TABLE 1

Genes differentially regulated under biofilm versus active dispersed conditions

Function group and geneDescriptionIAV dispersedHeat dispersedATP dispersed
Log2 fold changeP valueLog2 fold changeP valueLog2 fold changeP value
Competence/DNA transformation
    comFCCompetence protein−4.5<0.001−3.2<0.001−3.9<0.001
    comECPutative competence protein−2.30.009−3.0<0.001−3.00.008
    SPNINV200_16350Type IV prepilin peptidase family protein−2.2<0.001−1.40.006−2.0<0.001
    cinACinA-like protein−1.20.008−1.30.020−1.60.008
    SPNINV200_18610Competence protein ComGF−3.0<0.001−2.6<0.001−3.8<0.001
    SPNINV200_18630Putative competence protein−3.0<0.001−2.6<0.001−3.9<0.001
    ComicPutative competence protein−2.9<0.001−2.9<0.001−4.0<0.001
    SPNINV200_18650Putative competence protein−3.1<0.001−2.9<0.001−3.8<0.001
    SPNINV200_18660Putative competence protein−3.30.023−3.00.011−3.70.039
    comFALate competence protein−3.3<0.001−2.8<0.001−3.4<0.001
    comC2Competence-stimulating peptide (Csp-2)−1.4<0.001−2.2<0.001−5.1<0.001
Bacteriocins/immunity
    SPNINV200_01250Class IIb bacteriocin−3.8<0.001−3.7<0.001−5.6<0.001
    blpCPeptide pheromone BlpC3.8<0.0011.50.002−0.880.004
    blpBABC transporter BlpB3.7<0.0011.40.003−0.91<0.001
    blpA2Bacteriocin transporter BlpA23.4<0.0011.20.034−0.89<0.001
    pncGPutative immunity protein5.8<0.0012.2<0.001−0.720.045
    pncMPutative immunity protein4.5<0.0011.7<0.001−1.30.042
    blpXPutative immunity protein BlpX4.5<0.0011.7<0.001−1.40.020
    pncOBacteriocin ABC transporter transmembrane domain BlpY4.8<0.0011.7<0.001−1.1<0.001
    blpZPutative immunity protein BlpZ4.8<0.0011.6<0.001−0.94<0.001
    pncPABC transporter ATP-binding domain PncP4.9<0.0011.50.002−0.99<0.001
Amino acid synthesis and acquisition
    aliAExtracellular oligopeptide-binding protein−3.8<0.001−1.30.002−1.1<0.001
    alsSAcetolactate synthase large subunit−3.7<0.001−1.5<0.001−1.60.003
    ilvHAcetolactate synthase small subunit−4.0<0.001−1.6<0.001−1.70.002
    ilvCKetol-acid reductoisomerase−3.9<0.001−1.7<0.001−1.4<0.001
    ilvAThreonine dehydratase−4.1<0.001−1.7<0.001−1.4<0.001
    ilvDDihydroxy-acid dehydratase−1.8<0.001−1.20.007−0.690.004
    SPNINV200_06610Branched-chain amino acid ABC transporter−2.0<0.001−1.10.025−0.770.001
    SPNINV200_06620Branched-chain amino acid transport system permease−2.0<0.001−1.00.039−0.790.037
    SPNINV200_07520Putative branched-chain-amino acid aminotransferase−2.4<0.001−1.00.019−0.94<0.001
Nucleotide metabolic processes
    SPNINV200_02690Putative guanine/hypoxanthine permease−1.7<0.001−1.80.012−3.6<0.001
    pyrFOrotidine 5′-phosphate decarboxylase−3.3<0.001−3.2<0.001−2.7<0.001
    pyrEOrotate phosphoribosyltransferase−3.0<0.001−2.7<0.001−2.4<0.001
    pyrKDihydroorotate dehydrogenase electron transfer subunit−2.4<0.001−1.60.002−2.2<0.001
    pyrD2Dihydroorotate dehydrogenase, catalytic subunit−2.14<0.001−1.60.003−1.7<0.001
    SPNINV200_09870GMP reductase, purine nucleotide metabolic process−2.6<0.001−2.2<0.001−2.8<0.001
    carACarbamoyl-phosphate synthase small chain−1.9<0.001−1.8<0.001−1.5<0.001
    pyrBAspartate carbamoyltransferase−2.3<0.001−2.3<0.001−1.8<0.001
    pyrRBifunctional protein: pyrimidine operon regulatory protein, uracil phosphoribosyltransferase−2.6<0.001−2.7<0.001−1.9<0.001
    pyrPUracil permease−2.2<0.001−1.50.003−1.4<0.001
    xptPutative xanthine phosphoribosyltransferase−3.9<0.001−2.3<0.001−3.4<0.001
    pbuXPutative xanthine permease−3.0<0.001−1.9<0.001−3.4<0.001
Translation<0.001<0.001
    rpsP30S ribosomal protein S16−3.1<0.001−1.20.013−2.1<0.001
    SPNINV200_0758030S ribosomal protein S1−2.2<0.001−1.00.034−1.8<0.001
Carbohydrate/energy metabolism
    SPNINV200_02290DeoR family, glucitol operon repressor−1.8<0.001−1.6<0.001−1.0<0.001
    SPNINV200_02300Putative sugar-binding regulatory protein, Sor operon−1.4<0.001−1.40.003−1.0<0.001
    fhs1Formate-tetrahydrofolate ligase−1.1<0.001−1.60.003−2.2<0.001
    enoEnolase0.600.0031.40.0030.8<0.001
    dexBGlucan 1,6-α-glucosidase1.5<0.0011.20.0111.8<0.001
    pgkPhosphoglycerate kinase1.1<0.0011.40.0031.4<0.001
    glpF1Glycerol uptake facilitator protein 15.6<0.001−1.20.0231.4<0.001
    glpOα-Glycerophosphate oxidase5.9<0.001−1.20.0231.2<0.001
    glpKGlycerol kinase5.4<0.001−1.40.0030.90<0.001
Additional genes
    gdhNADP-specific glutamate dehydrogenase−2.8<0.001−2.0<0.001−0.89<0.001
    SPNINV200_12650Nicotinate phosphoribosyltransferase (NAPRTase) family protein0.560.0101.10.0151.6<0.001
    SPNINV200_13080ABC transporter3.3<0.0011.50.0021.0<0.001
    SPNINV200_14190DEAD box helicase family protein−2.7<0.001−1.30.002−1.7<0.001
    SPNINV200_14200Major facilitator superfamily protein−2.9<0.001−2.1<0.001−3.6<0.001
    mtsBMetal cation ABC transporter ATP-binding protein3.7<0.001−1.30.0310.700.002
    SPNINV200_15390ABC transporter, ATP-binding protein0.77<0.001−1.10.015−2.8<0.001
    SPNINV200_15760Putative sodium:dicarboxylate symporter family protein−2.1<0.001−1.5<0.001−1.1<0.001
    SPNINV200_16750Zinc-binding dehydrogenase4.6<0.0011.30.0162.6<0.001
    SPNINV200_17300Putative single-stranded DNA-binding protein−3.3<0.001−2.8<0.001−3.7<0.001
    SPNINV200_18310Putative nucleotide-binding protein−1.5<0.001−1.10.039−2.0<0.001
    SPNINV200_18590Putative methyltransferase (pseudogene)−3.0<0.001−2.6<0.001−3.8<0.001
    SPNINV200_19360Putative DNA-binding protein−2.9<0.001−1.50.002−1.00.005
    SPNINV200_19680Probable alcohol dehydrogenase4.9<0.0011.60.0022.5<0.001
    SPNINV200_20430TetR family regulatory protein−2.1<0.001−1.30.014−1.6<0.001
    SPNINV200_20440Putative response regulator protein−1.2<0.001−2.1<0.001−5.2<0.001
    SPNINV200_20450Putative sensor histidine kinase−1.3<0.001−2.4<0.001−5.1<0.001
Unknown function and hypothetical proteins
    SPNINV200_00180Hypothetical protein−0.690.006−1.8<0.001−3.2<0.001
    SPNINV200_01240Putative membrane protein−3.6<0.001−4.0<0.001−5.4<0.001
    SPNINV200_01590Putative membrane protein−0.85<0.001−1.9<0.001−0.60.012
    SPNINV200_01610Putative integral membrane protein−4.3<0.001−1.9<0.001−0.740.006
    SPNINV200_02700Putative CAAX amino terminal protease family membrane protein−2.8<0.001−1.80.014−3.7<0.001
    SPNINV200_03320Conserved hypothetical protein−0.850.011−1.20.045−1.10.021
    SPNINV200_03890Hypothetical protein0.580.005−1.8<0.001−4.4<0.001
    SPNINV200_03900Putative membrane protein0.98<0.001−1.9<0.001−4.1<0.001
    SPNINV200_03910Hypothetical protein0.96<0.001−1.8<0.001−4.1<0.001
    SPNINV200_04070Hypothetical protein−3.7<0.001−1.7<0.001−1.20.005
    SPNINV200_04080Hypothetical protein−3.1<0.001−1.7<0.001−1.10.008
    SPNINV200_04640Hypothetical protein6.1<0.0011.70.042−0.940.013
    SPNINV200_06850Hypothetical protein−2.7<0.001−1.4<0.001−1.6<0.001
    SPNINV200_06960Putative permease0.49<0.001−1.30.015−0.86<0.001
    SPNINV200_15770Putative membrane protein−1.5<0.001−1.10.023−0.600.026
    SPNINV200_18600Putative exported protein−2.9<0.001−2.6<0.001−3.8<0.001
    SPNINV200_18620Putative membrane protein−2.9<0.001−2.6<0.001−3.6<0.001
    SPNINV200_19370Conserved hypothetical protein−3.1<0.001−1.30.002−0.740.003
    SPNINV200_19380Hypothetical protein−1.8<0.001−1.20.011−0.85<0.001
    SPNINV200_19920Hypothetical protein5.7<0.001−1.50.0141.5<0.001