A repressor with similarities to prokaryotic and eukaryotic DNA helicases controls the assembly of the CAAT box binding complex at a photosynthesis gene promoter

A single nucleotide exchange in a promoter region located immediately upstr eam of the CAAT box of the spinach photosynthesis gene AtpC (gene product i s subunit gamma of the chloroplast ATP synthase) prevents the formation of a secondary structure and causes an unregulated, constitutive high level of expression (Kusnetsov, V,, Landsberger, M,, Oelmuller, R, (1999) J, Biol, Chem, 274, 36009-36014). We have isolated cDNAs for ATPC-2, a new polypepti de with homologies to pro- and eukaryotic helicases, which specifically bin ds to this promoter region. Binding of ATPC-2 competes strongly with that o f a CAAT box binding factor (CBF), consistent with the idea that both compl exes cannot be formed simultaneously because of sterical reasons, In gel mo bility shift assays, high binding activities of ATPC-2 and low binding acti vities of CBF were observed with nuclear extracts from tissue with low AtpC expression levels, and the opposite was observed with extracts from tissue s with high AtpC expression levels. Binding of ATPC-2 to the mutant sequenc e, which directs a constitutively high level expression in vivo and prevent s the formation of a secondary structure in vitro, is significantly weaker than binding to the wild-type sequence. Again, the opposite results were ob tained for the CBF, Thus, we conclude that the assembly of the CBF DNA comp lex stimulates transcription of AtpC and that CBF binding is prevented if A TPC-2 is bound to the promoter region. The novel mechanism of gene regulati on and the role of the helicase-like protein ATPC-2 as a potential transcri ptional repressor is discussed in relation to its modular structure.