Structure and function of virion RNA polymerase of a crAss-like phage

Arina V. Drobysheva, Sofia A. Panafidina, Matvei V. Kolesnik, Evgeny I. Klimuk, Leonid Minakhin, Maria V. Yakunina, Sergei Borukhov, Emelie Nilsson, Karin Holmfeldt, Natalya Yutin, Kira S. Makarova, Eugene V. Koonin, Konstantin V. Severinov (), Petr G. Leiman () and Maria L. Sokolova ()
Additional contact information
Arina V. Drobysheva: Skolkovo Institute of Science and Technology
Sofia A. Panafidina: Skolkovo Institute of Science and Technology
Matvei V. Kolesnik: Skolkovo Institute of Science and Technology
Evgeny I. Klimuk: Skolkovo Institute of Science and Technology
Leonid Minakhin: The State University of New Jersey
Maria V. Yakunina: Peter the Great St Petersburg Polytechnic University
Sergei Borukhov: Rowan University School of Osteopathic Medicine at Stratford
Emelie Nilsson: Linnaeus University
Karin Holmfeldt: Linnaeus University
Natalya Yutin: National Library of Medicine, National Institutes of Health
Kira S. Makarova: National Library of Medicine, National Institutes of Health
Eugene V. Koonin: National Library of Medicine, National Institutes of Health
Konstantin V. Severinov: Russian Academy of Sciences
Petr G. Leiman: University of Texas Medical Branch
Maria L. Sokolova: Skolkovo Institute of Science and Technology

Nature, 2021, vol. 589, issue 7841, 306-309

Abstract: Abstract CrAss-like phages are a recently described expansive group of viruses that includes the most abundant virus in the human gut1–3. The genomes of all crAss-like phages encode a large virion-packaged protein2,4 that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs)5. Here, using Cellulophaga baltica crAss-like phage phi14:2 as a model system, we show that this protein is a DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited state, which probably occurs before virion packaging. This conformation is attained with the help of a cleft-blocking domain that interacts with the active site and occupies the cavity in which the RNA–DNA hybrid binds. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs that are involved in RNA interference6,7, although most of the phi14:2 RNAP structure (nearly 1,600 residues) maps to a new region of the protein fold space. Considering this structural similarity, we propose that eukaryal RNA interference polymerases have their origins in phage, which parallels the emergence of the mitochondrial transcription apparatus8.

Date: 2021
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DOI: 10.1038/s41586-020-2921-5

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