Properties of the genome-scale (iRP911) and methylotrophic networks reconstructed for M. extorquens AM1

Range Table - link (1139 unique reactions and 977 metabolites)
Organism Methylobacterium extorquens
Reference Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais JC. Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC Syst Biol. 2011 Nov 10 5: 189. doi: 10.1186/1752-0509-5-189 p.4 table 2PubMed ID22074569
Method P.3 left column bottom paragraph: "The genome-scale (GS) metabolic network of M. extorquens AM1 was reconstructed according to previously established guidelines [ref 21]. The details of the process are given in material and methods and are schematically shown in Additional file 1 link . Briefly, the GS metabolic network was obtained by integrating relevant information collected from i) genome annotation [ref 20], ii) published physiological, genetic and biochemical studies in M. extorquens AM1 and closely related organisms iii) biochemical information contained in databases [refs 22, 23, 24], vi) complementary investigations (biomass quantification), and intensive refinement (Additional file 2, 3). The chemical composition of M. extorquens AM1 cell was determined experimentally or taken from available literature (Table 1 and Additional file 4) and used to define the biosynthetic needs and corresponding pathways."
Comments Abstract: "In this work, [investigators] report on the integrated, system-level investigation of the metabolic network of the facultative methylotroph Methylobacterium extorquens AM1, a valuable model of methylotrophic bacteria. The genome-scale metabolic network of the bacterium was reconstructed and contains 1139 reactions and 977 metabolites." P.4 left column top paragraph: "The final GS [genome-scale] network (iRP911) contained 1139 unique reactions and 977 metabolites, and was based on a gene-to-protein-to-reaction (GPR) association network that included 911 genes encoding 761 proteins (Table 2, Additional file 2, 3). The confidence in the network information was established by scoring the evidence currently available for each reaction [ref 21]. The confidence scores ranged from 0 (lowest) to 4 (highest), with the latter being assigned to a reaction with direct evidence for both gene product function and biochemical reaction (Table 2). The average confidence score over the final network score was 2.1." See also p.19 left column 4th paragraph: "The metabolic network - containing 1139 (m) reactions 977 (n) metabolites - was converted into a mathematical model corresponding to a m × n matrix defining the stoichiometric coefficient of reactions. Calculations of steady-state fluxes were performed using the software CellNetAnlyser [ref 25] and Matlab (Mathworks, Inc.). Flux Balance Analysis (FBA) calculations were performed using various objective functions, as indicated in the text."
Entered by Uri M
ID 114581