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An expanded computational model of cell envelope biogenesis for Escherichia coli

thesis
posted on 2025-01-31, 14:35 authored by Rui Afonso TavaresRui Afonso Tavares
A computational systems approach has been used to investigate the biogenesis of the outer envelope of Escherichia coli. Specifically, a deterministic model incorporating the lipopolysaccharide, peptidoglycan and phospholipid components. The expanded model now contains 195 reacting species, making up 145 biochemical reactions, making it the largest dynamic model published. The model was used to understand key regulatory elements underpinning pathway regulation and its findings extrapolated to account for phenotypic effects such as growth rates and cell envelope health. The model was capable of producing the known amounts of endpoint metabolites for each of the relevant pathways- Indicating that the parametrisation is reasonable for this network with steady state achieved for most reactions. However, there are numerous nodes which are fitted which can be a source of error. In order to test model predictions a strain library of tuneable CRISPR recombinant E. coli, which can downregulate specific genes (between 5-30%) within this network was generated. During strain validation it was found that genetic perturbation resulted in an associated accumulation at the metabolic level. This strongly suggests that the effect observed in these recombinant strains is likely a result of the perturbation of the specific gene of interest, making it an appropriate method to constrain the metabolic model. Intriguingly, one of the recombinant strains (MsbA- LPS flippase), when repressed caused a build up of DSMP which is the substrate for LpxK. This association has not been published previously and potentially represents a novel regulatory mechanism. However, more work is required in order to constrain and test the model accuracy.

History

Qualification name

  • PhD

Supervisor

George, John

Awarding Institution

Leeds Beckett University

Completion Date

2024-12-02

Qualification level

  • Doctoral

Language

  • eng

Publisher

Leeds Beckett University

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