title: Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast.
abstract: In the yeast Saccharomyces cerevisiae many genes involved in lipid biosynthesis are transcriptionally controlled by inositol-choline and the protein kinase Snf1. Here we undertook a global study on how inositol-choline and Snf1 interact in controlling lipid metabolism in yeast. Using both a reference strain (CEN.PK113-7D) and a snf1Δ strain cultured at different nutrient limitations (carbon and nitrogen), at a fixed specific growth rate of 0.1 h(-1), and at different inositol choline concentrations, we quantified the expression of genes involved in lipid biosynthesis and the fluxes towards the different lipid components. Through integrated analysis of the transcriptome, the lipid profiling and the fluxome, it was possible to obtain a high quality, large-scale dataset that could be used to identify correlations and associations between the different components. At the transcription level, Snf1 and inositol-choline interact either directly through the main phospholipid-involving transcription factors (i.e. Ino2, Ino4, and Opi1) or through other transcription factors e.g. Gis1, Mga2, and Hac1. However, there seems to be flux regulation at the enzyme levels of several lipid involving enzymes. The analysis showed the strength of using both transcriptome and lipid profiling analysis for mapping the co-influence of inositol-choline and Snf1 on phospholipid metabolism.
authors.affiliation: Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
authors.forename: Pramote
authors.initials: P
authors.lastname: Chumnanpuen
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Intawat
authors.initials: I
authors.lastname: Nookaew
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics; D002794:Choline / Q000378:metabolism*; D002851:Chromatography, High Pressure Liquid; D008401:Gas Chromatography-Mass Spectrometry; D007294:Inositol / Q000378:metabolism*; D008055:Lipids / Q000032:analysis / Q000096:biosynthesis*; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D017346:Protein Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D008055:Lipids; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D007294:Inositol; C071570:SNF1-related protein kinases; D017346:Protein Serine-Threonine Kinases; D002794:Choline