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Cost of rNTP/dNTP pool imbalance at the replication fork
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The concentration of ribonucleoside triphosphates (rNTPs) in cells is far greater than the concentration of deoxyribonucleoside triphosphates (dNTPs), and this pool imbalance presents a challenge for DNA polymerases (Pols) to select their proper substrate. This report examines the effect of nucleotide pool imbalance on the rate and fidelity of the Escherichia coli replisome. We find that rNTPs decrease replication fork rate by competing with dNTPs at the active site of the C-family Pol III replicase at a step that does not require correct base-pairing. The effect of rNTPs on Pol rate generalizes to B-family eukaryotic replicases, Pols δ and ε. Imbalance of the dNTP pool also slows the replisome and thus is not specific to rNTPs. We observe a measurable frequency of rNMP incorporation that predicts one rNTP incorporated every 2.3 kb during chromosome replication. Given the frequency of rNMP incorporation, the repair of rNMPs is likely rapid. RNase HII nicks DNA at single rNMP residues to initiate replacement with dNMP. Considering that rNMPs will mark the new strand, RNase HII may direct strand-specificity for mismatch repair (MMR). How the newly synthesized strand is recognized for MMR is uncertain in eukaryotes and most bacteria, which lack a methyl-directed nicking system. Here we demonstrate that Bacillus subtilis incorporates rNMPs in vivo, that RNase HII plays a role in their removal, and the RNase HII gene deletion enhances mutagenesis, suggesting a possible role of incorporated rNMPs in MMR.
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“Both replicative and translesion DNA polymerases make sugar errors”
From Ribonucleotide errors, RNase HII, and ribonucleotide excision repair (2026) · cites this paper as Yao et al. 2013
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“rNMPs may represent the most common nucleotide requiring removal from genomic DNA in organisms spanning all domains of life”
From Ribonucleotide errors, RNase HII, and ribonucleotide excision repair (2026) · cites this paper as Yao et al. 2013
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“it has been estimated that E. coli Pol III holoenzyme incorporates up to 2000 rNMPs per one round of chromosomal replication in vitro”
From Ribonucleotide errors, RNase HII, and ribonucleotide excision repair (2026) · cites this paper as Yao et al. 2013
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Metadata
- Authors
- Yao, N. Y., Schroeder, J. W., Yurieva, O., Simmons, L. A., & O’Donnell, M. E.
- Affiliations
- Rockefeller University (US)
- University of Michigan (US)
- Howard Hughes Medical Institute (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2013-07-23
- Volume
- 110
- Issue
- 32
- Pages
- 12942-12947
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3740908
- OpenAlex
- W1967720448
- Cited by
- 114
- References
- 41
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 7 · 2023: 10 · 2022: 8 · 2021: 8 · 2020: 4 · 2019: 13 · 2018: 8 · 2017: 10 · 2016: 8 · 2015: 11 · 2014: 17 · 2013: 1
- FWCI
- 5.53
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- National Institute of General Medical Sciences (GM38831, T32GM007544, R01GM038839)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- ribonucleoside triphosphates, DNA replication, DNA polymerase III, RNase HII, DNA mismatch repair, strand specificity, mutagenesis, Escherichia coli, Bacillus subtilis, DNA polymerase delta, DNA polymerase epsilon
- MeSH terms
- Bacillus subtilis, Binding, Competitive, Deoxyribonucleotides, DNA Polymerase III, DNA Repair, DNA Replication, DNA, Bacterial, Electrophoresis, Agar Gel, Escherichia coli, Models, Genetic, Mutation, Protein Binding, Ribonucleotides, Ribonuclease H, Escherichia coli Proteins
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