Table 3 RT-qPCR values of central metabolism and regulatory genes

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 and poxB shunt

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

gal regulon

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

pts operon

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