Table S3.
Decreases in Escherichia coli gene expression in response to 30-minute exposures to four independent zeolite supports containing silver nanoparticles versus E. coli exposed to four independent zeolite controls
| Gene name | Gene product | Fold change AgNP-ZM vs zeolite | Description |
|---|---|---|---|
| fliQ | Flagellar biosynthesis protein | −2 | Flagellar biosynthesis |
| mdtQ | Pseudo | −2 | orf, hypothetical protein |
| yhdE | Conserved protein | −2 | orf, hypothetical protein |
| yciT | Predicted DNA-binding transcriptional regulator | −2 | Putative DEOR-type transcriptional regulator |
| yjcC | Predicted signal transduction protein (EAL domain containing protein) | −2 | orf, hypothetical protein |
| yehE | Predicted protein | −2 | orf, hypothetical protein |
| sdiA | DNA-binding transcriptional activator | −2 | Transcriptional regulator of ftsQAZ gene cluster |
| yeeA | Conserved inner membrane protein | −2 | orf, hypothetical protein |
| yncH | Predicted protein | −2 | orf, hypothetical protein |
| ndk | Multifunctional nucleoside diphosphate kinase | −2 | Nucleoside diphosphate kinase |
| yebW | Predicted protein | −2 | orf, hypothetical protein |
| ycjW | Predicted DNA-binding transcriptional regulator | −2 | Putative LACI-type transcriptional regulator |
| ycgN | Conserved protein | −2.1 | orf, hypothetical protein |
| alsA | Fused D-allose transporter subunits of ABC superfamily: ATP-binding components | −2.1 | Putative ATP-binding component of a transport system |
| sugE | Multidrug efflux system protein | −2.1 | Suppresses groEL, may be chaperone |
| ybbD | pseudo | −2.1 | orf, hypothetical protein |
| yjhI | KpLE2 phage-like element; predicted DNAbinding transcriptional regulator | −2.1 | Putative regulator |
| glcF | Glycolate oxidase iron-sulfur subunit | −2.1 | Glycolate oxidase iron-sulfur subunit |
| ybdO | Predicted DNA-binding transcriptional regulator | −2.1 | Putative transcriptional regulator LYSR-type |
| mcrA | e14 prophage; 5-methylcytosine-specific restriction endonuclease B | −2.1 | Restriction of DNA at 5-methylcytosine residues; at locus of e14 element |
| efeB | Conserved protein | −2.1 | orf, hypothetical protein |
| yabP | Pseudo | −2.1 | orf, hypothetical protein |
| arnT | 4-amino-4-deoxy-L-arabinose transferase | −2.1 | orf, hypothetical protein |
| ais | Conserved protein | −2.1 | Protein induced by aluminum |
| rsxC | Fused predicted 4Fe-4S ferredoxin-type protein/conserved protein | −2.1 | Putative membrane protein |
| yagU | Conserved inner membrane protein | −2.1 | orf, hypothetical protein |
| yciF | Conserved protein | −2.1 | Putative structural proteins |
| yifK | Predicted transporter | −2.1 | Putative amino acid/amine transport protein |
| yncD | Predicted iron outer membrane transporter | −2.1 | Putative outer membrane receptor for iron transport |
| yhcO | Predicted barnase inhibitor | −2.1 | orf, hypothetical protein |
| elaD | Predicted enzyme | −2.1 | Putative sulfatase/phosphatase |
| eamA | Cysteine and O-acetyl-L-serine efflux system | −2.1 | orf, hypothetical protein |
| glcD | Glycolate oxidase subunit, FAD-linked | −2.1 | Glycolate oxidase subunit D |
| ydgC | Conserved inner membrane protein associated with alginate biosynthesis | −2.2 | orf, hypothetical protein |
| sugE | Multidrug efflux system protein | −2.2 | Suppresses groEL, may be chaperone |
| alsC | D-allose transporter subunit | −2.2 | Putative transport system permease protein |
| yifK | Predicted transporter | −2.2 | Putative amino acid/amine transport protein |
| yhhY | Predicted acetyltransferase | −2.2 | orf, hypothetical protein |
| fhuB | Fused iron-hydroxamate transporter subunits of ABC superfamily: membrane components | −2.2 | Hydroxamate-dependent iron uptake, cytoplasmic membrane component |
| hdeB | Acid-resistance protein | −2.2 | orf, hypothetical protein |
| yfhA | Predicted DNA-binding response regulator in two-component system | −2.2 | Putative 2-component transcriptional regulator |
| glgS | Predicted glycogen synthesis protein | −2.2 | Glycogen biosynthesis, rpoS dependent |
| ydaQ | Rac prophage; conserved protein | −2.2 | orf, hypothetical protein |
| ylbH | Pseudo | −2.2 | orf, hypothetical protein |
| rfaP | Kinase that phosphorylates core heptose of lipopolysaccharide | −2.2 | Lipopolysaccharide core biosynthesis; phosphorylation of core heptose |
| stpA | DNA binding protein, nucleoid-associated | −2.2 | DNA-binding protein; H-NS-like protein; chaperone activity |
| lpxT | Undecaprenyl pyrophosphate phosphatase | −2.2 | orf, hypothetical protein |
| ydhY | Predicted 4Fe-4S ferridoxin-type protein | −2.2 | Putative oxidoreductase, Fe-S subunit |
| yifK | Predicted transporter | −2.2 | Putative amino acid/amine transport protein |
| hisP | Histidine/lysine/arginine/ornithine transporter subunit | −2.2 | ATP-binding component of histidine transport |
| yhgE | Predicted inner membrane protein | −2.2 | Putative transport |
| thiQ | Thiamin transporter subunit | −2.2 | Putative ATP-binding component of a transport system |
| ycgZ | Predicted protein | −2.2 | orf, hypothetical protein |
| glcG | Conserved protein | −2.2 | orf, hypothetical protein |
| fliP | Flagellar biosynthesis protein | −2.2 | Flagellar biosynthesis |
| yibF | Predicted glutathione S-transferase | −2.2 | Putative S-transferase |
| rpiR | DNA-binding transcriptional repressor | −2.4 | Transcriptional repressor of rpiB expression |
| yojI | Fused predicted multidrug transport subunits of ABC superfamily | −2.4 | Putative ATP-binding component of a transport system |
| hsdS | Specificity determinant for hsdM and hsdR | −2.4 | Specificity determinant for hsdM and hsdR |
| racR | Rac prophage; predicted DNA-binding transcriptional regulator | −2.4 | orf, hypothetical protein |
| yceI | Predicted protein | −2.4 | orf, hypothetical protein |
| tonB | Membrane spanning protein in TonB-ExbBExbD complex | −2.4 | Energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages |
| rfaS | Lipopolysaccharide core biosynthesis protein | −2.5 | Lipopolysaccharide core biosynthesis |
| rutB | Predicted enzyme | −2.5 | Putative synthetase |
| yciI | Predicted enzyme | −2.5 | orf, hypothetical protein |
| wzyE | Predicted Wzy protein involved in ECA polysaccharide chain elongation | −2.5 | TDP-Fuc4NAc:lipidII transferase; synthesis of enterobacterial common Ag |
| nth | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III) | −2.5 | Endonuclease III; specific for apurinic and/or apyrimidinic sites |
| yncC | Predicted DNA-binding transcriptional regulator | −2.5 | orf, hypothetical protein |
| yifK | Predicted transporter | −2.5 | Putative amino acid/amine transport protein |
| yjhB | KpLE2 phage-like element; predicted transporter | −2.5 | Putative transport protein |
| yhjR | Conserved protein | −2.5 | orf, hypothetical protein |
| yfdI | CPS-53 (KpLE1) prophage; predicted inner membrane protein | −2.5 | putative ligase |
| yifN | pseudo | −2.6 | orf, hypothetical protein |
| caiF | DNA-binding transcriptional activator | −2.6 | Transcriptional regulator of cai operon |
| flgA | assembly protein for flagellar basal-body periplasmic P ring | −2.6 | Flagellar biosynthesis; assembly of basal-body periplasmic P ring |
| serA | D-3-phosphoglycerate dehydrogenase | −2.6 | D-3-phosphoglycerate dehydrogenase |
| can | Carbonic anhydrase | −2.7 | Putative carbonic anhdrase |
| yacC | Predicted protein | −2.7 | orf, hypothetical protein |
| ydbL | Conserved protein | −2.7 | orf, hypothetical protein |
| efeO | Conserved protein | −2.7 | orf, hypothetical protein |
| fliF | Flagellar basal-body MS-ring and collar protein | −2.7 | Flagellar biosynthesis; basal-body MS |
| flgC | Flagellar component of cell-proximal portion of basal-body rod | −2.7 | Flagellar biosynthesis, cell-proximal portion of basal-body rod |
| can | Carbonic anhydrase | −2.7 | Putative carbonic anhdrase |
| rsxD | Predicted inner membrane oxidoreductase | −2.7 | orf, hypothetical protein |
| fliM | Flagellar motor switching and energizing component | −2.7 | Flagellar biosynthesis, component of motor switch and energizing |
| ybaN | Conserved inner membrane protein | −2.8 | Putative gene 58 |
| proV | Glycine betaine transporter subunit | −2.8 | ATP-binding component of transport system for glycine, betaine and proline |
| fhuD | Iron-hydroxamate transporter subunit | −2.8 | Hydroxamate-dependent iron uptake, cytoplasmic membrane component |
| can | Carbonic anhydrase | −2.8 | Putative carbonic anhdrase |
| sufE | Sulfur acceptor protein | −2.8 | orf, hypothetical protein |
| sufS | Selenocysteine lyase, PLP-dependent | −2.8 | orf, hypothetical protein |
| ariR | Predicted protein | −2.8 | orf, hypothetical protein |
| wcaM | Predicted colanic acid biosynthesis protein | −2.8 | orf, hypothetical protein |
| ymgA | Predicted protein | −2.9 | orf, hypothetical protein |
| ybiX | Conserved protein | −2.9 | Putative enzyme |
| yacC | Predicted protein | −2.9 | orf, hypothetical protein |
| sufC | Component of SufBCD complex, ATP-binding component of ABC superfamily | −2.9 | Putative ATP-binding component of a transport system |
| can | Carbonic anhydrase | −2.9 | Putative carbonic anhydrase |
| yacC | Predicted protein | −3 | orf, hypothetical protein |
| fhuC | Iron-hydroxamate transporter subunit | −3 | ATP-binding component of hydroxymate-dependent iron transport |
| sodA | Superoxide dismutase, Mn | −3.1 | Superoxide dismutase, manganese |
| can | Carbonic anhydrase | −3.2 | Putative carbonic anhydrase |
| cbrB | Predicted inner membrane protein | −3.2 | orf, hypothetical protein |
| flgB | Flagellar component of cell-proximal portion of basal-body rod | −3.3 | Flagellar biosynthesis, cell-proximal portion of basal-body rod |
| ompT | DLP12 prophage; outer membrane protease VII (outer membrane protein 3b) | −3.3 | Outer membrane protein 3b |
| rsxE | Predicted inner membrane NADH-quinone reductase | −3.3 | orf, hypothetical protein |
| pqqL | Predicted peptidase | −3.3 | Putative peptidase |
| fliA | RNA polymerase, sigma 28 (sigma F) factor | −3.3 | Flagellar biosynthesis; alternative sigma factor 28 |
| yfdH | CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase | −3.5 | Putative glycan biosynthesis enzyme |
| yjgL | Predicted protein | −3.5 | orf, hypothetical protein |
| sufD | Component of SufBCD complex | −3.7 | orf, hypothetical protein |
| yfdH | CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase | −3.7 | Putative glycan biosynthesis enzyme |
| fepB | Iron-enterobactin transporter subunit | −3.7 | Ferric enterobactin |
| fliL | Flagellar biosynthesis protein | −3.7 | Flagellar biosynthesis |
| sufB | Component of SufBCD complex | −3.7 | orf, hypothetical protein |
| sufA | Fe-S cluster assembly protein | −3.8 | orf, hypothetical protein |
| ycgF | Predicted FAD-binding phosphodiesterase | −3.8 | orf, hypothetical protein |
| yfdH | CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase | −3.8 | Putative glycan biosynthesis enzyme |
| sufA | Fe-S cluster assembly protein | −3.9 | orf, hypothetical protein |
| ybdB | Conserved protein | −4 | orf, hypothetical protein |
| fhuE | Ferric-rhodotorulic acid outer membrane transporter | −4 | Outer membrane receptor for ferric iron uptake |
| sufA | Fe-S cluster assembly protein | −4.3 | orf, hypothetical protein |
| yfdH | CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase | −4.4 | Putative glycan biosynthesis enzyme |
| exbD | Membrane spanning protein in TonB-ExbBExbD complex | −4.5 | Uptake of enterochelin; tonB-dependent uptake of B colicins |
| yncE | Conserved protein | −4.5 | Putative receptor |
| fepD | Iron-enterobactin transporter subunit | −4.7 | Ferric enterobactin |
| sufA | Fe-S cluster assembly protein | −4.9 | orf, hypothetical protein |
| entB | Isochorismatase | −5 | 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochroismatase |
| entC | Isochorismate synthase 1 | −5.3 | Isochorismate hydroxymutase 2, enterochelin biosynthesis |
| tdcA | DNA-binding transcriptional activator | −5.3 | Transcriptional activator of tdc operon |
| fepA | Iron-enterobactin outer membrane transporter | −5.4 | Outer membrane receptor for ferric enterobactin |
| fepC | Iron-enterobactin transporter subunit | −5.6 | ATP-binding component of ferric enterobactin transport |
| fes | Enterobactin/ferric enterobactin esterase | −5.6 | Enterochelin esterase |
| exbB | Membrane spanning protein in TonB-ExbBExbD complex | −5.8 | Uptake of enterochelin; tonB-dependent uptake of B colicins |
| nrdH | Glutaredoxin-like protein | −5.8 | Glutaredoxin-like protein; hydrogen donor |
| fecR | KpLE2 phage-like element; transmembrane signal transducer for ferric citrate transport | −5.9 | Regulator for fec operon, periplasmic |
| entS | Predicted transporter | −6.6 | Putative transport |
| entF | Enterobactin synthase multienzyme complex component, ATP-dependent | −6.8 | ATP-dependent serine activating enzyme |
| cirA | Ferric iron-catecholate outer membrane transporter | −7.1 | Outer membrane receptor for iron-regulated colicin I receptor; porin |
| entA | 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase | −7.2 | 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase |
| entE | 2,3-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex | −7.4 | 2,3-dihydroxybenzoate-AMP ligase |
| yddB | Predicted porin protein | −7.9 | orf, hypothetical protein |
| fecI | KpLE2 phage-like element; RNA polymerase, sigma 19 factor | −8.5 | Probable RNA polymerase sigma factor |
| nrdI | Protein that stimulates ribonucleotide reduction | −8.8 | orf, hypothetical protein |
| ydiE | Conserved protein | −9.2 | orf, hypothetical protein |
| nrdE | Ribonucleoside-diphosphate reductase 2, alpha subunit | −10.4 | Ribonucleoside-diphosphate reductase 2, alpha subunit |
| bfd | Bacterioferritin-associated ferredoxin | −10.6 | orf, hypothetical protein |
| yddA | Fused predicted multidrug transporter subunits of ABC superfamily | −12.4 | Putative ATP-binding component of a transport system |
| fepG | Iron-enterobactin transporter subunit | −12.6 | Ferric enterobactin transport protein |
| fiu | Predicted iron outer membrane transporter | −13.7 | Putative outer membrane receptor for iron transport |
| nrdF | Ribonucleoside-diphosphate reductase 2, beta subunit, ferritin-like protein | −13.9 | Ribonucleoside-diphosphate reductase 2, beta chain, frag |
| fhuF | Ferric iron reductase involved in ferric hydroximate transport | −17.6 | orf, hypothetical protein |