‘PIPs’ in DNA polymerase: PCNA interaction affairs

2020 ◽  
Vol 48 (6) ◽  
pp. 2811-2822
Author(s):  
Narottam Acharya ◽  
Shraddheya Kumar Patel ◽  
Satya Ranjan Sahu ◽  
Premlata Kumari
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Interacting Proteins ◽  
Short Sequence ◽  
Hydrophobic Pocket ◽  
Interaction Sites ◽  
Binding Partners ◽  
Eukaryotic Dna ◽  
Multiple Ligands

Interaction of PCNA with DNA polymerase is vital to efficient and processive DNA synthesis. PCNA being a homotrimeric ring possesses three hydrophobic pockets mostly involved in an interaction with its binding partners. PCNA interacting proteins contain a short sequence of eight amino acids, popularly coined as PIP motif, which snuggly fits into the hydrophobic pocket of PCNA to stabilize the interaction. In the last two decades, several PIP motifs have been mapped or predicted in eukaryotic DNA polymerases. In this review, we summarize our understandings of DNA polymerase-PCNA interaction, the function of such interaction during DNA synthesis, and emphasize the lacunae that persist. Because of the presence of multiple ligands in the replisome complex and due to many interaction sites in DNA polymerases, we also propose two modes of DNA polymerase positioning on PCNA required for DNA synthesis to rationalize the tool-belt model of DNA replication.

Interactions of 1-[(S)-3-Hydroxy-2-(phosphonomethoxy)propyl]cytosine (Cidofovir) Diphosphate with DNA Polymerases α, δ and ε*

2001 ◽  
Vol 66 (11) ◽  
pp. 1698-1706 ◽  
Author(s):  
Gabriel Birkuš ◽  
Ivan Votruba ◽  
Miroslav Otmar ◽  
Antonín Holý
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Competitive Inhibitor ◽  
Dna Polymerase Δ ◽  
Eukaryotic Dna

The inhibitory and/or substrate activity of 1-[(S)-3-hydroxy-2-(phosphonomethoxy)propyl]cytosine [(S)-HPMPC, cidofovir, Vistide™] diphosphate towards eukaryotic DNA polymerases α, δ and ε* was examined. Cidofovir diphosphate is a weak competitive inhibitor of the above enzymes, approximately 3 to 7 times weaker than its adenine analogue (S)-HPMPApp. The enzymes also catalyze incorporation of (S)-HPMPC into DNA; after insertion of one (S)-HPMPC residue into DNA, another dNMP residue may incorporate. DNA polymerase δ and ε* can successively accommodate in the growing chain two (S)-HPMPC residues at the maximum, whereas pol α up to three residues.

scholarly journals Translesion DNA Synthesis Across Lesions Induced by Oxidative Products of Pyrimidines: An Insight into the Mechanism by Microscale Thermophoresis

2019 ◽  
Vol 20 (20) ◽  
pp. 5012 ◽  
Author(s):  
Ondrej Hrabina ◽  
Viktor Brabec ◽  
Olga Novakova
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Dna Duplexes ◽  
Translesion Dna Synthesis ◽  
Processing Enzymes ◽  
Microscale Thermophoresis ◽  
Oxidative Products ◽  
Dna Processing ◽  
Damaged Dna

Oxidative stress in cells can lead to the accumulation of reactive oxygen species and oxidation of DNA precursors. Oxidized nucleotides such as 2’-deoxyribo-5-hydroxyuridin (HdU) and 2’-deoxyribo-5-hydroxymethyluridin (HMdU) can be inserted into DNA during replication and repair. HdU and HMdU have attracted particular interest because they have different effects on damaged-DNA processing enzymes that control the downstream effects of the lesions. Herein, we studied the chemically simulated translesion DNA synthesis (TLS) across the lesions formed by HdU or HMdU using microscale thermophoresis (MST). The thermodynamic changes associated with replication across HdU or HMdU show that the HdU paired with the mismatched deoxyribonucleoside triphosphates disturbs DNA duplexes considerably less than thymidine (dT) or HMdU. Moreover, we also demonstrate that TLS by DNA polymerases across the lesion derived from HdU was markedly less extensive and potentially more mutagenic than that across the lesion formed by HMdU. Thus, DNA polymerization by DNA polymerase η (polη), the exonuclease-deficient Klenow fragment of DNA polymerase I (KF–), and reverse transcriptase from human immunodeficiency virus type 1 (HIV-1 RT) across these pyrimidine lesions correlated with the different stabilization effects of the HdU and HMdU in DNA duplexes revealed by MST. The equilibrium thermodynamic data obtained by MST can explain the influence of the thermodynamic alterations on the ability of DNA polymerases to bypass lesions induced by oxidative products of pyrimidines. The results also highlighted the usefulness of MST in evaluating the impact of oxidative products of pyrimidines on the processing of these lesions by damaged DNA processing enzymes.

scholarly journals Transcriptional Modulator NusA Interacts with Translesion DNA Polymerases in Escherichia coli

2008 ◽  
Vol 191 (2) ◽  
pp. 665-672 ◽  
Author(s):  
Susan E. Cohen ◽  
Veronica G. Godoy ◽  
Graham C. Walker
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Dna Synthesis ◽  
Dna Polymerase ◽  
Temperature Sensitivity ◽  
Dna Polymerases ◽  
Rna Polymerases ◽  
Translesion Dna Synthesis ◽  
Catalytic Activities ◽  
Translesion Dna

ABSTRACT NusA, a modulator of RNA polymerase, interacts with the DNA polymerase DinB. An increased level of expression of dinB or umuDC suppresses the temperature sensitivity of the nusA11 strain, requiring the catalytic activities of these proteins. We propose that NusA recruits translesion DNA synthesis (TLS) polymerases to RNA polymerases stalled at gaps, coupling TLS to transcription.

scholarly journals Palm Mutants in DNA Polymerases α and η Alter DNA Replication Fidelity and Translesion Activity

2004 ◽  
Vol 24 (7) ◽  
pp. 2734-2746 ◽  
Author(s):  
Atsuko Niimi ◽  
Siripan Limsirichaikul ◽  
Shonen Yoshida ◽  
Shigenori Iwai ◽  
Chikahide Masutani ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Pyrimidine Dimer ◽  
Replication Fidelity ◽  
Dna Polymerase Α ◽  
Replication Errors ◽  
Translesion Dna

ABSTRACT We isolated active mutants in Saccharomyces cerevisiae DNA polymerase α that were associated with a defect in error discrimination. Among them, L868F DNA polymerase α has a spontaneous error frequency of 3 in 100 nucleotides and 570-fold lower replication fidelity than wild-type (WT) polymerase α. In vivo, mutant DNA polymerases confer a mutator phenotype and are synergistic with msh2 or msh6, suggesting that DNA polymerase α-dependent replication errors are recognized and repaired by mismatch repair. In vitro, L868F DNA polymerase α catalyzes efficient bypass of a cis-syn cyclobutane pyrimidine dimer, extending the 3′ T 26,000-fold more efficiently than the WT. Phe34 is equivalent to residue Leu868 in translesion DNA polymerase η, and the F34L mutant of S. cerevisiae DNA polymerase η has reduced translesion DNA synthesis activity in vitro. These data suggest that high-fidelity DNA synthesis by DNA polymerase α is required for genomic stability in yeast. The data also suggest that the phenylalanine and leucine residues in translesion and replicative DNA polymerases, respectively, might have played a role in the functional evolution of these enzyme classes.

scholarly journals A sulphoquinovosyl diacylglycerol is a DNA polymerase epsilon inhibitor

2003 ◽  
Vol 370 (1) ◽  
pp. 299-305 ◽  
Author(s):  
Yoshiyuki MIZUSHINA ◽  
Xianai XU ◽  
Hitomi ASAHARA ◽  
Ryo TAKEUCHI ◽  
Masahiko OSHIGE ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Specific Inhibitor ◽  
Immunosuppressive Agent ◽  
Biochemical Properties ◽  
Selective Inhibitor ◽  
Dna Polymerase Epsilon ◽  
Eukaryotic Dna ◽  
Polymerase Epsilon

Sulphoquinovosyl diacylglycerol (SQDG) was reported as a selective inhibitor of eukaryotic DNA polymerases α and β [Hanashima, Mizushina, Ohta, Yamazaki, Sugawara and Sakaguchi (2000) Jpn. J. Cancer Res. 91, 1073—1083] and an immunosuppressive agent [Matsumoto, Sahara, Fujita, Shimozawa, Takenouchi, Torigoe, Hanashima, Yamazaki, Takahashi, Sugawara et al. (2002) Transplantation 74, 261—267]. The purpose of this paper is to elucidate the biochemical properties of the inhibition more precisely. As expected, SQDG could inhibit the activities of mammalian DNA polymerases such as α, Δ, η and κ in vitro in the range of 2—5μM, and β and λ in vitro in the range of 20—45μM. However, SQDG could inhibit only mammalian DNA polymerases ∊ (pol ∊) activity at less than 0.04μM. SQDG bound more tightly to mammalian pol ∊ than the other mammalian polymerases tested. Moreover, SQDG could inhibit the activities of all the polymerases from animals such as fish and insect, but not of the polymerases from plant and prokaryotes. SQDG should, therefore, be called a mammalian pol ∊-specific inhibitor or animal polymerase-specific inhibitor. To our knowledge, this represents the first report about an inhibitor specific to mammalian pol ∊.

scholarly journals Involvement of the essential yeast DNA polymerases in induced gene conversion.

1999 ◽  
Vol 46 (4) ◽  
pp. 862-872 ◽  
Author(s):  
A Hałas ◽  
A Ciesielski ◽  
J Zuk
Keyword(s):  
Dna Synthesis ◽  
Gene Conversion ◽  
Dna Polymerase ◽  
Dna Polymerases ◽  
Yeast Saccharomyces Cerevisiae ◽  
Dna Polymerase Alpha ◽  
Genes Encoding ◽  
Mitotic Gene Conversion ◽  
Dna Strand

In the yeast Saccharomyces cerevisiae three different DNA polymerases alpha, delta and epsilon are involved in DNA replication. DNA polymerase alpha is responsible for initiation of DNA synthesis and polymerases delta and epsilon are required for elongation of DNA strand during replication. DNA polymerases delta and epsilon are also involved in DNA repair. In this work we studied the role of these three DNA polymerases in the process of recombinational synthesis. Using thermo-sensitive heteroallelic mutants in genes encoding DNA polymerases we studied their role in the process of induced gene conversion. Mutant strains were treated with mutagens, incubated under permissive or restrictive conditions and the numbers of convertants obtained were compared. A very high difference in the number of convertants between restrictive and permissive conditions was observed for polymerases alpha and delta, which suggests that these two polymerases play an important role in DNA synthesis during mitotic gene conversion. Marginal dependence of gene conversion on the activity of polymerase epsilon indicates that this DNA polymerase may be involved in this process but rather as an auxiliary enzyme.

scholarly journals Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently

2017 ◽  
Vol 37 (21) ◽  
Author(s):  
Chuanhe Yu ◽  
Haiyun Gan ◽  
Zhiguo Zhang
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Genome Duplication ◽  
Dna Polymerases ◽  
Distinct Pattern ◽  
Replication Forks ◽  
Okazaki Fragments ◽  
Dna Replication Stress ◽  
Leading Strand ◽  
Stalled Replication Forks

ABSTRACT Three DNA polymerases, polymerases α, δ, and ε (Pol α, Pol δ, and Pol ε), are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has a distinct pattern of association with active and stalled replication forks. Pol α is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol δ contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol ε has greater contact with the nascent single-stranded DNA (ssDNA) of the leading strand on active forks than on stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitates the resumption of DNA synthesis after stress removal.

scholarly journals Biochemical aspects of cardiac muscle differentiation. Determination of deoxyribonucleic acid template availability and 3′-hydroxyl termini in nuclei and chromatin by using exogenous deoxyribonucleic acid polymerases

1978 ◽  
Vol 171 (2) ◽  
pp. 289-298 ◽  
Author(s):  
William C. Claycomb
Keyword(s):  
Dna Synthesis ◽  
Cardiac Muscle ◽  
Dna Polymerase ◽  
Deoxyribonucleic Acid ◽  
Dna Polymerases ◽  
Dna Polymerase Α ◽  
Dna Template ◽  
Hydroxyl Termini ◽  
Density Shift

Experiments were designed to determine whether DNA synthesis ceases in terminally differentiating cardiac muscle of the rat because the activity of the putative replicative DNA polymerase (DNA polymerase α) is lost or whether the activity of this enzyme is lost because DNA synthesis ceases. DNA-template availability and 3′-hydroxyl termini in nuclei and chromatin, isolated from cardiac muscle at various times during the developmental period in which DNA synthesis and the activity of DNA polymerase α are decreasing, were measured by using Escherichia coli DNA polymerase I, Micrococcus luteus DNA polymerase and DNA polymerase α under optimal conditions. Density-shift experiments with bromodeoxyuridine triphosphate and isopycnic analysis indicate that DNA chains being replicated semi-conservatively in vivo continue to be elongated in isolated nuclei by exogenous DNA polymerases. DNA template and 3′-hydroxyl termini available to exogenously added DNA polymerases do not change as cardiac muscle differentiates and the rate of DNA synthesis decreases and ceases in vivo. Template availability and 3′-hydroxyl termini are also not changed in nuclei isolated from cardiac muscle in which DNA synthesis had been inhibited by administration of isoproterenol and theophylline to newborn rats. DNA-template availability and 3′-hydroxyl termini, however, were substantially increased in nuclei and chromatin from cardiac muscle of adult rats. This increase is not due to elevated deoxyribonuclease activity in nuclei and chromatin of the adult. Electron microscopy indicates that this increase is also not due to dispersal of the chromatin or disruption of nuclear morphology. Density-shift experiments and isopycnic analysis of DNA from cardiac muscle of the adult show that it is more fragmented than DNA from cardiac-muscle cells that are, or have recently ceased, dividing. These studies indicate that DNA synthesis ceases in terminally differentiating cardiac muscle because the activity of a replicative DNA polymerase is lost, rather than the activity of this enzyme being lost because DNA synthesis ceases.

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