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y-family polymerase

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https://www.readbyqxmd.com/read/28739826/interleukin-17c-in-human-helicobacter-pylori-gastritis
#1
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-F) is involved in many inflammatory diseases. Although IL-17A is recognized as being involved in the pathophysiology of H. 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 biopsies. This was confirmed by quantitative reverse transcriptase-polymerase chain reaction in infected and uninfected gastric mucosa obtained from Bhutan and from the Dominican Republic...
July 24, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28720532/lipoid-proteinosis-a-clinical-and-molecular-study-in-egyptian-patients
#2
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...
July 15, 2017: Gene
https://www.readbyqxmd.com/read/28684739/dna-binding-strength-increases-the-processivity-and-activity-of-a-y-family-dna-polymerase
#3
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
#4
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...
June 21, 2017: Mutation Research
https://www.readbyqxmd.com/read/28655184/characterization-of-a-coupled-dna-replication-and-translesion-synthesis-polymerase-supraholoenzyme-from-archaea
#5
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...
June 26, 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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28557584/nhs-gene-mutations-in-ashkenazi-jewish-families-with-nance-horan-syndrome
#9
Nadav Shoshany, Isaac Avni, Yair Morad, Chen Weiner, Adi Einan-Lifshitz, Eran Pras
PURPOSE: To describe ocular and extraocular abnormalities in two Ashkenazi Jewish families with infantile cataract and X-linked inheritance, and to identify their underlying mutations. METHODS: Seven affected members were recruited. Medical history, clinical findings, and biometric measurements were recorded. Mutation analysis of the Nance-Horan syndrome (NHS) gene was performed by direct sequencing of polymerase chain reaction-amplified exons. RESULTS: An unusual anterior Y-sutural cataract was documented in the affected male proband...
May 30, 2017: Current Eye Research
https://www.readbyqxmd.com/read/28466855/a-domain-in-human-exog-converts-apoptotic-endonuclease-to-dna-repair-exonuclease
#10
Michal R Szymanski, Wangsheng Yu, Aleksandra M Gmyrek, Mark A White, Ian J Molineux, J Ching Lee, Y Whitney Yin
Human EXOG (hEXOG) is a 5'-exonuclease that is crucial for mitochondrial DNA repair; the enzyme belongs to a nonspecific nuclease family that includes the apoptotic endonuclease EndoG. Here we report biochemical and structural studies of hEXOG, including structures in its apo form and in a complex with DNA at 1.81 and 1.85 Å resolution, respectively. A Wing domain, absent in other ββα-Me members, suppresses endonuclease activity, but confers on hEXOG a strong 5'-dsDNA exonuclease activity that precisely excises a dinucleotide using an intrinsic 'tape-measure'...
May 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28458162/a-genetic-study-based-on-pcna-ubiquitin-fusions-reveals-no-requirement-for-pcna-polyubiquitylation-in-dna-damage-tolerance
#11
Judit Z Gervai, Judit Gálicza, Zoltán Szeltner, Judit Zámborszky, Dávid Szüts
Post-translational modifications of Proliferating Cell Nuclear Antigen (PCNA) play a key role in regulating the bypass of DNA lesions during DNA replication. PCNA can be monoubiquitylated at lysine 164 by the RAD6-RAD18 ubiquitin ligase complex. Through this modification, PCNA can interact with low fidelity Y family DNA polymerases to promote translesion synthesis. Monoubiquitylated PCNA can be polyubiquitylated on lysine 63 of ubiquitin by a further ubiquitin-conjugating complex. This modification promotes a template switching bypass process in yeast, while its role in higher eukaryotes is less clear...
April 14, 2017: DNA Repair
https://www.readbyqxmd.com/read/28436337/molecular-cloning-expression-and-characterization-of-e2f-transcription-factor-4-from-antheraea-pernyi
#12
M N Abbas, S Kausar, Y-X Sun, Y Sun, L Wang, C Qian, G-Q Wei, B-J Zhu, C-L Liu
The E2F transcription factor family is distributed widely in eukaryotes and has been well studied among mammals. In the present study, the E2F transcription factor 4 (E2F4) gene was isolated from fat bodies of Antheraea pernyi and sequenced. E2F4 comprised a 795 bp open reading frame encoding a deduced amino acid sequence of 264 amino acid residues. The recombinant protein was expressed in Escherichia coli (Transetta DE3), and anti-E2F4 antibodies were prepared. The deduced amino acid sequence displayed significant homology to an E2F4-like protein from Bombyx mori L...
April 24, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28423907/effects-of-active-site-mutations-on-specificity-of-nucleobase-binding-in-human-dna-polymerase-%C3%AE
#13
Melek N Ucisik, Sharon Hammes-Schiffer
Human DNA polymerase η (Pol η) plays a vital role in protection against skin cancer caused by damage from ultraviolet light. This enzyme rescues stalled replication forks at cyclobutane thymine-thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions. Residue R61 is conserved in the Pol η enzymes across species, but the corresponding residue, as well as its neighbor S62, is different in other Y-family polymerases, Pol ι and Pol κ. Herein, R61 and S62 are mutated to their Pol ι and Pol κ counterparts...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28412207/microrna-183-family-profiles-in-pheochromocytomas-are-related-to-clinical-parameters-and-sdhb-expression
#14
Suja Pillai, Chung Y Lo, Victor Liew, Minella Lalloz, Robert A Smith, Vinod Gopalan, Alfred King-Yin Lam
This study aims to examine the expression profiles of the miR-183 cluster (miR-96/182/183) in pheochromocytoma. Pheochromocytoma tissues were prospectively collected from 50 patients with pheochromocytoma. Expression of miR-183 cluster members and SDHB protein expression were analysed in these tissues by quantitative real-time polymerase chain reaction and immunohistochemistry respectively. The expression of miR-183 cluster members in pheochromocytomas was correlated with the clinical and pathological parameters of these patients...
April 12, 2017: Human Pathology
https://www.readbyqxmd.com/read/28402640/mutagenic-replication-of-n-2-deoxyguanosine-benzo-a-pyrene-adducts-by-escherichia-coli-dna-polymerase-i-and-sulfolobus-solfataricus-dna-polymerase-iv
#15
A S Prakasha Gowda, Jacek Krzeminski, Shantu Amin, Zucai Suo, Thomas E Spratt
Benzo[a]pyrene, a potent human carcinogen, is metabolized in vivo to a diol epoxide that reacts with the N(2)-position of guanine to produce N(2)-BP-dG adducts. These adducts are mutagenic causing G to T transversions. These adducts block replicative polymerases but can be bypassed by the Y-family translesion synthesis polymerases. The mechanisms by which mutagenic bypass occurs is not well-known. We have evaluated base pairing structures using atomic substitution of the dNTP with two stereoisomers, 2'-deoxy-N-[(7R,8S,9R,10S)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine and 2'-deoxy-N-[(7S,8R,9S,10R)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine...
May 15, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28401080/comparison-of-the-frequency-of-y-short-tandem-repeats-markers-between-sadat-and-non-sadat-populations-in-isfahan-province-of-iran
#16
Reihaneh Seyedebrahimi, Ebrahim Esfandiari, Bahman Rashidi, Rasoul Salehi, Ali Gholami Dahghi, Shahriar Dabiri, Majid Kheirollahi
BACKGROUND: Y chromosome is one of the two sex chromosomes and is male specific. Due to limited genetic exchange, the main part of that is passed virtually unchanged from one generation to next generation. The short tandem repeats (STRs) are almost constant on chromosomes that make them as an appropriate factor for use in population genetic studies. In this study, we used the STRs of Y chromosome markers in Sadat families and comparison with other families was investigated. MATERIALS AND METHODS: In this study, sampling was done from fifty unrelated males of Sadat families and fifty unrelated males of non-Sadat families...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28383109/simulating-the-fidelity-and-the-three-mg-mechanism-of-pol-%C3%AE-and-clarifying-the-validity-of-transition-state-theory-in-enzyme-catalysis
#17
Hanwool Yoon, Arieh Warshel
Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion...
April 6, 2017: Proteins
https://www.readbyqxmd.com/read/28364784/tty2-genes-deletions-as-genetic-risk-factor-of-male-infertility
#18
F Shaveisi-Zadeh, R Alibakhshi, R Asgari, Z Rostami-Far, M Bakhtiari, H Abdi, A Movafagh, R Mirfakhraie
Y chromosome has a number of genes that are expressed in testis and have a role in spermatogenesis. TTY2L12A and TTY2L2A are the members of testis transcript Y2 (TTY2) that are Y linked multi-copy gene families, located on Yp11 and Yq11 loci respectively. The aim of this study was to investigate frequency of TTY2L12A and TTY2L2A deletions in azoospermic patients compared with fertile males. This study was performed on 45 infertile males with idiopathic azoospermia without any AZF micro deletions (group A), 33 infertile males with azoospermia which do not screened for AZF micro deletions (group B) and 65 fertile males (group C), from October 2013 to April 2015 in west of Iran...
February 28, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28362993/association-between-interleukin-17-gene-polymorphisms-and-the-risk-of-laryngeal-cancer-in-a-chinese-population
#19
F Z Si, Y Q Feng, M Han
IL-17 is associated with the occurrence and development of laryngeal cancer. However, no study has reported the association between IL-17 polymorphisms and laryngeal cancer susceptibility. Therefore, we analyzed the association of three polymorphism loci (rs2275913, 197 G/A; rs3748067, 383 A/G; and rs763780, 7488 T/C) of IL-17A and IL-17F with laryngeal cancer in the Chinese population. A case-control study was performed with 325 patients and 325 controls. Polymorphisms were detected by polymerase chain reaction and sequencing methods...
March 30, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28333147/solute-carrier-family-12-member-5-promotes-tumor-invasion-metastasis-of-bladder-urothelial-carcinoma-by-enhancing-nf-%C3%AE%C2%BAb-mmp-7-signaling-pathway
#20
J Y Liu, Y B Dai, X Li, K Cao, D Xie, Z T Tong, Z Long, H Xiao, M K Chen, Y L Ye, B Liu, J Tan, J Tang, Z Z Xu, Y Gan, Y H Zhou, F Deng, L Y He
Solute carrier family 12 member 5 (SLC12A5), an integral membrane KCl cotransporter, which maintains chloride homeostasis in neurons, is aberrantly expressed and involved in the tumorigenesis of certain cancers. However, the clinical significance and biological role of SLC12A5 in human bladder urothelial carcinoma (BUC) remains unclear. In this study, the expression of SLC12A5 was examined in clinical specimens of primary BUC and in BUC cell lines using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), western blot and immunohistochemistry (IHC)...
March 23, 2017: Cell Death & Disease
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