7
    lp_0931hpaG2-Hydroxyhepta-2,4-diene-1,7-dioateisomerase/5-carboxymethyl-2-oxo-hex-3-ene-1,7-dioatedecarboxylase (putative)1−7.1−9.8−7.3
    lp_2658Glycosyltransferase (putative)2−4.5−3.8−3.2
    lp_2743ABC transporter, ATP-binding protein1−7.6−10.5−8
    lp_2744ABC transporter, permease protein1−7.6−10.5−8
    lp_3045Short-chain dehydrogenase/oxidoreductase1−6.6−4.8−3.1
    lp_3047Hypothetical protein1−6.6−4.8−3.1
    lp_3575Integral membrane protein1−6.7−11−7.5
    lp_3577Integral membrane protein2−4.6−3.8−3.7
    lp_3578katCatalase4−4.4−3.8−3.6
    lp_3580lamAResponse regulator; homologue of accessory gene3−2.7−4.7−2.8
Regulator protein A
    lp_3581lamCHistidine protein kinase; sensor protein3−2.7 (−2.3)−4.7 (−2.8)−2.8 (−2.7)
    lp_3581alamDHomologue of accessory gene regulator protein D, peptide pheromone precursor1−2.4−4.7−2.7
    lp_3582lamBHomologue of accessory gene regulator protein B1−2.4−4.7−2.7
    lp_3583clpLATP-dependent Clp protease, ATP-binding subunit ClpL3−21.6−27.6−11.7
    lp_3586loxLactate oxidase2−24.5−28.7−22.7
Cluster 3
    lp_1197cps2AExopolysaccharide biosynthesis protein140.5 (21.7)16.6 (9.9)19.0 (21.7)
    lp_1198cps2BExopolysaccharide biosynthesis protein; chain length determinator Wzz228.916.616.1
    lp_1199cps2CExopolysaccharide biosynthesis protein117.216.513.2
    lp_1200galE2UDP-glucose 4-epimerase326.614.318.5
    lp_1201cps2EPriming glycosyltransferase326.614.318.5
    lp_1202cps2FGlycosyltransferase237.012.513.3
    lp_1203cps2GGlycosyltransferase238.511.111.3
    lp_1204cps2HPolysaccharide polymerase228 (37)7.8 (10.4)8.1 (12.4)
    lp_1205cps2IRepeat unit transporter319.23.74.4
    lp_1206cps2JGlycosyltransferase1182.63.6
    lp_1207Hypothetical protein111.61.93.4
    lp_1208Hypothetical protein111.61.93.4
    lp_1210Hypothetical protein15.50.71.3
    lp_1211Hypothetical protein15.50.71.3
Cluster 4
    lp_0254cysESerine O-acetyltransferase2−0.15.55.4
    lp_0255metC1Cystathionine β-lyase3−0.45.85.4
    lp_0256cysKCysteine synthase2−0.65.95.7
    lp_2371pyrPUracil transport protein10.613.20.7
    lp_2684araT2Aromatic amino acid-specific aminotransferase20.60.819
    lp_2685dapA2Dihydrodipicolinate synthase20.60.819
    lp_2698pyrFOrotidine-5′-phosphate decarboxylase1−0.434.6−0.7
    lp_2699pyrDDihydroorotate oxidase2−0.646.6−0.7
    lp_2700pyrABCarbamoyl-phosphate synthase, pyrimidine specific, large chain4059.2−0.4
    lp_2701pyrAACarbamoyl-phosphate synthase, pyrimidine specific, small chain40.669.9−0.2
    lp_2702pyrCDihydroorotase3167.1−0.3
    lp_2703pyrBAspartate carbamoyltransferase1111.30
    lp_2704pyrR1Pyrimidine operon regulator1111.30
  • a Gene lp_ number from the Lactobacillus plantarum WCFS1 genome project (http://www.cmbi.kun.nl/lactobacillus).

  • b Previously reported gene name.

  • c Average change in the lamA mutant versus the wild-type strain during early (E), mid- (M), and late (L) logarithmic growth. Average of four arrays unless specified otherwise. Average of all significant clones encoding the gene. The values in parentheses are the fold changes determined by real-time RT-PCR.

  • d Average of three arrays instead of four arrays.

  • e PTS, phosphotransferase system; EIIBCA, enzyme IIBCA.