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 |