TY - JOUR
T1 - Reconstruction of a generic genome-scale metabolic network for chicken
T2 - Investigating network connectivity and finding potential biomarkers
AU - Salehabadi, Ehsan
AU - Motamedian, Ehsan
AU - Shojaosadati, Seyed Abbas
N1 - Publisher Copyright:
© 2022 Salehabadi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2022/3
Y1 - 2022/3
N2 - Chicken is the first sequenced avian that has a crucial role in human life for its meat and egg production. Because of various metabolic disorders, study the metabolism of chicken cell is important. Herein, the first genome-scale metabolic model of a chicken cell named iES1300, consists of 2427 reactions, 2569 metabolites, and 1300 genes, was reconstructed manually based on KEGG, BiGG, CHEBI, UNIPROT, REACTOME, and MetaNetX databases. Interactions of metabolic genes for growth were examined for E. coli, S. cerevisiae, human, and chicken metabolic models. The results indicated robustness to genetic manipulation for iES1300 similar to the results for human. iES1300 was integrated with transcriptomics data using algorithms and Principal Component Analysis was applied to compare context-specific models of the normal, tumor, lean and fat cell lines. It was found that the normal model has notable metabolic flexibility in the utilization of various metabolic pathways, especially in metabolic pathways of the carbohydrate metabolism, compared to the others. It was also concluded that the fat and tumor models have similar growth metabolisms and the lean chicken model has a more active lipid and carbohydrate metabolism.
AB - Chicken is the first sequenced avian that has a crucial role in human life for its meat and egg production. Because of various metabolic disorders, study the metabolism of chicken cell is important. Herein, the first genome-scale metabolic model of a chicken cell named iES1300, consists of 2427 reactions, 2569 metabolites, and 1300 genes, was reconstructed manually based on KEGG, BiGG, CHEBI, UNIPROT, REACTOME, and MetaNetX databases. Interactions of metabolic genes for growth were examined for E. coli, S. cerevisiae, human, and chicken metabolic models. The results indicated robustness to genetic manipulation for iES1300 similar to the results for human. iES1300 was integrated with transcriptomics data using algorithms and Principal Component Analysis was applied to compare context-specific models of the normal, tumor, lean and fat cell lines. It was found that the normal model has notable metabolic flexibility in the utilization of various metabolic pathways, especially in metabolic pathways of the carbohydrate metabolism, compared to the others. It was also concluded that the fat and tumor models have similar growth metabolisms and the lean chicken model has a more active lipid and carbohydrate metabolism.
UR - http://www.scopus.com/inward/record.url?scp=85126855535&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0254270
DO - 10.1371/journal.pone.0254270
M3 - Article
C2 - 35316277
AN - SCOPUS:85126855535
SN - 1932-6203
VL - 17
JO - PloS one
JF - PloS one
IS - 3 March
M1 - e0254270
ER -