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Structural basis for transcription elongation by bacterial RNA polymerase

Abstract

The RNA polymerase elongation complex (EC) is both highly stable and processive, rapidly extending RNA chains for thousands of nucleotides. Understanding the mechanisms of elongation and its regulation requires detailed information about the structural organization of the EC. Here we report the 2.5-Å resolution structure of the Thermus thermophilus EC; the structure reveals the post-translocated intermediate with the DNA template in the active site available for pairing with the substrate. DNA strand separation occurs one position downstream of the active site, implying that only one substrate at a time can specifically bind to the EC. The upstream edge of the RNA/DNA hybrid stacks on the β′-subunit ‘lid’ loop, whereas the first displaced RNA base is trapped within a protein pocket, suggesting a mechanism for RNA displacement. The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination.

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Figure 1: Overall structure of the ttEC.
Figure 2: Nucleic acid structure in the ttEC.
Figure 3: Schematic drawing of the protein/nucleic acid contacts.
Figure 4: Protein–nucleic acid interactions in the ttEC structure.
Figure 5: dwDNA and RNA/DNA hybrid strand separation.

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Acknowledgements

We thank D. Temiakov and M. Anikin for assistance in crystallization at the initial stage of the project. We are grateful to R. Landick for helpful discussions and critical reading of the manuscript. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Energy Research. This work was supported by NIH grants to D.G.V. and I.A.

Author Contributions D.G.V. determined and analysed the structure and guided the project. A.P. purified RNAP. M.N.V. and A.P performed crystallization and data collection. T.H.T assisted with data collection and analysis. I.A. contributed scaffold design and analysis. D.G.V. and I.A. jointly wrote the manuscript.

The atomic coordinates are deposited in the Protein Data Bank under accession number 2O5I

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The atomic coordinates are deposited in the Protein Data Bank under accession number 2O5I. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

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Vassylyev, D., Vassylyeva, M., Perederina, A. et al. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448, 157–162 (2007). https://doi.org/10.1038/nature05932

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