Table I. Proteins identified in the majority of BCG phagosome preparations that were not identified in any latex bead phagosome preparations.
No. BCG+ indicates the number of BCG phagosome preparations (out of five total) in which the indicated protein was identified. PM, plasma membrane; HA, hyaluronic acid; LFA-1, lymphocyte function associated antigen-1.
| Protein identified | Swiss-Prot accession no. | Reported locationa | Physiological functiona | No. BCG+ | Spectral/peptide countsb |
||||
|---|---|---|---|---|---|---|---|---|---|
| 3 h | 1 day | 3 days (a) | 3 days (b) | 5 days | |||||
| CD44 antigen | P16070 | PM | HA receptor | 4 | 0 | 1/1 | 1/1 | 1/1 | 2/2 |
| Erlin-2 (SPFH domain-containing protein 2) | O94905 | ER membrane, PM | Lipid raft-associated | 4 | 3/3 | 0 | 5/1 | 1/1 | 3/2 |
| Golgi apparatus protein 1 (E-selectin ligand 1) | Q92896 | Golgi and PM | Binds fibroblast growth factor and E-selectin | 4 | 0 | 2/2 | 4/4 | 24/24 | 11/11 |
| Intercellular adhesion molecule 1 | P05362 | PM | Ligand for LFA-1 protein | 4 | 0 | 1/1 | 2/2 | 3/3 | 1/1 |
| Protein FAM3C | Q92520 | Putative macrophage-secreted protein | Unknown; member of cytokine-like gene family; may be involved in cell differentiation and proliferation during embryogenesis | 4 | 0 | 4/4 | 2/2 | 4/4 | 4/4 |
| Ras GTPase-activating-like protein IQGAP1 | P46940 | Membrane | Integrates Ca2+/calmodulin and Cdc42 signaling | 4 | 0 | 3/3 | 5/4 | 9/9 | 14/14 |
| Ras-related protein Rab-6A | P20340 | Golgi | Golgi to ER traffic | 4 | 0 | 2/2 | 2/2 | 7/7 | 6/6 |
| Stress-induced-phosphoprotein 1 | P31948 | Cytoplasm, nucleus | Mediates the association of chaperones Hsc70 and Hsc90 | 4 | 0 | 6/6 | 2/2 | 5/5 | 8/8 |
| Transmembrane emp24 domain-containing protein 9 | Q9BVK6 | ER membrane | Unknown | 4 | 0 | 1/1 | 1/1 | 2/2 | 1/1 |
| Tubulin α-1C chain | Q9BQE3 | Cytoplasm | Cytoskeleton | 4 | 0 | 7/7 | 3/3 | 7/7 | 2/2 |
| Tubulin β chain | P07437 | Cytoplasm | Cytoskeleton | 4 | 0 | 13/12 | 12/11 | 12/12 | 4/4 |
| Tumor protein D54 | O43399 | Unknown | Unknown | 4 | 0 | 1/1 | 2/2 | 3/3 | 1/1 |
| Very long-chain-specific acyl-CoA dehydrogenase, mitochondrial | P49748 | Mitochondrion | Fatty acid β-oxidation system | 4 | 0 | 4/4 | 4/4 | 1/1 | 2/2 |
| ADP/ATP translocase 2 | P05141 | Mitochondrion | ATP/ADP translocation | 3 | 4/4 | 3/3 | 1/1 | 0 | 0 |
| α-Mannosidase 2 | Q16706 | Golgi | N-Glycosylation | 3 | 0 | 2/2 | 0 | 6/6 | 12/12 |
| Band 4.1-like protein 3 | Q9Y2J2 | Cytoplasm | Links membrane to cytoskeleton | 3 | 0 | 0 | 1/1 | 1/1 | 2/2 |
| Charged multivesicular body protein 4b | Q9H444 | Cytoplasm, endosome | MVB formation and sorting of endosomal cargo proteins into MVBs | 3 | 0 | 0 | 5/3 | 2/2 | 1/1 |
| Glutamate dehydrogenase 1, mitochondrial | P00367 | Mitochondrion | Oxidative deamination of glutamate to α-ketoglutarate | 3 | 4/3 | 2/2 | 2/2 | 0 | 0 |
| Guanine nucleotide-binding protein Gi/Gs/Gt subunit β-1 | P62873 | Membrane | Transmembrane signaling | 3 | 3/3 | 0 | 0 | 2/2 | 2/2 |
| Integrin α5 | P08648 | PM | Receptor for fibronectin and fibrinogen, present in endocytic pathway (36) | 3 | 1/1 | 3/3 | 1/1 | 0 | 0 |
| Nucleobindin-1 | Q02818 | Golgi, cytoplasm, membrane | Calcium homeostasis | 3 | 0 | 3/3 | 0 | 6/6 | 8/8 |
| Platelet endothelial cell adhesion molecule | P16284 | PM | Cell adhesion; signal transduction | 3 | 0 | 0 | 5/5 | 4/4 | 5/5 |
| Ras-related protein Rab-14 | P61106 | Membrane | Vesicular trafficking | 3 | 0 | 1/1 | 1/1 | 2/2 | 0 |
| Septin-7 | Q16181 | Cytoplasm | GTPase; associates with actin stress fibers; involved in cytokinesis and exocytosis | 3 | 0 | 0 | 2/2 | 2/2 | 4/4 |
| Synaptic vesicle membrane protein VAT-1 homolog | Q99536 | Membrane | Unknown; ATPase with homology to oxidoreductase and ξ-crystallin | 3 | 2/2 | 0 | 0 | 1/1 | 2/2 |
| Vacuolar proton pump subunit C 1 | P21283 | Intracellular compartments, endosome-lysosome | Compartment acidification | 3 | 6/6 | 0 | 0 | 1/1 | 1/1 |
| Vesicle-trafficking protein Sec22b | O75396 | ER-Golgi-intermediate compartment, melanosome | ER to Golgi targeting and fusion | 3 | 0 | 0 | 2/2 | 2/2 | 3/3 |
| 60 S ribosomal protein L35 | P42766c | Cytoplasm | Protein synthesis | 3 | 0 | 1/1 | 0 | 1/1 | 1/1 |
| 60 S ribosomal protein L8 | P62917c | Cytoplasm | Protein synthesis | 3 | 0 | 0 | 1/1 | 1/1 | 1/1 |
| Macrophage migration-inhibitory factor | P14174c | Macrophage-secreted protein | Proinflammatory immune modulator | 3 | 0 | 1/1 | 1/1 | 1/1 | 0 |
| Ras-related protein Ral-Bd | P11234c | Membrane | Signal transduction; regulation of exocytosis; activation of IκB kinase TBK1 | 3 | 1/1 | 0 | 0 | 1/1 | 1/1 |
| Translocon-associated protein subunit α | P43307c | ER | Binds Ca2+ to ER membrane; regulates retention of ER-resident proteins | 3 | 1/1 | 0 | 1/1 | 0 | 1/1 |
a Except where indicated by referenced citation, “Reported location” and “Physiological function” are abstracted from the Swiss-Prot database.
b 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 (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. 3 days (a) and 3 days (b) are biological replicates.
c Proteins identified by single peptide assignments.
d Ral-B (P11234) could not be differentiated from Ral-A (also see supplemental Table 1); 78% sequence identity between Ral-B and Ral-A (P11233).