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Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing

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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 [4]Collaborative Innovation Center for Natural Products and Biological Drugs of Yunnan, Kunming, Yunnan, China
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关键词: metabolic engineering metabolic network RNA sequencing Saccharomyces species

摘要:
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.

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出版当年[2016]版:
大类 | 4 区 生物
小类 | 4 区 生化与分子生物学
最新[2025]版:
大类 | 4 区 生物学
小类 | 4 区 生化与分子生物学
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出版当年[2015]版:
Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
最新[2023]版:
Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

影响因子: 最新[2023版] 最新五年平均 出版当年[2015版] 出版当年五年平均 出版前一年[2014版] 出版后一年[2016版]

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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
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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
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