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RNase L

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https://www.readbyqxmd.com/read/29297728/chronic-fatigue-and-immune-deficiency-syndrome-cfids-cellular-metabolism-and-ionizing-radiation-a-review-of-contemporary-scientific-literature-and-suggested-directions-for-future-research
#1
Andrej Rusin, Colin Seymour, Carmel Mothersill
PURPOSE: To investigate biochemical pathways known to be involved in radiation response and in CFIDS to determine if there might be common underlying mechanisms leading to symptoms experienced by those accidentally or deliberately exposed to radiation and those suffering from CFIDS. If such a link were established, to suggest testable hypotheses to investigate the mechanisms with the aim of identifying new therapeutic targets. CONCLUSIONS: Evidence for involvement of the alpha-synuclein, cytochrome c oxidiase, αB-crystallin, RNase L, and lactate dehydrogenase/STAT1 pathways is strong and suggests a common underlying mechanism involving mitochondrial dysfunction mediated by ROS and disruption of ATP production...
January 3, 2018: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/29290613/the-antiviral-and-cancer-genomic-dna-deaminase-apobec3h-is-regulated-by-an-rna-mediated-dimerization-mechanism
#2
Nadine M Shaban, Ke Shi, Kate V Lauer, Michael A Carpenter, Christopher M Richards, Daniel Salamango, Jiayi Wang, Michael W Lopresti, Surajit Banerjee, Rena Levin-Klein, William L Brown, Hideki Aihara, Reuben S Harris
Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA-editing enzymes function in innate immunity by restricting the replication of viruses and transposons. APOBEC3H also contributes to cancer mutagenesis. Here, we address the fundamental nature of RNA in regulating human APOBEC3H activities. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment enables strong DNA deaminase activity. RNA-binding-defective mutants demonstrate clear separation of function by becoming DNA hypermutators...
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29237844/hsv-1-dna-polymerase-rnase-h-activity-acts-in-a-3-5-direction-and-is-dependent-on-the-3-5-exonuclease-active-site
#3
Jessica L Lawler, Purba Mukherjee, Donald M Coen
The catalytic subunit (Pol) of herpes simplex virus-1 (HSV-1) DNA polymerase has been extensively studied both as a model for other family B DNA polymerases and for its differences from these enzymes as an antiviral target. Among the activities of HSV-1 Pol is an intrinsic RNase H activity that cleaves RNA from RNA:DNA hybrids. There has long been a controversy regarding whether this activity is due to the 3' -5' exonuclease of Pol or whether it is a separate activity, possibly acting on 5' RNA termini. To investigate this issue, we compared wild-type HSV-1 Pol and a 3' -5' exonuclease-deficient mutant, D368A, for DNA polymerase activity, 3' -5' exonuclease activity, and RNase H activity in vitro Additionally, we assessed the RNase H activity using differentially end-labeled templates with 5' or 3' RNA termini...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29169831/next-generation-sequencing-elucidates-cacao-badnavirus-diversity-and-reveals-the-existence-of-more-than-ten-viral-species
#4
E Muller, S Ravel, C Agret, F Abrokwah, H Dzahini-Obiatey, I Galyuon, K Kouakou, E C Jeyaseelan, J Allainguillaume, A Wetten
Cacao swollen shoot virus is a member of the family Caulimoviridae, genus Badnavirus and is naturally transmitted to Theobroma cacao (L.) by several mealybug species. CSSV populations in West African countries are highly variable and genetically structured into several different groups based on the diversity in the first part of ORF3 which encodes the movement protein. To unravel the extent of isolate diversity and address the problems of low titer and mixed viral sequences in samples, we used Illumina MiSeq and HiSeq technology...
November 21, 2017: Virus Research
https://www.readbyqxmd.com/read/29167539/genome-wide-analysis-shows-that-rnase-g-plays-a-global-role-in-the-stability-of-mrnas-in-stenotrophomonas-maltophilia
#5
Alejandra Bernardini, José L Martínez
Gene expression is determined by critical processes such as RNA synthesis and degradation. Ribonucleases participate in the coordinated and differential decay of messenger RNAs. We describe a suitable method of normalization and calculation of mRNAs half-life values quantified by RNA-Seq. We determined the mRNA half-lives of more than 2000 genes in Stenotrophomonas maltophilia D457 and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient strain, respectively...
November 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29117179/a-mutation-in-the-viral-sensor-2-5-oligoadenylate-synthetase-2-causes-failure-of-lactation
#6
Samantha R Oakes, David Gallego-Ortega, Prudence M Stanford, Simon Junankar, Wendy Wing Yee Au, Zoya Kikhtyak, Anita von Korff, Claudio M Sergio, Andrew M K Law, Lesley E Castillo, Stephanie L Allerdice, Adelaide I J Young, Catherine Piggin, Belinda Whittle, Edward Bertram, Matthew J Naylor, Daniel L Roden, Jesse Donovan, Alexei Korennykh, Christopher C Goodnow, Moira K O'Bryan, Christopher J Ormandy
We identified a non-synonymous mutation in Oas2 (I405N), a sensor of viral double-stranded RNA, from an ENU-mutagenesis screen designed to discover new genes involved in mammary development. The mutation caused post-partum failure of lactation in healthy mice with otherwise normally developed mammary glands, characterized by greatly reduced milk protein synthesis coupled with epithelial cell death, inhibition of proliferation and a robust interferon response. Expression of mutant but not wild type Oas2 in cultured HC-11 or T47D mammary cells recapitulated the phenotypic and transcriptional effects observed in the mouse...
November 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29117130/characterization-of-nucleoside-reverse-transcriptase-inhibitor-associated-mutations-in-the-rnase-h-region-of-hiv-1-subtype-c-infected-individuals
#7
Sinaye Ngcapu, Kristof Theys, Pieter Libin, Vincent C Marconi, Henry Sunpath, Thumbi Ndung'u, Michelle L Gordon
The South African national treatment programme includes nucleoside reverse transcriptase inhibitors (NRTIs) in both first and second line highly active antiretroviral therapy regimens. Mutations in the RNase H domain have been associated with resistance to NRTIs but primarily in HIV-1 subtype B studies. Here, we investigated the prevalence and association of RNase H mutations with NRTI resistance in sequences from HIV-1 subtype C infected individuals. RNase H sequences from 112 NRTI treated but virologically failing individuals and 28 antiretroviral therapy (ART)-naive individuals were generated and analysed...
November 8, 2017: Viruses
https://www.readbyqxmd.com/read/29036710/a-disulfide-bond-a-like-oxidoreductase-is-a-strong-candidate-gene-for-self-incompatibility-in-apricot-prunus-armeniaca-pollen
#8
Juan Vicente Muñoz-Sanz, Elena Zuriaga, María L Badenes, Carlos Romero
S-RNase based gametophytic self-incompatibility (SI) is a widespread prezygotic reproductive barrier in flowering plants. In the Solanaceae, Plantaginaceae and Rosaceae gametophytic SI is controlled by the pistil-specific S-RNases and the pollen S-locus F-box proteins but non-S-specific factors, namely modifiers, are also required. In apricot, Prunus armeniaca (Rosaceae), we previously mapped two pollen-part mutations that confer self-compatibility in cultivars Canino and Katy at the distal end of chromosome 3 (M-locus) unlinked to the S-locus...
September 25, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28986834/assays-to-demonstrate-the-roles-of-arenaviral-nucleoproteins-nps-in-viral-rna-synthesis-and-in-suppressing-type-i-interferon
#9
Qinfeng Huang, Junjie Shao, Yuying Liang, Hinh Ly
Arenaviruses, such as Lassa virus (LASV) and Pichindé virus (PICV), are enveloped viruses with a bi-segmented ambisense RNA genome. The large (L) genomic segment encodes the Z matrix protein and the L RNA-dependent RNA polymerase, whereas the small (S) genomic segment encodes the nucleoprotein (NP) and the glycoprotein (GPC). The NP encapsidates viral genome, is required for viral transcription and replication, and acts as a type I interferon (IFN) antagonist. This article describes assays to demonstrate that NP contains 3'-5' exoribonuclease (RNase) activity to degrade modeled RNA of the pathogen-associated molecular pattern type and suppresses the IFNβ promoter-driven luciferase reporter gene...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28977560/dynamic-nucleoplasmic-and-nucleolar-localization-of-mammalian-rnase-h1-in-response-to-rnap-i-transcriptional-r-loops
#10
Wen Shen, Hong Sun, Cheryl L De Hoyos, Jeffrey K Bailey, Xue-Hai Liang, Stanley T Crooke
An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migration of RNase H1 and R-loops from nucleoli to perinucleolar ring structures was observed upon inhibition of RNAP I transcription. Treatment with camptothecin which transiently stabilized nucleolar R-loops recruited RNase H1 to the nucleoli...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28970902/double-quick-double-click-reversible-peptide-stapling
#11
Claire M Grison, George M Burslem, Jennifer A Miles, Ludwig K A Pilsl, David J Yeo, Zeynab Imani, Stuart L Warriner, Michael E Webb, Andrew J Wilson
The development of constrained peptides for inhibition of protein-protein interactions is an emerging strategy in chemical biology and drug discovery. This manuscript introduces a versatile, rapid and reversible approach to constrain peptides in a bioactive helical conformation using BID and RNase S peptides as models. Dibromomaleimide is used to constrain BID and RNase S peptide sequence variants bearing cysteine (Cys) or homocysteine (hCys) amino acids spaced at i and i + 4 positions by double substitution...
July 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28929238/nuclease-integrated-kinase-super-assemblies-niks-and-their-role-in-rna-processing
#12
REVIEW
Monica C Pillon, Robin E Stanley
Here we highlight the Grc3/Las1 complex, an essential RNA processing machine that is well conserved across eukaryotes and required for processing the pre-ribosomal RNA (pre-rRNA). Las1 is an endoribonuclease that cleaves the pre-rRNA while Grc3 is a polynucleotide kinase that phosphorylates the Las1-cleaved RNA product. Recently we showed that Grc3 and Las1 assemble into a higher-order complex composed of a dimer of Grc3/Las1 heterodimers that is required for nuclease and kinase activity. Unexpectedly, we found that the Grc3/Las1 complex draws numerous parallels with two other eukaryotic nucleases, Ire1 and RNase L...
September 19, 2017: Current Genetics
https://www.readbyqxmd.com/read/28905148/building-a-pgc-lc-ms-n-glycan-retention-library-and-elution-mapping-resource
#13
Jodie L Abrahams, Matthew P Campbell, Nicolle H Packer
Porous graphitised carbon-liquid chromatography (PGC-LC) has been proven to be a powerful technique for the analysis and characterisation of complex mixtures of isomeric and isobaric glycan structures. Here we evaluate the elution behaviour of N-glycans on PGC-LC and thereby provide the potential of using chromatographic separation properties, together with mass spectrometry (MS) fragmentation, to determine glycan structure assignments more easily. We used previously reported N-glycan structures released from the purified glycoproteins Immunoglobulin G (IgG), Immunoglobulin A (IgA), lactoferrin, α1-acid glycoprotein, Ribonuclease B (RNase B), fetuin and ovalbumin to profile their behaviour on capillary PGC-LC-MS...
September 13, 2017: Glycoconjugate Journal
https://www.readbyqxmd.com/read/28893654/strain-specific-association-of-soybean-dwarf-virus-small-subgenomic-rna-with-virus-particles
#14
Thanuja Thekke-Veetil, Nancy K McCoppin, Leslie L Domier
Soybean dwarf virus (SbDV) produces a large subgenomic RNA (LsgRNA) for expression of structural and movement proteins and a small subgenomic RNA (SsgRNA) that does not contain an open reading frame. Sucrose gradient-purified SbDV virions from soybean plants systemically infected with SbDV by aphids and Nicotiana benthamiana leaves agroinfiltrated with infectious clones of two red clover SbDV isolates encapsidated genomic RNA and were associated with SsgRNA in a strain-specific manner. The LsgRNA was protected from RNase degradation, but not packaged into virions as indicated by its presence primarily in ELISA-negative fractions near the tops of sucrose gradients even in mutants that did not express coat protein...
September 8, 2017: Virus Research
https://www.readbyqxmd.com/read/28878087/novel-stable-ebola-virus-minigenome-replicon-reveals-remarkable-stability-of-the-viral-genome
#15
Wanyin Tao, Tianyu Gan, Mingzhe Guo, Yongfen Xu, Jin Zhong
Ebola virus (EBOV) causes severe hemorrhagic fever in humans and other primates with a high case fatality rate. No approved drug or vaccine of EBOV is available, which necessitates better understanding of the virus life cycle. Studies on EBOV have been hampered because experimentations involving live virus are restricted to biosafety level 4 (BSL-4) laboratories. EBOV minigenome system has provided researchers with the opportunity to study EBOV under BSL-2 conditions. Here, we developed a novel EBOV minigenome replicon which, to our knowledge, is the first EBOV cell culture system that can stably replicate and transcribe EBOV minigenome...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28854734/amide-linkages-mimic-phosphates-in-rna-interactions-with-proteins-and-are-well-tolerated-in-the-guide-strand-of-short-interfering-rnas
#16
Daniel Mutisya, Travis Hardcastle, Samwel K Cheruiyot, Pradeep S Pallan, Scott D Kennedy, Martin Egli, Melissa L Kelley, Anja van Brabant Smith, Eriks Rozners
While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute...
August 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28829437/control-of-phosphorothioate-stereochemistry-substantially-increases-the-efficacy-of-antisense-oligonucleotides
#17
Naoki Iwamoto, David C D Butler, Nenad Svrzikapa, Susovan Mohapatra, Ivan Zlatev, Dinah W Y Sah, Meena, Stephany M Standley, Genliang Lu, Luciano H Apponi, Maria Frank-Kamenetsky, Jason Jingxin Zhang, Chandra Vargeese, Gregory L Verdine
Whereas stereochemical purity in drugs has become the standard for small molecules, stereoisomeric mixtures containing as many as a half million components persist in antisense oligonucleotide (ASO) therapeutics because it has been feasible neither to separate the individual stereoisomers, nor to synthesize stereochemically pure ASOs. Here we report the development of a scalable synthetic process that yields therapeutic ASOs having high stereochemical and chemical purity. Using this method, we synthesized rationally designed stereopure components of mipomersen, a drug comprising 524,288 stereoisomers...
September 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28827284/rhinovirus-infection-of-ormdl3-transgenic-mice-is-associated-with-reduced-rhinovirus-viral-load-and-airway-inflammation
#18
Dae Jin Song, Marina Miller, Andrew Beppu, Peter Rosenthal, Sudipta Das, Maya Karta, Christine Vuong, Amit Kumar Mehta, Michael Croft, David H Broide
Orosomucoid like 3 (ORMDL3), a gene localized to chromosome 17q21, has been linked in epidemiologic studies to childhood asthma and rhinovirus (RV) infections. As the single nucleotide polymorphisms linking ORMDL3 to asthma are associated with increased expression of ORMDL3, we have used hORMDL3(zp3-Cre) mice (which have universal increased expression of human ORMDL3) to determine whether infection of these transgenic mice with RV influences levels of airway inflammation or RV viral load. RV infection of hORMDL3(zp3-Cre) mice resulted in reduced RV viral load assessed by quantitative real-time PCR (lung and airway epithelium), as well as reduced airway inflammation (total bronchoalveolar lavage cells, neutrophils, macrophages, and lymphocytes) compared with RV-infected wild-type mice...
October 1, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28808124/rapid-rnase-l-driven-arrest-of-protein-synthesis-in-the-dsrna-response-without-degradation-of-translation-machinery
#19
Jesse Donovan, Sneha Rath, David Kolet-Mandrikov, Alexei Korennykh
Mammalian cells respond to double-stranded RNA (dsRNA) by activating a translation-inhibiting endoribonuclease, RNase L. Consensus in the field indicates that RNase L arrests protein synthesis by degrading ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs). However, here we provide evidence for a different and far more efficient mechanism. By sequencing abundant RNA fragments generated by RNase L in human cells, we identify site-specific cleavage of two groups of noncoding RNAs: Y-RNAs, whose function is poorly understood, and cytosolic tRNAs, which are essential for translation...
November 2017: RNA
https://www.readbyqxmd.com/read/28804020/porcine-2-5-oligoadenylate-synthetase-2-inhibits-porcine-reproductive-and-respiratory-syndrome-virus-replication-in%C3%A2-vitro
#20
Mengmeng Zhao, Bo Wan, Huawei Li, Jian He, Xinxin Chen, Linjian Wang, Yinbiao Wang, Sha Xie, Songlin Qiao, Gaiping Zhang
Porcine reproductive and respiratory syndrome virus (PRRSV) is acknowledged a fulminating infectious pathogen affecting the pig farming industry, and current vaccines and drugs could hardly inhibit this virus. The 2', 5'-oligoadenylate synthetase (OASs) have antiviral activities, but the role(s) played by porcine OAS2 in protection against PRRSV infection are unknown. Here we found that endogenous expression of the porcine OAS2 gene could be promoted by interferon (IFN)-beta or PRRSV infection in porcine alveolar macrophages...
October 2017: Microbial Pathogenesis
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