Table 1 Genes significantly down-regulated in Escherichia coli O26:H11 21,765 in samples with microbiota compared to those without microbiota
Locus (ECO26H_v1_ #) | Gene name | Mean of normalized counts | FCa | adj. p b | Function or product |
|---|---|---|---|---|---|
Nitrate metabolism and nitrite detoxification | |||||
 180,052 | hcr | 90 | −2.3 | 0.003 | HCP oxidoreductase, NADH-dependent |
 110,034 | ybdL | 1542 | −2.1 | 3.3E-05 | Methionine aminotransferase, PLP-dependent |
 180,029 | grxA | 180 | −2.1 | 0.0006 | Glutaredoxin 1, redox coenzyme for ribonucleotide reductase (RNR1a) |
 520,050 | norR | 126 | −2.0 | 0.0002 | NO-responsive regulator |
  790008 | ytfE | 47 | −2.3 | 0.005 | Regulator of cell morphogenesis and NO sensing |
DNA repair | |||||
 740,026 | nfi | 590 | −2.0 | 1.6E-10 | Endonuclease V |
Amino acid transport and metabolism | |||||
 10,028 | carB | 490 | −2.3 | 3.8E-08 | Carbamoyl-phosphate synthase, large subunit |
 180,040 | artJ | 878 | −4.6 | 6.2E-25 | Arginine transporter subunit; periplasmic-binding component of ABC superfamily |
 20,008 | leuC | 96 | −2.1 | 0.0001 | 3-isopropylmalate dehydratase (isomerase), subunit with LeuD |
 270,021 | trpB | 302 | −2.0 | 0.0003 | Tryptophan synthase, beta subunit |
 270,022 | trpC | 244 | −2.0 | 0.002 | Fused indole-3-glycerolphosphate synthetase; N-(5-phosphoribosyl) anthranilate isomerase |
 270,023 | trpD | 222 | −2.1 | 0.0003 | Fused glutamine amidotransferase (component II) of anthranilate synthase; anthranilate phosphoribosyl transferase |
 270,024 | trpE | 173 | −2.8 | 1.0E-06 | Component I of anthranilate synthase |
 40,007 | metQ | 954 | −2.1 | 1.9E-05 | DL-methionine transporter subunit; periplasmic-binding component of ABC superfamily |
 40,009 | metN | 322 | −2.8 | 8.1E-11 | DL-methionine transporter subunit; ATP-binding component of ABC superfamily |
 430,005 | hisD | 257 | −2.3 | 1.0E-09 | Bifunctional histidinal dehydrogenase and histidinol dehydrogenase |
 430,006 | hisC | 59 | −2.5 | 0.0004 | Histidinol-phosphate aminotransferase |
 530,047 | argA | 172 | −2.6 | 6.7E-07 | Fused acetylglutamate kinase homolog (inactive); amino acid N-acetyltransferase |
 530,066 | lysA | 568 | −2.1 | 4.9E-05 | Diaminopimelate decarboxylase, PLP-binding |
 610,023 | argG | 754 | −2.5 | 6.0E-09 | Argininosuccinate synthetase |
 610,063 | gltD | 168 | −2.0 | 6.2E-05 | Glutamate synthase small chain |
 660,006 | metL | 2959 | −3.0 | 0.0003 | Fused asparto kinase II; homoserine dehydrogenase II |
 660,007 | metB | 251 | −2.1 | 0.0003 | Cystathionine gamma-synthase, PLP-dependent |
 700,021 | metE | 3087 | −2.5 | 2.1E-06 | 5-methyl tetra hydro pteroyl tri glutamate-homocysteine S-methyltransferase |
 700,022 | metR | 275 | −2.1 | 3.4E-05 | DNA-binding transcriptional activator, homocysteine-binding |
 700,077 | ilvC | 611 | −3.2 | 4.8E-11 | Ketol-acid reductoisomerase, NAD(P)-binding |
 700,079 | ilvA | 444 | −2.5 | 5.5E-09 | Threonine deaminase |
 700,081 | ilvE | 402 | −2.0 | 1.1E-05 | Branched-chain amino-acid aminotransferase |
 700,083 | ilvB(G) | 273 | −2.0 | 0.0002 | Acetolactate synthase I, large subunit |
 700,084 | ilvL | 5169 | −2.6 | 4.9E-17 | ilvG operon leader peptide |
 710,012 | asnA | 3488 | −2.1 | 1.1E-12 | Asparagine synthetase A |
 730,015 | argC | 450 | --3.2 | 1.9E-15 | N-acetyl-gamma-glutamylphosphate reductase, NAD(P)-binding |
 730,016 | argB | 154 | −2.6 | 2.6E-07 | Acetylglutamate kinase |
 730,017 | argH | 1040 | −3.5 | 2.1E-13 | Argininosuccinate lyase |
 760,070 | adiC | 582 | −3.7 | 2.1E-13 | Arginine/agmatine antiporter |
 760,072 | adiA | 224 | −2.6 | 3.1E-08 | Biodegradative arginine decarboxylase |
 800,012 | argI | 112 | −6.5 | 1.9E-20 | Ornithine carbamoyltransferase 1 |
Carbohydrate metabolism and energy production | |||||
 470,020 | glpA | 363 | −2.0 | 0.001 | sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)-binding |
 710,165 | lldD | 973 | −2.1 | 1.1E-12 | L-lactate dehydrogenase, FMN linked |
 710,166 | lldR | 123 | −2.5 | 6.5E-06 | DNA-binding transcriptional repressor |
 710,167 | lldP | 430 | −2.1 | 8.1E-06 | L-lactate permease |
bacterial pathogenicity | |||||
 230,055 | yccC | 1840 | −2.1 | 9.6E-07 | Cryptic autophosphorylating protein tyrosine kinase Etk |
 230,056 | etp | 214 | −2.1 | 0.002 | Phosphotyrosine-protein phosphatase |
Inorganic ion transport and metabolism | |||||
 430,088 | rncA | 68 | −2.0 | 0.003 | Nickel and cobalt resistance |
 560,020 | fecR | 116 | −3.0 | 1.7E-08 | Transmembrane signal transducer for ferric citrate transport; KpLE2 phage-like element |
 620,109 | feoB | 997 | −2.0 | 1.1E-05 | Fused ferrous iron transporter, protein B: GTP-binding protein; membrane protein |
 620,179 | nikB | 148 | −2.1 | 0.0004 | Nickel transporter subunit; membrane component of ABC superfamily |
 620,180 | nikC | 113 | −2.3 | 1.7E-05 | Nickel transporter subunit; membrane component of ABC superfamily |
 620,181 | nikD | 180 | −2.0 | 0.0006 | Nickel transporter subunit; ATP-binding component of ABC superfamily |
Cell wall/membrane biogenesis | |||||
 20,017 | ftsL | 485 | −2.3 | 1.3E-07 | Membrane bound cell division protein at septum containing leucine zipper motif |
 20,020 | murF | 436 | −2.3 | 5.5E-08 | UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase |
Transcription | |||||
 180,070 | lrp | 2442 | −3.0 | 1.7E-15 | DNA-binding transcriptional dual regulator, leucine-binding |