Table II. Proteins shared by BCG and latex bead phagosomes (proteins identified in at least four of five BCG and at least two of three latex bead phagosome preparations).
PM, plasma membrane; PKC, protein kinase C.
| Protein identified | Swiss-Prot accession no. | No. BCGa | No. beadb | Spectral/peptide countc |
Reported locationd | Physiological functiond | |
|---|---|---|---|---|---|---|---|
| BCG | Bead | ||||||
| 60-kDa heat shock protein, mitochondrial | P10809 | 5 | 3 | 9,19, 15, 2, 18/9, 19, 14, 2,18 | 12, 16, 5/12, 16, 5 | Mitochondrion, secretory granules | Chaperone; extramitochondrial localization reported (75–77) |
| 78-kDa glucose-regulated protein | P11021 | 5 | 3 | 5, 16, 6, 8, 13/5, 16, 6, 8, 13 | 5, 8, 16/5, 8, 16 | ER, melanosome | Chaperone; member of heat shock protein 70 family |
| ATP synthase subunit α | P25705 | 5 | 3 | 13, 12, 2, 4, 6/13, 12, 2, 4, 6 | 9, 7, 2/9, 7, 2 | Mitochondrion inner membrane | Ion transport; generation of ATP |
| Aminopeptidase N | P15144 | 5 | 3 | 13, 8, 31, 20, 21/13, 8, 20, 20, 21 | 9, 17, 9/9, 12, 9 | PM | Protein degradation |
| Calnexin | P27824 | 5 | 3 | 1, 2, 2, 1, 2/1, 2, 2, 1, 2 | 1, 1, 3/1, 1, 3 | ER | Chaperone; protein synthesis and folding |
| Endoplasmin | P14625 | 5 | 3 | 4, 11, 10, 14, 13/4, 11, 10, 14, 13 | 9, 10, 14/8, 9, 13 | ER | Protein synthesis and folding |
| Integrin β2 | P05107 | 5 | 3 | 5, 7, 8, 6, 12/5, 7, 8, 6, 12 | 3, 2, 2/3, 2, 2 | PM | Cell surface adhesion glycoprotein |
| Lysosome membrane protein 2 | Q14108 | 5 | 3 | 15, 3, 9, 12, 3/13, 3, 9, 12, 3 | 12, 5, 2/11, 5, 2 | Lysosome | Lysosomal receptor; scavenger receptor class B member 2 |
| Lysosome-associated membraneglycoprotein 1 | P11279 | 5 | 3 | 4, 2, 4, 6, 3/4, 2, 3, 6, 3 | 4, 3, 2/4, 3, 2 | Lysosome, endosome, PM | Presents carbohydrate ligands to selectins |
| Lysosome-associated membrane glycoprotein 2 | P13473 | 5 | 3 | 3, 1, 4, 2, 2/3, 1, 3, 2, 2 | 3, 5, 1/2, 3, 1 | Lysosome, endosome, PM | Protects lysosomal membrane from autodigestion |
| Moesin | P26038 | 5 | 3 | 3, 8, 3, 9, 12/3, 8, 3, 9, 12 | 4, 7, 14/4, 7, 14 | Cytoplasm | Connections of membrane to cytoskeleton |
| Peroxiredoxin-1 | Q06830 | 5 | 3 | 1, 2, 2, 6, 8/1, 2, 2, 5, 7 | 2, 1, 11/2, 1, 10 | Cytoplasm, melanosome | Redox regulation; detoxification |
| Protein-disulfide isomerase | P07237 | 5 | 3 | 3, 2, 5, 9, 7/3, 2, 5, 9, 7 | 2, 7, 11/2, 7, 11 | ER | Disulfide bond rearrangement |
| Protein-disulfide isomerase A3 | P30101 | 5 | 3 | 1, 2, 10, 9, 10/1, 2, 10, 9, 10 | 2, 7, 7/2, 6, 7 | ER | Disulfide bond rearrangement |
| Putative elongation factor 1α-like 3 | Q5VTE0 | 5 | 3 | 2, 5, 4, 3, 5/2, 5, 4, 3, 5 | 4, 8, 7/4, 7, 5 | Cytoplasm | Protein biosynthesis (by similarity) |
| Ras-related protein Rab-5C | P51148 | 5 | 3 | 4, 4, 5, 8, 3/4, 4, 5, 7, 3 | 4, 6, 1/4, 5, 1 | Early endosome | Vesicular trafficking |
| Acid ceramidase | Q13510 | 5 | 2 | 2, 1, 2, 2, 2/2, 1, 2, 2, 2 | 2, 2, 0/2, 2, 0 | Lysosome | Hydrolyzes ceramide into sphingosine and free fatty acid |
| CD63 antigen | P08962 | 5 | 2 | 2, 4, 2, 3, 2/2, 4, 2, 3, 2 | 3, 4, 0/3, 3, 0 | Late endosome-lysosome | Unknown; may regulate transport of other proteins |
| Coronin-1A | P31146 | 5 | 2 | 2, 1, 3, 3, 2/2, 1, 3, 3, 2 | 0, 4, 4/0, 3, 4 | Cytoplasm | Cytoskeleton component; important in membrane invaginations, protrusions, and cell locomotion |
| Erythrocyte band 7 integral membrane protein (stomatin) | P27105 | 5 | 2 | 1, 2, 2, 3, 4/1, 2, 2, 3, 4 | 6, 6, 0/6, 6, 0 | PM, melanosome | Regulates cation conductance; associates with actin and lipid rafts |
| Flotillin-1 | O75955 | 5 | 2 | 3, 1, 7, 1, 1/3, 1, 7, 1, 1 | 4, 9, 0/3, 9, 0 | PM, phagosomal membrane | Lipid rafts; clathrin-independent endocytosis; formation of caveolae or caveolae-like vesicles |
| Fructose-bisphosphate aldolase A | P04075 | 5 | 2 | 3, 8, 5, 14, 15/3, 8, 5, 12, 15 | 4, 0, 14/4, 0, 13 | Cytoplasm | Metabolism; interacts with cytoskeleton (78) |
| Heat shock protein HSP90-β | P08238 | 5 | 2 | 5, 10, 16, 22, 10/5, 10, 14, 22, 10 | 3, 0, 18/3, 0, 17 | Cytoplasm, melanosome | Chaperone |
| Proactivator polypeptide (prosaposin) | P07602 | 5 | 2 | 4, 1, 2, 4, 1/4, 1, 2, 4, 1 | 3, 3, 0/3, 3, 0 | Lysosome | Sphingolipid degradation |
| Ras-related protein Rab-11B | Q15907 | 5 | 2 | 1, 2, 2, 1, 1/1, 2, 2, 1, 1 | 1, 1, 0/1, 1, 0 | Recycling endosome, PM | Regulation of endosomal recycling |
| Stress-70 protein, mitochondrial | P38646 | 5 | 2 | 12, 3, 8, 5, 4/12, 3, 8, 5, 4 | 2, 6, 0/2, 6, 0 | Mitochondrion, cell surface | Chaperone; control of cell proliferation and cellular aging |
| Thioredoxin-dependent peroxide reductase, mitochondrial | P30048 | 5 | 2 | 2, 1, 1, 1, 1/1, 1, 1, 1, 1 | 1, 1, 0/1, 1, 0 | Mitochondrion, early endosome | Redox regulation; presence in endosomes reported (79) |
| Vacuolar ATP synthase subunit B | P21281 | 5 | 2 | 10, 2, 3, 7, 2/10, 2, 3, 7, 2 | 8, 15, 0/8, 11, 0 | Endosome-lysosome | Compartment acidification |
| Actin, cytoplasmic 1 | P60709 | 4 | 3 | 5, 0, 16, 16, 49/5, 0, 12, 13, 16 | 3, 2, 18/3, 2, 13 | Cytoplasm | Cytoskeleton |
| Annexin A2 | P07355 | 4 | 3 | 5, 0, 4, 9, 9/5, 0, 4, 9, 9 | 15, 8, 5/13, 6, 5 | Secreted, extracellular matrix, basement membrane | May cross-link PM phospholipids with actin cytoskeleton and be involved in exocytosis |
| Brain acid-soluble protein 1 | P80723 | 4 | 3 | 4, 0, 6, 3, 4/4, 0, 5, 3, 4 | 3, 5, 1/3, 5, 1 | Membrane | Signaling; regulation of actin dynamics; present in lipid rafts; has calmodulin binding site; is substrate for PKC |
| Cathepsin D | P07339 | 4 | 3 | 6, 0, 5, 8, 9/5, 0, 5, 8, 8 | 9, 15, 5/8, 11, 5 | Lysosome | Protein degradation |
| Glyceraldehyde-3-phosphate dehydrogenase | P04406 | 4 | 3 | 2, 0, 3, 3, 7/2, 0, 3, 3, 7 | 3, 3, 5/3, 3, 5 | Cytoplasm, membrane-associated | Glycolysis; membrane fusion; microtubule bundling; phosphotransferase activity; nuclear RNA export; DNA replication and DNA repair (80) |
| Heat shock cognate 71-kDa protein | P11142 | 4 | 3 | 6, 0, 9, 22, 8/6, 0, 9, 22, 8 | 3, 5, 11/3, 5, 11 | Cytoplasm, melanosome | Chaperone |
| Palmitoyl-protein thioesterase 1 | P50897 | 4 | 3 | 3, 0, 3, 3, 4/3, 0, 3, 3, 4 | 4, 6, 1/4, 5, 1 | Lysosome | Lipoprotein degradation |
| Plastin-2 | P13796 | 4 | 3 | 0, 10, 2, 12, 14/0, 10, 2, 12, 14 | 2, 3, 11/2, 3, 11 | Cytoplasm | Cytoskeleton |
| Ras-related protein Rab-7A | P51149 | 4 | 3 | 2, 0, 5, 4, 7/2, 0, 5, 4, 7 | 3, 3, 2/3, 3, 2 | Late endosome | Late endosomal transport; phagosome maturation |
| Vacuolar ATP synthase catalytic subunit A | P38606 | 4 | 3 | 3, 0, 1, 7, 4/3, 0, 1, 7, 4 | 4, 12, 1/4, 10, 1 | Endosome-lysosome | Compartment acidification |
| Vimentin | P08670 | 4 | 3 | 0, 5, 9, 2, 5/0, 5, 9, 2, 5 | 7, 8, 1/7, 8, 1 | Cytoplasm | Cytoskeleton; intermediate filament |
| Voltage-dependent anion-selective channel protein 1 | P21796 | 4 | 3 | 4, 0, 2, 5, 7/4, 0, 1, 5, 7 | 2, 3, 5/2, 3, 5 | Mitochondrion, PM | Channel for small hydrophilic molecules; present in secretory pathway and PM (81) |
| Voltage-dependent anion-selective channel protein 2 | P45880 | 4 | 3 | 2, 0, 3, 2, 5/2, 0, 3, 2, 5 | 2, 1, 2/2, 1, 2 | Mitochondrion | Channel for small hydrophilic molecules |
| 10-kDa heat shock protein, mitochondrial | P61604 | 4 | 2 | 6, 6, 4, 4, 0/6, 5, 4, 4, 0 | 3, 5, 0/3, 5, 0 | Mitochondrion and non-mitochondrial sites | Co-chaperone for Hsp60 in the protein folding process; also identified in non-mitochondrial sites, including secretory granules (82) |
| 40 S ribosomal protein SA (laminin receptor-1) | P08865 | 4 | 2 | 0, 1, 2, 3, 5/0, 1, 1, 3, 5 | 0, 1, 3/0, 1, 3 | Cytoplasm | Protein synthesis; cell adhesion |
| ADP-ribosylation factor-like protein 8Be | Q9NVJ2 | 4 | 2 | 3, 1, 1, 1, 0/3, 1, 1, 1, 0 | 2, 1, 0/2, 1, 0 | Late endosome-lysosome | Endosome and lysosome motility |
| α-Enolase | P06733 | 4 | 2 | 0, 1, 2, 6, 7/0, 1, 2, 6, 7 | 1, 0, 3/1, 0, 3 | Cytoplasm, PM, myofibril, sarcomere | Carbohydrate degradation; glycolysis; promotes vacuole fusion in yeast; may also function as a plasminogen receptor and activator on the PM |
| Cathepsin Z | Q9UBR2 | 4 | 2 | 3, 0, 1, 3, 2/3, 0, 1, 3, 2 | 2, 2, 0/2, 2, 0 | Lysosome | Carboxydipeptidase |
| Cofilin-1 | P23528 | 4 | 2 | 1, 2, 0, 2, 1/1, 2, 0, 2, 1 | 1, 0, 2/1, 0, 2 | Cytoplasm | Controls actin polymerization |
| Gelsolin | P06396 | 4 | 2 | 0, 1, 2, 8, 5/0, 1, 2, 8, 5 | 1, 0, 7/1, 0, 7 | Cytoplasm | Cytoskeleton |
| Hypoxia up-regulated protein 1 | Q9Y4L1 | 4 | 2 | 0, 2, 1, 2, 7/0, 1, 1, 2, 7 | 1, 0, 3/1, 0, 3 | ER lumen | Chaperone; induced by hypoxia |
| Lysosomal acid phosphatase | P11117 | 4 | 2 | 0, 1, 2, 1, 3/0, 1, 2, 1, 3 | 3, 5, 0/3, 5, 0 | Lysosome | Phosphate monoester hydrolysis |
| Lysosomal α-glucosidase | P10253 | 4 | 2 | 2, 0, 2, 1, 1/2, 0, 2, 1, 1 | 3, 2, 0/3, 2, 0 | Lysosome | Glycogen degradation |
| Malate dehydrogenase, mitochondrial | P40926 | 4 | 2 | 11, 0, 6, 2, 8/11, 0, 5, 2, 8 | 5, 5, 0/5, 5, 0 | Mitochondrion | Glycolysis; tricarboxylic acid cycle |
| Myosin-9 | P35579 | 4 | 2 | 0, 14, 5, 29, 15/0, 14, 5, 29, 15 | 0, 7, 34/0, 7, 34 | Cytoplasm | Cytoskeleton |
| N-Acetylglucosamine-6-sulfatase | P15586 | 4 | 2 | 8, 1, 1, 3, 0/8, 1, 1, 3, 0 | 3, 2, 0/3, 2, 0 | Lysosome | Heparan sulfate/keratan sulfate hydrolysis |
| Nicastrin | Q92542 | 4 | 2 | 2, 1, 2, 2, 0/2, 1, 2, 2, 0 | 4, 3, 0/4, 3, 0 | Golgi, ER, PM, melanosome | Component of the γ-secretase complex |
| Protein-disulfide isomerase A6 | Q15084 | 4 | 2 | 0, 3, 1, 4, 6/0, 3, 1, 4, 6 | 1, 0, 2/1, 0, 2 | ER, ER-Golgi intermediate compartment, melanosome | Disulfide bond rearrangement |
| Ras-related protein Rab-21 | Q9UL25 | 4 | 2 | 1, 0, 2, 2, 1/1, 0, 2, 2, 1 | 1, 2, 0/1, 2, 0 | Endosomes | Controls traffic of β1 integrins |
| Sulfide:quinone oxidoreductase, mitochondrial | Q9Y6N5 | 4 | 2 | 2, 0, 6, 4, 6/2, 0, 6, 4, 6 | 2, 2, 0/2, 2, 0 | Mitochondrion | Hydrogen sulfide oxidation |
| Vacuolar proton pump subunit d 1 | P61421 | 4 | 2 | 3, 0, 6, 5, 1/3, 0, 5, 5, 1 | 4, 5, 0/4, 4, 0 | Intracellular compartments, endosome-lysosome | Compartment acidification |
| Citrate synthase, mitochondrial | O75390f | 4 | 2 | 1, 0, 1, 1, 1/1, 0, 1, 1, 1 | 1, 1, 0/1, 1, 0 | Mitochondrion | Carbohydrate metabolism; tricarboxylic acid cycle |
| Interferon-induced transmembrane protein 3g | Q01628f | 4 | 2 | 1, 1, 1, 1, 0/1, 1, 1, 1, 0 | 1, 1, 0/1, 1, 0 | PM, Golgi, integral membrane protein | Cell differentiation and homing; immune response |
a No. BCG indicates the number of BCG phagosome (out of five total) in which the indicated protein was identified.
b No. bead indicates the number of latex bead phagosome preparations (out of three total) in which the indicated protein was identified.
c Spectral counts refer to all acquired precursor ions for a particular protein, whereas peptide counts only list the number of unique peptide sequences observed per protein in the phagosome preparation (for correlation of spectral counts to the relative protein concentration see Liu et al. (83)). For BCG, these are listed for 3 h, 1 days, 3 days (a), 3 days (b), and 5 days, respectively. For latex beads, these are listed for 3 h, 3 days, and 5 days, respectively. The spectral counts for the 5 BCG phagosome preparations are listed together and are separated by a slash (/) from the peptide counts of the same 5 preparations, which are listed in the same order. The same is done for the spectral and peptide counts, respectively, for the 3 latex bead phagosome preparations.
d Reported location and physiological function are abstracted from the Swiss-Prot on-line database except where indicated by cited references.
e Arl 8B (Q9NVJ2) could not be differentiated from ARL 8A (Q96BM9) (also see supplemental Table 1) in three of four BCG phagosome preparations and one of two latex bead phagosome preparations.
f Proteins identified by single peptide assignments.
g Interferon-induced transmembrane protein 3 (Q01628) could not be differentiated from interferon-induced transmembrane protein 1 (P13164) or interferon-induced transmembrane protein 2 (Q01629) (also see supplemental Table 1).