Archaeal transcription

After getting out of the promoter region, the RNAP moves into the elongation state, where it keeps growing the new RNA strand in a processive process. Double stranded DNA that enters from the front of the enzyme is unzipped to avail the template strand for RNA synthesis. For every DNA base pair separated by the advancing polymerase, one hybrid RNA:DNA base pair is immediately formed. DNA strands and nascent RNA chain exit from separate channels; the two DNA strands reunite at the trailing end of the transcription bubble while the single strand RNA emerges alone.^[2]

A number of elongation factors help with the rate and processivity of the RNAP. Factors of the Spt4/Spt5 family (bacterial homolog of Spt5 is called NusG) stimulate transcription by binding to the RNAP clamp on one side of the DNA channel and to the gate loop on the other. The resultant DSIF locks the clamp into a closed state to prevent the elongation complex (EC) from dissociating. Spt5 also has a NGN domain that helps the two strands separate. A KOW domain probably hooks the RNAP up to a ribosome so that translation and transcription happen together.^[2]

Some archaea have an Elf1 homolog that might also act as an elongation factor.^[2]

The RNAP occasionally stops and starts moving backwards when it encounters a roadblock or some difficult sequences. When this happens, the EC gets stuck because the reactive 3' edge of the RNA is out of the active site. The transcript cleavage factor TFS (a TFIIS homolog) helps resolve this issue by generating a cut so that a new 3' end is available in the active site. Some archaeon have up to 4 paralogs of TFS with divergent functions.^[2]

Not much is known about archaeal termination. Euryarchaeal RNAPs seem to terminate on their own when poly-U stretches appear.^[2]