Table 1

Proteins identified by LC-MS/MS analysis of tryptic fragments obtained after different treatments of intact E. faecalis V583.

Peptide hitsd


Gene

Pfama

Gene productb

Predicted localizationc

Un-treated 1 hour

Un-treated 2 hours

Trypsin 1 hour

Trypsin 2 hours

Beads 1 hour

Beads 2 hours

Total cover-age%


EF_B0004e

Bacterial extracellular solute-binding proteins, family 5

TraC protein

Cell wall

2

2

(1)

(1)

13.0

EF0071

Contains trehalase domain

Putative lipoprotein

Lipid anchor SP-II, VVS-CF

(3)

2

10.0

EF0123

Contains nine Clostridial hydro-phobic W domain

Hypothetical protein

Secreted SP-I, AYA-LE

5

2

9

7

(1)

4

23.2

EF0164

Putative lipoprotein

Lipid anchor SP-II, FTS-CG

2

3

2

3

2

32.3

EF0176f

Basic membrane protein

Hypothetical protein

Lipid anchor SP-II, LAA-CG

3

5

2

25.7

EF0177f

Basic membrane protein

Hypothetical protein

Lipid anchor SP-II, LAA-CG

5

7

2

32.1

EF0195g

Phospho-glycerate mutase 1

Cytoplasmic

2

(1)

10.5

EF0199g

30S ribosomal protein S7

Cytoplasmic

2

30.1

EF0200g

Elongation factor G

Cytoplasmic

(1)

7

7

22.4

EF0201fg

Elongation factor Tu

Cytoplasmic

(1)

2

11

8

5

4

47.1

EF0205

30S ribosomal protein S10

Cytoplasmic

2

(1)

29.4

EF0206g

50S ribosomal protein L3

Cytoplasmic

2

5

23.4

EF0207g

50S ribosomal protein L4

Cytoplasmic

(1)

2

15.9

EF0211

50S ribosomal protein L22

Cytoplasmic

(1)

2

2

(1)

(1)

17.4

EF0218g

50S ribosomal protein L5

Cytoplasmic

(1)

3

21.2

EF0221g

50S ribosomal protein L6

Cytoplasmic

(1)

3

27.0

EF0223

50S ribosomal protein L18

Cytoplasmic

(1)

2

39.0

EF0226

50S ribosomal protein L15

Cytoplasmic

(1)

(2)

2

(1)

(1)

(1)

21.2

EF0228

Adenylate kinase

Cytoplasmic

2

2

19.4

EF0234g

50S ribosomal protein L17

Cytoplasmic

2

(1)

26.0

EF0304

-

Putative lipoprotein

Lipid anchor SP-II, LSA-CS

(1)

2

2

20.5

EF0394

Cysteine-rich secretory protein family

Secreted antigen, putative

Secreted SP-I, ALA-DN

2

3

(1)

17.8

EF0417

-

Hypothetical protein

Secreted SP-I, VNA-LN

3

2

4

4

3

11.2

EF0502

-

Hypothetical protein

Multiple transmembrane proteins

2

7.9

EF0633

tyrosyl-tRNA synthetase

Cytoplasmic

2

6.9

EF0685f

Rotamase family protein

Lipid anchor SP-II, LAA-CS

2

10.8

EF0737

Amidase

N-terminal anchor

2

6.8

EF0907f

-

Peptide ABC transporter peptide-binding protein

Lipid anchor SP-II, LAA-CG

2

16.4

EF0916

50S ribosomal protein L20

Cytoplasmic

(1)

(1)

2

27.7

EF0970e

50S ribosomal protein L27

Cytoplasmic

2

2

34.7

EF0991

Penicillin-binding protein C

N-terminal anchor

(1)

2

11.2

EF1033

Lipoamidase

Cell wall anchored LPxTG SP-I, AQE-SI

2

2

4.7

EF1046g

Pyruvate kinase

Cytoplasmic

(2)

(2)

2

11.6

EF1167g

Fructose-bisphosphate aldolase

Cytoplasmic

(1)

(2)

2

4

3

(1)

30.8

EF1264f

Sulfatase domain-containing protein

Multiple trans-membrane proteins

2

10

11

(1)

5

29.8

EF1308fg

Dnak protein

Cytoplasmic

(1)

2

3

23.7

EF1319

-

Hypothetical protein

N-terminal anchor

(1)

3

23.3

EF1379

Alanyl-tRNA synthetase

Cytoplasmic

2

3.3

EF1420

-

Hypothetical protein

Lipid anchor SP-II, MTA-CS

2

(1)

15.6

EF1523e

-

Hypothetical protein

Cytoplasmic

(1)

3

6.4

EF1613fg

Formate acetyltransferase

Cytoplasmic

3

(2)

13.4

EF1818f

Coccolysin

Secreted SP-I, VAA-EE

8

3

8

5

(1)

2

45.1

EF1898

50S ribosomal protein L19

Cytoplasmic

(1)

2

30.4

EF1961fg

Enolase

Cytoplasmic

2

4

(1)

25.7

EF1964fg

Glycer-aldehyde-3-phosphate dehydrogenase (GAPDH)

Cytoplasmic

3

8

36.0

EF2144

-

Putative lipoprotein

Lipid anchor SP-II LTA-CS

(1)

2

(1)

2

22.4

EF2174

Glycosyl hydrolases family 25

Hypothetical protein

Secreted SP-I, ASG-EE

3

4.5

EF2398g

30S ribosomal protein S2

Cytoplasmic

(1)

2

4

2

(1)

19.2

EF2556f

Fumarate reductase flavoprotein subunit

Lipid anchor SP-II, ATG-CT

40

39

40

41

22

37

79.2

EF2718ge

50S ribosomal protein L1

Cytoplasmic

2

2

24.0

EF2746

DltD protein

N-terminal anchor

(1)

2

2

3

(1)

2

10.4

EF2860f

YkuD putative, peptido-glycan binding domain

Cell wall, SP-I VYF-QS,

2

6

5

9

(1)

7

36.3

EF2864

-

Hypothetical protein

Lipid anchor SP-II, LTA-CR

2

2

3

4

2

2

25.7

EF2925g

Cold-shock domain-contain protein

Cytoplasmic

(1)

2

(1)

2

45.5

EF3041f

Pheromone binding protein

Lipid anchor SP-II, LAA-CG

2

3

2

7

2

24.3

EF3256f

Pheromone cAD1 precursor lipoprotein

Lipid anchor SP-II, LAA-CG

(1)

2

19.4

EFA0003

TraC protein

Lipid anchor SP-II, LGA-CN

2

9.4


Further details on the Sequest-based protein identification process are provided in the Materials and Methods section and in Table S5 (Additional file 4).

aSignificant hits (or absence thereof, indicated by -) obtained after searches in Pfam [25] for putative and hypothetical proteins.

bAll data extracted from the LocateP database [12] with two exceptions: EF1033 (annotated as 6-aminohexanoate-cyclic-dimer hydrolase; annotated as putative, in LocateP) and EF2860 annotated as ErfK/YbiS/YcfS/YnhG family protein; annotated as putative, in LocateP).

cPredicted localization and potential cleavage site. Localization is based on LocateP annotations, with seven exceptions (for Tables 1 and 2 in total) that are all explicitly mentioned in the text. See also Table 3.

dThe column shows the number of peptide hits from four biological replicates. Protein identifications were considered significant using the criteria described in Materials and Methods. One criterium was the detection of at least two different peptides; another the detection of peptides in at least two independent parallels; these criteria are met for all listed proteins. Putative, non-significant additional identifications of these proteins (based on just one peptide and/or on just one parallel) are indicated in parentheses.

eSecretomeP value >0.5; this means that the protein is predicted to be secreted via a "non-classical" pathway.

fProteins that have been identified as being localised on the surface in a previous study of E. faecelis JH2-2 [13].

gCytoplasmic proteins that have been identified in other studies of the surface proteomes of Gram-positive bacteria. See text for references.

Bøhle et al. BMC Genomics 2011 12:135   doi:10.1186/1471-2164-12-135

Open Data