机构:[1]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, China[2]Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, China[3]Department of General Surgery, First People’s Hospital of Yunnan Province, Kunming, China云南省第一人民医院[4]Collaborative Innovation Center for Natural Products and Biological Drugs of Yunnan, Kunming, Yunnan, China
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.
基金:
This work was supported by the grants from National
Natural Science Foundation of China (Grant No.
81400084; Grant No. 31123005), National Basic
Research Program of China (2013CB835100).
第一作者机构:[1]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, China[*1]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming 650223 Yunnan, China
共同第一作者:
通讯作者:
通讯机构:[1]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, China[4]Collaborative Innovation Center for Natural Products and Biological Drugs of Yunnan, Kunming, Yunnan, China[*1]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming 650223 Yunnan, China
推荐引用方式(GB/T 7714):
Zhao Yuqi,Wang Yanjie,Zou Lei,et al.Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing[J].FEBS OPEN BIO.2016,6(4):264-275.doi:10.1002/2211-5463.12033.
APA:
Zhao, Yuqi,Wang, Yanjie,Zou, Lei&Huang, Jingfei.(2016).Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing.FEBS OPEN BIO,6,(4)
MLA:
Zhao, Yuqi,et al."Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing".FEBS OPEN BIO 6..4(2016):264-275