Metabolic network

A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions.

With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human. Several of these networks are available online: Kyoto Encyclopedia of Genes and Genomes (KEGG),[1] EcoCyc,[2] BioCyc[3] and metaTIGER.[4] Metabolic networks are powerful tools for studying and modelling metabolism.

Carbon fixation Photo- respiration Pentose phosphate pathway Citric acid cycle Glyoxylate cycle Urea cycle Fatty acid synthesis Fatty acid elongation Beta oxidation Peroxisomal beta oxidation Glyco- genolysis Glyco- genesis Glyco- lysis Gluconeo- genesis Pyruvate decarb- oxylation Fermentation Keto- lysis Keto- genesis feeders to gluconeo- genesis Direct / C4 / CAM carbon intake Light reaction Oxidative phosphorylation Amino acid deamination Citrate shuttle Lipogenesis Lipolysis Steroidogenesis MVA pathway MEP pathway Shikimate pathway Transcription & replication Translation Proteolysis Glycosyl- ation Sugar acids Double/multiple sugars & glycans Simple sugars Inositol-P Amino sugars & sialic acids Nucleotide sugars Hexose-P Triose-P Glycerol P-glycerates Pentose-P Tetrose-P Propionyl -CoA Succinate Acetyl -CoA Pentose-P P-glycerates Glyoxylate Photosystems Pyruvate Lactate Acetyl -CoA Citrate Oxalo- acetate Malate Succinyl -CoA α-Keto- glutarate Ketone bodies Respiratory chain Serine group Alanine Branched-chain amino acids Aspartate group Homoserine group & lysine Glutamate group & proline Arginine Creatine & polyamines Ketogenic & glucogenic amino acids Amino acids Shikimate Aromatic amino acids & histidine Ascorbate (vitamin C) δ-ALA Bile pigments Hemes Cobalamins (vitamin B12) Various vitamin Bs Calciferols (vitamin D) Retinoids (vitamin A) Quinones (vitamin K) & carotenoids (vitamin E) Cofactors Vitamins & minerals Antioxidants PRPP Nucleotides Nucleic acids Proteins Glycoproteins & proteoglycans Chlorophylls MEP MVA Acetyl -CoA Polyketides Terpenoid backbones Terpenoids & carotenoids (vitamin A) Cholesterol Bile acids Glycero- phospholipids Glycerolipids Acyl-CoA Fatty acids Glyco- sphingolipids Sphingolipids Waxes Polyunsaturated fatty acids Neurotransmitters & thyroid hormones Steroids Endo- cannabinoids Eicosanoids Major metabolic pathways in metro-style map. Click any text (name of pathway or metabolites) to link to the corresponding article. Single lines: pathways common to most lifeforms. Double lines: pathways not in humans (occurs in e.g. plants, fungi, prokaryotes). Orange nodes: carbohydrate metabolism. Violet nodes: photosynthesis. Red nodes: cellular respiration. Pink nodes: cell signaling. Blue nodes: amino acid metabolism. Grey nodes: vitamin and cofactor metabolism. Brown nodes: nucleotide and protein metabolism. Green nodes: lipid metabolism.

Uses

Metabolic networks can be used to detect comorbidity patterns in diseased patients.[5] Certain diseases, such as obesity and diabetes, can be present in the same individual concurrently, sometimes one disease being a significant risk factor for the other disease.[6] The disease phenotypes themselves are normally the consequence of the cell’s inability to breakdown or produce an essential substrate. However, an enzyme defect at one reaction may affect the fluxes of other subsequent reactions. These cascading effects couple the metabolic diseases associated with subsequent reactions resulting in comorbidity effects. Thus, metabolic disease networks can be used to determine if two disorders are connected due to their correlated reactions.[5]

See also

• Metabolic network modelling
• Metabolic pathway

References

1. "GenomeNet". www.genome.ad.jp. Archived from the original on 2009-02-24. Retrieved 2020-04-01.
2. "EcoCyc: Encyclopedia of E. coli Genes and Metabolic Pathways". www.ecocyc.org.
3. "BioCyc Pathway/Genome Database Collection". biocyc.org.
4. "metaTIGER - Home". www.bioinformatics.leeds.ac.uk. Archived from the original on 2012-03-04. Retrieved 2010-06-09.
5. Lee, D.- S.; Park, J.; Kay, K. A.; Christakis, N. A.; Oltvai, Z. N.; Barabasi, A.- L. (2008). "The implications of human metabolic network topology for disease comorbidity". Proceedings of the National Academy of Sciences. 105 (29): 9880–9885. doi:10.1073/pnas.0802208105. PMC 2481357. PMID 18599447.
6. Ross, R.; Dagnone, D.; Jones, P. J.; Smith, H.; Paddags, A.; Hudson, R.; Janssen, I. (2000). "Reduction in obesity and related comorbid conditions after diet-induced weight loss or exercise-induced weight loss in men. A randomized, controlled trial". Annals of Internal Medicine. 133 (2): 92–103. doi:10.7326/0003-4819-133-2-200007180-00008. PMID 10896648. S2CID 13415272.