Table 1. List of identified (by LC-MS/MS) proteins associated with cytosolic lipid droplets isolated from Caco-2/TC7 cells.
Caco-2/TC7 cells were cultured on semi-permeable filters for 3 weeks for differentiation and then supplied with lipid micelles for 24 h. Cell homogenates were centrifuged for 10 min at 1000 g and the supernatant was fractionated on a sucrose gradient. The top fraction, containing the cytosolic lipid droplets, was analysed by LC-MS/MS for protein identification. Proteins were identified with at least two unique peptides. A Mascot search was performed allowing 1 ‘max. missed cleavage’, 20 p.p.m. ‘peptides mass tolerance’, 0.3 ‘fragment mass tolerance’ and against Homo sapiens taxonomy (20401 sequences). Mascot search results were filtered by P=0.01 and false discovery rate below 1.6%. The proteins were identified in at least two out of three independent experiments. The proteins already reported in mammalian CLD proteome are indicated (a, reported in the recent review of Hodges and Wu, 2010; b, Moessinger et al., 2011). Proteins are grouped by function or localization and, inside a group, proteins are ranked by decreasing emPAI.
| Gene name | Entry name SwissProt | Protein name | Normalized emPAI | Reported in proteomic studies of lipid droplets |
|---|---|---|---|---|
| Lipid metabolism | ||||
| PLIN proteins | ||||
| PLIN2 | PLIN2_HUMAN | Perilipin-2, adipose differentiation-related protein, adipophilin | 6.97 | a |
| PLIN3 | PLIN3_HUMAN | Perilipin-3, mannose-6-phosphate receptor-binding protein, TIP47 | 3.42 | a |
| Fatty acid metabolism | ||||
| ACSL3 | ACSL3_HUMAN | Long-chain-fatty-acid-CoA ligase 3 | 2.65 | a |
| ACSL4 | ACSL4_HUMAN | Long-chain-fatty-acid-CoA ligase 4 | 0.15 | a |
| Acylglycerol metabolism | ||||
| MGLL | MGLL_HUMAN | Monoglyceride lipase | 0.67 | a |
| ABHD5 | ABHD5_HUMAN | 1-Acylglycerol-3-phosphate O-acyltransferase, abhydrolase domain-containing protein 5, CGI-58 | 0.31 | a |
| PNPLA2 | PLPL2_HUMAN | Patatin-like phospholipase domain-containing protein 2, adipose triacylglycerol lipase | 0.15 | a |
| Phospholipid metabolism | ||||
| PCYT1A | PCY1A_HUMAN | Choline-phosphate cytidylyltransferase A | 1.58 | |
| LPCAT2 | PCAT2_HUMAN | Lysophosphatidylcholine acyltransferase 2 | 0.30 | b |
| Sterol metabolism | ||||
| HSD17B11 | DHB11_HUMAN | Oestradiol 17-β-dehydrogenase 11 | 2.78 | a |
| LSS | ERG7_HUMAN | Lanosterol synthase | 2.46 | a |
| CYB5R3 | NB5R3_HUMAN | NADH–cytochrome b5 reductase 3 | 1.63 | a |
| NSDHL | NSDHL_HUMAN | Sterol-4-α-carboxylate 3-dehydrogenase, decarboxylating | 1.55 | a |
| EPHX1 | HYEP_HUMAN | Epoxide hydrolase 1 | 0.31 | |
| HSD3B1 | 3BHS1_HUMAN | 3-β-Hydroxysteroid dehydrogenase | 0.24 | |
| DHRS3 | DHRS3_HUMAN | Short-chain dehydrogenase/reductase 3 | 0.13 | a |
| DHCR7 | DHCR7_HUMAN | 7-Dehydrocholesterol reductase | 0.06 | |
| HSD17B7 | DHB7_HUMAN | 3-Oxo-steroid reductase | 0.04 | a |
| Lipoprotein metabolism | ||||
| APOA4 | APOA4_HUMAN | Apolipoprotein A-IV | 6.24 | |
| P4HB | PDIA1_HUMAN | Protein disulfide-isomerase | 4.71 | a |
| MTTP | MTP_HUMAN | Microsomal triacylglycerol transfer protein large subunit | 0.53 | |
| APOE | APOE_HUMAN | Apolipoprotein E | 0.48 | |
| Other lipidic metabolism | ||||
| FAF2 | FAF2_HUMAN | FAS-associated factor 2, UBXD8 | 1.77 | a |
| RDH10 | RDH10_HUMAN | Retinol dehydrogenase 10 | 1.24 | |
| DHRS1 | DHRS1_HUMAN | Dehydrogenase/reductase SDR family member 1 | 0.56 | a |
| ECHS1 | ECHM_HUMAN | Enoyl-CoA hydratase, mitochondrial | 0.17 | |
| SGPL1 | SGPL1_HUMAN | Sphingosine-1-phosphate lyase 1 | 0.11 | |
| TRAFFIC | ||||
| RAB7A | RAB7A_HUMAN | Ras-related protein Rab-7a | 2.78 | a |
| RAB1A | RAB1A_HUMAN | Ras-related protein Rab-1A | 1.75 | a |
| RAB5C | RAB5C_HUMAN | Ras-related protein Rab-5C | 1.66 | a |
| RAB10 | RAB10_HUMAN | Ras-related protein Rab-10 | 1.15 | a |
| RAB25 | RAB25_HUMAN | Ras-related protein Rab-25 | 1.02 | |
| RAB11A | RB11A_HUMAN | Ras-related protein Rab-11A | 0.68 | a |
| RAB15 | RAB15_HUMAN | Ras-related protein Rab-15 | 0.66 | |
| RAB6A | RAB6A_HUMAN | Ras-related protein Rab-6A | 0.20 | a |
| RAB33B | RB33B_HUMAN | Ras-related protein Rab-33B | 0.01 | a |
| ER (endoplasmic reticulum) | ||||
| ER lumen | ||||
| HSPA5 | GRP78_HUMAN | 78 kDa glucose-regulated protein | 5.76 | a |
| PDIA3 | PDIA3_HUMAN | Protein disulfide-isomerase A3 | 3.27 | a |
| CALR | CALR_HUMAN | Calreticulin | 1.97 | a |
| HSP90B | ENPL_HUMAN | Endoplasmin, heat-shock protein 90 kDa β member 1, 94 kDa glucose-regulated protein | 1.85 | a |
| PDIA6 | PDIA6_HUMAN | Protein disulfide-isomerase A6 | 1.52 | a |
| ERO1L | ERO1A_HUMAN | ERO1-like protein α | 0.82 | a |
| PDIA4 | PDIA4_HUMAN | Protein disulfide-isomerase A4 | 0.81 | a |
| SERPINH | SERPH_HUMAN | Serpin H1 | 0.38 | |
| ERP44 | ERP44_HUMAN | Endoplasmic reticulum resident protein ERp44 | 0.29 | |
| CALU | CALU_HUMAN | Calumenin | 0.28 | |
| POR | NCPR_HUMAN | NADPH–cytochrome P450 reductase | 0.27 | |
| PLOD2 | PLOD2_HUMAN | Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 | 0.19 | |
| UBXN4 | UBXN4_HUMAN | UBX domain-containing protein 4, UBX domain-containing protein 2, Erasin | 0.19 | a |
| ERP29 | ERP29_HUMAN | Endoplasmic reticulum protein ERp29 | 0.19 | a |
| LRPAP1 | AMRP_HUMAN | α-2-Macroglobulin receptor-associated protein, low-density lipoprotein receptor-related protein-associated protein 1 | 0.17 | |
| ER membrane, integral protein | ||||
| CANX | CALX_HUMAN | Calnexin | 0.66 | a |
| AUP1 | AUP1_HUMAN | Ancient ubiquitous protein 1 | 0.35 | a |
| RPN1 | RPN1_HUMAN | Dolichyl-diphospho-oligosaccharide–protein glycosyltransferase subunit 1 | 0.34 | a |
| UGT1A6 | UD16_HUMAN | UDP-glucuronosyltransferase 1-6 | 0.22 | |
| DDOST | OST48_HUMAN | Dolichyl-diphospho-oligosaccharide–protein glycosyltranferase 48 kDa subunit | 0.18 | a |
| RTN4 | RTN4_HUMAN | Reticulon-4 | 0.08 | |
| LRRC59 | LRC59_HUMAN | Leucine-rich repeat-containing protein 59 | 0.17 | |
| Unknown | ||||
| PRKCSH | GLU2B_HUMAN | Glucosidase 2 subunit β | 0.13 | |
| Mitochondria | ||||
| AIFM2 | AIFM2_HUMAN | Apoptosis-inducing factor 2, apoptosis-inducing factor-like mitochondrion-associated inducer of death | 1.87 | a |
| ATP5B | ATPB_HUMAN | ATP synthase subunit β, mitochondrial | 0.51 | |
| HSPA9 | GRP75_HUMAN | Stress-70 protein, mitochondrial | 0.24 | a |
| MDH2 | MDHM_HUMAN | Malate dehydrogenase, mitochondrial | 0.20 | |
| HSPD1 | CH60_HUMAN | 60 kDa heat-shock protein, mitochondrial | 0.18 | a |
| Lysosome | ||||
| PCYOX1 | PCYOX_HUMAN | Prenylcysteine oxidase 1 | 0.30 | |
| GNS | GNS_HUMAN | N-Acetylglucosamine-6-sulfatase | 0.20 | |
| Cytosol | ||||
| cytoskeleton | ||||
| TUBB2C | TBB2C_HUMAN | Tubulin β-2C chain | 6.04 | |
| TUBB | TBB5_HUMAN | Tubulin β chain | 5.39 | |
| TUBB2A | TBB2A_HUMAN | Tubulin β-2A chain | 3.43 | |
| ACTB | ACTB_HUMAN | Actin, cytoplasmic 1 | 2.70 | a |
| TUBA1B | TBA1B_HUMAN | Tubulin α-1B chain | 2.68 | |
| ACTN4 | ACTN4_HUMAN | α-Actinin-4 | 1.02 | |
| ANXA2 | ANXA2_HUMAN | Annexin A2 | 0.86 | a |
| ANXA4 | ANXA4_HUMAN | Annexin A4 | 0.35 | |
| ELMOD2 | ELMD2_HUMAN | ELMO domain-containing protein 2 | 0.34 | a |
| SLC9A3R1 | NHRF1_HUMAN | Na+/H+ exchange regulatory cofactor NHERF1 | 0.27 | |
| SEPT2 | SEPT2_HUMAN | Septin-2 | 0.17 | |
| Carbohydrate metabolism | ||||
| TPI1 | TPIS_HUMAN | Triosephosphate isomerase | 6.85 | |
| PGK1 | PGK1_HUMAN | Phosphoglycerate kinase 1 | 1.67 | |
| ENO1 | ENOA_HUMAN | α-Enolase | 1.47 | |
| ALDOA | ALDOA_HUMAN | Fructose-bisphosphate aldolase A | 1.40 | |
| GPI | G6PI_HUMAN | Glucose-6-phosphate isomerase | 1.08 | |
| GAPDH | G3P_HUMAN | Glyceraldehyde-3-phosphate dehydrogenase | 0.76 | a |
| Cytosolic chaperones | ||||
| HSPA8 | HSP7C_HUMAN | Heat-shock cognate 71 kDa protein | 1.89 | a |
| HSPA1A | HSP71_HUMAN | Heat-shock 70 kDa protein 1 | 1.78 | a |
| HSPA6 | HSP76_HUMAN | Heat-shock 70 kDa protein 6 | 0.52 | |
| HSP90AB1 | HS90B_HUMAN | Heat-shock protein HSP 90-β | 0.20 | a |
| Other function in cytoplasm | ||||
| CKB | KCRB_HUMAN | Creatine kinase B-type | 5.18 | |
| LGALS3 | LEG3_HUMAN | Galectin-3 | 1.62 | |
| GSTP1 | GSTP1_HUMAN | Glutathione transferase P | 0.57 | |
| GSTA1 | GSTA1_HUMAN | Glutathione transferase A1 | 0.44 | |
| NDRG1 | NDRG1_HUMAN | Protein NDRG1 | 0.26 | |
| TRIO | TRIO_HUMAN | Triple functional domain protein | 0.02 | |
| Miscellaneous | ||||
| METTL7B | MET7B_HUMAN | Methyltransferase-like protein 7B | 2.97 | a |
| METTL7A | MET7A_HUMAN | Methyltransferase-like protein 7A | 1.59 | a |
| SCCPDH | SCPDH_HUMAN | Probable saccharopine dehydrogenase | 1.56 | a |
| ATP1B1 P | AT1B1_HUMAN | Sodium/potassium-transporting ATPase subunit β-1 | 0.79 | |
| CDH17 | CAD17_HUMAN | Cadherin-17 | 0.68 | |
| GPA33 | GPA33_HUMAN | Cell-surface A33 antigen | 0.55 | |
| C2orf43 | CB043_HUMAN | UPF0554 protein C2 or f43 | 0.48 | a |
| GANAB | GANAB_HUMAN | Neutral α-glucosidase AB | 0.26 | |
| ATP1A1 | AT1A1_HUMAN | Sodium/potassium-transporting ATPase subunit α1 | 0.11 | |
| EEF1A1 | EF1A1_HUMAN | Elongation factor 1-α1 | 0.09 | a |
| KPNB1 | IMB1_HUMAN | Importin subunit β-1 | 0.07 | |
| CLIC1 | CLIC1_HUMAN | Chloride intracellular channel protein 1 | 0.01 |