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Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase

Author

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  • Alec Fraser

    (University of Texas Medical Branch)

  • Maria L. Sokolova

    (University of Texas Medical Branch
    Skolkovo Institute of Science and Technology)

  • Arina V. Drobysheva

    (Skolkovo Institute of Science and Technology)

  • Julia V. Gordeeva

    (Skolkovo Institute of Science and Technology)

  • Sergei Borukhov

    (Rowan University School of Osteopathic Medicine at Stratford)

  • John Jumper

    (DeepMind Technologies Limited)

  • Konstantin V. Severinov

    (Skolkovo Institute of Science and Technology
    Russian Academy of Sciences
    The State University of New Jersey)

  • Petr G. Leiman

    (University of Texas Medical Branch)

Abstract

Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the −10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the −10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

Suggested Citation

  • Alec Fraser & Maria L. Sokolova & Arina V. Drobysheva & Julia V. Gordeeva & Sergei Borukhov & John Jumper & Konstantin V. Severinov & Petr G. Leiman, 2022. "Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31214-6
    DOI: 10.1038/s41467-022-31214-6
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    References listed on IDEAS

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    1. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
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    1. Anastasiia Chaban & Leonid Minakhin & Ekaterina Goldobina & Brain Bae & Yue Hao & Sergei Borukhov & Leena Putzeys & Maarten Boon & Florian Kabinger & Rob Lavigne & Kira S. Makarova & Eugene V. Koonin , 2024. "Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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