Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination

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.

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Visualize Dynamics of Chromosome Structure Formation and DNA Repair/Recombination Coupled With DNA Replication: Tight Coupled Role of DNA Replication in Chromosome Compaction and DNA Recombination

Fundamental Aspects of DNA Replication ◽

10.5772/19131 ◽

2011 ◽

Author(s):

Eisuke Gotoh

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Structure Formation ◽

Chromosome Structure ◽

Dna Recombination

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Plant DNA Polymerases

International Journal of Molecular Sciences ◽

10.3390/ijms20194814 ◽

2019 ◽

Vol 20 (19) ◽

pp. 4814 ◽

Cited By ~ 4

Author(s):

Jose-Antonio Pedroza-Garcia ◽

Lieven De Veylder ◽

Cécile Raynaud

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Dna Sequences ◽

Nuclear Dna ◽

Protein Complexes ◽

Dna Polymerases ◽

Variable Number ◽

Dna Lesions ◽

Plant Dna ◽

Organellar Dna

Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.

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When DNA Polymerases Multitask: Functions Beyond Nucleotidyl Transfer

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.815845 ◽

2022 ◽

Vol 8 ◽

Author(s):

Denisse Carvajal-Maldonado ◽

Lea Drogalis Beckham ◽

Richard D. Wood ◽

Sylvie Doublié

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Dna Synthesis ◽

Extracurricular Activities ◽

Damage Tolerance ◽

Dna Polymerases ◽

Translesion Dna Synthesis ◽

Dna Strands ◽

Translesion Dna ◽

Central Reaction

DNA polymerases catalyze nucleotidyl transfer, the central reaction in synthesis of DNA polynucleotide chains. They function not only in DNA replication, but also in diverse aspects of DNA repair and recombination. Some DNA polymerases can perform translesion DNA synthesis, facilitating damage tolerance and leading to mutagenesis. In addition to these functions, many DNA polymerases conduct biochemically distinct reactions. This review presents examples of DNA polymerases that carry out nuclease (3ʹ—5′ exonuclease, 5′ nuclease, or end-trimming nuclease) or lyase (5′ dRP lyase) extracurricular activities. The discussion underscores how DNA polymerases have a remarkable ability to manipulate DNA strands, sometimes involving relatively large intramolecular movement.

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Eukaryotic DNA polymerases in DNA replication and DNA repair

Chromosoma ◽

10.1007/s004120050300 ◽

1998 ◽

Vol 107 (4) ◽

pp. 218-227 ◽

Cited By ~ 125

Author(s):

Peter M. J. Burgers

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Dna Polymerases ◽

Eukaryotic Dna

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Archaeal DNA polymerases: new frontiers in DNA replication and repair

Emerging Topics in Life Sciences ◽

10.1042/etls20180015 ◽

2018 ◽

Vol 2 (4) ◽

pp. 503-516 ◽

Cited By ~ 1

Author(s):

Christopher D.O. Cooper

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Dna Polymerase ◽

Dna Polymerases ◽

Dna Amplification ◽

Model Systems ◽

Genome Replication ◽

Sequencing Technologies ◽

Dna Replication And Repair ◽

Polymerase Chain

Archaeal DNA polymerases have long been studied due to their superior properties for DNA amplification in the polymerase chain reaction and DNA sequencing technologies. However, a full comprehension of their functions, recruitment and regulation as part of the replisome during genome replication and DNA repair lags behind well-established bacterial and eukaryotic model systems. The archaea are evolutionarily very broad, but many studies in the major model systems of both Crenarchaeota and Euryarchaeota are starting to yield significant increases in understanding of the functions of DNA polymerases in the respective phyla. Recent advances in biochemical approaches and in archaeal genetic models allowing knockout and epitope tagging have led to significant increases in our understanding, including DNA polymerase roles in Okazaki fragment maturation on the lagging strand, towards reconstitution of the replisome itself. Furthermore, poorly characterised DNA polymerase paralogues are finding roles in DNA repair and CRISPR immunity. This review attempts to provide a current update on the roles of archaeal DNA polymerases in both DNA replication and repair, addressing significant questions that remain for this field.

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Bacteriophage-Encoded DNA Polymerases—Beyond the Traditional View of Polymerase Activities

International Journal of Molecular Sciences ◽

10.3390/ijms23020635 ◽

2022 ◽

Vol 23 (2) ◽

pp. 635

Author(s):

Joanna Morcinek-Orłowska ◽

Karolina Zdrojewska ◽

Alicja Węgrzyn

Keyword(s):

Dna Repair ◽

Dna Replication ◽

Genetic Engineering ◽

Dna Synthesis ◽

Genetic Recombination ◽

Dna Polymerases ◽

Traditional View ◽

Even Start ◽

Viral Dna ◽

Viral Dna Replication

DNA polymerases are enzymes capable of synthesizing DNA. They are involved in replication of genomes of all cellular organisms as well as in processes of DNA repair and genetic recombination. However, DNA polymerases can also be encoded by viruses, including bacteriophages, and such enzymes are involved in viral DNA replication. DNA synthesizing enzymes are grouped in several families according to their structures and functions. Nevertheless, there are examples of bacteriophage-encoded DNA polymerases which are significantly different from other known enzymes capable of catalyzing synthesis of DNA. These differences are both structural and functional, indicating a huge biodiversity of bacteriophages and specific properties of their enzymes which had to evolve under certain conditions, selecting unusual properties of the enzymes which are nonetheless crucial for survival of these viruses, propagating as special kinds of obligatory parasites. In this review, we present a brief overview on DNA polymerases, and then we discuss unusual properties of different bacteriophage-encoded enzymes, such as those able to initiate DNA synthesis using the protein-priming mechanisms or even start this process without any primer, as well as able to incorporate untypical nucleotides. Apart from being extremely interesting examples of biochemical biodiversity, bacteriophage-encoded DNA polymerases can also be useful tools in genetic engineering and biotechnology.

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PrimPol (Primase/Polymerase), replicating enzyme – A mini review

Pak-Euro Journal of Medical and Life Sciences ◽

10.31580/pjmls.v2i4.956 ◽

2020 ◽

Vol 2 (4) ◽

pp. 89-92

Author(s):

Muhammad Amir ◽

Sabeera Afzal ◽

Alia Ishaq

Keyword(s):

Dna Replication ◽

Dna Polymerase ◽

Genetic Information ◽

Nuclear Dna ◽

De Novo ◽

Dna Polymerases ◽

Test Site ◽

Mitochondrial Dna Replication ◽

Dna Template ◽

Preliminary Phase

Polymerases were revealed first in 1970s. Most important to the modest perception the enzyme responsible for nuclear DNA replication that was pol , for DNA repair pol and for mitochondrial DNA replication pol DNA construction and renovation done by DNA polymerases, so directing both the constancy and discrepancy of genetic information. Replication of genome initiate with DNA template-dependent fusion of small primers of RNA. This preliminary phase in replication of DNA demarcated as de novo primer synthesis which is catalyzed by specified polymerases known as primases. Sixteen diverse DNA-synthesizing enzymes about human perspective are devoted to replication, reparation, mutilation lenience, and inconsistency of nuclear DNA. But in dissimilarity, merely one DNA polymerase has been called in mitochondria. It has been suggest that PrimPol is extremely acting the roles by re-priming DNA replication in mitochondria to permit an effective and appropriate way replication to be accomplished. Investigations from a numeral of test site have significantly amplified our appreciative of the role, recruitment and regulation of the enzyme during DNA replication. Though, we are simply just start to increase in value the versatile roles that play PrimPol in eukaryote.

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3′ → 5′ Exonucleases of DNA Polymerases ϵ and δ Correct Base Analog Induced DNA Replication Errors on Opposite DNA Strands in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/142.3.717 ◽

1996 ◽

Vol 142 (3) ◽

pp. 717-726 ◽

Cited By ~ 11

Author(s):

Polina V Shcherbakova ◽

Youri I Pavlov

Keyword(s):

Dna Replication ◽

Dna Polymerases ◽

Replication Errors ◽

Dna Strands ◽

Base Analog ◽

Chromosome Iii ◽

Dna Strand ◽

Dna Replication Errors ◽

Yeast Mutants ◽

Lagging Strand

Abstract The base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC → AT and AT → GC transitions that are enhanced in DNA polymerase ϵ and δ 3′ → 5′ exonuclease-deficient yeast mutants, pol2-4 and pol3-01, respectively. We have constructed a set of isogenic strains to determine whether the DNA polymerases δ and ϵ contribute equally to proofreading of replication errors provoked by HAP during leading and lagging strand DNA synthesis. Site-specific GC → AT and AT → GC transitions in a Pol→, pol2-4 or pol3-01 genetic background were scored as reversions of ura3 missense alleles. At each site, reversion was increased in only one proofreading-deficient mutant, either pol2-4 or pol3-01, depending on the DNA strand in which HAP incorporation presumably occurred. Measurement of the HAP-induced reversion frequency of the ura3 alleles placed into chromosome III near to the defined active replication origin ARS306 in two orientations indicated that DNA polymerases ϵ and δ correct HAP-induced DNA replication errors on opposite DNA strands.

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