Supplemental Table 1 List of genes induced and repressed more than 4.5-fold (P < 0.05) in biofilm cells of wild type BW25113 in LB after 7 h at 30°C vs. 37°C.
Group and gene / b number / Fold change / DescriptionIndole-related genes
tnaA / b3708 / 13.9 / tryptophan deaminase, PLP-dependent
tnaL / b3707 / 11.3 / tryptophanase leader peptide
tnaB / b3709 / 4.6 / low affinity tryptophan permease
UMP synthesis pathway and uracil transport
carA / b0032 / 6.1 / carbamoyl phosphate synthetase, glutamine amidotransferase small subunit
upp / b2498 / 5.3 / uracil phosphoribosyltransferase
pyrI / b4244 / 6.1 / aspartate carbamoyltransferase, regulatory subunit
pyrB / b4245 / 8.6 / aspartate carbamoyltransferase, catalytic subunit
Cell motility
flgB / b1073 / -12.1 / flagellar biosynthesis, cell-proximal portion of basal-body rod
flgI / b1080 / -18.4 / homolog of Salmonella P-ring of flagella basal body
motB / b1889 / -11.3 / enables flagellar motor rotation, linking torque machinery to cell wall
motA / b1890 / -5.3 / proton conductor component of motor, torque generator
fliD / b1924 / -5.3 / flagellar biosynthesis; filament capping protein, enables filament assembly
fliM / b1945 / -16.0 / flagellar biosynthesis, component of motor switch and energizing, enabling rotation and determining its direction
fliR / b1950 / -5.3 / flagellar biosynthesis
yehC / b2110 / -8.6 / putative chaperone
yfcV / b2339 / -9.2 / putative fimbrial-like protein
yraH / b3142 / -5.3 / putative fimbrial protein precursor
yhcD / b3216 / -5.3 / putative outer membrane protein
fimF / b4318 / -5.3 / fimbrial morphology
Cell wall/membrane biogenesis
crl / b0240 / 6.5 / transcriptional regulator of cryptic csgA gene for curli surface fibers
ompF / b0929 / 6.1 / outer membrane pore protein 1a (Ia;b;F)
ompA / b0957 / 6.1 / outer membrane protein 3a (II*;G;d)
spr / b2175 / 4.9 / putative lipoprotein
ompC / b2215 / 4.9 / outer membrane pore protein 1b (Ib;c)
Amino acid transport and metabolism
glnH / b0811 / 6.5 / high-affinity glutamine transport protein (ABC superfamily, peri_bind)
oppA / b1243 / 12.1 / oligopeptide transport protein (ABC superfamily, peri_bind)
oppB / b1244 / 7.0 / oligopeptide transport permease protein
ydcV / b1443 / 7.5 / putative ABC transporter permease protein
cstC / b1748 / 6.5 / acetylornithine delta-aminotransferase
Defense mechanisms
emrK / b2368 / -5.7 / multidrug resistance protein K
acrF / b3266 / -14.9 / integral transmembrane protein; acridine resistance
mcrC / b4345 / -6.5 / component of 5-methylcytosine-specific restriction enzyme McrBC
Signal transduction mechanisms
yeaG / b1783 / 5.3 / hypothetical protein
crp / b3357 / 4.6 / cyclic AMP receptor protein
uspA / b3495 / 5.3 / universal stress protein A
Inorganic ion transport and metabolism
cynT / b0339 / -5.3 / carbonic anhydrase
trkG / b1363 / -5.3 / Rac prophage; Trk system potassium uptake
sodB / b1656 / 4.6 / superoxide dismutase, iron
bfr / b3336 / 5.3 / bacterioferrin, an iron storage homoprotein
Replication, recombination and repair
t150 / b3558 / -6.1 / IS150 putative transposase
hupA / b4000 / 7.0 / DNA-binding protein HU-alpha (HU-2)
priB / b4201 / 4.9 / primosomal replication protein N
Transcription
cspD / b0880 / 5.3 / DNA replication inhibitor, nucleic acid-binding domain
umuD / b1183 / -4.6 / SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC
cspC / b1823 / 6.1 / cold shock protein
yfaH / b2238 / -4.6 / hypothetical protein
ygeH / b2852 / -9.2 / putative invasion (regulator) protein
rhaR / b3906 / -5.3 / positive regulator for rhaRS operon
cadC / b4133 / -5.3 / transcriptional activator of cad operon
Translation
rpsV / b1480 / 4.9 / 30S ribosomal subunit protein S22; stationary phase-induced ribosome-associated protein
infC / b1718 / 4.6 / protein chain initiation factor IF-3
thrS / b1719 / 4.9 / threonine tRNA synthetase
rplY / b2185 / 6.5 / 50S ribosomal subunit protein L25
rpsU / b3065 / 4.9 / 30S ribosomal subunit protein S21
yhbH / b3203 / 4.6 / probable sigma-54 modulation protein
rplM / b3231 / 5.3 / 50S ribosomal subunit protein L13
rpsE / b3303 / 4.6 / 30S ribosomal subunit protein S5
rplR / b3304 / 4.9 / 50S ribosomal subunit protein L18
rplF / b3305 / 5.3 / 50S ribosomal subunit protein L6
rpsH / b3306 / 5.3 / 30S ribosomal subunit protein S8, and regulator
rpsN / b3307 / 5.7 / 30S ribosomal subunit protein S14
rplE / b3308 / 5.3 / 50S ribosomal subunit protein L5
rplX / b3309 / 4.9 / 50S ribosomal subunit protein L24
rplN / b3310 / 4.9 / 50S ribosomal subunit protein L14
rplV / b3315 / 4.9 / 50S ribosomal subunit protein L22
rplB / b3317 / 4.9 / 50S ribosomal subunit protein L2
rplW / b3318 / 5.7 / 50S ribosomal subunit protein L23
rplD / b3319 / 5.3 / 50S ribosomal subunit protein L4, regulates expression of S10 operon
rplC / b3320 / 4.9 / 50S ribosomal subunit protein L3
rpsJ / b3321 / 4.9 / 30S ribosomal subunit protein S10
tufA / b3339 / 4.6 / protein chain elongation factor EF-Tu
fusA / b3340 / 4.6 / GTP-binding protein chain elongation factor EF-G
rpsG / b3341 / 5.7 / 30S ribosomal subunit protein S7, initiates assembly
rpsL / b3342 / 5.7 / 30S ribosomal subunit protein S12
rplK / b3983 / 4.9 / 50S ribosomal subunit protein L11
rplL / b3986 / 4.6 / 50S ribosomal subunit protein L7/L12
rpsF / b4200 / 4.9 / 30S ribosomal subunit protein S6
rpsR / b4202 / 5.7 / 30S ribosomal subunit protein S18
yjgF / b4243 / 5.7 / hypothetical protein
Lipid transport and metabolism
fabG / b1093 / 4.9 / 3-oxoacyl-[acyl-carrier-protein] reductase
acpP / b1094 / 6.1 / acyl carrier protein
Carbohydrate transport and metabolism
celB / b1737 / -6.1 / PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin
gapA / b1779 / 6.5 / glyceraldehyde-3-phosphate dehydrogenase A
manX / b1817 / 6.5 / PTS enzyme IIAB, mannose-specific
manY / b1818 / 6.1 / PTS enzyme IIC, mannose-specific
gnd / b2029 / 4.9 / gluconate-6-phosphate dehydrogenase, decarboxylating
gatC / b2092 / 6.5 / PTS family enzyme IIC, galactitol-specific
gatB / b2093 / 7.5 / PTS family enzyme IIB, galactitol-specific
gatA / b2094 / 7.5 / PTS family enzyme IIA, galactitol-specific
gatZ / b2095 / 8.6 / putative tagatose 6-phosphate kinase 1
gatY / b2096 / 4.6 / tagatose 6-phosphate aldolase 2, subunit with GatZ
mglB / b2150 / 8.6 / galactose transport protein (ABC superfamily, peri_bind)
ptsH / b2415 / 6.1 / PTS family Hpr protein, phosphohistidinoprotein-hexose phosphotransferase
yqaD / b2658 / -4.9 / hypothetical protein
pgk / b2926 / 4.9 / phosphoglycerate kinase
cmtB / b2934 / -4.9 / PTS family enzyme IIA, mannitol-specific, cryptic
agaI / b3141 / -4.9 / putative galactosamine-6-phosphate isomerase
yhfC / b3364 / -4.6 / putative transport
glvC / b3683 / -4.6 / PTS family enzyme IIC, glucose-glucoside-specific (arbutin-like)
rbsB / b3751 / 4.9 / D-ribose periplasmic binding protein
malE / b4034 / 5.3 / maltose transport protein, chemotaxis (ABC superfamily, peri_bind)
lamB / b4036 / 4.9 / maltoporin, high-affinity receptor for maltose and maltoseoligosaccharides; phage lambda receptor
Nucleotide transport and metabolism
adk / b0474 / 5.7 / adenylate kinase
ndk / b2518 / 6.1 / nucleoside diphosphate kinase
ygfP / b2883 / -4.9 / guanine deaminase
deoD / b4384 / 5.3 / purine-nucleoside phosphorylase
Amino acid transport and metabolism
aspC / b0928 / 4.6 / aspartate aminotransferase
oppC / b1245 / 5.7 / homolog of Salmonella oligopeptide transport permease protein
ydcS / b1440 / 4.6 / putative ABC transporter periplasmic binding protein
gatD / b2091 / 4.6 / galactitol-1-phosphate dehydrogenase
yqeG / b2845 / -4.9 / putative transport protein (HAAAP family)
gcvH / b2904 / 6.1 / glycine cleavage complex protein H, carrier of aminomethyl moiety via covalently bound lipoyl cofactor
gcvT / b2905 / 5.7 / aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system
yjdE / b4115 / -9.2 / putative amino acid/amine transport protein, cryptic
adiA / b4117 / -5.3 / arginine decarboxylase; inducible by acid, catabolic
cadA / b4131 / -6.1 / lysine decarboxylase 1
Energy production and conversion
cyoB / b0431 / 5.7 / cytochrome o ubiquinol oxidase subunit I
cyoA / b0432 / 7.0 / cytochrome o ubiquinol oxidase subunit II
ylbC / b0517 / -4.9 / ureidoglycolate dehydrogenase
sdhC / b0721 / 4.6 / succinate dehydrogenase, cytochrome b556
sdhD / b0722 / 6.1 / succinate dehydrogenase, hydrophobic subunit
sdhA / b0723 / 4.6 / succinate dehydrogenase, catalytic and NAD/flavoprotein subunit
sucA / b0726 / 5.3 / 2-oxoglutarate decarboxylase, component of the 2-oxoglutarate dehydrogenase complex, thiamin-binding
sucB / b0727 / 5.3 / 2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component)
sucC / b0728 / 4.9 / succinyl-CoA synthetase, beta subunit
icdA / b1136 / 5.7 / e14 prophage; isocitrate dehydrogenase, specific for NADP+
aldA / b1415 / 5.3 / aldehyde dehydrogenase A, NAD-linked
ydcW / b1444 / 7.5 / putative aldehyde dehydrogenase
osmC / b1482 / 4.9 / osmotically inducible protein
ydiQ / b1697 / -5.3 / putative electron transfer flavoprotein
ydiT / b1700 / -12.1 / hypothetical protein
nuoB / b2287 / 4.6 / NADH dehydrogenase I chain B
yfdW / b2374 / -11.3 / putative enzyme
mdh / b3236 / 5.7 / malate dehydrogenase
atpG / b3733 / 4.9 / membrane-bound ATP synthase, F1 sector, gamma-subunit
atpH / b3735 / 5.7 / membrane-bound ATP synthase, F1 sector, delta-subunit
atpF / b3736 / 6.1 / membrane-bound ATP synthase, F0 sector, subunit b
atpE / b3737 / 5.3 / membrane-bound ATP synthase, F0 sector, subunit c
atpB / b3738 / 4.9 / membrane-bound ATP synthase, F0 sector, subunit a
osmY / b4376 / 5.7 / hyperosmotically inducible periplasmic protein
General function prediction only
leuO / b0076 / -5.7 / probable transcriptional activator for leuABCD operon
yadK / b0136 / -5.7 / putative adhesin-like protein
yaeF / b0193 / -5.7 / hypothetical protein
yahO / b0329 / 9.8 / hypothetical protein
b0370 / b0370 / -4.6 / hypothetical protein
gcl / b0507 / -4.6 / glyoxylate carboligase
b0538 / b0538 / -6.1 / DLP12 prophage; putative sensory transduction regulator
ybcQ / b0551 / -4.6 / DLP12 prophage; putative antitermination protein Q
ybcV / b0558 / -9.2 / DLP12 prophage; putative envelope protein
ybcY / b0562 / -8.0 / DLP12 prophage; homolog of phage 21 head protein, putative methylase
ybeL / b0643 / 4.6 / hypothetical protein
ybeT / b0647 / -4.6 / hypothetical protein
ybfL / b0705 / -7.5 / putative receptor protein
ybfD / b0706 / -8.0 / hypothetical protein
ybgS / b0753 / 5.3 / hypothetical protein
ycaC / b0897 / 7.5 / hypothetical protein
yccE / b1001 / -4.9 / hypothetical protein
wrbA / b1004 / 4.6 / flavodoxin-like protein, trp repressor-binding protein
ycdF / b1005 / 6.1 / hypothetical protein
ycdU / b1029 / -7.5 / hypothetical protein
msyB / b1051 / 6.1 / acidic protein suppresses mutants lacking function of protein export
yceD / b1088 / 4.6 / hypothetical protein
lit / b1139 / -5.3 / e14 prophage; like phage T4 late gene expression
ymfM / b1148 / -4.9 / e14 prophage
ycgG / b1168 / -7.0 / hypothetical protein
ycgH_1 / b1169 / -4.9 / conserved protein; member of the Autotransporter family
hns / b1237 / 6.1 / DNA-binding protein HLP-II (HU, BH2, HD, NS); pleiotropic regulator
oppD / b1246 / 5.7 / homolog of Salmonella ATP-binding protein of oligopeptide ABC transport system
ydaQ / b1346 / -6.5 / Rac prophage
ydaS / b1357 / -5.7 / Rac prophage; repressor protein
rzpR / b1362 / -4.9 / Rac prophage; putative prophage lambda endopeptidase
ynaE / b1375 / -5.3 / Rac prophage
ynaF / b1376 / 8.6 / conserved hypothetical protein, adenine nucleotide-binding domain
yddK / b1471 / -12.1 / putative glycoportein
yddB / b1495 / -5.7 / hypothetical protein
yneK / b1527 / -4.9 / hypothetical protein
ydfO / b1549 / -5.3 / Qin prophage
dicB / b1575 / -4.9 / Qin prophage; inhibitior of cell division
ydfD / b1576 / -7.0 / Qin prophage
ydiN / b1691 / -8.0 / putative amino acid/amine transport protein
pheM / b1715 / -9.2 / phenylalanyl-tRNA synthetase (pheST) operon leader peptide
arpB_1 / b1720 / -6.5 / hypothetical protein
katE / b1732 / 4.6 / catalase; hydroperoxidase HPII (III), RpoS-dependent
ydjC / b1733 / -4.6 / hypothetical protein
osmE / b1739 / 4.9 / activator of ntrL gene
yeaC / b1777 / 5.7 / hypothetical protein
yeaA / b1778 / 6.1 / hypothetical protein
yobF / b1824 / 4.6 / hypothetical protein
yebF / b1847 / 4.6 / hypothetical protein
yedM / b1935 / -9.2 / hypothetical protein
yodB / b1974 / -4.6 / cytochrome b561 homolog 1
yeeL_2 / b1979 / -4.9 / putative transport protein
yehA / b2108 / -4.6 / hypothetical protein
molR_1 / b2115 / -6.5 / molybdate metabolism regulator, interrupted
elaB / b2266 / 6.1 / hypothetical protein
elaD / b2269 / -4.6 / hypothetical protein
yfbN / b2273 / -6.5 / hypothetical protein
yfbO / b2274 / -8.0 / hypothetical protein
yfbP / b2275 / -5.3 / hypothetical protein
nuoA / b2288 / 4.9 / NADH dehydrogenase I chain A
ypdI / b2376 / -4.6 / hypothetical protein
hyfC / b2483 / -7.0 / hydrogenase 4 membrane subunit
b2596 / b2596 / -7.5 / hypothetical protein
yfjZ / b2645 / -4.9 / CP4-57 prophage
pinH / b2648 / -10.6 / homolog of pin/cin, phage invertible sequence
ygaM / b2672 / 4.6 / hypothetical protein
ygcJ / b2758 / -5.7 / hypothetical protein
ygcG / b2778 / -8.0 / hypothetical protein
ygdI / b2809 / 4.9 / hypothetical protein
yqeK / b2849 / -8.6 / hypothetical protein
ygeG / b2851 / -8.6 / hypothetical protein
ygeI / b2853 / -7.5 / hypothetical protein
ygeO / b2858 / -5.3 / hypothetical protein
ygeO / b2859 / -6.1 / hypothetical protein
ygiW / b3024 / 5.3 / hypothetical protein
yqiH / b3047 / -5.3 / putative membrane protein
yqiI / b3048 / -4.9 / hypothetical protein
glgS / b3049 / 5.3 / glycogen biosynthesis, rpoS dependent
yqjC / b3097 / 5.3 / hypothetical protein
yqjD / b3098 / 6.1 / hypothetical protein
smg / b3284 / 4.9 / hypothetical protein
yhfL / b3369 / -5.7 / hypothetical protein
yhhH / b3483 / -6.1 / hypothetical protein
yhiJ / b3488 / -4.6 / hypothetical protein
yhiL / b3490 / -4.9 / hypothetical protein
yhiM / b3491 / -4.9 / hypothetical protein
yiaA / b3562 / -6.5 / hypothetical protein
yiaB / b3563 / -7.0 / hypothetical protein
yiaW / b3587 / -5.7 / hypothetical protein
aldB / b3588 / 5.7 / aldehyde dehydrogenase B (lactaldehyde dehydrogenase)
yidG / b3675 / -4.6 / hypothetical protein
yigG / b3818 / -5.7 / hypothetical protein
yihG / b3862 / -7.0 / putative endonuclease
yiiE / b3889 / -5.7 / hypothetical protein
sodA / b3908 / 4.6 / superoxide dismutase, manganese
b3975 / b3975 / -7.0 / hypothetical protein
yjbJ / b4045 / 5.3 / hypothetical protein
yjcB / b4060 / -4.6 / hypothetical protein
yjdJ / b4127 / 4.6 / hypothetical protein
ytfI / b4215 / -5.3 / hypothetical protein
yjgG / b4247 / -9.2 / hypothetical protein
yjgN / b4257 / -6.5 / hypothetical protein
yjhD / b4281 / -5.7 / KpLE2 phage-like element; conserved hypothetical protein
yjiH / b4330 / -4.6 / hypothetical protein
yjjM / b4357 / -6.5 / hypothetical protein
yjjB / b4363 / -9.2 / hypothetical protein
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