Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.

With the emergence of energy scarcity, the use of renewable energy sources such as biodiesel is becoming increasingly necessary. Recently, many researchers have focused their minds on Yarrowia lipolytica, a model oleaginous yeast, which can be employed to accumulate large amounts of lipids that coul...

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Autores principales:	Pengcheng Pan, Qiang Hua
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2fdf9e24b7d44dfbb597fa16ff318ad5
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spelling	oai:doaj.org-article:2fdf9e24b7d44dfbb597fa16ff318ad52021-11-18T08:05:53ZReconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.1932-620310.1371/journal.pone.0051535https://doaj.org/article/2fdf9e24b7d44dfbb597fa16ff318ad52012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23236514/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203With the emergence of energy scarcity, the use of renewable energy sources such as biodiesel is becoming increasingly necessary. Recently, many researchers have focused their minds on Yarrowia lipolytica, a model oleaginous yeast, which can be employed to accumulate large amounts of lipids that could be further converted to biodiesel. In order to understand the metabolic characteristics of Y. lipolytica at a systems level and to examine the potential for enhanced lipid production, a genome-scale compartmentalized metabolic network was reconstructed based on a combination of genome annotation and the detailed biochemical knowledge from multiple databases such as KEGG, ENZYME and BIGG. The information about protein and reaction associations of all the organisms in KEGG and Expasy-ENZYME database was arranged into an EXCEL file that can then be regarded as a new useful database to generate other reconstructions. The generated model iYL619_PCP accounts for 619 genes, 843 metabolites and 1,142 reactions including 236 transport reactions, 125 exchange reactions and 13 spontaneous reactions. The in silico model successfully predicted the minimal media and the growing abilities on different substrates. With flux balance analysis, single gene knockouts were also simulated to predict the essential genes and partially essential genes. In addition, flux variability analysis was applied to design new mutant strains that will redirect fluxes through the network and may enhance the production of lipid. This genome-scale metabolic model of Y. lipolytica can facilitate system-level metabolic analysis as well as strain development for improving the production of biodiesels and other valuable products by Y. lipolytica and other closely related oleaginous yeasts.Pengcheng PanQiang HuaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51535 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pengcheng Pan Qiang Hua Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.
description	With the emergence of energy scarcity, the use of renewable energy sources such as biodiesel is becoming increasingly necessary. Recently, many researchers have focused their minds on Yarrowia lipolytica, a model oleaginous yeast, which can be employed to accumulate large amounts of lipids that could be further converted to biodiesel. In order to understand the metabolic characteristics of Y. lipolytica at a systems level and to examine the potential for enhanced lipid production, a genome-scale compartmentalized metabolic network was reconstructed based on a combination of genome annotation and the detailed biochemical knowledge from multiple databases such as KEGG, ENZYME and BIGG. The information about protein and reaction associations of all the organisms in KEGG and Expasy-ENZYME database was arranged into an EXCEL file that can then be regarded as a new useful database to generate other reconstructions. The generated model iYL619_PCP accounts for 619 genes, 843 metabolites and 1,142 reactions including 236 transport reactions, 125 exchange reactions and 13 spontaneous reactions. The in silico model successfully predicted the minimal media and the growing abilities on different substrates. With flux balance analysis, single gene knockouts were also simulated to predict the essential genes and partially essential genes. In addition, flux variability analysis was applied to design new mutant strains that will redirect fluxes through the network and may enhance the production of lipid. This genome-scale metabolic model of Y. lipolytica can facilitate system-level metabolic analysis as well as strain development for improving the production of biodiesels and other valuable products by Y. lipolytica and other closely related oleaginous yeasts.
format	article
author	Pengcheng Pan Qiang Hua
author_facet	Pengcheng Pan Qiang Hua
author_sort	Pengcheng Pan
title	Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.
title_short	Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.
title_full	Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.
title_fullStr	Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.
title_full_unstemmed	Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.
title_sort	reconstruction and in silico analysis of metabolic network for an oleaginous yeast, yarrowia lipolytica.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/2fdf9e24b7d44dfbb597fa16ff318ad5
work_keys_str_mv	AT pengchengpan reconstructionandinsilicoanalysisofmetabolicnetworkforanoleaginousyeastyarrowialipolytica AT qianghua reconstructionandinsilicoanalysisofmetabolicnetworkforanoleaginousyeastyarrowialipolytica
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Reconstruction and in silico analysis of metabolic network for an oleaginous yeast, Yarrowia lipolytica.

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