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https://www.readbyqxmd.com/read/27924926/identification-of-protein-structural-elements-responsible-for-the-diversity-of-sequence-preferences-among-mini-iii-rnases
#1
Dawid Głów, Małgorzata Kurkowska, Justyna Czarnecka, Krzysztof Szczepaniak, Dariusz Pianka, Verena Kappert, Janusz M Bujnicki, Krzysztof J Skowronek
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920254/casein-kinase-2-is-linked-to-stress-granule-dynamics-through-phosphorylation-of-the-stress-granule-nucleating-protein-g3bp1
#2
Lucas C Reineke, Wei-Chih Tsai, Antrix Jain, Jason T Kaelber, Sung Yun Jung, Richard E Lloyd
Stress granules are large macromolecular aggregates that contain translation initiation complexes and mRNAs. Stress granule formation coincides with translational repression, and stress granules actively signal to mediate cell fate decisions by a) signaling to the translation apparatus to maintain translational repression, b) mount various transcriptional responses including innate immunity, and c) to repress apoptosis. Previous work showed G3BP1 is phosphorylated at serine 149, which regulates G3BP1 oligomerization, stress granule assembly, and RNase activity intrinsic to G3BP1...
December 5, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27920203/a-highly-active-isoform-of-lentivirus-restriction-factor-samhd1-in-mouse
#3
Nicolin Bloch, Sabine Gläsker, Poojitha Sitaram, Henning Hofmann, Caitlin N Shepard, Megan L Schultz, Baek Kim, Nathaniel R Landau
The triphosphohydrolase SAMHD1 restricts HIV-1 replication in nondividing myeloid cells by depleting the dNTP pool, preventing reverse transcription. SAMHD1 is also reported to have ribonuclease activity that degrades the virus genomic RNA. Human SAMHD1 is regulated by phosphorylation of its carboxy-terminus at T592, which abrogates its antiviral function yet has only a small effect on its phosphohydrolase activity. In the mouse, SAMHD1 is expressed as two isoforms (ISF1 and ISF2) that differ at the carboxy-terminus due to alternative splicing of the last coding exon...
December 5, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27911030/acellular-endocardium-as-a-novel-biomaterial-for-the-intima-of-tissue-engineered-small-caliber-vascular-grafts
#4
Feng Wang, Xin Guan, TianYi Wu, JianOu Qiao, ZhaoQing Han, JinLong Wu, XiaoWei Yu, QingJun You
We aimed to investigate whether acellular endocardium can be used as a useful biomaterial for the intima of engineered small-caliber vascular grafts. Fresh endocardium was harvested from the swine left atrium and was decellularized by digestion with the decellularization solution of Triton X-100 and SDS containing DNase I and RNase A. Surface morphological characteristics and Young's modulus were evaluated. To analyze the effect of mechanical characteristics on cell adhesion, the decellularized endocardium was stiffened with 2...
December 2016: Artificial Organs
https://www.readbyqxmd.com/read/27907832/modeling-of-the-catalytic-core-of-arabidopsis-thaliana-dicer-like-4-protein-and-its-complex-with-double-stranded-rna
#5
Agnieszka Mickiewicz, Joanna Sarzyńska, Maciej Miłostan, Anna Kurzyńska-Kokorniak, Agnieszka Rybarczyk, Piotr Łukasiak, Tadeusz Kuliński, Marek Figlerowicz, Jacek Błażewicz
Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA...
November 17, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27902925/targeted-inhibition-of-wrn-helicase-replication-stress-and-cancer
#6
REVIEW
Natalie Orlovetskie, Raphael Serruya, Ghada Abboud-Jarrous, Nayef Jarrous
WRN helicase has several roles in genome maintenance, such as replication, base excision repair, recombination, DNA damage response and transcription. These processes are often found upregulated in human cancers, many of which display increased levels of WRN. Therefore, directed inhibition of this RecQ helicase could be beneficial to selective cancer therapy. Inhibition of WRN is feasible by the use of small-molecule inhibitors or application of RNA interference and EGS/RNase P targeting systems. Remarkably, helicase depletion leads to a severe reduction in cell viability due to mitotic catastrophe, which is triggered by replication stress induced by DNA repair failure and fork progression arrest...
November 27, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27899605/poly-a-specific-ribonuclease-regulates-the-processing-of-small-subunit-rrnas-in-human-cells
#7
Hideaki Ishikawa, Harunori Yoshikawa, Keiichi Izumikawa, Yutaka Miura, Masato Taoka, Yuko Nobe, Yoshio Yamauchi, Hiroshi Nakayama, Richard J Simpson, Toshiaki Isobe
Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899559/division-of-labor-among-mycobacterium-smegmatis-rnase-h-enzymes-rnase-h1-activity-of-rnha-or-rnhc-is-essential-for-growth-whereas-rnhb-and-rnha-guard-against-killing-by-hydrogen-peroxide-in-stationary-phase
#8
Richa Gupta, Debashree Chatterjee, Michael S Glickman, Stewart Shuman
RNase H enzymes sense the presence of ribonucleotides in the genome and initiate their removal by incising the ribonucleotide-containing strand of an RNA:DNA hybrid. Mycobacterium smegmatis encodes four RNase H enzymes: RnhA, RnhB, RnhC and RnhD. Here, we interrogate the biochemical activity and nucleic acid substrate specificity of RnhA. We report that RnhA (like RnhC characterized previously) is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899035/delayed-seroconversion-to-htlv-ii-is-associated-with-a-stop-codon-mutation-in-the-pol-gene
#9
Syamalima Dube, Dipak K Dube, Lynn Abbott, Jordan Glaser, Bernard Poiesz
A known HIV-1 positive intravenous drug user was found to be HTLV-II DNA positive by PCR but seronegative in a screening ELISA assay. He was consistently DNA positive but took two years to fully seroconvert. Sequencing of the HTLV-II strain in his cultured T-lymphocytes indicated that it is a prototypical type A strain with no major differences in the LTR DNA sequence, nor major amino acid differences in the Gag, Env, Tax and Rex proteins. However, a mutation in its pol gene created a stop codon at amino acid 543 of the Pol protein, a region which encodes for the RNase function...
November 29, 2016: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/27894092/a-novel-fully-human-anti-ncl-immunornase-for-triple-negative-breast-cancer-therapy
#10
Chiara D'Avino, Dario Palmieri, Ashley Braddom, Nicola Zanesi, Cindy James, Sara Cole, Francesco Salvatore, Carlo M Croce, Claudia De Lorenzo
Breast cancer is the most common cancer in women worldwide. A new promising anti-cancer therapy involves the use of monoclonal antibodies specific for target tumor-associated antigens (TAAs). A TAA of interest for immunotherapy of Triple Negative Breast Cancer (TNBC) is nucleolin (NCL), a multifunctional protein, selectively expressed on the surface of cancer cells, which regulates the biogenesis of specific microRNAs (miRNAs) involved in tumor development and drug-resistance. We previously isolated a novel human anti-NCL scFv, called 4LB5, that is endowed with selective anti-tumor effects...
November 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27893764/virus-mediated-alterations-in-mirna-factors-and-degradation-of-viral-mirnas-by-mcpip1
#11
Christine Happel, Dhivya Ramalingam, Joseph M Ziegelbauer
Kaposi's sarcoma-associated herpesvirus (KSHV), the causative agent of Kaposi's sarcoma, encodes 25 mature viral miRNAs. MCP-1-induced protein-1 (MCPIP1), a critical regulator of immune homeostasis, has been shown to suppress miRNA biosynthesis via cleavage of precursor miRNAs through its RNase domain. We demonstrate that MCPIP1 can directly cleave KSHV and EBV precursor miRNAs and that MCPIP1 expression is repressed following de novo KSHV infection. In addition, repression with siRNAs to MCPIP1 in KSHV-infected cells increased IL-6 and KSHV miRNA expression, supporting a role for MCPIP1 in IL-6 and KSHV miRNA regulation...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27890900/in-vitro-and-in-vivo-biophysical-properties-of-oligonucleotides-containing-5-thio-nucleosides
#12
Md Ariful Islam, Reiko Waki, Aki Fujisaka, Kosuke Ramon Ito, Satoshi Obika
Phosphorothioate modification is one of the most widely investigated and promising chemical modifications in oligonucleotide (ON) based therapeutics. Structurally similar 5'-thio or phosphorothiolate-modified nucleotides, in which a 5'-bridging oxygen is replaced with a sulfur atom, are gaining importance for ON-based research. Several reports have been published describing the synthesis of 5'-thio-modified ONs but no detailed in vitro and in vivo data are available. Here, we report the synthesis of 5'-thio-modified 2'-deoxy-5-methylcytidine...
2016: Drug Discoveries & Therapeutics
https://www.readbyqxmd.com/read/27890678/hot-spot-mapping-of-protein-surfaces-with-tempol-bovine-pancreatic-rnase-a-as-a-model-system
#13
Neri Niccolai, Edoardo Morandi, Simone Gardini, Valentino Costabile, Roberta Spadaccini, Orlando Crescenzi, Delia Picone, Ottavia Spiga, Andrea Bernini
TEMPOL spin-label has been used to identify surface exposure of protein nuclei from NMR analysis of the induced paramagnetic relaxation enhancements (PRE). The absence of linear dependence between atom depths and observed PRE reveals that specific mechanisms drive the approach of the paramagnet to the protein surface. RNase A represents a unique protein system to explore the fine details of the information offered by TEMPOL induced PRE, due to the abundance of previous results, obtained in solution and in the crystal, dealing with surface dynamics behavior of this protein...
November 24, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27888443/the-effect-of-heat-and-free-chlorine-treatments-on-the-surface-properties-of-murine-norovirus
#14
Adrien Brié, Ravo Razafimahefa, Julie Loutreul, Aurélie Robert, Christophe Gantzer, Nicolas Boudaud, Isabelle Bertrand
Heat and free chlorine are among the most efficient and commonly used treatments to inactivate enteric viruses, but their global inactivation mechanisms have not been elucidated yet. These treatments have been shown to affect at least the capsid proteins of viruses and thus may affect the surface properties (i.e. electrostatic charge and hydrophobicity) of such particles. Our aim was to study the effects of heat and free chlorine on surface properties for a murine norovirus chosen as surrogate for human norovirus...
November 25, 2016: Food and Environmental Virology
https://www.readbyqxmd.com/read/27888105/efficient-ex%C3%A2-vivo-delivery-of-chemically-modified-messenger-rna-using-lipofection-and-magnetofection
#15
Zohreh Sadat Badieyan, Tamara Pasewald, Olga Mykhaylyk, Carsten Rudolph, Christian Plank
Recently, chemically modified mRNA (cmRNA) therapeutics have been the subject of extensive application-oriented research in both academia and industry as a safer alternative for gene and recombinant protein therapies. However, the lack of an efficient delivery system hinders widespread application. Here we used ∼100-nm lipoplexes and magnetic lipoplexes that can protect cmRNA from RNases and efficiently deliver it into muscle and fat tissues as well as to the endothelium of the carotid artery. Establishing magnetofection for ex vivo cmRNA delivery for the first time, we suggest this method for potential enhanced and targeted delivery of cmRNA...
November 22, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27886596/an-end-point-method-based-on-graphene-oxide-for-rnase-h-analysis-and-inhibitors-screening
#16
Chuan Zhao, Jialong Fan, Lan Peng, Lijian Zhao, Chunyi Tong, Wei Wang, Bin Liu
As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10(-3) units/ mL under optimal conditions...
November 16, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27881652/inhibition-of-human-cytomegalovirus-pul89-terminase-subunit-blocks-virus-replication-and-genome-cleavage
#17
Yan Wang, Lili Mao, Jayakanth Kankanala, Zhengqiang Wang, Robert J Geraghty
: Human cytomegalovirus terminase complex cleaves the concatemeric genomic DNA into unit lengths during genome packaging and particle assembly. This process is an attractive drug target because cleavage of concatemeric DNA is not required in mammalian cell DNA replication, indicating that drugs targeting the terminase complex could be safe and selective. One component of the human cytomegalovirus terminase complex, pUL89, provides the endonucleolytic activity for genome cleavage and the domain responsible is reported to have an RNase H-like fold...
November 23, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27881299/transient-rna-dna-hybrids-are-required-for-efficient-double-strand-break-repair
#18
Corina Ohle, Rafael Tesorero, Géza Schermann, Nikolay Dobrev, Irmgard Sinning, Tamás Fischer
RNA-DNA hybrids are a major internal cause of DNA damage within cells, and their degradation by RNase H enzymes is important for maintaining genomic stability. Here, we identified an unexpected role for RNA-DNA hybrids and RNase H enzymes in DNA repair. Using a site-specific DNA double-strand break (DSB) system in Schizosaccharomyces pombe, we showed that RNA-DNA hybrids form as part of the homologous-recombination (HR)-mediated DSB repair process and that RNase H enzymes are essential for their degradation and efficient completion of DNA repair...
November 3, 2016: Cell
https://www.readbyqxmd.com/read/27878651/messages-on-small-rna-duplexes-in-plants
#19
Taichiro Iki
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs...
November 23, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27875905/identification-of-novel-resistance-related-polymorphisms-in-hiv-1-subtype-c-rt-connection-and-rnase-h-domains-from-patients-under-virological-failure-in-brazil
#20
Maria Fernanda M Barral, Arielly K P Sousa, André F Santos, Celina M Abreu, Amilcar Tanuri, Marcelo A Soares
Mutations in the connection and RNase H C-terminal reverse transcriptase (RT) domains of HIV-1 have been shown to impact drug resistance to RT inhibitors. However, their impact in the context of non-B subtypes has been poorly assessed. This study aimed to characterize resistance-related mutations in the C-terminal portions of RT in treatment-failing patients from southern Brazil, a region with endemic HIV-1 subtype C (HIV-1C). Viral RNA was isolated and reverse transcribed from 280 infected subjects, and genomic regions were analyzed by PCR, DNA sequencing and phylogenetic analysis...
November 22, 2016: AIDS Research and Human Retroviruses
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