Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast

Nat Commun. 2020 Apr 20;11(1):1881. doi: 10.1038/s41467-020-15749-0.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bioreactors
  • Cell Engineering
  • Fermentation
  • Gene Expression Regulation, Fungal
  • Glucose / metabolism
  • Metabolic Networks and Pathways
  • Nitrogen / metabolism
  • Protein Biosynthesis*
  • Protein Processing, Post-Translational
  • Proteome / metabolism
  • Proteomics*
  • Ribosomal Proteins / metabolism
  • Saccharomyces cerevisiae / metabolism*

Substances

  • Proteome
  • Ribosomal Proteins
  • Glucose
  • Nitrogen