unIn silico Derivation of a Reduced Kinetic Model for Stationary or Oscillating Glycolysis in Escherichia coli Bacterium

Model-based Identification of Some Conditions Leading to Glycolytic Oscillations in E. coli Cells

“…Thus, the cell metabolic process complexity appears to be described by a succession of "locally" reduced models "enfolded" on the real process long time-interval dynamics. 4,11 Being quite versatile, the reduced mTRM model includes enough information to reproduce not only the cell energy potential through the total A(MDT)P level, but also the role played by ATP/ ADP ratio as a glycolysis driving force. The model can also reproduce the oscillatory behaviour depending on the external/internal conditions, as well as situations when homeostatic conditions are not fulfilled.…”

“…Simulations were made for the cell culture conditions given in Table 1, and for cells with [AM-DTP]total = 5.82 mM. 4,23 Following the discussion in the previous chapter on oscillations occurence, the influence of two main factors is studied here, that is:…”

“…[4][5][6] The CCM model is the 'core' part of any systematic and structured model-based analysis of the cell metabolism with immediate practical applications, such as target metabolite synthesis optimization, insilico re-programming of the cell metabolism to design new microorganisms for industrial bioprocess optimization, etc. [4][5][6][7][8][9][10][11][12] However, to cope with the astronomic complexity of cellular processes, of low observability, involving O(10 3 -10 4 ) number state variables (species conc. ), O(10 3 ) gene expression transcription factors TF, and O(10 4 -10 5 ) reactions, versatile models of 'building-blocks' like modular constructions, including individual and lumped species and reactions have been developed over decades.…”

“…[8][9][10] Consequently, understanding and simulation of the cell characteristics and environmental conditions leading to an oscillating glycolysis is an old subject, but still of high interest. 4 To simulate the glycolysis in bacteria, a large number of glycolysis models, of a reduced or extended form, have been proposed over decades (review of Maria 4 ). Recently, Maria 4 proposed a reduced glycolysis model (denoted by mTRM in the E. coli cells, including only 9 species, 7 lumped reactions, and 17 estimable parameters.…”

Setting Some Milestones when Modelling Cell Gene Expression Regulatory Circuits Under Variable-Volume Whole-cell Modelling Framework. I. Generalities

“…Comparatively to chemical systems, and lacking of enough and reproducible experimental data, the cell biochemical processes present the advantage of being approached in a modular way; every subsystem can be separately studied/modelled [6][7][8][9][10], that is: the central carbon metabolism phosphotransferase PTS-system for glucose transport into the cell, the pentose-phosphate pathway PPP for nucleotides and aminoacids production, and tricarboxylic acid cycle TCA, [10]); regulation of gene expression, cell cycle, signal transduction, and various metabolic pathways [6]. However, although these models made significant contributions to the development of in silico biology, the programs were only able to handle only specific subsystems, and it was difficult to combine different subsystem models into one single-cell model [6].…”