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https://www.readbyqxmd.com/read/28346450/structural-modeling-of-protein-rna-complexes-using-crosslinking-of-segmentally-isotope-labeled-rna-and-ms-ms
#1
Georg Dorn, Alexander Leitner, Julien Boudet, Sébastien Campagne, Christine von Schroetter, Ahmed Moursy, Ruedi Aebersold, Frédéric H-T Allain
Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach, crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS), to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on polypyrimidine tract binding protein 1 and U1 small nuclear RNP. Our method provides distance restraints to support integrative atomic-scale structural modeling and to gain mechanistic insights into RNP-regulated processes...
March 27, 2017: Nature Methods
https://www.readbyqxmd.com/read/28334779/targeted-gene-knock-in-by-homology-directed-genome-editing-using-cas9-ribonucleoprotein-and-aav-donor-delivery
#2
Thomas Gaj, Brett T Staahl, Gonçalo M C Rodrigues, Prajit Limsirichai, Freja K Ekman, Jennifer A Doudna, David V Schaffer
Realizing the full potential of genome editing requires the development of efficient and broadly applicable methods for delivering programmable nucleases and donor templates for homology-directed repair (HDR). The RNA-guided Cas9 endonuclease can be introduced into cells as a purified protein in complex with a single guide RNA (sgRNA). Such ribonucleoproteins (RNPs) can facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a single-stranded DNA oligonucleotide...
March 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28324866/long-term-bioavailability-of-redox-nanoparticles-effectively-reduces-organ-dysfunctions-and-death-in-whole-body-irradiated-mice
#3
Chitho P Feliciano, Koji Tsuboi, Kenshi Suzuki, Hiroyuki Kimura, Yukio Nagasaki
Radioprotective agents have been developed to protect patients against the damaging and lethal effects of ionizing radiation. However, in addition to the intrinsic ability to target reactive oxygen species (ROS), the ability to retain a significant level of bioavailability is desirable in radioprotective agents because that would increase and prolong their radioprotective efficacy and improve its safety. Here, we report the development of a novel nanoparticle-based radioprotective agent with improved bioavailability, which suppressed the adverse effects typically associated with low-molecular-weight (LMW) antioxidants...
March 14, 2017: Biomaterials
https://www.readbyqxmd.com/read/28324503/visualization-of-human-telomerase-localization-by-fluorescence-microscopy-techniques
#4
Eladio Abreu, Rebecca M Terns, Michael P Terns
Human telomerase is a ribonucleoprotein (RNP) that synthesizes DNA repeats at the ends of chromosomes and maintains telomere length and genome stability. The enzyme is comprised of telomerase RNA (hTR) (which provides the template for telomere addition) and several protein subunits including telomerase reverse transcriptase (hTERT) (the catalytic component). Intracellular trafficking of the enzyme has emerged as an important factor in the regulation of telomerase activity. Telomerase trafficking between nuclear Cajal bodies (proposed sites of telomerase biogenesis and regulation) and telomeres (sites of action) is regulated by the cell cycle in concordance with telomere synthesis during S phase...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28316014/rescue-of-recombinant-newcastle-disease-virus-a-short-history-of-how-it-all-started
#5
REVIEW
Aidin Molouki, Ben Peeters
Reverse genetics of viruses has come a long way, and many recombinant viruses have been generated since the first successful "rescues" were reported in the late 1970s. Recombinant Newcastle disease virus (rNDV), a non-segmented negative-sense RNA virus (NSNSV), was first rescued in 1999 using a reverse genetics approach similar to that reported for other recombinant viruses of the order Mononegavirales a few years before. The route from an original NDV isolate to the generation of its recombinant counterpart requires many steps that have to be sequentially and carefully completed...
March 18, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28315749/integrated-structural-biology-to-unravel-molecular-mechanisms-of-protein-rna-recognition
#6
REVIEW
Andreas Schlundt, Jan-Niklas Tants, Michael Sattler
Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation...
March 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28314893/integration-of-mrnp-formation-and-export
#7
REVIEW
Petra Björk, Lars Wieslander
Expression of protein-coding genes in eukaryotes relies on the coordinated action of many sophisticated molecular machineries. Transcription produces precursor mRNAs (pre-mRNAs) and the active gene provides an environment in which the pre-mRNAs are processed, folded, and assembled into RNA-protein (RNP) complexes. The dynamic pre-mRNPs incorporate the growing transcript, proteins, and the processing machineries, as well as the specific protein marks left after processing that are essential for export and the cytoplasmic fate of the mRNPs...
March 17, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28300534/identification-of-a-small-molecule-inhibitor-that-stalls-splicing-at-an-early-step-of-spliceosome-activation
#8
Anzhalika Sidarovich, Cindy L Will, Maria M Anokhina, Javier Ceballos, Sonja Sievers, Dmitry E Agafonov, Timur Samatov, Penghui Bao, Berthold Kastner, Henning Urlaub, Herbert Waldmann, Reinhard Lührmann
Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated B(act) complexes. Characterization of the stalled complexes (designated B(028)) revealed that U4/U6 snRNP proteins are released during activation before the U6 Lsm and B-specific proteins, and before recruitment and/or stable incorporation of Prp19/CDC5L complex and other B(act) complex proteins...
March 16, 2017: ELife
https://www.readbyqxmd.com/read/28296067/rna-binding-proteins-of-the-nxf-nuclear-export-factor-family-and-their-connection-with-the-cytoskeleton
#9
REVIEW
L A Mamon, V R Ginanova, S F Kliver, A O Yakimova, A A Atsapkina, E V Golubkova
The mutual relationship between mRNA and the cytoskeleton can be seen from two points of view. On the one hand, the cytoskeleton is necessary for mRNA trafficking and anchoring to subcellular domains. On the other hand, cytoskeletal growth and rearrangement require the translation of mRNAs that are connected to the cytoskeleton. β-actin mRNA localization may influence dynamic changes in the actin cytoskeleton. In the cytoplasm, long-lived mRNAs exist in the form of RNP (ribonucleoprotein) complexes, where they interact with RNA-binding proteins, including NXF (Nuclear eXport Factor)...
March 13, 2017: Cytoskeleton
https://www.readbyqxmd.com/read/28267329/boronic-acid-modifications-enhance-the-anti-influenza-a-virus-activities-of-novel-quindoline-derivatives
#10
Wei Wang, Ruijuan Yin, Meng Zhang, Rilei Yu, Cui Hao, Lijuan Zhang, Tao Jiang
The unique glycan-binding ability of chemically-synthesized boronic acid derivatives makes them emerging candidates for developing anti-influenza A virus (IAV) drugs. Herein we report the synthesis and the anti-IAV activities of 3 series of novel boronic acid-modified quindoline derivatives both in vitro and in vivo. Boronic acid-modified compounds 6a and 7a effectively prevented the entry of virus RNP into the nucleus, reduced virus titers in IAV infected cells, and also inhibited the activity of viral neuraminidase...
March 7, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28265061/amyotrophic-lateral-sclerosis-linked-mutations-increase-the-viscosity-of-liquid-like-tdp-43-rnp-granules-in-neurons
#11
Pallavi P Gopal, Jeffrey J Nirschl, Eva Klinman, Erika L F Holzbaur
Ribonucleoprotein (RNP) granules are enriched in specific RNAs and RNA-binding proteins (RBPs) and mediate critical cellular processes. Purified RBPs form liquid droplets in vitro through liquid-liquid phase separation and liquid-like non-membrane-bound structures in cells. Mutations in the human RBPs TAR-DNA binding protein 43 (TDP-43) and RNA-binding protein FUS cause amyotrophic lateral sclerosis (ALS), but the biophysical properties of these proteins have not yet been studied in neurons. Here, we show that TDP-43 RNP granules in axons of rodent primary cortical neurons display liquid-like properties, including fusion with rapid relaxation to circular shape, shear stress-induced deformation, and rapid fluorescence recovery after photobleaching...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28258033/rnp-transport-in-cell-biology-the-long-and-winding-road
#12
REVIEW
Carolina Eliscovich, Robert H Singer
Regulation of gene expression is key determinant to cell structure and function. RNA localization, where specific mRNAs are transported to subcellular regions and then translated, is highly conserved in eukaryotes ranging from yeast to extremely specialized and polarized cells such as neurons. Messenger RNA and associated proteins (mRNP) move from the site of transcription in the nucleus to their final destination in the cytoplasm both passively through diffusion and actively via directed transport. Dysfunction of RNA localization, transport and translation machinery can lead to pathology...
February 28, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28254838/the-7sk-snrnp-associates-with-the-little-elongation-complex-to-promote-snrna-gene-expression
#13
Sylvain Egloff, Patrice Vitali, Michael Tellier, Raoul Raffel, Shona Murphy, Tamás Kiss
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes...
March 2, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28248800/mixed-connective-tissue-disease-and-epitope-spreading-an-historical-cohort-study
#14
Laura Escolà-Vergé, Iago Pinal-Fernandez, Andreu Fernandez-Codina, Eduardo L Callejas-Moraga, Juan Espinosa, Ana Marin, Moises Labrador-Horrillo, Albert Selva-O'Callaghan
OBJECTIVES: Mixed connective tissue disease (MCTD) is characterized by the presence of anti-U1-snRNP autoantibodies and a variable set of associated clinical features. Some MCTD patients test positive over time to autoantibodies against Sm, proteins spatially related with U1-snRNP. This situation has been attributed to expanding of the autoimmune response by a phenomenon known as epitope spreading. Our aim was to study the frequency of this phenomenon in MCTD patients and the specific clinical features of those with epitope spreading...
April 2017: Journal of Clinical Rheumatology: Practical Reports on Rheumatic & Musculoskeletal Diseases
https://www.readbyqxmd.com/read/28239624/p-body-and-stress-granule-quantification-in-caenorhabditis-elegans
#15
Matthias Rieckher, Nektarios Tavernarakis
Eukaryotic cells contain various types of cytoplasmic, non-membrane bound ribonucleoprotein (RNP) granules that consist of non-translating mRNAs and a versatile set of associated proteins. One prominent type of RNP granules are Processing bodies (P bodies), which majorly harbors translationally inactive mRNAs and an array of proteins mediating mRNA degradation, translational repression and cellular mRNA transport (Sheth and Parker, 2003). Another type of RNP granules, the stress granules (SGs), majorly contain mRNAs associated with translation initiation factors and are formed upon stress-induced translational stalling (Kedersha et al...
January 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28235408/the-chinese-prescription-lianhuaqingwen-capsule-exerts-anti-influenza-activity-through-the-inhibition-of-viral-propagation-and-impacts-immune-function
#16
Yuewen Ding, Lijuan Zeng, Runfeng Li, Qiaoyan Chen, Beixian Zhou, Qiaolian Chen, Pui Leng Cheng, Wang Yutao, Jingping Zheng, Zifeng Yang, Fengxue Zhang
BACKGROUND: Lianhuaqingwen Capsule (LH-C) is a traditional Chinese medicine (TCM) formula used to treat respiratory tract infectious diseases in Chinese. The aim of this study was to determine the antiviral activity of LH-C and its immunomodulatory effects on viral infection. METHOD: The in vitro cytotoxicity and antiviral activity of LH-C was determined by MTT and Plaque reduction assays. Time course study under single-cycle virus growth conditions were used to determine which stage of viral replication was blocked...
February 24, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28228619/a-case-of-anti-3-hydroxy-3-methylglutaryl-coenzyme-a-reductase-antibody-positive-paraneoplastic-necrotizing-myopathy-associated-with-advanced-gastric-cancer-that-responded-to-intravenous-immunoglobulin-therapy
#17
Tomohisa Yamaguchi, Akiko Matsunaga, Masamichi Ikawa, Norimichi Shirafuji, Ichizo Nishino, Tadanori Hamano
A 49-year-old woman presented with progressive muscle weakness of the limbs and dysphagia. Her past and family medical history were unremarkable and she did not take statins or any other medications. Laboratory tests showed that serum levels of creatine kinase were elevated (13,565 IU/l) and anti-3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) antibodies were detected in the serum. Other autoantibodies to the nuclear (ANA), RNP, aminoacyl-tRNA synthetases (ARS), and signal recognition particle (SRP) were negative...
February 22, 2017: Rinshō Shinkeigaku, Clinical Neurology
https://www.readbyqxmd.com/read/28223024/construction-of-a-library-of-structurally-diverse-ribonucleopeptides-with-catalytic-groups
#18
Tomoki Tamura, Shun Nakano, Eiji Nakata, Takashi Morii
Functional screening of structurally diverse libraries consisting of proteins or nucleic acids is an effective method to obtain receptors or aptamers with unique molecular recognition characteristics. However, further modification of these selected receptors to exert a newly desired function is still a challenging task. We have constructed a library of structurally diverse ribonucleopeptides (RNPs) that are modified with a catalytic group, in which the catalytic group aligns with various orientations against the ATP binding pocket of RNA subunit...
February 10, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28206738/defective-ribonucleoproteins-mistakes-in-rna-processing-and-diseases
#19
Mia K Mihailovic, Angela Chen, Juan C Gonzalez-Rivera, Lydia M Contreras
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell...
March 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28202765/the-lateral-organization-of-influenza-virus-proteins-in-the-budozone-region-of-the-plasma-membrane
#20
George P Leser, Robert A Lamb
Influenza virus assembles and buds at the plasma membrane of virus-infected cells. The viral proteins assemble at the same site on the plasma membrane for budding to occur. This involves a complex web of interactions among viral proteins. Some, like HA, NA, and M2 are integral membrane proteins. M1 is peripherally membrane associated, whereas NP associates with the viral RNA to form an RNP complex that associates with the cytoplasmic face of the plasma membrane. Furthermore, HA and NP have been shown to be concentrated in cholesterol-rich membrane raft domains whereas M2, although containing a cholesterol binding motif, is not raft associated...
February 15, 2017: Journal of Virology
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