Skip to main content

Table 3 Abundance differences of Y. pestis proteins profiled in cytoplasmic fractions of iron-rich vs. iron-starved cells

From: Proteomic analysis of iron acquisition, metabolic and regulatory responses of Yersinia pestis to iron starvation

Spot No a)

Gene locus

b)

gene name

c)

Protein description c)

Subc. Loc.

d)

Fur/RyhB e)

Mascot Score

f)

exp Mr (Da)

exp pI

26°C, Vs (-Fe) g)

26°C, Vs (+Fe) h)

26-ratio -Fe/+Fe i)

26°C P-value j)

37-ratio -Fe/+Fe k)

1

y0015

aceB

malate synthase A

CY

Fur

688

63974

5.86

0.06

1.73

0.036

0.000

0.421

2

y0016

aceA

isocitrate lyase

CY

 

741

54571

5.47

0.38

4.19

0.090

0.000

0.408

3

y0047

glpK

glycerol kinase

CY

 

828

60235

6.01

0.07

0.33

0.198

0.000

0.570

4

y0320

oxyR

DNA-binding transcriptional regulator OxyR

CY

 

510

36649

5.82

0.49

0.40

1.237

0.004

0.791

5

y0548

metF2

putative methylenetetrahydrofolate reductase

U

 

321

31848

5.73

1.77

1.06

1.677

0.000

0.543

6

y0617

frdA

fumarate reductase, anaerobic, flavoprotein subunit

PP

 

437

80764

5.77

-

0.23

< 0.05

N.D.

0.339

7

y0668

mdh

malate dehydrogenase

ML

 

2170

34545

5.55

1.03

1.80

0.576

0.001

1.253

8

y0771

acnB

aconitate hydrase B

CY

RyhB

1408

95757

5.13

0.22

0.98

0.220

0.000

0.229

9

y0801

erpA

iron-sulfur cluster insertion protein ErpA

U

 

76

10730

4.41

1.41

0.57

2.492

0.008

1.260

10

y0818

cysJ

sulfite reductase subunit alpha

U

 

340

72332

4.97

-

0.20

< 0.05

N.D.

< 0.05

11

y0854

fumA

fumarase A

CY

RyhB

255

68184

6.02

-

0.50

< 0.05

N.D.

< 0.05

12

y0870

katY

catalase; hydroperoxidase HPI(I)

U

 

768

78569

6.32

0.11

0.48

0.231

0.000

0.081

13

y0888

luxS

predicted S-ribosylhomocysteinase

CY

 

670

19733

5.46

0.79

0.30

2.617

0.000

2.164

14

y0988

ahpC

putative peroxidase

CY

 

898

24298

5.75

5.02

6.10

0.823

0.202

1.376

15

y1069

ymt

murine toxin

U

 

7052

67771

5.64

13.61

9.61

1.415

0.143

1.359

16

y1069

ymt

murine toxin, C-t. fragment

U

 

245

33893

5.30

0.89

0.19

4.634

0.000

N.D.

17

y1069

ymt

murine toxin, N-t. fragment

U

 

164

39074

6.11

0.84

0.17

4.860

0.000

N.D.

18

y1208

fur

ferric uptake regulator

CY

 

95

13425

6.16

0.11

0.17

0.651

0.055

N.D.

19

y1282

yfiD

formate acetyltransferase, glycyl radical cofactor GrcA

CY

 

521

13866

4.75

1.27

2.27

0.560

0.000

0.456

20

y1334

iscS

selenocysteine lyase/cysteine desulfurase

U

 

408

51519

5.96

-

-

N.D.

N.D.

0.59

21

y1339

hscA

chaperone protein HscA

CY

 

384

49149

5.53

-

-

N.D.

N.D.

0.48

22

y1342

pepB

aminopeptidase B

U

 

855

52355

5.69

0.12

0.75

0.153

0.000

0.681

23

y1452

ypeA

predicted acyltransferase

CY

 

188

12771

4.83

0.39

0.14

2.844

0.000

3.300

24

y1677

dps

DNA starvation/stationary phase protection protein

U

 

724

14844

5.94

0.27

0.80

0.337

0.000

0.808

25

y1791

pepT

putative peptidase T

CY

 

310

51106

5.89

-

0.18

< 0.05

N.D.

N.D.

26

y1802

icdA

isocitrate dehydrogenase, specific for NADP+

CY

 

459

53760

5.46

0.92

1.80

0.511

0.002

1.238

27

y1934

sufA

iron-sulfur cluster assembly scaffold protein SufA

U

Fur

156

13330

4.48

0.13

-

> 20

N.D.

2.170

28

y1935

sufB

cysteine desulfurase activator complex subunit SufB

U

Fur

330

70431

4.69

0.25

0.06

4.022

0.000

3.836

29

y1938

sufS

selenocysteine lyase

U

Fur

369

46479

5.55

0.65

0.15

4.294

0.000

2.420

30

y1944

pykF

pyruvate kinase I

CY

 

525

62400

5.93

0.38

1.23

0.309

0.525

1.265

31

y1951

sodB

superoxide dismutase, iron

U

RyhB

285

21541

5.75

0.16

0.94

0.172

0.000

>20

32

y1968

gst

glutathionine S-transferase

CY

 

1326

25438

6.25

3.15

2.14

1.471

0.054

1.247

33

y1990

tpx

thiol peroxidase

U

 

479

18655

5.13

3.02

3.06

0.986

0.816

1.198

34

y2063

acnA

aconitate hydratase A

CY

RyhB

565

97825

6.08

-

0.22

< 0.05

N.D.

< 0.05

35

y2255

yebC

hypothetical protein y2255

U

 

219

39957

4.74

0.11

0.40

0.285

0.000

0.777

36

y2524

ftnA

ferritin iron storage complex protein

CY

RyhB

223

14143

4.99

2.67

1.61

1.656

0.000

1.275

37

y2790

pflB

formate acetyltransferase 1

CY

 

804

80979

5.49

0.63

1.38

0.454

0.000

0.980

38

y2802

trxB

thioredoxin reductase

ML

 

702

37892

5.21

0.96

0.99

0.967

0.446

1.037

39

y2821

poxB

pyruvate oxidase

CY

 

448

67362

5.91

1.89

0.33

5.722

0.000

3.710

40

y2981

katE

catalase; hydroperoxidase HPII(III)

CY

RyhB

481

66313

6.09

0.04

1.20

0.032

0.000

0.113

41

y3064

sucD

succinyl-CoA synthetase, alpha subunit

CY

 

597

33015

6.04

0.33

0.91

0.363

0.000

0.472

42

y3067

sucA

2-oxoglutarate dehydrogenase (decarboxylase component)

CY

 

1153

102739

5.98

-

0.43

< 0.05

N.D.

0.277

43

y3069

sdhA

succinate dehydrogenase, flavoprotein subunit

ML

RyhB

965

75497

5.56

0.05

0.21

0.248

0.000

0.207

44

y3142

fldA3

predicted flavodoxin

CY

 

267

11842

4.37

0.93

0.39

2.395

0.003

1.502

45

y3499

yqhD

NADP-dependent dehydrogenase

CY

 

369

46727

5.76

0.35

1.922

0.179

0.001

1.404

46

y3600

uxaC

D-glucuronate/D-galacturonate isomerase

U

 

842

56072

5.75

0.09

-

> 20

N.D.

2.383

47

y3673

hcp1

hemolysin-coregulated protein

U

 

508

14459

5.16

8.35

4.38

1.908

0.001

N.D.

48

y3675

-

putative type VI secretion protein

CY

 

392

25923

4.62

0.43

0.16

2.735

0.001

N.D.

49

y3802

bipA

putative GTP-binding factor

CY

 

435

82945

5.27

-

-

N.D.

N.D.

4.096

50

y3966

tauD

taurine dioxygenase

U

 

228

40946

6.12

0.50

0.16

3.129

0.001

N.D.

51

y3988

bfr

bacterioferritin, iron storage and detoxification protein

CY

RyhB

143

17087

4.92

0.22

0.29

0.779

0.006

0.927

52

y4080

sodA

superoxide dismutase, manganese

U

 

597

25405

5.86

4.11

5.10

0.805

0.074

0.877

75

y2402

ybtT

yersiniabactin thioesterase

U

Fur

123

34389

5.88

0.10

-

> 20

N.D.

12.08

111

y3066

sucB

2-oxoglutarate dehydrogenase (dihydrolipoyltranssuccinase E2 component)

CY

 

789

58844

5.38

0.29

0.76

0.38

0.0468

0.38

  1. a) spot number as denoted in Figure 4; b) protein accession number and locus tag as listed in Y. pestis KIM genome database (NCBI); c) gene name and protein description from the KIM database or a conserved E. coli K12 ortholog http://www.ecocyc.org, if >65 pct. sequence identity; d) subcellular localization based on PSORTb data: CY, cytoplasm; ML: multiple localizations; PP, periplasm; U: unknown; e) proven or putative regulation by Fur or a Fur-dependent small RNA (e.g. RyhB); f) highest Mascot score for a protein from LC-MS/MS or MALDI data; g) Vs (-Fe): average spot volume (n ≥ 3) in 2D gels for iron-depleted growth conditions at 26°C as shown in Figure 4; h) Vs (+Fe): average spot volume (n ≥ 3) in 2D gels for iron-supplemented growth conditions at 26°C; i) spot volume ratio (-Fe/+Fe) at 26°C, N.D.: not determined; -: no spot detected; j) two-tailed t-test p-value for spot abundance change at 26°C, 0.000 stands for < 0.001; k) average spot volume ratio (-Fe/+Fe) at 37°C; additional data for the statistical spot analysis at 37°C are part of Additional Table 1.