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"Rna Rearrangement"

Yi Zhou, Sharmishtha Musalgaonkar, Arlen W Johnson, David W Taylor
The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation...
February 27, 2019: Nature Communications
Olga Kossinova, Alexey Malygin, Alain Krol, Galina Karpova
Chemical approaches are very powerful tools for investigating the molecular structure and architecture of large ribonucleoprotein complexes involving ribosomes and other components of the translation system. Application of RNA nucleotide-specific and cross-linking reagents of a broad specificity range allows the researcher to obtain information on the sites of ligand binding to the ribosome and to each other as well as on the RNA rearrangements caused by the binding. Here, we describe specific chemical approaches including chemical probing and site-directed or bifunctional reagent-mediated cross-linking, which have been used for exploring the mechanism of selenocysteine insertion into a polypeptide chain by mammalian ribosomes...
2018: Methods in Molecular Biology
Franziska Theresia Edelmann, Andreas Schlundt, Roland Gerhard Heym, Andreas Jenner, Annika Niedner-Boblenz, Muhammad Ibrahim Syed, Jean-Christophe Paillart, Ralf Stehle, Robert Janowski, Michael Sattler, Ralf-Peter Jansen, Dierk Niessing
mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p...
February 2017: Nature Structural & Molecular Biology
W Luke Ward, Rick Russell
Cellular RNAs depend on proteins for efficient folding to specific functional structures and for transitions between functional structures. This dependence arises from intrinsic properties of RNA structure. Specifically, RNAs possess stable local structure, largely in the form of helices, and they have abundant opportunities to form alternative helices and tertiary contacts and therefore to populate alternative structures. Proteins with RNA chaperone activity, either ATP-dependent or ATP-independent, can promote structural transitions by interacting with single-stranded RNA (ssRNA) to compete away partner interactions and then release ssRNA so that it can form new interactions...
2015: Methods in Molecular Biology
Cynthia Pan, Jeffrey P Potratz, Brian Cannon, Zachary B Simpson, Jessica L Ziehr, Pilar Tijerina, Rick Russell
DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA-protein complexes (RNPs) in many essential cellular processes. Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices, it is not known how they disrupt RNA tertiary structure. Here, we use single molecule fluorescence to show that the DEAD-box protein CYT-19 disrupts tertiary structure in a group I intron using a helix capture mechanism. CYT-19 binds to a helix within the structured RNA only after the helix spontaneously loses its tertiary contacts, and then CYT-19 uses ATP to unwind the helix, liberating the product strands...
October 2014: PLoS Biology
Vito Martella, Pierfrancesco Pinto, Fabio Tummolo, Simona De Grazia, Giovanni M Giammanco, Maria C Medici, Balasubramanian Ganesh, Yvan L'Homme, Tibor Farkas, Ferenc Jakab, Krisztián Bányai
Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5' or 3' end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established...
December 2014: Archives of Virology
Jie Zhou, Laura Lancaster, John Paul Donohue, Harry F Noller
Coupled translocation of messenger RNA and transfer RNA (tRNA) through the ribosome, a process catalyzed by elongation factor EF-G, is a crucial step in protein synthesis. The crystal structure of a bacterial translocation complex describes the binding states of two tRNAs trapped in mid-translocation. The deacylated P-site tRNA has moved into a partly translocated pe/E chimeric hybrid state. The anticodon stem-loop of the A-site tRNA is captured in transition toward the 30S P site, while its 3' acceptor end contacts both the A and P loops of the 50S subunit, forming an ap/ap chimeric hybrid state...
September 5, 2014: Science
Rick Russell, Inga Jarmoskaite, Alan M Lambowitz
DEAD-box proteins are superfamily 2 helicases that function in all aspects of RNA metabolism. They employ ATP binding and hydrolysis to generate tight, yet regulated RNA binding, which is used to unwind short RNA helices non-processively and promote structural transitions of RNA and RNA-protein substrates. In the last few years, substantial progress has been made toward a detailed, quantitative understanding of the structural and biochemical properties of DEAD-box proteins. Concurrently, progress has been made toward a physical understanding of the RNA rearrangements and folding steps that are accelerated by DEAD-box proteins in model systems...
January 2013: RNA Biology
Dona Sleiman, Valérie Goldschmidt, Pierre Barraud, Roland Marquet, Jean-Christophe Paillart, Carine Tisné
HIV-1 reverse transcription is initiated from a tRNA(Lys)(3) molecule annealed to the viral RNA at the primer binding site (PBS). The annealing of tRNA(Lys)(3) requires the opening of its three-dimensional structure and RNA rearrangements to form an efficient initiation complex recognized by the reverse transcriptase. This annealing is mediated by the nucleocapsid protein (NC). In this paper, we first review the actual knowledge about HIV-1 viral RNA and tRNA(Lys)(3) structures. Then, we summarize the studies explaining how NC chaperones the formation of the tRNA(Lys)(3)/PBS binary complex...
November 2012: Virus Research
Daniela Hahn, Jean D Beggs
RNA helicases are involved in many cellular processes. Pre-mRNA splicing requires eight different DExD/H-box RNA helicases, which facilitate spliceosome assembly and remodelling of the intricate network of RNA rearrangements that are central to the splicing process. Brr2p, one of the spliceosomal RNA helicases, stands out through its unusual domain architecture. In the present review we highlight the advances made by recent structural and biochemical studies that have important implications for the mechanism and regulation of Brr2p activity...
August 2010: Biochemical Society Transactions
Gwendoline Cartier, Florence Lorieux, Frédéric Allemand, Marc Dreyfus, Thierry Bizebard
Spontaneous rearrangements of RNA structures are usually characterized by large activation energies and thus become very slow at low temperatures, yet RNA structure must remain dynamic even in cold-adapted (psychrophilic) organisms. DEAD-box proteins constitute a ubiquitous family of RNA-dependent ATPases that can often unwind short RNA duplexes in vitro (helicase activity), hence the belief that one of their major (though not exclusive) roles in vivo is to assist in RNA rearrangements. Here, we compare two Escherichia coli DEAD-box proteins and their orthologs from the psychrophilic bacteria Pseudoalteromonas haloplanktis and Colwellia psychrerythraea from the point of view of enzymatic properties...
March 30, 2010: Biochemistry
Lily Novak Frazer, Simon C Lovell, Raymond T O'Keefe
Conformational changes of snRNAs in the spliceosome required for pre-mRNA splicing are regulated by eight ATPases and one GTPase Snu114p. The Snu114p guanine state regulates U4/U6 unwinding during spliceosome activation and U2/U6 unwinding during spliceosome disassembly through the ATPase Brr2p. We investigated 618 genetic interactions to identify an extensive genetic interaction network between SNU114 and snRNAs. Snu114p G domain alleles were exacerbated by mutations that stabilize U4/U6 base pairing. G domain alleles were made worse by U2 and U6 mutations that stabilize or destabilize U2/U6 base pairing in helix I...
October 2009: Genetics
Zuopeng Wu, Xinying Jia, Laura de la Cruz, Xun-Cheng Su, Bruz Marzolf, Pamela Troisch, Daniel Zak, Adam Hamilton, Belinda Whittle, Di Yu, Daniel Sheahan, Edward Bertram, Alan Aderem, Gottfried Otting, Christopher C Goodnow, Gerard F Hoyne
Differentiation of memory cells involves DNA-sequence changes in B lymphocytes but is less clearly defined in T cells. RNA rearrangement is identified here as a key event in memory T cell differentiation by analysis of a mouse mutation that altered the proportions of naive and memory T cells and crippled the process of Ptprc exon silencing needed to generate CD45RO in memory T cells. A single substitution in a memory-induced RNA-binding protein, hnRNPLL, destabilized an RNA-recognition domain that bound with micromolar affinity to RNA containing the Ptprc exon-silencing sequence...
December 19, 2008: Immunity
Michelle Alvarez, Jack Ballantyne
OBJECTIVE: In the course of developing assays for the molecular prediction of biological age, we serendipitously discovered four novel isoforms of gamma hemoglobin mRNA, designated HBG1n1, HBG1n2, HBG2n2, and HBG2n3, collectively termed HBGn isoforms. Here we report the molecular characterization and tissue expression of these isoforms. MATERIALS AND METHODS: RNA obtained from human peripheral blood and various fetal and adult tissues was amplified with duplex reverse transcription polymerase chain reaction (RT-PCR) assays to determine the expression profiles of the HBGn isoforms...
February 2009: Experimental Hematology
Rujun Song, Jafar Kafaie, Long Yang, Michael Laughrea
We have characterized the viral RNA conformation in wild-type, protease-inactive (PR-) and SL1-defective (DeltaDIS) human immunodeficiency virus type 1 (HIV-1), as a function of the age of the viruses, from newly released to grown-up (>or=24 h old). We report evidence for packaging HIV-1 genomic RNA (gRNA) in the form of monomers in PR- virions, viral RNA rearrangement (not maturation) within PR- HIV-1, protease-dependent formation of thermolabile dimeric viral RNAs, a new form of immature gRNA dimer at about 5 h post virion release, and slow-acting dimerization signals in SL1-defective viruses...
August 24, 2007: Journal of Molecular Biology
Carolin Jalal, Heike Uhlmann-Schiffler, Hans Stahl
The DEAD box proteins encoded by the genes ddx5 (p68) and ddx17 (isoforms p72 and p82) are more closely related to each other than to any other member of their family. We found that p68 negatively controls p72/p82 gene expression but not vice versa. Knocking down of either gene does not affect cell proliferation, in case of p68 suppression, however, only on condition that p72/p82 overexpression was granted. In contrast, co-silencing of both genes causes perturbation of nucleolar structure and cell death. In mutant studies, the apparently redundant role(s) of p68 and p72/p82 correspond to their ability to catalyze RNA rearrangement rather than RNA unwinding reactions...
2007: Nucleic Acids Research
Pierre Barraud, Cyril Gaudin, Frédéric Dardel, Carine Tisné
HIV-1 reverse transcriptase uses the host tRNA3(Lys) as a primer for the synthesis of the minus DNA strand. The first event in viral replication is thus the annealing of tRNA to the primer binding site (PBS) in the 5' UTR of the viral RNA. This event requires a major RNA rearrangement which is chaperoned by the viral NC protein. The binding of NC to nucleic acids is essentially non-specific, however, NC is known to bind selectively to hairpins located in the 5' region of the viral RNA. In a previous study, using an NMR approach in which the reaction is slowed down by controlling temperature, we were able to follow details in this RNA unfolding/refolding process and to uncover an intermediate state...
October 2007: Biochimie
Victor Croitoru, Katharina Semrad, Silvia Prenninger, Lukas Rajkowitsch, Max Vejen, Brian Søgaard Laursen, Hans Uffe Sperling-Petersen, Leif A Isaksson
Translation initiation factor IF1 is an indispensable protein for translation in prokaryotes. No clear function has been assigned to this factor so far. In this study we demonstrate an RNA chaperone activity of this protein both in vivo and in vitro. The chaperone assays are based on in vivo or in vitro splicing of the group I intron in the thymidylate synthase gene (td) from phage T4 and an in vitro RNA annealing assay. IF1 wild-type and mutant variants with single amino acid substitutions have been analyzed for RNA chaperone activity...
December 2006: Biochimie
Kakoli Mitra, Christiane Schaffitzel, Felcy Fabiola, Michael S Chapman, Nenad Ban, Joachim Frank
In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements...
May 19, 2006: Molecular Cell
Carine Tisné
To promote the initiation of reverse transcription, the HIV-1 virus uses a host tRNA as a primer, tRNA(3Lys). The annealing of tRNA(3Lys) to the viral RNA requires the breaking of the 3D structure of the tRNA and RNA rearrangements, to form a stable initiation complex recognised by the reverse transcriptase. The annealing is mediated by a viral factor, the nucleocapsid protein. This protein has been studied for a long while to define the role of its different sub-domains and their mode of action. Only recently, a consensus view seems to emerge...
April 2005: Current HIV Research
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