| Wang CW, et al. (2014) Control of lipid droplet size in budding yeast requires the collaboration between Fld1 and Ldb16. J Cell Sci 127(Pt 6):1214-28 |
| Oshiro J, et al. (2000) Regulation of the DPP1-encoded diacylglycerol pyrophosphate (DGPP) phosphatase by inositol and growth phase. Inhibition of DGPP phosphatase activity by CDP-diacylglyceron and activation of phosphatidylserine synthase activity by DG |
| Ko J, et al. (1994) Regulation of phosphatidylinositol:ceramide phosphoinositol transferase in Saccharomyces cerevisiae. J Bacteriol 176(16):5181-3 |
| Rojas M, et al. (2008) Selective inhibition of yeast regulons by daunorubicin: a transcriptome-wide analysis. BMC Genomics 9:358 |
| Iwanyshyn WM, et al. (2004) Regulation of phospholipid synthesis in Saccharomyces cerevisiae by zinc. J Biol Chem 279(21):21976-83 |
| Villa-Garcia MJ, et al. (2011) Genome-wide screen for inositol auxotrophy in Saccharomyces cerevisiae implicates lipid metabolism in stress response signaling. Mol Genet Genomics 285(2):125-49 |
| Li Z and Brendel M (1993) Co-regulation with genes of phospholipid biosynthesis of the CTR/HNM1-encoded choline/nitrogen mustard permease in Saccharomyces cerevisiae. Mol Gen Genet 241(5-6):680-4 |
| Pascual F, et al. (2013) PAH1-encoded Phosphatidate Phosphatase Plays a Role in the Growth Phase- and Inositol-mediated Regulation of Lipid Synthesis in Saccharomyces cerevisiae. J Biol Chem 288(50):35781-92 |
| Chumnanpuen P, et al. (2012) Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast. Mol Genet Genomics 287(7):541-54 |
| Howe AG and McMaster CR (2001) Regulation of vesicle trafficking, transcription, and meiosis: lessons learned from yeast regarding the disparate biologies of phosphatidylcholine. Biochim Biophys Acta 1534(2-3):65-77 |
| He Y, et al. (2012) Transcription regulation of the Saccharomyces cerevisiae PHO5 gene by the Ino2p and Ino4p basic helix-loop-helix proteins. Mol Microbiol 83(2):395-407 |
| Donahue TF and Henry SA (1981) Inositol Mutants of SACCHAROMYCES CEREVISIAE: Mapping the ino1 Locus and Characterizing Alleles of the ino1, ino2 and ino4 Loci. Genetics 98(3):491-503 |
| Beskow A and Wright AP (2006) Comparative analysis of regulatory transcription factors in Schizosaccharomyces pombe and budding yeasts. Yeast 23(13):929-35 |
| Dettmann A, et al. (2010) Mediator subunits and histone methyltransferase Set2 contribute to Ino2-dependent transcriptional activation of phospholipid biosynthesis in the yeast Saccharomyces cerevisiae. Mol Genet Genomics 283(3):211-21 |
| Donahue TF and Henry SA (1981) myo-Inositol-1-phosphate synthase. Characteristics of the enzyme and identification of its structural gene in yeast. J Biol Chem 256(13):7077-85 |
| Zhao Y, et al. (2008) Development of a Novel Oligonucleotide Array-Based Transcription Factor Assay Platform for Genome-Wide Active Transcription Factor Profiling in Saccharomyces cerevisiae. J Proteome Res 7(3):1315-1325 |
| Chumnanpuen P, et al. (2013) Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast. BMC Syst Biol 7(Suppl 3):S7 |
| Wu WS and Chen BS (2009) Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. Bioinform Biol Insights 1():137-45 |
| Lamping E, et al. (1991) Coordinate regulation of phosphatidylserine decarboxylase in Saccharomyces cerevisiae. J Bacteriol 173(20):6432-7 |
| Baile MG, et al. (2014) The topology and regulation of cardiolipin biosynthesis and remodeling in yeast. Chem Phys Lipids 179():25-31 |
| Carman GM (2005) Regulation of phospholipid synthesis in yeast by zinc. Biochem Soc Trans 33(Pt 5):1150-3 |
| Bailis AM, et al. (1992) Cis and trans regulatory elements required for regulation of the CHO1 gene of Saccharomyces cerevisiae. Nucleic Acids Res 20(6):1411-8 |
| Block-Alper L, et al. (2002) IN02, a positive regulator of lipid biosynthesis, is essential for the formation of inducible membranes in yeast. Mol Biol Cell 13(1):40-51 |
| Babbitt GA (2010) Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts. Gene 466(1-2):43-8 |
| Kersting MC, et al. (2004) Regulation of the yeast EKI1-encoded ethanolamine kinase by inositol and choline. J Biol Chem 279(34):35353-9 |
| Nielsen J (2009) Systems biology of lipid metabolism: from yeast to human. FEBS Lett 583(24):3905-13 |
| Lai K and McGraw P (1994) Dual control of inositol transport in Saccharomyces cerevisiae by irreversible inactivation of permease and regulation of permease synthesis by INO2, INO4, and OPI1. J Biol Chem 269(3):2245-51 |
| Henry SA, et al. (2014) The response to inositol: Regulation of glycerolipid metabolism and stress response signaling in yeast. Chem Phys Lipids 180C():23-43 |
| Li BZ, et al. (2010) Transcriptome analysis of differential responses of diploid and haploid yeast to ethanol stress. J Biotechnol 148(4):194-203 |
| Hirsch JP and Henry SA (1986) Expression of the Saccharomyces cerevisiae inositol-1-phosphate synthase (INO1) gene is regulated by factors that affect phospholipid synthesis. Mol Cell Biol 6(10):3320-8 |
| Sugimoto H, et al. (2008) Transcriptional regulation of phosphatidylcholine biosynthesis. Prog Lipid Res 47(3):204-20 |
| Nostramo R, et al. (2015) The Catalytic Activity of the Ubp3 Deubiquitinating Protease Is Required for Efficient Stress Granule Assembly in Saccharomyces cerevisiae. Mol Cell Biol 36(1):173-83 |
| Chen L and Lopes JM (2010) Multiple bHLH proteins regulate CIT2 expression in Saccharomyces cerevisiae. Yeast 27(6):345-59 |
| Novo M, et al. (2013) Genome-Wide Study of the Adaptation of Saccharomyces cerevisiae to the Early Stages of Wine Fermentation. PLoS One 8(9):e74086 |
| Nohturfft A and Zhang SC (2009) Coordination of lipid metabolism in membrane biogenesis. Annu Rev Cell Dev Biol 25:539-66 |
| Nikawa J and Kamiuto J (2004) The promoter of the yeast OPI1 regulatory gene. J Biosci Bioeng 97(6):369-73 |
| Ebbert R, et al. (1999) The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol Microbiol 32(4):741-51 |
| Ashburner BP and Lopes JM (1995) Autoregulated expression of the yeast INO2 and INO4 helix-loop-helix activator genes effects cooperative regulation on their target genes. Mol Cell Biol 15(3):1709-15 |
| Shen H and Dowhan W (1998) Regulation of phosphatidylglycerophosphate synthase levels in Saccharomyces cerevisiae. J Biol Chem 273(19):11638-42 |
| Dietz M, et al. (2003) 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 48(4):1119-30 |
| Schuller HJ, et al. (1995) DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor: structural requirements as defined by saturation mutagenesis. FEBS Lett 370(1-2):149-52 |
| Tavassoli S, et al. (2013) Plasma membrane-endoplasmic reticulum contact sites regulate phosphatidylcholine synthesis. EMBO Rep 14(5):434-40 |
| Kumme J, et al. (2008) Dimerization of yeast transcription factors Ino2 and Ino4 is regulated by precursors of phospholipid biosynthesis mediated by Opi1 repressor. Curr Genet 54(1):35-45 |
| Brandman O, et al. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell 151(5):1042-54 |
| Lipford JR, et al. (2005) A putative stimulatory role for activator turnover in gene expression. Nature 438(7064):113-6 |
| Kennedy MA, et al. (1999) Transcriptional regulation of the squalene synthase gene (ERG9) in the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1445(1):110-22 |
| Zhong Q and Greenberg ML (2003) Regulation of phosphatidylglycerophosphate synthase by inositol in Saccharomyces cerevisiae is not at the level of PGS1 mRNA abundance. J Biol Chem 278(36):33978-84 |
| Santiago TC and Mamoun CB (2003) Genome expression analysis in yeast reveals novel transcriptional regulation by inositol and choline and new regulatory functions for Opi1p, Ino2p, and Ino4p. J Biol Chem 278(40):38723-30 |
| Lu CC, et al. (2008) Extracting transcription factor binding sites from unaligned gene sequences with statistical models. BMC Bioinformatics 9 Suppl 12:S7 |
| Carman GM and Henry SA (2007) Phosphatidic acid plays a central role in the transcriptional regulation of glycerophospholipid synthesis in Saccharomyces cerevisiae. J Biol Chem 282(52):37293-7 |
| Miller C, et al. (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7():458 |
| Hiesinger M, et al. (1997) The acetyl-CoA synthetase gene ACS2 of the yeast Saccharomyces cerevisiae is coregulated with structural genes of fatty acid biosynthesis by the transcriptional activators Ino2p and Ino4p. FEBS Lett 415(1):16-20 |
| Loewen CJ (2012) Lipids as conductors in the orchestra of life. F1000 Biol Rep 4():4 |
| Schuck S, et al. (2009) Membrane expansion alleviates endoplasmic reticulum stress independently of the unfolded protein response. J Cell Biol 187(4):525-36 |
| Dzugasova V, et al. (1998) Phosphatidylglycerolphosphate synthase encoded by the PEL1/PGS1 gene in Saccharomyces cerevisiae is localized in mitochondria and its expression is regulated by phospholipid precursors. Curr Genet 34(4):297-302 |
| Bailis AM, et al. (1987) The membrane-associated enzyme phosphatidylserine synthase is regulated at the level of mRNA abundance. Mol Cell Biol 7(1):167-76 |
| Swift S and McGraw P (1995) INO1-100: an allele of the Saccharomyces cerevisiae INO1 gene that is transcribed without the action of the positive factors encoded by the INO2, INO4, SWI1, SWI2 and SWI3 genes. Nucleic Acids Res 23(8):1426-33 |
| Robinson KA, et al. (2000) A network of yeast basic helix-loop-helix interactions. Nucleic Acids Res 28(22):4460-6 |
| Ambroziak J and Henry SA (1994) INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 269(21):15344-9 |
| Chen M, et al. (2007) Transcriptional regulation of yeast phospholipid biosynthetic genes. Biochim Biophys Acta 1771(3):310-21 |
| Robinson KA and Lopes JM (2000) The promoter of the yeast INO4 regulatory gene: a model of the simplest yeast promoter. J Bacteriol 182(10):2746-52 |
| Homann MJ, et al. (1987) Coordinate regulation of phospholipid biosynthesis by serine in Saccharomyces cerevisiae. J Bacteriol 169(7):3276-80 |
| Bachhawat N, et al. (1995) Functional characterization of an inositol-sensitive upstream activation sequence in yeast. A cis-regulatory element responsible for inositol-choline mediated regulation of phospholipid biosynthesis. J Biol Chem 270(42):25087-95 |
| Yu T and Li KC (2005) Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 21(21):4033-8 |
| Shirra MK, et al. (2005) The Snf1 protein kinase and Sit4 protein phosphatase have opposing functions in regulating TATA-binding protein association with the Saccharomyces cerevisiae INO1 promoter. Genetics 169(4):1957-72 |
| Fei W, et al. (2011) A role for phosphatidic Acid in the formation of "supersized" lipid droplets. PLoS Genet 7(7):e1002201 |
| Grauslund M, et al. (1999) Expression of GUT1, which encodes glycerol kinase in Saccharomyces cerevisiae, is controlled by the positive regulators Adr1p, Ino2p and Ino4p and the negative regulator Opi1p in a carbon source-dependent fashion. Nucleic Acids |
| Schwank S, et al. (1997) Influence of gene dosage and autoregulation of the regulatory genes INO2 and INO4 on inositol/choline-repressible gene transcription in the yeast Saccharomyces cerevisiae. Curr Genet 31(6):462-8 |
| Shetty A and Lopes JM (2010) Derepression of INO1 Transcription Requires Cooperation between the Ino2p-Ino4p Heterodimer and Cbf1p and Recruitment of the ISW2 Chromatin-Remodeling Complex. Eukaryot Cell 9(12):1845-55 |
| de Kroon AI, et al. (2013) Checks and balances in membrane phospholipid class and acyl chain homeostasis, the yeast perspective. Prog Lipid Res 52(4):374-94 |
| Loewy BS and Henry SA (1984) The INO2 and INO4 loci of Saccharomyces cerevisiae are pleiotropic regulatory genes. Mol Cell Biol 4(11):2479-85 |
| Pan J, et al. (2011) A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation. Cell 144(5):719-31 |
| Torma A, et al. (2009) Concordant gene regulation related to perturbations of three GDP-mannose-related genes. FEMS Yeast Res 9(1):63-72 |
| Reynolds TB (2006) The Opi1p transcription factor affects expression of FLO11, mat formation, and invasive growth in Saccharomyces cerevisiae. Eukaryot Cell 5(8):1266-75 |
| Hofbauer HF, et al. (2014) Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Dev Cell 29(6):729-39 |
| Jesch SA, et al. (2005) Genome-wide analysis reveals inositol, not choline, as the major effector of Ino2p-Ino4p and unfolded protein response target gene expression in yeast. J Biol Chem 280(10):9106-18 |
| McMaster CR (2001) Lipid metabolism and vesicle trafficking: more than just greasing the transport machinery. Biochem Cell Biol 79(6):681-92 |
| Carman GM (2011) The discovery of the fat-regulating phosphatidic acid phosphatase gene. Front Biol 6(3):172-176 |
| Nikawa JI, et al. (2006) Ternary complex formation of ino2p-ino4p transcription factors and apl2p adaptin Beta subunit in yeast. Biosci Biotechnol Biochem 70(11):2604-12 |
| Asif HM and Sanguinetti G (2013) Simultaneous inference and clustering of transcriptional dynamics in gene regulatory networks. Stat Appl Genet Mol Biol 12(5):545-57 |
| Schwank S, et al. (1995) 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 |
| Almaguer C, et al. (2004) Glycerophosphoinositol, a novel phosphate source whose transport is regulated by multiple factors in Saccharomyces cerevisiae. J Biol Chem 279(30):31937-42 |
| Swiecilo A (2016) Cross-stress resistance in Saccharomyces cerevisiae yeast-new insight into an old phenomenon. Cell Stress Chaperones () |
| Lopes JM and Henry SA (1991) Interaction of trans and cis regulatory elements in the INO1 promoter of Saccharomyces cerevisiae. Nucleic Acids Res 19(14):3987-94 |
| Wenz P, et al. (2001) A downstream regulatory element located within the coding sequence mediates autoregulated expression of the yeast fatty acid synthase gene FAS2 by the FAS1 gene product. Nucleic Acids Res 29(22):4625-32 |
| Ouyang Q, et al. (1999) The REG1 gene product is required for repression of INO1 and other inositol-sensitive upstream activating sequence-containing genes of yeast. Genetics 152(1):89-100 |
| Tabuchi M, et al. (2006) The phosphatidylinositol 4,5-biphosphate and TORC2 binding proteins Slm1 and Slm2 function in sphingolipid regulation. Mol Cell Biol 26(15):5861-75 |
| Morozov AV and Siggia ED (2007) Connecting protein structure with predictions of regulatory sites. Proc Natl Acad Sci U S A 104(17):7068-73 |
| Wagner C, et al. (1999) Overproduction of the Opi1 repressor inhibits transcriptional activation of structural genes required for phospholipid biosynthesis in the yeast Saccharomyces cerevisiae. Yeast 15(10A):843-54 |
| Brickner JH and Walter P (2004) Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2(11):e342 |
| Dasgupta A, et al. (2005) Mot1-mediated control of transcription complex assembly and activity. EMBO J 24(9):1717-29 |
| Graves JA and Henry SA (2000) Regulation of the yeast INO1 gene. The products of the INO2, INO4 and OPI1 regulatory genes are not required for repression in response to inositol. Genetics 154(4):1485-95 |
| Hoppen J, et al. (2005) Comparative analysis of promoter regions containing binding sites of the heterodimeric transcription factor Ino2/Ino4 involved in yeast phospholipid biosynthesis. Yeast 22(8):601-13 |
| Gururaj C, et al. (2013) Orm proteins integrate multiple signals to maintain sphingolipid homeostasis. J Biol Chem 288(28):20453-63 |
| Addinall SG, et al. (2008) A Genomewide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae. Genetics 180(4):2251-66 |
| Bussereau F, et al. (2006) The Kluyveromyces lactis repertoire of transcriptional regulators. FEMS Yeast Res 6(3):325-35 |
| Robinson KA and Lopes JM (2000) SURVEY AND SUMMARY: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes. Nucleic Acids Res 28(7):1499-505 |
| Hanano A, et al. (2014) Removal of petroleum-crude oil from aqueous solution by Saccharomyces cerevisiae SHSY strain necessitates at least an inducible CYP450ALK homolog gene. J Basic Microbiol 54(5):358-68 |
| Yu X, et al. (2006) Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. Nucleic Acids Res 34(3):917-27 |
| Hoppen J, et al. (2007) Ribosomal protein genes in the yeast Candida albicans may be activated by a heterodimeric transcription factor related to Ino2 and Ino4 from S. cerevisiae. Mol Genet Genomics 278(3):317-30 |
| Shetty A, et al. (2013) Transcription regulation of a yeast gene from a downstream location. J Mol Biol 425(3):457-65 |
| Hasslacher M, et al. (1993) Acetyl-CoA carboxylase from yeast is an essential enzyme and is regulated by factors that control phospholipid metabolism. J Biol Chem 268(15):10946-52 |
| Soto A and Carman GM (2008) Regulation of the Saccharomyces cerevisiae CKI1-encoded Choline Kinase by Zinc Depletion. J Biol Chem 283(15):10079-88 |
| Jothi R, et al. (2009) Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol 5:294 |
| Su X and Dowhan W (2006) Regulation of cardiolipin synthase levels in Saccharomyces cerevisiae. Yeast 23(4):279-91 |
| Henry SA, et al. (2012) Metabolism and Regulation of Glycerolipids in the Yeast Saccharomyces cerevisiae. Genetics 190(2):317-49 |
| Barajas D, et al. (2014) Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast. Virology 471-473():72-80 |
| Ottosson LG, et al. (2010) Sulfate Assimilation Mediates Tellurite Reduction and Toxicity in Saccharomyces cerevisiae. Eukaryot Cell 9(10):1635-1647 |
| Fukuda R (2013) Metabolism of Hydrophobic Carbon Sources and Regulation of It in n-Alkane-Assimilating Yeast Yarrowia lipolytica. Biosci Biotechnol Biochem 77(6):1149-1154 |
| Han SH, et al. (2005) Regulation of the PIS1-encoded phosphatidylinositol synthase in Saccharomyces cerevisiae by zinc. J Biol Chem 280(32):29017-24 |
| Sharma M, et al. (2011) Inhibition of phospholipid biosynthesis decreases the activity of the tombusvirus replicase and alters the subcellular localization of replication proteins. Virology 415(2):141-52 |
| Chen M and Lopes JM (2007) Multiple Basic Helix-Loop-Helix Proteins Regulate Expression of the ENO1 Gene of Saccharomyces cerevisiae. Eukaryot Cell 6(5):786-96 |
| Patton-Vogt JL and Henry SA (1998) GIT1, a gene encoding a novel transporter for glycerophosphoinositol in Saccharomyces cerevisiae. Genetics 149(4):1707-15 |
| Jiang F, et al. (1999) Cardiolipin synthase expression is essential for growth at elevated temperature and is regulated by factors affecting mitochondrial development. Mol Microbiol 31(1):373-9 |
| Young BP, et al. (2010) Phosphatidic acid is a pH biosensor that links membrane biogenesis to metabolism. Science 329(5995):1085-8 |
| Cok SJ, et al. (1998) Transcription of INO2 and INO4 is regulated by the state of protein N-myristoylation in Saccharomyces cerevisiae. Nucleic Acids Res 26(12):2865-72 |
| Kundaje A, et al. (2006) A classification-based framework for predicting and analyzing gene regulatory response. BMC Bioinformatics 7 Suppl 1():S5 |