Table 1.
S-palmitoylated liver proteins involved in fatty acid synthesis, amino acid metabolism, neutrophil degranulation and hemostasis whose S-palmitoylation extent changed after 4 and/or 12 weeks of HPD feeding.
| Protein ID | Gene ID | Protein Name | 4-Week HPDpalm/RDpalm |
4-Week HPDp/RDp |
12-Week HPDpalm/RDpalm |
12-Week HPDp/RDp |
|---|---|---|---|---|---|---|
| Fatty acid synthesis | ||||||
| Q62264 | Thrsp | Thyroid hormone-inducible hepatic protein | >100 | 0.60 | 0.62 | 0.76 |
| Q9JLJ4 * | Elovl2 | Elongation of very long chain fatty acids protein 2 | 2.26 | 0.68 | 4.51 | 0.73 |
| P19096 * | Fasn | Fatty acid synthase | 2.55 | 0.50 | 1.01 | 0.83 |
| Q8K2C9 * | Hacd3 | Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase 3 | 1.62 | 0.95 | 0.88 | 1.17 |
| Q91V92 | Acly | ATP-citrate synthase | 1.52 | 0.50 | 1.03 | 0.88 |
| Amino acid synthesis | ||||||
| Q9CQT1 | Mir1 | Methylthioribose-1-phosphate isomerase | 0.01 | 0.93 | 1.13 | 1.09 |
| Q8VBT2 | Sds | L-serine dehydratase/L-threonine deaminase | 0.29 | 0.87 | 0.97 | 0.93 |
| O35490 | Bhmt | Betaine-homocysteine S-methyltransferase 1 | 0.33 | 1.85 | 0.67 | 1.40 |
| P15105 | Glul | Glutamine synthetase | 0.56 | 1.27 | 1.09 | 1.12 |
| Amino acid degradation | ||||||
| Q9D2G2 * | Dlst | 2-oxoglutarate dehydrogenase complex component E2, mitochondrial | 0.34 | 1.23 | 1.32 | 0.95 |
| Q9D7B6 | Acad8 | Isobutyryl-CoA dehydrogenase, mitochondrial | 0.37 | 1.01 | 4.09 | 0.92 |
| Q8BH00 | Aldh8a1 | Aldehyde dehydrogenase family 8 member A1 | 0.46 | 1.26 | 0.77 | 0.99 |
| Q8BWF0 * | Aldh5a1 | Succinate-semialdehyde dehydrogenase, mitochondrial | 0.47 | 1.13 | 0.73 | 1.11 |
| O09173 | Hgd | Homogentisate 1,2-dioxygenase | 0.49 | 1.28 | 0.97 | 0.96 |
| P11725 | Otc | Ornithine carbamoyltransferase, mitochondrial | 0.49 | 1.36 | 0.94 | 0.95 |
| Q61425 | Hadh | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 0.51 | 1.40 | 0.96 | 1.16 |
| P61922 | Abat | 4-aminobutyrate aminotransferase, mitochondrial | 0.52 | 1.31 | 1.32 | 1.03 |
| P26443 | Glud1 | Glutamate dehydrogenase 1, mitochondrial | 0.50 | 1.27 | 0.98 | 1.12 |
| Q91XD4 | Ftcd | Formimidoyltransferase-cyclodeaminase | 0.59 | 1.25 | 0.99 | 0.98 |
| Q8VC12 | Uroc1 | Urocanate hydratase | 0.60 | 1.24 | 0.84 | 1.02 |
| Q3ULD5 | Mccc2 | Methylcrotonoyl-CoA carboxylase β chain, mitochondrial | 0.63 | 1.12 | 0.84 | 1.07 |
| P49429 | Hpd | 4-Hydroxyphenylpyruvate dioxygenase | 0.64 | 1.27 | 1.28 | 1.08 |
| Q9DBA8 | Amdhd1 | Probable imidazolonepropionase | 0.79 | 1.13 | 6.28 | 0.95 |
| O88986 * | Gcat | 2-amino-3-ketobutyrate CoA ligase, mitochondria | 1.24 | 0.84 | 1.81 | 0.9 |
| Neutrophil degranulation | ||||||
| Q9Z0K8 | Vnn1 | Pantetheinase | >100 | 1.51 | 29.5 | 1.18 |
| Q8C7E7 | Stbd1 | Starch-binding domain-containing protein 1 | 6.50 | 0.87 | 0.18 | 1.10 |
| P60904 | Dnajc5 | DnaJ homolog subfamily C member 5 | 5.19 | 1.00 | >100 | 1.06 |
| Q3TDN2 | Faf2 | FAS-associated factor 2 | 3.52 | 0.94 | 0.96 | 1.02 |
| Q99JI6 | Rap1b | Ras-related protein Rap-1b | 2.74 | 0.93 | 0.16 | 1.00 |
| O08807 | Prdx4 | Peroxiredoxin-4 | 0.64 | 1.09 | 2.83 | 0.88 |
| Q08857 | Cd36 | Platelet glycoprotein 4 | 0.45 | 1.12 | 6.05 | 1.28 |
| Q91W90 | Txndc5 | Thioredoxin domain-containing protein 5 | 0.25 | 1.19 | 0.52 | 0.99 |
| P63158 | Hmgb1 | High mobility group protein B1 | 0.24 | 1.04 | 1.62 | 1.06 |
| O09044 | Snap23 | Synaptosomal-associated protein 23 | 0.18 | 1.12 | 2.16 | 1.00 |
| P18242 | Ctsd | Cathepsin D | 0.13 | 1.02 | 2.25 | 0.96 |
| Q91W53 | Golga7 | Golgin subfamily A member 7 | 0.11 | 1.00 | 0.36 | 0.86 |
| Q64310 | Surf4 | Surfeit locus protein 4 | 0.96 | 0.98 | 2.45 | 0.84 |
| P11835 | Itgb2 | Integrin β-2 | 0.94 | 0.99 | 0.13 | 0.93 |
| Hemostasis | ||||||
| O08677 | Kng1 | Kininogen-1 | >100 | 0.95 | 0.41 | 1.03 |
| P04441 * | Cd74 | H-2 class II histocompatibility antigen γ chain | >100 | 1.00 | >100 | 1.00 |
| O35678 * | Mgll | Monoglyceride lipase | 3.31 | 0.93 | 7.37 | 0.94 |
| Q01339 | Apoh | β-2-glycoprotein 1 | 2.61 | 1.00 | 1.29 | 1.06 |
| Q76MZ3 | Ppp2r1a | Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A α isoform | 2.39 | 0.96 | 0.72 | 1.00 |
| P21279 | Gnaq | Guanine nucleotide-binding protein G(q) subunit α | 2.32 | 0.97 | 0.41 | 0.95 |
| Q9DC51 | Gnai3 | Guanine nucleotide-binding protein G(i) subunit α-3 | 2.10 | 1.01 | 0.71 | 0.93 |
| P14094 | Atp1b1 | Sodium/potassium-transporting ATPase subunit β-1 | 1.56 | 0.91 | 1.14 | 0.98 |
| P47757 | Capzb | F-actin-capping protein subunit β | 1.82 | 0.97 | 1.82 | 0.92 |
| O08715 | Akap1 | A-kinase anchor protein 1, mitochondrial | 0.77 | 0.96 | 0.38 | 1.11 |
| Q61411 | Hras | GTPase HRas | 0.66 | 0.98 | 3.49 | 0.96 |
| P27601 | Gna13 | Guanine nucleotide-binding protein subunit α-13 | 0.63 | 0.89 | 1.49 | 0.89 |
| P09055 | Itgb1 | Integrin β-1 | 0.53 | 0.96 | 1.08 | 1.07 |
| Q08857 | Cd36 | Platelet glycoprotein 4 | 0.45 | 1.12 | 6.05 | 1.28 |
| E9PV24 | Fga | Fibrinogen α chain | 0.43 | 1.08 | 1.94 | 0.83 |
| Q8VCM7 | Fgg | Fibrinogen γ chain | 0.43 | 1.15 | 0.87 | 0.85 |
| Q91WC9 * | Daglb | sn1-specific diacylglycerol lipase β | 0.38 | 0.93 | 1.49 | 1.00 |
| P63001 | Rac1 | Ras-related C3 botulinum toxin substrate 1 | 0.29 | 1.05 | 0.99 | 1.00 |
| Q8K0E8 | Fgb | Fibrinogen β chain | 0.28 | 1.28 | 0.58 | 0.86 |
| Q64727 | Vcl | Vinculin | 1.27 | 1.02 | 3.21 | 1.08 |
| P25911 | Lyn | Tyrosine-protein kinase Lyn | 1.43 | 0.99 | 0.63 | 0.98 |
| P21278 | Gna11 | Guanine nucleotide-binding protein subunit α-11 | 1.01 | 0.94 | 0.41 | 1.01 |
| P18572 | Bsg | Basigin | 1.07 | 0.98 | 0.32 | 1.11 |
| Q04736 | Yes1 | Tyrosine-protein kinase Yes | 0.73 | 0.93 | 2.32 | 0.95 |
The proteins were selected basing on the STRING-Reactome/REACTOME functional analysis; proteins which were detected after both 4 and 12 weeks of feeding are shown. Proteins whose S-palmitoylation extent was up-regulated (HPDpalm/RDpalm ratio ≥ 1.5) are highlighted with green font, those with the S-palmitoylation extent down-regulated (HPDpalm/RDpalm ratio ≤ 0.67)-with red font. For neutrophil degranulation only the most strongly up-regulated and down-regulated proteins at 4 or 12 weeks are included. Full characteristics of the proteins involved in lipid and amino acid metabolism, and in innate and adaptive immune responses is given in Supplemental Table S3, sheets 3–5. * Potentially false positive, see text for explanation.