scholarly journals Noncanonical DNA polymerization by aminoadenine-based siphoviruses

Science ◽  
2021 ◽  
Vol 372 (6541) ◽  
pp. 520-524
Author(s):  
Valerie Pezo ◽  
Faten Jaziri ◽  
Pierre-Yves Bourguignon ◽  
Dominique Louis ◽  
Deborah Jacobs-Sera ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Life Forms ◽  
Chemical Diversity ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
Dna Viruses ◽  
Bacterial Dna ◽  
Dna Polymerization ◽  
Deoxynucleoside Triphosphate ◽  
Polymerase I

Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3′-exonuclease but lacks 5′-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.

scholarly journals Synthetic Nucleotides as Probes of DNA Polymerase Specificity

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Jason M. Walsh ◽  
Penny J. Beuning
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Polymerase Activity ◽  
Chemical Diversity ◽  
Dna Polymerase I ◽  
Mutagenic Potential ◽  
Natural Agents ◽  
Polymerase I ◽  
Y Family ◽  
Insight Into

The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example,Escherichia coliDNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides.

scholarly journals Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa

Pathogens ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 257 ◽  
Author(s):  
Ryo Harada ◽  
Yoshihisa Hirakawa ◽  
Akinori Yabuki ◽  
Yuichiro Kashiyama ◽  
Moe Maruyama ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Dna Polymerase I ◽  
Bacterial Dna ◽  
Polymerase Gamma ◽  
Origin And Evolution ◽  
Dna Polymerase Gamma ◽  
Unique Biology ◽  
Organellar Dna ◽  
Polymerase I

The order Trypanosomatida has been well studied due to its pathogenicity and the unique biology of the mitochondrion. In Trypanosoma brucei, four DNA polymerases, namely PolIA, PolIB, PolIC, and PolID, related to bacterial DNA polymerase I (PolI), were shown to be localized in mitochondria experimentally. These mitochondrion-localized DNA polymerases are phylogenetically distinct from other family A DNA polymerases, such as bacterial PolI, DNA polymerase gamma (Polγ) in human and yeasts, “plant and protist organellar DNA polymerase (POP)” in diverse eukaryotes. However, the diversity of mitochondrion-localized DNA polymerases in Euglenozoa other than Trypanosomatida is poorly understood. In this study, we discovered putative mitochondrion-localized DNA polymerases in broad members of three major classes of Euglenozoa—Kinetoplastea, Diplonemea, and Euglenida—to explore the origin and evolution of trypanosomatid PolIA-D. We unveiled distinct inventories of mitochondrion-localized DNA polymerases in the three classes: (1) PolIA is ubiquitous across the three euglenozoan classes, (2) PolIB, C, and D are restricted in kinetoplastids, (3) new types of mitochondrion-localized DNA polymerases were identified in a prokinetoplastid and diplonemids, and (4) evolutionarily distinct types of POP were found in euglenids. We finally propose scenarios to explain the inventories of mitochondrion-localized DNA polymerases in Kinetoplastea, Diplonemea, and Euglenida.

Uracil Glycol Deoxynucleoside Triphosphate Is a Better Substrate for DNA Polymerase I Klenow Fragment Than Thymine Glycol Deoxynucleoside Triphosphate†

Biochemistry ◽  
1998 ◽  
Vol 37 (1) ◽  
pp. 330-338 ◽  
Author(s):  
Andrei A. Purmal ◽  
Jeffrey P. Bond ◽  
Barbara A. Lyons ◽  
Yoke Wah Kow ◽  
Susan S. Wallace
Keyword(s):  
Dna Polymerase ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
Thymine Glycol ◽  
Deoxynucleoside Triphosphate ◽  
Polymerase I

scholarly journals Processive Incorporation of Deoxynucleoside Triphosphate Analogs by Single-Molecule DNA Polymerase I (Klenow Fragment) Nanocircuits

2015 ◽  
Vol 137 (30) ◽  
pp. 9587-9594 ◽  
Author(s):  
Kaitlin M. Pugliese ◽  
O. Tolga Gul ◽  
Yongki Choi ◽  
Tivoli J. Olsen ◽  
Patrick C. Sims ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Single Molecule ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
Deoxynucleoside Triphosphate ◽  
Polymerase I

scholarly journals Crystallization and preliminary X-ray analysis of thePlasmodium falciparumapicoplast DNA polymerase

2015 ◽  
Vol 71 (3) ◽  
pp. 333-337 ◽  
Author(s):  
Morgan E. Milton ◽  
Jun-yong Choe ◽  
Richard B. Honzatko ◽  
Scott W. Nelson
Keyword(s):  
Dna Polymerase ◽  
Structural Information ◽  
Klenow Fragment ◽  
X Ray Diffraction ◽  
Dna Polymerase I ◽  
X Ray ◽  
Cell Parameters ◽  
A Genome ◽  
Reported Data ◽  
Polymerase I

Infection by the parasitePlasmodium falciparumis the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment ofEscherichia coliDNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals ofP. falciparumapPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space groupP6522 (unit-cell parametersa=b= 141.8,c= 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress.

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