Projects

“Uncovering Thermodynamic Bottlenecks in Essential Metabolic Pathways in E. coli”

Ismael Maximiliano De Los Santos Huesca, Jose Utrilla Carreri
Center of Genomic Sciences, National Autonomous University of Mexico

Status: 2025 - Ongoing

E. coli proteome optimization through the identification of energy bottlenecks and the use of Keio-deficient strains of these bottleneck genes in order to evaluate E. coli growth at different induction levels and assess proteome liberation. The goal of this project is to free cellular energy by knocking out genes identified as bottlenecks in the E. coli proteome.

“Testing Proteome Liberation Using Isocost Lines in E. coli”

Ismael Maximiliano De Los Santos Huesca, Gabriela Perez Segura, Jose Utrilla Carreri
Center of Genomic Sciences, National Autonomous University of Mexico

Status: 2025 - Ongoing

E. coli transcription factor-deficient strains identified using the ReProMin tool, combined with a CRISPR-dCas9-like system to downregulate previously identified bottleneck genes in order to redirect the liberated energy toward a heterologous pathway.

“Quantifying Step-Limiting Enzymes in E. coli”

Ismael Maximiliano De Los Santos Huesca, Donaji Hernández Moreno, Jose Utrilla Carreri
Center of Genomic Sciences, National Autonomous University of Mexico

Status: 2026 - Ongoing

This project focuses on a computational approach to model the E. coli proteome using ME-models implemented in Python scripts in order to quantify the proteome fraction of enzymes that act as step-limiting factors in E. coli metabolism.