Roles of the Four DNA Polymerases of the Crenarchaeon Sulfolobus solfataricus and Accessory Proteins in DNA Replication

Choi, J.-Y.,Eoff, R.L.,Pence, M.G.,Wang, J.,Martin, M.V.,Kim, E.-J.,Folkmann, L.M.,Guengerich, F.P. The American Society for Biochemistry and Molecula 2011 The Journal of biological chemistry Vol.286 No.36

EXISTENCE UNIQUENESS AND STABILITY OF NONLOCAL NEUTRAL STOCHASTIC DIFFERENTIAL EQUATIONS WITH RANDOM IMPULSES AND POISSON JUMPS

CHALISHAJAR, DIMPLEKUMAR,RAMKUMAR, K.,RAVIKUMAR, K.,COX, EOFF The Korean Society for Computational and Applied M 2022 Journal of applied and pure mathematics Vol.4 No.3/4

This manuscript aims to investigate the existence, uniqueness, and stability of non-local random impulsive neutral stochastic differential time delay equations (NRINSDEs) with Poisson jumps. First, we prove the existence of mild solutions to this equation using the Banach fixed point theorem. Next, we demonstrate the stability via continuous dependence initial value. Our study extends the work of Wang, and Wu [16] where the time delay is addressed by the prescribed phase space 𝓑 (defined in Section 3). To illustrate the theory, we also provide an example of our methods. Using our results, one could investigate the controllability of random impulsive neutral stochastic differential equations with finite/infinite states. Moreover, one could extend this study to analyze the controllability of fractional-order of NRINSDEs with Poisson jumps as well.

Biochemical Analysis of Six Genetic Variants of Error-Prone Human DNA Polymerase ι Involved in Translesion DNA Synthesis

Kim, Jinsook,Song, Insil,Jo, Ara,Shin, Joo-Ho,Cho, Hana,Eoff, Robert L.,Guengerich, F. Peter,Choi, Jeong-Yun American Chemical Society 2014 Chemical research in toxicology Vol.27 No.10

<P/><P>DNA polymerase (pol) ι is the most error-prone among the Y-family polymerases that participate in translesion synthesis (TLS). Pol ι can bypass various DNA lesions, e.g., <I>N</I><SUP>2</SUP>-ethyl(Et)G, <I>O</I><SUP>6</SUP>-methyl(Me)G, 8-oxo-7,8-dihydroguanine (8-oxoG), and an abasic site, though frequently with low fidelity. We assessed the biochemical effects of six reported genetic variations of human pol ι on its TLS properties, using the recombinant pol ι (residues 1–445) proteins and DNA templates containing a G, <I>N</I><SUP>2</SUP>-EtG, <I>O</I><SUP>6</SUP>-MeG, 8-oxoG, or abasic site. The Δ1–25 variant, which is the <I>N</I>-terminal truncation of 25 residues resulting from an initiation codon variant (c.3G > A) and also is the formerly misassigned wild-type, exhibited considerably higher polymerase activity than wild-type with Mg<SUP>2+</SUP> (but not with Mn<SUP>2+</SUP>), coinciding with its steady-state kinetic data showing a ∼10-fold increase in <I>k</I><SUB>cat</SUB>/<I>K</I><SUB>m</SUB> for nucleotide incorporation opposite templates (only with Mg<SUP>2+</SUP>). The R96G variant, which lacks a R96 residue known to interact with the incoming nucleotide, lost much of its polymerase activity, consistent with the kinetic data displaying 5- to 72-fold decreases in <I>k</I><SUB>cat</SUB>/<I>K</I><SUB>m</SUB> for nucleotide incorporation opposite templates either with Mg<SUP>2+</SUP> or Mn<SUP>2+</SUP>, except for that opposite <I>N</I><SUP>2</SUP>-EtG with Mn<SUP>2+</SUP> (showing a 9-fold increase for dCTP incorporation). The Δ1–25 variant bound DNA 20- to 29-fold more tightly than wild-type (with Mg<SUP>2+</SUP>), but the R96G variant bound DNA 2-fold less tightly than wild-type. The DNA-binding affinity of wild-type, but not of the Δ1–25 variant, was ∼7-fold stronger with 0.15 mM Mn<SUP>2+</SUP> than with Mg<SUP>2+</SUP>. The results indicate that the R96G variation severely impairs most of the Mg<SUP>2+</SUP>- and Mn<SUP>2+</SUP>-dependent TLS abilities of pol ι, whereas the Δ1–25 variation selectively and substantially enhances the Mg<SUP>2+</SUP>-dependent TLS capability of pol ι, emphasizing the potential translational importance of these pol ι genetic variations, e.g., individual differences in TLS, mutation, and cancer susceptibility to genotoxic carcinogens.</P>

Human Rev1 polymerase disrupts G-quadruplex DNA

Eddy, Sarah,Ketkar, Amit,Zafar, Maroof K.,Maddukuri, Leena,Choi, Jeong-Yun,Eoff, Robert L. Oxford University Press 2014 Nucleic acids research Vol.42 No.5

<P>The Y-family DNA polymerase Rev1 is required for successful replication of G-quadruplex DNA (G4 DNA) in higher eukaryotes. Here we show that human Rev1 (hRev1) disrupts G4 DNA structures and prevents refolding <I>in vitro</I>. Nucleotidyl transfer by hRev1 is not necessary for mechanical unfolding to occur. hRev1 binds G4 DNA substrates with <I>K</I><SUB>d,DNA</SUB> values that are 4–15-fold lower than those of non-G4 DNA substrates. The pre-steady-state rate constant of deoxycytidine monophosphate (dCMP) insertion opposite the first tetrad-guanine by hRev1 is ∼56% as fast as that observed for non-G4 DNA substrates. Thus, hRev1 can promote fork progression by either dislodging tetrad guanines to unfold the G4 DNA, which could assist in extension by other DNA polymerases, or hRev1 can prevent refolding of G4 DNA structures. The hRev1 mechanism of action against G-quadruplexes helps explain why replication progress is impeded at G4 DNA sites in Rev1-deficient cells and illustrates another unique feature of this enzyme with important implications for genome maintenance.</P>

Effects of Twelve Germline Missense Variations on DNA Lesion and G-Quadruplex Bypass Activities of Human DNA Polymerase REV1

Yeom, Mina,Kim, In-Hyeok,Kim, Jae-Kwon,Kang, KyeongJin,Eoff, Robert L.,Guengerich, F. Peter,Choi, Jeong-Yun American Chemical Society 2016 Chemical research in toxicology Vol.29 No.3

<P>The Y-family DNA polymerase REV1 is involved in replicative bypass of damaged DNA and G-quadruplex (G4) DNA. In addition to a scaffolding role in the replicative bypass, REV1 acts in a catalytic role as a deoxycytidyl transferase opposite some replication stall sites, e.g., apurinic/apyrimidinic (AP) sites, N2-guanyl lesions, and G4 sites. We characterized the biochemical properties of 12 reported germline missense variants of human REV1, including the N373S variant associated with high risk of cervical cancer, using the recombinant REV1 (residues 330-833) proteins and DNA templates containing a G, AP site, N-2-CH2(2-naphthyl)G (N-2-NaphG), or G4. In steady-state kinetic analyses, the F427L, R434Q, M656V, D700N, R704Q, and P831L variants displayed 2- to 8-fold decreases in k(cat)/K-m for dCTP insertion opposite all four templates, compared to that of wild-type, while the N373S, M407L, and N497S showed 2- to 3-fold increases with all four and the former three or two templates, respectively. The F427L, R434Q, M656V, and R704Q variants also had 2- to 3-fold lower binding affinities to DNA substrates containing G, an AP site, and/or N-2-NaphG than wild-type. Distinctively, the N373S variant had a 3-fold higher binding affinity to G4 DNA than the wild-type, as well as a 2-fold higher catalytic activity opposite the first tetrad G, suggesting a facilitating effect of this variation on replication of G4 DNA sequences in certain human papillomavirus genomes. Our results suggest that the catalytic function of REV1 is moderately or slightly altered by at least nine genetic variations, and the G4 DNA processing function of REV1 is slightly enhanced by the N373S variation, which might provide the possibility that certain germline missense REV1 variations affect the individual susceptibility to carcinogenesis by modifying the capability of REV1 for replicative bypass past DNA lesions and G4 motifs derived from chemical and viral carcinogens.</P>

Leukotriene Biosynthesis Inhibitor MK886 Impedes DNA Polymerase Activity

Ketkar, Amit,Zafar, Maroof K.,Maddukuri, Leena,Yamanaka, Kinrin,Banerjee, Surajit,Egli, Martin,Choi, Jeong-Yun,Lloyd, R. Stephen,Eoff, Robert L. American Chemical Society 2013 Chemical research in toxicology Vol.26 No.2

<P>Specialized DNA polymerases participate in replication stress responses and in DNA repair pathways that function as barriers against cellular senescence and genomic instability. These events can be co-opted by tumor cells as a mechanism to survive chemotherapeutic and ionizing radiation treatments and as such, represent potential targets for adjuvant therapies. Previously, a high-throughput screen of ∼16,000 compounds identified several first generation proof-of-principle inhibitors of human DNA polymerase kappa (hpol κ). The indole-derived inhibitor of 5-lipoxygenase activating protein (FLAP), MK886, was one of the most potent inhibitors of hpol κ discovered in that screen. However, the specificity and mechanism of inhibition remained largely undefined. In the current study, the specificity of MK886 against human Y-family DNA polymerases and a model B-family DNA polymerase was investigated. MK886 was found to inhibit the activity of all DNA polymerases tested with similar IC<SUB>50</SUB> values, the exception being a 6- to 8-fold increase in the potency of inhibition against human DNA polymerase iota (hpol ι), a highly error-prone enzyme that uses Hoogsteen base-pairing modes during catalysis. The specificity against hpol ι was partially abrogated by inclusion of the recently annotated 25 a.a. N-terminal extension. On the basis of Michaelis–Menten kinetic analyses and DNA binding assays, the mechanism of inhibition by MK886 appears to be mixed. <I>In silico</I> docking studies were used to produce a series of models for MK886 binding to Y-family members. The docking results indicate that two binding pockets are conserved between Y-family polymerases, while a third pocket near the thumb domain appears to be unique to hpol ι. Overall, these results provide insight into the general mechanism of DNA polymerase inhibition by MK886.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/crtoec/2013/crtoec.2013.26.issue-2/tx300392m/production/images/medium/tx-2012-00392m_0005.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/tx300392m'>ACS Electronic Supporting Info</A></P>