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Table 2 List of differentially expressed genes showing altered metabolic profile of E. coli O157:H7 Congo red-positive isolate

From: Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism

Gene group/genea Gene IDb Known or predicted functionb Fold change P value
Transport
 phoE Z0302 Outer membrane phosphoporin protein −1.89 0.027
 ybaL Z0597 Cation:proton antiport protein −1.48 0.004
 ybbA Z0648 ABC transporter ATP-binding protein −1.59 5.4E-04
 ybbP Z0649 Oxidoreductase −1.7 0.02
 nagE Z0826 N-acetylglucosamine PTS permease −2.30 0.022
 glnQ Z1031 Glutamine ABC transporter ATP-binding −3.09 0.006
 glnH Z1033 Glutamine ABC transporter periplasmic protein −3.66 0.004
 potF Z1081 Putrescine ABC transporter periplasmic-binding protein −4.42 4.0E-04
 potG Z1082 Putrescine ABC transporter ATP-binding protein −4.00 9.0E-04
 potH Z1083 Putrescine ABC transporter membrane protein −2.98 1.5E-02
 potI Z1084 Putrescine ABC transporter membrane −2.92 9.0E-03
 lolA Z1237 Periplasmic chaperone for translocation of lipoproteins to outer membrane −1.48 0.037
 ompA Z1307 Outer membrane porin A −2.50 8.6E-06
 ybaL Z1672 Cation:proton antiporter −1.48 0.004
 VybbA Z1673 ATP-binding protein of ABC transporter −1.59 5.0E-04
 ybbP Z1677 Membrane component of ABC transporter protein −1.59 5.0E-04
 yceL (mdtH) Z1702 Multidrug efflux transporter +1.40 0.024
 narK Z2000 Nitrite/nitrate antiporter +2.79 0.059
 gabP Z3961 Gamma-aminobutyrate transporter −5.33 1.0E-03
 yhaO Z4463 Permease for D-serine transport +2.76 0.01
 livF Z4824 Leucine/isoleucine/valine transporter ATP-binding subunit −2.06 0.04
 nirC Z4728 Transport of nitrite +3.95 0.03
 dppF Z4957 Dipeptide transporter ABC-binding unit −2.61 0.03
 dppD Z4958 Dipeptide transporter ABC-binding unit −2.40 0.04
 dppA Z4961 Dipeptide transporter protein −2.52 0.03
 yigM Z5348 Biotin transporter +1.36 0.03
Amino acid biosynthesis
 thrB Z0003 Homoserine kinase −2.18 0.01
 thrC Z0004 Threonine synthase −2.17 0.03
 leuD Z0080 Isopropylmalate isomerase small subunit −2.66 0.01
 leuC Z0081 Isopropylmalate isomerase large subunt −2.34 0.04
 asnB Z0821 Asparagine synthetase B −3.07 0.049
Z2491 Glutamine synthetase −2.93 0.02
 hisC Z3183 Histidinol-phosphate aminotransferase −1.79 0.03
 hisH Z3185 Imidazolr glycerol phosphate synthase −1.78 0.03
 hisA Z3186 Imidazole-4-carboxamide isomerase −1.84 0.02
 hisF Z3187 Imidazole glycerol phosphate synthase −1.86 0.01
 hisI Z3188 Bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase −1.82 0.02
 lysA Z4156 Diaminopimelate decarboxylase +2.39 0.03
 ilvN Z5164 Acetolactate synthase I regulatory subunit −2.08 0.02
 ilvB Z5165 Isoleucine/valine biosynthesis −2.02 0.01
 asnA Z5245 Asparagine synthetase −3.47 0.04
 aspA Z5744 Aspartate ammonia-lyase +2.04 0.04
Amino acid degradation
 goaG Z2486 4-aminobutyrate transferase −6.75 2.5E-04
 ordL Z2487 γ-glutamylputrescine oxidase −6.79 0.01
 aldH Z2488 γ-glutamyl-γ-aminobutyraldehyde −5.52 1.1E-03
 gabD Z3959 Succinate-semialdehyde dehydrogenase I −4.12 5.0E-03
 gabT Z3960 4-aminobutyrate aminotransferase −5.66 5.0E-03
Carbohydrate/Energy metabolism
 aceF Z0125 Dihydrolipoamide acetyltransferase −2.00 0.02
 yaeM Z0184 1-deoxy-D-xylulose 5-phosphate reductoisomerase −1.33 0.03
 malZ Z0501 Maltodextrin glucosidase −2.13 0.041
 ybdR Z0752 Zn-dependent oxidoreductase −2.70 3.0E-04
 sdhA Z0877 Succinate dehydrogenase flavoprotein subunit −3.11 0.044
 sucA Z0880 2-oxoglutarate dehydrogenase E1 −2.73 0.047
 sucB Z0881 Dihydrolipoamide succinyltransferase −2.62 0.039
 sucC Z0882 Succinyl-CoA synthetase subunit beta −2.64 0.029
 sucD Z0883 Succinyl-CoA synthetase subunit alpha −2.37 0.054
 nadA Z0919 Quinolate synthetase −1.82 0.002
 galM Z0926 Galactose-1-epimerase −1.33 0.047
 galE Z0929 UDP-galactose-4-epimerase −1.46 0.019
 ybjW Z1107 Hydroxylamine reductase +1.98 9/0E-03
 galU Z2012 UTP-glucose-1-phosphate uridylyltransferase −2.11 0.006
 adhE Z2016 Aldehyde-alcohol dehydrogenase +2.29 0.01
 manX Z2860 PTS system mannose-specific transporter unit AB +1.47 0.035
 manY Z2861 PTS enzyme IIC, mannose-specific +1.55 0.007
 manZ Z2862 PTS system mannose-specific transporter subunit IID +1.50 0.02
 yghA Z4356 Oxidoreductase −2.72 0.01
 ugpB Z4822 Glycerol-3-phosphate transporter periplasmic-binding protein −2.74 0.01
 uhpT Z5156 Sugar phosphate antiporter +3.22 6.9E-05
 mdoB Z5959 Phosphoglycerol transferase I −3.00 3.0E-04
Fatty acid and lipid metabolism
 pgsA Z3000 Phosphatidylglycerophosphate synthetase +1.47 0.01
 plsC Z4372 1-acyl-sn-glycerol-3-phosphate +1.30 2.3E-03
 yrbB Z4554 Phospholipid ABC transporter −1.87 2.0E-03
 yrbC Z4555 Phospholipid ABC transporter −1.97 3.0E-04
Phosphate metabolism
 phoU Z5215 Transcriptional regulator −2.09 4.0E-03
 pstB Z5216 Phosphate transporter ATP-binding protein −2.02 0.02
 pstA Z5217 Phosphate transport permease subunit PstA −2.70 2.0E-03
 pstC Z5218 Phosphate transport permease subunit PstC −2.52 3.0E-04
 pstS Z5219 Phosphate ABC transporter substrate-binding protein −5.84 1.4E-07
Sulfur metabolism
 cysZ Z3679 Sulfate transport protein −1.47 0.03
 cysA Z3687 Sulfate/thiosulfate transporter +1.50 0.02
 cysW Z3688 Sulfate/thiosulfate permease +2.16 3.4E-03
 cysN Z4059 Sulfate adenylyltransferase subunit 1 +1.65 0.03
 cysJ Z4074 Sulfite reductase subunit alpha +2.12 1.2E-03
Protein metabolism
 yaeJ Z0203 Peptidyl-tRNA hydrolase domain-containing protein −1.36 0.03
 rpmE Z5484 50S ribosomal protein L31 −2.20 0.019
 pepA Z5872 Leucyl aminopeptidase −1.58 0.02
DNA/RNA metabolism
 hisT Z3580 tRNA pseudouridine synthase A −1.51 0.02
 deoD Z5986 Purine nucleoside phosphorylase −1.37 0.04
 mazG Z4096 Nucleoside triphosphate pyrophospho-hydrolase +1.49 0.02
Cell wall/cell division/cell cycle
 murD Z0098 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase −1.58 0.02
 uppP Z4410 Undecaprenyl pyrophosphate phosphatase −1.72 0.01
Cofactors, vitamins, protheticgroups
 yaeM Z0184 1-deoxy-D-xylulose 5-phosphate −1.33 0.04
 nadA Z0919 Quinolinate synthetase reductoisomerase −1.82 0.002
 btuR Z2540 Cobinamide adenosyltransferase −1.31 0.04
 nadB Z3856 L-aspartate oxidase −1.63 4.0E-03
 ggt Z4813 Gamma-glutamyltranspeptidase −1.76 2.0E-03
Transcriptional regulation
 ykgK Z0361 LuxR-type transcriptional regulator −2.49 0.049
 marA Z2170 DNA-binding transcriptional activator MarA −1.52 0.039
 marR Z2172 MarR family transcriptional repressor −1.56 0.053
 yhgG Z4765 Transcriptional regulator +2.12 0.04
Signal transduction
 phoB Z0497 Response regulator belonging to PhoB/PhoR two-component system −1.53 0.031
 phoR Z0498 Signal sensor component of PhoB/PhoR two-component system −1.47 0.036
 narL Z1996 Nitrate/citrate response regulator −1.48 0.064
 narK Z2000 Nitrite/nitrate antiporter +2.79 0.059
Virulence
 cutF (nlpE) Z0204 Lipoprotein involved with copper homeostasis and adhesion −1.63 0.004
 ykfE Z0277 C-lysozyme inhibitor −7.09 5.6E-06
 nleB Z4328 Type III effector +1.72 0.04
 nleE Z4329 Type III effector +1.86 0.02
 efa-1` Z4332 Cytotoxin +1.84 0.01
Z4333 Cytotoxin +1.93 0.03
  1. aGene group/gene designations were selected from RAST Server [44]
  2. bGene ID and known or predicted functions are based on the annotated sequence of E. coli O157:H7 EDL 933 [92]. Symbols + and – represent upregulated and downregulated gene expression, respectively