Table 1. Pathways encompassed by the differentially expressed enzymes in the LD proteome and the whole-cell proteome.
| Pathway | Differentially expressed enzymes in LD proteome | Differentially expressed enzymes in whole-cell proteome |
|---|---|---|
| Carbohydrate Metabolism Related Pathways | ||
| Starch and sucrose metabolism | EC:2.4.1.25-disproportionating enzyme ↓ EC:2.7.7.9-uridylyltransferase ↓ EC:3.2.1.33-amylo-1,6-glucosidase ↓ | EC:3.2.1.28-trehalase ↓ EC:2.4.1.1-phosphorylase ↓ EC:5.4.2.2-(alpha-D-glucose-1,6-bisphosphate-dependent) ↓ EC:2.7.7.9-uridylyltransferase ↓ |
| Galactose metabolism | EC:2.7.7.9-uridylyltransferase ↓ EC:2.7.7.64-uridylyltransferase ↓ | EC:2.7.7.64-uridyltransferase ↓ EC:2.7.7.9-uridylyltransferase ↓ EC:5.4.2.2-(alpha-D-glucose-1,6-bisphosphate-dependent) ↓ |
| Citrate cycle (TCA cycle) | EC:2.3.3.8-citrate synthase ↓ | EC:1.8.1.4-dehydrogenase ↓ EC:4.1.1.49-carboxykinase(ATP) ↓ EC:1.2.4.2-dehydrogenase(succinyl-transferring) ↓ EC:1.1.1.42-dehydrogenase(NADP+) ↓ EC:1.1.1.41-dehydrogenase(NAD+) ↓ |
| Pentose and glucuronate interconversions | EC:2.7.7.9-uridylyltransferase ↓ EC:2.7.7.64-uridylyltransferase ↓ | EC:2.7.7.9-uridylyltransferase ↓ EC:2.7.7.64-uridylyltransferase ↓ |
| Pyruvate metabolism | EC:1.8.1.4-dehydrogenase ↓ EC:6.4.1.2-carboxylase ↓ EC:4.1.1.49-carboxykinase(ATP) ↓ EC:1.1.1.39-dehydrogenase(decarboxylating) ↓ EC:1.1.1.38-dehydrogenase(oxaloacetate-decarbosylating) ↓ | |
| Glycolysis | EC:5.4.2.2-(alpha-D-glucose-1,6-bisphosphate-dependent) ↓ EC:4.2.1.11-hydratase ↓ EC:4.1.1.49-carboxykinase(ATP) ↓ EC:1.8.1.4-dehydrogenase ↓ | |
| Pentose phosphate pathway | EC:5.4.2.2-alpha-D-glucose-1,6-bisphosphate-dependent ↓ | |
| Fructose and mannose metabolism | EC:4.2.1.47–4,6-dehydratase ↑ EC:1.1.1.271-synthase ↑ | |
| Fatty Acid Metabolism Related Pathways | ||
| Fatty acid biosynthesis | EC:2.3.1.85-synthase ↓ EC:6.4.1.2-carboxylase ↓ | EC:6.4.1.2-carboxylase ↓ |
| Biosynthesis of unsaturated fatty acids | EC 1.14.19.1-desaturase ↓ EC 1.14.19.3-desaturase ↓ EC 1.14.19.6-desaturase ↓ | EC 1.14.19.3-desaturase ↓ EC:4.2.1.17-hydratase ↑ |
| Glycerophospholipid metabolism | EC:3.1.1.5-lecithinase B ↑ | EC:2.7.8.8-O-phosphatidyltransferase ↓ |
| Lipid catabolic process | EC 3.1.1.5-lysophospholipase ↑ | |
| Fatty acid elongation | EC:4.2.1.17-hydratase ↑ | |
| Propanoate metabolism | EC:1.8.1.4-dehydrogenase ↓ EC:6.4.1.2-carboxylase ↓ EC:4.2.1.17-hydratase ↑ | |
| Alpha-linolenic acid metabolism | EC:4.2.1.17-hydratase ↑ | |
| Glyoxylate and dicarboxylate metabolism | EC:6.3.1.2-ligase ↑ EC:2.1.2.1-hydroxymethyltransferase ↑ | |
| Amino Acid Metabolism Related Pathways | ||
| Cysteine and methionine metabolism | EC:2.5.1.6-adenosyltransferase ↓ | EC:3.3.1.1-S-adenosylhomocysteine synthase ↓ |
| Phenylalanine, tyrosine and tryptophan biosynthesis | EC:2.5.1.54-synthase ↓ | EC:4.2.1.20-synthase ↓ |
| Arginine biosynthesis | EC:6.3.1.2-ligase ↑ | EC:6.3.4.5-synthase ↑ EC:3.5.3.1-arginine amidinase ↓ |
| Glycine, serine and threonine metabolism | EC:2.1.2.1-hydroxymethyltransferase ↑ | EC:4.2.1.20-synthase ↓ EC:1.8.1.4-dehydrogenase ↓ EC:1.1.1.95-dehydrogenase ↓ EC:2.7.8.8-O-phosphatidyltransferase ↓ |
| Alanine, aspartate and glutamate metabolism | EC:6.3.1.2-ligase ↑ | EC:2.6.1.16-transaminase(isomerizing) ↓ EC:6.3.4.5-synthase ↑ EC:1.4.1.14-synthase ↓ EC:1.4.1.14-synthase(NADH) ↓ EC:1.4.1.13-synthase(NADPH) ↓ |
| Cyano amino acid metabolism | EC:2.1.2.1-hydroxymethyltransferase ↑ | |
| Valine, leucine and isoleucine degradation | EC:1.8.1.4-dehydrogenase ↓ EC:4.2.1.17-hydratase ↑ EC:1.1.1.35-dehydrogenase ↑ EC:1.1.1.35-dehydrogenase ↑ | |
| Lysine degradation | EC:1.2.4.2-dehydrogenase(succinyl-transferring) ↓ EC:4.2.1.17-hydratase ↑ EC:1.1.1.35-dehydrogenase ↑ | |
| Tryptophane metabolism | EC:1.2.4.2-dehydrogenase(succinyl-transferring) ↓ EC:4.2.1.17-hydratase ↑ EC:1.1.1.35-dehydrogenase ↑ | |
| Beta-alanine metabolism | EC:4.2.1.17-hydratase ↑ | |
| Arginine and proline metabolism | EC:3.5.3.1-arginine amidinase ↓ | |
| Valine, leucine and isoleucine Biosynthesis | EC:4.2.1.33-dehydratase ↓ | |
| Phenylalanine metabolism | EC:4.2.1.17-hydratase ↑ | |
| Histidine metabolism | EC:4.2.1.19-dehydratase ↓ | |
| Other Metabolic Pathways | ||
| Amino sugar and nucleotide sugar metabolism | EC:2.7.7.9-uridylytransferase ↓ EC:2.7.7.64-uridylyltransferase ↓ EC:4.2.1.47–4,6-dehydratase ↑ EC:1.1.1.271-synthase ↑ | EC:3.5.99.6-deaminase ↑ EC:2.6.1.16-transaminase(isomerizing) ↓ EC:2.7.7.64-uridylyltransferase ↓ EC:2.4.1.16-synthase ↑ EC:5.4.2.2-(alpha-D-glucose-1,6-bisphosphate-dependent) ↓ EC:2.7.7.9-uridylyltransferase ↓ |
| Purine metabolism | EC:3.6.1.3-adenylpyrophosphatase ↑ EC:3.6.1.15-phosphatase ↑ | |
| Pantothenate and CoA biosynthesis | EC:2.7.8.7-synthase ↓ | |
| Glutathione metabolism | EC:1.1.1.42-dehydrogenase(NADP+) ↓ EC:1.11.1.15-thioredoxin peroxidase ↓ | |
| Oxidative phosphorylation | EC:1.6.99.3-dehydrogenase ↓ EC:1.6.5.3-reductase (H+-translocating) ↓ EC:3.6.1.1-diphosphatase ↑ EC:3.6.3.6-ATPase ↓ | |
Note: Up-regulated enzymes were labelled with ↑; down-regulated enzymes were labelled with ↓.