A network of yeast basic helix-loop-helix interactions

Abstract

The Ino4 protein belongs to the basic helix-loop-helix (bHLH) family of proteins. It is known to form a dimer with Ino2p, which regulates phospholipid biosynthetic genes. Mammalian bHLH proteins have been shown to form multiple dimer combinations. However, this flexibility in dimerization had not been documented for yeast bHLH proteins. Using the yeast two-hybrid assay and a biochemical assay we show that Ino4p dimerizes with the Pho4p, Rtg1p, Rtg3p and Sgc1p bHLH proteins. Screening a yeast cDNA library identified three additional proteins that interact with Ino4p: Bck2p, YLR422W and YNR064C. The interaction with Bck2p prompted us to examine if any of the Bck2p-associated functions affect expression of phospholipid biosynthetic genes. We found that hyperosmotic growth conditions altered the growth phase regulation of a phospholipid biosynthetic gene, CHO1. There are two recent reports of initial whole genome yeast two-hybrid interactions. Interestingly, one of these reports identified five proteins that interact with Ino4p: Ino2p, Hcs1p, Apl2p, YMR317W and YNL279W. Ino2p is the only protein in common with the data presented here. Our finding that Ino4p interacts with five bHLH proteins suggests that Ino4p is likely to be a central player in the coordination of multiple biological processes.

IN02, A Positive Regulator of Lipid Biosynthesis, Is Essential for the Formation of Inducible Membranes in Yeast

“…In the case of Ino4p, there is some evidence for multiple partners. Yeast-two-hybrid analysis recently revealed interactions with four other known yeast bHLH proteins that have not been implicated in lipid biosynthesis: Pho4p, Rtg1p, Rtg3p, and Sgc1p (Robinson et al, 2000). Ino4p has also been implicated in functioning independently of Ino2p in the synthesis of the sphingolipid biosynthetic enzyme, IPC synthase (Ko et al, 1994).…”

The Essential Basic Helix-Loop-Helix Protein FIT1 Is Required for the Iron Deficiency Response

“…The identity of nonconserved amino acids in the basic region of bHLH transcription factors determine the affinity for specific E-box sequences in the promoters of regulated genes, the most common being the G-box 59-CACGTG-39 (Robinson et al, 2000). Upon examination of specific residues in the bHLH domain, FIT1 is predicted to belong to a subgroup of bHLHs that recognize the E-box 59-CANNTG-39, but not the G-box in the promoters of target genes (Toledo-Ortiz et al, 2003).…”

Genome-Wide Analysis of Basic/Helix-Loop-Helix Transcription Factor Family in Rice and Arabidopsis

“…Some bHLH proteins have been shown to bind to sequences containing a consensus core element called the E box (5#-CANNTG-3#), with the G box (5#-CACGTG-3#) being the most common form. In addition, the nucleotides flanking the core element may also have a role in binding specificity (Atchley et al, 1999;MartinezGarcia et al, 2000;Massari and Murre, 2000;Robinson et al, 2000).…”