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https://www.readbyqxmd.com/read/28525600/a-novel-double-kink-turn-module-in-euryarchaeal-rnase-p-rnas
#1
Lien B Lai, Akiko Tanimoto, Stella M Lai, Wen-Yi Chen, Ila A Marathe, Eric Westhof, Vicki H Wysocki, Venkat Gopalan
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525279/double-winged-3-hydroxypyrimidine-2-4-diones-potent-and-selective-inhibition-against-hiv-1-rnase-h-with-significant-antiviral-activity
#2
Sanjeev Kumar V Vernekar, Jing Tang, Bulan Wu, Andrew D Huber, Mary C Casey, Nataliya S Myshakina, Daniel J Wilson, Jayakanth Kankanala, Karen A Kirby, Michael A Parniak, Stefan G Sarafianos, Zhengqiang Wang
Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function yet to be exploited as an antiviral target. One of the possible challenges may be that targeting HIV RNase H is confronted with a steep substrate barrier. We have previously reported a 3-hydroxypyrimidine-2,4-dione (HPD) subtype that potently and selectively inhibited RNase H without inhibiting HIV in cell culture. We report herein a critical redesign of the HPD chemotype featuring an additional wing at the C5 position that led to drastically improved RNase H inhibition and significant antiviral activity...
May 19, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28524158/sequencing-of-dicer1-in-sarcomas-identifies-biallelic-somatic-dicer1-mutations-in-an-adult-onset-embryonal-rhabdomyosarcoma
#3
Leanne de Kock, Barbara Rivera, Timothée Revil, Paul Thorner, Catherine Goudie, Dorothée Bouron-Dal Soglio, Catherine S Choong, John R Priest, Paul J van Diest, Jantima Tanboon, Anja Wagner, Jiannis Ragoussis, Peter Fm Choong, William D Foulkes
BACKGROUND: Sarcomas are rare and heterogeneous cancers. We assessed the contribution of DICER1 mutations to sarcoma development. METHODS: The coding region of DICER1 was sequenced in 67 sarcomas using a custom Fluidigm Access Array. The RNase III domains were Sanger sequenced in six additional sarcomas to identify hotspot DICER1 variants. RESULTS: The median age of sarcoma diagnosis was 45.7 years (range: 3 months to 87.4 years). A recurrent embryonal rhabdomyosarcoma (ERMS) of the broad ligament, first diagnosed at age 23 years, harboured biallelic pathogenic somatic DICER1 variants (1 truncating and 1 RNase IIIb missense)...
May 18, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28522867/movement-protein-of-apple-chlorotic-leaf-spot-virus-is-genetically-unstable-and-negatively-regulated-by-ribonuclease-e-in-e-coli
#4
Rahul Mohan Singh, Dharam Singh, Vipin Hallan
Movement protein (MP) of Apple chlorotic leaf spot virus (ACLSV) belongs to "30 K" superfamily of proteins and members of this family are known to show a wide array of functions. In the present study this gene was found to be genetically unstable in E. coli when transformed DH5α cells were grown at 28 °C and 37 °C. However, genetic instability was not encountered at 20 °C. Heterologous over expression failed despite the use of different transcriptional promoters and translational fusion constructs...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28512205/phorbol-12-myristate-13-acetate-mediated-stabilization-of-leukemia-inhibitory-factor-lif-mrna-involvement-of-nucleolin-and-pcbp1
#5
Alina Chakraborty, Srimoyee Mukherjee, Sucharita Saha, Soumasree De, Sumita Sengupta Bandyopadhyay
LIF is a potent pleiotropic cytokine involved in diverse biological activities, thereby requiring precise spatial and temporal control of its expression. The present study reveals that enhanced expression of Leukemia Inhibitory Factor in response to PMA (phorbol-12-myristate-13-acetate) in human histiocytic lymphoma cell-line U937 largely happens through stabilization of its mRNA. Functional characterization of the long 3'-untranslated region (3'-UTR) of human lif -mRNA revealed several conserved sequences with conventional cis -acting elements...
May 16, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28511060/a-comparison-study-on-rnase-a-oligomerization-induced-by-cisplatin-carboplatin-and-oxaliplatin
#6
Delia Picone, Federica Donnarumma, Giarita Ferraro, Giovanni Gotte, Andrea Fagagnini, Giovanna Butera, Massimo Donadelli, Antonello Merlino
Cisplatin (CDDP) can form interprotein cross-links, leading to the formation of platinated oligomers. A dimer, a trimer and higher oligomers of bovine pancreatic ribonuclease (RNase A) obtained upon reaction with CDDP in 1:10 protein to metal ratio at 37°C have been previously characterized. Here, we verify the ability of carboplatin and oxaliplatin to induce RNase A oligomerization under the same experimental conditions. The amount of formed RNase A oligomers was compared with that obtained in the reaction of the protein with CDDP...
May 9, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28509532/nanodiamonds-mediate-oral-delivery-of-proteins-for-stem-cell-activation-and-intestinal-remodeling-in-drosophila
#7
Xingjie Hu, Xiaojiao Li, Min Yin, Ping Li, Ping Huang, Lihua Wang, Yiguo Jiang, Hui Wang, Nan Chen, Chunhai Fan, Haiyun Song
Introduction of exogenous bio-macromolecules into living systems is of great interest in genome editing, cancer immunotherapy and stem cell reprogramming. Whereas current strategies generally depend on nucleic acids transfection, direct delivery of functional proteins that provides enhanced specificity, increased safety, fast and temporal regulation is highly desirable. Nevertheless, intracellular delivery of intact and bioactive proteins, especially in vivo, remains poorly explored. In this study, we developed a nanodiamonds (NDs)-based protein delivery system in cultured cells and in Drosophila, which showed high adsorption, high efficiency and effective cytosolic release of fully functional proteins...
May 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28508084/clinicopathologic-and-molecular-spectrum-of-rnaseh1-related-mitochondrial-disease
#8
Enrico Bugiardini, Olivia V Poole, Andreea Manole, Alan M Pittman, Alejandro Horga, Iain Hargreaves, Cathy E Woodward, Mary G Sweeney, Janice L Holton, Jan-Willem Taanman, Gordon T Plant, Joanna Poulton, Massimo Zeviani, Daniele Ghezzi, John Taylor, Conrad Smith, Carl Fratter, Meena A Kanikannan, Arumugam Paramasivam, Kumarasamy Thangaraj, Antonella Spinazzola, Ian J Holt, Henry Houlden, Michael G Hanna, Robert D S Pitceathly
OBJECTIVE: Pathologic ribonuclease H1 (RNase H1) causes aberrant mitochondrial DNA (mtDNA) segregation and is associated with multiple mtDNA deletions. We aimed to determine the prevalence of RNase H1 gene (RNASEH1) mutations among patients with mitochondrial disease and establish clinically meaningful genotype-phenotype correlations. METHODS: RNASEH1 was analyzed in patients with (1) multiple deletions/depletion of muscle mtDNA and (2) mendelian progressive external ophthalmoplegia (PEO) with neuropathologic evidence of mitochondrial dysfunction, but no detectable multiple deletions/depletion of muscle mtDNA...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28501587/functional-requirements-for-djla-and-rraa-mediated-enhancement-of-recombinant-membrane-protein-production-in-the-engineered-escherichia-coli-strains-suptoxd-and-suptoxr
#9
Dimitra Gialama, Dafni Chrysanthi Delivoria, Myrsini Michou, Artemis Giannakopoulou, Georgios Skretas
In previous work, we have generated the engineered Escherichia coli strains SuptoxD and SuptoxR, which upon co-expression of the effector genes djlA or rraA, respectively, are capable of suppressing the cytotoxicity caused by membrane protein (MP) overexpression and producing dramatically enhanced yields for a variety of recombinant MPs of both prokaryotic and eukaryotic origin. Here, we investigated the functional requirements for DjlA- and RraA-mediated enhancement of recombinant MP production in these strains and show that: (i) DjlA and RraA act independently, i...
May 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28499021/protein-only-rnase-p-function-in-escherichia-coli-viability-processing-defects-and-differences-between-prorp-isoenzymes
#10
Markus Gößringer, Marcus Lechner, Nadia Brillante, Christoph Weber, Walter Rossmanith, Roland K Hartmann
The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli...
May 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28498974/strong-transcription-blockage-mediated-by-r-loop-formation-within-a-g-rich-homopurine-homopyrimidine-sequence-localized-in-the-vicinity-of-the-promoter
#11
Boris P Belotserkovskii, Jane Hae Soo Shin, Philip C Hanawalt
Guanine-rich (G-rich) homopurine-homopyrimidine nucleotide sequences can block transcription with an efficiency that depends upon their orientation, composition and length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand. We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase transcription by more than an order of magnitude when positioned close (9 bp) to the promoter, in comparison to that for a distal (∼250 bp) location of the same sequence...
May 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28496054/days-weaving-the-lagging-strand-synthesis-of-dna-a-personal-recollection-of-the-discovery-of-okazaki-fragments-and-studies-on-discontinuous-replication-mechanism
#12
Tsuneko Okazaki
At DNA replication forks, the overall growth of the antiparallel two daughter DNA chains appears to occur 5'-to-3' direction in the leading-strand and 3'-to-5' direction in the lagging-strand using enzyme system only able to elongate 5'-to-3' direction, and I describe in this review how we have analyzed and proved the lagging strand multistep synthesis reactions, called Discontinuous Replication Mechanism, which involve short RNA primer synthesis, primer-dependent short DNA chains (Okazaki fragments) synthesis, primer removal from the Okazaki fragments and gap filling between Okazaki fragments by RNase H and DNA polymerase I, and long lagging strand formation by joining between Okazaki fragments with DNA ligase...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28495858/comparative-functional-analysis-of-ribonuclease-1-homologs-molecular-insights-into-evolving-vertebrate-physiology
#13
Jo E Lomax, Chelcie H Eller, Ronald T Raines
Pancreatic-type ribonucleases (ptRNases) comprise a class of highly conserved secretory endoribonucleases in vertebrates. The prototype of this enzyme family is ribonuclease 1 (RNase 1). Understanding the physiological roles of RNase 1 is becoming increasingly important, as engineered forms of the enzyme progress through clinical trials as chemotherapeutic agents for cancer. Here we present an in-depth biochemical characterization of RNase 1 homologs from a broad range of mammals (human, bat, squirrel, horse, cat, mouse, and cow) and non-mammalian species (chicken, lizard, and frog)...
May 11, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28490179/-living-dynamics-of-filamentous-bacteria-on-an-adherent-surface-under-hydrodynamic-exposure
#14
Justin P Jahnke, Austin M Smith, Nicole E Zander, Victoria Wiedorn, Kenneth E Strawhecker, Jessica L Terrell, Dimitra N Stratis-Cullum, Xuanhong Cheng
The potential advantages of cell-based biohybrid devices over conventional nonliving systems drive the interest to control the behavior of the underlying biological cells in microdevices. Here, the authors studied how shear influenced the geometry and elongation of fimbriated filaments on affinity substrates. The cells were engineered to express FimH, which binds to mannose with a high affinity. A microfluidic channel was functionalized with RNAse B, which is rich in mannose residues, and the device was used to control the hydrodynamic force on live Escherichia coli under filamentous growth...
May 10, 2017: Biointerphases
https://www.readbyqxmd.com/read/28484023/coronavirus-nonstructural-protein-15-mediates-evasion-of-dsrna-sensors-and-limits-apoptosis-in-macrophages
#15
Xufang Deng, Matthew Hackbart, Robert C Mettelman, Amornrat O'Brien, Anna M Mielech, Guanghui Yi, C Cheng Kao, Susan C Baker
Coronaviruses are positive-sense RNA viruses that generate double-stranded RNA (dsRNA) intermediates during replication, yet evade detection by host innate immune sensors. Here we report that coronavirus nonstructural protein 15 (nsp15), an endoribonuclease, is required for evasion of dsRNA sensors. We evaluated two independent nsp15 mutant mouse coronaviruses, designated N15m1 and N15m3, and found that these viruses replicated poorly and induced rapid cell death in mouse bone marrow-derived macrophages. Infection of macrophages with N15m1, which expresses an unstable nsp15, or N15m3, which expresses a catalysis-deficient nsp15, activated MDA5, PKR, and the OAS/RNase L system, resulting in an early, robust induction of type I IFN, PKR-mediated apoptosis, and RNA degradation...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28479722/influence-of-capsaicin-on-inflammatory-cytokines-induced-by-lipopolysaccharide-in-myoblast-cells-under-in-vitro-environment
#16
Ke Shang, Touseef Amna, Musarat Amina, Nawal M Al-Musayeib, Salem S Al-Deyab, Inho Hwang
BACKGROUND: ellular damage initiated by reactive oxygen species (ROS) is the main cause of numerous severe diseases and therefore for this reason, the natural antioxidants have note worthy significance in human health. Capsaicin possesses noteworthy analgesic and anti-inflammatory properties. It also possesses healing effects for treatment of arthritis, diabetic neuropathy, gastric lesions, and cardiac excitability that is why it is incorporated in creams and gels. OBJECTIVE: The present study was carried out to estimate the in vitro antioxidant and ROS scavenging activities of capsaicin against muscle precursor cells...
January 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28477335/2-%C3%AE-fluoro-tricyclo-nucleic-acids-2-f-tc-ana-thermal-duplex-stability-structural-studies-and-rnase-h-activation
#17
Alena Istrate, Adam Katolik, Andrei Istrate, Christian Joerg Leumann
We describe the synthesis, thermal stability and structural and RNase H activation properties of 2'β-fluoro-tricyclo nucleic acids (2'F-tc-ANA). Three 2'F-tc-ANA nucleosides (T, 5MeC and A) were synthesized starting from a previously described fluorinated tricyclo sugar intermediate. NMR analysis and quantum mechanical calculations indicate that 2'F-tc-ANA nucleosides prefer sugar conformations in the East and South regions of the pseudorotational cycle. UV-melting experiments revealed that non-consecutive insertions of 2'F-tc-ANA units in DNA reduce the affinity to DNA and RNA complements...
May 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28474844/one-pot-synthesis-of-multiple-protein-encapsulated-dna-flowers-and-their-application-in-intracellular-protein-delivery
#18
Eunjung Kim, Limor Zwi-Dantsis, Natalie Reznikov, Catherine S Hansel, Shweta Agarwal, Molly M Stevens
Inspired by biological systems, many biomimetic methods suggest fabrication of functional materials with unique physicochemical properties. Such methods frequently generate organic-inorganic composites that feature highly ordered hierarchical structures with intriguing properties, distinct from their individual components. A striking example is that of DNA-inorganic hybrid micro/nanostructures, fabricated by the rolling circle technique. Here, a novel concept for the encapsulation of bioactive proteins in DNA flowers (DNF) while maintaining the activity of protein payloads is reported...
May 5, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28465635/berberine-displays-antitumor-activity-in-esophageal-cancer-cells-in-vitro
#19
Shu-Xian Jiang, Bo Qi, Wen-Jian Yao, Cheng-Wei Gu, Xiu-Feng Wei, Yi Zhao, Yu-Zhen Liu, Bao-Sheng Zhao
AIM: To investigate the effects of berberine on esophageal cancer (EC) cells and its molecular mechanisms. METHODS: Human esophageal squamous cell carcinoma cell line KYSE-70 and esophageal adenocarcinoma cell line SKGT4 were used. The effects of berberine on cell proliferation were evaluated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. For cell cycle progression, KYSE-70 cells were stained with propidium iodide (PI) staining buffer (10 mg/mL PI and 100 mg/mL RNase A) for 30 min and cell cycle was analyzed using a BD FACSCalibur flow cytometer...
April 14, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28465261/challenges-in-the-evaluation-of-thiol-reactive-inhibitors-of-human-protein-disulfide-isomerase
#20
Celia K Foster, Colin Thorpe
This paper addresses how to evaluate the efficacy of the growing inventory of thiol-reactive inhibitors of mammalian protein disulfide Isomerase (PDI) enzymes under realistic concentrations of potentially competing thiol-containing peptides and proteins. For this purpose, we introduce a variant of the widely-used reductase assay by using a commercially-available cysteine derivative (BODIPY FL L-Cystine; BD-SS) that yields a 55-fold increase in fluorescence (excitation/emission; 490/513nm) on scission of the disulfide bond...
April 30, 2017: Free Radical Biology & Medicine
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