The activity reaction core and plasticity of metabolic networks Almaas e. oltvai z N.& barabasi A-L 01/04/2006
The activity reaction core and plasticity of metabolic networks Almaas E., Oltvai Z.N. & Barabasi A.-L. 01/04/2006
The idea To examine the utilization and relative flux rates of each metabolic reaction in a wide range of simulated environmental conditions 30,000 randomly and uniformly chosen optimal growth conditions(randomly assigning values for metabolic-uptake reactions and all single-carbon-source minimal medium conditions sufficient for growth Using fba on in silico models H pylori ■E.cOl ■S. cerevisiae
The idea ◼ To examine the utilization and relative flux rates of each metabolic reaction in a wide range of simulated environmental conditions ◼ 30,000 randomly and uniformly chosen optimal growth conditions (randomly assigning values for metabolic-uptake reactions) ◼ and all single-carbon-source minimal medium conditions sufficient for growth ◼ Using FBA on in silico models: ◼ H. pylori ◼ E. coli ◼ S. cerevisiae
Observations ■ Flux plastici Changes in the fluxes of already active reactions when the organism is shifted from one growth condition to another a Structural plasticity Changes in the active reaction set
Observations ◼ Flux plasticity ◼ Changes in the fluxes of already active reactions when the organism is shifted from one growth condition to another ◼ Structural plasticity ◼ Changes in the active reaction set
Metabolic core Definition The set of reactions that are active under all conditions Metabolic cores in different organisms H. pylori:138of381(36.200) ■E.coi:90of758(11.900 S cerevisiae: 33 of 1172(2.8%o) a Property The reactions in the metabolic core form a single connected cluster
Metabolic core ◼ Definition ◼ The set of reactions that are active under all conditions ◼ Metabolic cores in different organisms: ◼ H. pylori: 138 of 381 (36.2%) ◼ E. coli: 90 of 758 (11.9%) ◼ S. cerevisiae: 33 of 1172 (2.8%) ◼ Property ◼ The reactions in the metabolic core form a single connected cluster
The metabolic core of e. coli 3DDAH7P T3P2 E4P UDPNAM 13DPG DHSK ALA 2PG ESP MDA 3PSME 4PPNCYSH DALA CHOR UNPTDO 4PPNTE ADCHOR DPCOA COA )Ey AHTD PNAG O6R PSP UDPGG2A ACA 2) A6RPSP THE C140ACP C120ACP C141ACP C160ACP C161ACP C181ACI A6RP6P2 UoPg23a A6RP DISAC1P PEP PGP RIBFLV KPo CMPKDO K2LIPIV CDPETN LPS GLYCOGEN ADPGLC GIP UDPG AOPHEP NAD NMN一PP1 UTP UDP METTHE OTHIO TTHE RTHIO NADPH GMP CoP DTTP一 DTDp OTMI
The metabolic core of E. coli