Structural basis of RNA polymerase inhibition by viral and host factors

RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors.

figure1
Fig: The complete structure of the crenarchaeal RNA polymerase: a Cryo-EM map and cartoon representation of Sulfolobus acidocaldariusRNA polymerase. This composite map is illustrated as semi-trasparent surface and obtained by merging the cryo-EM map of apo-RNA polymerase with the stalk resulting from the multi-body refinement of the TFS4-bound RNA polymerase. Each subunit is highlighted according to the colour code shown on the left, the cryo-EM map is illustrated as semi-transparent surface. b Details of the apo-RNAP map showing the coordination system of the [3Fe-4S] cluster with sulphur atoms in yellow spheres and iron in dark red. Rpo3 residues are shown as sticks in red as in a, while the map is shown in mesh. c Cartoon representation of Rpo8 bound to Rpo1´ within the cryo-em map shown here in semi-transparency. The β
β5–6 loop is highlighted in red, and the conserved GGLLM motif in orange. The corresponding sequence alignment is reported in Supplementar
y.

However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition.

Pilotto, S., Fouqueau, T., Lukoyanova, N. et al. Structural basis of RNA polymerase inhibition by viral and host factors. Nat Commun 12,5523 (2021). https://doi.org/10.1038/s41467-021-25666-5