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Transcription. 2012 Sep-Oct;3(5):260-9. doi: 10.4161/trns.22307. Epub 2012 Sep 1.

RNA polymerase stalls in a post-translocated register and can hyper-translocate.

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Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.


Exonuclease (Exo) III was used to probe translocation states of RNA polymerase (RNAP) ternary elongation complexes (TECs). Escherichia coli RNAP stalls primarily in a post-translocation register that makes relatively slow excursions to a hyper-translocated state or to a pre-translocated state. Tagetitoxin (TGT) strongly inhibits hyper-translocation and inhibits backtracking, so, as indicated by Exo III mapping, TGT appears to stabilize both the pre- and probably a partially post-translocation state of RNAP. Because the pre-translocated to post-translocated transition is slow at many template positions, these studies appear inconsistent with a model in which RNAP makes frequent and rapid (i.e., millisecond phase) oscillations between pre- and post-translocation states. Nine nucleotides (9-nt) and 10-nt TECs, and TECs with longer nascent RNAs, have distinct translocation properties consistent with a 9-10 nt RNA/DNA hybrid. RNAP mutant proteins in the bridge helix and trigger loop are identified that inhibit or stimulate forward and backward translocation.


NTP analogues; RNA polymerase; bridge helix; hyper-translocation; tagetitoxin; translocation; trigger loop

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