Development and validation of the genome-scale metabolic model of Trypanosoma cruzi: comparative in silico analysis of the metabolic flux of epimastigotes, trypomastigotes and amastigotes

• Grant number: 23/07306-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: April 01, 2024
• End date: March 31, 2026
• Field of knowledge: Biological Sciences - Parasitology - Protozoology of Parasites
• Principal Investigator: Ariel Mariano Silber
• Grantee: Bruno Ribeiro Pinto
• Host Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 21/12938-0 - Amino acid metabolism in Trypanosoma cruzi: a toolbox to survive in hostile environments, AP.TEM

Abstract

Trypanosoma cruzi is the causative agent of Chagas disease, a neglected tropical disease that affects many countries in the Americas. This trypanosomatid, throughout its life cycle, transits between two different hosts and needs to survive in limited nutrient conditions. T. cruzi is capable of using both glucose, amino acids and fatty acids to generate energy. For this, it has transporters and enzymes that catalyze various reactions of metabolic pathways, allowing the uptake and oxidation of these nutrients from the extracellular environment, generating energy and biomass to adapt and complete its life cycle. Analyzing manually, in a systemic way, the interaction of the reactions that make up the metabolic network of this parasite under different conditions is a complex task. However, genomic-scale metabolic modeling allows us, through genomic data, to reconstruct in silico the metabolic network of a given organism and to predict the metabolic fluxes of this network. Thus, making it possible to systematically analyze the metabolic interactions in different conditions. Metabolic flux simulations allow us to clarify different aspects of metabolism, identifying essential reactions and genes that can be studied and experimentally validated as putative new therapeutic targets. This project aims to expand the metabolic model of T. cruzi iIS312, through an extensive review of data present in databases and literature, expanding the model in a curated way, adding new reactions, genes, metabolites and context-specific modeling of epimastigote, trypomastigote and amastigote forms. As well as the formulation of specific biomass equations for the infectious stages of T. cruzi, using experimental data for the determination of cell components such as RNA, DNA, proteins and lipids. From the curation and expansion of the model, it will be possible to generate a mathematical model of the metabolic network. This model will allow us to simulate biomass production under different conditions, thus making it possible to systematically visualize the metabolic flux of different pathways, and perform in silico knockouts, which will be experimentally validated using the CRISPR-Cas9 genome editing technique. Thus generating a tool that will allow in silico studies of the metabolism of T. cruzi that will be available to the scientific community. (AU)