Transcriptional regulation at a distance in bacteria

Transcriptional enhancers are cis-acting DNA elements that are binding sites for regulatory proteins and function at large distances from promoter elements to stimulate transcription. Once thought to be unique to eukaryotes, enhancer-like elements have been discovered in a wide variety of bacteria. The regulatory proteins that bind to these bacterial enhancers must contact RNA polymerase to activate transcription. In principle, interactions between bacterial enhancer-binding proteins and RNA polymerase can occur by either DNA looping or tracking of the enhancer-binding protein along the DNA. Paradigms for each of these methods are found in bacterial systems. Activators of sigma(54)-RNA polymerase holoenzyme contact polymerase by DNA looping, while bacteriophage T4 gp45 functions as a sliding clamp that tracks along DNA until it engages RNA polymerase. Significant advances have been made over the last few years towards understanding the mechanisms by which bacterial enhancer-binding proteins activate transcription, but important aspects of these mechanisms are still poorly defined.