scholarly journals Plant organellar DNA polymerases bypass thymine glycol using two conserved lysine residues

2020 ◽  
Vol 477 (5) ◽  
pp. 1049-1059 ◽  
Author(s):  
Noe Baruch-Torres ◽  
Junpei Yamamoto ◽  
Víctor Juárez-Quintero ◽  
Shigenori Iwai ◽  
Luis G. Brieba
Keyword(s):  
Structural Model ◽  
Dna Polymerases ◽  
Lesion Bypass ◽  
Thymine Glycol ◽  
Abasic Sites ◽  
Organellar Dna ◽  
Lysine Residues ◽  
Exogenous Agents ◽  
Replicative Polymerases ◽  
Bacterial Replication

Plant organelles cope with endogenous DNA damaging agents, byproducts of respiration and photosynthesis, and exogenous agents like ultraviolet light. Plant organellar DNA polymerases (DNAPs) are not phylogenetically related to yeast and metazoan DNAPs and they harbor three insertions not present in any other DNAPs. Plant organellar DNAPs from Arabidopsis thaliana (AtPolIA and AtPolIB) are translesion synthesis (TLS) DNAPs able to bypass abasic sites, a lesion that poses a strong block to replicative polymerases. Besides abasic sites, reactive oxidative species and ionizing radiation react with thymine resulting in thymine glycol (Tg), a DNA adduct that is also a strong block to replication. Here, we report that AtPolIA and AtPolIB bypass Tg by inserting an adenine opposite the lesion and efficiently extend from a Tg-A base pair. The TLS ability of AtPolIB is mapped to two conserved lysine residues: K593 and K866. Residue K593 is situated in insertion 1 and K866 is in insertion 3. With basis on the location of both insertions on a structural model of AtPolIIB, we hypothesize that the two positively charged residues interact to form a clamp around the primer-template. In contrast with nuclear and bacterial replication, where lesion bypass involves an interplay between TLS and replicative DNA polymerases, we postulate that plant organellar DNAPs evolved to exert replicative and TLS activities.

scholarly journals Enzymatic Switching Between Archaeal DNA Polymerases Facilitates Abasic Site Bypass

2021 ◽  
Vol 12 ◽  
Author(s):  
Xu Feng ◽  
Baochang Zhang ◽  
Ruyi Xu ◽  
Zhe Gao ◽  
Xiaotong Liu ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Enzyme Kinetics ◽  
Dna Polymerases ◽  
Dna Lesions ◽  
Abasic Site ◽  
Lesion Bypass ◽  
Translesion Dna Synthesis ◽  
Kinetics Studies ◽  
Abasic Sites ◽  
Y Family

Abasic sites are among the most abundant DNA lesions encountered by cells. Their replication requires actions of specialized DNA polymerases. Herein, two archaeal specialized DNA polymerases were examined for their capability to perform translesion DNA synthesis (TLS) on the lesion, including Sulfolobuss islandicus Dpo2 of B-family, and Dpo4 of Y-family. We found neither Dpo2 nor Dpo4 is efficient to complete abasic sites bypass alone, but their sequential actions promote lesion bypass. Enzyme kinetics studies further revealed that the Dpo4’s activity is significantly inhibited at +1 to +3 site past the lesion, at which Dpo2 efficiently extends the primer termini. Furthermore, their activities are inhibited upon synthesis of 5–6 nt TLS patches. Once handed over to Dpo1, these substrates basically inactivate its exonuclease, enabling the transition from proofreading to polymerization of the replicase. Collectively, by functioning as an “extender” to catalyze further DNA synthesis past the lesion, Dpo2 bridges the activity gap between Dpo4 and Dpo1 in the archaeal TLS process, thus achieving more efficient lesion bypass.

scholarly journals Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism

2018 ◽  
Vol 87 (1) ◽  
pp. 239-261 ◽  
Author(s):  
Wei Yang ◽  
Yang Gao
Keyword(s):  
Genome Stability ◽  
Dna Polymerases ◽  
Error Rates ◽  
Dna Lesions ◽  
End Joining ◽  
Lesion Bypass ◽  
Replicative Polymerases ◽  
And Function ◽  
Dna Ends ◽  
Intrinsic Error

The number of DNA polymerases identified in each organism has mushroomed in the past two decades. Most newly found DNA polymerases specialize in translesion synthesis and DNA repair instead of replication. Although intrinsic error rates are higher for translesion and repair polymerases than for replicative polymerases, the specialized polymerases increase genome stability and reduce tumorigenesis. Reflecting the numerous types of DNA lesions and variations of broken DNA ends, translesion and repair polymerases differ in structure, mechanism, and function. Here, we review the unique and general features of polymerases specialized in lesion bypass, as well as in gap-filling and end-joining synthesis.

scholarly journals Arabidopsis thaliana PrimPol is a primase and lesion bypass DNA polymerase with the biochemical characteristics to cope with DNA damage in the nucleus, mitochondria, and chloroplast

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paola L. García-Medel ◽  
Antolín Peralta-Castro ◽  
Noe Baruch-Torres ◽  
Alma Fuentes-Pascacio ◽  
José A. Pedroza-García ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Polymerase ◽  
De Novo ◽  
Dna Lesions ◽  
Lesion Bypass ◽  
Exogenous Dna ◽  
Thymine Glycol ◽  
Abasic Sites ◽  
Dna Primers

AbstractPrimPol is a novel Primase–Polymerase that synthesizes RNA and DNA primers de novo and extents from these primers as a DNA polymerase. Animal PrimPol is involved in nuclear and mitochondrial DNA replication by virtue of its translesion DNA synthesis (TLS) and repriming activities. Here we report that the plant model Arabidopsis thaliana encodes a functional PrimPol (AtPrimPol). AtPrimPol is a low fidelity and a TLS polymerase capable to bypass DNA lesions, like thymine glycol and abasic sites, by incorporating directly across these lesions or by skipping them. AtPrimPol is also an efficient primase that preferentially recognizes the single-stranded 3′-GTCG-5′ DNA sequence, where the 3′-G is cryptic. AtPrimPol is the first DNA polymerase that localizes in three cellular compartments: nucleus, mitochondria, and chloroplast. In vitro, AtPrimPol synthesizes primers that are extended by the plant organellar DNA polymerases and this reaction is regulated by organellar single-stranded binding proteins. Given the constant exposure of plants to endogenous and exogenous DNA-damaging agents and the enzymatic capabilities of lesion bypass and re-priming of AtPrimPol, we postulate a predominant role of this enzyme in avoiding replication fork collapse in all three plant genomes, both as a primase and as a TLS polymerase.

scholarly journals Plant organellar DNA polymerases paralogs exhibit dissimilar nucleotide incorporation fidelity

FEBS Journal ◽  
2018 ◽  
Vol 285 (21) ◽  
pp. 4005-4018 ◽  
Author(s):  
Víctor M. Ayala‐García ◽  
Noe Baruch‐Torres ◽  
Paola L. García‐Medel ◽  
Luis G. Brieba
Keyword(s):  
Dna Polymerases ◽  
Nucleotide Incorporation ◽  
Organellar Dna

scholarly journals Plant Organellar DNA Polymerases Evolved Multifunctionality through the Acquisition of Novel Amino Acid Insertions

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1370
Author(s):  
Antolín Peralta-Castro ◽  
Paola L. García-Medel ◽  
Noe Baruch-Torres ◽  
Carlos H. Trasviña-Arenas ◽  
Víctor Juarez-Quintero ◽  
...  
Keyword(s):  
Dna Repair ◽  
Amino Acid ◽  
Dna Replication ◽  
Excision Repair ◽  
Dna Polymerases ◽  
Strand Displacement ◽  
End Joining ◽  
Apparent Contradiction ◽  
Organellar Dna ◽  
Base Excision

The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS DNAPs. Furthermore, plant organellar DNA polymerases from the plant model Arabidopsis thaliana (AtPOLIs) execute repair of double-stranded breaks by microhomology-mediated end-joining and perform Base Excision Repair (BER) using lyase and strand-displacement activities. AtPOLIs harbor three unique insertions in their polymerization domain that are associated with TLS, microhomology-mediated end-joining (MMEJ), strand-displacement, and lyase activities. We postulate that AtPOLIs are able to execute those different functions through the acquisition of these novel amino acid insertions, making them multifunctional enzymes able to participate in DNA replication and DNA repair.

scholarly journals Plant organellar DNA primase-helicase synthesizes RNA primers for organellar DNA polymerases using a unique recognition sequence

2017 ◽  
Vol 45 (18) ◽  
pp. 10764-10774 ◽  
Author(s):  
Antolín Peralta-Castro ◽  
Noe Baruch-Torres ◽  
Luis G. Brieba
Keyword(s):  
Dna Polymerases ◽  
Recognition Sequence ◽  
Dna Primase ◽  
Organellar Dna

scholarly journals Efficient and Error-Free Replication past a Minor-Groove N2-Guanine Adduct by the Sequential Action of Yeast Rev1 and DNA Polymerase ζ

2004 ◽  
Vol 24 (16) ◽  
pp. 6900-6906 ◽  
Author(s):  
M. Todd Washington ◽  
Irina G. Minko ◽  
Robert E. Johnson ◽  
Lajos Haracska ◽  
Thomas M. Harris ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Close Contact ◽  
Dna Polymerases ◽  
Minor Groove ◽  
Synthetic Activity ◽  
Oxidation Reactions ◽  
Lesion Bypass ◽  
Dna Minor Groove

ABSTRACT Rev1, a member of the Y family of DNA polymerases, functions in lesion bypass together with DNA polymerase ζ (Polζ). Rev1 is a highly specialized enzyme in that it incorporates only a C opposite template G. While Rev1 plays an indispensable structural role in Polζ-dependent lesion bypass, the role of its DNA synthetic activity in lesion bypass has remained unclear. Since interactions of DNA polymerases with the DNA minor groove contribute to the nearly equivalent efficiencies and fidelities of nucleotide incorporation opposite each of the four template bases, here we examine the possibility that unlike other DNA polymerases, Rev1 does not come into close contact with the minor groove of the incipient base pair, and that enables it to incorporate a C opposite the N 2-adducted guanines in DNA. To test this idea, we examined whether Rev1 could incorporate a C opposite the γ-hydroxy-1,N 2-propano-2′deoxyguanosine DNA minor-groove adduct, which is formed from the reaction of acrolein with the N 2 of guanine. Acrolein, an α,β-unsaturated aldehyde, is generated in vivo as the end product of lipid peroxidation and from other oxidation reactions. We show here that Rev1 efficiently incorporates a C opposite this adduct from which Polζ subsequently extends, thereby completing the lesion bypass reaction. Based upon these observations, we suggest that an important role of the Rev1 DNA synthetic activity in lesion bypass is to incorporate a C opposite the various N 2-guanine DNA minor-groove adducts that form in DNA.

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