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https://www.readbyqxmd.com/read/29165591/translation-can-affect-the-antisense-activity-of-rnase-h1-dependent-oligonucleotides-targeting-mrnas
#1
Xue-Hai Liang, Joshua G Nichols, Hong Sun, Stanley T Crooke
RNase H1-dependent antisense oligonucleotides (ASOs) can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. Here we show that mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29163435/evolutionary-analysis-of-hiv-1-pol-proteins-reveals-representative-residues-for-viral-subtype-differentiation
#2
Shohei Nagata, Junnosuke Imai, Gakuto Makino, Masaru Tomita, Akio Kanai
RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29159954/unraveling-the-mechanistic-complexity-of-the-glomerulocystic-phenotype-in-dicer-conditional-ko-mice-by-2d-gel-electrophoresis-coupled-mass-spectrometry
#3
Claudia Vincenza Fiumara, Domenica Scumaci, Anna Iervolino, Angela Mena Perri, Antonio Concolino, Laura Tammè, Federica Petrillo, Giovambattista Capasso, Giovanni Cuda
PURPOSE: Dicer, an RNase III type endonuclease, is a key enzyme involved in miRNA biogenesis. It has been shown that this enzyme is essential for several aspects of postnatal kidney functions and homeostasis. In this study, we have examined conditional knockout (cKO) mice for Dicer in Pax8 (Paired-box gene 8) expressing cells to investigate the kidney protein profile. This specific model develops a glomerulocystic phenotype coupled with urinary concentration impairment, proteinuria and severe renal failure...
November 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29157732/rnase-7-strongly-promotes-tlr9-mediated-dna-sensing-by-human-plasmacytoid-dendritic-cells
#4
V Kopfnagel, S Wagenknecht, J Harder, K Hofmann, M Kleine, A Buch, B Sodeik, T Werfel
Plasmacytoid dendritic cells (pDCs) were described to accumulate in the skin of patients with psoriasis and to be recruited into the dermis upon allergen challenge in atopic dermatitis. Importantly, activation of pDCs in the skin has been identified as important initiator of psoriasis development. RNase 7 is one of the major antimicrobial peptides (AMP) secreted by keratinocytes and is expressed in significantly higher amounts in lesional skin of patients with atopic dermatitis or psoriasis than in healthy individuals...
November 17, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29152711/the-burst-phase-folding-intermediate-of-ribonuclease-h-changes-conformation-over-evolutionary-history
#5
Shion A Lim, Susan Marqusee
The amino acid sequence encodes the energy landscape of a protein. Therefore, we expect evolutionary mutations to change features of the protein energy landscape, including the conformations adopted by a polypeptide as it folds to its native state. Ribonucleases H (RNase H) from Escherichia coli and Thermus thermophilus both fold via a partially folded intermediate in which the core region of the protein (helices A-D and strands 4-5) is structured. Strand 1, however, uniquely contributes to the T. thermophilus RNase H folding intermediate (Icore+1 ), but not the E...
November 20, 2017: Biopolymers
https://www.readbyqxmd.com/read/29149301/use-of-domain-swapping-to-identify-candidate-amino-acids-involved-in-differential-interactions-between-two-allelic-variants-of-type-1%C3%A2-s-locus-f-box-protein-and-s3-rnase-in-petunia-inflata
#6
Lihua Wu, Justin S Williams, Ning Wang, Wasi A Khatri, Daniele San Román, Teh-Hui Kao
Petunia inflata possesses a self-incompatibility (SI) mechanism, which involves S-RNase and multiple S-locus F-box (SLF) genes at the polymorphic S-locus. For a given S-haplotype, each SLF is thought to interact with some of its non-self S-RNases, but not with its self-S-RNase. In this work, we studied an allelic pair of SLF1, S2-SLF1 and S3-SLF1, which differ in 44 amino acids and show differential interactions with S3-RNase. We first used an in vivo transgenic assay to determine whether four chimeric proteins of S2-SLF1 and S3-SLF1, each with one of the three functional domains swapped, interact with S3-RNase...
November 15, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29148824/biobanking-of-fresh-frozen-cancer-tissue-rna-is-stable-independent-of-tissue-type-with-less-than-1-hour-of-cold-ischemia
#7
Sang Yong Song, Jonghyun Jun, Miyeon Park, Seo Kyu Park, Wonju Choi, Kyunghee Park, Kee-Taek Jang, Myoyong Lee
BACKGROUND: The effects of preanalytical variables in tissue processing and storage periods on RNA quality of tissues have been well documented in each type of cancer. However, few studies have been performed on a comparative assessment of the impacts across different cancer tissues, even though it is well known that RNase activity is highly variable in various tissue types and RNase-rich tissues have been found to yield low-quality RNA. METHODS: We investigated the impacts of cold ischemia times and long-term storage on RNA integrity in various types of cancer tissue, which had been fresh-frozen and collected at the Samsung Medical Center Biobank...
November 17, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/29146908/lrpprc-mediated-folding-of-the-mitochondrial-transcriptome
#8
Stefan J Siira, Henrik Spåhr, Anne-Marie J Shearwood, Benedetta Ruzzenente, Nils-Göran Larsson, Oliver Rackham, Aleksandra Filipovska
The expression of the compact mammalian mitochondrial genome requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, and here we use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA-protein interactions in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29139200/allosteric-mechanism-of-quinoline-inhibitors-for-hiv-rt-associated-rnase-with-md-simulation-and-dynamics-fluctuation-network
#9
Yi Cai, Hao Liu, Haifeng Chen
The human immunodeficiency virus (HIV) is a retrovirus which infects T lymphocyte of human body and causes Immunodeficiency. Reverse transcriptase inhibitors (RTIs) can inhibit some functions of RT, preventing virus synthesis (double-stranded DNA), so that HIV virus replication can be reduced. Experimental results indicate a series of benzimidazole-based inhibitors which target HIV RT-associate RNase to inhibit the reverse transcription of HIV virus. However, the allosteric mechanism is still unclear. Here, molecular dynamics simulations and dynamics fluctuation network analysis were used to reveal the binding mode between the inhibitors and RT-associate RNase...
November 15, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29139109/%C3%AE-cyclodextrin-encapsulated-polyphenols-as-effective-antioxidants
#10
Pritam Roy, Amit Kumar Dinda, Susmitnarayan Chaudhury, Swagata Dasgupta
Formation of dityrosine (DT) cross-linkages in proteins is one of the most widely used markers of oxidative stress. Ribonuclease A (RNase A) has 6 Tyr residues and shows a characteristic DT fluorescence peak upon oxidation in addition to major changes in its secondary structure. DT formation can be prevented by using polyphenols (GA, ECG, and EGCG) which are known to have strong antioxidant activity. However, it has been observed that ECG and EGCG initiate protein oligomerization due to protein-polyphenol cross-linkages...
November 15, 2017: Biopolymers
https://www.readbyqxmd.com/read/29136196/analysis-of-the-natively-unstructured-rna-protein-recognition-core-in-the-escherichia-coli-rna-degradosome-and-its-interactions-with-regulatory-rna-hfq-complexes
#11
Heather A Bruce, Dijun Du, Dijana Matak-Vinkovic, Katarzyna J Bandyra, R William Broadhurst, Esther Martin, Frank Sobott, Alexander V Shkumatov, Ben F Luisi
The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126318/rnase-h-sequence-preferences-influence-antisense-oligonucleotide-efficiency
#12
Lukasz J Kielpinski, Peter H Hagedorn, Morten Lindow, Jeppe Vinther
RNase H cleaves RNA in RNA-DNA duplexes. It is present in all domains of life as well as in multiple viruses and is essential for mammalian development and for human immunodeficiency virus replication. Here, we developed a sequencing-based method to measure the cleavage of thousands of different RNA-DNA duplexes and thereby comprehensively characterized the sequence preferences of HIV-1, human and Escherichia coli RNase H enzymes. We find that the catalytic domains of E. coli and human RNase H have nearly identical sequence preferences, which correlate with the efficiency of RNase H-recruiting antisense oligonucleotides...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29124095/circular-transcriptome-sequencing-of-the-middle-silk-gland-and-posterior-silk-gland-in-the-bombyx-mori
#13
Huaiyan Gan, Tieshan Feng, Yuqian Wu, Chun Liu, Qingyou Xia, Tingcai Cheng
Circular transcriptome sequencing of the middle silk gland (MSG) and posterior silk gland (PSG) in the Bombyx mori are presented. The middle silk gland and posterior silk gland were collected from the third day of fifth-instar B.mori larvae. The circular RNAs enriched by using RNase R to degrade the linear RNA molecules, and circular RNA sequencing (circRNA-seq) was performed using an Illumina Hiseq. 2500 sequencing platform. Samples are described in the SRA portal (SRP100385) and FASTQ files have been deposited in Sequence Read Archive (accession numbers: SRX2577343 and SRX2577342)...
December 2017: Data in Brief
https://www.readbyqxmd.com/read/29123201/insecticidal-effects-of-dsrna-targeting-the-diap1-gene-in-dipteran-pests
#14
Michelle Powell, Prashant Pyati, Min Cao, Howard Bell, John A Gatehouse, Elaine Fitches
The Drosophila melanogaster (fruit fly) gene Diap1 encodes a protein referred to as DIAP1 (D rosophila Inhibitor of Apoptosis Protein 1) that acts to supress apoptosis in "normal" cells in the fly. In this study we investigate the use of RNA interference (RNAi) to control two dipteran pests, Musca domestica and Delia radicum, by disrupting the control of apoptosis. Larval injections of 125-500 ng of Diap1 dsRNA resulted in dose-dependent mortality which was shown to be attributable to down-regulation of target mRNA...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29122886/mechanism-of-polypurine-tract-primer-generation-by-hiv-1-reverse-transcriptase
#15
Małgorzata Figiel, Miroslav Krepl, Sangwoo Park, Jarosław Poznański, Krzysztof Skowronek, Agnieszka Gołąb, Taekjip Ha, Jiři Šponer, Marcin Nowotny
HIV-1 reverse transcriptase (HIV-1 RT) possesses both DNA polymerase activity and RNase H activity that act in concert to convert single-stranded RNA of the viral genome to double-stranded DNA that is then integrated into the DNA of the infected cell. Reverse transcriptase-catalyzed reverse transcription critically relies on the proper generation of a polypurine tract (PPT) primer. However, the mechanism of PPT primer generation and the features of the PPT sequence that are critical for its recognition by HIV-1 RT remain unclear...
November 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29118447/influenza-virus-segment-5-rna-secondary-structure-and-new-targets-for-antiviral-strategies
#16
Marta Soszynska-Jozwiak, Paula Michalak, Walter N Moss, Ryszard Kierzek, Julita Kesy, Elzbieta Kierzek
Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29117179/a-mutation-in-the-viral-sensor-2-5-oligoadenylate-synthetase-2-causes-failure-of-lactation
#17
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
#18
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/29116782/inner-sphere-coordination-of-divalent-metal-ion-with-nucleobase-in-catalytic-rna
#19
Xin Liu, Yu Chen, Carol A Fierke
Identification of the function of metal ions and the RNA moieties, particularly nucleobases, that bind metal ions are important questions in RNA catalysis. Here we combine single-atom and abasic substitutions to probe functions of conserved nucleobases in ribonuclease P (RNase P). Structural and biophysical studies of bacterial RNase P propose direct coordination of metal ions by the nucleobases of conserved uridine and guanosine in helix P4 of the RNA subunit (P RNA). To biochemically probe the function of metal ion interactions, we substituted the universally conserved bulged uridine (U51) in the P4 helix of circularly permuted Bacillus subtilis P RNA with 4-thiouridine, 4-deoxyuridine and abasic modifications and G378/379 with 2-aminopurine, N7-deazaguanosine, and 6-thioguanosine...
November 8, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29111294/oxygen-binding-isotope-effects-of-triazole-based-hiv-1-reverse-transcriptase-inhibitors-indicate-the-actual-binding-site
#20
Agnieszka Krzemińska, Tomasz Frączek, P Paneth
Binding isotope effects (BIEs) associated with binding of four triazole-based ligands to HIV-1 reverse transcriptase have been calculated at the QM/MM MD level of theory. Two main binding sites: allosteric cavity and RNase H active site, as well as three other sites reported in the literature (the Knuckles, the NNRTI Adjacent, and Incoming Nucleotide Binding) have been considered. The interactions between inhibitors and these protein sites have been quantified by binding free energies obtained from free energy perturbation (FEP) calculations, supported by interaction energy analysis...
December 1, 2017: Archives of Biochemistry and Biophysics
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