Table 1.
Unique proteins found in this study. Salient features of mass spectrometry experiments are contained in Supplementary Table 1. Peptides matched in Mascot searches are listed in Supplementary Table 2. Fragmentation spectra for single-peptide protein indentifications are shown in Supplementary Figure 2.
| Protein name | Locus in Enterococcus faecalis OG1RF (a) |
Cellular location (b) |
TMs (c) | Type (d) |
|---|---|---|---|---|
| Proteins involved in transport | ||||
| Peptide ABC transporter | Contig 35 (24586–25509) | M | 6 | ABC1 |
| Peptide ABC transporter | Contig 35 (26499–27443) | S | 0 | ABC1 |
| Peptide ABC transporter | Contig 35 (27451–28450) | S | 0 | ABC1 |
| Cobalt import ATP-binding protein CbiO 1 | Contig 10 (31446–32285) | S | 0 | ABC2 |
| Cobalt import ATP-binding protein CbiO 2 | Contig 10 (30601–31476) | S | 0 | ABC2 |
| Cobalt transport family protein | Contig 10 (29807–30604) | M | 5 | ABC2 |
| Amino acid ABC transporter | Contig 5 (209776–210513) | S | 0 | ABC3 |
| Amino acid ABC transporter | Contig 5 (211684–212683) | M | 6 | ABC3 |
| ABC transporter, ATP-binding protein | Contig 10 (72643–73276) | S | 0 | ABC4 |
| ABC transporter, permease protein | Contig 10 (71091–72090) | M | 7 | ABC4 |
| ABC transporter | Contig 27 (10556–10969) | M | 5 | ABC5 |
| ABC transporter | Contig 27 (10974–11849) | M | 6 | ABC5 |
| ABC transporter | Contig 36 (11529–12271) | L | 0 | ABC6 |
| ABC transporter | Contig 36 (12552–13460) | M | 5 | ABC6 |
| ABC transporter | Contig 36 (13487–14425) | M | 4 | ABC6 |
| Amino acid ABC transporter | Contig 10 (23469–24468) | M | 3 | ABC7 |
| ABC transporter | Contig 5 (242535–243096) | M | 5 | ABC8 |
| ABC transporter | Contig 5 (243812–244811) | M | 5 | ABC8 |
| Peptide ABC transporter | Contig 4 (9909–10908) | L | 0 | ABC9 |
| Phosphate import ATP-binding protein pstB 1 | Contig 8 (185123–185881) | S | 0 | ABC10 |
| Phosphate import ATP-binding protein pstB 2 | Contig 8 (184303–185112) | S | 0 | ABC10 |
| Cell division ABC transporter | Contig 8 (180445–181329) | M | 4 | ABC11 |
| ABC transporter | Contig 27 (23767–24766) | M | 5 | ABC12 |
| ABC transporter | Contig 27 (25491–26490) | M | 6 | ABC12 |
| Glycine betaine/L-proline ABC transporter | Contig 32 (97401–99107) | M | 7 | ABC13 |
| PTS system, mannose-specific IIAB components | Contig 11 (5988–6947) | S | 0 | PTS1 |
| PTS system, mannose-specific IIC component | Contig 11 (7015–7818) | M | 7 | PTS1 |
| PTS system, mannose-specific IID component | Contig 11 (7841–8752) | M | 5 | PTS1 |
| PTS system, fructose-specific family, IIABC components | Contig 5 (165638–166637) | M | 8 | PTS2 |
| PTS family glucose porter, IICBA component | Contig 3 (52672–53671) | M | 9 | PTS3 |
| PTS system, IIC component | Contig 7 (40824–41823) | M | 8 | PTS4 |
| PTS system, IIC component | Contig 3 (73328–74327) | M | 10 | PTS5 |
| PTS system, IID component | Contig 8 (141368–142177) | M | 5 | PTS6 |
| C4-dicarboxylate transporter, putative | Contig 11 (97235–98159) | M | 8 | IT1 |
| Citrate transporter | Contig 23 (2321–3320) | M | 10 | IT2 |
| Major facilitator family transporter | Contig 11 (65570–66569) | M | 11 | MFS1 |
| Amino acid permease family protein | Contig 37 (11438–12437) | M | 12 | MFS2 |
| Amino acid permease family protein | Contig 5 (76782–77781) | M | 11 | |
| Formate/nitrite transporter family protein | Contig 41 (2254–3057) | M | 5 | |
| Mn2+/Fe2+ transporter, NRAMP family | Contig 13 (12302–13301) | M | 12 | |
| Na+/H+ antiporter | Contig 26 (63390–64389) | M | 11 | |
| Cation-transporting ATPase, E1–E2 family | Contig 8 (39552–40551) | M | 8 | |
| Large-conductance mechanosensitive channel | Contig 35 (74751–75200) | M | 2 | |
| V-type ATPase, subunit K | Contig 3 (30122–30595) | M | 3 | |
| V-type ATPase, subunit I | Contig 3 (28115–29114) | M | 8 | |
| Proteins involved in biogenesis | ||||
| Preprotein translocase, SecY subunit | Contig 10 (39044–40043) | M | 9 | |
| OG1RF_Possible O-antigen polymerase | Contig 30 (31004–32003) | M | 12 | |
| Septation ring formation regulator ezrA | Contig 26 (26980–27979) | M | 1 | |
| Cell division protein DivIVA | Contig 7 (57857–58558) | S | 0 | |
| Penicillin-binding protein 4 | Contig 32 (211716–212715) | S | 0 | |
| Penicillin-binding protein 2A | Contig 5 (126101–127100) | M | 1 | |
| Penicillin-binding protein 2B | Contig 18 (13934–14933) | M | 1 | |
| Preprotein translocase, YajC subunit | Contig 4 (20567–20944) | M | 1 | |
| Amidase, putative | Contig 5 (187646–188645) | S | 0 | |
| DltD protein | Contig 17 (5604–6603) | S | 0 | |
| Foldase protein prsA | Contig 5 (134096–134800) | L | 0 | |
| Proteins involved in metabolism | ||||
| ATP synthase subunit alpha | Contig 32 (122707–123706) | S | 0 | |
| ATP synthase subunit beta | Contig 32 (125269–126268) | S | 0 | |
| ATP synthase gamma chain | Contig 32 (124279–125187) | S | 0 | |
| ATP synthase epsilon chain | Contig 32 (126692–127111) | S | 0 | |
| ATP synthase subunit b | Contig 32 (121619–122149) | M | 1 | |
| Oxidoreductase, pyridine nucleotide-disulfide family | Contig 34 (7771–8770) | M | 5 | |
| Formate acetyltransferase | Contig 39 (81299–82298) | S | 0 | |
| Enolase | Contig 8 (18945–19944) | S | 0 | |
| Glucose-6-phosphate isomerase | Contig 3 (25333–26332) | S | 0 | |
| Ornithine carbamoyltransferase | Contig 11 (94338–95337) | S | 0 | |
| Decarboxylase | Ccontig 5 (74669–75668) | S | 0 | |
| 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | Contig 10 (58445–59131) | S | 0 | |
| Glyceraldehyde 3-phosphate dehydrogenases | Contig 8 (15688–16687) | S | 0 | |
| Thiamin biosynthesis lipoprotein ApbE | Contig 34 (5310–6309) | L | 0 | |
| Fumarate reductase flavoprotein subunit | Contig 32 (179927–180597) | L | 0 | |
| Proteins involved in signalling | ||||
| Probable protease eep | Contig 38 (3317–4016) | M | 4 | |
| Serine/threonine-protein kinase PrkC | Contig 35 (43308–44307) | M | 1 | |
| Sensor histidine kinase | Contig 7 (797–1796) | M | 2 | |
| Pheromone cAD1 lipoprotein | Contig 34 (6564–7272) | L | 0 | |
| Pheromone binding protein | Contig 28 (61901–62900) | L | 0 | |
| Proteins involved in lipid biosynthesis | ||||
| Glycerophosphoryl diester phosphodiesterase family protein | Contig 8 (75630–76629) | M | 9 | |
| (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase 1 | Contig 43 (1042–1476) | S | 0 | |
| (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase 2 | Contig 18 (35776–36201) | S | 0 | |
| Proteins involved in other processes | ||||
| Regulatory protein pfoR, putative | Contig 11 (86464–86967) | M | 8 | |
| Transcriptional regulator, PSR protein | Contig 39 (33224–33935) | M | 1 | |
| Transcriptional regulator lytR | Contig 1 (102661–103572) | S | 0 | |
| Bacterial sugar transferase | Contig 30 (42555–43341) | M | 5 | |
| Proteins with no annotated function | ||||
| hypothetical protein EF2929 | Contig 27 (32738–33728) | M | 11 | |
| Putative uncharacterized protein | Contig 39 (151365–151832) | M | 1 | |
| Membrane protein | Contig 11 (20435–21434) | M | 12 | |
| hypothetical protein OG1RF_0150 [Enterococcus faecalis OG1RF] | Contig 30 (18903–19902) | M | 10 | |
| Membrane protein | Contig 30 (1279–1750) | M | 10 | |
| Putative uncharacterized protein | Contig 15 (106536–106931) | M | 3 | |
| YitT family protein | Contig 39 (20040–20923) | M | 6 | |
| Putative uncharacterized protein | Contig 27 (19139–19838) | M | 1 | |
| Putative uncharacterized protein | Contig 15 (54450–55181) | M | 3 | |
| Putative uncharacterized protein | Contig 18 (7102–7677) | M | 4 | |
| Putative uncharacterized protein | Contig 8 (194308–194714) | M | 1 | |
| conserved hypothetical protein [Enterococcus faecalis ATCC 29200] | Contig 32 (88786–89658) | M | 12 | |
| Phage infection protein | Contig 4 (65550–68213) | M | 6 | |
| PIN domain protein | Contig 11 (28478–29477) | M | 4 | |
| Cell wall surface anchor family protein | Contig 35 (105859–106858) | M | 1 | |
| Putative uncharacterized protein | Contig 30 (12932–13931) | S | 0 | |
| Putative uncharacterized protein | Contig 1 (61273–61944) | S | 0 | |
| Basic membrane protein family | Contig 10 (73934–74933) | L | 0 | |
| Basic membrane protein family | Contig 10 (75061–76060) | L | 0 | |
(a)
As the OG1X sequence is not publically available we verified the location of each protein in the closely related OG1RF strain (http://blast.hgsc.bcm.tmc.edu/blast.hgsc?organism=EfaecalisOG1).
(b)
Membrane (M), soluble (S), lipoprotein (L).
(c)
The number of predicted transmembrane helices for each protein was obtained by analyzing the amino acid sequence with SCAMPI (http://scampi.cbr.su.se/) and SignalP 3.0 (http://www.cbs.dtu.dk/services/SignalP/).
(d)
Type of transporter: ABC, amino acid binding cassette; PTS, phosphoenolpyruvate:sugar phosphotransferase system; IT, ion transporter; MFS, major facilitator superfamily. Transporters were grouped according to the Transporter Classification Database (http://www.tcdb.org/superfamily.php) and numbered arbitrarily.