Model-Based Re-Design of some Genetic Regulatory Circuits to get Genetic Modified Micro-organisms (GMO) by using Engineering Computational Tools

Abstract

The paper is aiming at reviewing the main math modelling and computational tools developed by to in-silico redesign genetic regulation circuits (GRC) in living cells to get GMOs of desired characteristics. A number of suggestive examples (case studies) are mentioned as well.

Concepts and Tools to Model GRCs, and Some Essential CCM Pathways in Living Cells 1. Generalities

“…The 3&4 parts [14] of the work proves, by means of several demonstrative relevant examples the superiority of using MSDKM and HSMDM dynamic math models when solving various bioengineering problems (i) to in-silico off-line optimize the operating policy of various types of bioreactors, and (ii) to insilico design/check some GMO-s of industrial use able to improve the performances of several bioprocess/bioreactors. By contrast, by considering only the macroscopic keyvariables of the process (biomass, substrate, and product concentrations), the unstructured (apparent, global) math models do not adequately reflect the metabolic changes of the bioreactor biomass, being inadequate to accurately predict the cellular response to the medium disturbances through the self-regulated cellular metabolism.…”

“…These structured models can satisfactorily represent the key steps of the central carbon metabolism (CCM) at a cell scale, by also including reaction modules responsible for the synthesis of cellular metabolites of interest for the industrial biosynthesis. As proved ny Maria [11][12][13][14]32], and Yang et al [175], the modular structured kinetic models can reproduce the dynamics of complex metabolic syntheses inside living cells. This is why, the modular GRC and CCM dynamic models, of an adequate mathematical representation, seem to be the most comprehensive mean for a rational design of the regulatory GRC with desired behaviour [110].…”

“…By contrast, the current (classical/ default) approach in biochemical engineering and bioengineering practice for solving design, optimization and control problems based on the math models of industrial biological reactors is to use unstructured Monod (for cell culture reactor) or Michaelis-Menten (if only enzymatic reactions are retained) global kinetic models by ignoring detailed representations of metabolic cellular processes. The applied engineering rules to develop MSDKM and HSMDM dynamic math models presented in the 1-st and 2-nd parts of this work [14] are similar to those used in the CBE, and in the control theory of nonlinear systems (NSCT). This 1-st part of the work presents some general concepts of CBE, of the NSCT, and of Bioinformatics used to derive MSDKM and HSMDM models, with continuous variables and based on cellular metabolic reaction mechanisms.…”

“…The 2-nd part of the work [14] will briefly reviews the 'wholecell of variable-volume' (WCVV) modelling framework introduced and promoted by the author in previous works. Also, this 2-nd part [14] points-out the features of the deterministic WCVV models, and its advantages when simulating GERM-s, and GRC-s dynamics in living cells, by contrast to the classical (default) WCCV (wholecell constant-volume modelling framework); P.I.-s of GERM-s; rules to link GERM-s when modelling GRC-s, and other related theoretical aspects necessary to construct MSDKM and HSMDM models.…”

“…[Bottom-right] Production cost structure in the case of biosyntheses with free enzyme (or biomass) compared to those with immobilized enzyme (or biomass). Adapted from [164,14].…”