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Table 1 List of differentially expressed genes mediating biofilm formation, cell envelope and global stress responses in Congo red-binding isolate of E. coli O157:H7

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
Biofilm related
 Curli biosynthesis
  csgF Z1671 Curli assembly protein +2.40 0.03
  csgE Z1672 Curli assembly/transport +2.14 0.09
  csgD Z1673 Positive regulator of curli genes +2.07 0.05
  csgC Z1677 Autoagglutination protein +5.70 0.06
 Motility and chemotaxis
  flgL Z1721 Flagellar hook-associated protein +1.40 0.03
  cheR Z2938 Chemotaxi methyltransferase +2.40 1.5E-04
  tap Z2939 Methyl-accepting protein IV +4.25 6.6E-09
  tar Z2940 Methyl-accepting chemotaxis protein II +4.48 1.7E-11
  cheA Z2942 Chemotaxis protein CheA +2.82 1.8E-07
  motA Z2944 Flagellar motor protein MotA +3.74 3.3E-08
  flhC Z2945 Transcriptional activator FlhC +2.55 9.0E-04
  flhD Z2946 Transcriptional activator FlhD +2.58 0.01
  fliZ Z3011 Flagellar biosynthesis protein FliZ +1.57 0.05
  fliC Z3013 Flagellin +2.54 2.4E-07
  fliD Z3014 Flagellar capping protein +2.88 1.8E-07
  yfiR Z3897 Periplasmic protein +1.55 0.03
  ykgK Z0361 Negative regulator of motility −2.49 0.05
  bssR Z1062 Biofilm formation regulatory protein +2.57 0.08
  ydeH Z2163 Putative diguanylate cyclase −2.20 1.2E-05
  bdm Z2229 Biofilm-dependent modulation protein −11.53 2.0E-07
  ydiV Z2736 Anti-FlhDC factor +1.64 0.01
  qseB Z4377 Response regulator −1.60 0.03
 Cell envelope
  nlpE (cutF) Z0204 Surface adhesion −1.63 0.004
  ompA Z1307 Outer membrane protein −2.50 8.6E-06
  ycfJ Z1749 Membrane protein −24.98 1.5E-14
  ycfT Z1756 Inner membrane protein −3.25 6.5E-04
  ygiB Z4394 Outer membrane protein −1.55 0.01
  uppP Z4410 Undecaprenyl pyrophosphate phosphatase −1.72 0.01
  yjbE Z5624 Predicted protein mediating extracellular polysaccharide biosynthesis −19.61 1.0E-03
  yjbF Z5625 Predicted protein mediating extracellular polysaccharide biosynthesis −14.61 3.0E-04
  yjbG Z5626 Predicted protein mediating extracellular polysaccharide biosynthesis −12.87 2.0E-03
  yjbH Z5627 Predicted protein mediating extracellular polysaccharide biosynthesis −7.24 2.1E-05
Stress related
 Acid stress
  gadB Z2215 Glutamate decarboxylase −14.41 3.0E-03
  xasA Z2216 Acid sensitivity protein GadC −17.72 7.5E-05
  yhiM Z4890 Inner membrane protein −14.43 0.01
  yhiD Z4920 Mg2+ transport ATPase −12.48 0.01
  hdeD Z4923 Acid-resistance membrane protein −13.47 5.0E-03
  gadA Z4930 Glutamate decarboxylase −13.99 0.01
 Oxidative stress
  ybjW Z1107 Hydroxylamine reductase +1.98 0.01
  marA Z2170 Transcriptional activator −1.52 0.04
  marR Z2171 Transcriptional regulator −1.56 0.05
  katE Z2761 Hydroxyperoxidase or catalase II −3.18 6.7E-05
  cspD Z2117 Stationary phase/starvation-inducible +1.65 0.02
  csiD Z3956 Carbon starvation-inducible protein −5.85 3.1E-03
  yjiY Z5953 Carbon starvation protein −5.74 7.0E-05
 Cell envelope stress
  ykfE Z0277 C-lysozyme inhibitor −7.09 5.6E-06
  yccA Z1322 Putative carrier/transport protein −1.54 4.0E-03
  ycfS (idtC) Z1752 L, D-transpeptidase −2.73 5.5E-04
  spy Z2775 Protease/chaperone −14.70 3.9E-09
  cpxP Z5458 Inhibitor of CpxA of CpxRA pathway −3.76 3.5E-07
  slt Z5994 lytic murein transglycosylase −1.54 0.01
Heat, osmotic and desiccation stress
  htrA (degP) Z0173 Serine endoprotease −2.39 0.01
  hslJ Z2330 Heat-shock outer membrane protein −5.41 1.7E-11
  pspE Z2477 Thiosulfate:cyanide sulfur transferase −2.23 9.3E-05
  pspD Z2478 Inner membrane phage shock protein −3.38 6.9E-06
  pspC Z2479 Transcriptional activator −3.42 3.2E-05
  pspB Z2480 Phage shock protein −3.65 8.6E-06
  pspA Z2482 Phage shock protein −3.29 2.0E-04
  pspF Z2484 Transcriptional regulator of phage shock proteins operon −1.27 0.04
  htpX Z2876 Heat shock protein −2.66 2.1E-05
  rpoH Z4835 Sigma factor σ32 −1.35 0.03
  rcsA Z3041 Positive regulator of colanic acid biosynthesis −15.51 8.6E-04
  wzzB Z3189 Regulator of O-antigen component of LPS chains −1.41 0.04
  wcaM Z3207 Colanic acid biosynthesis protein −6.36 0.01
  wcaK Z3209 Pyruvyl transferase −12.75 0.03
  cpsG Z3212 Phosphomannomutase −14.59 3.4E-03
  cspB Z3213 Mannose-1-phosphate guanylly-trasferase −13.91 7.0E-04
  wcaI Z3214 Glycosyl transferase −14.28 4.0E-03
  wcaH Z3215 GDP-D-mannose dehydratase −13.95 3.1E-03
  wcaG Z3216 Nucleotide di-P-sugar epimerase −16.20 0.03
  gmd Z3217 GDP-D-mannose dehydratase −15.73 0.04
  wcaF Z3218 Colanic acid biosynthesis acetyl-transferase −12.03 0.01
  wcaE Z3219 Glycosyl transferase −13.67 0.03
  wcaD Z3220 Colanic acid biosynthesis protein −9.84 0.01
  wcaC Z3221 Glycosyl transferase −8.14 9.6E-05
  wcaA Z3223 Glycosyl transferase −16.40 1.1E-03
  wzc Z3224 Tyrosine kinase −18.28 4.0E-03
  wzb Z3226 Tyrosine phosphatase −18.15 0.01
  wza Z3227 Polysaccharide export protein −19.40 9.0E-03
  osmY Z5977 Periplasmic chaperone −2.44 0.02
  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