Hold on!: RNA polymerase interactions with the nascent RNA modulate transcription elongation and termination

Evolutionary related multisubunit RNA polymerases from all three domains of life, Eukarya, Archaea and Bacteria, have common structural and functional properties. We have recently shown that two RNAP subunits, F/E (RPB4/7)-which are conserved between eukaryotes and Archaea but have no bacterial homologues-interact with the nascent RNA chain and thereby profoundly modulate RNAP activity. Overall F/E increases transcription processivity, but it also stimulates transcription termination in a sequence-dependent manner. In addition to RNA-binding, these two apparently opposed processes are likely to involve an allosteric mechanism of the RNAP clamp. Spt4/5 is the only known RNAP-associated transcription factor that is conserved in all three domains of life, and it stimulates elongation similar to RNAP subunits F/E. Spt4/5 enhances processivity in a fashion that is independent of the nontemplate DNA strand, by interacting with the RNAP clamp. Whereas the molecular mechanism of Spt4/5 is universally conserved in evolution, the added functionality of F/E-like complexes has emerged after the split of the bacterial and archaeoeukaryotic lineages. Interestingly, bacteriophage-encoded antiterminator proteins could, in theory, fulfil an analogous function in the bacterial RNAP.