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. 2014 Nov;82(11):4607–4619. doi: 10.1128/IAI.02225-14

TABLE 1.

Genes differentially regulated under biofilm versus active dispersed conditions

Function group and gene Description IAV dispersed
 Heat dispersed
 ATP dispersed
Log2 fold change P value Log2 fold change P value Log2 fold change P value
Competence/DNA transformation
    comFC Competence protein −4.5 <0.001 −3.2 <0.001 −3.9 <0.001
    comEC Putative competence protein −2.3 0.009 −3.0 <0.001 −3.0 0.008
    SPNINV200_16350 Type IV prepilin peptidase family protein −2.2 <0.001 −1.4 0.006 −2.0 <0.001
    cinA CinA-like protein −1.2 0.008 −1.3 0.020 −1.6 0.008
    SPNINV200_18610 Competence protein ComGF −3.0 <0.001 −2.6 <0.001 −3.8 <0.001
    SPNINV200_18630 Putative competence protein −3.0 <0.001 −2.6 <0.001 −3.9 <0.001
    Comic Putative competence protein −2.9 <0.001 −2.9 <0.001 −4.0 <0.001
    SPNINV200_18650 Putative competence protein −3.1 <0.001 −2.9 <0.001 −3.8 <0.001
    SPNINV200_18660 Putative competence protein −3.3 0.023 −3.0 0.011 −3.7 0.039
    comFA Late competence protein −3.3 <0.001 −2.8 <0.001 −3.4 <0.001
    comC2 Competence-stimulating peptide (Csp-2) −1.4 <0.001 −2.2 <0.001 −5.1 <0.001
Bacteriocins/immunity
    SPNINV200_01250 Class IIb bacteriocin −3.8 <0.001 −3.7 <0.001 −5.6 <0.001
    blpC Peptide pheromone BlpC 3.8 <0.001 1.5 0.002 −0.88 0.004
    blpB ABC transporter BlpB 3.7 <0.001 1.4 0.003 −0.91 <0.001
    blpA2 Bacteriocin transporter BlpA2 3.4 <0.001 1.2 0.034 −0.89 <0.001
    pncG Putative immunity protein 5.8 <0.001 2.2 <0.001 −0.72 0.045
    pncM Putative immunity protein 4.5 <0.001 1.7 <0.001 −1.3 0.042
    blpX Putative immunity protein BlpX 4.5 <0.001 1.7 <0.001 −1.4 0.020
    pncO Bacteriocin ABC transporter transmembrane domain BlpY 4.8 <0.001 1.7 <0.001 −1.1 <0.001
    blpZ Putative immunity protein BlpZ 4.8 <0.001 1.6 <0.001 −0.94 <0.001
    pncP ABC transporter ATP-binding domain PncP 4.9 <0.001 1.5 0.002 −0.99 <0.001
Amino acid synthesis and acquisition
    aliA Extracellular oligopeptide-binding protein −3.8 <0.001 −1.3 0.002 −1.1 <0.001
    alsS Acetolactate synthase large subunit −3.7 <0.001 −1.5 <0.001 −1.6 0.003
    ilvH Acetolactate synthase small subunit −4.0 <0.001 −1.6 <0.001 −1.7 0.002
    ilvC Ketol-acid reductoisomerase −3.9 <0.001 −1.7 <0.001 −1.4 <0.001
    ilvA Threonine dehydratase −4.1 <0.001 −1.7 <0.001 −1.4 <0.001
    ilvD Dihydroxy-acid dehydratase −1.8 <0.001 −1.2 0.007 −0.69 0.004
    SPNINV200_06610 Branched-chain amino acid ABC transporter −2.0 <0.001 −1.1 0.025 −0.77 0.001
    SPNINV200_06620 Branched-chain amino acid transport system permease −2.0 <0.001 −1.0 0.039 −0.79 0.037
    SPNINV200_07520 Putative branched-chain-amino acid aminotransferase −2.4 <0.001 −1.0 0.019 −0.94 <0.001
Nucleotide metabolic processes
    SPNINV200_02690 Putative guanine/hypoxanthine permease −1.7 <0.001 −1.8 0.012 −3.6 <0.001
    pyrF Orotidine 5′-phosphate decarboxylase −3.3 <0.001 −3.2 <0.001 −2.7 <0.001
    pyrE Orotate phosphoribosyltransferase −3.0 <0.001 −2.7 <0.001 −2.4 <0.001
    pyrK Dihydroorotate dehydrogenase electron transfer subunit −2.4 <0.001 −1.6 0.002 −2.2 <0.001
    pyrD2 Dihydroorotate dehydrogenase, catalytic subunit −2.14 <0.001 −1.6 0.003 −1.7 <0.001
    SPNINV200_09870 GMP reductase, purine nucleotide metabolic process −2.6 <0.001 −2.2 <0.001 −2.8 <0.001
    carA Carbamoyl-phosphate synthase small chain −1.9 <0.001 −1.8 <0.001 −1.5 <0.001
    pyrB Aspartate carbamoyltransferase −2.3 <0.001 −2.3 <0.001 −1.8 <0.001
    pyrR Bifunctional protein: pyrimidine operon regulatory protein, uracil phosphoribosyltransferase −2.6 <0.001 −2.7 <0.001 −1.9 <0.001
    pyrP Uracil permease −2.2 <0.001 −1.5 0.003 −1.4 <0.001
    xpt Putative xanthine phosphoribosyltransferase −3.9 <0.001 −2.3 <0.001 −3.4 <0.001
    pbuX Putative xanthine permease −3.0 <0.001 −1.9 <0.001 −3.4 <0.001
Translation <0.001 <0.001
    rpsP 30S ribosomal protein S16 −3.1 <0.001 −1.2 0.013 −2.1 <0.001
    SPNINV200_07580 30S ribosomal protein S1 −2.2 <0.001 −1.0 0.034 −1.8 <0.001
Carbohydrate/energy metabolism
    SPNINV200_02290 DeoR family, glucitol operon repressor −1.8 <0.001 −1.6 <0.001 −1.0 <0.001
    SPNINV200_02300 Putative sugar-binding regulatory protein, Sor operon −1.4 <0.001 −1.4 0.003 −1.0 <0.001
    fhs1 Formate-tetrahydrofolate ligase −1.1 <0.001 −1.6 0.003 −2.2 <0.001
    eno Enolase 0.60 0.003 1.4 0.003 0.8 <0.001
    dexB Glucan 1,6-α-glucosidase 1.5 <0.001 1.2 0.011 1.8 <0.001
    pgk Phosphoglycerate kinase 1.1 <0.001 1.4 0.003 1.4 <0.001
    glpF1 Glycerol uptake facilitator protein 1 5.6 <0.001 −1.2 0.023 1.4 <0.001
    glpO α-Glycerophosphate oxidase 5.9 <0.001 −1.2 0.023 1.2 <0.001
    glpK Glycerol kinase 5.4 <0.001 −1.4 0.003 0.90 <0.001
Additional genes
    gdh NADP-specific glutamate dehydrogenase −2.8 <0.001 −2.0 <0.001 −0.89 <0.001
    SPNINV200_12650 Nicotinate phosphoribosyltransferase (NAPRTase) family protein 0.56 0.010 1.1 0.015 1.6 <0.001
    SPNINV200_13080 ABC transporter 3.3 <0.001 1.5 0.002 1.0 <0.001
    SPNINV200_14190 DEAD box helicase family protein −2.7 <0.001 −1.3 0.002 −1.7 <0.001
    SPNINV200_14200 Major facilitator superfamily protein −2.9 <0.001 −2.1 <0.001 −3.6 <0.001
    mtsB Metal cation ABC transporter ATP-binding protein 3.7 <0.001 −1.3 0.031 0.70 0.002
    SPNINV200_15390 ABC transporter, ATP-binding protein 0.77 <0.001 −1.1 0.015 −2.8 <0.001
    SPNINV200_15760 Putative sodium:dicarboxylate symporter family protein −2.1 <0.001 −1.5 <0.001 −1.1 <0.001
    SPNINV200_16750 Zinc-binding dehydrogenase 4.6 <0.001 1.3 0.016 2.6 <0.001
    SPNINV200_17300 Putative single-stranded DNA-binding protein −3.3 <0.001 −2.8 <0.001 −3.7 <0.001
    SPNINV200_18310 Putative nucleotide-binding protein −1.5 <0.001 −1.1 0.039 −2.0 <0.001
    SPNINV200_18590 Putative methyltransferase (pseudogene) −3.0 <0.001 −2.6 <0.001 −3.8 <0.001
    SPNINV200_19360 Putative DNA-binding protein −2.9 <0.001 −1.5 0.002 −1.0 0.005
    SPNINV200_19680 Probable alcohol dehydrogenase 4.9 <0.001 1.6 0.002 2.5 <0.001
    SPNINV200_20430 TetR family regulatory protein −2.1 <0.001 −1.3 0.014 −1.6 <0.001
    SPNINV200_20440 Putative response regulator protein −1.2 <0.001 −2.1 <0.001 −5.2 <0.001
    SPNINV200_20450 Putative sensor histidine kinase −1.3 <0.001 −2.4 <0.001 −5.1 <0.001
Unknown function and hypothetical proteins
    SPNINV200_00180 Hypothetical protein −0.69 0.006 −1.8 <0.001 −3.2 <0.001
    SPNINV200_01240 Putative membrane protein −3.6 <0.001 −4.0 <0.001 −5.4 <0.001
    SPNINV200_01590 Putative membrane protein −0.85 <0.001 −1.9 <0.001 −0.6 0.012
    SPNINV200_01610 Putative integral membrane protein −4.3 <0.001 −1.9 <0.001 −0.74 0.006
    SPNINV200_02700 Putative CAAX amino terminal protease family membrane protein −2.8 <0.001 −1.8 0.014 −3.7 <0.001
    SPNINV200_03320 Conserved hypothetical protein −0.85 0.011 −1.2 0.045 −1.1 0.021
    SPNINV200_03890 Hypothetical protein 0.58 0.005 −1.8 <0.001 −4.4 <0.001
    SPNINV200_03900 Putative membrane protein 0.98 <0.001 −1.9 <0.001 −4.1 <0.001
    SPNINV200_03910 Hypothetical protein 0.96 <0.001 −1.8 <0.001 −4.1 <0.001
    SPNINV200_04070 Hypothetical protein −3.7 <0.001 −1.7 <0.001 −1.2 0.005
    SPNINV200_04080 Hypothetical protein −3.1 <0.001 −1.7 <0.001 −1.1 0.008
    SPNINV200_04640 Hypothetical protein 6.1 <0.001 1.7 0.042 −0.94 0.013
    SPNINV200_06850 Hypothetical protein −2.7 <0.001 −1.4 <0.001 −1.6 <0.001
    SPNINV200_06960 Putative permease 0.49 <0.001 −1.3 0.015 −0.86 <0.001
    SPNINV200_15770 Putative membrane protein −1.5 <0.001 −1.1 0.023 −0.60 0.026
    SPNINV200_18600 Putative exported protein −2.9 <0.001 −2.6 <0.001 −3.8 <0.001
    SPNINV200_18620 Putative membrane protein −2.9 <0.001 −2.6 <0.001 −3.6 <0.001
    SPNINV200_19370 Conserved hypothetical protein −3.1 <0.001 −1.3 0.002 −0.74 0.003
    SPNINV200_19380 Hypothetical protein −1.8 <0.001 −1.2 0.011 −0.85 <0.001
    SPNINV200_19920 Hypothetical protein 5.7 <0.001 −1.5 0.014 1.5 <0.001