Acetyl Phosphate Functions as a Global Signal
during Biofilm Development
Supplemental Tables
Table 1. Genes significantly up-regulated in a pta
ackA mutant compared to an ackA mutant
|
Gene
|
b#
|
Pta/Ack
ratio
|
Pta/Ack
log10
|
Pta/WT
ratio
|
Pta/WT
log10
|
Ack/WT
ratio
|
Ack/WT
log10
|
Gene Product |
Flagellar regulon
| fliC |
1923 |
30.93 |
1.49
|
11.76 |
1.07
|
-2.63
|
-0.42
|
flagellin (filament) |
| flgE |
1076 |
8.89
|
0.95
|
3.95
|
0.60
|
-2.25
|
-0.35
|
hook |
| fliD |
1924 |
5.81
|
0.76
|
4.12
|
0.62
|
-1.41
|
-0.15
|
filament cap |
| flgC |
1074 |
5.49
|
0.74
|
3.10
|
0.49
|
-1.77
|
-0.25
|
basal body-rod |
| flgB |
1073 |
5.41
|
0.73
|
2.64
|
0.42
|
-2.05
|
-0.31
|
basal body-rod |
| flgK |
1082 |
4.13
|
0.62
|
3.15
|
0.50
|
-1.31
|
-0.12
|
hook-filament junction |
| flgG |
1078 |
4.09
|
0.61
|
2.45
|
0.39
|
-1.67
|
-0.22
|
basal body-rod |
| flgD |
1075 |
3.55
|
0.55
|
2.18
|
0.34
|
-1.63
|
-0.21
|
hook assembly initiation |
| flgL |
1083 |
3.37
|
0.53
|
2.36
|
0.37
|
-1.43
|
-0.16
|
hook-filament junction |
| fliA |
1922 |
3.42
|
0.53
|
1.89
|
0.28
|
-1.81
|
-0.26
|
flagellar-specific regulation; sigma factor |
| fliL |
1944 |
3.13
|
0.50
|
1.35
|
0.13
|
-2.32
|
-0.37
|
flagellar biosynthesis |
| flgA |
1072 |
2.72
|
0.42
|
1.60
|
0.20
|
-1.70
|
-0.23
|
basal body assembly |
| flgF |
1077 |
2.49
|
0.40
|
1.79
|
0.25
|
-1.39
|
-0.14
|
basal body-rod |
| fliM |
1945 |
2.49
|
0.40
|
1.50
|
0.17
|
-1.66
|
-0.22
|
motor switch; energy transduction |
| cheY |
1882 |
2.33
|
0.37
|
2.33
|
0.37
|
1.00
|
0 |
chemotactic signaling |
| tar |
1886 |
2.15
|
0.33
|
1.94
|
0.29
|
-1.11
|
-0.05
|
chemoreceptor |
| flgJ |
1081 |
2.11
|
0.32
|
1.80
|
0.26
|
-1.17
|
-0.07
|
flagellar biosynthesis |
| flhC |
1891 |
1.92
|
0.28
|
1.30
|
0.11
|
-1.48
|
-0.17
|
with FlhD, activator of flagellar biosynthesis |
| fliS |
1925 |
1.82
|
0.26
|
1.16
|
0.06
|
-1.57
|
-0.20
|
repressor of class 3a and 3b operons |
| cheB |
1883 |
1.68
|
0.22
|
1.66
|
0.22
|
-1.01
|
<-0.01 |
chemotactic signaling |
| flgN |
1070 |
1.67
|
0.22
|
-1.38
|
-0.14
|
-2.30
|
-0.36
|
chaperone of flagellar biosynthesis |
| cheZ |
1881 |
1.65
|
0.22
|
1.95
|
0.29
|
1.18
|
0.07
|
chemotactic signaling |
| cheR |
1884 |
1.61
|
0.21
|
1.80
|
0.25
|
1.12
|
0.05
|
chemotactic signaling |
| flhB |
1880 |
1.61
|
0.21
|
-1.03
|
-0.02
|
-1.66
|
-0.22
|
putative part of flagellar export apparatus |
| fliZ |
1921 |
1.57
|
0.20
|
1.47
|
0.17
|
-1.07
|
-0.03
|
hypothetical ORF |
| fliY |
1920 |
1.56
|
0.19
|
1.93
|
0.29
|
1.24
|
0.10
|
putative periplasmic binding transport |
| trg |
1421 |
1.54
|
0.19
|
1.57
|
0.20
|
1.02
|
<0.01
|
chemoreceptor |
| motB |
1889 |
1.53
|
0.19
|
1.17
|
0.07
|
-1.31
|
-0.12
|
energy transduction |
| fliI |
1941 |
1.46
|
0.17
|
1.22
|
0.09
|
-1.20
|
-0.08
|
flagellar biosynthesis; flagellum-specific ATP synthase |
| fliJ |
1942 |
1.44
|
0.16
|
-1.09
|
-0.04
|
-1.57
|
-0.20
|
flagellar biosynthesis |
| fliK |
1943 |
1.43
|
0.15
|
1.24
|
0.09
|
-1.15
|
-0.06
|
flagellar biosynthesis; flagellar hook length control protein |
| flhD |
1892 |
1.42
|
0.15
|
-1.89
|
-0.28
|
-2.68
|
-0.43
|
with FlhC, activator of flagellar biosynthesis |
Other genes
| rbsB |
3751 |
1.86
|
0.27
|
1.95
|
0.29
|
1.05
|
0.02
|
D-ribose periplasmic binding protein |
| b1966 |
1966 |
1.74
|
0.24
|
1.24
|
0.09
|
-1.40
|
-0.15
|
Putative outer membrane protein |
| prsA |
1207 |
1.69
|
0.23
|
1.79
|
0.25
|
1.06
|
0.03
|
phosphoribosylpyrophosphate synthetase |
| purU |
1232 |
1.68
|
0.23
|
1.97
|
0.30
|
1.17
|
0.07
|
Formyltetrahydrofolate deformylase; for purT-dependent FGAR
synthesis |
| ompF |
0929 |
1.68
|
0.22
|
-1.68
|
-0.23
|
-2.82
|
-0.45
|
outer membrane protein 1a; porin |
| ompC |
2215 |
1.66
|
0.22
|
1.46
|
0.16
|
-1.14
|
-0.06
|
outer membrane protein 1b; porin |
| malT |
3418 |
1.59
|
0.20
|
-1.72
|
-0.23
|
-2.73
|
-0.44
|
positive regulator of mal regulon |
| caiF |
0034 |
1.56
|
0.19
|
2.72
|
0.43
|
1.74
|
0.24
|
transcriptional regulator of cai operon |
| yqiH |
3047 |
1.54
|
0.19
|
-1.61
|
-0.21
|
-2.48
|
-0.39
|
putative membrane protein |
|
|
|
|
|
|
|
|
|
| glpD |
3426 |
1.53
|
0.19
|
1.38
|
0.14
|
-1.11
|
-0.04
|
sn-glycerol-3-phosphate dehydrogenase (aerobic) |
| rplV |
3315 |
1.51
|
0.18
|
1.62
|
0.21
|
1.07
|
0.03
|
50S ribosomal subunit protein L22 |
| dnaK |
0014 |
1.46
|
0.16
|
2.68
|
0.43
|
1.84
|
0.27
|
chaperone Hsp70 |
| caiD |
0036 |
1.45
|
0.16
|
-1.40
|
-0.15
|
-2.03
|
-0.31
|
carnitine racemase |
| mopB |
4142 |
1.44
|
0.16
|
2.21
|
0.35
|
0.53
|
0.19
|
chaperone GroES; binds Hsp60 |
| rfbX |
2037 |
1.42
|
0.15
|
2.10
|
0.32
|
1.48
|
0.17
|
putative O-antigen transporter |
| rbsD |
3748 |
1.40
|
0.15
|
-3.53
|
-0.55
|
-4.95
|
-0.69
|
D-ribose high-affinity transport system |
| b3027 |
3027 |
1.40
|
0.15
|
-1.36
|
-0.13
|
-1.90
|
-0.28
|
hypothetical protein |
| mopA |
4143 |
1.41
|
0.15
|
1.47
|
0.17
|
1.04
|
0.02
|
chaperone GroEL/Hsp60 |
Table 2. Genes significantly up-regulated in an ackA mutant
compared to a pta ackA mutant.
|
Gene
|
b#
|
Pta/Ack
ratio
|
Pta/Ack
log10
|
Pta/WT
ratio
|
Pta/WT
log10
|
Ack/WT
ratio
|
Ack/WT
log10
|
Gene Product |
Genes that respond positively to AcP
| osmB |
1283 |
-10.85
|
-1.03
|
-1.07
|
-0.03
|
10.14
|
1.01
|
osmotically inducible lipoprotein |
| yjbE |
4026 |
-3.55
|
-0.55
|
1.01
|
<0.01
|
3.59
|
0.56
|
hypothetical protein |
| rcsA |
1951 |
-3.51
|
-0.55
|
1.02
|
<0.01
|
3.58
|
0.55
|
colanic acid biosynthesis, positive regulator |
| wcaE |
2055 |
-3.49
|
-0.54
|
-1.07
|
-0.03
|
3.26
|
0.51
|
colanic acid biosynthesis, putative glycosyl transferase |
| gmd |
2053 |
-3.35
|
-0.53
|
-1.11
|
-0.05
|
3.02
|
0.48
|
colanic acid biosynthesis, GDP-D-mannose dehydratase, |
| ycfJ |
1110 |
-2.55
|
-0.41
|
1.01
|
<0.01
|
2.58
|
0.41
|
hypothetical protein |
| ybdG |
0577 |
-2.15
|
-0.33
|
-1.12
|
-0.05
|
1.92
|
0.28
|
putative transport protein |
| fimC |
4316 |
-2.12
|
-0.33
|
-1.05
|
-0.02
|
2.02
|
0.31
|
type I pilus; periplasmic chaperone |
| b2833 |
2833 |
-2.06
|
-0.31
|
1.07
|
0.03
|
2.20
|
0.34
|
hypothetical protein |
| eco |
2209 |
-2.02
|
-0.31
|
-1.06
|
-0.02
|
1.91
|
0.28
|
ecotin; serine protease inhibitor |
| ydhA |
1639 |
-1.96
|
-0.29
|
1.05
|
0.02
|
2.06
|
0.31
|
hypothetical protein |
| b1171 |
1171 |
-1.92
|
-0.28
|
1.09
|
0.04
|
2.09
|
0.32
|
hypothetical protein |
| b2391 |
2391 |
-1.83
|
-0.26
|
-1.08
|
-0.03
|
1.69
|
0.23
|
hypothetical protein |
| b1550 |
1550 |
-1.82
|
-0.26
|
1.09
|
0.04
|
1.98
|
0.30
|
hypothetical protein |
| wcaD |
2056 |
-1.73
|
-0.24
|
-1.14
|
-0.06
|
1.52
|
0.18
|
colanic acid biosynthesis, putative polymerase |
| menC |
2261 |
-1.59
|
-0.20
|
-1.09
|
-0.04
|
1.46
|
0.17
|
o-succinylbenzoyl-CoA synthase |
| yafY |
0251 |
-1.52
|
-0.18
|
1.05
|
0.02
|
1.60
|
0.20
|
hypothetical protein |
| ygaC |
2671 |
-1.49
|
-0.17
|
-1.00
|
<-0.01
|
1.49
|
0.17
|
hypothetical protein |
| ugd |
2028 |
-1.44
|
-0.16
|
1.00
|
<0.01
|
1.44
|
0.16
|
colanic acid biosynthesis; UDP-glucose 6-dehydrogenase |
| b1592 |
1592 |
-1.43
|
-0.16
|
1.15
|
0.06
|
1.65
|
0.22
|
putative chloride channel |
Genes that respond positively to both AcCoA and AcP
| yfkE |
0220 |
-5.48
|
-0.74
|
1.96
|
0.29
|
10.75
|
1.03
|
hypothetical protein |
| osmY |
4376 |
-4.63
|
-0.67
|
1.77
|
0.25
|
8.19
|
0.91
|
hyperosmotically inducible periplamic protein |
| yafP |
0234 |
-3.41
|
-0.53
|
1.21
|
0.08
|
4.13
|
0.62
|
hypothetical protein |
| sfmC |
0531 |
-2.71
|
-0.43
|
1.26
|
0.10
|
3.41
|
0.53
|
putative fimbrial chaperone |
| fimG |
4319 |
-2.70
|
-0.43
|
1.82
|
0.26
|
4.92
|
0.69
|
type I pilus; morphology |
| b1172 |
1172 |
-2.66
|
-0.43
|
1.30
|
0.11
|
3.46
|
0.54
|
hypothetical protein |
| osmC |
1482 |
-2.63
|
-0.42
|
1.39
|
0.14
|
3.65
|
0.56
|
osmotically inducible protein |
| dps |
0812 |
-2.35
|
-0.37
|
3.52
|
0.55
|
8.27
|
0.92
|
starvation, gobal regulator |
| hslJ |
1379 |
-2.29
|
-0.36
|
1.37
|
0.14
|
3.14
|
0.50
|
heat shock protein |
| fimI |
4315 |
-2.28
|
-0.36
|
1.63
|
0.21
|
3.72
|
0.57
|
type I pilus; minor protein? |
| fimA |
4314 |
-2.18
|
-0.34
|
1.68
|
0.23
|
3.67
|
0.56
|
type I pilus;major subunit (pilin) |
| fimH |
4320 |
-2.09
|
-0.32
|
1.52
|
0.18
|
3.17
|
0.50
|
type I pilus; D-mannose-specific adhesin |
| fimF |
4318 |
-2.04
|
-0.31
|
1.40
|
0.15
|
2.86
|
0.46
|
type I pilus; morphology |
| ompX |
0814 |
-1.77
|
-0.25
|
1.23
|
0.09
|
2.18
|
0.34
|
outer membrane protein |
| ytfK |
4217 |
-1.67
|
-0.22
|
1.20
|
0.08
|
2.00
|
0.30
|
hypothetical protein |
| gor |
3500 |
-1.45
|
-0.16
|
1.39
|
0.14
|
2.01
|
0.30
|
glutathione oxidoreductase |
| sfsA |
0146 |
-1.41
|
-0.15
|
1.23
|
0.09
|
1.74
|
0.24
|
probable regulator of maltose metabolism |
Genes that respond negatively to AcCoA and positively to
AcP
| b0943 |
0943 |
-3.01
|
-0.48
|
-1.26
|
-0.10
|
2.39
|
0.38
|
putative fimbrial protein |
| yiaD |
3552 |
-2.33
|
-0.37
|
-1.25
|
-0.10
|
1.87
|
0.27
|
putative outer membrane protein |
Genes that respond negatively to AcP
| rplK |
3983 |
-1.64
|
-0.22
|
-1.06
|
-0.03
|
-1.74
|
-0.24
|
50S ribosomal subunit protein L11 |
Genes that respond negatively to both AcCoA and AcP
| b0795 |
0795 |
-1.53
|
-0.18
|
-1.80
|
-0.26
|
-1.18
|
-0.07
|
putative membrane protein |
| fdhF |
4079 |
-1.48
|
-0.17
|
-1.95
|
-0.29
|
-1.32
|
-0.12
|
selenopolypeptide subunit; formate dehydrogenase-H |
| wcaM |
2043 |
-1.41
|
-0.15
|
-2.60
|
-0.41
|
-1.84
|
-0.26 |
?colanic acid biosynthesis; hypothetical protein |
| endA |
2945 |
-1.41
|
-0.15
|
-2.13
|
-0.33
|
-1.51
|
-0.18
|
DNA-specific endonuclease I |
| ycaI |
3382 |
-1.40
|
-0.15
|
-1.89
|
-0.28
|
-1.35
|
-0.13
|
hypothetical protein |
| ilvL |
3766 |
-1.40
|
-0.15
|
-1.70
|
-0.23
|
-1.21
|
-0.08
|
ilvGEDA operon leader peptide |
Table 3. Genes significantly up-regulated in both mutants
compared to wild-type.
|
Gene
|
b#
|
Pta/Ack
ratio
|
Pta/Ack
log10
|
Pta/WT
ratio
|
Pta/WT
log10
|
Ack/WT
ratio
|
Ack/WT
log10
|
Gene Product |
| hdeA |
3510 |
-1.03
|
-0.01
|
45.01 |
1.65
|
45.94 |
1.66
|
acid stress response periplasmic protein |
| hdeB |
3509 |
-1.03
|
-0.01
|
24.96 |
1.40
|
25.81 |
1.41
|
acid stress response periplasmic protein |
| yhiE |
3512 |
1.38
|
0.14
|
4.51
|
0.65
|
3.26
|
0.51
|
hypothetical protein; slp-hde-gad region |
| mdh |
3236 |
1.22
|
0.09
|
4.18
|
0.62
|
3.42
|
0.53
|
hypothetical protein |
| yfiD |
2579 |
-1.15
|
-0.06
|
3.12
|
0.50
|
3.59
|
0.56
|
putative formate acetyltransferase |
| slp |
3506 |
1.25
|
0.10
|
3.10
|
0.49
|
2.48
|
0.40
|
outer membrane protein induced after carbon starvation |
| b0725 |
0725 |
1.21
|
0.08
|
3.01
|
0.48
|
2.48
|
0.40
|
hypothetical protein |
| lpdA |
0116 |
1.38
|
0.14
|
3.15
|
0.50
|
2.28
|
0.36
|
lipoamide dehydrogenase (NADH) |
| b1777 |
1777 |
1.04
|
0.02
|
2.63
|
0.42
|
2.52
|
0.40
|
hypothetical protein |
| ompT |
0565 |
1.30
|
0.11
|
2.89
|
0.46
|
2.22
|
0.35
|
outer membrane protein 3b; protease VII |
| ftn |
1905 |
1.04
|
0.02
|
2.48
|
0.40
|
2.38
|
0.38
|
cytoplasmic ferritin |
| icdA |
1136 |
1.10
|
0.04
|
2.49
|
0.40
|
2.27
|
0.36
|
isocitrate dehydrogenase |
| gapA |
1779 |
1.19
|
0.07
|
2.56
|
0.41
|
2.16
|
0.33
|
glyceraldehyde-3-phosphate dehydrogenase A |
| b0105 |
0105 |
1.31
|
0.12
|
2.68
|
0.43
|
2.05
|
0.31
|
hypothetical protein |
| clpB |
2592 |
1.17
|
0.07
|
2.47
|
0.39
|
2.11
|
0.33
|
heat shock protein |
| sucA |
0726 |
1.19
|
0.08
|
2.45
|
0.39
|
2.06
|
0.32
|
2-oxoglutarate dehydrogenase
(decarboxylase component)
|
| gltA |
0720 |
1.22
|
0.09
|
2.47
|
0.39
|
2.02
|
0.31
|
citrate synthase |
| yeaA |
1778 |
1.11
|
0.04
|
2.37
|
0.37
|
2.14
|
0.33
|
hypothetical protein |
| yfiA |
2597 |
-1.18
|
-0.07
|
2.06
|
0.31
|
2.43
|
0.39
|
putative yhbH sigma-54 modulator |
| tra8_3 |
4284 |
1.12
|
0.05
|
2.35
|
0.37
|
2.10
|
0.32
|
IS30 transposase |
| sucD |
0729 |
1.34
|
0.13
|
2.53
|
0.40
|
1.89
|
0.28
|
succinyl-CoA synthetase, alpha subunit |
| crl |
0240 |
1.05
|
0.02
|
2.22
|
0.35
|
2.12
|
0.33
|
transcriptional regulator of cryptic csgA gene for curli surface
fibers |
| guaC |
0104 |
1.24
|
0.09
|
2.36
|
0.37
|
1.91
|
0.28
|
GMP reductase |
| yafA |
0239 |
1.11
|
0.04
|
2.19
|
0.34
|
1.98
|
0.30
|
hypothetical protein |
| b4285 |
4285 |
-1.32
|
-0.12
|
1.83
|
0.26
|
2.42
|
0.38
|
putative transposase |
| rseA |
2572 |
-1.16
|
-0.07
|
1.91
|
0.28
|
2.22
|
0.35
|
negative regulator of sigma E |
| sgbU |
3582 |
-1.09
|
-0.04
|
1.97
|
0.29
|
2.15
|
0.33
|
probable 3-hexulose-6-phosphate isomerase |
Table 4. Genes significantly up-regulated in the wild-type
than compared to both mutants
|
Gene
|
b#
|
Pta/Ack
ratio
|
Pta/Ack
log10
|
Pta/WT
ratio
|
Pta/WT
log10
|
Ack/WT
ratio
|
Ack/WT
log10
|
Gene Product |
| b2862 |
2862 |
1.04
|
0.02
|
-2.59
|
-0.41
|
-2.70
|
-0.43
|
hypothetical protein |
| b0671 |
0671 |
1.15
|
0.06
|
-2.44
|
-0.39
|
-2.80
|
-0.45
|
putative RNA |
| yhhQ |
3471 |
1.06
|
0.02
|
-2.36
|
-0.37
|
-2.49
|
-0.40
|
hypothetical protein |
| secG |
3175 |
-1.01
|
<-0.01 |
-2.33
|
-0.37
|
-2.31
|
-0.36
|
protein export |
| yaiV |
0375 |
1.05
|
0.02
|
-2.23
|
-0.35
|
-2.34
|
-0.37
|
hypothetical protein |
| iadA |
4328 |
1.29
|
0.11
|
-2.01
|
-0.30
|
-2.59
|
-0.41
|
isoaspartyl dipeptidase |
| rbfA |
3167 |
1.16
|
0.07
|
-1.97
|
-0.30
|
-2.38
|
-0.38
|
ribosome-binding factor A |
| ymfR |
1150 |
1.08
|
0.03
|
-2.05
|
-0.31
|
-2.21
|
-0.35
|
hypothetical protein |
| b1030 |
1030 |
-1.07
|
-0.03
|
-2.21
|
-0.34
|
-2.06
|
-0.31
|
hypothetical protein |
| rpmE |
3936 |
1.31
|
0.12
|
-1.80
|
-0.26
|
-2.36
|
-0.37
|
50S ribosomal subunit protein L31 |
| yacG |
0101 |
-1.02
|
-0.01
|
-2.03
|
-0.31
|
-2.00
|
-0.30
|
hypothetical protein |
| hisF |
2025 |
1.18
|
0.07
|
-1.84
|
-0.27
|
-2.18
|
-0.34
|
subunit of imidazole glycerol phosphate synthase; with HisH |
| cspC |
1823 |
1.17
|
0.07
|
-1.86
|
-0.27
|
-2.18
|
-0.34
|
cold shock protein |
| ykfB |
0250 |
-1.24
|
-0.09
|
-2.23
|
-0.35
|
-1.80
|
-0.25
|
hypothetical protein |
| yaeJ |
0191 |
1.05
|
0.02
|
-1.94
|
-0.29
|
-2.04
|
-0.31
|
hypothetical protein |
| b1436 |
1436 |
-1.07
|
-0.03
|
-2.04
|
-0.31
|
-1.90
|
-0.28
|
hypothetical protein |
| yhfY |
3382 |
1.06
|
0.02
|
-1.91
|
-0.28
|
-2.02
|
-0.31
|
hypothetical protein |
| ampE |
0111 |
1.03
|
0.01
|
-1.97
|
-0.30
|
-1.91
|
-0.28
|
regulates ampC |
| glvC |
3683 |
1.09
|
0.04
|
-1.88
|
-0.27
|
-2.04
|
-0.31
|
PTS system; arbutin-like IIC component |
| yfhL |
2562 |
1.10
|
0.04
|
-1.87
|
-0.27
|
-2.06
|
-0.31
|
hypothetical protein |
| ybcO |
0549 |
-1.05
|
-0.02
|
-1.98
|
-0.30
|
-1.88
|
-0.27
|
hypothetical protein |
| metE |
3829 |
1.11
|
0.05
|
-1.83
|
-0.26
|
-2.04
|
-0.31
|
methionine biosynthesis; tetrahydropteroyltriglutamate methyltransferase |
| rpmG |
3636 |
-1.12
|
-0.05
|
-2.01
|
-0.30
|
-1.80
|
-0.26
|
50S ribosomal subunit protein L33 |
| 
