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2-Compound Loop in E. coli Model iJR904

2-Compound Loop in E. coli Model iJR904. The Metabolic Network. From Palsson’s group 1075 reactions and 762 compounds. The Mostly Connected Nodes.

kamal-rosario
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2-Compound Loop in E. coli Model iJR904

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  1. 2-Compound Loop in E. coli Model iJR904

  2. The Metabolic Network • From Palsson’s group • 1075 reactions and 762 compounds

  3. The Mostly Connected Nodes Using the objective function proposed by Palsson’s group: H[c] is the only compound whose free drainage increases biomass production significantly. Compounds removed are: Atp, adp, nad, nadh, nadp, nadph, ppi, co2, fe2, h, h2o, k, na, nh4, pi, so4, and all other external compounds which have single-transport reaction.

  4. Loop-Finding Algorithm • Breadth-first search in Matlab • A 2-compound loop is composed of two metabolites and two reactions, in the form of C1R1C2R2C1. • A loop has directionality. C1R1C2R2C1 and C1R1C2R2C1 are considered to be two distinct loop.

  5. Loops of Different Sizes Count of loops increases sharply as more compounds are allowed to be included. If all connections which make up 2-compound loops are removed, the number of larger loops reduces dramatically.

  6. Most Frequently Observed 2-Compound Pairs • Many of the 2R2C loops have exactly the same set of 2C. For the 820 2R2C loops, 128 unique compound pairs are identified.

  7. The 2-Compound Pairs

  8. Co-activation of Reactions in 2R2C Loop • The conditions tested are Glc_aer, ac_aer, akg_aer, glyc_aer, lac-D_aer, lac-L_aer, mal-L_aer, pyr_aer, succ_aer, and glc_ana, where aer stands for aerobic and ana for anaerobic.

  9. All the 2R2C loops and their activation pattern

  10. Classification of Connectivities of 2R2C Elements • Order all the loop in the format of CRCR. 1connected; 0not connected to other components in the network. • The majority (624 out of 820) have all component nodes connected.

  11. 7-node: 8-arc 18678 5-node: 6-arc 12860 8-arc 5492 4-node: 4-arc 820 8-arc 160 6-node: 7-arc 542 6-node: 8-arc 67400

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