Cost of rNTP/dNTP pool imbalance at the replication fork
Open accessAbstract
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.
“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
The paper’s introduction says DNA polymerases incorporate ribonucleotides at low frequency, and its results document this sugar error for the replicative polymerase Pol III. It does not specifically report that translesion polymerases make sugar errors; its reference to a family Y polymerase concerns discrimination against ribonucleotides. (LLM, conf=0.78)
Experimental — accuracy not yet measuredrNMPs are the most common nucleotide requiring removal/repair from genomic DNA in organisms across all domains of life, owing in part to high rNTP:dNTP ratios and high incorporation rates.
“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
The introduction reports high cellular rNTP:dNTP ratios and abundant rNMP incorporation, and the Discussion says rNMPs are frequent in bacteria as well as yeast. The copy does not establish that rNMPs are the most common nucleotides requiring removal from DNA or extend that conclusion to all domains of life (pages not provided). (LLM, conf=0.83)
Experimental — accuracy not yet measuredE. coli Pol III holoenzyme incorporates up to 2000 rNMPs per round of chromosomal replication in vitro.
“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
The section headed “Incorporation of 2,000 rNMPs Predicted During Replication of the E. coli Genome” estimates about 2,000 rNMPs per daughter chromosome. That figure is extrapolated from in vitro selectivity measurements using in vivo nucleotide concentrations; the paper does not report an in vitro round of chromosomal replication incorporating up to 2,000 rNMPs. Page numbers are not provided in our copy. (LLM, conf=0.88)
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RNase HI Is Essential for Survival of Mycobacterium smegmatis
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Replication Rapidly Recovers and Continues in the Presence of Hydroxyurea in Escherichia coli
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Bacillus subtilis PcrA Helicase Removes Trafficking Barriers
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Bacterial Genome Containing Chimeric DNA–RNA Sequences
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The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria
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Genetic stability of Mycobacterium smegmatis under the stress of first-line antitubercular agentsPreprint
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Ribonucleotide errors, RNase HII, and ribonucleotide excision repair
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“RNase HII/H2 is the sole RNase H protein responsible for the repair of single rNMPs, which are incorporated in the genome when DNA polymerases make errors (Nick McElhinny et al. 2010; Yao et al. 2013).”
InfluentialSelf-citationPotenski, C. J., & Klein, H. L. (2014)
How MutS finds a needle in a haystack
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Liao, Y. (2015) · Deep Blue (University of Michigan)
A timidilát bioszintézis és a genomi integritás preventív védelme
Hírmondó, R. (2015) · Eötvös Loránd Tudományegyetem · doi:10.15476/elte.2015.115
- 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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