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Table 1 Differential expression pattern at pH 9 in comparison to pH 7.5

From: Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Genes induced at pH 9

 

Transcriptome4

Proteome5

Regulators6

        

cytoplasma

envelope

membrane

 

No

gene ID1

op2

gene

function

TMH3

pH 6

pH 9

6

7.5

9

6

7.5

9

6

7.5

9

 

1

cg0077

  

Hypothetical protein

0

n.d.

1.04

-0.6

-

-

-

-

-

-0.9

-

-

 

2

cg0105

  

Hypothetical protein Cgl0077

0

-0.83

1.65

-

-

-

-0.4

-

-

-

-

-

 

3

cg0310

 

katA

Catalase

0

-0.62

1.73

4.2

5.1

6.4

-

-

0.0

-

-

-0.6

RipA

4

cg0444

 

ramB

Regulator of acetate metabolism

0

0.76

1.11

-

-

-0.8

-

0.7

3.5

-

-

-

RamA, RamB

5

cg0445

c

sdhCD

Succinate dehydrogenase component CD

5

-1.31

1.31

-

-

-

1.8

1.4

2.4

3.2

4.0

5.0

RipA, DtxR, RamA*, RamB*

6

cg0446

c

sdhA

Succinate dehydrogenase A

0

-1.08

1.47

1.0

2.7

1.7

6.7

7.0

9.0

8.5

9.0

9.9

RipA, DtxR, RamA*, RamB*

7

cg0447

c

sdhB

Succinate dehydrogenase B

0

-1.43

1.14

-

-0.4

-

4.6

5.0

6.7

3.5

3.4

5.3

RipA, DtxR, RamA*, RamB*

8

cg0448

c

 

Conserved hypothetical membrane protein

2

-0.98

1.18

-

-

-

-0.4

0.8

1.7

-

-

-

RipA*, DtxR, RamB*

9

cg0778

 

fecC

putative iron or siderophore ABC-type transporter, permease component

8

-0.05

1.07

-

-

-

-

-

-

-

-

-

 

10

cg0825

  

Dehydrogenases with different specificities

0

-0.19

1.07

4.1

4.6

5.0

-0.4

-0.3

1.8

-0.7

-

-0.4

 

11

cg0858

  

putative gamma subunit of the nitrate reductase

1

-0.28

1.22

-

-

-

-

-

-

-

-

-

 

12

cg1095

  

Hypothetical protein

0

0.32

1.28

-

-

-

-

-

-

-

-

-

 

13

cg1136

  

Hypothetical protein

0

0.15

1.02

1.6

0.5

2.2

-

-

-

-

-

-

 

14

cg1206

  

PEP phosphonomutase or related enzyme

0

0.38

1.05

2.6

2.8

2.7

-

-

-

-

-

-

 

15

cg1292

r

 

Flavin-containing monoxygenase 3

0

n.d.

3.87

-

-

2.4

-

-

4.4

-

-

-0.6

 

16

cg1293

r

 

Hypothetical membrane protein

3

n.d.

1.71

-

-

-

-

-

-

-

-

-

 

17

cg1312

  

Hypothetical membrane protein

4

n.d.

1.32

-

-

-0.2

1.9

2.1

4.7

5.3

4.4

6.3

 

18

cg1344

s

narG

Nitrate dehydrogenases 2 (Fe4S4 containing)

0

1.36

1.94

-

-

-0.6

-

-

-

-

-

-0.4

RipA, GlxR*

19

cg1345

s

narK

putative nitrate/nitrite transporter

12

n.d.

1.66

-

-

-

-0.4

-

3.0

1.5

-0.6

3.0

RipA, GlxR*

20

cg1695

  

SAM dependent methyltransferase

0

n.d.

1.72

-

-

-

-

-

-

-

-

-

 

21

cg1737

 

acn

Aconitase A

0

-0.58

1.66

4.4

5.3

6.2

4.4

5.0

4.9

2.2

2.6

2.5

RipA, RamA*, RamB*

22

cg1759

x

sufX

Predicted metal-sulfur cluster biosynthetic enzyme

0

0.94

1.34

-

-

-0.8

-0.4

-

-

-

-

-

SufR, SigM

23

cg1761

x

nifS2

Cysteine desulfhydrase, Selenocysteine lyase

0

0.44

1.47

2.3

2.0

3.2

-0.4

-

-

-

-

-

SufR, SigM

24

cg1762

x

sufC

Suf related ABC-type transporter, ATPase component

0

0.81

1.51

3.7

3.4

4.6

3.4

4.4

4.1

0.1

2.9

2.1

SufR, SigM

25

cg1764

x

sufB

Suf related ABC-type transporter SufB, permease component

0

0.93

1.81

2.8

3.4

5.0

3.4

3.4

3.8

0.1

0.4

1.6

SufR, SigM

26

cg1765

x

sufR

transcriptional regulator SufR

0

0.76

1.53

-

-

-

-

-

-

-

-

-

SufR, SigM

27

cg1790

 

pgk

Phosphoglycerate kinase

0

0.15

1.07

4.8

4.2

5.0

5.0

4.8

5.0

2.5

2.7

3.3

SigB*

28

cg1884

  

putative copper export protein CopC

2

-0.39

1.12

-

-

-

-

-

-

-

-

-

LexA

29

cg1904

  

ABC-type transporter, permease component

6

0.09

1.12

-

-

-

-

-

-

-

-0.6

1.2

 

30

cg2191

  

putative 3-demethylubiquinone-9 3-methyltransferase

0

n.d.

1.02

-

-

-

-

-

-

-

-

-

 

31

cg2274

ab

 

Hypothetical protein

0

-0.17

1.15

-0.6

0.4

1.8

-

-

-

-

-

-

 

32

cg2275

ab

 

Hypothetical protein

0

-0.28

1.03

1.0

2.4

1.3

-

-

-

-0.9

-

-

 

33

cg2320

  

ArsR type transcriptional regulator

0

-0.26

1.25

-

-

-

-

-

-

-

-

-

 

34

cg2572

  

Hypothetical protein

0

0.45

1.44

-

-

-

-

-

-

-

-

-

 

35

cg2636

 

catA1

Protocatechuate 3,4-dioxygenase beta subunit

0

n.d.

3.09

-

-

1.6

-

-

-

-

-

-

RipA, GlxR*

36

cg2736

 

bcp

putative 3-demethylubiquinone-9 3-methyltransferase

0

0.12

1.12

0.5

-0.5

0.4

-

-

-

-

-

-

 

37

cg2782

 

ftn

Ferritin-like protein

0

0.56

1.29

-

-

0.8

-

-

-

-

-

-

DtxR

38

cg2853

  

Hypothetical protein

0

0.41

1.4

0.6

-0.5

1.8

-

-

-

-

-

-

 

39

cg3117

ai

cysX

Hypothetical protein

0

3.5

1.08

-

-

-

-

-

-

-

-

-

DtxR, McbR*, CysR*

40

cg3118

ai

cysI

Sulfite reductase hemoprotein beta-component

0

3.5

1.06

0.6

1.5

2.4

3.5

2.1

-0.3

-

-

-

DtxR, McbR, CysR*

41

cg3236

  

MFS-type transporter

0

1.27

1.01

-

-

-0.8

-

-

-

-

-

-

 

42

cg3331

 

ogt

Methylated DNA-protein cysteine methyltransferase

0

0.2

1.34

-

-0.8

-

-0.1

-

1.3

-

-

-

 

Genes repressed at pH 9

1

cg0071

  

Metallo-beta-lactamase superfamily

0

n.d.

-1.01

-

-

-

-

-

-

-

-

-

 

2

cg0133

 

abgT

P-aminobenzoyl-glutamate transporter

13

-0.86

-1.02

-

-

-

-

-

-

0.3

3.7

2.1

 

3

cg0202

 

iolD

Putative acetolactate synthase

0

n.d.

-1.13

-

-

-

-

-

-

-

-

-

 

4

cg0265

  

putative ABC-type molybdate transporter, ATPase component

0

-0.22

-1.08

-

-

-

-

-

-

-

-

-

 

5

cg0303

 

leuA

2-isopropylmalate synthase

0

-0.97

-1.06

4.3

4.7

4.5

-

-0.3

-

-

-

-

 

6

cg0404

b

 

putative nitroreductase

0

1.77

-1.50

3.4

2.5

0.9

0.9

-

-

-0.9

-

-

 

7

cg0467

  

ABC-type cobalamin/Fe3+-siderophores transporter, periplasmic component

0

-0.50

-1.10

-

0.2

-

-

0.7

-

0.2

1.0

-0.4

DtxR

8

cg0527

  

ArsR type transcriptional regulator

0

-0.32

-1.13

-

-

-

-

-

-

-

-

-

DtxR

9

cg0589

  

ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component

0

-0.15

-1.01

-

-

-

1.2

-

-

0.1

-

-

DtxR

10

cg0623

  

putative ABC-type cobalt transporter, permease components

8

-1.05

-1.35

-

-

-

-

-

-

-

-

-

 

11

cg0624

h

 

Hypothetical membrane protein

2

-1.09

-1.09

-

-

-

-

-

-

1.3

1.6

-0.4

 

12

cg0625

h

 

putative terpenoide cylase

1

-1.28

-1.04

-

2.2

0.0

2.8

3.6

2.2

-

-0.6

-0.4

 

13

cg0723

 

crtE

Geranylgeranyl-pyrophosphate sythase

0

0.66

-1.01

-

-

-

-

-0.2

-

-

-

-

 

14

cg0748

  

ABC-type Fe3+-siderophores transporter, periplasmic components

0

-1.07

-2.14

-0.3

1.3

-

1.2

0.7

-

0.1

-0.6

-

DtxR

15

cg0756

 

cstA

putative carbon starvation protein A

16

-0.83

-1.56

-

-

-

1.9

2.1

1.0

2.1

2.8

-0.6

 

16

cg0767

m

 

Siderophore-interacting protein

0

-0.34

-2.99

0.5

-0.8

-

-

-

-

-

-

-

DtxR, RamB*

17

cg0768

m

 

ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component

0

-0.17

-2.03

-

-

-

1.7

1.7

-

-

-0.6

-

DtxR, RamB*

18

cg0924

n

 

ABC-type cobalamin/Fe3+-siderophores transporter, periplasmic component

0

-0.60

-2.91

4.8

5.2

2.7

3.6

4.1

0.7

5.1

4.5

3.4

DtxR

19

cg0927

n

 

ABC-type cobalamin/Fe3+-siderophores transporter, permease component

9

-0.10

-2.08

-

-

-

1.2

-0.2

0.0

3.0

3.3

-

DtxR

20

cg0928

n

 

ABC-type cobalamin/Fe3+-siderophores transporter, ATPase component

0

-0.14

-2.35

-

-0.8

-

3.3

4.0

-

1.8

1.0

-

DtxR

21

cg0952

o

mctB

putative monocarboxylate transporter subunit

2

-2.55

-1.32

-

0.5

-

2.4

4.7

4.1

-

2.1

-0.6

RamA, RamB

22

cg0953

o

mctC

monocarboxylate transporter

13

-2.44

-1.01

-

3.0

-0.2

1.9

4.7

4.7

3.2

4.5

3.2

RamA, RamB

23

cg1091

  

Hypothetical protein

0

0.95

-1.18

-

-

-

-

-

-

-

-

-

SigM*

24

cg1167

 

metS

putative methionine transporter subunit

0

-1.04

-1.43

-

-

-

-

-

-

-0.9

-

-0.6

 

25

cg1290

 

metE

5-methyltetrahydropteroyltri-glutamate-homocystein-emethyltransferase

0

0.65

-1.06

8.2

6.8

6.4

8.0

8.0

6.5

6.2

6.4

4.2

McbR*

26

cg1365

t

atpH

F0F1 ATP synthase delta subunit

0

-1.26

-1.03

1.9

2.3

1.3

3.9

4.8

4.7

3.2

4.1

3.4

SigH*

27

cg1367

t

atpG

F0F1 ATP synthase gamma subunit

0

-1.71

-1.11

1.1

4.2

3.4

3.3

4.9

4.7

4.0

4.0

2.5

SigH*

28

cg1451

 

serA

Phosphoglycerate dehydrogenase

0

-0.22

-1.10

6.5

5.4

6.1

7.7

7.5

7.2

5.3

5.3

4.2

 

29

cg1537

 

ptsM

PTS system mannose-specific EIIBCA component

10

-0.39

-1.06

2.6

3.5

1.8

5.9

5.6

6.0

6.6

6.4

6.1

RamB*, GlxR*

30

cg1859

  

Putative secreted protein

0

0.04

-1.34

-

1.7

-

-

3.6

1.5

0.1

5.0

-0.4

 

31

cg1930

z

 

Putative secreted hydrolase

0

-1.18

-3.26

-

-

-

-

-

-

-

-

-

DtxR

32

cg1931

z

 

Hypothetical protein

0

-0.88

-2.55

-

-

-

-

-

-

-0.7

-0.6

-

DtxR

33

cg2283

  

Hypothetical protein

0

0.00

-1.51

4.2

4.3

3.4

-

-0.2

-

-

-

-

 

34

cg2336

  

Putative secreted protein

0

-0.09

-1.31

-

-

-

-

2.1

-

3.6

3.9

1.9

 

35

cg2445

 

hmuO

putative heme oxygenase

0

-0.93

-1.19

-0.2

2.5

-

-

-0.2

-

-

-0.6

-

DtxR

36

cg2560

ad

aceA

Isocitrate lyase

0

-2.73

-2.19

-

4.9

2.4

-

-0.3

-

-

-

-

RamA, RamB

37

cg2962

  

Uncharacterized enzyme involved in biosynthesis of extracellular polysaccharides

0

0.45

-1.18

-0.3

0.2

-

-

-

-

-

-

-

 

38

cg3156

 

htaA

secreted protein implicated in iron acquisition and transport

0

-2.50

-2.76

-

-

-

-

-

-0.3

2.7

5.7

-

DtxR

39

cg3254

  

Hypothetical membrane protein

3

0.07

-1.29

-

-

-

-

-

-

-0.5

-

-

 
  1. Genes for which an increased or decreased mRNA level was found at pH 9 in comparison to pH 7.5. The gene locus tag, organisation in operons, the gene name, the (proposed) function of the protein as well as the predicted number of transmembrane helices are given. The results of the transcriptome analysis are given as induction factor at pH 6 and pH 9 in comparison to pH 7.5. Results of the proteome analysis are indicated for the soluble, membrane and envelope fraction. Regulators of particular genes are given based on the CoryneRegNet data base.
  2. 1 The geneID according to the accession number BX927147 was used.
  3. 2 Genes known to form an operon and closely adjacent, equally oriented genes that likely form an operon were indicated by equal Latin letters.
  4. 3 Prediction of transmembrane helices were performed by using the TMHMM 2.0 sever at http://www.cbs.dtu.dk/services/TMHMM/.
  5. 4 The induction factors are given as log2 values of the ration of mRNA levels at pH 6 and pH 9 in comparison to pH 7.5, respectively.
  6. 5 The determined relative peptide numbers are given as log2 values in order to allow calculation of ratios by simple subtraction of values. Peptide numbers found to be significantly altered at pH 6 and pH 9 in comparison to pH 7.5 are shown in bold and peptide numbers found to be significantly altered at pH 6 in comparison to pH 9 are shown in italic (see M&M section for the details of calculation).
  7. 6 Data whether a particular gene was experimentally proven or predicted (*) to be regulated by a transcription factor was obtained by using the data base CoryneRegNet http://coryneregnet.cebitec.uni-bielefeld.de/v4/.
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BMC Genomics

ISSN: 1471-2164

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