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https://www.readbyqxmd.com/read/28937734/discovery-of-oligonucleotide-signaling-mediated-by-crispr-associated-polymerases-solves-two-puzzles-but-leaves-an-enigma
#1
Eugene V Koonin, Kira S Makarova
The signature component of type III CRISPR-Cas systems is the Cas10 protein that consists of two Palm domains homologous to those of DNA and RNA polymerases, and nucleotide cyclases, and an HD nuclease domain. However, until very recently, the activity of the Palm domains and their role in CRISPR function have not been experimentally established. Most of the type III CRISPR-Cas systems and some type I systems also encompass proteins containing the CARF (CRISPR-associated Rossmann fold) domain that has been predicted to regulate CRISPR functions via nucleotide binding but its function in CRISPR-Cas remained obscure...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28936661/isolation-of-rice-sperm-cells-for-transcriptional-profiling
#2
Scott D Russell, Daniel S Jones, Sarah Anderson, Xinkun Wang, Venkatesan Sundaresan, Xiaoping Gou
The male germline of flowering plants displays unexpectedly divergent transcriptional profiles compared to other cell types and tissues of plants. As these are among the smallest cells, and are harbored within pollen, isolating a pure collection of germline RNA presents unusual challenges. The sperm cells of rice represent a particularly challenging subject for study as the pollen are unusually short lived upon release from the anther, and the marker gene sequences that make FACS possible in Arabidopsis have not yet been introduced into rice...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28935594/self-replicating-rna-vaccine-functionality-modulated-by-fine-tuning-of-polyplex-delivery-vehicle-structure
#3
Thomas Démoulins, Thomas Ebensen, Kai Schulze, Pavlos C Englezou, Panagiota Milona, Maria Pelliccia, Carlos A Guzmán, Nicolas Ruggli, Kenneth C McCullough
The major limitations with large and complex self-amplifying RNA vaccines (RepRNA) are RNase-sensitivity and inefficient translation in dendritic cells (DCs). Condensing RepRNA with polyethylenimine (PEI) gave positive in vitro readouts, but was largely inferior to virus-like replicon particles (VRP) or direct electroporation. In the present study, we improved such polyplex formulation and determined that fine-tuning of the polyplex structure is essential for ensuring efficacious translation. Thereby, three parameters dominate: (i) PEI molecular weight (MW); (ii) RepRNA:PEI (weight:weight) ratio; and (iii) inclusion of cell penetrating peptides (CPPs)...
September 18, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28935369/a-three-dimensional-model-of-rnase-p-in-the-hyperthermophilic-archaeon-pyrococcus-horikoshii-ot3
#4
Xuzhu Gao, Kosuke Oshima, Toshifumi Ueda, Takashi Nakashima, Makoto Kimura
Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5'-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model of PhopRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available...
September 18, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28931690/conformational-changes-in-the-5-end-of-the-hiv-1-genome-dependent-on-the-debranching-enzyme-dbr1-during-early-stages-of-infection
#5
Alvaro E Galvis, Hugh E Fisher, Hung Fan, David Camerini
Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation, but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5' end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 shRNA followed 48 hours later by infection with an HIV-1 derived vector containing an RNase H deficient reverse transcriptase...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28929238/nuclease-integrated-kinase-super-assemblies-niks-and-their-role-in-rna-processing
#6
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/28927503/learning-induces-the-translin-trax-rnase-complex-to-express-activin-receptors-for-persistent-memory
#7
Alan Jung Park, Robbert Havekes, Xiuping Fu, Rolf Hansen, Jennifer C Tudor, Lucia Peixoto, Zhi Li, Yen-Ching Wu, Shane G Poplawski, Jay M Baraban, Ted Abel
Long-lasting forms of synaptic plasticity and memory require de novo protein synthesis. Yet, how learning triggers this process to form memory is unclear. Translin/trax is a candidate to drive this learning-induced memory mechanism by suppressing microRNA-mediated translational silencing at activated synapses. We find that mice lacking translin/trax display defects in synaptic tagging, which requires protein synthesis at activated synapses, and long-term memory. Hippocampal samples harvested from these mice following learning show increases in several disease-related microRNAs targeting the activin A receptor type 1C (ACVR1C), a component of the transforming growth factor-β receptor superfamily...
September 20, 2017: ELife
https://www.readbyqxmd.com/read/28926591/no-evidence-for-the-presence-of-epstein-barr-virus-in-squamous-cell-carcinoma-of-the-mobile-tongue
#8
Torben Wilms, Gulfaraz Khan, Philip J Coates, Nicola Sgaramella, Robin Fåhraeus, Asma Hassani, Pretty S Philip, Lena Norberg Spaak, Luigi Califano, Giuseppe Colella, Katarina Olofsson, Christos Loizou, Renato Franco, Karin Nylander
Squamous cell carcinoma of the head and neck (SCCHN) comprises a large group of cancers in the oral cavity and nasopharyngeal area that typically arise in older males in association with alcohol/tobacco usage. Within the oral cavity, the mobile tongue is the most common site for tumour development. The incidence of tongue squamous cell carcinoma (TSCC) is increasing in younger people, which has been suggested to associate with a viral aetiology. Two common human oncogenic viruses, human papilloma virus (HPV) and Epstein-Barr virus (EBV) are known causes of certain types of SCCHN, namely the oropharynx and nasopharynx, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28926069/rna-directed-off-on-switch-of-rnase-h-activity-using-boronic-ester-formation
#9
Maëva Reverte, Ivan Barvik, Jean-Jacques Vasseur, Michael Smietana
RNase H is a non-specific endonuclease which degrades selectively the RNA strand in DNA/RNA duplexes. We demonstrate in the present study that 5'-boronic acid modified oligonucleotides hybridized to a RNA target sequence converts RNase H to an inactivated enzyme complex. The dynamic formation of a boronate ester upon addition of a diol moiety disrupts the enzyme-inhibitor complex and reactivates RNase H. Moreover, we show that reactivation of RNase H function can also be engineered through short RNA trimers inputs that fashion RNase H from a non-specific DNA-guided enzyme into an informational and programmable RNA-guided one...
September 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28924504/the-evolutionary-history-of-plant-t2-s-type-ribonucleases
#10
Karolis Ramanauskas, Boris Igić
A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context...
2017: PeerJ
https://www.readbyqxmd.com/read/28921966/tool-for-rapid-analysis-of-glycopeptide-by-permethylation-trap-via-one-pot-site-mapping-and-glycan-analysis
#11
Asif Shajahan, Nitin Tatyaso Supekar, Christian Heiss, Mayumi Ishihara, Parastoo Azadi
To overcome the challenges in the analysis of protein glycosylation, we have developed a comprehensive and universal tool through permethylation of glycopeptides and their tandem mass spectrometric analysis. This method has the potential to simplify glycoprotein analysis by integrating glycan sequencing and glycopeptide analysis in a single experiment. Moreover, glycans with unique glycosidic linkages, particularly from prokaryotes, which are resistant to enzymatic or chemical release, could also be detected and analyzed by this methodology...
September 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28918041/gapmer-antisense-oligonucleotides-suppress-the-mutant-allele-of-col6a3-and-restore-functional-protein-in-ullrich-muscular-dystrophy
#12
Elena Marrosu, Pierpaolo Ala, Francesco Muntoni, Haiyan Zhou
Dominant-negative mutations in the genes that encode the three major α chains of collagen type VI, COL6A1, COL6A2, and COL6A3, account for more than 50% of Ullrich congenital muscular dystrophy patients and nearly all Bethlem myopathy patients. Gapmer antisense oligonucleotides (AONs) are usually used for gene silencing by stimulating RNA cleavage through the recruitment of an endogenous endonuclease known as RNase H to cleave the RNA strand of a DNA-RNA duplex. In this study, we exploited the application of the allele-specific silencing approach by gapmer AON as a potential therapy for Collagen-VI-related congenital muscular dystrophy (COL6-CMD)...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28918028/human-dmbt1-derived-cell-penetrating-peptides-for-intracellular-sirna-delivery
#13
Martina Tuttolomondo, Cinzia Casella, Pernille Lund Hansen, Ester Polo, Luciana M Herda, Kenneth A Dawson, Henrik J Ditzel, Jan Mollenhauer
Small interfering RNA (siRNA) is a promising molecule for gene therapy, but its therapeutic administration remains problematic. Among the recently proposed vectors, cell-penetrating peptides show great promise in in vivo trials for siRNA delivery. Human protein DMBT1 (deleted in malignant brain tumor 1) is a pattern recognition molecule that interacts with polyanions and recognizes and aggregates bacteria. Taking advantage of these properties, we investigated whether specific synthetic DMBT1-derived peptides could be used to formulate nanoparticles for siRNA administration...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28918018/locked-nucleic-acid-gapmers-and-conjugates-potently-silence-adam33-an-asthma-associated-metalloprotease-with-nuclear-localized-mrna
#14
Hannah M Pendergraff, Pranathi Meda Krishnamurthy, Alexandre J Debacker, Michael P Moazami, Vivek K Sharma, Liisa Niitsoo, Yong Yu, Yen Nee Tan, Hans Michael Haitchi, Jonathan K Watts
Two mechanisms dominate the clinical pipeline for oligonucleotide-based gene silencing, namely, the antisense approach that recruits RNase H to cleave target RNA and the RNAi approach that recruits the RISC complex to cleave target RNA. Multiple chemical designs can be used to elicit each pathway. We compare the silencing of the asthma susceptibility gene ADAM33 in MRC-5 lung fibroblasts using four classes of gene silencing agents, two that use each mechanism: traditional duplex small interfering RNAs (siRNAs), single-stranded small interfering RNAs (ss-siRNAs), locked nucleic acid (LNA) gapmer antisense oligonucleotides (ASOs), and novel hexadecyloxypropyl conjugates of the ASOs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917670/morphological-characterization-and-biocontrol-effects-of-vibrio-vulnificus-phages-against-vibriosis-in-the-shrimp-aquaculture-environment
#15
P Srinivasan, P Ramasamy
The re-emerging field of phage therapy is the potential biocontrol agents for the transfer of virulence factor and to kill their bacterial hosts. In this study, the lytic Vibrio vulnificus phages were studied to provide a better understanding of phage-host interactions and development of phage therapy. Four new V. vulnificus phages were detected from shrimp aquaculture system, named VV1, VV2, VV3 and VV4. All lytic V. vulnificus phages are the Tecviruses of the family Tectiviridae with typical double layered elongated icosahedral head and tailless morphology...
September 13, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28917142/reactions-of-tobacco-genotypes-with-different-antioxidant-capacities-to-powdery-mildew-and-tobacco-mosaic-virus-infections
#16
Gábor Gullner, Csilla Juhász, Adél Németh, Balázs Barna
The interactions of powdery mildew (Golovinomyces orontii) and Tobacco mosaic virus (TMV) with tobacco lines having down or upregulated antioxidants were investigated. Xanthi-nc, its salicylic acid-deficient NahG mutant, a paraquat-sensitive Samsun (PS) and its paraquat tolerant (PT) mutant were used. Cell membrane damage caused by H2O2 was significantly higher in NahG than Xanthi, whereas it was lower in PT than in PS. Leakage of ions from PT was reduced by the powdery mildew infection. On the other hand TMV inoculation led to a 6-fold and 2-fold elevation of ion leakage from hypersensitive resistant NahG and Xanthi leaves, respectively, whereas ion leakage increased slightly from susceptible PS leaves...
September 8, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28917037/identification-and-characterization-of-proteins-that-bind-to-selenoprotein-3-utrs
#17
Eric M Cockman, Donna M Driscoll
This chapter explains the use of RNase-assisted RNA chromatography. RNA affinity chromatography is a powerful technique that is used to isolate and identify proteins that bind to a specific RNA ligand. The RNA of interest is attached to beads before protein lysates are passed over the column. In traditional RNA chromatography, bound proteins are eluted with high salt or harsh detergent, which can also release proteins that are nonspecifically bound to the beads. To avoid this, a new method was developed in which RNases are used to cleave RNA from the beads, releasing only RNA binding proteins (RBPs) and leaving behind proteins that are bound to the beads (Michlewski and Caceres, RNA 16(8):1673-1678, 2010)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28916654/biallelic-dicer1%C3%A2-loss-mediated-by-ap2-cre-drives-angiosarcoma
#18
Jason A Hanna, Catherine J Drummond, Matthew R Garcia, Jonathan C Go, David Finkelstein, Jerold E Rehg, Mark E Hatley
Angiosarcoma is an aggressive vascular sarcoma with an extremely poor prognosis. Due to the relative rarity of this disease, its molecular drivers and optimal treatment strategies are obscure. DICER1 is an RNase III endoribonuclease central to microRNA biogenesis, and germline DICER1 mutations result in a cancer predisposition syndrome, associated with an increased risk of many tumor types. Here we show that biallelic Dicer1 deletion with aP2-Cre drives aggressive and metastatic angiosarcoma independent of other genetically engineered oncogenes or tumor suppressor loss...
September 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28915552/dicer-suppresses-cytoskeleton-remodeling-and-tumorigenesis-of-colorectal-epithelium-by-mir-324-5p-mediated-suppression-of-hmgxb3-and-wasf-2
#19
Li Na Sun, Cheng Xing, Zheng Zhi, Yao Liu, Liang-Yan Chen, Tong Shen, Qun Zhou, Yu Hong Liu, Wen Juan Gan, Jing-Ru Wang, Yong Xu, Jian Ming Li
Emerging evidence indicates that microRNAs, a class of small and well-conserved noncoding RNAs, participate in many physiological and pathological processes. RNase III endonuclease DICER is one of the key enzymes for microRNA biogenesis. Here, we found that DICER was downregulated in tumor samples of colorectal cancer (CRC) patients at both mRNA and protein levels. Importantly, intestinal epithelial cell (IEC)-specific deletion of Dicer mice got more tumors after azoxymethane and dextran sulfate sodium (DSS) administration...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28911227/a-fluorescence-assay-for-ribonuclease-h-based-on-non-labeled-substrate-and-dnazyme-assisted-cascade-amplification
#20
Lanbo Wang, Hongyan Zhou, Bin Liu, Chuan Zhao, Jialong Fan, Wei Wang, Chunyi Tong
As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA-RNA chimeric strands. DNAzyme, a synthetic single-stranded DNA consisting of binding and catalytic sites, can cleave RNA in the presence of cofactors. In this study, we establish a highly sensitive RNase H assay assisted with DNAzyme's cleavage property. A DNA-RNA chimeric strand, which contains DNAzyme sequences, is used as the hydrolysis substrate of RNase H. The RNase H hydrolysis of the chimeric substrate results in the release of DNAzyme...
September 15, 2017: Analytical Chemistry
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