TABLE 2.

Summary of changes in E. coli O157:H7 biofilm gene expression

Gene type or function and nameRelative change in expression (n-fold) after exposure to:aDescription
EPINEIND
AI-2 group
    c19931.41.41.6Putative integral membrane transport protein
    lsrA −9.8 −5.3 1.0Fused AI-2 transporter subunits of ABC superfamily; ATP-binding components
    lsrB −7.0 −5.3 −1.4Putative LACI-type transcriptional regulator
    lsrC −4.3 −2.3 1.2AI-2 transporter
    lsrD −3.2 −1.41.5AI-2 transporter
    lsrG −3.2 −3.0 −1.1AI-2 modifying protein LsrG
    lsrK −2.8 −2.3 1.2AI-2 kinase
    lsrR −3.7 −3.7 1.1 lsr operon transcriptional repressor
Phosphate related
    phnD −2.1 1.2 2.1 Phosphonates-binding periplasmic protein precursor
    phnG−1.11.5 2.3 PhnG protein
    phnP−1.21.3 2.1 PhnP protein
    phoB 2.1 3.0 −2.6 Phosphate regulon transcriptional regulatory protein phoB
    phoH −4.9 −4.6 −1.9PhoH protein
    phoR 2.6 3.5 −1.6Phosphate regulon sensor protein phoR
    phoU1.9 2.1 −3.7 Phosphate transport system protein phoU
    pstA 2.5 2.6 −3.2 Phosphate transport system permease protein pstA
    pstB1.31.5 −3.7 Phosphate transport ATP-binding protein pstB
    pstC 2.6 3.0 −2.3 Phosphate transport system permease protein pstC
    pstS1.11.1 −4.6 Phosphate-binding periplasmic protein precursor
    purE 3.0 3.7 1.4Phosphoribosylaminoimidazole carboxylase catalytic subunit
    purK1.2 2.6 1.6Phosphoribosylaminoimidazole carboxylase ATPase subunit
    purT−1.4 2.5 2.1 Phosphoribosylglycinamide formyltransferase 2
Hydrognease
    hyaA −3.0 −3.2 1.1Hydrogenase-1 large chain
    hyaB −4.0 −3.5 1.2Hydrogenase-1 operon protein hyaE
    hyaC −3.7 −3.0 1.1Hydrogenase-1 operon protein hyaF
    hyaD −3.2 −2.8 1.2Hydrogenase-1 small chain precursor
    hyaE −3.5 −2.5 1.3Hydrogenase-1 large chain
    hyaF −3.0 −2.6 1.1Hydrogenase-1 operon protein hyaE
PTS
    mtlA −13.9 −11.3 1.0PTS system; mannitol-specific IIABC component
    manX −4.6 −3.5 1.1PTS system; mannose-specific IIAB component
    manY −2.8 −2.3 1.1PTS system; mannose-specific IIC component
    manZ −2.8 −2.1 1.2PTS system; mannose-specific IID component
    fruB−1.7 −2.1 1.2PTS system; fructose-specific IIA/FPr component
Glycerol related
    glgC −2.5 −3.0 −1.3Glucose-1-phosphate adenylyltransferase
    glpA −4.9 −1.71.7Anaerobic glycerol-3-phosphate dehydrogenase subunit A
    glpD −9.2 −18.4 1.3sn-Glycerol-3-phosphate dehydrogenase (aerobic)
    glpF −5.7 −5.7 1.3Glycerol uptake facilitator protein
    glpK −7.5 −6.1 1.1Glycerol kinase
    glpQ −2.1 −2.5 −1.1Glycerophosphoryl diester phosphodiesterase; periplasmic precursor
    glpR−1.6 −2.1 −1.1Glycerol-3-phosphate regulon repressor
    ugpB −7.0 −6.1 −1.4Glycerol-3-phosphate-binding periplasmic protein precursor
Histidine biosynthesis
    hisA −2.1 −2.8 −1.61-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
    hisB −2.3 −2.6 −2.1 Bifunctional: histidinol-phosphatase (N terminus) and imidazoleglycerol-phosphate dehydratase (C terminus)
    hisC −4.0 −4.6 −2.8 Histidinol-phosphate aminotransferase
    hisD −4.3 −4.3 −2.6 Histidine biosynthesis
    hisF −3.0 −3.0 −2.0 Imidazole glycerol phosphate synthase subunit hisF
    hisG1.1−1.3 −2.8 ATP phosphoribosyltransferase
    hisH−1.6 −2.1 −2.0 Imidazole glycerol phosphate synthase subunit hisH
    hisI −2.1 −2.0 −1.9Histidine biosynthesis
    hisL 3.0 1.1 −3.7 His operon leader peptide
    hisLEDL1.7−1.2 −3.5 Histidine biosynthesis; hisL gene from strain EDL933
    hisP −2.5 −1.4−1.1Nucleotide binding
Two-component signal transduction
    dos1.3 2.1 1.4Putative phosphodiesterase, oxygen-sensing protein
    evgS −3.2 −1.5−1.2Two-component signal transduction system (phosphorelay)
    fimZ1.1 2.1 3.0 Fimbiral protein Z; putative transcriptional regulator of fimbrial expression (LuxR/UhpA family)
    glnL 3.2 2.5 −1.9Two-component signal transduction system (phosphorelay)
    narL −2.6 −2.0 −1.4Nitrate/nitrite response regulator protein narL
    prpR −3.5 −3.7 1.1Regulator for prp operon
    rstA 2.5 1.9−1.3Transcriptional Regulatory protein rstA
    yedV1.4 2.6 2.0 Putative two-component sensor protein
    ygeV −2.1 −1.4−1.5Two-component signal transduction system (phosphorelay)
Sulfate
    cysD −3.0 −3.0 −1.6Sulfate adenylyltransferase (ATP) activity
    cysI −3.5 −3.0 −1.2Sulfite reductase [NADPH] hemoprotein beta-component
    cysJ −4.3 −2.8 1.0Sulfite reductase [NADPH] flavoprotein alpha-component
    sseA −2.1 −1.91.43-Mercaptopyruvate sulfurtransferase
Motility/chemotaxis
    acs −8.0 −4.3 1.1Acetyl-coenzyme A synthetase
    c2129 3.0 2.5 1.5Cell division activator cedA
    c40041.32.11.1Hypothetical protein
    csgA −4.3 −2.8 1.5Cell adhesion
    csgB −5.7 −4.6 −1.1Minor curlin subunit precursor
    csgF −3.7 −2.5 −1.4Curli production assembly/transport component csgF precursor
    fimZ1.12.1 3.0 Fimbiral protein Z; putative transcriptional regulator of fimbrial expression (LuxR/UhpA family)
    fliD 2.0 2.1 1.4Cell motility
    fliR−1.11.9 2.3 Flagellar biosynthetic protein fliR
    gidB1.4 2.1 1.5Methyltransferase gidB
    motB −2.3 −1.21.3Chemotaxis motB protein
    mreC1.5 2.1 1.2Rod shape-determining protein mreC
    sfmA−1.21.5 2.1 Putative fimbrial-like protein
    sfmF1.01.5 2.3 Putative fimbrial-like protein
    sfmH −2.0 1.0 2.5 Fimbrial assembly protein
    yhhP1.7 2.5 1.5SirA protein
    Z00201.5 2.5 2.1 Cell adhesion
    Z4971−1.9 3.7 1.9Cell adhesion
Cytochrome
    appB −3.0 −2.3 1.2Cytochrome bd II oxidase subunit II
    appC −2.5 −2.1 1.1Cytochrome bd II oxidase subunit I
    cyoC −2.1 −3.0 1.0Cytochrome o ubiquinol oxidase subunit III
    nrfA −3.2 −1.51.5Cytochrome c-552 precursor
    nrfB −2.8 1.01.5Cytochrome c-type protein nrfB precursor
Cold shock protein
    cspA1.51.5 −3.2 Cold shock protein cspA
    cspE 2.3 2.5 −1.1Cold shock-like protein cspE
    cspG 8.0 6.1 −4.0 Cold shock-like protein cspG
    cspH 22.6 21.1 −2.5 Cold shock-like protein cspH
    deaD 2.1 2.6 −1.2Cold shock DEAD-box protein A
Antisense RNA
    dsrA 3.5 4.9 1.3Antisense RNA; silencer of rcsA gene, interacts with rpoS translation
    rdlD 4.0 4.0 −2.5 Antisense RNA; trans-acting regulator of ldrD translation
    sokB 9.2 7.0 −1.1Antisense RNA blocking mokB and hokB translation
    sokC 2.0 2.6 −1.6Antisense RNA blocking mokC (orf69) and hokC (gef) translation
Glutamine/glutamate
    c0018 24.3 24.3 5.7 Putative glutamate dehydrogenase
    glnA1.61.3 −2.3 Glutamine synthetase
    glnH−1.21.0 −2.1 Glutamine-binding periplasmic protein precursor
    glnP 2.5 3.0 −1.9Glutamine transport system permease protein glnP
    gltJ 3.7 4.3 −1.6Glutamate/aspartate transport system permease protein gltJ
    gltK 2.6 2.6 −1.6Glutamate/aspartate transport system permease protein gltK
    gltL1.41.7−1.9Glutamate/aspartate transport ATP-binding protein gltL
    ybeJ−1.3−1.1 −2.5 Glutamate/aspartate periplasmic binding protein precursor
Iron related
    c3773 2.0 2.1 1.6Putative iron compound permease protein of ABC transporter family
    cydA 2.0 2.8 −1.1Cytochrome d ubiquinol oxidase subunit I
    cydB1.9 2.8 −1.2Cytochrome d ubiquinol oxidase subunit II
    feoA 2.5 2.6 −1.3Ferrous iron transport protein A
    feoB 2.0 3.2 1.0Ferrous iron transport protein B
    fhuB1.3 2.5 1.1Ferrichrome transport system permease protein fhuB
    fhuC1.6 2.5 1.0Ferrichrome transport ATP-binding protein fhuC
    fhuD 2.5 4.6 1.1Ferrichrome-binding periplasmic protein precursor
    yodB 2.5 2.6 −1.3Cytochrome b561 homolog 1
NADH dehydrogenase
    nuoA−1.3 −2.5 1.1NADH dehydrogenase I chain A
    nuoB −2.0 −3.5 1.0NADH dehydrogenase I chain B
    nuoC−1.7 −4.0 −1.1NADH dehydrogenase I chain C/D
    nuoE −2.0 −4.3 −1.1NADH dehydrogenase I chain E
    nuoI−1.1 −2.5 1.1NADH dehydrogenase I chain I
    nuoJ−1.3 −2.5 1.3NADH dehydrogenase I chain J
    nuoK−1.3 −2.3 1.4NADH dehydrogenase I chain K
    nuoL−1.2 −2.3 1.4NADH dehydrogenase I chain L
Tricarboxylic acid cycle
    sdhD −13.0 −21.1 1.1Succinate dehydrogenase hydrophobic membrane anchor protein
    sdhC −12.1 −18.4 1.1Succinate dehydrogenase cytochrome b-556 subunit
    sdhA −11.3 −16.0 1.3Succinate dehydrogenase, catalytic and NAD/flavoprotein subunit
    sdhB −10.6 −12.1 1.0Succinate dehydrogenase iron-sulfur protein
    sucA −7.5 −11.3 1.12-Oxoglutarate dehydrogenase E1 component
    sucB −7.0 −9.2 −1.1Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex
    sucD −6.5 −8.6 1.0Succinyl-coenzyme A synthetase alpha chain
    sucC −6.5 −8.6 1.0Succinyl-coenzyme A synthetase beta chain
    acnB −2.0 −4.3 1.0Aconitate hydratase activity
    icdA−1.9 −2.6 1.1Isocitrate dehydrogenase [NADP]
    yojH−1.2 −2.3 −1.5Malate:quinone oxidoreductase
    mdh −2.0 −2.1 −1.1Malate dehydrogenase
  • a Important changes are shown in boldface. IND, indole.