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
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 |
 Regulators | ||||
  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 |