Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast
Journal article, 2020
Cells maintain reserves in their metabolic and translational capacities as a strategy to quickly respond to changing environments. Here we quantify these reserves by stepwise reducing nitrogen availability in yeast steady-state chemostat cultures, imposing severe restrictions on total cellular protein and transcript content. Combining multi-omics analysis with metabolic modeling, we find that seven metabolic superpathways maintain >50% metabolic capacity in reserve, with glucose metabolism maintaining >80% reserve capacity. Cells maintain >50% reserve in translational capacity for 2490 out of 3361 expressed genes (74%), with a disproportionately large reserve dedicated to translating metabolic proteins. Finally, ribosome reserves contain up to 30% sub-stoichiometric ribosomal proteins, with activation of reserve translational capacity associated with selective upregulation of 17 ribosomal proteins. Together, our dataset provides a quantitative link between yeast physiology and cellular economics, which could be leveraged in future cell engineering through targeted proteome streamlining.
Author
Tao Yu
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Kate Campbell
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Rui Pereira
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Johan Björkeroth
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Qi Qi
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Egor Vorontsov
University of Gothenburg
C. Sihlbom
University of Gothenburg
Jens B Nielsen
Technical University of Denmark (DTU)
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
BioInnovation Institute
Nature Communications
2041-1723 (ISSN) 20411723 (eISSN)
Vol. 11 1 1881Subject Categories
Cell Biology
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Other Industrial Biotechnology
DOI
10.1038/s41467-020-15749-0
PubMed
32312967