Table 3

RT-qPCR values of central metabolism and regulatory genes
Gene PB11* PB12* JM101ΔrppH PB11ΔrppH PB11ΔrpoS* PB12ΔrpoS* PB11ΔarcA*
Glycolysis
aceE + 0.40 ± 0.02 1.40 ± 0.02 1.57 ± 0.23 1.32 ± 0.21 0.20 ± 0.00 0.85 ± 0.00 0.40 ± 0.00
aceF + 0.60 ± 0.00 1.20 ± 0.00 2.66 ± 0.51 1.00 ± 0.12 0.40 ± 0.10 0.70 ± 0.00 0.60 ± 0.00
eno 0.50 ± 0.10 0.50 ± 0.14 0.89 ± 0.01 1.28 ± 0.41 0.20 ± 0.00 0.37 ± 0.00 0.30 ± 0.00
fbaA 0.90 ± 0.00 1.10 ± 0.05 0.82 ± 0.08 1.46 ± 0.18 0.90 ± 0.00 0.37 ± 0.10 0.40 ± 0.00
gapA 0.40 ± 0.10 1.70 ± 0.20 6.98 ± 1.17 3.76 ± 0.67 0.10 ± 0.00 1.40 ± 0.20 0.30 ± 0.00
glk 1.00 ± 0.00 2.20 ± 0.10 3.43 ± 0.72 6.04 ± 0.03 0.70 ± 0.10 1.70 ± 0.10 0.80 ± 0.10
gpmA 0.90 ± 0.00 1.80 ± 0.00 3.07 ± 0.21 2.46 ± 0.13 0.60 ± 0.10 1.70 ± 0.30 0.50 ± 0.00
lpdA + 1.10 ± 0.10 2.00 ± 0.10 2.33 ± 0.00 3.16 ± 0.36 1.30 ± 0.30 1.70 ± 0.10 2.00 ± 0.10
pfkA 0.30 ± 0.00 0.50 ± 0.00 1.49 + 0.11 1.48 + 0.11 0.00 ± 0.00 0.20 ± 0.00 0.10 ± 0.00
pgi 1.00 ± 0.10 6.60 ± 0.30 3.47 ± 0.10 7.71 ± 0.91 0.40 ± 0.10 3.70 ± 0.10 0.40 ± 0.00
pgk 0.70 ± 0.00 1.20 ± 0.00 1.24 ± 0.20 1.08 ± 0.11 N.D. N.D. 0.80 ± 0.00
ppc 0.60 ± 0.05 0.80 ± 0.00 3.81 ± 0.27 1.97 ± 0.40 0.80 ± 0.10 0.50 ± 0.10 N.D.
pykA 0.40 ± 0.00 1.00 ± 0.00 1.16 ± 0.12 0.83 ± 0.03 0.10 ± 0.00 0.51 ± 0.10 0.50 ± 0.10
pykF 0.80 ± 0.00 0.90 ± 0.00 0.89 ± 0.31 2.00 ± 0.26 0.20 ± 0.00 0.50 ± 0.10 0.40 ± 0.00
tpiA 0.50 ± 0.00 1.80 ± 0.00 4.84 ± 0.12 8.83 ± 2.61 0.20 ± 0.00 0.30 ± 0.00 0.40 ± 0.00
Gene TCA cycle
acnA 5.20 ± 0.60 5.70 ± 0.20 2.88 ± 0.31 10.80 ± 1.63 0.70 ± 0.10 3.50 ± 0.30 4.30 ± 0.20
acnB + 1.70 ± 0.36 1.70 ± 0.42 1.76 ± 0.06 24.80 ± 2.18 0.20 ± 0.00 0.70 ± 0.00 2.60 ± 0.30
fumA + 3.30 ± 0.67 3.60 ± 0.67 2.62 ± 0.72 24.07 ± 3.41 2.30 ± 0.50 3.80 ± 0.10 2.10 ± 0.10
gltA + 0.80 ± 0.10 1.30 ± 0.20 1.73 ± 0.31 6.68 ± 0.13 1.30 ± 0.20 1.20 ± 0.20 1.70 ± 0.10
icdA + 1.00 ± 0.10 1.90 ± 0.00 1.03 ± 0.11 4.66 ± 0.78 1.20 ± 0.00 2.40 ± 0.00 1.30 ± 0.00
mdh 1.20 ± 0.10 1.80 ± 0.50 1.93 ± 0.16 3.64 ± 0.32 1.40 ± 0.30 1.40 ± 0.10 1.10 ± 0.10
sdhA + 0.90 ± 0.00 2.00 ± 0.30 4.75 ± 0.98 5.96 ± 0.67 3.70 ± 0.20 4.00 ± 0.00 2.60 ± 0.10
sdhB + 0.80 ± 0.00 1.70 ± 0.00 4.40 ± 0.86 8.05 ± 0.86 2.20 ± 0.00 2.40 ± 0.30 1.30 ± 0.00
sucA + 1.40 ± 0.10 1.70 ± 0.10 3.28 ± 0.20 5.42 ± 1.39 1.20 ± 0.20 1.00 ± 0.00 1.20 ± 0.00
sucB + 0.80 ± 0.00 1.40 ± 0.10 3.31 ± 0.62 8.28 ± 1.91 N.D. N.D. 1.20 ± 0.00
sucC + 0.90 ± 0.10 1.60 ± 0.00 1.99 ± 0.43 7.41 ± 1.21 1.30 ± 0.10 1.50 ± 0.00 1.20 ± 0.20
sucD + 1.00 ± 0.20 1.40 ± 0.30 1.89 ± 0.32 7.16 ± 0.11 1.70 ± 0.20 1.00 ± 0.10 1.10 ± 0.10
Gene Gluconeogenic, glyoxylate andpoxBshunt
aceA + 12.00 ± 1.20 1.90 ± 0.20 1.66 ± 0.38 24.20 ± 3.16 9.10 ± 2.80 0.80 ± 0.10 8.81 ± 1.00
aceB + 15.60 ± 2.50 3.70 ± 0.30 2.54 ± 0.09 28.65 ± 5.91 11.00 ± 2.10 0.74 ± 0.00 24.20 ± 2.60
acs 5.60 ± 0.74 8.00 ± 0.13 1.83 ± 0.19 21.82 ± 3.20 4.10 ± 0.10 3.40 ± 0.10 11.90 ± 0.10
glcB + 11.70 ± 1.4 3.70 ± 0.50 1.04 ± 0.28 12.62 ± 0.93 2.50 ± 0.20 1.80 ± 0.20 7.60 ± 0.30
maeB 1.20 ± 0.20 2.50 ± 0.03 1.18 ± 0.26 10.06 ± 1.19 1.60 ± 0.00 1.70 ± 0.00 N.D.
pckA 0.80 ± 0.06 2.30 ± 0.02 0.83 ± 0.21 2.81 ± 0.89 0.90 ± 0.20 1.30 ± 0.10 N.D.
poxB 4.20 ± 0.35 5.70 ± 0.48 3.30 ± 0.48 5.30 ± 0.56 1.50 ± 0.10 0.50 ± 0.00 2.80 ± 0.90
ppsA 3.70 ± 0.21 2.40 ± 0.09 7.34 ± 2.08 5.57 ± 1.34 3.30 ± 0.20 1.10 ± 0.20 N.D.
sfcA 1.90 ± 0.33 1.70 ± 0.10 2.56 ± 0.85 3.72 ± 0.28 1.10 ± 0.10 1.00 ± 0.00 N.D.
Gene galregulon
galE 38.80 ± 6.80 46.60 ± 6.50 0.53 ± 0.12 40.25 ± 1.97 1.40 ± 0.10 25.00 ± 2.10 N.D.
galK 39.00 ± 2.30 48.21 ± 4.00 2.12 ± 0.09 43.78 ± 3.43 N.D. N.D. N.D.
galM 8.10 ± 3.94 3.30 ± 0.70 0.96 ± 0.18 2.67 ± 0.85 N.D. N.D. N.D.
galP 12.40 ± 1.08 13.10 ± 1.86 1.98 ± 0.36 25.11 ± 0.98 N.D. N.D. 11.70 ± 1.90
galR*** 3.20 ± 0.10 1.20 ± 0.40 2.04 ± 0.25 5.20 ± 0.10 N.D. N.D. N.D.
galS 4.90 ± 0.47 3.20 ± 0.52 4.14 ± 0.35 23.48 ± 0.07 N.D. N.D. N.D.
galT 35.60 ± 2.37 42.50 ± 4.00 1.10 ± 0.12 64.34 ± 5.20 N.D. N.D. N.D.
galU 1.70 ± 0.30 2.10 ± 0.36 1.27 ± 0.01 2.36 ± 0.22 N.D. N.D. N.D.
Gene Respiration
cyoA + 0.60 ± 0.01 1.40 ± 0.07 2.16 ± 0.07 4.33 ± 0.38 N.D. N.D. 1.10 ± 0.10
cyoB + 0.30 ± 0.00 1.40 ± 0.10 2.42 ± 0.58 3.11 ± 0.04 N.D. N.D. N.D.
cyoC + 0.30 ± 0.00 1.20 ± 0.20 2.93 ± 0.19 2.77 ± 0.55 N.D. N.D. N.D.
cyoD + 0.30 ± 0.02 1.10 ± 0.10 1.90 ± 0.43 3.05 ± 0.03 N.D. N.D. N.D.
nuoA + 0.40 ± 0.00 2.40 ± 0.10 3.53 ± 0.54 9.67 ± 1.98 N.D. N.D. 1.00 ± 0.00
nuoF + 0.40 ± 0.10 1.40 ± 0.10 4.68 ± 0.11 6.84 ± 0.28 N.D. N.D. N.D.
nuoN + 0.40 ± 0.02 1.00 ± 0.08 0.44 ± 0.02 1.55 ± 0.18 N.D. N.D. N.D.
ubiE + 0.40 ± 0.00 1.60 ± 0.00 4.39 ± 1.31 12.01 ± 1.26 N.D. N.D. N.D.
Gene ppGpp metabolism
gpp 1.40 ± 1.20 5.20 ± 0.30 9.17 ± 1.65 4.77 ± 0.93 0.00 ± 0.00 0.10 ± 0.00 N.D.
ndk 0.40 ± 0.00 3.10 ± 0.10 3.49 ± 0.52 11.08 ± 0.43 0.50 ± 0.00 3.30 ± 0.10 N.D.
ppa 1.00 ± 0.00 6.10 ± 1.40 7.42 ± 0.33 9.29 ± 0.32 0.50 ± 0.10 3.80 ± 0.10 N.D.
relA 1.30 ± 0.00 1.60 ± 0.20 3.13 ± 0.20 1.51 ± 0.00 0.90 ± 0.10 1.10 ± 0.00 N.D.
spoT 1.10 ± 0.20 4.80 ± 0.20 6.00 ± 0.77 7.36 ± 0.82 0.50 ± 0.10 0.70 ± 0.10 N.D.
Gene ptsoperon
crr 0.00 ± 0.00 0.00 ± 0.00 2.46 ± 0.37 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
ptsH 0.00 ± 0.00 0.00 ± 0.00 1.07 ± 0.12 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
ptsI 0.00 ± 0.00 0.00 ± 0.00 1.34 ± 0.14 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00
Gene Genes in deleted chromosomal fragment in PB12
galR*** 3.20 ± 0.10 1.20 ± 0.40 2.04 ± 0.25 5.20 ± 0.10 N.D. N.D. N.D.
lplT*** 3.95 ± 0.53 0.00 ± 0.00 0.95 ± 0.12 2.83 ± 0.32 N.D. N.D. N.D.
mutH*** 2.76 ± 0.02 0.00 ± 0.00 16.49 ± 0.22 30.48 ± 0.00 N.D. N.D. N.D.
rppH*** 1.84 ± 0.20 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 N.D. N.D. N.D.
ptsP*** 1.80 ± 0.20 0.00 ± 0.00 0.55 ± 0.07 0.30 ± 0.06 N.D. N.D. N.D.
tas*** 1.31 ± 0.07 0.00 ± 0.00 1.07 ± 0.21 12.80 ± 2.44 N.D. N.D. N.D.
ygdQ*** 8.86 ± 1.86 0.00 ± 0.00 1.92 ± 0.06 6.10 ± 1.58 N.D. N.D. N.D.
Gene Genes with point mutations in PB12
arcB** 2.30 ± 0.70 1.30 ± 0.72 0.99 ± 0.06 1.23 ± 0.19 N.D. N.D. N.D.
barA** 4.14 ± 0.91 3.46 ± 0.46 3.25 ± 0.09 2.30 ± 0.53 N.D. N.D. N.D.
rna** 0.89 ± 0.18 3.40 ± 0.75 2.06 + 0.42 8.03 ± 0.00 N.D. N.D. N.D.
rssA** 4.89 ± 1.27 4.04 ± 0.43 6.45 ± 0.31 6.07 ± 0.95 N.D. N.D. N.D.
rpoD** 1.00 ± 0.20 0.90 ± 0.20 1.00 ± 0.20 1.18 ± 0.24 0.70 ± 0.20 1.10 ± 0.10 N.D.
rpoS + 2.90 ± 0.86 2.20 ± 0.20 2.03 ± 0.07 4.62 ± 0.34 0.10 ± 0.00 0.20 ± 0.00 2.60 ± 0.10
yjjU** 0.86 ± 0.26 8.51 ± 0.00 1.44 ± 0.03 4.31 ± 0.35 N.D. N.D. N.D.
ypdA** 1.59 ± 0.49 1.38 ± 0.15 1.20 ± 0.31 1.36 ± 0.11 N.D. N.D. N.D.
Gene Regulators
arcA 1.02 ± 0.02 1.30 ± 0.09 1.68 ± 0.49 3.86 ± 0.60 0.70 ± 0.00 1.10 ± 0.10 0.00 ± 0.00
arcB** 2.30 ± 0.70 1.30 ± 0.72 0.99 ± 0.06 1.23 ± 0.19 N.D. N.D. N.D.
barA** 4.14 ± 0.91 3.46 ± 0.46 3.25 ± 0.09 2.30 ± 0.53 N.D. N.D. N.D.
crp 0.80 ± 0.02 1.00 ± 0.05 1.38 ± 0.01 2.22 ± 0.64 N.D. N.D. N.D.
cyaA 1.40 ± 0.10 1.80 ± 0.10 2.37 ± 0.78 3.62 ± 0.68 N.D. N.D. N.D.
fadR 0.60 ± 0.03 1.60 ± 0.08 3.52 ± 0.03 3.34 ± 0.19 N.D. N.D. N.D.
fruR 1.30 ± 0.00 1.50 ± 0.07 1.41 + 0.02 4.34 + 0.34 N.D. N.D. N.D.
galR*** 3.20 ± 0.10 1.20 ± 0.40 2.04 ± 0.25 5.20 ± 0.10 N.D. N.D. N.D.
iclR 0.40 ± 0.03 1.40 ± 0.07 0.81 ± 0.20 2.62 ± 0.39 N.D. N.D. N.D.
ihfA 1.80 ± 0.04 1.70 ± 0.06 1.97 ± 0.32 2.07 ± 0.22 N.D. N.D. N.D.
ihfB 1.00 ± 0.00 1.00 ± 0.00 1.00 ± 0.00 1.00 ± 0.00 N.D. N.D. N.D.
mlc 1.10 ± 0.00 1.70 ± 0.06 2.37 ± 0.49 10.66 ± 2.07 N.D. N.D. N.D.
rpoD** 1.00 ± 0.20 0.90 ± 0.20 1.00 ± 0.20 1.18 ± 0.22 0.70 ± 0.20 1.10 ± 0.10 N.D.
rpoS + 2.90 ± 0.86 2.20 ± 0.20 2.03 ± 0.07 4.62 ± 0.34 0.10 ± 0.00 0.20 ± 0.00 2.60 ± 0.10

Relative mRNA concentrations of central metabolism and regulatory genes of JM101, PB11, PB12 and their derivatives strains, grown in glucose as the sole carbon source, were determined by RT-qPCR. Most of these values have previously been reported (*) and are presented here for discussion and comparison purposes [9-11]. ArcA/B regulated genes are marked with (+). Data in this table are reported as relative expression levels of the parental JM101 strain, assigning it the value of one (see Materials and Methods). The RT-qPCR values of mutated (**) or deleted (***) genes in the PB12 strain have not been reported, with the exception of arcB and rpoS. N.D. Not determinate.

Aguilar et al.

Aguilar et al. BMC Genomics 2012 13:385   doi:10.1186/1471-2164-13-385

Open Data