Cited by 7Bacterial Genetics and BiotechnologyGenomics and Chromatin DynamicsRNA and protein synthesis mechanisms

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

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Fraser, Alec, Sokolova, Maria L., Drobysheva, Arina V., Gordeeva, Julia V., Borukhov, Sergei, Jumper, John, Severinov, Konstantin V., Leiman, Petr G.·2022·Nature Communications

Published version of a preprint

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.

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Authors
Fraser, A., Sokolova, M. L., Drobysheva, A. V., Gordeeva, J. V., Borukhov, S., Jumper, J., Severinov, K. V., & Leiman, P. G.
Affiliations
  • The University of Texas Medical Branch at Galveston (US)
  • Skolkovo Institute of Science and Technology (RU)
  • Rowan University (US)
  • Rutgers, The State University of New Jersey (US)
Corresponding author
  • Sokolova, Maria L.
  • Severinov, Konstantin V.
  • Leiman, Petr G.
Venue
Nature Communications
Published
2022-06-20
Volume
13
Issue
1
Pages
3526-3526
ISSN
2041-1723 (ISSN-L)
OpenAlex
W4283157815
Cited by
7
References
87
Citations by year
2026: 1 · 2025: 2 · 2024: 3 · 2023: 1
FWCI
0.91
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • University of Texas Medical Branch
  • UTMB Sealy Center for Structural Biology and Molecular Biophysics
  • Russian Science Foundation (19-74-00011)
  • Skolkovo Institute of Science and Technology
  • Russian Foundation for Basic Research (20-34-90079)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
sigma factor, promoter identification, deoxyuridine, template strand, transcription initiation
MeSH terms
Viral Replicase Complex Proteins, Deoxyuridine, Promoter Regions, Genetic, DNA-Directed RNA Polymerases, RNA, Viral, Sigma Factor, Transcription, Genetic

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