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Table 1 Genes significantly down-regulated in Escherichia coli O26:H11 21,765 in samples with microbiota compared to those without microbiota

From: Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

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
  1. aFC is the fold change of the genes that exhibit significant (FC ≤ −2, false discovery rate (FDR) ≤ 0.005, minimum normalized read count = 10) differential expression. Only discussed genes in our study are shown on this table
  2. bAdjusted p-value for multiple testing with the Benjamini-Hochberg procedure which controls FDR