Transcriptional elongation involves the rapid extension of RNA chains by DNA-dependent RNA polymerases, but structural information on the mechanistic basis of this process has been lacking. Vassylyev et al. determined the first high-resolution structure of a bacterial transcription elongation complex (EC) that comprises the RNA polymerase core enzyme bound to a nucleic-acid scaffold that contains 14 base pairs (bp) of downstream DNA, a 9-bp RNA–DNA hybrid and seven nucleotides of the displaced RNA transcript. The most notable rearrangement of the core enzyme in the EC is the closure of the pincers of the crab-claw-like structure of RNA polymerase, which substantially reduces the size of the main channel that accommodates the downstream DNA and the RNA–DNA hybrid. The channel closure might increase the surface complementarity between the polymerase and nucleic-acid chains, favouring high stability and processivity of the EC.
Each elongation cycle involves the separation of 1 bp of the downstream DNA, accompanied by the displacement of one nucleotide of the nascent RNA from the DNA template at the upstream edge of the RNA–DNA hybrid. The structure reveals that DNA-strand separation occurs one position downstream of the active site, which implies that only one substrate at a time can bind to the EC. The upstream edge of the 9-bp RNA–DNA hybrid interacts with the so-called lid loop, which is thought to sterically block further growth of the hybrid while stabilizing the upstream hybrid base pair. The first displaced RNA from the DNA template is trapped in a hydrophobic protein pocket, providing a clue to the possible mechanism of RNA separation.
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