Initiator recognition in a primitive eukaryote: IBP39, an initiator-binding protein from Trichomonas vaginalis

While considerable progress has been made in understanding the mechanisms o f transcription in higher eukaryotes, transcription in single-celled, primi tive eukaryotes remains poorly understood. Promoters of protein-encoding ge nes in the parasitic protist Trichomonas vaginalis, which represents one of the deepest-branching eukaryotic lineages, have a bipartite structure with gene-specific regulatory elements and a conserved core promoter encompassi ng the transcription start site. Core promoters in T. vaginalis appear to c onsist solely of a highly conserved initiator (Inr) element that is both a structural and a functional homologue of its metazoan counterpart. Using DN A affinity chromatography, we have isolated an Inr-binding protein from T. vaginalis. Cloning of the gene encoding the Inr binding protein identified a novel 39-kDa protein (IBP39). We show that IBP39 binds to both double and single Inr motifs found in T. vaginalis genes and that binding requires th e conserved nucleotides necessary for Inr function in vivo. Analyses of the cloned IBP39 gene revealed no homology at the protein sequence level with identified proteins in other organisms or the presence of known DNA-binding domains. The relationship between IBP39 and Inr-binding proteins in metazo a presents interesting evolutionary questions.