Table I. Acylated proteins up-regulated and downregulated in LPS-stimulated cell selected depending on frequency of their identification.
Cells were labeled with 50 μm 17ODYA or exposed to 0.05% DMSO carrier for 4 h then stimulated with 100 ng/ml LPS for 60 min or left unstimulated and labeled proteins were captured on streptavidin-coupled beads. Subsequently, mass spectrometry was performed, as described in Fig. 1. Three sets of experiments were performed, followed by statistical analysis of the data based on spectral counts. Fatty-acylated proteins identified with high and medium confidence are listed in supplemental Table 3, and those considered to be up-regulated or downregulated in LPS-stimulated cells based on the RL value are listed in supplemental Table 4. The proteins shown have been selected from those in supplemental Table 4, taking into account the number of experiments in which they were identified. Up-regulated proteins: acylated proteins identified in two or three experiments in stimulated cells and absent or found only once in unstimulated cells. Downregulated proteins: acylated proteins identified in two or three experiments in unstimulated cells and absent or found only once in stimulated cells. Numbers in columns A, B, C, D indicate in how many experiments represented by those symbols (see text) a given protein was identified.* Protein with GPI anchor or an enzyme involved in GPI anchor attachment that can incorporate 17ODYA into the GPI anchor.
| UP-REGULATED |
DOWNREGULATED |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UniProt accession number | UniProt protein name | No. in A | No. in B | No. in C | No. in D | RL | UniProt accession number | UniProt protein name | No. in A | No. in B | No. in C | No. in D | RL |
| P06804 | Tumor necrosis factor | 0 | 0 | 3 | 0 | 119.000 | O35381 | Acidic leucine-rich nuclear phosphoprotein 32 family member A | 2 | 0 | 1 | 0 | 0.500 |
| Q8BGY2 | Eukaryotic translation initiation factor 5A-2 | 0 | 0 | 2 | 0 | 84.000 | Q9EST5 | Acidic leucine-rich nuclear phosphoprotein 32 family member B | 2 | 0 | 1 | 0 | 0.500 |
| *O08603 | Retinoic acid early-inducible protein 1-beta | 0 | 0 | 2 | 0 | 46.000 | Q80YP0, P30285 | Cyclin-dependent kinase | 2 | 0 | 1 | 0 | 0.500 |
| *Q9CXY9 | GPI-anchor transamidase | 0 | 0 | 3 | 0 | 37.000 | P97377 | Cyclin-dependent kinase 2 | 2 | 0 | 1 | 0 | 0.500 |
| Q9R1J0 | Sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating | 0 | 0 | 2 | 0 | 33.000 | Q69ZN6 | N-acetylglucosamine-1-phosphotransferase subunits alpha/beta | 3 | 0 | 1 | 0 | 0.500 |
| O88693 | Ceramide glucosyltransferase | 0 | 0 | 2 | 0 | 28.000 | Q8VC90 | Probable palmitoyltransferase ZDHHC12 | 2 | 0 | 1 | 0 | 0.500 |
| Q8R480 | Nuclear pore complex protein Nup85 | 0 | 0 | 3 | 0 | 23.000 | Q8CIG8 | Protein arginine N-methyltransferase 5 | 2 | 0 | 1 | 0 | 0.500 |
| Q8K4Z5 | Splicing factor 3A subunit 1 | 0 | 0 | 2 | 0 | 15.000 | Q8CGC6 | RNA-binding protein 28 | 2 | 0 | 1 | 0 | 0.500 |
| Q8BHN3 | Neutral alpha-glucosidase AB | 1 | 1 | 3 | 0 | 8.941 | Q571J5 | Zinc finger protein 354C | 2 | 0 | 1 | 0 | 0.500 |
| Q91W98 | Solute carrier family 15 member 4 | 1 | 0 | 3 | 0 | 8.428 | Q8C827 | Zinc finger protein 62 | 2 | 0 | 1 | 0 | 0.500 |
| P15920 | V-type proton ATPase 116 kDa subunit a isoform 2 | 1 | 0 | 3 | 0 | 6.500 | E9Q9A9 | 2′-5′-oligoadenylate synthase 2 | 2 | 0 | 1 | 0 | 0.400 |
| Q91WU6 | Palmitoyltransferase ZDHHC7 | 1 | 0 | 3 | 0 | 6.333 | P49710 | Hematopoietic lineage cell-specific protein | 2 | 0 | 1 | 0 | 0.372 |
| P0DOV2 | Interferon-activable protein 204 | 1 | 0 | 3 | 0 | 6.000 | Q6ZQL4 | WD repeat-containing protein 43 | 2 | 0 | 1 | 0 | 0.353 |
| Q8K1M6 | Dynamin-1-like protein | 1 | 0 | 2 | 0 | 5.400 | Q9QUJ7 | Long-chain-fatty-acid–CoA ligase 4 | 3 | 0 | 1 | 0 | 0.333 |
| P59268 | Palmitoyltransferase ZDHHC9 | 1 | 0 | 3 | 0 | 5.200 | O55234 | Proteasome subunit beta type-5 | 2 | 0 | 1 | 0 | 0.326 |
| P48962 | ADP/ATP translocase 1 | 1 | 0 | 3 | 0 | 5.154 | Q8R016 | Bleomycin hydrolase | 2 | 0 | 1 | 0 | 0.320 |
| P00493, Q64531 | Hypoxanthine-guanine phosphoribosyltransferase | 1 | 0 | 3 | 0 | 3.846 | P60122 | RuvB-like 1 | 2 | 0 | 1 | 0 | 0.320 |
| Q9R1C6 | Diacylglycerol kinase epsilon | 1 | 0 | 2 | 0 | 3.167 | Q3UEB3 | Poly(U)-binding-splicing factor PUF60 | 2 | 0 | 1 | 0 | 0.318 |
| Q8VEE4 | Replication protein A 70 kDa DNA-binding subunit | 1 | 0 | 2 | 0 | 3.167 | A2AVZ9 | Solute carrier family 43 member 3 | 2 | 0 | 1 | 0 | 0.318 |
| Q9CPY7 | Cytosol aminopeptidase | 1 | 0 | 2 | 0 | 3.143 | Q8BJS4 | SUN domain-containing protein 2 | 2 | 0 | 1 | 0 | 0.313 |
| O08917 | Flotillin-1 | 1 | 0 | 2 | 0 | 3.111 | Q921H8, Q8VCH0 | 3-ketoacyl-CoA thiolase | 2 | 0 | 1 | 0 | 0.250 |
| Q9Z0H4 | CUGBP Elav-like family member2 | 1 | 0 | 2 | 0 | 3.000 | Q8VCM8 | Nicalin | 3 | 0 | 1 | 0 | 0.250 |
| Q8BH24 | Transmembrane 9 superfamily member 4 | 1 | 0 | 2 | 0 | 3.000 | Q5SSI6 | U3 small nucleolar RNA-associated protein 18 homolog | 2 | 0 | 1 | 0 | 0.250 |
| Q8VEC4 | Calcium homeostasis modulator protein 2 | 1 | 0 | 3 | 0 | 2.520 | Q9JJ00 | Phospholipid scramblase 1 | 3 | 0 | 1 | 0 | 0.245 |
| P68033, P68134 | Actin | 1 | 0 | 3 | 0 | 2.364 | Q8CIF6 | SID1 transmembrane family member 2 | 3 | 0 | 1 | 0 | 0.235 |
| P22892 | AP-1 complex subunit gamma-1 | 1 | 0 | 2 | 0 | 2.111 | P62317 | Small nuclear ribonucleoprotein Sm D2 | 2 | 0 | 1 | 0 | 0.194 |
| Q9JL26 | Formin-like protein 1 | 1 | 0 | 2 | 0 | 2.000 | Q99LG1 | Transmembrane protein 51 | 3 | 0 | 1 | 0 | 0.185 |
| D3Z7P3 | Glutaminase kidney isoform, mitochondrial | 1 | 0 | 2 | 0 | 2.000 | Q5SYD0 | Unconventional myosin-Id | 2 | 0 | 1 | 0 | 0.182 |
| Q9CPP6 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | 1 | 0 | 2 | 0 | 2.000 | P52332 | Tyrosine-protein kinase JAK1 | 2 | 0 | 1 | 0 | 0.150 |
| Q8VEK2 | Rhomboid domain-containing protein 2 | 1 | 0 | 3 | 0 | 2.000 | Q6T707 | Acyl-CoA desaturase 4 | 2 | 0 | 1 | 1 | 0.071 |
| Q924S7 | Sprouty-related, EVH1 domain-containing protein 2 | 1 | 0 | 2 | 0 | 2.000 | Q922F4 | Tubulin beta-6 chain | 2 | 0 | 0 | 0 | 0.040 |
| P12382 | ATP-dependent 6-phosphofructokinase, liver type | 1 | 0 | 2 | 0 | 1.500 | O35153 | BET1-like protein | 2 | 0 | 0 | 0 | 0.009 |
| Q8CBQ5 | Phosphatidylinositol 4-kinase type 2-beta | 1 | 0 | 2 | 0 | 1.500 | |||||||
| P54823 | Probable ATP-dependent RNA helicase DDX6 | 1 | 0 | 2 | 0 | 1.500 | |||||||