The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
Open accessPreprint — published as 10.1038/s41467-022-31214-6 · Paper page
Abstract
Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by their sigma subunits that first bind to a double-stranded DNA element ~35 to ~14 nucleotides upstream of the transcription start site (TSS) and then capture several bases of the non-template strand ~10 nucleotides upstream of the TSS. Here, we shift this paradigm and explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes a −10 promoter element in the template strand directly. Together, the AR9 nvRNAP sigma-like subunit, the enzyme core, and the template strand itself form two nucleotide base-accepting pockets whose shapes dictate the AR9 nvRNAP’s deoxyuridine promoter requirement. A single amino acid substitution in the promoter specificity subunit allows one of these pockets to accept a thymine base thus expanding the enzyme’s promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to control host takeover.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Leiman, P., Fraser, A., Sokolova, M., Drobysheva, A., Gordeeva, J., Borukhov, S., Team, A., & Severinov, K.
- Affiliations
- The University of Texas Medical Branch at Galveston (US)
- Skolkovo Institute of Science and Technology (RU)
- Rowan University (US)
- DeepMind Technologies Limited
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Leiman, Petr
- Sokolova, Maria
- Severinov, Konstantin
- Venue
- Nature Communications
- Published
- 2021-11-04
- Volume
- 13
- Issue
- 1
- Pages
- 3526-3526
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC9209446
- OpenAlex
- W4283157815
- Cited by
- 7
- References
- 1
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 3 · 2023: 1
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- 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
- Howard Hughes Medical Institute (DE-AC02-05CH11231)
- U.S. Department of Energy (DE‐ AC02‐06CH11357, -AC02-05CH11231, Contract No. DE-AC02-06CH11357., Contract No. DE-AC02-05-CH11231, AC02‐06CH11357, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, 085P1000817, 06CH11357, No. DE-AC02-06CH11357, DE-AC02-)
- Michigan Economic Development Corporation (085P1000817, DE-AC02-06CH11357, Grant 085P1000817)
- University of Texas Medical Branch
- Russian Foundation for Basic Research (20-34-90079)
- Russian Science Foundation (075-10-2021-114, 19-74-00011)
- Skolkovo Institute of Science and Technology
- National Institutes of Health (DE-AC02–05CH11231, DE-AC02–06CH11357, 085P1000817)
- Office of Science (No. DE-AC02- 05-CH11231, Contract No. DE-AC02-06CH11357, AC02‐06CH11357, DEAC02–05CH11231, AC02-05CH11231, DE-AC02, No. DE-AC02-06CH11357., 085P1000817, 05CH11231, 06CH11357, Contract No. DE-AC02-05CH11231, DE-AC02-06CH11357)
- Department of Mechanical Engineering, University of Texas at Austin
- Michigan Technology Tri-Corridor (DE-AC02-06CH11357, 085P1000817, DE-AC02-05CH11231)
- Simons Center for the Social Brain, Massachusetts Institute of Technology
- National Institute of General Medical Sciences (R01GM139034, R01GM130942)
- Argonne National Laboratory (DE- AC02-06-CH11357, DE-AC02, AC02–06CH11357, 085P1000817, DE-AC02-05CH11231, No. DE-AC02-06CH11357, 06CH11357, Contract No. DE-AC02-06CH11357.)
- SLAC National Accelerator Laboratory (DE-AC02-05-CH11231, DE-AC02-06CH11357)
- 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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