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

Alec Fraser, Maria L. Sokolova (), Arina V. Drobysheva, Julia V. Gordeeva, Sergei Borukhov, John Jumper, Konstantin V. Severinov () and Petr G. Leiman ()
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Alec Fraser: University of Texas Medical Branch
Maria L. Sokolova: University of Texas Medical Branch
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
Petr G. Leiman: University of Texas Medical Branch

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-31214-6

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