A Dictyostelium protein binds to distinct oligo(dA)center dot oligo(dT) DNA sequences in the C-module of the retrotransposable element DRE

The genome of the eukaryotic microbe Dictyostelium discoideum contains some 200 copies of the nonlong-terminal repeat retrotransposon DRE. Among sever al unique features of this retroelement, DRE is transcribed in both directi ons leading to the formation of partially overlapping plus strand and minus strand RNAs. The synthesis of minus strand RNAs is controlled by the C-mod ule, a 134-bp DNA sequence located at the 3'-end of DRE. A nuclear protein (CMBF) binds to the C-module via interaction with two almost homopolymeric 24 bp oligo(dA).oligo(dT) sequences. The DNA-binding drugs distamycin and n etropsin, which bind to A.T-rich DNA sequences in the minor groove, compete d efficiently for the binding of CMBF to the C-module. The CMBF-encoding ge ne, cbfA, was isolated and a DNA-binding domain was mapped to a 25-kDa C-te rminal region of the protein. A peptide motif involved in the binding of AT -rich DNA by high mobility group-I proteins ('GRP' box) was identified in t he deduced CMBF protein sequence, and exchange of a consensus arginine resi due for alanine within the CMBF GRP box abolished the interaction of CMBF w ith the C-module. The current data support the theory that CMBF binds to th e C-module by detecting its long-range DNA conformation and interacting wit h AT base pairs in the minor groove of oligo(dA).oligo(dT) stretches.