Structural basis of RNA polymerase inhibition by viral and host factors View Full Text


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Article Info

DATE

2021-09-17

AUTHORS

Simona Pilotto, Thomas Fouqueau, Natalya Lukoyanova, Carol Sheppard, Soizick Lucas-Staat, Luis Miguel Díaz-Santín, Dorota Matelska, David Prangishvili, Alan C. M. Cheung, Finn Werner

ABSTRACT

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. 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. More... »

PAGES

5523

References to SciGraph publications

  • 2019-12-05. Molecular insight into RNA polymerase I promoter recognition and promoter melting in NATURE COMMUNICATIONS
  • 2020-02-17. Structural basis for RNA polymerase III transcription repression by Maf1 in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2013-10-23. Crystal structure of the 14-subunit RNA polymerase I in NATURE
  • 2013-10-23. RNA polymerase I structure and transcription regulation in NATURE
  • 2021-02-08. Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2009-10-09. RNA polymerase II–TFIIB structure and mechanism of transcription initiation in NATURE
  • 2020-11-30. Direct binding of TFEα opens DNA binding cleft of RNA polymerase in NATURE COMMUNICATIONS
  • 2017-11-22. Structural basis for the initiation of eukaryotic transcription-coupled DNA repair in NATURE
  • 2017-02-27. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy in NATURE METHODS
  • 2017-09-11. Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2011-02-23. Structural basis of RNA polymerase II backtracking, arrest and reactivation in NATURE
  • 2008-01-30. The X-ray crystal structure of RNA polymerase from Archaea in NATURE
  • 2017-12-04. The transcript cleavage factor paralogue TFS4 is a potent RNA polymerase inhibitor in NATURE COMMUNICATIONS
  • 2017-02-06. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination in NATURE METHODS
  • 2017-07-05. Structure and mechanisms of viral transcription factors in archaea in EXTREMOPHILES
  • 2016-05-11. Near-atomic resolution visualization of human transcription promoter opening in NATURE
  • 2007-06-20. Structural basis for transcription elongation by bacterial RNA polymerase in NATURE
  • 2007-06-20. Structural basis for substrate loading in bacterial RNA polymerase in NATURE
  • 2016-11-24. Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP in NATURE COMMUNICATIONS
  • 2010-12-01. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein in NATURE
  • 2020-01-06. A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2016-11-14. Structure of RNA polymerase I transcribing ribosomal DNA genes in NATURE
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-021-25666-5

    DOI

    http://dx.doi.org/10.1038/s41467-021-25666-5

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1141189131

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34535646


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