文献类型：期刊文献

英文题名：Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation

作者：Xia, Jianye[1,2,3];Sanchez, Benjamin J.[2];Chen, Yu[1,2];Campbell, Kate[2];Kasvandik, Sergo[4];Nielsen, Jens[2,5]

机构：[1]East China Univ Sci & Technol, State Key Lab Bioreactor Engn, Shanghai 200237, Peoples R China;[2]Chalmers Univ Technol, Dept Biol & Biol Engn, SE-41296 Gothenburg, Sweden;[3]Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China;[4]Univ Tartu, Inst Technol, EE-50411 Tartu, Estonia;[5]BioInnovat Inst, Ole Maaloes Vej 3, DK-2200 Copenhagen, Denmark

年份：2022

卷号：13

期号：1

外文期刊名：NATURE COMMUNICATIONS

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000799632400011)】；

基金：The authors would like to acknowledge the Project 21776082 (J.X. and J.N.) supported by National Natural Science Foundation of China, the Knut and Alice Wallenberg Foundation, the Novo Nordisk Foundation (grant no. NNF10CC1016517, J.N.), the Swedish Foundation for Strategic Research and DD-DeCaF (Horizon2020 project 686070, J.N.). We would like to thank Anna Koza for conducting the RNA-Seq measurement of our samples, Petri-Jaan Lahtvee for his help on the absolute transcriptome and proteome measurement method discussion, Yongjun Wei for his help on the experiment conducting and large amount of omics samples collection.

语种：英文

摘要：Saccharomyces cerevisiae is a widely used cell factory; therefore, it is important to understand how it organizes key functional parts when cultured under different conditions. Here, we perform a multiomics analysis of S. cerevisiae by culturing the strain with a wide range of specific growth rates using glucose as the sole limiting nutrient. Under these different conditions, we measure the absolute transcriptome, the absolute proteome, the phosphoproteome, and the metabolome. Most functional protein groups show a linear dependence on the specific growth rate. Proteins engaged in translation show a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins show a linear decrease under respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates; at the same time, an overall increased flux through these pathways is observed. Further analysis show that even though mRNA levels do not correlate with protein levels for all individual genes, the transcriptome level of functional groups correlates very well with its corresponding proteome. Finally, using enzyme-constrained genome-scale modeling, we find that enzyme usage plays an important role in controlling flux in amino acid biosynthesis. Understanding how yeast organizes its functional proteome is a fundamental task in systems biology. Here, the authors conduct a multiomics analysis on yeast cells cultured with different growth rates, identifying a linear dependence of the functional proteome on the growth rate.