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y-family polymerase

Eunjeong Lee, Jason D Fowler, Zucai Suo, Zhengrong Wu
Sulfolobus solfataricus DNA polymerase IV (Dpo4), a model Y-family DNA polymerase, bypasses a wide range of DNA lesions in vitro and in vivo. In this paper, we report the backbone chemical shift assignments of the full length Dpo4 in its binary complex with a 14/14-mer DNA substrate. Upon DNA binding, several β-stranded regions in the isolated catalytic core and little finger/linker fragments of Dpo4 become more structured. This work serves as a foundation for our ongoing investigation of conformational dynamics of Dpo4 and future determination of the first solution structures of a DNA polymerase and its binary and ternary complexes...
October 13, 2016: Biomolecular NMR Assignments
Cigdem Donmez, Ece Konac, Batuhan T Aydogan, Cenk Y Bilen
PURPOSE: To study whether -160 C > A (rs16260) and -347 G > GA (rs5030625) single nucleotide polymorphisms of the regulatory region (rSNPs) of CDH1 gene modulate the risk of nephrolithiasis. METHODS: Genomic DNA of 101 patients with calcium oxalate nephrolithiasis and 114 healthy controls were screened for both polymorphisms, using polymerase chain reaction-restriction fragments length polymorphism method (PCR-RLFP). Haplotype frequencies were also analyzed...
2016: SpringerPlus
Zhuoran Zhang, Enzhuo Yang, Chunmiao Hu, Han Cheng, Crystal Y Chen, Dan Huang, Richard Wang, Yue Zhao, Lijun Rong, Marco Vignuzzi, Hongbo Shen, Ling Shen, Zheng W Chen
While we are approaching the global eradication of circulating wild-type polioviruses(PV), vaccination with oral poliovirus vaccine (OPV) has led to emergence of circulating vaccine-derived poliovirus (cVDPV) and vaccine-associated paralytic poliomyelitis (VAPP). Complete cessation of all poliovirus infections may require stopping use of OPV and formulating improved vaccines and new antiviral drugs. Currently, no licensed drugs are available to treat chronically infected poliovirus excretors. Here, we created a modified PV expressing Gaussia Luciferase (PV-GLuc) and developed a cell-based high-throughput screening (HTS) antiviral assay...
October 12, 2016: ACS Infectious Diseases
S Chen, X C Zhu, Y L Liu, C Wang, K G Zhang
We carried out a hospital-based case-control study to investigate the role of XRCC1 gene Arg399Gln, Arg280His, and Arg194Trp polymorphisms in susceptibility to gastric cancer. A total of 214 gastric cancer patients and 247 control subjects were recruited between March 2013 and March 2015, and polymorphism genotype frequencies were determined by polymerase chain reaction-restriction fragment length polymorphism. Using the chi-square test, we detected statistically significant differences in age (chi-square = 22...
September 9, 2016: Genetics and Molecular Research: GMR
N M A Rahman, H T Fu, S M Sun, H Qiao, S Jin, H K Bai, W Y Zhang, G X Liang, Y S Gong, Y W Xiong, Y Wu
Nitric oxide synthase (NOS) produces nitric oxide (NO) by catalyzing the conversion of l-arginine to l-citrulline, with the concomitant oxidation of nicotinamide adenine dinucleotide phosphate. Recently, various studies have verified the importance of NOS invertebrates and invertebrates. However, the NOS gene family in the oriental river prawn Macrobrachium nipponense is poorly understood. In this study, we cloned the full-length NOS complementary DNA from M. nipponense (MnNOS) and characterized its expression pattern in different tissues and at different developmental stages...
August 29, 2016: Genetics and Molecular Research: GMR
Zhan Zhao, Yadong Xue, Huili Yang, Huimin Li, Gaoyang Sun, Xiaofeng Zhao, Dong Ding, Jihua Tang
Internode length is one of the decisive factors affecting plant height (PH) and ear height (EH), which are closely associated with the lodging resistance, biomass and grain yield of maize. miRNAs, currently recognized as important transcriptional/ post-transcriptional regulators, play an essential role in plant growth and development. However, their roles in developing internodes under maize ears remain unclear. To identify the roles of miRNAs and their targets in the development of internodes under maize ears, six miRNA and two degradome libraries were constructed using the 7th, 8th and 9th internodes of two inbred lines, 'Xun928' and 'Xun9058', which had significantly different internode lengths...
2016: PloS One
Amritaj Patra, Qianqian Zhang, F Peter Guengerich, Martin Egli
O6-Methyl-2(prime)-deoxyguanosine (O6-MeG) is a ubiquitous DNA lesion, formed not only by xenobiotic carcinogens but also by the endogenous methylating agent S-adenosylmethionine. It can introduce mutations during DNA replication, with different DNA polymerases displaying different ratios of correct or incorrect incoporation opposite this nucleoside. Of the "translesion" Y-family human DNA polymerases (hpols), hpol η is most efficient in incorporating equal numbers of correct and incorrect C and T bases. However, the mechanistic basis for this specific yet indescriminate activity is not known...
September 30, 2016: Journal of Biological Chemistry
Austin T Raper, Zucai Suo
DNA polymerases catalyze DNA synthesis through a stepwise kinetic mechanism that begins with binding to DNA, followed by selection, binding, and incorporation of a nucleotide into an elongating primer. It is hypothesized that subtle active site adjustments in a polymerase to align reactive moieties limit the rate of correct nucleotide incorporation. DNA damage can impede this process for many DNA polymerases, causing replication fork stalling, genetic mutations, and potentially cell death. However, specialized Y-family DNA polymerases are structurally evolved to efficiently bypass DNA damage in vivo, albeit at the expense of replication fidelity...
October 10, 2016: Biochemistry
Rajendra Prasad, Vladimir Poltoratsky, Esther W Hou, Samuel H Wilson
Rev1 is a member of the Y-family of DNA polymerases and is known for its deoxycytidyl transferase activity that incorporates dCMP into DNA and its ability to function as a scaffold factor for other Y-family polymerases in translesion bypass events. Rev1 also is involved in mutagenic processes during somatic hypermutation of immunoglobulin genes. In light of the mutation pattern consistent with dCMP insertion observed earlier in mouse fibroblast cells treated with a base excision repair-inducing agent, we questioned whether Rev1 could also be involved in base excision repair (BER)...
September 28, 2016: Nucleic Acids Research
Y Zhang, Y Shi, H Yu, J Li, Y Quan, T Shu, Z Nie, Y Zhang, W Yu
Baculoviridae is a family of invertebrate viruses with large double-stranded DNA genomes. Proteins encoded by some late expression factor (lef ) genes are involved in the regulation of viral gene expression. Lef-9 is one of four transcription-specific Lefs, which are components of the virus-encoded RNA polymerase, and can initiate and transcribe late and very late genes. As a multifunctional protein encoded by the Bombyx mori nucleopolyhedrovirus (BmNPV), Lef-9 may be involved in the regulation of viral propagation...
2016: Acta Virologica
E John Tokarsky, Varun V Gadkari, Walter J Zahurancik, Chanchal K Malik, Ashis K Basu, Zucai Suo
3-Nitrobenzanthrone (3-NBA), a byproduct of diesel exhaust, is highly present in the environment and poses a significant health risk. Exposure to 3-NBA results in formation of N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG(C8-)(N)(-ABA)), a bulky DNA lesion that is of particular importance due to its mutagenic and carcinogenic potential. If not repaired or bypassed during genomic replication, dG(C8-)(N)(-ABA) can stall replication forks, leading to senescence and cell death. Here we used pre-steady-state kinetic methods to determine which of the four human Y-family DNA polymerases (hPolη, hPolκ, hPolι, or hRev1) are able to catalyze translesion synthesis of dG(C8-)(N)(-ABA)in vitro...
October 2016: DNA Repair
Tatiana Kent, Timur D Rusanov, Trung M Hoang, Willem A Velema, Andrew T Krueger, William C Copeland, Eric T Kool, Richard T Pomerantz
DNA polymerase θ (Polθ) is a unique A-family polymerase that is essential for alternative end-joining (alt-EJ) of double-strand breaks (DSBs) and performs translesion synthesis. Because Polθ is highly expressed in cancer cells, confers resistance to ionizing radiation and chemotherapy agents, and promotes the survival of homologous recombination (HR) deficient cells, it represents a promising new cancer drug target. As a result, identifying substrates that are selective for this enzyme is a priority. Here, we demonstrate that Polθ efficiently and selectively incorporates into DNA large benzo-expanded nucleotide analogs (dxAMP, dxGMP, dxTMP, dxAMP) which exhibit canonical base-pairing and enhanced base stacking...
September 2, 2016: Nucleic Acids Research
D K O'Flaherty, A Patra, Y Su, F P Guengerich, M Egli, C J Wilds
DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O (4)-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4-O (4) bond on processing by human DNA polymerase η (hPol η) was studied for oligonucleotides containing O (4)-methylthymidine, O (4)-ethylthymidine, and analogs restricting the O (4)-methylene group in an anti-orientation. Primer extension assays revealed that the O (4)-alkyl orientation influences hPol η bypass...
August 1, 2016: Chemical Science
Amritraj Patra, Dustin A Politica, Arindom Chatterjee, E John Tokarsky, Zucai Suo, Ashis Basu, Michael P Stone, Martin Egli
The environmental pollutant 3-nitrobenzanthrone produces bulky aminobenzanthrone (ABA) DNA adducts with both guanine and adenine nucleobases. A major product occurs at the C8 position of guanine (C8-dG-ABA). These adducts present a strong block to replicative polymerases but, remarkably, can be bypassed in a largely error-free manner by the human Y-family polymerase(hPol ). Here we report the crystal structure of a ternary Pol*DNA*dCTP complex between a C8-dG-ABA containing template: primer duplex and hPol ...
August 24, 2016: Chembiochem: a European Journal of Chemical Biology
Jeong-Yun Choi, Amritaj Patra, Mina Yeom, Young-Sam Lee, Qianqian Zhang, Martin Egli, F Peter Guengerich
DNA polymerase (pol) ι is a Y-family polymerase involved in translesion synthesis, exhibiting higher catalytic activity with Mn(2+) than Mg(2+) The human germline R96G variant impairs both Mn(2+)-dependent and Mg(2+)-dependent activities of pol ι, whereas the Δ1-25 variant selectively enhances its Mg(2+)-dependent activity. We analyzed pre-steady-state kinetic and structural effects of these two metal ions and genetic variations on pol ι using pol ι core (residues 1-445) proteins. The presence of Mn(2+) (0...
September 30, 2016: Journal of Biological Chemistry
Y-S L Cheng, L Jordan, H-S Chen, D Kang, L Oxford, J Plemons, H Parks, T Rees
BACKGROUND AND OBJECTIVE: More than 100 salivary constituents have been found to show levels significantly different in patients with oral squamous cell carcinoma (OSCC) from those found in healthy controls, and therefore have been suggested to be potential salivary biomarkers for OSCC detection. However, many of these potential OSCC salivary biomarkers are also involved in chronic inflammation, and whether the levels of these biomarkers could be affected by the presence of chronic periodontitis was not known...
August 23, 2016: Journal of Periodontal Research
Sarah Eddy, Magdalena Tillman, Leena Maddukuri, Amit Ketkar, Maroof K Zafar, Robert L Eoff
We have investigated the in vitro properties of human Y-family polymerase κ (hpol κ) on G-quadruplex DNA (G4 DNA). Similar to hpol η, another Y-family member implicated in replication of G4 motifs, hpol κ bound G4 DNA with a 5.7-fold preference over control, non-G4 DNA. Results from pol extension assays are consistent with the notion that G-quadruplexes present a stronger barrier to DNA synthesis by hpol κ than they do to that by hpol η. However, kinetic analysis revealed that hpol κ activity increases considerably when the enzyme is 2-3 nucleotides from the G4 motif, a trend that was reported previously for hpol η, though the increase was less pronounced...
September 20, 2016: Biochemistry
Keiji Hashimoto, Radha Bonala, Francis Johnson, Arthur P Grollman, Masaaki Moriya
Translesion DNA synthesis (TLS) operates when replicative polymerases are blocked by DNA lesions. To investigate the mechanism of mammalian TLS, we employed a plasmid bearing a single 7-(deoxyadenosine-N(6)-yl)-aristolactam I (dA-AL-I) adduct, which is generated by the human carcinogen, aristolochic acid I, and genetically engineered mouse embryonic fibroblasts. This lesion induces A to T transversions at a high frequency. The simultaneous knockouts of the Polh, Poli and Polk genes did not influence the TLS efficiency or the coding property of dA-AL-I, indicating that an unknown DNA polymerase(s) can efficiently catalyze the insertion of a nucleotide opposite the adduct and subsequent extension...
October 2016: DNA Repair
Tetsuya Toyono, Tomohiko Usui, Guadalupe Villarreal, Laura Kallay, Mario Matthaei, Lucas M M Vianna, Angela Y Zhu, Masahiko Kuroda, Shiro Amano, Albert S Jun
PURPOSE: MicroRNAs are small noncoding RNAs that regulate gene expression at the posttranscriptional level. We reported that levels of microRNA (miR)-29 family are decreased in corneas of patients with Fuchs endothelial corneal dystrophy (FECD). The miR-29 family regulates the production of extracellular matrix (ECM) proteins. Accumulation of ECM proteins in Descemet membrane is an important pathologic change in FECD. In this study, we transfected miR-29b into human corneal endothelial cells and tissues and evaluated ECM protein expression levels...
November 2016: Cornea
Yicheng Long, Maria G Abad, Erik D Olson, Elisabeth Y Carrillo, Jane E Jackman
The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties...
September 30, 2016: Nucleic Acids Research
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