Proteome allocations change linearly with specific growth rate of Saccharomyces cerevisiae under glucose-limitation

Abstract

Saccharomyces cerevisiae is widely used as a cell factory and it is therefore important to understand how it organizes key functional parts when cultured under different conditions. Here we performed a multi-omics analysis of S. cerevisiae by culturing the strain under a wide range of specific growth rates using glucose as the sole limited nutrient. At these different conditions we measured the absolute transcriptome, the absolute proteome, the phosphproteome, and the metabolome. Most functional protein groups showed linear dependence on the cell specific growth rate. Proteins engaged with translation showed a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins showed a linear decrease at respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates, resulting in an overall increased activity that is associated with increased flux through these pathways. Further analysis showed that proteome allocation was primarily determined at the transcriptome level. Finally, using enzyme constraint genome scale modeling we found that enzyme usage play an important role for controlling flux in amino acid biosynthesis.

System-level analysis of flux regulation of yeast show that glycolytic flux is controlled by allosteric regulation and enzyme phosphorylation

“…For yeast growing under aerobic glucose-limited chemostat, repression of genes involved in oxidative metabolism 17 , together with lower translation e ciency of ribosome 18 led to lower mitochondrial protein levels and a better correlation between protein concentration and metabolic ux was observed. On the contrary, metabolites and protein phosphorylation level were correlated better with metabolic uxes for EMP and PP pathways, since the majority of physiologically relevant allosteric regulators and functional phosphorylation sites were identi ed in these pathways 20,29 .…”

“…This was consistent with the previous ndings that functional phosphorylation events mostly clustered among glycolytic enzymes within the CCM pathways 24,25 . Although it was impossible to calculate the ratio of this part FREs as phosphatase was not protein speci c, our pervious study has veri ed protein phosphorylation likely affected the majority of protein activities of glycolysis 20 . Our analysis here showed again protein phosphorylation caused FREs seemed to take the priority for EMP pathway ux regulation.…”

“…To decipher ux differences of S. cerevisiae between respiration and respiro-fermentation conditions, chemostat experiments under 9 different speci c growth rates (µ = 0.027h − 1 , 0.051h − 1 , 0.118h − 1 , 0.154h − 1 , 0.207h − 1 , 0.249h − 1 , 0.316h − 1 , 0.355h − 1 , 0.385h − 1 ), were carried out as described earlier 20 .…”

“…We therefore evaluated FREs of enzyme phosphorylation levels using phosphorylation regulation analysis 24 . Phosphorylation data were obtained from our previous published study (4 of the 9 dilution rates had phosphorylation data and they were 0.027h − 1 , 0.154h − 1 , 0.355h − 1 , 0.385h − 1 ) 20 . We observed that enzyme phosphorylation regulation seemed pathway dependent.…”

An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State

“…The past decade has seen a flurry of experimental studies further establishing the importance of protein synthesis in defining growth. Approaches include modern "-omics" techniques with molecular-level resolution [25][26][27][28][29][30][31][32][33][34][35][36][37][38], measurements of many core physiological processes and their coordination [38][39][40][41][42][43][44][45][46], and the perturbation of major cellular processes like translation [39,[47][48][49]. Together, these studies advanced a more thorough description of how cells allocate their ribosomes to the synthesis of different proteins depending on their metabolic state and the environmental conditions they encounter, called ribosomal allocation.…”