Proteome overabundance enables respiration but limitation onsets carbon overflow

Abstract

Central carbon metabolism produces energy and precursor metabolites for biomass in heterotrophs. Carbon overflow yields metabolic byproducts and, here, we examined its dependency on nutrient and growth using the unicellular eukaryotic model organism Saccharomyces cerevisiae. We performed quantitative proteomics analysis together with metabolic modeling and found that proteome overabundance enabled respiration, and variation in energy efficiency caused distinct composition of biomass at different carbon to nitrogen ratio and growth rate. Our results showed that ceullar resource allocation for ribosomes was determinative of growth rate, but energy constrains on protein synthesis incepted carbon overflow by prioritizing abundance of ribosomes and glycolysis over mitochondria. We proved that glycolytic efficiency affected energy metabolism by making a trade-off between low and high energy production pathways. Finally, we summarized cellular energy budget underlying nutrient-responsive and growth rate-dependent carbon overflow, and suggested implications of results for bioprocesses and pathways relevant in cancer metabolism in humans.

Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery

“…For ADA, ribosomal protein allocation was already reduced to a lower level and decreased further, forming only 21% under the nutrient-limiting conditions in P3. As ribosomes are essential for achieving faster cell growth, the trade-off between allocation toward ribosomal proteins or energy generation pathways has been demonstrated previously ( Nilsson and Nielsen, 2016 ; Sánchez et al, 2017; Kumar and Lahtvee , 2020 ). Interestingly, glycolysis was increased to the same extent under nitrogen-limiting conditions in the presence and absence of oxidative stress, but mitochondria and amino acid metabolism demonstrated significantly increased allocation for the ADA.…”

“…Heavy labelling of the proteinogenic lysine was measured at 96.6% (data not shown). Absolute proteomics and internal heavy-labelled standard preparation and analyses were performed similarly as described in Lahtvee et al (2017) and Kumar and Lahtvee (2020) . Briefly, cells were resuspended in the lysis buffer (6 mol/L guanidine HCl, 100 mmol/L Tris–HCl pH 8.5 and 100 mmol/L dithiothreitol) and homogenised with glass beads using the FastPrep24 device.…”

Characterization of potassium, sodium and their interactions effects in yeasts

“…The trace element solution contained, per litre (pH = 4), EDTA (sodium salt), 15.0g; ZnSO 4 ·7H 2 O, 4.5g; MnCl 2 ·2H 2 O, 0.84g; CoCl 2 ·6H 2 O,0.3g; CuSO 4 ·5H 2 O, 0.3g; Na 2 MoO 4 ·2H 2 O, 0.4g; CaCl 2 ·2H 2 O, 4.5g; FeSO 4 ·7H 2 O, 3.0g; H 3 BO 3 , 1.0g; and KI, 0.10g. The vitamin solution contained, per litre (pH = 6.5), biotin, 0.05g; p-amino benzoic acid, 0.2g; nicotinic acid, 1g; Ca-pantothenate, 1g; pyridoxine-HCl, 1g; thiamine-HCl, 1g; and myoinositol, 25g (62). The culture medium pH was adjusted to 6 with 1.9 ml per litre of 2M KOH.…”

Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery

“…Heavy labelling of the proteinogenic lysine was measured at 96.6% (data not shown). Absolute proteomics and internal heavy-labelled standard preparation and analyses were performed similarly as described in Lahtvee et al (2017) and Kumar and Lahtvee (2020). Briefly, cells were resuspended in the lysis buffer (6 mol/L guanidine HCl, 100 mmol/L Tris-HCl pH 8.5 and 100 mmol/L dithiothreitol) and homogenised with glass beads using the FastPrep24 device.…”