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Molecular Genetics and Genomics

, Volume 287, Issue 7, pp 541–554 | Cite as

Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol–choline and Snf1 in controlling lipid biosynthesis in yeast

  • Pramote Chumnanpuen
  • Jie Zhang
  • Intawat Nookaew
  • Jens NielsenEmail author
Original Paper

Abstract

In the yeast Saccharomyces cerevisiae many genes involved in lipid biosynthesis are transcriptionally controlled by inositolcholine and the protein kinase Snf1. Here we undertook a global study on how inositolcholine 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 inositolcholine 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 inositolcholine and Snf1 on phospholipid metabolism.

Keywords

Inositolcholine Snf1 Co-influence Lipid profiling Transcriptome 

Abbreviations

AcCoA

Acetyl coenzyme A

AceAcCoA

Acetoacetyl coenzyme A

CDP-DAG

Cytidine diphosphate-diacylglycerol

Cho

Choline

DAG

Diacylglycerol

Etn

Ethanolamine

ES

Ergosterol

FA

Fatty acid or fatty acyl-CoA

Glc-6-P

Glucose 6-phosphate

G-3-P

Glycerol 3-phosphate

HIC

High inositolcholine

IC

Inositolcholine

LIC

Low inositolcholine

MaCoA

Malonyl coenzyme A

PA

Phosphatidic acids

PC

Phosphatidylcholine

PE

Phosphatidylethanolamine

PI

Phosphatidylinositiol

PL

Phospholipids

PS

Phosphatidylserine

Pyr

Pyruvate

SE

Sterylester

ST

Strain factor

TAG

Triacylglycerol

TF

Transcription factor

UASINO

Inositol-sensitive upstream activating sequence

Notes

Acknowledgments

This work was financed by Chalmers Foundation, the Knut and Alice Wallenberg Foundation and the Swedish Research Council (Vetenskapsrådet). We also acknowledge funding from the EU-funded project UNICELLSYS. Pramote Chumnanpuen also would like to thank the Office of the Higher Education Commission, Thailand for support by a stipend for his Ph.D. program under the program Strategic Scholarships for Frontier Research Network. We also thank Nils-Gunnar Carlsson for valuable assistance with running the HPLC-CAD, Tobias Österlund and Klaas Buijs for helpful suggestions on manuscript preparation.

Supplementary material

438_2012_697_MOESM1_ESM.doc (1.5 mb)
Supplementary material 1 (DOC 1586 kb)

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Pramote Chumnanpuen
    • 1
  • Jie Zhang
    • 1
  • Intawat Nookaew
    • 1
  • Jens Nielsen
    • 1
    Email author
  1. 1.Systems and Synthetic Biology, Department of Chemical and Biological EngineeringChalmers University of TechnologyGothenburgSweden

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