A competitive transcription factor binding mechanism determines the timing of late cell cycle-dependent gene expression

Abstract

Transcriptional 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.

Figure 1

Yox1p Forms a Complex with Mcm1p on the SPO12 Promoter In Vitro (A) Schematic representation of the SPO12 promoter illustrating the relative positions and sequences of the Yox1p-, Mcm1p-, and Fkh2p-binding sites within the fragments used for DNA binding studies. (B) Immobilized template binding assay of full-length in vitro-translated Yox1p binding to the SPO12 promoter sequence in the presence or absence of recombinant Mcm1p(1–98). Control reactions contained streptavidin beads but no biotinylated oligonucleotides. Ten percent input is shown. (C) Schematic illustration of full-length and truncated Yox1p proteins, illustrating the position of the homeodomain (HD). (D and E) Gel retardation analysis of recombinant Flag-tagged Yox1p(151–274) binding to the SPO12 site in the presence or absence of (D) recombinant Mcm1p or (E) Fkh2p(312–458). Where indicated, Flag antibody was added. (F) Gel retardation analysis of the indicated in vitro-translated Yox1p proteins binding to a SPO12 promoter fragment in the presence or absence of recombinant Mcm1p(1–98). The bands corresponding to Mcm1p alone (black arrow) and Yox1p-Mcm1p complexes (white arrows) are indicated. (G) MBP pull-down assays of the indicated recombinant Flag-tagged Yox1p derivatives with MBP-Mcm1p(1–96). Yox1p proteins were detected by western analysis with anti-Flag antibody. Input lanes contain 10% total input protein. See also Figure S1.

Figure 2

The Yox1p-Binding Site Is Required for Ternary Complex Formation (A) Schematic representation of the wild-type and mutant SPO12 promoter. The cross indicates that the Yox1p-binding site has been mutated, and the sequence of the mutated site is indicated (mutated bases underlined). (B) Gel retardation analysis of in vitro-translated Yox1p(151–274) and Fkh2p(1–458) binding to the wild-type (WT) and mutant (mut) SPO12 promoter in the presence or absence of recombinant Mcm1p(1–98). (C) Gel retardation analysis of recombinant Yox1p(151–274) binding to the wild-type (WT) and indicated spacer mutant versions of the SPO12 promoter (shown diagrammatically above the figure; additional nucleotides are underlined) in the presence or absence of recombinant Mcm1p(1–98). The bands corresponding to Mcm1p alone (black arrow), Mcm1p-Yox1p complexes (white arrow), and Mcm1p-Fkh2p complexes (gray arrow) are indicated.

Figure 3

Identification of Amino Acids in Yox1p Critical for Interaction with Mcm1p (A) Schematic illustration of Yox1p(151–274) highlighting the sequence N terminal to the homeodomain (HD). Mutated versions of Yox1p(151–274) are indicated. (B) MBP pull-down assays of the indicated in vitro-translated Yox1p(151–274) derivatives with MBP-Mcm1p(1–96). (C) Gel retardation analysis of the indicated in vitro-translated Yox1p proteins binding to the SPO12 promoter fragment in the presence (lanes 6–10) or absence (lanes 1–5) of recombinant Mcm1p(1–98). The bands corresponding to Mcm1p alone (black arrow), Yox1p-Mcm1p complexes (white arrow), and Yox1p alone (gray arrow) are indicated. See also Figure S2.

Figure 4

Mutant Yox1p Proteins Are Defective in Promoter Binding and Transcriptional Repression (A) Western analysis of Yox1p expression in logarithmically growing yox1Δyhp1Δ cells containing the YCplac-based plasmids pAS2563 and pAS2568 encoding the wild-type (WT) and F155A mutant myc-tagged Yox1p derivatives, respectively. The loading control is tubulin (bottom). (B) Real-time RT-PCR analysis of the indicated genes in yox1Δyhp1Δ cells containing plasmids encoding either wild-type (WT-pAS2563) (black lines) or F155A (pAS2568) (gray lines) myc-tagged Yox1p derivatives, following release from α factor block at the indicated times. Data are normalized to ACT1 levels. (C) ChIP analysis of myc-tagged Yox1p derivatives binding to the indicated gene promoters in yox1Δyhp1Δ cells containing plasmids expressing either wild-type (WT) (white bars) or F155A (black bars) Yox1p derivatives (pAS2563 or pAS2568), following release from α factor block at the indicated times. Data are shown relative to the background binding to each gene promoter in control cells harboring untagged wild-type Yox1p (control, gray bar) (taken as 1) and are the average (± SEM) of two independent experiments performed in duplicate. See also Figure S3.

Figure 5

Yox1p and Fkh2p Binding to Mcm1p Are Mutually Exclusive (A) Schematic illustration of full-length and truncated Yox1p proteins. (B–D) Gel retardation analyses using the SPO12 promoter fragment and (B) in vitro-translated Fkh2p(1–862) in the presence of recombinant Mcm1p(1–96) and increasing amounts of recombinant Yox1p proteins (1, 5, and 10 molar equivalents; indicated by a triangle above the lanes), (C) in vitro-translated Yox1p(151–274) in the presence of recombinant Mcm1p(1–96) and increasing amounts of in vitro-translated Fkh2p(1–862) proteins (1, 2, and 4 molar equivalents; indicated by a triangle above the lanes), or (D) the indicated combinations of recombinant versions of Mcm1p(1–96), Fkh2p(325–458), and increasing amounts of Yox1p(151–274) or Yox1p(176–274) proteins (1 and 2.5 molar equivalents; indicated by a triangle above each set of lanes; lanes 6 and 9 contain the same quantity as lanes 5 and 8). The bands corresponding to Mcm1p and Fkh2p alone (black arrows), binary Yox1p-Mcm1p or Fkh2p-Mcm1p complexes (gray arrows), or ternary Mcm1p-Fkh2p-Yox1p complexes (white arrow) are indicated. Complexes containing Yox1p alone are indicated by #. ^, a higher-order complex. ^∗, a nonspecific band arising from the rabbit reticulocyte lysate. See also Figure S4.

Figure 6

Yox1p Determinants for Competition with Fkh2p for Mcm1p Binding (A and B) Gel retardation analysis of in vitro-translated Fkh2p(1–862) binding to the wild-type (WT) and Yox1p site mutant (mut) SPO12 promoter fragments in the presence of recombinant Mcm1p(1–98) and increasing amounts of the indicated recombinant Yox1p(151–274) proteins (1, 5, and 25 molar equivalents in A and 1, 5, and 10 molar equivalents in B; indicated by a triangle above each set of lanes). The bands corresponding to Mcm1p alone (black arrows), Yox1p-Mcm1p complexes (white arrows), and Fkh2p-Mcm1p complexes (gray arrows) are indicated. Complexes containing Mcm1p and two Yox1p molecules are indicated by #. ^∗, a nonspecific band arising from the rabbit reticulocyte lysate. See also Figure S5.

Figure 7

Yox1p Displaces Fkh2p from Promoters In Vivo (A) Reporter gene assay of SPO12 promoter activity in cells (AP18) containing either integrated pAS2000 (wild-type [WT] SPO12 promoter) or pAS2001 (mutant [mut] SPO12 promoter). Data are shown relative to the activity of the wild-type SPO12 promoter (taken as 1) and are the average (± SEM) of five independent experiments. (B–D) ChIP assays of occupancy of either the CLB2 promoter in its normal endogenous context or the SPO12 promoter in the SPO12-LACZ fusion (B and C) or the SPO12 promoter in its normal endogenous context (D). ChIP was performed using either anti-Myc (to detect Myc-tagged Fkh2p) or anti-Pk (to detect Pk-tagged Ndd1p) antibodies and extracts isolated from logarithmically growing AP16 (B) or AP180 (C) cells containing either integrated pAS2000 (wild-type [WT] SPO12 promoter) or pAS2001 (mutant [mut] SPO12 promoter), or in (D), AP180 cells containing empty vector (−) or plasmids expressing either GAL1 promoter-driven wild-type (WT-pAS2573) or F155A (pAS2574) Yox1p derivatives. In (D), cells were grown in galactose-containing media for 4 hr before sample collection. Data are shown relative to the background binding to the CLB2 or SPO12 promoters in control cells (W303-1a) harboring untagged wild-type Fkh2p (B and C) or Ndd1p (D, control) (white bars) (taken as 1) and are the average (± SEM) of at least two independent experiments. (E) Re-ChIP analysis of Mcm1p, Pk-tagged Yox1p, and Myc-tagged Fkh2p binding to the indicated promoters following a first-round ChIP with either Pk (for Yox1p) or Myc (for Fkh2p) antibodies. Data are average of two independent experiments. (F) Model of how Yox1p represses cell cycle-dependent transcription. In the case of a subset of CLB2 cluster genes, Yox1p binding causes the displacement of the activator protein Fkh2p (top). On genes expressed at the M/G1 phase border (bottom), Fkh2p is not present at the promoter, and Yox1p might act through displacement of an unknown (co-)activator (indicated as X) or through direct repressive effects. Potential protein-DNA interactions are indicated by a dotted arrow. See also Figure S6.