Template strand gap bypass is a general property of prokaryotic RNA polymerases: implications for elongation mechanisms

It has previously been shown that T7 RNA polymerase is capable of bypassing gaps on the template strand ranging in size from 1 to 24 nucleotides. This as well as other observations suggested a role for the nontemplate strand during elongation. To establish the generality of this gap bypassing event, we have extended these studies to SP6 and Escherichia coli RNA polymerases. SP6 RNA polymerase bypasses template gaps from 1 to 19 nucleotides in size with various degrees of efficiency and produces runoff transcripts of decreasing length corresponding to increasing gap size. RNA sequence analysis of the resulting runoff transcripts revealed that SP6 RNA polymerase faithfully transcribed both parts of the template strand flanking the gapped region. Similar experiments were carried out with E. coli RNA polymerase (a multiple subunit enzyme) and indicate that it is also capable of gap bypass albeit with reduced efficiency compared to T7 and SP6 RNA polymerases. It appears that the ability to bypass gaps present on the DNA template strand is a general property of prokaryotic RNA polymerases. These results have implications with respect to the mechanism of elongation and the role of the nontemplate strand in transcription.