Table 2

Additional proteins identified using the SDS-PAGE approach after different treatments.

Peptide hitsd


Gene

Pfama

Gene productsb

Predicted localizationc

Untreated 2 hours

Trypsin 2 hours

Beads 2 hours

Coverage%


EF0517f

2-dehydropantoate 2-reductase

Cytoplasmic

2

13.1

EF0968f

50S ribosomal protein L21

Cytoplasmic

2

35.3

EF2221

ABC transporter. substrate-binding protein

Lipid anchor SP-II, LSA-CG

2

8.8

EF2224

Four DUF11 repeats

Cell wall surface anchor family protein

Cell wall, LPxTG, SP-I, MNA-FA

2

1.4

EF2633f

Chaperonin. GroEL

Cytoplasmic

4

9.2

EF2713

Gram positive anchor

Cell wall surface anchor family protein

Cell wall, LPxTG, SP-I VWA-ED

2

9.4

EF2715f

Ribosomal protein L7/L12

Cytoplasmic

2

29.5

EF2857e

Penicillin-binding protein 2B

N-terminal anchor

3

4.8

EF2903e

ABC transporter, substrate-binding protein

Lipid anchor SP-II, LGA-CG

6

2

20.2

EF3106e

Peptide ABC transporter. peptide-binding protein

Lipid anchor SP-II, LAA-CG

2

3.4

EF3257

Pyridine nucleotide-disulfide family oxidoreductase

Multiple transmembrane proteins

2

7.3

EFA0052

Surface exclusion protein Sea1

Cell wall LPxTG SP-1, VQA-AE

2

2

2

6.3


The gel approach yielded 25 unique proteins in total but only 12 of these were novel compared to the list of Table 1; see Additional file 2 for more details. Further details on the Sequest-based protein identification process are provided in the Materials and Methods section and in Table S6 (Additional file 5).

aSignificant hits obtained after searches in Pfam [25] for putative and hypothetical proteins.

bData extracted from the LocateP database [12].

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.

dNumber of peptide hits in each of the three treatments. Protein identifications were considered significant using the criteria described in Materials and Methods. Proteins were only considered a significant hit if at least two unique peptides were found.

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

fCytoplasmic 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

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