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y-family polymerase

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https://www.readbyqxmd.com/read/29129138/the-role-of-zn-complex-in-binding-of-transcription-factors-to-operator-dna-mouse%C3%A2-egr-1-from-the-cys2his2-family
#1
Y N Chirgadze, E A Boshkova, R V Polozov, V S Sivozhelezov, A V Dzyabchenko, M B Kuzminsky, V A Stepanenko, V V Ivanov
The mouse factor Zif268, known also as early growth response protein EGR-1, is a classical representative for the Cys2His2 transcription factor family. It is required for binding the RNA polymerase with operator dsDNA to initialize the transcription process. We have shown that only in this family of total six Zn-finger protein families the Zn complex plays a significant role in the protein-DNA binding. Electrostatic feature of this complex in the binding of factor Zif268 from Mus musculus with operator DNA has been considered...
November 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29116069/-participation-of-the-pirna-pathway-in-recruiting-a-component-of-rna-polymerase-i-transcription-initiation-complex-to-germline-cell-nucleoli
#2
E A Fefelova, A D Stolyarenko, E Y Yakushev, V A Gvozdev, M S Klenov
Proteins of the Piwi family and short Piwi-interacting RNAs (piRNAs) ensure the protection of the genome from transposable elements. We have previously shown that nuclear Piwi protein tends to concentrate in the nucleoli of the cells of Drosophila melanogaster ovaries. It could be hypothesized that the function of Piwi in the nucleolus is associated with the repression of R1 and R2 retrotransposons inserted into the rDNA cluster. Here, we show that Piwi participates in recruiting Udd protein to nucleoli. Udd is a component of the conserved Selectivity Factor I-like (SL1-like) complex, which is required for transcription initiation by RNA polymerase I...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29040737/calcium-driven-dna-synthesis-by-a-high-fidelity-dna-polymerase
#3
Céline Ralec, Etienne Henry, Mélanie Lemor, Tom Killelea, Ghislaine Henneke
Divalent metal ions, usually Mg2+, are required for both DNA synthesis and proofreading functions by DNA polymerases (DNA Pol). Although used as a non-reactive cofactor substitute for binding and crystallographic studies, Ca2+ supports DNA polymerization by only one DNA Pol, Dpo4. Here, we explore whether Ca2+-driven catalysis might apply to high-fidelity (HiFi) family B DNA Pols. The consequences of replacing Mg2+ by Ca2+ on base pairing at the polymerase active site as well as the editing of terminal nucleotides at the exonuclease active site of the archaeal Pyrococcus abyssi DNA Pol (PabPolB) are characterized and compared to other (families B, A, Y, X, D) DNA Pols...
October 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28978678/pufa-status-and-methylmercury-exposure-are-not-associated-with-leukocyte-telomere-length-in-mothers-or-their-children-in-the-seychelles-child-development-study
#4
Alison J Yeates, Sally W Thurston, Huiqi Li, Maria S Mulhern, Emeir M McSorley, Gene E Watson, Conrad F Shamlaye, J J Strain, Gary J Myers, Philip W Davidson, Edwin van Wijngaarden, Karin Broberg
Background: Leukocyte telomere length (TL) is associated with age-related diseases and early mortality, but there is a lack of data on the determinants of TL in early life. Evidence suggests that dietary intake of marine n-3 (ω-3) polyunsaturated fatty acids (PUFAs) is protective of telomere attrition, yet the effect of methylmercury exposure, also found in fish, on TL is unknown.Objective: The aim of this study was to investigate the associations between prenatal PUFA status, methylmercury exposure, and TL in mothers and children in the SCDS (Seychelles Child Development Study), for whom fish consumption is high...
November 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28972162/human-dna-polymerase-%C3%AE-accommodates-rna-for-strand-extension
#5
Yan Su, Martin Egli, F Peter Guengerich
Ribonucleotides are the natural analogs of deoxyribonucleotides, which can be misinserted by DNA polymerases, leading to the most abundant DNA lesions in genomes. During replication, DNA polymerases tolerate patches of ribonucleotides on the parental strands to different extents. The majority of human DNA polymerases have been reported to misinsert ribonucleotides into genomes. However, only PrimPol, DNA polymerase α, telomerase, and the mitochondrial human DNA polymerase (hpol) γ have been shown to tolerate an entire RNA strand...
November 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28950778/first-report-of-a-novel-deletion-due-to-%C3%AE%C2%B5%C3%AE-%C3%AE-%C3%AE-thalassemia-in-a-chinese-family
#6
Annie S Y Hui, Patrick K C Au, Yuen-Ha Ting, Anita S Y Kan, Yvonne K Y Cheng, Alex W K Leung, Kelvin Y K Chan, Chi-Kong Li, Mary H Y Tang, Tak-Yeung Leung
A fetus of Chinese descent presented with ultrasound features of anemia at 20 weeks' gestation. Father had low a mean corpuscular volume (MCV) level. Multiplex gap-polymerase chain reaction (gap-PCR) excluded common α-thalassemia (α-thal) deletions and mutations and PCR sequencing of the α1- and α2-globin genes were negative. The fetus had a normal karyotype. Array comparative genomic hybridization (aCGH) showed a single copy loss of 189.87 kb in chromosome 11p15.4, involving the whole β-globin gene cluster, inherited from the father...
May 2017: Hemoglobin
https://www.readbyqxmd.com/read/28910570/nine-novel-pax9-mutations-and-a-distinct-tooth-agenesis-genotype-phenotype
#7
S-W Wong, D Han, H Zhang, Y Liu, X Zhang, M Z Miao, Y Wang, N Zhao, L Zeng, B Bai, Y-X Wang, H Liu, S A Frazier-Bowers, H Feng
Tooth agenesis is one of the most common developmental anomalies affecting function and esthetics. The paired-domain transcription factor, Pax9, is critical for patterning and morphogenesis of tooth and taste buds. Mutations of PAX9 have been identified in patients with tooth agenesis. Despite significant progress in the genetics of tooth agenesis, many gaps in knowledge exist in refining the genotype-phenotype correlation between PAX9 and tooth agenesis. In the present study, we complete genetic and phenotypic characterization of multiplex Chinese families with nonsyndromic (NS) tooth agenesis...
September 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28895416/associations-of-the-variable-number-of-tandem-repeats-polymorphism-in-the-smyd3-gene-with-risk-and-prognosis-of-esophageal-cancer-a-case-control-study
#8
H F Wang, Y L Qu, L Y Ma, Y Tang
The aim of this study was to explore the associations between the variable number of tandem repeats (VNTR) polymorphism in the SMYD3 gene and the risk and prognosis of esophageal cancer (EC). A total of 546 EC patients (case group) and 580 healthy individuals (control group) were recruited for this study. Direct DNA sequencing of polymerase chain reaction (PCR) products was applied to detect the SMYD3 VNTR genotypes. A non-conditional logistic regression model was used to analyze the associations between different VNTR genotypes and clinicopathological features with the risk of EC...
September 12, 2017: Neoplasma
https://www.readbyqxmd.com/read/28860552/identification-of-amino-acid-residues-involved-in-the-drp-lyase-activity-of-human-pol-%C3%AE
#9
Nataliya Miropolskaya, Ivan Petushkov, Andrey Kulbachinskiy, Alena V Makarova
Besides X-family DNA polymerases (first of all, Pol β) several other human DNA polymerases from Y- and A- families were shown to possess the dRP-lyase activity and could serve as backup polymerases in base excision repair (Pol ι, Rev1, Pol γ and Pol θ). However the exact position of the active sites and the amino acid residues involved in the dRP-lyase activity in Y- and A- family DNA polymerases are not known. Here we carried out functional analysis of fifteen amino acid residues possibly involved in the dRP-lyase activity of human Pol ι...
August 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28834688/innate-immune-genes-in-persistent-mating-induced-endometritis-in-horses
#10
Christina D Marth, Simon M Firestone, Dave Hanlon, Lisa Y Glenton, Glenn F Browning, Neil D Young, Natali Krekeler
Persistent mating-induced endometritis (PMIE) severely decreases fertility in horses. The aim of the present study was to evaluate differences between horses susceptible to PMIE and a control group in terms of the expression of selected immune response and effector genes, and the effects of oestrous cycle stage on this expression. Endometrial biopsies from 18 uterine samples of mares in the control group (eight in dioestrus, 10 in oestrus) and 16 PMIE-susceptible mares (four in dioestrus, 12 in oestrus) were analysed by quantitative real-time reverse transcription-polymerase chain reaction...
August 24, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28806503/identification-of-the-dimer-exchange-interface-of-the-bacterial-dna-damage-response-protein-umud
#11
David A Murison, Rebecca C Timson, Bilyana N Koleva, Michael Ordazzo, Penny J Beuning
The Escherichia coli SOS response, an induced DNA damage response pathway, confers survival on bacterial cells by providing accurate repair mechanisms as well as the potentially mutagenic pathway translesion synthesis (TLS). The umuD gene products are upregulated after DNA damage and play roles in both nonmutagenic and mutagenic aspects of the SOS response. Full-length UmuD is expressed as a homodimer of 139-amino-acid subunits, which eventually cleaves its N-terminal 24 amino acids to form UmuD'. The cleavage product UmuD' and UmuC form the Y-family polymerase DNA Pol V (UmuD'2C) capable of performing TLS...
September 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28753597/urotensin-2-in-kawasaki-disease-pathogenesis
#12
Cassidy Y Huang, Jane C Burns, Chisato Shimizu
BackgroundGenetic variation in calcium signaling pathways is associated with Kawasaki disease (KD) susceptibility and coronary artery aneurysms (CAA). Expression quantitative trait locus analysis for KD-associated variants in calcium/sodium channel gene solute carrier family 8 member 1 (SLC8A1) revealed an effect on expression of urotensin 2 (UTS2). We speculated that UTS2 is influenced by genetic variation in SLC8A1 and contributes to disease pathogenesis.MethodsWe measured levels of UTS2 and its receptor in blood and tissues using quantitative reverse transcription-polymerase chain reaction, enzyme-linked immunosorbent assay, and immunohistochemical staining...
December 2017: Pediatric Research
https://www.readbyqxmd.com/read/28739826/interleukin-17c-in-human-helicobacter-pylori-gastritis
#13
Shingo Tanaka, Hiroyuki Nagashima, Modesto Cruz, Tomohisa Uchida, Takahiro Uotani, José A Jiménez Abreu, Varocha Mahachai, Ratha-Korn Vilaichone, Thawee Ratanachu-Ek, Lotay Tshering, David Y Graham, Yoshio Yamaoka
The interleukin-17 (IL-17) family of cytokines (IL-17A to IL-17F) is involved in many inflammatory diseases. Although IL-17A is recognized as being involved in the pathophysiology of Helicobacter pylori-associated diseases, the role of other IL-17 cytokine family members remains unclear. Microarray analysis of IL-17 family cytokines was performed in H. pylori-infected and uninfected gastric biopsy specimens. IL-17C mRNA was upregulated approximately 4.5-fold in H. pylori-infected gastric biopsy specimens. This was confirmed by quantitative reverse transcriptase PCR in infected and uninfected gastric mucosa obtained from Bhutan and from the Dominican Republic...
October 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28720532/lipoid-proteinosis-a-clinical-and-molecular-study-in-egyptian-patients
#14
Hanan H Afifi, Khalda S Amr, Angie M S Tosson, Tarak A Hassan, Mennat I Mehrez, Ghada Y El-Kamah
Lipoid proteinosis (LP) is an autosomal recessive disorder caused by the loss of function of ECM1 gene. Clinical features include varying degrees of skin thickening, hoarseness of voice and less frequently neuropsychiatric abnormalities. Twelve patients from ten unrelated families with a clinical diagnosis of lipoid proteinosis were enrolled in this study. Extraction of DNA samples of the 12 patients and their parents from peripheral blood by standard methods was performed. Polymerase chain reaction (PCR) amplification of the ECM1 gene was conducted using eight pairs of primers spanning over the 10 exons and splice junctions...
September 10, 2017: Gene
https://www.readbyqxmd.com/read/28684739/dna-binding-strength-increases-the-processivity-and-activity-of-a-y-family-dna-polymerase
#15
Jing Wu, Alexandra de Paz, Bradley M Zamft, Adam H Marblestone, Edward S Boyden, Konrad P Kording, Keith E J Tyo
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28666590/regulation-of-dna-damage-tolerance-in-mammalian-cells-by-post-translational-modifications-of-pcna
#16
REVIEW
Rie Kanao, Chikahide Masutani
DNA damage tolerance pathways, which include translesion DNA synthesis (TLS) and template switching, are crucial for prevention of DNA replication arrest and maintenance of genomic stability. However, these pathways utilize error-prone DNA polymerases or template exchange between sister DNA strands, and consequently have the potential to induce mutations or chromosomal rearrangements. Post-translational modifications of proliferating cell nuclear antigen (PCNA) play important roles in controlling these pathways...
October 2017: Mutation Research
https://www.readbyqxmd.com/read/28655184/characterization-of-a-coupled-dna-replication-and-translesion-synthesis-polymerase-supraholoenzyme-from-archaea
#17
Matthew T Cranford, Aurea M Chu, Joshua K Baguley, Robert J Bauer, Michael A Trakselis
The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28652326/trar-directly-regulates-transcription-initiation-by-mimicking-the-combined-effects-of-the-global-regulators-dksa-and-ppgpp
#18
Saumya Gopalkrishnan, Wilma Ross, Albert Y Chen, Richard L Gourse
The Escherichia coli F element-encoded protein TraR is a distant homolog of the chromosome-encoded transcription factor DksA. Here we address the mechanism by which TraR acts as a global regulator, inhibiting some promoters and activating others. We show that TraR regulates transcription directly in vitro by binding to the secondary channel of RNA polymerase (RNAP) using interactions similar, but not identical, to those of DksA. Even though it binds to RNAP with only slightly higher affinity than DksA and is only half the size of DksA, TraR by itself inhibits transcription as strongly as DksA and ppGpp combined and much more than DksA alone...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28622825/mutagenicity-of-%C3%AF-3-fatty-acid-peroxidation-products-in-the-ames-test
#19
Petr Grúz, Masatomi Shimizu, Kei-Ichi Sugiyama, Masamitsu Honma
Polyunsaturated fatty acids (PUFA) represent one of the main building blocks of cellular membranes and their varying composition impacts lifespan as well as susceptibility to cancer and other degenerative diseases. Increased intake of ω-3 PUFA is taught to compensate for the abundance of ω-6 PUFA in modern human diet and prevent cardiocirculatory diseases. However, highly unsaturated PUFA of marine and seed origin easily oxidize to aldehydic products which form DNA adducts. With increased PUFA consumption it is prudent to re-evaluate ω-3 PUFA safety and the genotoxic hazards of their metabolites...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28620358/the-transcriptional-regulators-of-the-crp-family-regulate-different-essential-bacterial-functions-and-can-be-inherited-vertically-and-horizontally
#20
REVIEW
Gloria Soberón-Chávez, Luis D Alcaraz, Estefanía Morales, Gabriel Y Ponce-Soto, Luis Servín-González
One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3'-5'-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species...
2017: Frontiers in Microbiology
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