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Vol. 15, No. 18, pp. 2445-2456, September 15, 2001
Department of Biomolecular Chemistry, University of Wisconsin,
Madison, Wisconsin 53706, USA
The roles of DNA and Mcm1p interactions in determining the
overlapping and distinct functions of the yeast cell cycle regulatory transcription factors Fkh1p and Fkh2p were examined. Full-length recombinant Fkh1p and Fkh2p were purified and their binding to bona
fide promoters examined in vitro. Each protein bound a variety of
target promoters with similar specificity in vitro, consistent with the
observation that these proteins bind common promoters in vivo. However,
in vivo, the Fkh1p and Fkh2p occupied different target promoters to
different extents, suggesting that each was primarily responsible for
controlling a different set of genes. Additional in vitro studies
provided a mechanistic explanation for this differential
promoter-occupancy. Specifically, the Fkh2p, but not the Fkh1p, was
capable of binding cooperatively with Mcm1p. The Mcm1p-Fkh2p
cooperative binding was enhanced by, but did not require, the presence
of a Mcm1p-binding site within a target promoter. Consistent with these
data, Mcm1p was present at Fkh-controlled promoters in vivo regardless
of whether they contained Mcm1p-binding sites, suggesting a role for
Mcm1p at promoters not thought previously to be under Mcm1p control.
Analysis of Fkh1p and Fkh2p binding to promoter targets in vivo by use
of mutant strains indicated that the two proteins compete for
promoter-occupancy at a number of target promoters. We postulate that
Fkh1p and a stable Fkh2p/Mcm1p complex compete for binding to target
promoters and that the levels and/or binding activity of Fkh1p, but not
Fkh2p, are most limiting for promoter-occupancy in vivo. Interestingly,
the in vitro DNA-binding assays, using a variety of promoter targets,
revealed that bona fide Fkh target promoters contained two or more
Fkh-binding sites that allowed the Fkh1p and Fkh2p proteins to form
multiple protein-DNA complexes in vitro. Multiple Fkh-binding sites
may be a distinguishing feature of bona fide Fkh promoters in yeast and
other organisms.
[Key Words: Forkhead; Mcm1p; cell cycle; SFF; transcription; yeast]
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