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Investigating uncharacterised genes in Saccharomyces cerevisiae using Robot Scientists

ABSTRACT:

Despite extensive research on Saccharomyces cerevisiae functional genomics, approximately 880 out of ~6,000 open reading frames (ORFs) remain uncharacterised. In this study we propose a method for characterising genes with limited prior functional knowledge using an automated laboratory platform, in conjunction with several hypothesis instantiation methods. We demonstrate this method by investigating YGR067C, an uncharacterised ORF hypothesised to regulate respiration during the diauxic shift. Predictions of the first-order effects of deletion were obtained by curating a list of pathways relevant to the hypothesis. Higher-order effects were predicted using simulation models based on the GEM Yeast9. The predictions were tested using empirical data from biological experiments performed in the Robot Scientist Eve, which generated OD560, transcriptomics, and metabolomics data.

We observed that YGR067C deletion led to downregulation of transcripts in some ethanol consuming respiratory pathways during the glucose phase. During the ethanol phase we observed that NAD+, NADP+ and NADH accumulated, and several amino acid biosynthesis pathways were enriched for the ygr067c∆ strain, suggesting longer term consequences of YGR067C mediated regulation. Based on these observations we propose that the role of YGR067C during the diauxic shift is to regulate genes related to ethanol consumption and respiration in the glucose phase.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS12663 | MetaboLights | 2025-12-03

REPOSITORIES: MetaboLights

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			Action	DRS
	a_MTBLS12663_LC-MS_negative_reverse-phase_metabolite_profiling.txt	Txt
	a_MTBLS12663_LC-MS_positive_reverse-phase_metabolite_profiling.txt	Txt
	i_Investigation.txt	Txt
	m_MTBLS12663_LC-MS_negative_reverse-phase_metabolite_profiling_v2_maf.tsv	Tabular
	m_MTBLS12663_LC-MS_positive_reverse-phase_metabolite_profiling_v2_maf.tsv	Tabular

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Project description:This SuperSeries is composed of the following subset Series: GSE3205: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1 GSE3206: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2 Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. Judging from the patterns of gene expression, the state of the cells growing at steady state in glucose-limited chemostats corresponds most closely with the state of cells in batch cultures just before they undergo this "diauxic shift." Essentially the same pattern was found between chemostats having a fivefold difference in steady-state growth rate (the lower rate approximating that of the second phase respiratory growth rate in batch cultures). Although in both cases the cells in the chemostat consumed most of the glucose, in neither case did they seem to be metabolizing it primarily through respiration. Although there was some indication of a modest oxidative stress response, the chemostat cultures did not exhibit the massive environmental stress response associated with starvation that also is observed, at least in part, during the diauxic shift in batch cultures. We conclude that despite the theoretical possibility of a switch to fully aerobic metabolism of glucose in the chemostat under conditions of glucose scarcity, homeostatic mechanisms are able to carry out metabolic adjustment as if fermentation of the glucose is the preferred option until the glucose is entirely depleted. These results suggest that some aspect of actual starvation, possibly a component of the stress response, may be required for triggering the metabolic remodeling associated with the diauxic shift. Refer to individual Series

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Investigating uncharacterised genes in Saccharomyces cerevisiae using Robot Scientists

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