| The basic helix-loop-helix (bHLH) eukaryotic transcription factors have the ability to form multiple dimer combinations. This property together with the limited DNA-binding specificity to the E-box (CANNTG) makes them ideally suited for combinatorial control of gene expression. I tested the ability of all 9 Saccharomyces cerevisiae bHLH proteins to regulate the enolase-encoding gene, ENO1. ENO1 was known to be activated by the bHLH protein, Sgc1p. Here, we show that expression of an ENO1-lacZ reporter was also regulated by the other 8 bHLH proteins: Ino2p, Ino4p, Cbf1p, Rtg1p, Rtg3p, Pho4p, Hms1p, and Ygr290wp. ENO1-lacZ expression was also repressed by growth in inositol/choline-containing (I+C+) media. Epistatic analysis and ChIP experiments showed that regulation by Sgc1p, Ino2p, Ino4p, Cbf1p, and repression by inositol/choline required three distal E-boxes: E1, E2, and E3. The pattern of bHLH binding to the 3 E-boxes and experiments with two dominant-negative mutant alleles of INO4 and INO2 support the model that bHLH dimer selection affects ENO1-lacZ expression.;Ino4p and Sgc1p were known to regulate the phospholipid biosynthetic pathway and glycolytic pathway, respectively. However, their ability to dimerize suggested that they might regulate overlapping gene sets. To test this, microarray-based expression analysis was performed to identify the Ino4p and Sgc1p transcriptomes. These studies were carried out under four different growth conditions known to affect bHLH proteins function: presence and absence of inositol/choline and low and high phosphate (Pi) concentrations. These experiments identified several target gene regulated by both Ino4p and Sgc1p under each condition. The Sgc1p transcriptome included genes involved in different pathways including sulfur amino acid biosynthesis, nitrogen utilization, and mating. ChIP experiments showed that Ino4p and Sgc1p do bind to the promoters of some of the target genes. These results support the model that bHLH proteins can coordinate different biological pathways. |
