Open AccessReconstruction and applications of consensus yeast metabolic network based on RNA sequencing
Author(s) -
Zhao Yuqi,
Wang Yanjie,
Zou Lei,
Huang Jingfei
Publication year - 2016
Publication title -
febs open bio
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.718
H-Index - 31
ISSN - 2211-5463
DOI - 10.1002/2211-5463.12033
Subject(s) - biology , computational biology , yeast , transcriptome , metabolic network , gene , genome , saccharomyces cerevisiae , metabolic engineering , model organism , sequence assembly , genetics , gene expression
One practical application of genome‐scale metabolic reconstructions is to interrogate multispecies relationships. Here, we report a consensus metabolic model in four yeast species ( Saccharomyces cerevisiae , S. paradoxus , S. mikatae , and S. bayanus ) by integrating metabolic network simulations with RNA sequencing ( RNA ‐seq) datasets. We generated high‐resolution transcriptome maps of four yeast species through de novo assembly and genome‐guided approaches. The transcriptomes were annotated and applied to build the consensus metabolic network, which was verified using independent RNA ‐seq experiments. The expression profiles reveal that the genes involved in amino acid and lipid metabolism are highly coexpressed. The diverse phenotypic characteristics, such as cellular growth and gene deletions, can be simulated using the metabolic model. We also explored the applications of the consensus model in metabolic engineering using yeast‐specific reactions and biofuel production as examples. Similar strategies will benefit communities studying genome‐scale metabolic networks of other organisms.