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Polymerase substrate specificity

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https://www.readbyqxmd.com/read/28922369/crimean-congo-hemorrhagic-fever-virus-nucleocapsid-protein-has-dual-rna-binding-modes
#1
Subbiah Jeeva, Sean Pador, Brittany Voss, Safder Saieed Ganaie, Mohammad Ayoub Mir
Crimean Congo hemorrhagic fever, a zoonotic viral disease, has high mortality rate in humans. There is currently no vaccine for Crimean Congo hemorrhagic fever virus (CCHFV) and chemical interventions are limited. The three negative sense genomic RNA segments of CCHFV are specifically encapsidated by the nucleocapsid protein into three ribonucleocapsids, which serve as templates for the viral RNA dependent RNA polymerase. Here we demonstrate that CCHFV nucleocapsid protein has two distinct binding modes for double and single strand RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28893909/processive-searching-ability-varies-among-members-of-the-gap-filling-dna-polymerase-x-family
#2
Michael J Howard, Samuel H Wilson
DNA repair proteins must locate rare damaged sites within the genome. DNA polymerase beta (Pol β), a member of the DNA polymerase X family that is involved in base excision repair, uses a processive hopping search mechanism to locate substrates. This effectively enhances its search footprint on DNA, increasing the probability of locating damaged sites. Processive searching has been reported or proposed for many DNA-binding proteins, raising the question of how widespread or specific to certain enzymes the ability to perform this function is...
September 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28886759/epigenetic-regulation-of-the-kappa-opioid-receptor-by-child-abuse
#3
Pierre-Eric Lutz, Jeffrey A Gross, Sabine K Dhir, Gilles Maussion, Jennie Yang, Alexandre Bramoulle, Michael J Meaney, Gustavo Turecki
BACKGROUND: Experiences of abuse and neglect during childhood are major predictors of the emergence of depressive and suicidal behaviors throughout life. The underlying biological mechanisms, however, remain poorly understood. Here, we focused on the opioid system as a potential brain substrate mediating these effects. METHODS: Postmortem samples from three brain structures regulating social bonds and emotions were analyzed. Groups were constituted of depressed individuals who died by suicide, with or without a history of severe child abuse, and of psychiatrically healthy control subjects...
July 27, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28863261/characterization-of-hsp90-co-chaperone-p23-cleavage-by-caspase-7-uncovers-a-peptidase-substrate-interaction-involving-intrinsically-disordered-regions
#4
Cyrielle Martini, Mikaël Bédard, Pierre Lavigne, Jean-Bernard Denault
Caspases are cysteinyl peptidases involved in inflammation and apoptosis during which hundreds of proteins are cleaved by executioner caspase-3 and -7. Despite the fact that caspase-3 has a higher catalytic activity, caspase-7 is more proficient at cleaving poly(ADP ribose) polymerase 1 (PARP1) because it uses an exosite within its N-terminal domain (NTD). Here, we demonstrate that molecular determinants also located in the NTD enhance the recognition and proteolysis of the Hsp90 co-chaperone p23. Structure-activity relationship analyses using mutagenesis of caspase-7 NTD and kinetics show that residues 36 to 45 of caspase-7, which overlap with residues necessary for efficacious PARP1 cleavage, participate in p23 recognition...
September 1, 2017: Biochemistry
https://www.readbyqxmd.com/read/28860671/polyphasic-taxonomy-of-aspergillus-section-aspergillus-formerly-eurotium-and-its-occurrence-in-indoor-environments-and-food
#5
A J Chen, V Hubka, J C Frisvad, C M Visagie, J Houbraken, M Meijer, J Varga, R Demirel, Ž Jurjević, A Kubátová, F Sklenář, Y G Zhou, R A Samson
Aspergillus section Aspergillus (formerly the genus Eurotium) includes xerophilic species with uniseriate conidiophores, globose to subglobose vesicles, green conidia and yellow, thin walled eurotium-like ascomata with hyaline, lenticular ascospores. In the present study, a polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of this section. Over 500 strains from various culture collections and new isolates obtained from indoor environments and a wide range of substrates all over the world were identified using calmodulin gene sequencing...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/28845000/-application-of-transcription-mediated-amplification-and-real-time-reverse-transcription-polymerase-chain-reaction-in-detection-of-human-immunodeficiency-virus-rna
#6
Daxian Wu, Shuhui Tao, Shuiping Liu, Jiebin Zhou, Deming Tan, Zhouhua Hou
To observe the sensitivity of transcription mediated amplification (TMA), and to compare its performance with real-time reverse transcription polymerase chain reaction (real-time RT-PCR) in detecting human immunodeficiency virus RNA (HIV RNA).
 Methods: TMA system was established with TaqMan probes, specific primers, moloney murine leukemia virus (MMLV) reverse transcriptase, T7 RNA polymerase, and reaction substrates. The sensitivity of TMA was evaluated by amplifying a group of 10-fold diluted HIV RNA standards which were transcribed in vitro...
July 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/28840566/photo-induced-oxidative-stress-impairs-mitochondrial-metabolism-in-neurons-and-astrocytes
#7
Elena Berezhnaya, Maria Neginskaya, Anatoly B Uzdensky, Andrey Y Abramov
Photodynamic therapy is selective destruction of cells stained with a photosensitizer upon irradiation with light at a specific wavelength in the presence of oxygen. Cell death upon photodynamic treatment is known to occur mainly due to free radical production and subsequent development of oxidative stress. During photodynamic therapy of brain tumors, healthy cells are also damaged; considering this, it is important to investigate the effect of the treatment on normal neurons and glia. We employed live-cell imaging technique to investigate the cellular mechanism of photodynamic action of radachlorin (200 nM) on neurons and astrocytes in primary rat cell culture...
August 24, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28811334/argonaute-8-ago8-mediates-the-elicitation-of-primary-defense-against-herbivory
#8
Maitree Pradhan, Priyanka Pandey, Klaus Gase, Murali Shraff, Ravi K Singh, Avinash Sethi, Ian T Baldwin, Shree P Pandey
In Nicotiana attenuata, specific RNA directed RNA polymerase (RdR1) and the Dicer-like proteins (DCL3 and 4) are recruited during herbivore attack to mediate the regulation of defense responses. However, the identity and role(s) of Argonautes (AGOs) involved in herbivory remains unknown. Of the 11 AGOs in the N. attenuata genome, we silenced the expression of 10. Plants silenced in NaAGO8 expression grew normally but were highly susceptible to herbivore attack. Larvae of the Manduca sexta grew faster when consuming irAGO8 plants, but did not differ from WT when consuming plants silenced in AGO1 (a, b and c), AGO2, AGO4 (a and b), AGO7, or AGO10 expression...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28808059/linchpin-dna-binding-residues-serve-as-go-no-go-controls-in-the-replication-factor-c-catalyzed-clamp-loading-mechanism
#9
Juan Liu, Yayan Zhou, Manju M Hingorani
DNA polymerases depend on circular sliding clamps for processive replication. Clamps must be loaded onto primer-template DNA (ptDNA) by clamp loaders that open and close clamps around ptDNA in an ATP-fueled reaction. All clamp loaders share a core structure in which five subunits form a spiral chamber that binds the clamp at its base in a twisted open form and encloses ptDNA within, while binding and hydrolyzing ATP to topologically link the clamp and ptDNA. To understand how clamp loaders perform this complex task, here we focused on conserved arginines that might play a central coordinating role in the mechanism, since they can alternately contact ptDNA or Walker B glutamate in the ATPase site, and lie close to the clamp loader-clamp binding interface...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28790447/wheat-tapub1-modulates-plant-drought-stress-resistance-by-improving-antioxidant-capability
#10
Guangqiang Zhang, Meng Zhang, Zhongxian Zhao, Yuanqing Ren, Qinxue Li, Wei Wang
E3 ligases play significant roles in plant stress tolerance by targeting specific substrate proteins for post-translational modification. In a previous study, we cloned TaPUB1 from Triticum aestivum L., which encodes a U-box E3 ligase. Real-time polymerase chain reaction revealed that the gene was up-regulated under drought stress. To investigate the function of TaPUB1 in the response of plants to drought, we generated transgenic Nicotiana benthamiana (N. benthamiana) plants constitutively expressing TaPUB1 under the CaMV35S promoter...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28769016/favipiravir-t-705-a-broad-spectrum-inhibitor-of-viral-rna-polymerase
#11
Yousuke Furuta, Takashi Komeno, Takaaki Nakamura
Favipiravir (T-705; 6-fluoro-3-hydroxy-2-pyrazinecarboxamide) is an anti-viral agent that selectively and potently inhibits the RNA-dependent RNA polymerase (RdRp) of RNA viruses. Favipiravir was discovered through screening chemical library for anti-viral activity against the influenza virus by Toyama Chemical Co., Ltd. Favipiravir undergoes an intracellular phosphoribosylation to be an active form, favipiravir-RTP (favipiravir ribofuranosyl-5'-triphosphate), which is recognized as a substrate by RdRp, and inhibits the RNA polymerase activity...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28752801/virus-directed-enzyme-prodrug-therapy-and-the-assessment-of-the-cytotoxic-impact-of-some-benzimidazole-derivatives
#12
Michał Szewczuk, Karolina Boguszewska, Marta Żebrowska, Ewa Balcerczak, Marta Stasiak, Maria Świątkowska, Katarzyna Błaszczak-Świątkiewicz
Virus-directed enzyme prodrug therapy is one of the major strategy of increasing cytotoxicity of bioreductive agents. This research intended to examine new selected benzimidazole derivatives as a substrate for nitroreductase, the enzyme involved in nitroreduction which is responsible to the production of cytotoxic metabolites. In this way, the selectivity and strength of cytotoxicity can be raised. The effect of benzimidazoles on virus transfected cells and non-virus transfected cells A549 cell line was established by Annexin V + propidium iodide test, western blot, and polymerase chain reaction analysis of specific pro- and anti-apoptotic proteins in the corresponding gene expression and additionally nitroreductase gene expression...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28751463/dual-src-kinase-pretubulin-inhibitor-kx-01-sensitizes-er%C3%AE-negative-breast-cancers-to-tamoxifen-through-er%C3%AE-re-expression
#13
Muralidharan Anbalagan, Mei Sheng, Brian Fleischer, Yifang Zhang, Yuanjun Gao, Van T Hoang, Margarite D Matossian, Hope E Burks, Matthew E Burow, Bridgette M Collins-Burow, David Hangauer, Brian G Rowan
Unlike breast cancer that is positive for estrogen receptor-α (ERα), there are no targeted therapies for triple negative breast cancer (TNBC). ERα is silenced in TNBC through epigenetic changes including DNA methylation and histone acetylation. Restoring ERα expression in TNBC may sensitize patients to endocrine therapy. Expression of c-Src and ERα are inversely correlated in breast cancer suggesting that c-Src inhibition may lead to re-expression of ERα in TNBC. KX-01 is a peptide substrate-targeted Src/pretubulin inhibitor in clinical trials for solid tumors...
July 27, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28695520/use-of-inosine-monophosphate-dehydrogenase-activity-assay-to-determine-the-specificity-of-parp-1-inhibitors
#14
Sajitha Anthony, Jeffrey R Peterson, Yingbiao Ji
Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme involved in purine nucleotide biosynthesis. It is responsible for catalyzing the oxidation of inosine monophosphate (IMP) into xanthosine monophosphate (XMP). Concurrently, the cofactor NAD(+) is reduced to NADH. Poly(ADP-ribose) polymerase 1 (PARP-1) also utilizes NAD(+) as a substrate to synthesize poly(ADP-ribose). It has been demonstrated that inhibition of PARP-1 activity can be an effective cancer therapeutic. However, most PARP-1 inhibitors, including olaparib, were developed as NAD(+) analogs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28695506/using-clickable-nad-analogs-to-label-substrate-proteins-of-parps
#15
Lu Zhang, Hening Lin
ADP-ribosylation has been well known as an important posttranslational modification, which is catalyzed by a family of enzymes called poly(ADP-ribose) polymerases (PARPs). PARPs transfer of a single or multiple adenine diphosphate ribose (ADP-ribose) units from nicotinamide adenine dinucleotide (NAD(+)) to specific amino acids on substrate proteins. Through mono- or poly-ADP-ribosylation enzymatic activities, PARPs regulate various biological processes, including DNA damage repair, chromatin remodeling, transcriptional regulation, RNA processing and metabolism...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28695500/quantification-of-parp-activity-in-human-tissues-ex-vivo-assays-in-blood-cells-and-immunohistochemistry-in-human-biopsies
#16
Eszter M Horvath, Zsuzsanna K Zsengellér, Csaba Szabo
Poly(ADP-ribosyl)ation of proteins is a posttranslational modification mediated by poly(ADP-ribose) polymerases (PARPs) that use NAD(+) as substrate to form the negatively charged polymer of poly(ADP-ribose) (PAR). After DNA damage, PARP-1 is responsible for approximately 90% of the total cellular PARylation activity. Numerous studies showed activation of PARP-1 in various conditions associated with oxidative and nitrosative stress, such as ischemia-reperfusion injury, diabetes mellitus, and inflammation, and also proved the beneficial effects of PARP inhibitors...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28678845/polymerase-free-measurement-of-microrna-122-with-single-base-specificity-using-single-molecule-arrays-detection-of-drug-induced-liver-injury
#17
David M Rissin, Barbara López-Longarela, Salvatore Pernagallo, Hugh Ilyine, A D Bastiaan Vliegenthart, James W Dear, Juan J Díaz-Mochón, David C Duffy
We have developed a single probe method for detecting microRNA from human serum using single molecule arrays, with sequence specificity down to a single base, and without the use of amplification by polymerases. An abasic peptide nucleic acid (PNA) probe-containing a reactive amine instead of a nucleotide at a specific position in the sequence-for detecting a microRNA was conjugated to superparamagnetic beads. These beads were incubated with a sample containing microRNA, a biotinylated reactive nucleobase-containing an aldehyde group-that was complementary to the missing base in the probe sequence, and a reducing agent...
2017: PloS One
https://www.readbyqxmd.com/read/28665322/pre-replicative-repair-of-oxidized-bases-maintains-fidelity-in-mammalian-genomes-the-cowcatcher-role-of-neil1-dna-glycosylase
#18
Suganya Rangaswamy, Arvind Pandey, Sankar Mitra, Muralidhar L Hegde
Genomic fidelity in the humans is continuously challenged by genotoxic reactive oxygen species (ROS) generated both endogenously during metabolic processes, and by exogenous agents. Mispairing of most ROS-induced oxidized base lesions during DNA replication induces mutations. Although bulky base adducts induced by ultraviolet light and other environmental mutagens block replicative DNA polymerases, most oxidized base lesions do not block DNA synthesis. In 8-oxo-G:A mispairs generated by the incorporation of A opposite unrepaired 8-oxo-G, A is removed by MutYH (MYH) for post-replicative repair, and other oxidized base lesions must be repaired prior to replication in order to prevent mutation fixation...
June 30, 2017: Genes
https://www.readbyqxmd.com/read/28659472/crystal-structure-and-thermostability-characterization-of-enterovirus-d68-3d-pol
#19
Chunnian Wang, Caiyan Wang, Qing Li, Zhong Wang, Wei Xie
Enterovirus D68 (EV-D68) is one of the many nonpolio enteroviruses that cause mild to severe respiratory illness. The nonstructural protein 3D(pol) is an RNA-dependent RNA polymerase (RdRP) of EV-D68 which plays a critical role in the replication of the viral genome and represents a promising drug target. Here, we report the first three-dimensional crystal structure of the RdRP from EV-D68 in complex with the substrate GTP to 2.3-Å resolution. The RdRP structure is similar to structures of other viral RdRPs, where the three domains, termed the palm, fingers, and thumb, form a structure resembling a cupped right hand...
September 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28641560/functional-and-catalytic-characterization-of-the-detoxifying-enzyme-haloalkane-dehalogenase-from-rhizobium-leguminosarum
#20
Nikolaos Georgakis, Evangelia Chronopoulou, Maria Anna Gad, Dimitrios Skliros, Rodica Efrose, Emmanouil Flemetakis, Nikolaos E Labrou
BACKGROUND: Haloalkane dehalogenases (EC 3.8.1.5, HLDs) are α/β-hydrolases which catalyze the irreversible cleavage of carbon-halogen bonds of haloalkanes, producing an alcohol, a halide and a hydrogen ion. Haloalkanes are acutely toxic to animals and humans and their toxic effects are mainly observed in the liver, kidneys and central nervous system. OBJECTIVE: In the present work, the haloalkane dehalogenase from Rhizobium leguminosarum bv. trifolii (DrlA) was characterized...
2017: Protein and Peptide Letters
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