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Background  In the yeast  Saccharomyces cerevisiae , genes containing UAS INO  sequences are regulated by the Ino2/Ino4 and Opi1 transcription factors, and this regulation controls lipid biosynthesis. The expression level of  INO2  and  INO4  genes ( INO -level) at different nutrient limited conditions might lead to various responses in yeast lipid metabolism.    Methods  In this study, we undertook a global study on how  INO -levels (transcription level of  INO2  and  INO4 ) affect lipid metabolism in yeast and we also studied the effects of single and double deletions of the two  INO -genes (deficient effect). Using 2 types of nutrient limitations (carbon and nitrogen) in chemostat cultures operated at a fixed specific growth rate of 0.1 h-1 and strains having different  INO -level, we were able to see the effect on expression level of the genes involved in lipid biosynthesis and the fluxes towards the different lipid components. Through combined measurements of the transcriptome, metabolome, and lipidome it was possible to obtain a large dataset that could be used to identify how the  INO -level controls lipid metabolism and also establish correlations between the different components.    Results  In this study, we undertook a global study on how  INO -levels (transcription level of  INO2  and  INO4 ) affect lipid metabolism in yeast and we also studied the effects of single and double deletions of the two  INO -genes (deficient effect). Using 2 types of nutrient limitations (carbon and nitrogen) in chemostat cultures operated at a fixed specific growth rate of 0.1 h-1 and strains having different  INO -level, we were able to see the effect on expression level of the genes involved in lipid biosynthesis and the fluxes towards the different lipid components. Through combined measurements of the transcriptome, metabolome, and lipidome it was possible to obtain a large dataset that could be used to identify how the  INO -level controls lipid metabolism and also establish correlations between the different components.    Conclusions  Our analysis showed the strength of using a combination of transcriptome and lipidome analysis to illustrate the effect of  INO -levels on phospholipid metabolism and based on our analysis we established a global regulatory map.

Integrated analysis, transcriptome-lipidome, reveals the effects of INO- level (INO2 and INO4) on lipid metabolism in yeast