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RNase L

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https://www.readbyqxmd.com/read/28092684/biallelic-mutations-in-the-3-exonuclease-toe1-cause-pontocerebellar-hypoplasia-and-uncover-a-role-in-snrna-processing
#1
Rea M Lardelli, Ashleigh E Schaffer, Veerle R C Eggens, Maha S Zaki, Stephanie Grainger, Shashank Sathe, Eric L Van Nostrand, Zinayida Schlachetzki, Basak Rosti, Naiara Akizu, Eric Scott, Jennifer L Silhavy, Laura Dean Heckman, Rasim Ozgur Rosti, Esra Dikoglu, Anne Gregor, Alicia Guemez-Gamboa, Damir Musaev, Rohit Mande, Ari Widjaja, Tim L Shaw, Sebastian Markmiller, Isaac Marin-Valencia, Justin H Davies, Linda de Meirleir, Hulya Kayserili, Umut Altunoglu, Mary Louise Freckmann, Linda Warwick, David Chitayat, Susan Blaser, Ahmet Okay Çağlayan, Kaya Bilguvar, Huseyin Per, Christina Fagerberg, Henrik T Christesen, Maria Kibaek, Kimberly A Aldinger, David Manchester, Naomichi Matsumoto, Kazuhiro Muramatsu, Hirotomo Saitsu, Masaaki Shiina, Kazuhiro Ogata, Nicola Foulds, William B Dobyns, Neil C Chi, David Traver, Luigina Spaccini, Stefania Maria Bova, Stacey B Gabriel, Murat Gunel, Enza Maria Valente, Marie-Cecile Nassogne, Eric J Bennett, Gene W Yeo, Frank Baas, Jens Lykke-Andersen, Joseph G Gleeson
Deadenylases are best known for degrading the poly(A) tail during mRNA decay. The deadenylase family has expanded throughout evolution and, in mammals, consists of 12 Mg(2+)-dependent 3'-end RNases with substrate specificity that is mostly unknown. Pontocerebellar hypoplasia type 7 (PCH7) is a unique recessive syndrome characterized by neurodegeneration and ambiguous genitalia. We studied 12 human families with PCH7, uncovering biallelic, loss-of-function mutations in TOE1, which encodes an unconventional deadenylase...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28076346/cryo-em-structure-of-a-human-spliceosome-activated-for-step-2-of-splicing
#2
Karl Bertram, Dmitry E Agafonov, Wen-Ti Liu, Olexandr Dybkov, Cindy L Will, Klaus Hartmuth, Henning Urlaub, Berthold Kastner, Holger Stark, Reinhard Lu Hrmann
Spliceosome rearrangements facilitated by RNA helicase Prp16 before catalytic step 2 of splicing are poorly understood. Here we report a 3D cryo-electron microscopy structure of the human spliceosomal C complex stalled directly after Prp16 action (C*). The architecture of the catalytic U2-U6 RNP core of the human C* spliceosome is highly similar to that of the yeast pre-Prp16 C complex. However, in C* the branched intron region is separated (by ~20 Å) from the catalytic centre, and its position close to the U6 snRNA ACAGA box is stabilised by interactions with the Prp8 RNase H-like and Prp17 WD40 domains...
January 11, 2017: Nature
https://www.readbyqxmd.com/read/28074027/a-unique-cis-encoded-small-noncoding-rna-is-regulating-legionella-pneumophila-hfq-expression-in-a-life-cycle-dependent-manner
#3
Giulia Oliva, Tobias Sahr, Monica Rolando, Maike Knoth, Carmen Buchrieser
: Legionella pneumophila is an environmental bacterium that parasitizes protozoa, but it may also infect humans, thereby causing a severe pneumonia called Legionnaires' disease. To cycle between the environment and a eukaryotic host, L. pneumophila is regulating the expression of virulence factors in a life cycle-dependent manner: replicating bacteria do not express virulence factors, whereas transmissive bacteria are highly motile and infective. Here we show that Hfq is an important regulator in this network...
January 10, 2017: MBio
https://www.readbyqxmd.com/read/28067412/broadening-the-phenotypic-spectrum-of-pop1-skeletal-dysplasias-identification-of-pop1-mutations-in-a-mild-and-severe-skeletal-dysplasia
#4
Jimena Barraza-García, Carlos I Rivera-Pedroza, Alfonso Hisado-Oliva, Alberta Belinchón-Martínez, Lucia Sentchordi-Montané, Emma L Duncan, Graeme R Clark, Angela Del Pozo, Kristina Ibáñez-Garikano, Amaka Offiah, Pablo Prieto-Matos, Valerie Cormier-Daire, Karen E Heath
POP1 is a large protein common to the RNase-MRP and RNase-P (RMRP) endoribonucleoprotein complexes. Although its precise function is unknown, it appears to participate in the assembly or stability of both complexes. Numerous RMRP mutations have been reported in individuals with cartilage hair hypoplasia (CHH) but, to date, only three POP1 mutations have been described in two families with features similar to anauxetic dysplasia (AD). We present two further individuals, one with severe short stature and a relatively mild skeletal dysplasia and another in whom AD was suspected...
January 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28064315/-activation-of-biosynthesis-of-guanyl-specific-ribonuclease-secreted-by-bacillus-circulans-under-salt-stress
#5
M A Kharitonova, L V Kipenskaya, O N Ilinskaya
The gene transcription of guanyl-specific ribonucleases (RNases), which provide available phosphate to cells of Bacillus, is controlled by the signal transduction system PhoP-PhoR. However, the biosynthesis of B. circulans RNase does not depend on the signal-transduction regulatory proteins of Pho regulon. It has been found that raising the salt molar concentration in culture medium increases the level of extracellular guanyl-specific ribonuclease Bci synthesized by B. circulans. Sequences homologous to the binding sites of the regulatory protein DegU were found in RNase Bci promoter...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28053103/cytokines-elevated-in-hiv-elite-controllers-reduce-hiv-replication-in-vitro-and-modulate-hiv-restriction-factor-expression
#6
Evan S Jacobs, Sheila M Keating, Mohamed Abdel-Mohsen, Stuart L Gibb, John W Heitman, Heather C Inglis, Jeffrey N Martin, Jinbing Zhang, Zhanna Kaidarova, Xutao Deng, Shiquan Wu, Kathryn Anastos, Howard Crystal, Maria C Villacres, Mary Young, Ruth M Greenblatt, Alan L Landay, Stephen J Gange, Steven G Deeks, Elizabeth T Golub, Satish K Pillai, Philip J Norris
: A subset of HIV infected individuals termed elite controllers (ECs) maintain CD4+ T cell counts and control viral replication in the absence of antiretroviral therapy (ART). Systemic cytokine responses may differentiate ECs from subjects with uncontrolled viral replication or those who require ART to suppress viral replication. We measured 87 cytokines in four groups of women: 73 EC, 42 with pharmacologically suppressed viremia (ART), 42 with uncontrolled viral replication (noncontrollers, NC), and 48 HIV uninfected (NEG) subjects...
January 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28003490/lineage-a-betacoronavirus-ns2-proteins-and-homologous-torovirus-berne-pp1a-carboxyterminal-domain-are-phosphodiesterases-that-antagonize-activation-of-rnase-l
#7
Stephen A Goldstein, Joshua M Thornbrough, Rong Zhang, Babal K Jha, Yize Li, Ruth Elliott, Katherine Quiroz-Figueroa, Annie I Chen, Robert H Silverman, Susan R Weiss
: Viruses in the family Coronaviridae, with the Nidovirus order, are etiologic agents of a range of human and animal diseases, including both mild and severe respiratory disease in humans. These viruses encode conserved replicase and structural proteins, and more diverse accessory proteins in the 3' end of their genomes that often act as host cell antagonists. We have previously shown that 2', 5' phosphodiesterases (PDE) encoded by the prototypical Betacoronavirus, mouse hepatitis virus (MHV), Middle East respiratory syndrome-associated coronavirus antagonize the oligoadenylate - ribonuclease L (OAS-RNase L) pathway...
December 21, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27920203/a-highly-active-isoform-of-lentivirus-restriction-factor-samhd1-in-mouse
#8
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/27888443/the-effect-of-heat-and-free-chlorine-treatments-on-the-surface-properties-of-murine-norovirus
#9
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/27836995/small-rna-interactome-of-pathogenic-e-%C3%A2-coli-revealed-through-crosslinking-of-rnase-e
#10
Shafagh A Waters, Sean P McAteer, Grzegorz Kudla, Ignatius Pang, Nandan P Deshpande, Timothy G Amos, Kai Wen Leong, Marc R Wilkins, Richard Strugnell, David L Gally, David Tollervey, Jai J Tree
RNA sequencing studies have identified hundreds of non-coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high-throughput analysis of RNA-RNA interactions in bacteria. Here we demonstrate that in vivo sRNA-mRNA duplexes can be recovered using UV-crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs...
November 11, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27834201/identification-of-ybey-protein-interactions-involved-in-16s-rrna-maturation-and-stress-regulation-in-escherichia-coli
#11
Maarten Vercruysse, Caroline Köhrer, Yang Shen, Sandra Proulx, Anubrata Ghosal, Bryan W Davies, Uttam L RajBhandary, Graham C Walker
: YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3' end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology...
November 8, 2016: MBio
https://www.readbyqxmd.com/read/27831565/a-link-between-adipogenesis-and-innate-immunity-rnase-l-promotes-3t3-l1-adipogenesis-by-destabilizing-pref-1-mrna
#12
Yi-Ting Wang, Hou-Hsien Chiang, Ying-Shing Huang, Chia-Lang Hsu, Po-Jen Yang, Hsueh-Fen Juan, Wei-Shiung Yang
Ribonuclease L (RNase-L) is an endoribonuclease well known for its roles in innate immunity. Recently it has been shown to regulate several cellular functions by modulating the levels of specific mRNAs. In this study, we investigated whether RNase-L may regulate adipocyte functions. We showed that knockdown of RNase-L reduced 3T3-L1 adipocyte differentiation and lipid accumulation. After mRNA profiling, we found that upregulation of Pref-1 mRNA, an inhibitory regulator of adipogenesis, could explain the reduced adipocyte differentiation with RNase-L downregulation...
November 10, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27789644/genome-sequence-of-the-multiple-protease-producing-strain-geobacillus-thermoleovorans-n7-a-thermophilic-bacterium-isolated-from-paniphala-hot-spring-west-bengal-india
#13
Sucharita Bose, Trinetra Mukherjee, Urmimala Sen, Chayan Roy, Moidu Jameela Rameez, Wriddhiman Ghosh, Subhra Kanti Mukhopadhyay
Here, we present the draft genome sequence of Geobacillus thermoleovorans strain N7 (MCC 3175), isolated from Paniphala Hot Spring, West Bengal, India, which contains genes that encode several industrially and medically important thermostable enzymes like neutral protease, xylose isomerase, rhamnogalacturonan acetylesterase, nitrate and nitrite reductase, l-asparaginase, glutaminase, and RNase P.
October 27, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27765358/sennoside-a-derived-from-the-traditional-chinese-medicine-plant-rheum-l-is-a-new-dual-hiv-1-inhibitor-effective-on-hiv-1-replication
#14
Francesca Esposito, Ilaria Carli, Claudia Del Vecchio, Lijia Xu, Angela Corona, Nicole Grandi, Dario Piano, Elias Maccioni, Simona Distinto, Cristina Parolin, Enzo Tramontano
BACKGROUND: Despite the availability of effective antiretroviral therapies, drugs for HIV-1 treatment with new mode of action are still needed. An innovative approach is aimed to identify dual HIV-1 inhibitors, small molecules that can inhibit two viral functions at the same time. Rhubarb, originated from Rheum palmatum L. and Rheum officinale Baill., is one of the earliest and most commonly used medicinal plants in Traditional Chinese Medicine (TCM) practice. We wanted to explore TCM for the identification of new chemical scaffolds with dual action abilities against HIV-1...
November 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/27729457/molecular-basis-for-cytoplasmic-rna-surveillance-by-uridylation-triggered-decay-in-drosophila
#15
Madalena M Reimão-Pinto, Raphael A Manzenreither, Thomas R Burkard, Pawel Sledz, Martin Jinek, Karl Mechtler, Stefan L Ameres
The posttranscriptional addition of nucleotides to the 3' end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that in flies, 3' terminal RNA uridylation triggers the processive, 3'-to-5' exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, terminal RNA uridylation-mediated processing (TRUMP) complex that functionally cooperates in the degradation of structured RNA RNA immunoprecipitation and high-throughput sequencing reveals a variety of TRUMP complex substrates, including abundant non-coding RNA, such as 5S rRNA, tRNA, snRNA, snoRNA, and the essential RNase MRP Based on genetic and biochemical evidence, we propose a key function of the TRUMP complex in the cytoplasmic quality control of RNA polymerase III transcripts...
November 15, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27704074/signal-amplification-of-micrornas-with-modified-strand-displacement-based-cycling-probe-technology
#16
Huning Jia, Ying Bu, Bingjie Zou, Jianping Wang, Shalen Kumar, Janet L Pitman, Guohua Zhou, Qinxin Song
Micro ribose nucleic acids (miRNAs) play an important role in biological processes such as cell differentiation, proliferation and apoptosis. Therefore, miRNAs are potentially a powerful marker for monitoring cancer and diagnosis. Here, we present sensitive signal amplification for miRNAs based on modified cycling probe technology with strand displacement amplification. miRNA was captured by the template coupled with beads, and then the first cycle based on SDA was repeatedly extended to the nicking end, which was produced by the extension reaction of miRNA...
September 30, 2016: Analyst
https://www.readbyqxmd.com/read/27663720/the-role-of-mouse-2-5-oligoadenylate-synthetase-1-paralogs
#17
Enas Elkhateeb, Hassan T Tag-El-Din-Hassan, Nobuya Sasaki, Daisuke Torigoe, Masami Morimatsu, Takashi Agui
The interferon-induced oligoadenylate synthetase (OAS) family is one of the most important immune response proteins to the viral infection. The OAS protein binds dsRNA and is activated to produce 2',5'-oligoadenylates, which lead to the activation of latent form of RNase L, resulting in degradation of cellular and viral RNA and inhibition of viral replication. In mice, the Oas gene family locates on chromosome 5. The mouse Oas gene locus undergoes a recent series of duplication event, leading to the presence of eight paralogs of Oas1 genes (Oas1a through Oas1h) that forms Oas gene cluster with the Oas2, Oas3 and two OasL (OasL1 and OasL2) genes...
September 21, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27643814/atomic-modeling-of-the-its2-ribosome-assembly-subcomplex-from-cryo-em-together-with-mass-spectrometry-identified-protein-protein-crosslinks
#18
Shan Wu, Dan Tan, John L Woolford, Meng-Qiu Dong, Ning Gao
The assembly of ribosomal subunits starts in the nucleus, initiated by co-transcriptional folding of nascent ribosomal RNA (rRNA) transcripts and binding of ribosomal proteins and assembly factors. The internal transcribed spacer 2 (ITS2) is a precursor sequence to be processed from the intermediate 27S rRNA in the nucleoplasm; its removal is required for nuclear export of pre-60S particles. The proper processing of the ITS2 depends on multiple associated assembly factors and RNases. However, none of the structures of the known ITS2-binding factors is available...
January 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27634929/topology-independent-comparison-of-rna-3d-structures-using-the-click-algorithm
#19
Minh N Nguyen, Adelene Y L Sim, Yue Wan, M S Madhusudhan, Chandra Verma
RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting...
September 14, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27595182/new-advances-in-our-understanding-of-the-unique-rnase-l-in-host-pathogen-interaction-and-immune-signaling
#20
Elona Gusho, Danika Baskar, Shuvojit Banerjee
Ever since the discovery of the existence of an interferon (IFN)-regulated ribonuclease, significant advances have been made in understanding the mechanism and associated regulatory effects of its action. What had been studied initially as a "unique" endoribonuclease is currently known as ribonuclease L (RNase L where "L" stands for latent). Some of the key developments include discovery of the RNase L signaling pathway, its structural characterization, and its molecular cloning. RNase L has been implicated in antiviral and antibacterial defense, as well as in hereditary prostate cancer...
August 29, 2016: Cytokine
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