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Table 1 Identified proteins of E. faecalis V583 whose abundance is affected by the presence of 1% bovine bile—the three columns to the right show the results for cells harvested at three different time points (20, 60 and 120 minutes)

From: Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile

Spot no.

Functional class a

Putative function a

ORF

Mass (kDa)

pI b

Coverage c

No. of peptides matched

Fold ratio d

T(20) T(60) T(120)

1 e

Fatty acid and phospholipid metabolsim

Enoyl-(acyl carrier protein) reductase

EF0282

26.9

5.29

42

14

1.01

0.67

0.3

2 e

 

Acetyl_coA carboxylase, biotin carboxyl carrier protein

EF2879

17.6

4.23

40

8

0.92

0.39

0.28

3 e

 

(3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase

EF0284

16.4

5.73

22

5

1.09

0.71

0.49

4 e

 

3-oxoacyl-(acyl-carrier-protein) synthase II

EF0283

43.5

5.11

40

12

0.51

0.87

0.41

5 e

 

3-ketoacyl-(acyl-carrier-protein) reductase

EF2881

26.1

5.92

35

10

1.70

0.37

0.55

6

Transport and binding protein

Phosphocarrier protein HPr

EF0709

9.3

4.92

13

11

0.99

0.70

0.52

7 e

 

PTS system, mannose-specific IIAB components

EF0020

35.5

5.11

50

22

1.62

3.06

0.90

8

 

peptide ABC transporter, ATP-binding protein

EF0912

35.9

5.97

20

7

1.10

1,00

0.46

9 e

Amino acid biosynthesis

Ornithine carbamoyltransferase

EF0105

38.1

5.02

18

5

1.03

0.64

3.48

10 e

 

Decarboxylase, putative

EF0634

71.96

5.14

47

29

0.52

1.21

1.86

11

Other cellular processes

Glutathione reductase

EF3270

49.6

5.23

21

10

2.42

0.96

0.87

12

 

Dps family protein

EF3233

17.9

4.56

46

6

0.51

0.81

1.23

13

 

General stress protein, putative

EF1744

20.5

4.61

31

6

0.88

0.66

0.52

14

 

Cell division protein DivIVA

EF1002

26.6

4.53

62

16

0.61

1.21

3.5

15 e

Energy metabolism

Deoxyribose-phosphate aldolase

EF0174

23.3

4.65

48

10

1.39

1.28

0.47

16 f

 

Formate acetyltransferase

EF1613

84.5

5.31

11

8

1.00

0.95

2.87

17 e

 

Fumarate reductase flavoprotein subunit

EF2556

53.8

5.26

10

6

0.86

1.57

2.26

18

 

Phosphoglycerate mutase 1

EF0195

26.0

5.09

41

11

0.87

1.13

0.36

19 f

 

Formate acetyltransferase

EF1613

84.7

5.31

14

11

0.94

1.21

2.09

20 e

 

V-type ATP synthase subunit B

EF1499

51.3

5.03

18

8

0.59

2.02

1.29

21

 

Pyruvate kinase

EF1046

62.6

4.99

41

25

2.99

3.61

1.09

22

 

Enolase

EF1961

46.5

4.56

54

22

1.46

0.98

0.45

23

 

Thioredoxin

EF1405

11.7

4.35

66

9

1.49

0.40

0.60

24 e

Cell wall/membrane biogenesis

D-fructose-6-phosphate amidotransferase

EF2151

65.7

4.93

24

12

1.93

1.13

2.12

25

Coenzyme transport and metabolism

Naphthoate synthase

EF0445

30.0

5.24

39

10

0.89

1.46

0.43

26 e

 

2-dehydropantoate 2-reductase

EF2445

34.7

5.08

3

1 (39)g

1.32

1.40

0.46

27 e

Transcription and translation

Transcriptional regulator, AraC family

EF0432

34.6

6.76

25

7

0.91

2.64

0.18

28

 

Cold-shock domain-contain protein

EF2925

7.3

4.35

60

5

0.97

0.33

0.37

29

 

Peptide deformylase

EF3066

21.0

5.08

48

6

1.15

0.77

0.5

30

 

30S ribosomal protein S2

EF2398

29.5

5

24

8

2.82

1.87

0.81

31 e

 

Ribosomal protein L31

EF1171

10.1

5.57

95

10

1.65

0.36

0.29

32

 

Elongation factor G

EF0200

76.6

4.8

23

19

0.93

0.87

1.97

33

 

30S ribosomal protein S3

EF0212

24.4

9.8

12

3

0.86

2.19

0.68

34

 

Phenylalanyl-tRNA synthetase subunit beta

EF1116

88.8

4.76

12

11

0.87

0.97

2.18

35

 

Methionyl-tRNA formyltransferase

EF3123

34.3

6.06

3

1 (48)g

0.96

1.29

0.41

36

Hypothetical protein

Hypothetical protein EF1967

EF1967

20.7

5.98

20

5

0.51

0.86

0.25

37

 

Hypothetical protein EF2909

EF2909

12.1

4.33

52

7

0.99

0.47

0.69

38

 

Hypothetical protein EF2763

EF2763

12.1

4.7

43

5

1.25

0.43

0.66

39

 

Hypothetical protein EF2888

EF2888

8.9

4.54

42

6

1.07

0.32

0.43

40 e

 

Hypothetical protein EF3184

EF3184

26.4

4.86

28

7

0.80

0.31

0.38

41 e

 

Hypothetical protein EF3186

EF3186

25.7

4.91

28

8

1.44

1.80

0.44

42

 

Hypothetical protein EF0123

EF0123

85.5

7.23

4

3

1.89

2.11

0.43

43

 

Hypothetical protein EF0352

EF0352

29.3

6.91

4

1 (61)g

1.44

2.18

0.48

44

 

Hypothetical protein EF2174

EF2174

99.6

8.68

36

33

1.54

1.41

0.32

45

 

Hypothetical protein EF 2104

EF2104

43.6

4.88

18

6

0.82

2.36

1.17

46

Protein fate

Glutamyl-aminopeptidase

EF3037

39.4

5.68

22

8

0.87

1.90

1.01

47 e

 

DnaK protein

EF1308

65.5

4.59

56

31

1.11

1.20

2.21

48 e

 

Heat shock protein GrpE

EF1307

20.1

4.5

26

8

1.10

0.30

0.30

49 f

Nucleotid metabolism

Ribose-phosphate pyrophosphokinase

EF3163

35.4

6.16

22

9

1.21

2.5

0.47

50

 

Inositol-5-monophosphate dehydrogenase

EF3293

52.8

5.7

50

84

1.24

2.0

1.05

51 f

 

Ribose-phosphate pyrophosphokinase

EF3163

35.5

6.16

15

7

0.95

1.21

0.38

52

Unknown function

DNAbinding response regulator VicR

EF1193

26.9

5.17

15

6

0.87

1.20

0.51

53

 

Glyoxalase family protein

EF2591

31.7

4.85

50

15

1.04

0.99

0.30

54

 

PhnA protein

EF1374

12.4

5.01

66

6

0.9

0.55

0.47

55

 

Oxidoreductase, aldo/keto reductase family

EF1138

31.0

5.28

18

5

0.97

1.22

0.44

  1. a The putative function is based on the JCVI Comprehensive Microbial Resource database http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi.
  2. bThe pI values are theoretical values calculated from the protein sequences
  3. c The coverage shows the percentage of the protein that is covered by the identified peptides.
  4. d Proteins with values over 1 are up-regulated in response to bile, proteins with values below 1 are down-regulated. Values representing a change larger than 1.9-fold are printed in bold face.
  5. e Proteins that also were shown to be regulated in a transcriptome study of bile responses in E. faecalis V583 [15]; see text for details.
  6. f Note that proteins EF3163 (spots 49 & 51) and EF1613 (spots 16 & 19) were identified twice.
  7. gThe value in parenthesis shows the probability-based Mowse score for proteins that were identified by only one peptide (in all cases using the LC-LTQ Orbitrap). The Mowse score equals -10*Log (P), where P is the probability that the observed match is a random event; Mowse scores greater than 38 indicate identity or extensive homology (p < 0.05).
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