Probing the nucleobase selectivity of RNA polymerases with dual-coding substrates

Mäkinen, Janne J.; Rosenqvist, Petja; Virta, Pasi; Metsä-Ketelä, Mikko; Belogurov, Georgiy A.

Abstract

Formycin A (FOR) and pyrazofurin A (PYR) are nucleoside analogs with antiviral and antitumor properties. They are known to interfere with nucleic acid metabolism, but their direct effect on transcription is less understood. We explored how RNA polymerases (RNAPs) from bacteria, mitochondria, and viruses utilize FOR, PYR, and oxidized purine nucleotides. All tested polymerases incorporated FOR in place of adenine and PYR in place of uridine. FOR also exhibited surprising dual-coding behavior, functioning as a cytosine substitute, particularly for viral RNAP. In contrast, 8-oxoadenine and 8-oxoguanine were incorporated in place of uridine in addition to their canonical Watson–Crick codings. Our data suggest that the interconversion of canonical anti and alternative syn conformers underlies dual-coding abilities of FOR and oxidized purines. Structurally distinct RNAPs displayed varying abilities to utilize syn conformers during transcription. By examining base pairings that led to substrate incorporation and the entire spectrum of geometrically compatible pairings, we have gained new insights into the nucleobase selection processes employed by structurally diverse RNAPs. These insights may pave the way for advancements in antiviral therapies.

Citation

Mäkinen, J. J., Rosenqvist, P., Virta, P., Metsä-Ketelä, M., & Belogurov, G. A. (2024). Probing the nucleobase selectivity of RNA polymerases with dual-coding substrates. Journal of Biological Chemistry, 300(10), Article 107755. https://doi.org/10.1016/j.jbc.2024.107755

• Journal Article Type: Article
• Acceptance Date: Jun 17, 2024
• Online Publication Date: Sep 9, 2024
• Publication Date: 2024-10
• Deposit Date: Jan 13, 2025
• Publicly Available Date: Jan 13, 2025
• Journal: Journal of Biological Chemistry
• Print ISSN: 0021-9258
• Electronic ISSN: 1083-351X
• Publisher: American Society for Biochemistry and Molecular Biology
• Peer Reviewed: Peer Reviewed
• Volume: 300
• Issue: 10
• Article Number: 107755
• DOI: https://doi.org/10.1016/j.jbc.2024.107755
• Public URL: https://durham-repository.worktribe.com/output/3333542