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 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) 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 and all single-carbon-source minimal medium conditions sufficient for growth Using FBA on in silico models: Using FBA on in silico models: H. pylori H. pylori E. coli E. coli S. cerevisiae S. cerevisiae

Observations Flux plasticity Flux plasticity Changes in the fluxes of already active reactions when the organism is shifted from one growth condition to another Changes in the fluxes of already active reactions when the organism is shifted from one growth condition to another Structural plasticity Structural plasticity Changes in the active reaction set Changes in the active reaction set

Metabolic core Definition Definition The set of reactions that are active under all conditions The set of reactions that are active under all conditions Metabolic cores in different organisms: Metabolic cores in different organisms: H. pylori: 138 of 381 (36.2%) H. pylori: 138 of 381 (36.2%) E. coli: 90 of 758 (11.9%) E. coli: 90 of 758 (11.9%) S. cerevisiae: 33 of 1172 (2.8%) S. cerevisiae: 33 of 1172 (2.8%) Property Property The reactions in the metabolic core form a single connected cluster. The reactions in the metabolic core form a single connected cluster.

The metabolic core of E. coli

Essentiality of reactions in metabolic core Two types of reactions in metabolic core Two types of reactions in metabolic core Reactions that are essential for growth under all conditions Reactions that are essential for growth under all conditions H. pylori: no data in the paper H. pylori: no data in the paper E. coli: 81 out of 90 E. coli: 81 out of 90 Experimental data: 74.7% of the enzymes that catalyze core metabolic reactions are essential, compared with a 19.6% lethality fraction of the noncore enzymes. Experimental data: 74.7% of the enzymes that catalyze core metabolic reactions are essential, compared with a 19.6% lethality fraction of the noncore enzymes. S. cerevisiae: all 33 S. cerevisiae: all 33 Experimental data: 84% of the core enzymes are essential, whereas 15.6% of noncore enzymes are essential. Experimental data: 84% of the core enzymes are essential, whereas 15.6% of noncore enzymes are essential. Reactions that are required for optimal metabolic performance Reactions that are required for optimal metabolic performance When assuming a 10% reduction in the growth rate, the size of the metabolic core becomes 83 in E. coli. When assuming a 10% reduction in the growth rate, the size of the metabolic core becomes 83 in E. coli.

Size of the metabolic cores Metabolic cores in different organisms: Metabolic cores in different organisms: H. pylori: 36.2% H. pylori: 36.2% E. coli: 11.9% E. coli: 11.9% S. cerevisiae: 2.8% S. cerevisiae: 2.8% Explanation Explanation Little flexibility for biomass production in H. pylori Little flexibility for biomass production in H. pylori 61% of the H. pylori reactions are active on average. 61% of the H. pylori reactions are active on average. Higher metabolic flexibility in E. coli and S. cerevisiae Higher metabolic flexibility in E. coli and S. cerevisiae On average, 35.3% and 19.7% of the reactions are required in E. coli and S. cerevisiae, respectively. On average, 35.3% and 19.7% of the reactions are required in E. coli and S. cerevisiae, respectively. Alternative pathways: 20 out of the 51 biomass constituents in E. coli are not produced by the core. Alternative pathways: 20 out of the 51 biomass constituents in E. coli are not produced by the core. The more reactions a metabolic network possesses, the stronger is the network-induced redundancy, and the smaller is the core. The more reactions a metabolic network possesses, the stronger is the network-induced redundancy, and the smaller is the core.

Conservation of the metabolic core The average core enzyme in E. coli has orthologs in 71.7% of the 32 reference bacteria. While the noncore enzymes have an evolutionary retention of only 47.7%. This difference is not a simple consequence of the high-lethality fraction of the core enzymes. Random selection of 90 enzymes with a 74.7% lethality ratio has an average evolutionary retetion of only 63.4% Maintaining the core ’ s integrity is a collective need of the organism.

Regulatory control on metabolic core mRNA half-lives mRNA half-lives Average half-life for the core enzymes: 14.0 min Average half-life for the core enzymes: 14.0 min Average half-life for the noncore enzymes: 10.5 min Average half-life for the noncore enzymes: 10.5 min Activating and repressive regulatory links Activating and repressive regulatory links Extended core: a set of 234 reactions that are active in more than 90% of the 30,000 simulated growth conditions Extended core: a set of 234 reactions that are active in more than 90% of the 30,000 simulated growth conditions Core enzyme-encoding operons: 52.3% repressive; 35.7% activating; and 10% dual interactions Core enzyme-encoding operons: 52.3% repressive; 35.7% activating; and 10% dual interactions Noncore enzyme-encoding operons: 45% repressive; 45% activating; and 10% dual interactions Noncore enzyme-encoding operons: 45% repressive; 45% activating; and 10% dual interactions Synchronization Synchronization Flux correlation Flux correlation mRNA expression correlation mRNA expression correlation All data are of E. coli.

Practical implications The core enzymes may prove effective antibiotic targets. The core enzymes may prove effective antibiotic targets. Currently used antibiotics: Currently used antibiotics: Fosfomycin and cycloserine inhibit cell-wall peptidoglycan. Fosfomycin and cycloserine inhibit cell-wall peptidoglycan. Sulfonamides and trimethoprim inhibit tetrahydrofolte biosynthesis. Sulfonamides and trimethoprim inhibit tetrahydrofolte biosynthesis. Both pathways are present in H. pylori and E. coli. Both pathways are present in H. pylori and E. coli.

Summary of our previous work Production efficiency of amino acids Production efficiency of amino acids Energy requirement Energy requirement Redox balance Redox balance Charge balance Charge balance Carrier molecules Carrier molecules Internal structure of the network Internal structure of the network Coupling mechanisms in amino acid synthesis Coupling mechanisms in amino acid synthesis Complementary needs in currency/carrier molecules Complementary needs in currency/carrier molecules Irreversible flow of energy/redox potential Irreversible flow of energy/redox potential

Further work Extend the analysis to all biomass constituents instead of only amino acids Extend the analysis to all biomass constituents instead of only amino acids Straightforward extension but attention should be paid to constituent molecules with large number of carbon atoms.. Straightforward extension but attention should be paid to constituent molecules with large number of carbon atoms.. Coupling mechanisms Coupling mechanisms Quite complicated for yeast and E.coli Quite complicated for yeast and E.coli It might be okay if the problem is not completely solved now. It might be okay if the problem is not completely solved now.