A BACTERIAL ATP-DEPENDENT, ENHANCER-BINDING PROTEIN THAT ACTIVATES THE HOUSEKEEPING RNA-POLYMERASE

A commonly accepted view of gene regulation in bacteria that has emerg ed over the last decade is that promoters are transcriptionally activa ted by one of two general mechanisms. The major type involves activato r proteins that bind to DNA adjacent to where the RNA polymerase (RNAP ) holoenzyme binds, usually assisting in recruitment of the RNAP to th e promoter. This holoenzyme uses the housekeeping sigma(70) or a relat ed factor, which directs the core RNAP to the promoter and assists in melting the DNA near the RNA start site. A second type of mechanism in volves the alternative sigma factor (called sigma(54) or sigma(N)) tha t directs RNAP to highly conserved promoters. Era these cases, an acti vator protein with an ATPase function oligomerizes at tandem sires far upstream from the promoter. The nitrogen regulatory protein (NtrC) fr om enteric bacteria has been the model for this family of activators. Activation of the RNBP/sigma(54) holoenzyme to form the open complex i s mediated by the activator, which is tethered upstream. Hence, this c lass of protein is sometimes called the enhancer binding protein famil y or the NtrC class. We describe here a third system that has properti es of each of these two types. The NtrC enhancer binding protein from the photosynthetic bacterium, Rhodobacter capsulatus, is shown in vitr o to activate the housekeeping RNAP/sigma(70) holoenzyme. Transcriptio nal activation by this NtrC requires ATP binding but not hydrolysis. O ligomerization at distant tandem binding sites on a supercoiled templa te is also necessary. Mechanistic and evolutionary questions of these systems are discussed.