当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

Abstract：

:RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-binding proteins Yra1, Nab2, and Mex67 onto poly(A)(+)RNA. We also found that Yra1 associates directly with Dbp2 and functions as an inhibitor of Dbp2-dependent duplex unwinding, suggestive of a cycle of unwinding and inhibition by Dbp2. To test this, we undertook a series of experiments to shed light on the order of events for Dbp2 in co-transcriptional mRNP assembly. We now show that Dbp2 is recruited to chromatin via RNA and forms a large, RNA-dependent complex with Yra1 and Mex67. Moreover, single-molecule fluorescence resonance energy transfer and bulk biochemical assays show that Yra1 inhibits unwinding in a concentration-dependent manner by preventing the association of Dbp2 with single-stranded RNA. This inhibition prevents over-accumulation of Dbp2 on mRNA and stabilization of a subset of RNA polymerase II transcripts. We propose a model whereby Yra1 terminates a cycle of mRNP assembly by Dbp2.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Ma WK,Paudel BP,Xing Z,Sabath IG,Rueda D,Tran EJ

doi

10.1016/j.jmb.2016.02.005

subject

Has Abstract

pub_date

2016-03-27 00:00:00

pages

1091-1106

issue

6

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(16)00110-8

journal_volume

428

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding.

    abstract：:The mutants P235A and F236A have been generated and their crystal structure was determined to resolutions of 2.38 and 2.35 A, respectively, in order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A-ATP synthase from Pyrococcus horikoshii OT3. Both the structures sho...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.06.070

    authors： Kumar A,Manimekalai MS,Balakrishna AM,Priya R,Biuković G,Jeyakanthan J,Grüber G

    更新日期：2010-09-03 00:00:00

  • Crystal structures of artocarpin, a Moraceae lectin with mannose specificity, and its complex with methyl-alpha-D-mannose: implications to the generation of carbohydrate specificity.

    abstract：:The seeds of jack fruit (Artocarpus integrifolia) contain two tetrameric lectins, jacalin and artocarpin. Jacalin was the first lectin found to exhibit the beta-prism I fold, which is characteristic of the Moraceae plant lectin family. Jacalin contains two polypeptide chains produced by a post-translational proteolysi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5432

    authors： Pratap JV,Jeyaprakash AA,Rani PG,Sekar K,Surolia A,Vijayan M

    更新日期：2002-03-22 00:00:00

  • Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase.

    abstract：:Peptide deformylase (PDF) has received considerable attention during the last few years as a potential target for a new type of antibiotics. It is an essential enzyme in eubacteria for the removal of the formyl group from the N terminus of the nascent polypeptide chain. We have solved the X-ray structures of four memb...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00596-5

    authors： Kreusch A,Spraggon G,Lee CC,Klock H,McMullan D,Ng K,Shin T,Vincent J,Warner I,Ericson C,Lesley SA

    更新日期：2003-07-04 00:00:00

  • Temperature dependence and Arrhenius activation energy of F-actin velocity generated in vitro by skeletal myosin.

    abstract：:The effect of temperature on the velocity of rhodamine phalloidin-labelled F-actin moving in vitro on rabbit skeletal myosin has been studied. Translating actin filaments were visualized by epi-fluorescence in an inverted microscope, equipped with temperature control (+/- 0.2 K) of the stage and objective. Images were...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90467-x

    authors： Anson M

    更新日期：1992-04-20 00:00:00

  • Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.

    abstract：:Comparisons of the structures of glutamate dehydrogenase (GluDH) and leucine dehydrogenase (LeuDH) have suggested that two substitutions, deep within the amino acid binding pockets of these homologous enzymes, from hydrophilic residues to hydrophobic ones are critical components of their differential substrate specifi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2335

    authors： Stillman TJ,Migueis AM,Wang XG,Baker PJ,Britton KL,Engel PC,Rice DW

    更新日期：1999-01-15 00:00:00

  • Identification of a B-cell epitope of hyaluronidase, a major bee venom allergen, from its crystal structure in complex with a specific Fab.

    abstract：:The major allergens of honeybee venom, hyaluronidase (Hyal) and phospholipase A2, can induce life-threatening IgE-mediated allergic reactions in humans. Although conventional immunotherapy is effective, up to 40% of patients develop allergic side effects including anaphylaxis and thus, there is a need for an improved ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.02.036

    authors： Padavattan S,Schirmer T,Schmidt M,Akdis C,Valenta R,Mittermann I,Soldatova L,Slater J,Mueller U,Markovic-Housley Z

    更新日期：2007-05-04 00:00:00

  • Heterocyst-forming filamentous cyanobacteria encode proteins that resemble eukaryotic RNA-binding proteins of the RNP family.

    abstract：:Heterocyst-forming cyanobacteria have multiple genes encoding proteins that are similar to the RNP family of eukaryotic RNA-binding proteins. Three genes from two strains of cyanobacteria (Anabaena and Chlorogloeopsis) have been sequenced. All three putative gene products contain a single RNA Recognition Motif (RRM) t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1070

    authors： Mulligan ME,Jackman DM,Murphy ST

    更新日期：1994-01-21 00:00:00

  • The activation defect of a lambda cI positive control mutant.

    abstract：:"Positive control" mutants of the cI protein of bacteriophage lambda (lambda cI) bind DNA but, unlike the wild-type protein, fail to activate transcription. According to the original interpretation of Ptashne and co-workers, these mutants bear amino acid substitutions that disrupt a stimulatory interaction between lam...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0735

    authors： Whipple FW,Ptashne M,Hochschild A

    更新日期：1997-01-24 00:00:00

  • Structure and function of the F plasmid genes essential for partitioning.

    abstract：:The F plasmid in Escherichia coli has its own partition mechanism controlled by the sopA and sopB genes, and by the cis-acting sopC region. The DNA sequence of the entire partition region and its flanking regions is described here. Two large open reading frames coding for 43,700 Mr and 35,400 Mr proteins correspond to...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90459-6

    authors： Mori H,Kondo A,Ohshima A,Ogura T,Hiraga S

    更新日期：1986-11-05 00:00:00

  • In vitro packaging of DNA of the Bacillus subtilis bacteriophage SPP1.

    abstract：:In vitro packaging of bacteriophage SPP1 DNA into procapsids is described and the requirements of this process were determined. Combination of proheads with an extract supplying terminase, DNA and phage tails yielded up to 10(7 )viable phages per milliliter of in vitro reaction under optimized conditions. The presence...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3449

    authors： Dröge A,Tavares P

    更新日期：2000-02-11 00:00:00

  • A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding.

    abstract：:The denatured states of barnase that are induced by urea, acid, and high temperature and acid have been assigned and characterised by high resolution heteronuclear NMR. The assignment was completed using a combination of triple-resonance and magnetisation-transfer methods. The latter was facilitated by selecting a sui...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0618

    authors： Arcus VL,Vuilleumier S,Freund SM,Bycroft M,Fersht AR

    更新日期：1995-11-24 00:00:00

  • Negatively stained 50 S ribosomal subunits of Escherichia coli.

    abstract：:Ribosomes are large nucleoproteins of approximately 3 X 10(6) Mr. In contrast to helical or spherical nucleoproteins (viruses) of similar size (which consist of several hundred small asymmetric units reproduced by symmetry), ribosomes are completely asymmetric; therefore, the amount of structural information (defined ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90366-9

    authors： Hoppe W,Oettl H,Tietz HR

    更新日期：1986-11-20 00:00:00

  • The structure of interleukin-23 reveals the molecular basis of p40 subunit sharing with interleukin-12.

    abstract：:Interleukin (IL)-23 is a recently identified member of the IL-12 family of heterodimeric cytokines that modulate subpopulations of T helper cells, and both IL-12 and IL-23 are attractive targets for therapy of autoimmune diseases. IL-23 is a binary complex of a four-helix bundle cytokine (p19) and a soluble class I cy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.07.051

    authors： Lupardus PJ,Garcia KC

    更新日期：2008-10-17 00:00:00

  • The Role of RNA Interference in Stem Cell Biology: Beyond the Mutant Phenotypes.

    abstract：:Complex gene regulation systems ensure the maintenance of cellular identity during early development in mammals. Eukaryotic small RNAs have emerged as critical players in RNA interference (RNAi) by mediating gene silencing during embryonic stem cell self-renewal. Most of the proteins involved in the biogenesis of smal...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2017.01.014

    authors： Bodak M,Cirera-Salinas D,Luitz J,Ciaudo C

    更新日期：2017-05-19 00:00:00

  • Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion.

    abstract：:Influenza viral entry into the host cell cytoplasm is accomplished by a process of membrane fusion mediated by the viral hemagglutinin protein. Hemagglutinin acts in a pH-triggered fashion, inserting a short fusion peptide into the host membrane followed by refolding of a coiled-coil structure to draw the viral envelo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2018.01.006

    authors： Zawada KE,Okamoto K,Kasson PM

    更新日期：2018-03-02 00:00:00

  • Principles governing amino acid composition of integral membrane proteins: application to topology prediction.

    abstract：:A new method is suggested here for topology prediction of helical transmembrane proteins. The method is based on the hypothesis that the localizations of the transmembrane segments and the topology are determined by the difference in the amino acid distributions in various structural parts of these proteins rather tha...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2107

    authors： Tusnády GE,Simon I

    更新日期：1998-10-23 00:00:00

  • Structure of a foreign peptide displayed on the surface of bacteriophage M13.

    abstract：:The use of filamentous bacteriophage M13 as a vehicle for display of foreign peptides and proteins provides a means for the construction of therapeutic, diagnostic and technological tools of broad utility. The usefulness of this technology is dependent on the ability of an inserted peptide to act as a ligand when fuse...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1489

    authors： Kishchenko G,Batliwala H,Makowski L

    更新日期：1994-08-12 00:00:00

  • Hsp70 and Hsp90 of E. coli Directly Interact for Collaboration in Protein Remodeling.

    abstract：:Hsp90 is a highly conserved molecular chaperone that remodels hundreds of client proteins, many involved in the progression of cancer and other diseases. It functions with the Hsp70 chaperone and numerous cochaperones. The bacterial Hsp90 functions with an Hsp70 chaperone, DnaK, but is independent of Hsp90 cochaperone...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.10.010

    authors： Genest O,Hoskins JR,Kravats AN,Doyle SM,Wickner S

    更新日期：2015-12-04 00:00:00

  • Activation of the lac promoter and its variants. Synergistic effects of catabolite activator protein and supercoiling in vitro.

    abstract：:Escherichia coli lac promoter variants are shown to be subject to large synergistic transcriptional activation by catabolite activator protein (CRP) and DNA supercoiling in vitro. Activation was studied for the lac wild-type promoter, a promoter with a variant spacing (lac delta l) and two promoters with variant -10 r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90236-2

    authors： Meiklejohn AL,Gralla JD

    更新日期：1989-06-20 00:00:00

  • A novel mutation in the neurofibromatosis type 1 (NF1) gene promotes skipping of two exons by preventing exon definition.

    abstract：:Using a protein truncation assay, we have identified a new mutation in the neurofibromatosis type 1 (NF1) gene that causes a severe defect in NF1 pre-mRNA splicing. The mutation, which consists of a G to A transition at position +1 of the 5' splice site of exon 12a, is associated with the loss of both exons 11 and 12a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4561

    authors： Fang LJ,Simard MJ,Vidaud D,Assouline B,Lemieux B,Vidaud M,Chabot B,Thirion JP

    更新日期：2001-04-13 00:00:00

  • Organization and evolution of a higher plant alphoid-like satellite DNA sequence.

    abstract：:Two recombinant plasmids containing, respectively, three and eight tandem repeats of a 177 base-pair (bp) element from radish nuclear DNA have been isolated. These plasmids were used as probes to investigate the organization and the copy number of this element within the genome. This sequence is present in congruent t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90329-3

    authors： Grellet F,Delcasso D,Panabieres F,Delseny M

    更新日期：1986-02-20 00:00:00

  • Crystallization of halophilic malate dehydrogenase from Halobacterium marismortui.

    abstract：:Malate dehydrogenase from the extreme halophile Halobacterium marismortui crystallizes in highly concentrated phosphate solution in space group 12 with cell dimensions a = 113.8 A, b = 122.8 A, c = 126.7 A, beta = 98.1 degrees. The halophilic enzyme was found to be unstable at lower concentrations of phosphate. It ass...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90547-5

    authors： Harel M,Shoham M,Frolow F,Eisenberg H,Mevarech M,Yonath A,Sussman JL

    更新日期：1988-04-05 00:00:00

  • Evolution of protein binding modes in homooligomers.

    abstract：:The evolution of protein interactions cannot be deciphered without a detailed analysis of interaction interfaces and binding modes. We performed a large-scale study of protein homooligomers in terms of their symmetry, interface sizes, and conservation of binding modes. We also focused specifically on the evolution of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.10.052

    authors： Dayhoff JE,Shoemaker BA,Bryant SH,Panchenko AR

    更新日期：2010-01-29 00:00:00

  • An amphipathic alpha-helix at a membrane interface: a structural study using a novel X-ray diffraction method.

    abstract：:The amphipathic alpha-helix is a recurrent feature of membrane-active proteins, peptides, and toxins. Despite extensive biophysical studies, the structural details of its affinity for membrane interfaces remain rather vague. We report here the first results of an effort to obtain detailed structural information about ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2840

    authors： Hristova K,Wimley WC,Mishra VK,Anantharamiah GM,Segrest JP,White SH

    更新日期：1999-07-02 00:00:00

  • Order-disorder phenomena in myelinated nerve sheaths. I. A physical model and its parametrization: exact and approximate determination of the parameters.

    abstract：:An algorithm is developed for the analysis of the X-ray scattering spectra of lamellar systems, by reference to a precise physical model. The model consists of identical planar lamellae (the motif), all parallel and stacked in a one-dimensional crystal with four types of defect: stacking disorder, finite size of the c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(05)80358-4

    authors： Luzzati V,Mateu L

    更新日期：1990-10-05 00:00:00

  • Structural polymorphism of Methanothermobacter thermautotrophicus MCM.

    abstract：:The minichromosome maintenance (MCM) proteins are essential for replication initiation and elongation in eukarya and archaea. There are six MCM proteins in eukaryotes, and MCM complexes are believed to unwind DNA during chromosomal DNA replication. However, the mechanism and structure of the MCM complexes are not know...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.11.076

    authors： Chen YJ,Yu X,Kasiviswanathan R,Shin JH,Kelman Z,Egelman EH

    更新日期：2005-02-18 00:00:00

  • Oligomerization of the SPP1 scaffolding protein.

    abstract：:Viral scaffolding proteins direct polymerization of major capsid protein subunits into icosahedral procapsid structures. The scaffolding protein of bacteriophage SPP1 was engineered with a C-terminal hexahistidine tag (gp11-His(6)) and purified. The protein is an alpha-helical-rich molecule with a very elongated shape...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.02.028

    authors： Poh SL,el Khadali F,Berrier C,Lurz R,Melki R,Tavares P

    更新日期：2008-05-02 00:00:00

  • Defining the requirements for an antibody epitope on influenza virus neuraminidase: how tolerant are protein epitopes?

    abstract：:To determine the conformational requirements for antibody recognition and extent of flexibility within a protein epitope, a chimeric influenza A virus neuraminidase (NA) has been constructed in which five discontinuous polypeptide segments from a subtype N9 NA, which comprise the monoclonal antibody NC41 epitope, have...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1025

    authors： Nuss JM,Air GM

    更新日期：1994-01-14 00:00:00

  • Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes.

    abstract：:Nonstandard nucleotide triphosphate pyrophosphatase (NTPase) can efficiently hydrolyze nonstandard purine nucleotides in the presence of divalent cations. The crystal structures of the NTPase from Pyrococcus horikoshii OT3 (PhNTPase) have been determined in two unliganded forms and in three liganded forms with inosine...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.11.018

    authors： Lokanath NK,Pampa KJ,Takio K,Kunishima N

    更新日期：2008-01-25 00:00:00

  • On the nature of conformational openings: native and unfolded-state hydrogen and thiol-disulfide exchange studies of ferric aquomyoglobin.

    abstract：:Native-state amide hydrogen exchange (HX) of proteins in the presence of denaturant has provided valuable details on the structures of equilibrium folding intermediates. Here, we extend HX theory to model thiol group exchange (SX) in single cysteine-containing variants of sperm whale ferric aquomyoglobin. SX is comple...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5117

    authors： Feng Z,Butler MC,Alam SL,Loh SN

    更新日期：2001-11-16 00:00:00