Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis.
BMC Microbiol
; 21(1): 292, 2021 10 25.
Article
em En
| MEDLINE
| ID: mdl-34696732
ABSTRACT
BACKGROUND:
Graph-based analysis (GBA) of genome-scale metabolic networks has revealed system-level structures such as the bow-tie connectivity that describes the overall mass flow in a network. However, many pathways obtained by GBA are biologically impossible, making it difficult to study how the global structures affect the biological functions of a network. New method that can calculate the biologically relevant pathways is desirable for structural analysis of metabolic networks.RESULTS:
Here, we present a new method to determine the bow-tie connectivity structure by calculating possible pathways between any pairs of metabolites in the metabolic network using a flux balance analysis (FBA) approach to ensure that the obtained pathways are biologically relevant. We tested this method with 15 selected high-quality genome-scale metabolic models from BiGG database. The results confirmed the key roles of central metabolites in network connectivity, locating in the core part of the bow-tie structure, the giant strongly connected component (GSC). However, the sizes of GSCs revealed by GBA are significantly larger than those by FBA approach. A great number of metabolites in the GSC from GBA actually cannot be produced from or converted to other metabolites through a mass balanced pathway and thus should not be in GSC but in other subsets of the bow-tie structure. In contrast, the bow-tie structural classification of metabolites obtained by FBA is more biologically relevant and suitable for the study of the structure-function relationships of genome scale metabolic networks.CONCLUSIONS:
The FBA based pathway calculation improve the biologically relevant classification of metabolites in the bow-tie connectivity structure of the metabolic network, taking us one step further toward understanding how such system-level structures impact the biological functions of an organism.Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Genoma
/
Redes e Vias Metabólicas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
BMC Microbiol
Assunto da revista:
MICROBIOLOGIA
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
China