initiates the synthesis of short RNA fragments (Section 6.6, Figure 6.17). Often the initiation is an abortive
‘futile’ cycle in which only short nucleotides of two to six bases are synthesized. With the synthesis of
10–12-nucleotide fragments, the elongation phase commences and transcription proceeds processively.
The polymerase does not dissociate until the termination stage is reached. The transition to the longer
RNA fragments appears to force the RNA polymerase to undergo an allosteric transition to a shape that
creates an engulfing exit tunnel, which accounts for the processivity of the enzyme. Hence, a number of
seemingly wasteful futile cycles are required while the polymerase awaits the proper structural switch. In
the prokaryotic polymerase, the -factor is jettisoned, and this causes an analogous allosteric switch that
ensures processivity. The -factor is composed of multiple domains, which individually might associate
weakly, but when compacted, collectively bind tightly. Consequently, they can be dissociated sequentially.
The structure of a bacterial RNA polymerase in a complex with -factor and with a DNA promoter
shows that sequence-specific interactions are mediated by the subunit; and that explains how the enzyme
complex can recognize the10 and35 elements of promoters. The protein undergoes large conforma-
tional changes during engagement of the substrate, which may be required during the elongation so as to
maintain processivity of transcription. Similar allosteric transitions are observed for the eukaryotic poly-
merase from yeast and the phage T7 RNA polymerase.45,46Formation of the transcription bubble is a key
step to the initiation of transcription. A conserved tryptophan residue in the -factor stacks on the exposed
downstream edge of the transcription bubble at position12 relative to the start site. One of the domains
of the -factor is essential for DNA melting to form the ‘transcription bubble’. Here, the -factor forms
single strand, sequence-specific contacts with the non-template strand.
The yeast RNA polymerase II (Figure 10.18) and eubacterial polymerase have two metal ions at the active
site, which are probably both magnesium ions. One metal ion is persistent and the other may possibly exit
412 Chapter 10
Figure 10.18 Structure of the elongation complex of yeast RNA polymerase II (PDB: 1I6H). Each protein subunit is
colour coded differently. The view is along the axis of the central RNA–DNA heteroduplex (green and
purple)