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Table 2 Genes with significantly altered expression as a result of endogenous and heterologous proteins overproduction in B. subtilis cells a,b

From: Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins

Gene

Description

Overproduced proteins

Membrane proteins

Lipoproteins

Secreted proteins

XylP

LmrA

MntA

YcdH

XynA

NprE

Usp45

Bla

UPREGULATED

        

Cell envelope stress response

        

cssR

two-component response regulator (class V)

0.96

1.06

6.82

1.38

5.97

1.08

2.90

1.85

cssS

two-component sensor histidine kinase (class V)

0.95

1.11

3.10

1.54

2.67

0.99

2.37

1.66

htrB

similar to HtrA-like serine protease (class V)

0.67

1.03

1.70

7.37

10.86

1.12

0.44

7.52

htrA

Quality control serine protease (heat-shock protein) (class V)

0.76

1.17

3.17

5.18

14.88

0.78

46.70

7.23

sigM

RNA polymerase ECF-type sigma factor

1.17

0.94

3.01

2.51

0.62

1.49

1.67

1.21

liaI (yvqI)

permease

2.38

1.07

1.31

2.55

1.59

2.03

8.96

23.44

liaH (yvqH)

modulator of liaIHGFSR (yvqIHGFEC) operon expression

2.32

1.08

1.19

3.40

1.47

2.51

9.43

29.75

liaG (yvqG)

hypothetical protein

1.48

1.06

2.27

2.67

0.82

2.65

4.55

13.38

liaF (yvqF)

integral inner membrane protein

0.89

1.07

2.14

1.94

0.92

2.56

4.16

10.93

liaS (yvqE)

two-component sensor histidine kinase [YvqC] sensing cell wall stress

1.14

NA

2.42

1.93

0.89

NA

5.88

6.61

liaR (yvqC)

two-component response regulator [YvqE] responding to cell wall stress

0.94

1.04

1.91

2.57

0.79

1.96

2.19

4.76

ykrL

Homolog of HtpX, membrane protease

10.35

3.62

1.66

0.88

2.15

0.90

2.98

1.85

sigW

RNA polymerase ECF-type sigma factor

4.52

5.50

1.95

1.77

1.62

1.05

1.73

2.44

rsiW (ybbM)

sigmaW anti-sigma factor

5.54

4.11

2.43

1.72

2.31

0.84

1.89

2.61

yuaF

putative membrane integrity integral inner membrane protein

6.93

2.65

1.09

0.23

1.41

1.31

2.15

2.36

yuaG

similar to flotillin 1

12.21

3.43

0.66

0.75

1.87

1.00

4.52

2.40

yuaI

putative acetyl-transferase

15.16

6.62

0.40

0.81

2.80

0.78

5.01

2.70

ydjG

putative phage replication protein

7.70

2.85

0.59

1.85

1.93

1.01

3.09

1.46

ydjH

hypothetical protein

6.88

3.92

0.60

0.48

1.68

1.09

2.19

1.86

ydjI

hypothetical protein

6.78

4.55

0.59

0.75

1.86

0.57

2.84

2.40

yeaA

conserved hypothetical protein

5.58

3.28

0.93

0.42

1.41

2.36

1.35

2.10

ydjP

similar to chloroperoxydase

7.41

4.67

1.16

0.91

2.55

1.53

4.56

3.00

ydjO

unknown

3.81

7.59

1.14

1.08

1.99

1.46

2.97

2.57

sppA

signal peptide peptidase

4.25

3.12

0.33

0.26

1.18

0.39

1.70

1.80

yteJ

integral inner membrane protein

4.48

4.16

0.31

0.29

1.27

0.34

2.27

1.77

pbpE

penicillin-binding protein 4

11.25

8.56

0.95

0.97

2.08

0.49

6.37

2.72

racX

amino acid racemase

8.99

8.09

0.78

0.95

2.06

0.45

6.00

2.39

yaaN

hypothetical protein

4.03

6.82

1.07

0.43

1.15

2.64

1.51

1.82

yceC

putative stress adaptation protein

2.44

3.05

2.06

NA

NA

0.54

NA

1.64

yceD

putative stress adaptation protein

5.29

7.02

0.81

0.76

2.04

0.92

3.14

1.55

yceE

putative stress adaptation protein

4.55

5.36

0.82

0.67

2.08

0.89

3.71

2.34

yceF

putative stress adaptation protein

5.30

4.91

0.70

0.78

2.07

0.73

4.27

1.79

yceG

hypothetical protein

3.99

3.02

0.79

1.07

1.94

1.04

3.29

1.22

yceH

hypothetical protein

3.72

4.09

0.64

0.99

1.99

0.60

3.68

2.15

yjoB

ATPase possibly involved in protein degradation

7.16

2.98

1.28

0.65

1.45

0.94

1.74

2.44

yknW

permease

2.51

3.06

0.67

0.36

1.12

0.84

1.14

1.46

yknY

ABC transporter ATP-binding protein

2.63

2.54

0.49

0.33

1.31

0.57

1.51

1.64

ythQ

putative ABC transporter (permease)

10.01

5.75

0.80

NA

2.21

NA

3.21

3.19

yqfB

hypothetical protein

6.37

6.24

1.12

0.56

1.66

0.39

3.10

2.93

yvlA

hypothetical protein

4.11

3.06

1.49

0.59

1.23

1.34

1.39

2.04

yvlB

hypothetical protein

6.13

9.56

0.99

0.66

1.76

0.91

3.84

2.10

yvlC

putative regulator (stress mediated)

3.83

7.71

0.99

0.61

1.61

0.76

2.24

2.05

yvlD

putative integral inner membrane protein

4.26

6.66

1.60

0.65

1.22

0.74

2.98

1.87

yxjI

unknown

10.12

5.20

0.96

0.55

1.60

1.46

1.38

1.83

hrcA

transcriptional repressor of class I heat-shock genes

11.08

2.23

1.89

12.62

0.96

1.30

2.33

2.12

groES

class I heat-shock protein (chaperonin)

8.37

7.17

0.10

6.85

3.15

1.11

3.68

3.07

groEL

class I heat-shock protein (chaperonin)

8.38

4.17

0.35

5.07

2.73

1.14

3.00

2.66

nfrA

FMN-containing NADPH-linked nitro/flavin reductase (class VI)

7.36

3.32

0.47

1.67

10.37

0.98

13.77

1.85

ywcH

putative monooxygenase (class VI)

10.29

2.91

1.04

6.03

5.29

0.86

NA

2.46

trxB

thioredoxin reductase

4.71

1.59

0.88

2.98

3.97

0.72

3.56

1.36

trxA

thioredoxin

2.29

1.94

0.86

1.68

3.08

1.13

3.11

1.31

ctsR

transcriptional regulator of class III stress genes

0.71

0.55

1.39

NA

NA

NA

NA

NA

mcsA

modulator of CtsR repression

10.38

3.47

0.87

5.12

1.72

1.57

4.63

3.11

mcsB

modulator of CtsR repression

6.92

4.11

0.83

5.09

2.46

1.09

2.68

2.63

clpC

class III stress response-related ATPase

5.65

3.24

0.65

4.63

2.03

0.80

3.28

2.80

radA

DNA repair protein

2.79

1.97

0.75

3.86

1.82

1.26

3.14

2.19

clpE

Class III, ATP-dependent Clp protease-like

74.08

1.89

0.98

4.54

0.77

1.24

5.95

4.79

fdhD

required for formate dehydrogenase activity

2.89

1.26

2.99

4.65

1.93

1.65

1.67

0.94

cydB

cytochrome bd ubiquinol oxidase (subunit II)

0.75

2.28

1.39

0.51

2.93

4.50

0.74

0.64

kinD

TCS sensor histidine kinase; initiation of sporulation

1.35

1.20

3.18

2.76

1.49

1.81

1.05

1.05

yabT

putative serine/threonine-protein kinase

2.19

1.14

NA

1.56

2.55

2.65

1.26

1.04

yceK

putative transcriptional regulator (ArsR family)

2.58

2.54

0.81

1.35

1.07

1.06

2.10

1.92

yjbI

putative thiol management oxidoreductase component

3.93

0.99

1.45

2.95

3.23

1.33

3.61

1.46

yloC

unknown

1.65

1.09

3.56

3.51

1.47

1.36

1.57

1.05

yndN

fosfomycin resistance protein FosB

6.66

13.17

0.94

0.32

1.60

0.56

3.49

3.04

yrkA

putative membrane associated protein

3.20

3.75

1.51

0.96

1.48

0.97

1.13

1.30

yvdT

uncharacterized transcriptional regulator (TetR/AcrR family)

2.94

3.28

1.82

2.19

1.37

1.80

2.26

1.92

yvdS

similar to molecular chaperone, putative membrane protein

7.12

2.12

1.20

1.14

1.08

1.26

3.43

1.96

yvdR

similar to molecular chaperone, putative membrane protein

6.32

2.66

2.46

1.39

1.01

1.36

3.99

1.81

cydC

ABC membrane transporter ATP-binding protein

3.22

3.76

0.87

0.32

2.92

2.36

2.25

1.12

yhaT

K+/H + antiporter for K + efflux

15.45

3.48

2.16

2.91

2.47

1.22

4.80

2.54

yhaU

K+/H + antiporter for K + efflux

15.49

2.19

2.38

1.84

2.56

1.00

5.14

1.97

Unknown

         

ydiN

unknown

4.44

2.76

0.22

5.11

1.75

1.75

2.41

3.51

yomP

hypothetical protein

3.57

3.21

0.92

3.33

0.89

2.60

1.40

0.82

yomT

hypothetical protein

2.92

2.60

0.83

2.90

0.72

2.47

1.24

0.85

yceI

putative transporter

2.92

3.55

1.49

0.80

1.75

0.69

2.89

2.26

yhaS

K+/H + antiporter for K + efflux

9.48

2.13

2.08

1.76

2.42

0.96

3.41

1.94

yomV

hypothetical protein

3.59

3.37

1.05

3.92

0.73

2.55

1.43

0.88

yomW

hypothetical protein

3.19

3.38

0.97

4.57

0.65

2.79

1.31

0.78

yomY

hypothetical protein

3.66

2.53

1.09

3.64

0.77

2.60

1.66

0.82

yonB

hypothetical protein

3.22

2.92

0.96

2.61

1.01

2.26

1.24

0.79

yonC

hypothetical protein

2.92

2.64

0.83

2.84

0.96

2.41

1.43

0.84

yvkN

hypothetical protein

3.21

2.69

0.89

0.61

1.83

1.07

1.88

1.69

ywmB

hypothetical protein

1.32

1.18

3.00

2.67

1.30

2.43

0.55

1.16

sdpA (yvaW)

export of killing factor SdpC

15.28

2.78

4.29

3.96

3.54

1.54

14.19

4.35

sdpB (yvaX)

exporter of killing factor SdpC

19.87

4.06

3.26

5.34

3.96

1.49

13.85

4.00

sdpC (yvaY)

killing factor SdpC

8.12

2.75

2.45

12.90

11.51

1.21

26.62

5.56

sppA

signal peptide peptidase

0.24

0.32

3.03

3.89

0.85

2.56

0.59

0.56

yteJ

putative integral inner membrane protein

0.22

0.24

3.18

3.51

0.79

2.93

0.44

0.56

gltT

proton/sodium-glutamate symport protein

3.36

3.12

2.52

1.63

0.82

1.96

8.35

1.20

pbuX

xanthine permease

3.32

2.74

0.45

1.76

1.47

1.50

4.45

1.61

yhaQ

Na + −effluxABCtransporterATP-bindingprotein

2.07

1.55

3.73

4.51

2.19

2.10

1.65

1.32

yoaG

putative permease

0.13

0.67

3.13

3.68

1.20

1.15

0.66

0.53

ctaB

cytochrome caa3 oxydase assembly factor

1.18

1.63

0.66

1.16

1.34

1.15

3.48

1.17

ctaC

cytochrome caa3 oxidase subunit II

4.37

1.13

4.74

2.68

1.08

1.91

5.52

1.20

ctaD

cytochrome caa3 oxidase subunit I

3.71

1.37

3.58

3.14

NA

1.81

3.33

1.27

ctaE

cytochrome caa3 oxidase subunit III

3.57

1.44

2.40

3.02

1.90

2.08

4.21

1.10

ctaF

cytochrome caa3 oxidase subunit IV

4.33

1.91

2.05

3.86

2.68

2.32

4.24

1.41

ctaG

cytochrome aa3 assembly factor

4.61

NA

2.40

1.83

NA

1.19

2.67

NA

bdbB

bacteriophage SPbeta thiol-disulfide oxidoreductase

3.59

2.79

6.00

2.57

3.05

1.16

14.00

2.00

wapA

cell wall-associated protein precursor

2.88

1.07

1.15

8.19

2.50

0.91

6.38

1.15

yxxG

hypothetical protein

4.04

0.99

1.22

8.68

4.20

0.87

5.25

1.08

wprA

cell wall-associated protease

2.45

1.05

4.87

4.19

2.27

1.85

9.13

1.27

Unknown

         

yisL

hypothetical protein

2.00

1.13

2.58

4.59

1.41

1.96

0.73

1.11

yokE

hypothetical protein

1.56

1.76

7.19

2.84

2.74

1.50

4.35

1.28

ytxG

hypothetical protein

1.80

0.76

2.98

2.56

0.83

1.00

0.48

0.93

yukE

hypothetical protein

1.37

1.56

3.25

2.67

0.92

2.04

1.60

1.02

yxbC

hypothetical protein

3.55

0.69

3.22

5.71

0.72

1.30

2.06

1.11

  1. a Significant changes (p value < 0.01, fold > 2.5) are shown in bold.
  2. b Endogenous proteins: MntA, YcdH, XynA, NprE; heterologous proteins: XylP (Lb. pentosus), LmrA and Usp45 (L. lactis), Bla (TEM-1 β-lactamase, E. coli).
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