A Competitive Transcription Factor Binding Mechanism Determines the Timing of Late Cell Cycle-Dependent Gene Expression

Abstract

SummaryTranscriptional control is exerted by the antagonistic activities of activator and repressor proteins. In Saccharomyces cerevisiae, transcription factor complexes containing the MADS box protein Mcm1p are key regulators of cell cycle-dependent transcription at both the G2/M and M/G1 transitions. The homeodomain repressor protein Yox1p acts in a complex with Mcm1p to control the timing of gene expression. Here, we show that Yox1p interacts with Mcm1p through a motif located N terminally to its homeodomain. Yox1p functions as a transcriptional repressor by competing with the forkhead transcription activator protein Fkh2p for binding to Mcm1p through protein-protein interactions at promoters of a subset of Mcm1p-regulated genes. Importantly, this competition is not through binding the same DNA site that is commonly observed. Thus, this study describes a different mechanism for determining the timing of cell cycle-dependent gene expression that involves competition between short peptide motifs in repressor and activator proteins for interaction with a common binding partner.

Topology and Control of the Cell-Cycle-Regulated Transcriptional Circuitry

“…Mcm1 is regulated by one of two transcriptional repressors, the homeodomain proteins Yox1 or Yhp1, that hold expression of this cluster of genes in check outside of the M/G1 interval by binding directly to Mcm1 and a DNA element that flanks the ECB (Mai et al 2002;Pramila 2002) (Figure 4). Their interaction with both Mcm1 and DNA is required to stabilize the repressive complex (Darieva et al 2010). Consistent with the need to repress M/G1 cluster expression from G1 through M phase, YOX1 is expressed as a G1/S cluster gene during G1 and YHP1 somewhat later, perhaps as a consequence of the presence of Fkh2 sites in its promoter (Spellman et al 1998;Pramila 2002).…”

“…In fact, some genes within the cluster exhibit different behaviors in the mitotic cyclin mutants, suggesting that more than one regulatory mechanism exists for triggering transcription . It has recently been recognized that other members of the family, including SPO12, despite being Mcm1/Fkh2 targets, are subject to an additional level of regulation by the homeodomain-containing repressor protein, Yox1 (Pramila 2002;Darieva et al 2010). Yox1 was previously recognized as an important repressor in the regulation of the M/G1 gene cluster (see below).…”

“…Yox1 was previously recognized as an important repressor in the regulation of the M/G1 gene cluster (see below). However, in addition to having a consensus DNA-binding site for Fkh2 downstream of that for Mcm1, some G2/M genes have a Yox1-binding site upstream, suggesting that Yox1 also plays a role in their transcriptional regulation (Darieva et al 2010). In fact, occupancy of that Yox1-binding site precludes the binding of Fkh2.…”

“…Consequently, Yox1 represses those genes having a Yox1-binding site in a manner similar to its effect on members of the M/G1 gene cluster. The basis for the mutual exclusivity of binding sites for Yox1 and Fkh2 remains unclear but presumably involves competition between Yox1 and Fkh2 for binding sites on Mcm1 and not the geometry of the DNAbinding sites themselves (Boros et al 2003;Darieva et al 2010). Regardless, this regulatory circuit is clearly effective in repressing gene expression at those loci and shifting the expression of those genes later in the cell cycle relative to the other members of the G2/M gene cluster (Pramila 2002).…”

“…Expression of Mcm1 target genes does not occur until the Yox1 and Yhp1 repressor proteins are eliminated, presumably by APC-dependent ubiquitylation, during late M phase (Pramila 2002). Whereas Yox1 appears to repress gene expression at some G2/M cluster promoters by displacing Fkh2-Ndd1, no similar mechanism is known for M/G1 cluster genes (Darieva et al 2010). Nevertheless, renewed accumulation of Yox1 and Yhp1 at the beginning of the next cell cycle certainly contributes to M/G1 gene repression.…”