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 Beyond the Lesion: Back to High Fidelity DNA Synthesis

2022 ◽  
Vol 8 ◽  
Author(s):  
Joseph D. Kaszubowski ◽  
Michael A. Trakselis
Keyword(s):  
Dna Damage ◽  
Dna Synthesis ◽  
Dna Polymerases ◽  
Translesion Synthesis ◽  
Structural Features ◽  
Dna Bases ◽  
High Fidelity ◽  
Nucleotide Incorporation ◽  
Hand Off ◽  
Enzymatic Mechanisms

High fidelity (HiFi) DNA polymerases (Pols) perform the bulk of DNA synthesis required to duplicate genomes in all forms of life. Their structural features, enzymatic mechanisms, and inherent properties are well-described over several decades of research. HiFi Pols are so accurate that they become stalled at sites of DNA damage or lesions that are not one of the four canonical DNA bases. Once stalled, the replisome becomes compromised and vulnerable to further DNA damage. One mechanism to relieve stalling is to recruit a translesion synthesis (TLS) Pol to rapidly synthesize over and past the damage. These TLS Pols have good specificities for the lesion but are less accurate when synthesizing opposite undamaged DNA, and so, mechanisms are needed to limit TLS Pol synthesis and recruit back a HiFi Pol to reestablish the replisome. The overall TLS process can be complicated with several cellular Pols, multifaceted protein contacts, and variable nucleotide incorporation kinetics all contributing to several discrete substitution (or template hand-off) steps. In this review, we highlight the mechanistic differences between distributive equilibrium exchange events and concerted contact-dependent switching by DNA Pols for insertion, extension, and resumption of high-fidelity synthesis beyond the lesion.

scholarly journals Deoxynucleotide Triphosphate Binding Mode Conserved in Y Family DNA Polymerases

2003 ◽  
Vol 23 (8) ◽  
pp. 3008-3012 ◽  
Author(s):  
Robert E. Johnson ◽  
José Trincao ◽  
Aneel K. Aggarwal ◽  
Satya Prakash ◽  
Louise Prakash
Keyword(s):  
Dna Polymerase ◽  
Close Contact ◽  
Dna Polymerases ◽  
Binding Mode ◽  
Nucleotide Incorporation ◽  
The Family ◽  
And Function ◽  
High Degree ◽  
Y Family ◽  
Deoxynucleotide Triphosphate

ABSTRACT Although DNA polymerase η (Polη) and other Y family polymerases differ in sequence and function from classical DNA polymerases, they all share a similar right-handed architecture with the palm, fingers, and thumb domains. Here, we examine the role in Saccharomyces cerevisiae Polη of three conserved residues, tyrosine 64, arginine 67, and lysine 279, which come into close contact with the triphosphate moiety of the incoming nucleotide, in nucleotide incorporation. We find that mutational alteration of these residues reduces the efficiency of correct nucleotide incorporation very considerably. The high degree of conservation of these residues among the various Y family DNA polymerases suggests that these residues are also crucial for nucleotide incorporation in the other members of the family. Furthermore, we note that tyrosine 64 and arginine 67 are functionally equivalent to the deoxynucleotide triphosphate binding residues arginine 518 and histidine 506 in T7 DNA polymerase, respectively.

Conservation of POPs, the Plant Organellar DNA Polymerases, in Eukaryotes

Protist ◽  
2011 ◽  
Vol 162 (1) ◽  
pp. 177-187 ◽  
Author(s):  
Takashi Moriyama ◽  
Kimihiro Terasawa ◽  
Naoki Sato
Keyword(s):  
Dna Polymerases ◽  
Organellar Dna

scholarly journals Plant organellar DNA polymerases repair double-stranded breaks by microhomology-mediated end-joining

2019 ◽  
Vol 47 (6) ◽  
pp. 3028-3044 ◽  
Author(s):  
Paola L García-Medel ◽  
Noe Baruch-Torres ◽  
Antolín Peralta-Castro ◽  
Carlos H Trasviña-Arenas ◽  
Alfredo Torres-Larios ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
End Joining ◽  
Organellar Dna

A Reexamination of the Nucleotide Incorporation Fidelity of DNA Polymerases†

Biochemistry ◽  
2002 ◽  
Vol 41 (34) ◽  
pp. 10571-10576 ◽  
Author(s):  
Alexander K. Showalter ◽  
Ming-Daw Tsai
Keyword(s):  
Dna Polymerases ◽  
Nucleotide Incorporation
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