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https://www.readbyqxmd.com/read/28438387/structural-insights-into-the-mechanism-of-group-ii-intron-splicing
#1
REVIEW
Chen Zhao, Anna Marie Pyle
While the major architectural features and active-site components of group II introns have been known for almost a decade, information on the individual stages of splicing has been lacking. Recent advances in crystallography and cryo-electron microscopy (cryo-EM) have provided major new insights into the structure of intact lariat introns. Conformational changes that mediate the steps of splicing and retrotransposition are being elucidated, revealing the dynamic, highly coordinated motions that are required for group II intron activity...
April 21, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28429401/synthesis-of-l-threitol-based-crown-ethers-and-their-application-as-enantioselective-phase-transfer-catalyst-in-michael-additions
#2
Zsolt Rapi, Tamás Nemcsok, Ádám Pálvölgyi, György Keglevich, Alajos Grün, Péter Bakó
A few new l-threitol-based lariat ethers incorporating a monoaza-15-crown-5 unit were synthesized starting from diethyl l-tartrate. These macrocycles were used as phase transfer catalysts in asymmetric Michael addition reactions under mild conditions to afford the adducts in a few cases in good to excellent enantioselectivities. The addition of 2-nitropropane to trans-chalcone, and the reaction of diethyl acetamidomalonate with β-nitrostyrene resulted in the chiral Michael adducts in good enantioselectivities (90% and 95%, respectively)...
April 21, 2017: Chirality
https://www.readbyqxmd.com/read/28421220/a-highly-selective-colorimetric-and-environment-sensitive-optical-potassium-ion-sensor
#3
Guangjie Song, Ruofan Sun, Jiqing Du, Meiwan Chen, Yanqing Tian
Potassium ions (K(+)) play vital roles in many biological processes and thus highly selective sensors for K(+) are critical for disease diagnosis and health monitoring. Herein, we report a colorimetric K(+) sensor (KS7) in which a hemicyanine dye was used as a fluorophore and phenylaza-[18]crown-6 lariat ether (ACLE) was utilized as a K(+) ligand. The maximum absorption peak of KS7 shifted hypsochromically by 77 nm (from 515 to 438 nm) with an isosbestic point at 452 nm upon the addition of K(+) to its aqueous solution accompanied by a color change from red to yellow...
April 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28416677/structural-toggle-in-the-rnaseh-domain-of-prp8-helps-balance-splicing-fidelity-and-catalytic-efficiency
#4
Megan Mayerle, Madhura Raghavan, Sarah Ledoux, Argenta Price, Nicholas Stepankiw, Haralambos Hadjivassiliou, Erica A Moehle, Senén D Mendoza, Jeffrey A Pleiss, Christine Guthrie, John Abelson
Pre-mRNA splicing is an essential step of eukaryotic gene expression that requires both high efficiency and high fidelity. Prp8 has long been considered the "master regulator" of the spliceosome, the molecular machine that executes pre-mRNA splicing. Cross-linking and structural studies place the RNaseH domain (RH) of Prp8 near the spliceosome's catalytic core and demonstrate that prp8 alleles that map to a 17-aa extension in RH stabilize it in one of two mutually exclusive structures, the biological relevance of which are unknown...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28368002/macrocycle-peptides-delineate-locked-open-inhibition-mechanism-for-microorganism-phosphoglycerate-mutases
#5
Hao Yu, Patricia Dranchak, Zhiru Li, Ryan MacArthur, Matthew S Munson, Nurjahan Mehzabeen, Nathan J Baird, Kevin P Battalie, David Ross, Scott Lovell, Clotilde K S Carlow, Hiroaki Suga, James Inglese
Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >10(12) members...
April 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28262556/rapid-discovery-of-potent-and-selective-glycosidase-inhibiting-de-novo-peptides
#6
Seino A K Jongkees, Sami Caner, Christina Tysoe, Gary D Brayer, Stephen G Withers, Hiroaki Suga
Human pancreatic α-amylase (HPA) is responsible for degrading starch to malto-oligosaccharides, thence to glucose, and is therefore an attractive therapeutic target for the treatment of diabetes and obesity. Here we report the discovery of a unique lariat nonapeptide, by means of the RaPID (Random non-standard Peptides Integrated Discovery) system, composed of five amino acids in a head-to-side-chain thioether macrocycle and a further four amino acids in a 310 helical C terminus. This is a potent inhibitor of HPA (Ki = 7 nM) yet exhibits selectivity for the target over other glycosidases tested...
March 16, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28185365/circular-rnas-biogenesis-properties-roles-and-their-relationships-with-liver-diseases
#7
REVIEW
Ting Yao, Qingqing Chen, Liyun Fu, Junming Guo
Circular RNAs (circRNAs) are a class of new-found RNA molecules that have a special covalent loop structure without a 5' cap and 3' tail. Researchers have found that circRNAs may be generated by intron-pairing-driven or lariat-driven circularization. They are cleared up by way of extracellular vesicles. They have some advantages such as stability, conservation, and tissue specificity. By serving as sponges of microRNAs, interacting with long non-coding RNAs, mRNA, or proteins, circRNAs regulate gene expression at transcriptional and post-transcriptional levels and contribute to carcinogenesis...
February 10, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28159804/lariat-capping-as-a-tool-to-study-5-cap-functions-of-individual-yeast-mrna-species-in-vivo
#8
Nicolai Krogh, Max Pietschmann, Manfred Schmid, Torben Heick Jensen, Henrik Nielsen
The 5' cap structure of eukaryotic mRNA is critical for its processing, transport, translation and stability. The many functions of the cap and the fact that most, if not all, mRNA carries the same type of cap makes it difficult to analyse cap function in vivo at individual steps of gene expression. We have used the lariat capping ribozyme (LCrz) from the myxomycete Didymium to replace the mRNA m7G cap of a single reporter mRNA species with a tiny lariat in which the first and the third nucleotide are joined by a 2', 5' phosphodiester bond...
February 3, 2017: RNA
https://www.readbyqxmd.com/read/28119336/large-scale-analysis-of-branchpoint-usage-across-species-and-cell-lines
#9
Allison J Taggart, Chien-Ling Lin, Barsha Shrestha, Claire Heintzelman, Seongwon Kim, William G Fairbrother
The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2-5 linkage...
April 2017: Genome Research
https://www.readbyqxmd.com/read/28076345/structure-of-a-spliceosome-remodelled-for-exon-ligation
#10
Sebastian M Fica, Chris Oubridge, Wojciech P Galej, Max E Wilkinson, Xiao-Chen Bai, Andrew J Newman, Kiyoshi Nagai
The spliceosome excises introns from pre-mRNAs in two sequential transesterifications-branching and exon ligation-catalysed at a single catalytic metal site in U6 small nuclear RNA (snRNA). Recently reported structures of the spliceosomal C complex with the cleaved 5' exon and lariat-3'-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5' splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site...
February 16, 2017: Nature
https://www.readbyqxmd.com/read/28055181/fluorescent-branched-rnas-for-high-throughput-analysis-of-dbr1-enzyme-kinetics-and-inhibition
#11
Adam Katolik, Nathaniel E Clark, Nobuhiro Tago, Eric J Montemayor, P John Hart, Masad J Damha
We have developed fluorescent 2',5' branched RNAs (bRNA) that permit real time monitoring of RNA lariat (intron) debranching enzyme (Dbr1) kinetics. These compounds contain fluorescein (FAM) on the 5' arm of the bRNA that is quenched by a dabcyl moiety on the 2' arm. Dbr1-mediated hydrolysis of the 2',5' linkage induces a large increase in fluorescence, providing a convenient assay for Dbr1 hydrolysis. We show that unlabeled bRNAs with non-native 2',5'-phosphodiester linkages, such as phosphoramidate or phosphorothioate, can inhibit Dbr1-mediated debranching with IC50 values in the low nanomolar range...
January 18, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28053119/short-intron-derived-ncrnas
#12
Florent Hubé, Damien Ulveling, Alain Sureau, Sabrina Forveille, Claire Francastel
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2)...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27980089/structure-of-a-yeast-step-ii-catalytically-activated-spliceosome
#13
Chuangye Yan, Ruixue Wan, Rui Bai, Gaoxingyu Huang, Yigong Shi
Each cycle of precursor messenger RNA (pre-mRNA) splicing comprises two sequential reactions, first freeing the 5' exon and generating an intron lariat-3' exon and then ligating the two exons and releasing the intron lariat. The second reaction is executed by the step II catalytically activated spliceosome (known as the C* complex). Here, we present the cryo-electron microscopy structure of a C* complex from Saccharomyces cerevisiae at an average resolution of 4.0 angstroms. Compared with the preceding spliceosomal complex (C complex), the lariat junction has been translocated by 15 to 20 angstroms to vacate space for the incoming 3'-exon sequences...
January 13, 2017: Science
https://www.readbyqxmd.com/read/27940559/functional-link-between-deah-rha-helicase-prp43-activation-and-atp-base-binding
#14
Julien Robert-Paganin, Maral Halladjian, Magali Blaud, Simon Lebaron, Lila Delbos, Florian Chardon, Régine Capeyrou, Odile Humbert, Yves Henry, Anthony K Henras, Stéphane Réty, Nicolas Leulliot
The DEAH box helicase Prp43 is a bifunctional enzyme from the DEAH/RHA helicase family required both for the maturation of ribosomes and for lariat intron release during splicing. It interacts with G-patch domain containing proteins which activate the enzymatic activity of Prp43 in vitro by an unknown mechanism. In this work, we show that the activation by G-patch domains is linked to the unique nucleotide binding mode of this helicase family. The base of the ATP molecule is stacked between two residues, R159 of the RecA1 domain (R-motif) and F357 of the RecA2 domain (F-motif)...
December 9, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27934709/crystal-structures-of-a-group-ii-intron-lariat-primed-for-reverse-splicing
#15
Maria Costa, Hélène Walbott, Dario Monachello, Eric Westhof, François Michel
The 2'-5' branch of nuclear premessenger introns is believed to have been inherited from self-splicing group II introns, which are retrotransposons of bacterial origin. Our crystal structures at 3.4 and 3.5 angstrom of an excised group II intron in branched ("lariat") form show that the 2'-5' branch organizes a network of active-site tertiary interactions that position the intron terminal 3'-hydroxyl group into a configuration poised to initiate reverse splicing, the first step in retrotransposition. Moreover, the branchpoint and flanking helices must undergo a base-pairing switch after branch formation...
December 2, 2016: Science
https://www.readbyqxmd.com/read/27930312/metal-dependence-and-branched-rna-cocrystal-structures-of-the-rna-lariat-debranching-enzyme-dbr1
#16
Nathaniel E Clark, Adam Katolik, Kenneth M Roberts, Alexander B Taylor, Stephen P Holloway, Jonathan P Schuermann, Eric J Montemayor, Scott W Stevens, Paul F Fitzpatrick, Masad J Damha, P John Hart
Intron lariats are circular, branched RNAs (bRNAs) produced during pre-mRNA splicing. Their unusual chemical and topological properties arise from branch-point nucleotides harboring vicinal 2',5'- and 3',5'-phosphodiester linkages. The 2',5'-bonds must be hydrolyzed by the RNA debranching enzyme Dbr1 before spliced introns can be degraded or processed into small nucleolar RNA and microRNA derived from intronic RNA. Here, we measure the activity of Dbr1 from Entamoeba histolytica by using a synthetic, dark-quenched bRNA substrate that fluoresces upon hydrolysis...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27923990/regulation-of-prp43-mediated-disassembly-of-spliceosomes-by-its-cofactors-ntr1-and-ntr2
#17
Jean-Baptiste Fourmann, Marcel J Tauchert, Ralf Ficner, Patrizia Fabrizio, Reinhard Lührmann
The DEAH-box NTPase Prp43 disassembles spliceosomes in co-operation with the cofactors Ntr1/Spp382 and Ntr2, forming the NTR complex. How Prp43 is regulated by its cofactors to discard selectively only intron-lariat spliceosomes (ILS) and defective spliceosomes and to prevent disassembly of earlier and properly assembled/wild-type spliceosomes remains unclear. First, we show that Ntr1΄s G-patch motif (Ntr1GP) can be replaced by the GP motif of Pfa1/Sqs1, a Prp43΄s cofactor in ribosome biogenesis, demonstrating that the specific function of Ntr1GP is to activate Prp43 for spliceosome disassembly and not to guide Prp43 to its binding site in the spliceosome...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898435/percutaneous-left-atrial-appendage-closure-current-state-of-the-art
#18
Mohammad-Ali Jazayeri, Venkat Vuddanda, Valay Parikh, Dhanunjaya R Lakkireddy
PURPOSE OF REVIEW: The authors reviewed the seminal and more recent literature surrounding the major modalities for percutaneous left atrial appendage closure used in contemporary practice, with particular emphasis on safety and efficacy, technical challenges, and future developments. RECENT FINDINGS: Along with the continued practice of surgical left atrial appendage closure, which has evolved substantially with the advent of clipping techniques, a number of percutaneous methods have been developed to close the left atrial appendage with endocardial, epicardial, and hybrid approaches...
January 2017: Current Opinion in Cardiology
https://www.readbyqxmd.com/read/27875300/the-fission-yeast-pre-mrna-processing-factor-18-prp18-has-intron-specific-splicing-functions-with-links-to-g1-s-cell-cycle-progression
#19
Nagampalli Vijaykrishna, Geetha Melangath, Rakesh Kumar, Piyush Khandelia, Pushpinder Bawa, Raghavan Varadarajan, Usha Vijayraghavan
The fission yeast genome, which contains numerous short introns, is an apt model for studies on fungal splicing mechanisms and splicing by intron definition. Here we perform a domain analysis of the evolutionarily conserved Schizosaccharomyces pombe pre-mRNA-processing factor, SpPrp18. Our mutational and biophysical analyses of the C-terminal α-helical bundle reveal critical roles for the conserved region as well as helix five. We generate a novel conditional missense mutant, spprp18-5 To assess the role of SpPrp18, we performed global splicing analyses on cells depleted of prp18(+) and the conditional spprp18-5 mutant, which show widespread but intron-specific defects...
December 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27870853/intron-lariat-rna-inhibits-microrna-biogenesis-by-sequestering-the-dicing-complex-in-arabidopsis
#20
Ziwei Li, Shengpeng Wang, Jinping Cheng, Chuanbin Su, Songxiao Zhong, Qi Liu, Yuda Fang, Yao Yu, Hong Lv, Yun Zheng, Binglian Zheng
Lariat RNAs formed as by-products of splicing are quickly degraded by the RNA debranching enzyme 1 (DBR1), leading to their turnover. Null dbr1 mutants in both animals and plants are embryo lethal, but the mechanism underlying the lethality remains unclear. Here we characterized a weak mutant allele of DBR1 in Arabidopsis, dbr1-2, and showed that a global increase in lariat RNAs was unexpectedly accompanied by a genome-wide reduction in miRNA accumulation. The dbr1-2 mutation had no effects on expression of miRNA biogenesis genes or primary miRNAs (pri-miRNAs), but the association of pri-miRNAs with the DCL1/HYL1 dicing complex was impaired...
November 2016: PLoS Genetics
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