TABLE 2.

Top 30 most up-regulated genes during biofilm growth in urine of E. coli 83972 and VR50 compared to that during planktonic growth in MOPS and urine

GeneCodeFunction and/or productFC in BFaSignal intensity in BFb
cspGb0990Homolog of Salmonella cold shock protein80.74,659
cspHb0989Cold shock-like protein56.52,532
ibpBb3686Heat shock protein33.65,787
marRb1530Multiple antibiotic resistance protein; repressor of mar operon31.54,859
yqiJb3050Putative oxidoreductase30.61,522
oxySb4458Global regulatory RNA OxyS30.53,916
c2422c2422Putative inner membrane ABC transporter28.11,096
ddgb2378Palmitoleoyl-acyl carrier protein-dependent acyltransferase, cold-induced gene26.21,859
ygiDb3039Putative enzyme with dioxygenase domain23.43,863
c3685c3685Hypothetical protein22.5791
aaeXb3242Hypothetical protein21.23,905
grxAb0849Glutaredoxin 1 redox coenzyme for glutathione-dependent ribonucleotide reductase21.14,675
c2436c2436Putative pesticin receptor precursor, homologous to fyuA19.81,196
c2424c2424Putative peptide synthetase19.61,408
yfiPb2583Hypothetical protein19.01,863
yqjFc3859Hypothetical protein18.93,664
mdtLb3710Drug/chloramphenicol transport protein (MFS family)18.31,862
yhcNb3238Hypothetical protein17.35,790
yqgAb2966Putative transport membrane protein17.21,010
rydBb4430Small toxic membrane polypeptide17.11,167
sgaBb4194Putative PTS family enzyme II component, possibly ascorbate-specific16.52,167
pflEb0824Putative pyruvate formate lyase activating enzyme16.4891
marBb1532Multiple antibiotic resistance protein16.32,173
sgaEb4198l-ribulose 5-phosphate 4-epimerase16.21,405
ybaOZ0555Putative transcriptional regulator15.92,505
ytfHb4212Putative transcriptional regulator15.92,383
cspAb3556Cold shock protein 7.4, transcriptional activator of hns15.96,387
yjfYb4199Hypothetical protein15.2960
c3865c3865Hypothetical protein14.7676
fxsAb4140Suppress F exclusion of bacteriophage T713.42,475
  • a Fold change (FC) in biofilm (BF) was calculated from all 6 biofilm arrays using all 12 planktonic arrays as the baseline.

  • b Signal intensity was calculated from all six biofilm arrays treated as one single sample group.