TABLE 3.

Top 50 most expressed 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 productSignal intensityaFC in BFb
rrfHb02055S rRNA11,2231.2
rrlGZ387523S rRNA9,568−1.0
rrsGb259116S rRNA8,0621.1
ssrAb262110Sa RNA (tmRNA); tags incomplete translation products for degradation7,9241.1
ssrSb29116S RNA7,6014.6
rnpBb3123RNase P, RNA component; M1 RNA7,5591.2
csrBb4408CsrB regulatory RNA6,6381.2
ahpCb0605Alkyl hydroperoxide reductase, detoxification of hydroperoxides6,6221.3
rhoLb3782rho operon leader peptide6,4761.8
cspAb3556Cold shock protein 7.4, transcriptional activator of hns6,38715.9
ibpAb3687Heat shock protein6,1208.7
t44b4414Small toxic membrane polypeptide6,0251.0
folEb2153GTP cyclohydrolase I5,9421.2
ybiJb0802Hypothetical protein5,8178.2
ycfRb1112Hypothetical protein5,8049.3
yhcNb3238Hypothetical protein5,79017.3
ibpBb3686Heat shock protein5,78733.6
bfdb3337Regulatory or redox component complexing with Bfr, in iron storage and mobility5,5825.2
rplUb318650S ribosomal subunit protein L215,5481.1
rplNb331050S ribosomal subunit protein L145,323−1.0
dpsb0812Global regulator, starvation conditions5,2742.6
trxCb2582Putative thioredoxin-like protein5,2358.1
marAb1531Multiple antibiotic resistance; transcriptional activator of defense systems5,1648.2
furb0683Negative regulator5,1452.7
asnAb3744Asparagine synthetase A5,1295.5
yhaKb3106Predicted pirin-related protein5,10312.1
dnaKb0014Chaperone Hsp70 in DNA biosynthesis/cell division5,1011.7
csrCb4457CsrC regulatory RNA5,0141.3
fnrb1334Transcriptional regulation of aerobic, anaerobic respiration, osmotic balance4,9812.1
rplMb323150S ribosomal subunit protein L134,955−1.1
marRb1530Multiple antibiotic resistance protein; repressor of mar operon4,85931.5
rhob3783Transcription termination factor Rho; polarity suppressor4,7681.9
ffsb04554.5S RNA; component of ribonucleoprotein particle4,7525.9
rpoDb3067RNA polymerase, sigma 70 factor4,7512.1
glgSb3049Glycogen biosynthesis, rpoS dependent4,7475.3
groEb4142GroES, binds to Hsp60 in presence of Mg-ATP, suppressing its ATPase activity4,7311.2
nlpIb3163NlpI lipoprotein involved in cell division4,6983.7
infCZ2747Initiation factor IF-34,677−1.1
grxAb0849Glutaredoxin 1 redox coenzyme for glutathione-dependent ribonucleotide reductase4,67521.1
cspGb0990Homolog of Salmonella cold shock protein4,65980.7
rpmHb370350S ribosomal subunit protein L344,6481.8
bfrb3336Bacterioferrin, an iron storage homoprotein4,6444.5
yhhWc4228Protein YhhW, putative pirin protein4,64412.3
pdhRb0113Transcriptional regulator for pyruvate dehydrogenase complex4,5905.5
rplKb398350S ribosomal subunit protein L114,576−1.2
iscRb2531Fe-S cluster-containing transcription factor4,5642.3
rseAb2572Sigma E (sigma 24) factor, negative regulator4,5301.9
yceDb1088Hypothetical protein4,522−1.0
ryhBb4451Regulatory RNA mediating Fur regulon4,5092.4
Z5401Z5401Hypothetical protein4,4851.3
  • a Signal intensity was calculated from all six biofilm arrays treated as one single sample group.

  • b Fold change (FC) in biofilm (BF) was calculated from all 6 biofilm arrays using all 12 planktonic arrays as the baseline. Boldface indicates significant change.