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Table 2 Partial list of genes induced and repressed more than 2-fold after 24 h in (i) K-12 yceP biofilms upon addition of 600 μM indole in LB glu medium (experiment performed in duplicate, and one standard deviation is shown), (ii) K-12 biofilms due to the trpE mutation in LB glu medium, and (iii) K-12 biofilms due to the tnaA mutation in LB medium.

From: Indole is an inter-species biofilm signal mediated by SdiA

Gene b # Fold change upon indole addition Fold change upon trpE deletion Fold change upon tnaA deletion Description Protein Size, aa
Transcription
sdiA b 1916 2.9 ± 0.8 1.0* 1.2 AHL transcriptional activator (LuxR/TraR family) 240
ygaV b 2667 2.2 ± 0.2 1.1* -1.1* hypothetical protein 99
soxS b 4062 2.3 ± 0.3 -2.8 -1.2 regulation of superoxide response regulon 107
cspA b 3556 1.8 ± 0.4 -4.6 -1.2* cold shock protein 7.4, transcriptional activator of hns 70
mtlR b 3601 1.3* ± 0.4 -2.6 -1.4* MtlR transcriptional repressor 195
yjcT b 4084 -1.1* ± 0.1 1.5* -3.5 D-allose kinase 309
rhoL b 3782 2.2 ± 0.1 -1.1* 1.1* rho operon leader peptide 33
Cell motility and secretion
hha b 0460 4.9 ± 0.0 -1.4 -1.4 haemolysin expression modulating protein 72
ybaJ b 0461 5.2 ± 0.8 -1.1* 1.0* conserved hypothetical protein 124
mqsR b 3022 2.8 ± 0.7 1.1* 1.4 master regulator of chemotaxis via AI-2; interacts with QseB 98
sfmA b 0530 -1.3* ± 0.1 1.0* -2.3 putative fimbrial-like protein 191
sfmC b 0531 -1.1* ± 0.1 -1.1* -2.3 putative chaperone 230
sfmH b 0533 -1.2* ± 0.1 1.1* -2.0 fimbrial assembly protein 325
flgA b 1072 1.1* ± 0.1 1.2* -2.1 flagellar biosynthesis; assembly of basal-body periplasmic P ring 219
yehA b 2108 1.1* ± 0.0 -1.1* -2.1 hypothetical protein 344
yhcA b 3215 1.1* ± 0.0 -1.7 -2.0 putative chaperone 224
yfcP b 2333 1.1* ± 0.1 1.3* -2.0 putative fimbrial-like protein 179
Colanic acid synthesis genes
ypdI b 2376 -1.2* ± 0.2 1.3* -2.5 YpdI colanic acid synthesis lipoprotein 91
Acid resistance
gadE b 3512 -4.3 ± 1.4 -1.6 1.1* activator of acid resistance genes and putative LuxR transcriptional activator 175
gadA b 3517 -4.0 ± 1.3 -2.3 1.2* glutamate decarboxylase A, isozyme, PLP-dependent 466
gadB b 1493 -2.8 ± 0.7 -2.6 1.2* glutamate decarboxylase isozyme 466
gadC b 1492 -3.7 ± 0.0 -1.6 1.2* acid sensitivity protein, putative transporter, encoding a γ-aminobutyrate antiporter 511
gadX b 3516 -2.0 ± 0.4 -1.2 -1.2 activator of gadA and gadBC 274
hdeA b 3510 -4.8 ± 0.2 -2.3 1.0* periplasmic chaperone of acid-denatured protein 110
hdeB b 3509 -3.9 ± 0.6 -2.3 1.2* 10K-L protein, periplasmic protein related to acid resistance protein 112
hdeD b 3511 -3.0 ± 0.5 -1.6 -1.5 protein involved in acid resistance 190
Phage-related genes
cspI b 1552 1.8 ± 0.7 1.0* -3.7 Qin prophage; cold shock-like protein 70
ypjF b 2646 1.4* ± 0.2 1.2* -12.1 CP4-57 prophage 109
ymfI b 1143 1.1* ± 0.1 1.1* -5.7 E14 prophage 113
ydaY b 1366 1.0* ± 0.0 1.0* -4.6 Rac prophage 119
ydfP b 1553 -1.2* ± 0.2 1.2* -2.6 Qin prophage 165
ydfE b 1577 1.0* ± 0.1 1.3* -2.5 Qin prophage 255
yeeV b 2005 -1.5* ± 0.5 1.1* -2.5 CP4-44 prophage 124
stfE b 1157 1.4* ± 0.4 -1.1* -2.3 E14 prophage; putative tail fiber protein 166
b 1364 b 1364 1.2* ± 0.1 1.1* -2.3 Rac prophage 93
yfjW b 2642 1.4* ± 0.4 -1.1* -2.1 CP4-57 prophage 567
yeeU b 2004 1.0* ± 0.0 -1.1* -2.0 CP4-44 prophage; putative structural protein 122
yfjT b 2637 -1.4* ± 0.6 1.1* -2.0 CP4-57 prophage 155
ynaE b 1375 1.8 ± 0.6 -1.9 -2.0 Rac prophage 88
Amino acid transport and metabolism
tnaA b 3708 1.7 ± 0.0 -1.3* -14.9 tryptophan deaminase, PLP-dependent 476
tnaC b 3707 1.5 ± 1.1 1.1* 32.0 tryptophanase leader peptide 24
mtr b 3161 -1.1* ± 0.1 -1.3 -5.7 Mtr tryptophan ArAAP transporter 414
aroP b 0112 1.0* ± 0.0 -1.2* -5.3 AroP phenylalanine/tyrosine/tryptophan APC transporter 457
proC b 0386 -1.2 ± 0.0 1.0* -3.0 pyrroline-5-carboxylate-reductase 269
Carbohydrate transport and metabolism
melB b 4120 1.2* ± 0.1 1.1* -7.5 melibiose permease II 469
eno b 2779 -1.9 ± 0.2 -1.2* 1.1* Enolase 432
yegB b 2077 -1.2* ± 0.2 1.1* -3.2 multidrug transport protein (MFS family)  
prpB b 0331 -2.4 ± 0.6 -1.1* 1.0* putative carboxyphosphonoenolpyruvate mutase 296
Other metabolism
htrL b 3618 2.2 ± 0.1 1.1* -1.2* involved in lipopolysaccharide biosynthesis 290
pyrG b 2780 -2.2 ± 0.2 1.0* 1.0* CTP synthetase 545
pheL b 2598 -1.2 ± 0.1 -4.9 2.3 chorismate mutase-P-prephenate dehydratase leader peptide 15
yodA b 1973 1.5 ± 0.4 1.0* -7.5 cadmium-induced metal binding protein 216
chaA b 1216 -1.4* ± 0.4 1.2* -7.0 sodium-calcium/proton antiporter 366
nhaA b 0019 -1.2* ± 0.0 -1.4 -3.2 Na+/H antiporter, pH dependent 388
ybdS b 0612 -1.3* ± 0.3 -1.2* -3.2 citrate carrier 487
Energy production and conversion
rsxA b 1627 1.1* ± 0.0 -1.1* -14.9 integral membrane protein of SoxR-reducing complex 193
ynbA b 1408 1.1* ± 0.0 1.4* -4.6 putative diacylglycerol cholinephosphotransferase 203
Posttranslational modification, protein turnover, chaperones
htpX b 1829 2.8 ± 1.1 -1.1* 1.1* heat shock protein, integral membrane protein 293
Translation
ksgA b 0051 -1.9 ± 0.6 -1.3* -3.0 S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase 273
infA b 0884 1.0* ± 0.1 -1.3* -3.0 protein chain initiation factor IF-1 72
Defense mechanisms
soda b 3908 1.2* ± 0.3 -3.2 1.1* superoxide dismutase, manganese 206
Poorly-characterized genes
ycfR b 1112 2.7 ± 0.8 1.0* -1.4 hypothetical protein 85
ylaD b 0459 2.3 ± 0.3 1.0* -2.8* maltose O-acetyltransferase 183
yebE b 1846 2.4 ± 0.1 1.1* -2.1 hypothetical protein 219
yncJ b 1436 2.7 ± 0.5 -1.1* -1.2 hypothetical protein 76
yejG b 2181 2.4 ± 0.4 -1.5 -1.2* hypothetical protein 114
ybjM b 0848 -1.3* ± 0.3 -1.4 -8.6 hypothetical protein 125
b 0309 b 0309 -1.5* ± 0.6 -1.4 -4.6 hypothetical protein 70
ypjB b 2649 1.1* ± 0.0 1.2* -3.7 hypothetical protein 263
apaG b 0050 -2.2 ± 0.9 -1.3 -3.7 hypothetical protein 125
ydiY b 1722 -1.1* ± 0.1 1.2* -3.5 hypothetical protein 252
ymfA b 1122 -1.1* ± 0.1 1.0* -3.5 hypothetical protein 156
yeiU b 2174 1.2* ± 0.1 -1.2* -3.0 hypothetical protein 249
yahO b 0329 -1.8 ± 0.4 1.3 1.3 hypothetical protein 91
psiF b 0384 -1.9 ± 0.3 -1.1* -1.3 induced by phosphate starvation; pho regulon member, requiring phoRB system 112
ycdF b 1005 -2.0 ± 0.1 1.1* -1.2 hypothetical protein 76
yciG b 1259 -2.1 ± 0.1 1.2* 1.6 hypothetical protein 78
ycgZ b 1164 -2.9 ± 0.6 1.3 1.7 hypothetical protein 78
ymgC b 1167 -2.1 ± 0.3 1.2* 1.5 hypothetical protein 82
ymgA b 1165 -2.4 ± 1.3 1.1 1.7 hypothetical protein 90
ymgB b 1166 -5.2 ± 1.3 1.2 1.5 hypothetical protein, putative acid-resistance protein 88
  1. Full data available using GEO accession number 4562. Asterisk indicates p value greater than 0.05 (data are less reliable but included for completeness). Negative values indicate repressed genes. b # indicates the Blattner number for each gene. Boldface indicates most significant fold changes.