TABLE 2.
Summary of changes in E. coli O157:H7 biofilm gene expression
| Gene type or function and name | Relative change in expression (n-fold) after exposure to:a
|
Description | ||
|---|---|---|---|---|
| EPI | NE | IND | ||
| AI-2 group | ||||
| c1993 | 1.4 | 1.4 | 1.6 | Putative integral membrane transport protein |
| lsrA | −9.8 | −5.3 | 1.0 | Fused AI-2 transporter subunits of ABC superfamily; ATP-binding components |
| lsrB | −7.0 | −5.3 | −1.4 | Putative LACI-type transcriptional regulator |
| lsrC | −4.3 | −2.3 | 1.2 | AI-2 transporter |
| lsrD | −3.2 | −1.4 | 1.5 | AI-2 transporter |
| lsrG | −3.2 | −3.0 | −1.1 | AI-2 modifying protein LsrG |
| lsrK | −2.8 | −2.3 | 1.2 | AI-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 | −1.1 | 1.5 | 2.3 | PhnG protein |
| phnP | −1.2 | 1.3 | 2.1 | PhnP protein |
| phoB | 2.1 | 3.0 | −2.6 | Phosphate regulon transcriptional regulatory protein phoB |
| phoH | −4.9 | −4.6 | −1.9 | PhoH protein |
| phoR | 2.6 | 3.5 | −1.6 | Phosphate regulon sensor protein phoR |
| phoU | 1.9 | 2.1 | −3.7 | Phosphate transport system protein phoU |
| pstA | 2.5 | 2.6 | −3.2 | Phosphate transport system permease protein pstA |
| pstB | 1.3 | 1.5 | −3.7 | Phosphate transport ATP-binding protein pstB |
| pstC | 2.6 | 3.0 | −2.3 | Phosphate transport system permease protein pstC |
| pstS | 1.1 | 1.1 | −4.6 | Phosphate-binding periplasmic protein precursor |
| purE | 3.0 | 3.7 | 1.4 | Phosphoribosylaminoimidazole carboxylase catalytic subunit |
| purK | 1.2 | 2.6 | 1.6 | Phosphoribosylaminoimidazole carboxylase ATPase subunit |
| purT | −1.4 | 2.5 | 2.1 | Phosphoribosylglycinamide formyltransferase 2 |
| Hydrognease | ||||
| hyaA | −3.0 | −3.2 | 1.1 | Hydrogenase-1 large chain |
| hyaB | −4.0 | −3.5 | 1.2 | Hydrogenase-1 operon protein hyaE |
| hyaC | −3.7 | −3.0 | 1.1 | Hydrogenase-1 operon protein hyaF |
| hyaD | −3.2 | −2.8 | 1.2 | Hydrogenase-1 small chain precursor |
| hyaE | −3.5 | −2.5 | 1.3 | Hydrogenase-1 large chain |
| hyaF | −3.0 | −2.6 | 1.1 | Hydrogenase-1 operon protein hyaE |
| PTS | ||||
| mtlA | −13.9 | −11.3 | 1.0 | PTS system; mannitol-specific IIABC component |
| manX | −4.6 | −3.5 | 1.1 | PTS system; mannose-specific IIAB component |
| manY | −2.8 | −2.3 | 1.1 | PTS system; mannose-specific IIC component |
| manZ | −2.8 | −2.1 | 1.2 | PTS system; mannose-specific IID component |
| fruB | −1.7 | −2.1 | 1.2 | PTS system; fructose-specific IIA/FPr component |
| Glycerol related | ||||
| glgC | −2.5 | −3.0 | −1.3 | Glucose-1-phosphate adenylyltransferase |
| glpA | −4.9 | −1.7 | 1.7 | Anaerobic glycerol-3-phosphate dehydrogenase subunit A |
| glpD | −9.2 | −18.4 | 1.3 | sn-Glycerol-3-phosphate dehydrogenase (aerobic) |
| glpF | −5.7 | −5.7 | 1.3 | Glycerol uptake facilitator protein |
| glpK | −7.5 | −6.1 | 1.1 | Glycerol kinase |
| glpQ | −2.1 | −2.5 | −1.1 | Glycerophosphoryl diester phosphodiesterase; periplasmic precursor |
| glpR | −1.6 | −2.1 | −1.1 | Glycerol-3-phosphate regulon repressor |
| ugpB | −7.0 | −6.1 | −1.4 | Glycerol-3-phosphate-binding periplasmic protein precursor |
| Histidine biosynthesis | ||||
| hisA | −2.1 | −2.8 | −1.6 | 1-(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 |
| hisG | 1.1 | −1.3 | −2.8 | ATP phosphoribosyltransferase |
| hisH | −1.6 | −2.1 | −2.0 | Imidazole glycerol phosphate synthase subunit hisH |
| hisI | −2.1 | −2.0 | −1.9 | Histidine biosynthesis |
| hisL | 3.0 | 1.1 | −3.7 | His operon leader peptide |
| hisLEDL | 1.7 | −1.2 | −3.5 | Histidine biosynthesis; hisL gene from strain EDL933 |
| hisP | −2.5 | −1.4 | −1.1 | Nucleotide binding |
| Two-component signal transduction | ||||
| dos | 1.3 | 2.1 | 1.4 | Putative phosphodiesterase, oxygen-sensing protein |
| evgS | −3.2 | −1.5 | −1.2 | Two-component signal transduction system (phosphorelay) |
| fimZ | 1.1 | 2.1 | 3.0 | Fimbiral protein Z; putative transcriptional regulator of fimbrial expression (LuxR/UhpA family) |
| glnL | 3.2 | 2.5 | −1.9 | Two-component signal transduction system (phosphorelay) |
| narL | −2.6 | −2.0 | −1.4 | Nitrate/nitrite response regulator protein narL |
| prpR | −3.5 | −3.7 | 1.1 | Regulator for prp operon |
| rstA | 2.5 | 1.9 | −1.3 | Transcriptional Regulatory protein rstA |
| yedV | 1.4 | 2.6 | 2.0 | Putative two-component sensor protein |
| ygeV | −2.1 | −1.4 | −1.5 | Two-component signal transduction system (phosphorelay) |
| Sulfate | ||||
| cysD | −3.0 | −3.0 | −1.6 | Sulfate adenylyltransferase (ATP) activity |
| cysI | −3.5 | −3.0 | −1.2 | Sulfite reductase [NADPH] hemoprotein beta-component |
| cysJ | −4.3 | −2.8 | 1.0 | Sulfite reductase [NADPH] flavoprotein alpha-component |
| sseA | −2.1 | −1.9 | 1.4 | 3-Mercaptopyruvate sulfurtransferase |
| Motility/chemotaxis | ||||
| acs | −8.0 | −4.3 | 1.1 | Acetyl-coenzyme A synthetase |
| c2129 | 3.0 | 2.5 | 1.5 | Cell division activator cedA |
| c4004 | 1.3 | 2.1 | 1.1 | Hypothetical protein |
| csgA | −4.3 | −2.8 | 1.5 | Cell adhesion |
| csgB | −5.7 | −4.6 | −1.1 | Minor curlin subunit precursor |
| csgF | −3.7 | −2.5 | −1.4 | Curli production assembly/transport component csgF precursor |
| fimZ | 1.1 | 2.1 | 3.0 | Fimbiral protein Z; putative transcriptional regulator of fimbrial expression (LuxR/UhpA family) |
| fliD | 2.0 | 2.1 | 1.4 | Cell motility |
| fliR | −1.1 | 1.9 | 2.3 | Flagellar biosynthetic protein fliR |
| gidB | 1.4 | 2.1 | 1.5 | Methyltransferase gidB |
| motB | −2.3 | −1.2 | 1.3 | Chemotaxis motB protein |
| mreC | 1.5 | 2.1 | 1.2 | Rod shape-determining protein mreC |
| sfmA | −1.2 | 1.5 | 2.1 | Putative fimbrial-like protein |
| sfmF | 1.0 | 1.5 | 2.3 | Putative fimbrial-like protein |
| sfmH | −2.0 | 1.0 | 2.5 | Fimbrial assembly protein |
| yhhP | 1.7 | 2.5 | 1.5 | SirA protein |
| Z0020 | 1.5 | 2.5 | 2.1 | Cell adhesion |
| Z4971 | −1.9 | 3.7 | 1.9 | Cell adhesion |
| Cytochrome | ||||
| appB | −3.0 | −2.3 | 1.2 | Cytochrome bd II oxidase subunit II |
| appC | −2.5 | −2.1 | 1.1 | Cytochrome bd II oxidase subunit I |
| cyoC | −2.1 | −3.0 | 1.0 | Cytochrome o ubiquinol oxidase subunit III |
| nrfA | −3.2 | −1.5 | 1.5 | Cytochrome c-552 precursor |
| nrfB | −2.8 | 1.0 | 1.5 | Cytochrome c-type protein nrfB precursor |
| Cold shock protein | ||||
| cspA | 1.5 | 1.5 | −3.2 | Cold shock protein cspA |
| cspE | 2.3 | 2.5 | −1.1 | Cold 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 | −1.2 | Cold shock DEAD-box protein A |
| Antisense RNA | ||||
| dsrA | 3.5 | 4.9 | 1.3 | Antisense 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 | −1.1 | Antisense RNA blocking mokB and hokB translation |
| sokC | 2.0 | 2.6 | −1.6 | Antisense RNA blocking mokC (orf69) and hokC (gef) translation |
| Glutamine/glutamate | ||||
| c0018 | 24.3 | 24.3 | 5.7 | Putative glutamate dehydrogenase |
| glnA | 1.6 | 1.3 | −2.3 | Glutamine synthetase |
| glnH | −1.2 | 1.0 | −2.1 | Glutamine-binding periplasmic protein precursor |
| glnP | 2.5 | 3.0 | −1.9 | Glutamine transport system permease protein glnP |
| gltJ | 3.7 | 4.3 | −1.6 | Glutamate/aspartate transport system permease protein gltJ |
| gltK | 2.6 | 2.6 | −1.6 | Glutamate/aspartate transport system permease protein gltK |
| gltL | 1.4 | 1.7 | −1.9 | Glutamate/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 | 1.6 | Putative iron compound permease protein of ABC transporter family |
| cydA | 2.0 | 2.8 | −1.1 | Cytochrome d ubiquinol oxidase subunit I |
| cydB | 1.9 | 2.8 | −1.2 | Cytochrome d ubiquinol oxidase subunit II |
| feoA | 2.5 | 2.6 | −1.3 | Ferrous iron transport protein A |
| feoB | 2.0 | 3.2 | 1.0 | Ferrous iron transport protein B |
| fhuB | 1.3 | 2.5 | 1.1 | Ferrichrome transport system permease protein fhuB |
| fhuC | 1.6 | 2.5 | 1.0 | Ferrichrome transport ATP-binding protein fhuC |
| fhuD | 2.5 | 4.6 | 1.1 | Ferrichrome-binding periplasmic protein precursor |
| yodB | 2.5 | 2.6 | −1.3 | Cytochrome b561 homolog 1 |
| NADH dehydrogenase | ||||
| nuoA | −1.3 | −2.5 | 1.1 | NADH dehydrogenase I chain A |
| nuoB | −2.0 | −3.5 | 1.0 | NADH dehydrogenase I chain B |
| nuoC | −1.7 | −4.0 | −1.1 | NADH dehydrogenase I chain C/D |
| nuoE | −2.0 | −4.3 | −1.1 | NADH dehydrogenase I chain E |
| nuoI | −1.1 | −2.5 | 1.1 | NADH dehydrogenase I chain I |
| nuoJ | −1.3 | −2.5 | 1.3 | NADH dehydrogenase I chain J |
| nuoK | −1.3 | −2.3 | 1.4 | NADH dehydrogenase I chain K |
| nuoL | −1.2 | −2.3 | 1.4 | NADH dehydrogenase I chain L |
| Tricarboxylic acid cycle | ||||
| sdhD | −13.0 | −21.1 | 1.1 | Succinate dehydrogenase hydrophobic membrane anchor protein |
| sdhC | −12.1 | −18.4 | 1.1 | Succinate dehydrogenase cytochrome b-556 subunit |
| sdhA | −11.3 | −16.0 | 1.3 | Succinate dehydrogenase, catalytic and NAD/flavoprotein subunit |
| sdhB | −10.6 | −12.1 | 1.0 | Succinate dehydrogenase iron-sulfur protein |
| sucA | −7.5 | −11.3 | 1.1 | 2-Oxoglutarate dehydrogenase E1 component |
| sucB | −7.0 | −9.2 | −1.1 | Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex |
| sucD | −6.5 | −8.6 | 1.0 | Succinyl-coenzyme A synthetase alpha chain |
| sucC | −6.5 | −8.6 | 1.0 | Succinyl-coenzyme A synthetase beta chain |
| acnB | −2.0 | −4.3 | 1.0 | Aconitate hydratase activity |
| icdA | −1.9 | −2.6 | 1.1 | Isocitrate dehydrogenase [NADP] |
| yojH | −1.2 | −2.3 | −1.5 | Malate:quinone oxidoreductase |
| mdh | −2.0 | −2.1 | −1.1 | Malate dehydrogenase |
a
Important changes are shown in boldface. IND, indole.