Mechanisms of action of RNA polymerase-binding transcription factors that do not bind to DNA

The mechanisms regulating gene expression are a vigorously expanding area of research. DNA-dependent RNA polymerase (RNAP) is the enzyme of transcription, the first stage of gene expression, and a major target of regulation. There is a class of transcription factors-including the prokaryotic proteins GreA, GreB, Gfh1, Rnk, DksA, TraR and the eukaryotic TFIIS-that do not bind to DNA but directly interact with RNAP: through the secondary channel of the enzyme they reach the catalytic center and modulate its activity. GreA, GreB, and TFIIS act by stimulating the intrinsic endonucleolytic activity of the RNAP catalytic center. This activity allows RNAP to read through transcription pauses and arrest sites. The biochemical activities of other factors of this class are less clear. In this work, the data that accumulated during the last 15 years of research on this exciting group of factors are reviewed.