Identification of surface proteins in Enterococcus faecalis V583

BMC Genomics

Table 2 Additional proteins identified using the SDS-PAGE approach after different treatments.

				Peptide hits^d
Gene	Pfam^a	Gene products^b	Predicted localization^c	Untreated 2 hours	Trypsin 2 hours	Beads 2 hours	Coverage%
EF0517^f		2-dehydropantoate 2-reductase	Cytoplasmic			2	13.1
EF0968^f		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
EF2633^f		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
EF2715^f		Ribosomal protein L7/L12	Cytoplasmic			2	29.5
EF2857^e		Penicillin-binding protein 2B	N-terminal anchor			3	4.8
EF2903^e		ABC transporter, substrate-binding protein	Lipid anchor SP-II, LGA-CG		6	2	20.2
EF3106^e		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.

ISSN: 1471-2164