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

• Cells maintain reserves in their metabolic and translational capacities as a strategy to quickly respond to changing environments. Here we quantify these reserves by stepwisereducing 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. © 2020, The Author(s).

Subject headings

NATURVETENSKAP  -- Biologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences (hsv//eng)

NATURVETENSKAP  -- Biologi -- Cellbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Cell Biology (hsv//eng)

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinsk bioteknologi -- Medicinsk bioteknologi (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Medical Biotechnology -- Medical Biotechnology (hsv//eng)

TEKNIK OCH TEKNOLOGIER  -- Industriell bioteknik -- Annan industriell bioteknik (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Industrial Biotechnology -- Other Industrial Biotechnology (hsv//eng)

Keyword

cell protein

proteome

ribosome protein

transcriptome

bioengineering

cell component

chemostat

crassulacean acid metabolism

glucose

metabolism

nitrogen

protein

proteomics

yeast

Article

biomass production

cell engineering

data processing

fungal cell culture

gene expression

glucose metabolism

high performance liquid chromatography

liquid chromatography-mass spectrometry

metabolic capacity

metabolic flux analysis

metabolomics

multiomics

nitrogen availability

nitrogen limitation

nitrogen metabolism

nonhuman

nutrient limitation

protein analysis

protein expression

quantitative analysis

RNA analysis

RNA extraction

RNA translation

Saccharomyces cerevisiae

steady state

transcriptome sequencing

transcriptomics

upregulation

Publication and Content Type

ref (subject category)

art (subject category)