ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Autor(es)

Tamasco, Gustavo ; Kumar, Manish ; Zengler, Karsten ; Silva-Rocha, Rafael ; da Silva, Ricardo Roberto

• Tipo de documento: Artigo Científico
• Fonte: BMC Bioinformatics; v. 23, n. 1, p. 13-pg., 2022-11-30.

Resumo

Background Genome-scale metabolic reconstruction tools have been developed in the last decades. They have helped to reconstruct eukaryotic and prokaryotic metabolic models, which have contributed to fields, e.g., genetic engineering, drug discovery, prediction of phenotypes, and other model-driven discoveries. However, the use of these programs requires a high level of bioinformatic skills. Moreover, the functionalities required to build models are scattered throughout multiple tools, requiring knowledge and experience for utilizing several tools. Results Here we present ChiMera, which combines tools used for model reconstruction, prediction, and visualization. ChiMera uses CarveMe in the reconstruction module, generating a gap-filled draft reconstruction able to produce growth predictions using flux balance analysis for gram-positive and gram-negative bacteria. ChiMera also contains two modules for metabolic network visualization. The first module generates maps for the most important pathways, e.g., glycolysis, nucleotides and amino acids biosynthesis, fatty acid oxidation and biosynthesis and core-metabolism. The second module produces a genome-wide metabolic map, which can be used to retrieve KEGG pathway information for each compound in the model. A module to investigate gene essentiality and knockout is also present. Conclusions Overall, ChiMera uses automation algorithms to combine a variety of tools to automatically perform model creation, gap-filling, flux balance analysis (FBA), and metabolic network visualization. ChiMera models readily provide metabolic insights that can aid genetic engineering projects, prediction of phenotypes, and model-driven discoveries. (AU)

• Processo FAPESP: 17/18934-0 - Expressão de lipases e pectinases pelo fungo patogênico Puccinia psidii durante a diferenciação in vitro
• Beneficiário: Gustavo Tamasco
• Modalidade de apoio: Bolsas no Brasil - Iniciação Científica
• Processo FAPESP: 17/18922-2 - Desenvolvimento de uma plataforma computacional modular extensível para análises de experimentos de metabolômica e metagenômica: inovando com a descoberta de novas atividades enzimáticas e produtos naturais de interesse farmacêutico derivados
• Beneficiário: Ricardo Roberto da Silva
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Jovens Pesquisadores
• Processo FAPESP: 19/05026-4 - Desenvolvimento de uma plataforma computacional modular extensível para análises de experimentos de metabolômica e metagenômica: Inovando com a descoberta de novas atividades enzimáticas e produtos naturais de interesse farmacêutico derivados
• Beneficiário: Ricardo Roberto da Silva
• Modalidade de apoio: Bolsas no Brasil - Programa BIOTA - Jovens Pesquisadores
• Processo FAPESP: 19/15675-0 - Desvendando a complexidade das redes de regulação gênica microbianas
• Beneficiário: Rafael Silva Rocha
• Modalidade de apoio: Auxílio à Pesquisa - Temático