Transcriptional regulation of yeast phospholipid biosynthetic genes

doi:10.1016/j.bbalip.2006.05.017

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids

Volume 1771, Issue 3, March 2007, Pages 310-321

https://doi.org/10.1016/j.bbalip.2006.05.017 Get rights and content

Abstract

The last several years have been witness to significant developments in understanding transcriptional regulation of the yeast phospholipid structural genes. The response of most phospholipid structural genes to inositol is now understood on a mechanistic level. The roles of specific activators and repressors are also well established. The knowledge of specific regulatory factors that bind the promoters of phospholipid structural genes serves as a foundation for understanding the role of chromatin modification complexes. Collectively, these findings present a complex picture for transcriptional regulation of the phospholipid biosynthetic genes. The INO1 gene is an ideal example of the complexity of transcriptional control and continues to serve as a model for studying transcription in general. Furthermore, transcription of the regulatory genes is also subject to complex and essential regulation. In addition, databases resulting from a plethora of genome-wide studies have identified regulatory signals that control one of the essential phospholipid biosynthetic genes, PIS1. These databases also provide significant clues for other regulatory signals that may affect phospholipid biosynthesis. Here, we have tried to present a complete summary of the transcription factors and mechanisms that regulate the phospholipid biosynthetic genes.

Section snippets

Transcriptional regulation of INO1 expression

The de novo synthesis of phosphatidylinositol (PI) from glucose-6-phosphate requires the INO1 structural gene that encodes inositol-3-phosphate synthase (IPS) (Fig. 1) [1], [2]. IPS is responsible for the conversion of glucose-6-phosphate to inositol-3-phosphate, which is then dephosphorylated to produce inositol [3], [4]. INO1 is regulated at the level of transcription by the soluble precursors inositol and choline. INO1 is maximally expressed in the absence of inositol and choline, partially

Transcriptional regulation of PIS1 expression

The final step in the de novo synthesis of PI requires the essential PIS1 structural gene that encodes PI synthase (PIS) (Fig. 1) [76], [77], [78], [79], [80]. PIS catalyzes the formation of PI from inositol and CDP-DAG (Fig. 1) [81], [82]. Transcriptional regulation of the PIS1 gene is understudied relative to that of the other phospholipid structural genes. This is partly because its expression is not coordinated with other phospholipid biosynthetic genes in response to inositol and choline

Transcriptional regulation of de novo PC synthesis

In Saccharomyces cerevisiae, PC can be synthesized using the CDP-diacylglycerol (CDP-DAG) de novo pathway (Fig. 1). De novo synthesis requires five genes (Fig. 1). While most of these genes are also regulated in response to inositol and choline, they have not been studied to nearly the same degree as INO1. However, several other transcription factors have been defined mostly by genome-wide strategies.

Transcriptional regulation of the PC Kennedy pathway

The Kennedy pathway utilizes ethanolamine (E) and choline (C) to synthesize PC (Fig. 1) [123]. There are six structural genes in this pathway and some of them are highly regulated in response to inositol and choline. The EKI1 and CKI1 genes are required in the first steps in the Kennedy pathway. EKI1 and CKI1 encode ethanolamine kinase and choline kinase, respectively. Both genes are regulated at the transcriptional level in response to inositol and choline in a pattern similar to that of INO1

Ino2p and Ino4p

It is generally accepted that INO2 gene is auto-regulated in response to inositol and choline. Several studies show that INO2 transcript levels, INO2-lacZ and INO2-cat reporters, and Ino2p protein levels are repressed ∼12-fold in response to inositol and choline [39], [63], [127], [128], [129], [130], [131], [132], [133], [134], [135]. However, there is one study that reports constitutive expression of Ino2p protein levels in a wild type strain [17]. The reason for this discrepancy was not

Future directions

Considerable strides have been made in recent years towards understanding the mechanisms that regulate transcription of the phospholipid structural and regulatory genes. However, many new questions emerge from these developments. The regulation of INO1 transcription is remarkable in that it involves a large number of transcription factors that bind DNA and/or regulate chromatin structure. Why there is a need for so many factors remains to be answered. It will be important to determine if these

Acknowledgements

We thank members of the Lopes lab for helpful discussions and assistance with editing. We also thank Dr. George Carman (Rutgers Univ.) for his longtime support and encouragement. We are grateful to our colleague down the hall, Dr. Miriam Greenberg, for being a constant source of inspiration and to members of her lab for continuous discussions. We are also grateful for the reviewers' helpful comments. Work in the Lopes lab is supported by a grant from the National Science Foundation to J.M.L.

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Citation Excerpt :
The cellular consequences of inositol depletion have also been studied in mammalian cells and compared to yeast in the context of exposure to inositol depleting drugs lithium and valproic acid (Deranieh and Greenberg, 2009). Various aspects of regulation and signaling related to lipid and inositol metabolism in yeast have been extensively reviewed (Carman and Han, 2011; Carman and Henry, 1999; Chen et al., 2007; Dickson, 2008; Gaspar et al., 2007; Greenberg and Lopes, 1996; Henneberry and Sturley, 2005; Henry et al., 2012; Jesch and Henry, 2005; Majerus and York, 2009; Strahl and Thorner, 2007; Tsui and York, 2010). Thus it is not the intention of this article to provide a comprehensive coverage of the broader topics of lipid and inositol metabolism in regulation and signaling in eukaryotic cells in general.
This article focuses on discoveries of the mechanisms governing the regulation of glycerolipid metabolism and stress response signaling in response to the phospholipid precursor, inositol. The regulation of glycerolipid lipid metabolism in yeast in response to inositol is highly complex, but increasingly well understood, and the roles of individual lipids in stress response are also increasingly well characterized. Discoveries that have emerged over several decades of genetic, molecular and biochemical analyses of metabolic, regulatory and signaling responses of yeast cells, both mutant and wild type, to the availability of the phospholipid precursor, inositol are discussed.

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¹: These authors contributed equally to this work.

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ReviewTranscriptional regulation of yeast phospholipid biosynthetic genes

Abstract

Section snippets

Transcriptional regulation of INO1 expression

Transcriptional regulation of PIS1 expression

Transcriptional regulation of de novo PC synthesis

Transcriptional regulation of the PC Kennedy pathway

Ino2p and Ino4p

Future directions

Acknowledgements

J. Biol. Chem.

FEBS Lett.

J. Biol. Chem.

J. Biol. Chem.

Curr. Opin. Genet. Dev.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Cell

Cell

Cell

Cell

Curr. Opin. Genet. Dev.

Biochim. Biophys. Acta

J. Biol. Chem.

Cell

Mutat. Res.

Curr. Opin. Cell Biol.

J. Biol. Chem.

Cell

Cell

J. Biol. Chem.

J. Biol. Chem.

Biochim. Biophys. Acta

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

J. Biol. Chem.

Inositol mutants of Saccharomyces cerevisiae: mapping the ino1 locus and characterizing alleles of ino1, ino2 and ino4 loci

Genetics

Isolation of the yeast INO1 gene: located on an autonomously replicating plasmid

Proc. Natl. Acad. Sci. U. S. A.

Control of inositol biosynthesis in Saccharomyces cerevisiae: properties of a repressible enzyme system in extracts of wild type (Ino+) cells

J. Bacteriol.

Expression of yeast INM1 encoding inositol monophosphatase is regulated by inositol, carbon source and growth stage and is decreased by lithium and valproate

Mol. Microbiol.

Expression of the Saccharomyces cerevisiae inositol-1-phosphate synthase (INO1) gene is regulated by factors that affect phospholipid synthesis

Mol. Cell. Biol.

Functional characterization of the repeated UASINO element in the promoters of the INO1 and CHO2 genes of yeast

Yeast

Interaction of trans and cis regulatory elements in the INO1 promoter of Saccharomyces cerevisiae

Nucleic Acids Res.

The INO2 gene of Saccharomyces cerevisiae encodes a helix–loop–helix protein that is required for activation of phospholipid synthesis

Nucleic Acids Res.

A network of yeast basic helix–loop–helix interactions

Nucleic Acids Res.

Saccharomyces cerevisiae basic helix–loop–helix proteins regulate diverse biological processes

Nucleic Acids Res.

Yeast transcriptional activator INO2 interacts as an Ino2p/Ino4p basic helix–loop–helix heteromeric complex with the inositol/choline-responsive element necessary for expression of phospholipid biosynthetic genes in Saccharomyces cerevisiae

Nucleic Acids Res.

TFIIB and subunits of the SAGA complex are involved in transcriptional activation of phospholipid biosynthetic genes by the regulatory protein Ino2 in the yeast Saccharomyces cerevisiae

Mol. Microbiol.

Gene recruitment of the activated INO1 locus to the nuclear membrane

PLoS Biol.

Inhibition of acetyl coenzyme A carboxylase activity restores expression of the INO1 gene in a snf1 mutant strain of Saccharomyces cerevisiae

Mol. Cell. Biol.

The Snf1 protein kinase and Sit4 protein phosphatase have opposing functions in regulating TATA-binding protein association with the Saccharomyces cerevisiae INO1 promoter

Genetics

Snf1-a histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription

Science

Histone H3 phosphorylation can promoter TBP recruitment through distinct promoter-specific mechanisms

EMBO J.

Regulatory mutations of inositol biosynthesis in yeast: isolation of inositol-excreting mutants

Genetics

Role of the yeast VAP homolog, Scs2p, in INO1 expression and phospholipid metabolism

J. Biochem.

Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid

Science

Review
Transcriptional regulation of yeast phospholipid biosynthetic genes

Functional characterization of the repeated UAS_INO element in the promoters of the INO1 and CHO2 genes of yeast