Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability

Park, Joon; Baruch‐Torres, Noe; Iwai, Shigenori; Herrmann, Geoffrey K.; Brieba, Luis G.; Yin, Yajiang

doi:10.3389/fmolb.2022.808036

Cited by 4 publications

(4 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Regulation by divalent cations has been described for other DNA Pols, such as human mitochondrial Pol γ, that has an enhanced ability to perform translesion synthesis (TLS) in the presence of Mn 2+ compared to Mg 2+ . 46 In another example, Pol η shifts its activity to ribonucleotide incorporation through an increased affinity to rNTPs in the presence of Mn 2+ . 47 This modulation in activity for both proteins is likely due to a conformational change of the active site that is allowed due to the more relaxed coordination requirement of Mn 2+ .…”

Section: ■ Discussionmentioning

confidence: 99%

“…Another mechanism that could be altering POLIB activity is the use of different available divalent cations. Regulation by divalent cations has been described for other DNA Pols, such as human mitochondrial Pol γ, that has an enhanced ability to perform translesion synthesis (TLS) in the presence of Mn 2+ compared to Mg 2+ . In another example, Pol η shifts its activity to ribonucleotide incorporation through an increased affinity to rNTPs in the presence of Mn 2+ .…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Trypanosoma brucei Mitochondrial DNA Polymerase POLIB Contains a Novel Polymerase Domain Insertion That Confers Dominant Exonuclease Activity

et al. 2022

View full text Add to dashboard Cite

Trypanosoma brucei and related parasites contain an unusual catenated mitochondrial genome known as kinetoplast DNA (kDNA) composed of maxicircles and minicircles. The kDNA structure and replication mechanism are divergent and essential for parasite survival. POLIB is one of three Family A DNA polymerases independently essential to maintain the kDNA network. However, the division of labor among the paralogs, particularly which might be a replicative, proofreading enzyme, remains enigmatic. De novo modeling of POLIB suggested a structure that is divergent from all other Family A polymerases, in which the thumb subdomain contains a 369 amino acid insertion with homology to DEDDh DnaQ family 3′–5′ exonucleases. Here we demonstrate recombinant POLIB 3′–5′ exonuclease prefers DNA vs RNA substrates and degrades single- and double-stranded DNA nonprocessively. Exonuclease activity prevails over polymerase activity on DNA substrates at pH 8.0, while DNA primer extension is favored at pH 6.0. Mutations that ablate POLIB polymerase activity slow the exonuclease rate suggesting crosstalk between the domains. We show that POLIB extends an RNA primer more efficiently than a DNA primer in the presence of dNTPs but does not incorporate rNTPs efficiently using either primer. Immunoprecipitation of Pol I-like paralogs from T. brucei corroborates the pH selectivity and RNA primer preferences of POLIB and revealed that the other paralogs efficiently extend a DNA primer. The enzymatic properties of POLIB suggest this paralog is not a replicative kDNA polymerase, and the noncanonical polymerase domain provides another example of exquisite diversity among DNA polymerases for specialized function.

show abstract

Section: ■ Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Trypanosoma brucei Mitochondrial DNA Polymerase POLIB Contains a Novel Polymerase Domain Insertion That Confers Dominant Exonuclease Activity

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Regulation by divalent cations has been described for other DNA Pols, such as human mitochondrial Pol g, that has an enhanced ability to perform translesion synthesis (TLS) in the presence of Mn 2+ compared to Mg 2+ . 46 In another example, Pol h shifts its activity to ribonucleotide incorporation through an increased affinity to rNTPs in the presence of Mn 2+ . 47 This modulation in activity for both proteins is likely due to a conformational change of the active site that is allowed due to the more relaxed coordination requirement of Mn 2+ .…”

Section: Discussionmentioning

confidence: 99%

Trypanosoma brucei Mitochondrial DNA Polymerase POLIB Contains a Novel Thumb Insertion That Confers Dominant Exonuclease Activity

Klingbeil

Nelson²,

Frost

et al. 2022

Preprint

View full text Add to dashboard Cite

Trypanosoma brucei and related parasites contain an unusual catenated mitochondrial genome known as kinetoplast DNA (kDNA) composed of maxicircles and minicircles. The kDNA structure and replication mechanism are divergent and essential for parasite survival. POLIB is one of three Family A DNA polymerases independently essential to maintain the kDNA network. However, the division of labor among the paralogs, particularly which might fulfill the role of a replicative, proofreading enzyme remains enigmatic. De novo modeling of POLIB revealed a structure divergent from all other Family A polymerases in which the thumb subdomain contains a 369 amino acid insertion with homology to DEDDh DnaQ family 3'-5' exonucleases. Here we demonstrate recombinant POLIB 3'-5' exonuclease prefers DNA vs. RNA substrates and degrades single- and double-stranded DNA in a non processive manner. The exonuclease activity prevails over polymerase activity on DNA substrates at pH 8.0, while DNA primer extension is favored at pH 6.0. Mutations that ablate POLIB polymerase activity slow the exonuclease rate suggesting crosstalk between the domains. We show that POLIB is able to extend an RNA primer more efficiently than a DNA primer in the presence of dNTPs but does not incorporate rNTPs efficiently using either primer. Immunoprecipitation of Pol I-like paralogs from T. brucei corroborate the pH selectivity and RNA primer preferences of POLIB and revealed that the other paralogs efficiently extend a DNA primer. The unique POLIB thumb insertion influences the balance between polymerase and exonuclease activity and provides another example of exquisite diversity among DNA polymerases for specialized function.

show abstract

“…The work by Park et al demonstrates that mitochondrial DNA polymerase gamma is capable of efficiently bypassing a CPD lesion at physiological concentrations of Mn 2+ ( Park et al, 2022 ). This ability is specific to polymerase gamma, not a general property of A-family DNA polymerases, underscoring the diversity of polymerases and emphasizing the role of cellular conditions in regulating activity.…”

mentioning

confidence: 99%