Cited by 46DNA Repair MechanismsBacterial Genetics and BiotechnologyEnzyme Structure and Function

Characterization of three mycobacterial DinB (DNA polymerase IV) paralogs highlights DinB2 as naturally adept at ribonucleotide incorporation

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Ordonez, Heather, Uson, Maria Loressa, Shuman, Stewart·2014·Nucleic Acids Research

Abstract

This study unveils Mycobacterium smegmatis DinB2 as the founder of a clade of Y-family DNA polymerase that is naturally adept at incorporating ribonucleotides by virtue of a leucine in lieu of a canonical aromatic steric gate. DinB2 efficiently scavenges limiting dNTP and rNTP substrates in the presence of manganese. DinB2's sugar selectivity factor, gauged by rates of manganese-dependent dNMP versus rNMP addition, is 2.7- to 3.8-fold. DinB2 embeds ribonucleotides during DNA synthesis when rCTP and dCTP are at equimolar concentration. DinB2 can incorporate at least 16 consecutive ribonucleotides. In magnesium, DinB2 has a 26- to 78-fold lower affinity for rNTPs than dNTPs, but only a 2.6- to 6-fold differential in rates of deoxy versus ribo addition (kpol). Two other M. smegmatis Y-family polymerases, DinB1 and DinB3, are characterized here as template-dependent DNA polymerases that discriminate strongly against ribonucleotides, a property that, in the case of DinB1, correlates with its aromatic steric gate side chain. We speculate that the unique ability of DinB2 to utilize rNTPs might allow for DNA repair with a 'ribo patch' when dNTPs are limiting. Phylogenetic analysis reveals DinB2-like polymerases, with leucine, isoleucine or valine steric gates, in many taxa of the phylum Actinobacteria.

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Crossref · 10.1093/nar/gku752

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  • Oxidatively damaged lesions may occur in RNA if rNMP incorporation numbers are high.

    “Oxidatively-damaged lesions may also occur in RNA provided that rNMP incorporation numbers are high”

    From Ribonucleotide errors, RNase HII, and ribonucleotide excision repair (2026) · cites this paper as Ordonez et al. 2014

    The Results section, “DinB2 can embed ribonucleotides during DNA synthesis” (page unavailable), reports substantial rNMP incorporation in laboratory reactions. It does not say that oxidative lesions occur in RNA or connect their occurrence to high rNMP incorporation numbers; the measured incorporation was into DNA. (LLM, conf=0.79)

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Research works printed but not linked: 2

  1. [21]Shuman S. Glickman M.S. Bacterial DNA repair by nonhomologous end joining Nat. Rev. Microbiol. 2007 5 852 861 17938628
  2. [30]Bjedov I. Dasgupta C.N. Slade D. Le Blastier S. Selva M. Matic I. Involvement of Escherichia coli DNA polymerase IV in tolerance of cytotoxic alkylating DNA lesions in vivo Genetics 2007 176 1431 4140 17483416 PMC1931539

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Authors
Ordonez, H., Uson, M. L., & Shuman, S.
Affiliations
Memorial Sloan Kettering Cancer Center (US)
Corresponding author
Shuman, Stewart
Venue
Nucleic Acids Research
Published
2014-09-08
Volume
42
Issue
17
Pages
11056-11070
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W2010483150
Cited by
46
References
41
Citations by year
2026: 4 · 2025: 2 · 2024: 1 · 2023: 5 · 2022: 6 · 2021: 3 · 2020: 3 · 2019: 4 · 2018: 4 · 2017: 9 · 2016: 1 · 2015: 2 · 2014: 2
FWCI
1.91
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • National Cancer Institute (P30CA008748)
  • National Institute of Allergy and Infectious Diseases (AI 64693, R01AI064693)
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
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords
DinB, Y-family DNA polymerases, Mycobacterium smegmatis, ribonucleotide incorporation, DNA repair, actinobacteria, paralogs
MeSH terms
Bacterial Proteins, Cations, Divalent, Deoxyribonucleotides, DNA, Manganese, Mycobacterium tuberculosis, Ribonucleotides, RNA, Templates, Genetic, DNA Primers, Amino Acid Substitution, DNA Polymerase beta, Mycobacterium smegmatis

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