Table 5.
Average expression data of upregulated genes during STA1/STA2 comparison based on resultant FDR value from the RP analysis equal or less to 0.05 in compared growth phases during SA production cultures
| Gene | Locus | Protein name a | Cellular function GO b | Average expression |
|---|---|---|---|---|
|
argA |
b2818 |
Acetylglutamate synthase |
Amino acid metabolism |
87.9837 |
|
argB |
b3959 |
N-acetylglutamate kinase |
Amino acid metabolism |
45.8143 |
|
argC |
b3958 |
N-acetylglutamylphosphate reductase |
Amino acid metabolism |
53.4932 |
|
argD |
b3359 |
N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase |
Amino acid metabolism |
21.9053 |
|
argE |
b3957 |
Acetylornithine deacetylase |
Amino acid metabolism |
18.7485 |
|
argG |
b3172 |
Argininosuccinate synthase |
Amino acid metabolism |
65.2192 |
|
argH |
b3960 |
Argininosuccinate lyase |
Amino acid metabolism |
23.7859 |
|
argI |
b4254 |
Ornithine carbamoyltransferase chain I |
Amino acid metabolism |
33.2672 |
|
carA |
b0032 |
Polypeptide: CarA |
Amino acid metabolism |
107.7785 |
|
carB |
b0033 |
Polypeptide: CarB |
Amino acid metabolism |
23.9781 |
|
ilvG_1 |
b3767 |
Acetolactate synthase II, large subunit, N-ter fragment |
Amino acid metabolism |
75.4038 |
|
ilvG_2 |
b3768 |
Acetolactate synthase II, large subunit, N-ter fragment |
Amino acid metabolism |
24.6648 |
|
ilvM |
b3769 |
Polypeptide: IlvM |
Amino acid metabolism |
16.9332 |
|
metE |
b3829 |
Cobalamin-independent homocysteine transmethylase |
Amino acid metabolism |
59.0097 |
|
serA |
b2913 |
α-Ketoglutarate reductase/D-3-phosphoglycerate dehydrogenase |
Amino acid metabolism |
15.4266 |
|
ybaS |
b0485 |
Glutaminase |
Amino acid metabolism |
27.4637 |
|
fimC |
b4316 |
Periplasmic chaperone, required for type 1 fimbriae |
Cell envelope |
20.5382 |
|
ydiQ |
b1697 |
Putative subunit of YdiQ-YdiR flavoprotein |
Electron carrier activity |
32.4583 |
|
ydiR |
b1698 |
Putative subunit of YdiQ-YdiR flavoprotein |
Electron carrier activity |
32.3715 |
|
ydiT |
b1700 |
Putative ferredoxin |
Electron carrier activity |
28.0548 |
|
arnB |
b2253 |
UDP-L-Ara4O C-4′ transaminase |
Lipid metabolism |
20.7697 |
|
arnC |
b2254 |
Undecaprenyl phosphate-L-Ara4FN transferase |
Lipid metabolism |
33.1058 |
|
yhiD |
b3508 |
Predicted Mg(2+) transport ATPase |
Lipid metabolism |
52.2858 |
|
narY |
b1467 |
Nitrate reductase Z, β subunit |
Other metabolic process |
18.7104 |
|
narZ |
b1468 |
Nitrate reductase Z, α subunit |
Other metabolic process |
13.4094 |
|
yciE |
b1257 |
Conserved protein |
Other metabolic process |
18.9020 |
|
ydiS |
b1699 |
Putative flavoprotein |
Other metabolic process |
20.0646 |
|
ygdI |
b2809 |
Putative lipoprotein |
Out of OGs |
15.8477 |
|
slp |
b3506 |
Starvation lipoprotein |
Out of OGs |
16.3895 |
|
ybaY |
b0453 |
Predicted OM lipoprotein |
Out of OGs |
31.4852 |
|
yhjR |
b3535 |
Conserved protein |
Out of OGs |
17.5298 |
|
yhiE |
b3512 |
GadE DNA-binding transcriptional activator |
Regulatory |
224.6027 |
|
yhiF |
b3507 |
Polypeptide: predicted DNA-binding transcriptional regulator |
Regulatory |
33.7016 |
|
yhiW |
b3515 |
GadW DNA-binding transcriptional dual regulator |
Regulatory |
33.4367 |
|
ykfE |
b0220 |
Inhibitor of vertebrate C-type lysozyme |
Regulatory |
40.8144 |
|
gadB |
b1493 |
Glutamate decarboxylase B |
Stress response |
94.5462 |
|
hdeA |
b3510 |
HdeA dimer, inactive form of acid-resistance protein |
Stress response |
125.3695 |
|
hdeB |
b3509 |
Acid stress chaperone |
Stress response |
104.9129 |
|
hdeD |
b3511 |
Acid-resistance membrane protein |
Stress response |
140.6337 |
|
katE |
b1732 |
Heme d synthase/hydroperoxidase |
Stress response |
15.6533 |
|
cysD |
b2752 |
Polypeptide: CysD |
Sulfur metabolism |
34.5193 |
|
cysH |
b2762 |
3′-Phospho-adenylylsulfate reductase |
Sulfur metabolism |
15.6801 |
|
hisP |
b2306 |
Lysine/arginine/ornithine ABC transporter/histidine ABC transporter - ATP binding subunit |
Transport |
17.8485 |
|
potG |
b0855 |
Putrescine ABC transporter - ATP binding subunit |
Transport |
18.0562 |
|
artJ |
b0860 |
Arginine ABC transporter - periplasmic binding protein |
Transport |
120.3908 |
|
gadC |
b1492 |
Glutamic acid: 4-aminobutyrate antiporter |
Transport |
28.9528 |
|
hisM |
b2307 |
Lysine/arginine/ornithine ABC transporter/histidine ABC transporter - membrane subunit |
Transport |
44.5442 |
|
narU |
b1469 |
NarU MFS nitrate/nitrite antiporter |
Transport |
62.1767 |
|
ompC |
b2215 |
OMP C |
Transport |
37.5373 |
| yggB | b2924 | Mechano sensitive channel MscS | Transport | 22.3863 |
aRetrieved from EcoCyc database, bBiological functions were assigned according to the EcoCyc database for E. coli strain MG1655 and broadly grouped on the basis of GO terms [17].