Two MalT binding sites in direct repeat: A structural motif involved in the activation of all the promoters of the maltose regulons in Escherichia coli and Klebsiella pneumoniae

Abstract

The maltose regulons of Escherichia coli and Klebsiella pneumoniae are very similar, comprising three operons that code for the proteins required for the utilization of maltodextrins as a carbon source. The maltose regulon of K. pneumoniae contains two additional operons, pulAB and pulC-O, which allow the use of starch as a carbon source. The promoters of all of these operons are strictly controlled by the activator protein MalT. In this paper, we report a detailed study of the structure and the functional role of the MalT binding sites located in the adjacent and divergent pulAp and pulCp promoters. By biochemical and genetic experiments, we show that the 134 base-pair region separating the transcription start sites of pulAp and pulCp contains four MalT binding sites, which leads us to propose a revised consensus for the asymmetrical nucleotide sequence recognized by MalT (5′-GGGGAT/GGAGG). MalT binds co-operatively to these four sites, contacting the major groove of the DNA helix. The genetic dissection of the pulAp-pulCp region shows that the promoters partially overlap: the two central MalT binding sites, which are in direct repeat, are required for the activation of both promoters. We further show that an analogous pair of directly repeated MalT binding sites is also involved in the activation of two other promoters of the regulon, malEp and malKp. This study, which confirms the striking structural diversity of the promoters of the maltose regulon, suggests that the motif formed by two MalT binding sites in direct repeat is a recurrent feature of these promoters and plays a crucial role in their activation.