Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
Elife. 2021 Mar 15;10:e65722. doi: 10.7554/eLife.65722.
In addition to controlled expression of genes by specific regulatory circuits, the abundance of proteins and transcripts can also be influenced by physiological states of the cell such as growth rate and metabolism. Here we examine the control of gene expression by growth rate and metabolism, by analyzing a multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and amino acids in 22 steady-state yeast cultures. We find that transcription and translation are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but they are independently controlled by nitrogen metabolism via amino acid and nucleotide availabilities. Genes in central carbon metabolism, however, are distinctly regulated and do not respond to the cell growth rate or nitrogen metabolism as all other genes. Understanding these effects allows the confounding factors of growth rate and metabolism to be accounted for in gene expression profiling studies.
除了通过特定的调控回路来控制基因的表达外，蛋白质和转录本的丰度也会受到细胞生理状态的影响，如生长速度和代谢。在这里，我们通过分析由 22 种稳定酵母培养物的转录组、蛋白质组和氨基酸的绝对定量丰度组成的多组学数据集，研究了基因表达受生长速度和代谢的控制。我们发现，转录和翻译通过 RNA 聚合酶 II 和核糖体的丰度被细胞生长速度协同控制，但通过氨基酸和核苷酸的可用性被氮代谢独立控制。然而，中心碳代谢基因的调节方式明显不同，它们不响应细胞生长速度或氮代谢，而其他所有基因都响应。了解这些影响可以在基因表达谱研究中考虑到生长速度和代谢的混杂因素。
