Structural basis for single-stranded RNA recognition and cleavage by C3PO.

Abstract:

:Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced silencing complex, the effector complex of RNA interference (RNAi). Here, we report three crystal structures of Nanoarchaeum equitans (Ne) C3PO. The apo-NeC3PO structure adopts an open form and unravels a potential substrates entryway for the first time. The NeC3PO:ssRNA and NeC3PO:ssDNA complexes fold like closed football with the substrates captured at the inner cavities. The NeC3PO:ssRNA structure represents the only catalytic form C3PO complex available to date; with mutagenesis and in vitro cleavage assays, the structure provides critical insights into the substrate binding and the two-cation-assisted catalytic mechanisms that are shared by eukaryotic C3POs. The work presented here further advances our understanding on the RNAi pathway.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Zhang J,Liu H,Yao Q,Yu X,Chen Y,Cui R,Wu B,Zheng L,Zuo J,Huang Z,Ma J,Gan J

doi

10.1093/nar/gkw776

subject

Has Abstract

pub_date

2016-11-02 00:00:00

pages

9494-9504

issue

19

eissn

0305-1048

issn

1362-4962

pii

gkw776

journal_volume

44

pub_type

杂志文章
  • Z-DNA-binding proteins from bull testis.

    abstract::Three Z-DNA-binding proteins of Mr 31, 33 and 58 kD were isolated from mature bull testis. They were obtained in a native state suitable for binding studies. These are the first examples of Z-DNA-binding proteins from a mammalian tissue. Purification involved tissue extraction with 0.35 M NaCl, cation exchange chromat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.23.9691

    authors: Gut SH,Bischoff M,Hobi R,Kuenzle CC

    更新日期:1987-12-10 00:00:00

  • Recognition of base pairs by polar peptides in double stranded DNA.

    abstract::The resonance Raman spectrum of native DNA has been obtained using excitation at 257 nm. In a first part, the spectral lines are assigned to the different nucleotide bases which provide the resonance effect. In a second part, the interactions of DNA with basic peptides (Arginine Methylester, Lysine Methylester, Arginy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.5.1707

    authors: Laigle A,Chinsky L,Turpin PY

    更新日期:1982-03-11 00:00:00

  • Identification and partial characterization of an endogenous form of mouse mammary tumor virus that is transcribed into the virion-associated RNA genome.

    abstract::Restriction mapping demonstrated the presence of several distinct proviral forms of mouse mammary tumor virus in the genome of GR mice. One of these proviruses (GR-MTV-2) was highly amplified in GR 3A cells, a cell line derived from a GR mammary tumor. By the criterion of restriction mapping, the amplified GR-MTV-2 pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.23.5715

    authors: Fanning TG,Puma JP,Cardiff RD

    更新日期:1980-12-11 00:00:00

  • Selection of bacteriophage lambda integrases with altered recombination specificity by in vitro compartmentalization.

    abstract::In vitro compartmentalization (IVC) was employed for the first time to select for novel bacteriophage lambda integrase variants displaying significantly enhanced recombination activity on a non-cognate target DNA sequence. These variants displayed up to 9-fold increased recombination activity over the parental enzyme,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1089

    authors: Tay Y,Ho C,Droge P,Ghadessy FJ

    更新日期:2010-03-01 00:00:00

  • Multiplex accurate sensitive quantitation (MASQ) with application to minimal residual disease in acute myeloid leukemia.

    abstract::Measuring minimal residual disease in cancer has applications for prognosis, monitoring treatment and detection of recurrence. Simple sequence-based methods to detect nucleotide substitution variants have error rates (about 10-3) that limit sensitive detection. We developed and characterized the performance of MASQ (m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa090

    authors: Moffitt AB,Spector MS,Andrews P,Kendall J,Alexander J,Stepansky A,Ma B,Kolitz J,Chiorazzi N,Allen SL,Krasnitz A,Wigler M,Levy D,Wang Z

    更新日期:2020-04-17 00:00:00

  • A gene-specific DNA sequencing chip for exploring molecular evolutionary change.

    abstract::Sequencing by hybridization (SBH) approaches to DNA sequencing face two conflicting constraints. First, in order to ensure that the target DNA binds reliably, the oligonucleotide probes that are attached to the chip array must be >15 bp in length. Secondly, the total number of possible 15 bp oligonucleotides is too la...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh210

    authors: Fedrigo O,Naylor G

    更新日期:2004-02-18 00:00:00

  • The evolution of the ribosome biogenesis pathway from a yeast perspective.

    abstract::Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome biogenesis factors (RBFs) exists only for Saccharomyces cerevisiae. Far less is known for other fungi, animals or plants, and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1137

    authors: Ebersberger I,Simm S,Leisegang MS,Schmitzberger P,Mirus O,von Haeseler A,Bohnsack MT,Schleiff E

    更新日期:2014-02-01 00:00:00

  • Laminin-database v.2.0: an update on laminins in health and neuromuscular disorders.

    abstract::The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt901

    authors: Golbert DC,Santana-van-Vliet E,Mundstein AS,Calfo V,Savino W,de Vasconcelos AT

    更新日期:2014-01-01 00:00:00

  • The signal recognition particle database (SRPDB).

    abstract::The SRPDB (signal recognition particle database) provides aligned SRP RNA and protein sequences, annotated and phylogenetically ordered. This release includes 82 SRP RNAs (including 22 bacterial and 9 archaeal homologs) and a total of 20 protein sequences representing SRP9, SRP14, SRP19, SRP54, SRP68, and SRP72. The o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.17.3483

    authors: Zwieb C,Larsen N

    更新日期:1994-09-01 00:00:00

  • The use of R-looping for structural gene identification and mRNA purification.

    abstract::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.7.2483

    authors: Woolford JL Jr,Rosbash M

    更新日期:1979-06-11 00:00:00

  • Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes.

    abstract::We have used paired-end sequencing of yeast nucleosomal DNA to obtain accurate genomic maps of nucleosome positions and occupancies in control cells and cells treated with 3-aminotriazole (3AT), an inducer of the transcriptional activator Gcn4. In control cells, 3AT-inducible genes exhibit a series of distinct nucleos...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr643

    authors: Cole HA,Howard BH,Clark DJ

    更新日期:2011-12-01 00:00:00

  • In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding.

    abstract::The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki546

    authors: Fauzi H,Jack KD,Hines JV

    更新日期:2005-05-06 00:00:00

  • Interactions of replication initiator RctB with single- and double-stranded DNA in origin opening of Vibrio cholerae chromosome 2.

    abstract::Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa826

    authors: Chatterjee S,Jha JK,Ciaccia P,Venkova T,Chattoraj DK

    更新日期:2020-11-04 00:00:00

  • The regulatory region of the divergent argECBH operon in Escherichia coli K-12.

    abstract::The nucleotide sequence of the control region of the divergent argECBH operon has been established in the wild type and in mutants affecting expression of these genes. The argE and argCBH promoters face each other and overlap with an operator region containing two domains which may act as distinct repressor binding si...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.24.8031

    authors: Piette J,Cunin R,Boyen A,Charlier D,Crabeel M,Van Vliet F,Glansdorff N,Squires C,Squires CL

    更新日期:1982-12-20 00:00:00

  • SIRT1 is regulated by a PPAR{γ}-SIRT1 negative feedback loop associated with senescence.

    abstract::Human Silent Information Regulator Type 1 (SIRT1) is an NAD(+)-dependent deacetylase protein which is an intermediary of cellular metabolism in gene silencing and aging. SIRT1 has been extensively investigated and shown to delay senescence; however, less is known about the regulation of SIRT1 during aging. In this stu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq609

    authors: Han L,Zhou R,Niu J,McNutt MA,Wang P,Tong T

    更新日期:2010-11-01 00:00:00

  • The mechanism of mutation induction by a hydrogen bond ambivalent, bicyclic N4-oxy-2'-deoxycytidine in Escherichia coli.

    abstract::The triphosphate of the nucleoside deoxyribosyl dihydropyrimido[4,5-c][1,2]oxazin-7-one (dP) is known to be incorporated into DNA efficiently by Taq polymerase and is a useful tool for polymerase-mediated in vitro mutagenesis. It is shown here that dP is a potent mutagen in Escherichia coli and Salmonella typhimurium ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.8.1548

    authors: Negishi K,Williams DM,Inoue Y,Moriyama K,Brown DM,Hayatsu H

    更新日期:1997-04-15 00:00:00

  • Human ADA3 regulates RARalpha transcriptional activity through direct contact between LxxLL motifs and the receptor coactivator pocket.

    abstract::The alternation/deficiency in activation-3 (ADA3) is an essential component of the human p300/CBP-associated factor (PCAF) and yeast Spt-Ada-Gcn5-acetyltransferase (SAGA) histone acetyltransferase complexes. These complexes facilitate transactivation of target genes by association with transcription factors and modifi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq269

    authors: Li CW,Ai N,Dinh GK,Welsh WJ,Chen JD

    更新日期:2010-09-01 00:00:00

  • Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA.

    abstract::Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome's subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1253

    authors: Scheunemann AE,Graham WD,Vendeix FA,Agris PF

    更新日期:2010-05-01 00:00:00

  • Global landscape of mouse and human cytokine transcriptional regulation.

    abstract::Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky787

    authors: Carrasco Pro S,Dafonte Imedio A,Santoso CS,Gan KA,Sewell JA,Martinez M,Sereda R,Mehta S,Fuxman Bass JI

    更新日期:2018-10-12 00:00:00

  • Inherited disorders of cobalamin metabolism disrupt nucleocytoplasmic transport of mRNA through impaired methylation/phosphorylation of ELAVL1/HuR.

    abstract::The molecular mechanisms that underlie the neurological manifestations of patients with inherited diseases of vitamin B12 (cobalamin) metabolism remain to date obscure. We observed transcriptomic changes of genes involved in RNA metabolism and endoplasmic reticulum stress in a neuronal cell model with impaired cobalam...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky634

    authors: Battaglia-Hsu SF,Ghemrawi R,Coelho D,Dreumont N,Mosca P,Hergalant S,Gauchotte G,Sequeira JM,Ndiongue M,Houlgatte R,Alberto JM,Umoret R,Robert A,Paoli J,Jung M,Quadros EV,Guéant JL

    更新日期:2018-09-06 00:00:00

  • Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions.

    abstract::Structures of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5'/5" have been assigned stereospecifically. All 3JH,H and 3JP,H coupling constants have been measured. The structures were dete...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.22.4589

    authors: Popenda M,Biala E,Milecki J,Adamiak RW

    更新日期:1997-11-15 00:00:00

  • Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations.

    abstract::We present a general method for isolating molecular markers specific to any region of a chromosome using existing mapping populations. Two pools of DNA from individuals homozygous for opposing alleles for a targeted chromosomal interval, defined by two or more linked RFLP markers, are constructed from members of an ex...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.23.6553

    authors: Giovannoni JJ,Wing RA,Ganal MW,Tanksley SD

    更新日期:1991-12-11 00:00:00

  • Roles for TbDSS-1 in RNA surveillance and decay of maturation by-products from the 12S rRNA locus.

    abstract::The Trypanosoma brucei exoribonuclease, TbDSS-1, has been implicated in multiple aspects of mitochondrial RNA metabolism. Here, we investigate the role of TbDSS-1 in RNA processing and surveillance by analyzing 12S rRNA processing intermediates in TbDSS-1 RNAi cells. RNA fragments corresponding to leader sequence upst...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm690

    authors: Mattiacio JL,Read LK

    更新日期:2008-01-01 00:00:00

  • Determination of the number of superhelical turns by the hyperchromicity of partially denatured covalently-closed DNA molecules.

    abstract::A novel method of determining the number of superhelical turns of a covalently-closed plasmid DNA is described. It relies on the determination of the hyperchromicity, and hence the proportion of unstacked basepairs, of a partially heat-denatured sample which co-migrates during electrophoresis with nicked circular dupl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.2.525

    authors: Dougherty G,Koller T

    更新日期:1982-01-22 00:00:00

  • A method for generating subtractive cDNA libraries retaining clones containing repetitive elements.

    abstract::Here we describe a two-stepped photobiotin-based procedure to enrich a target (canine retinal) cDNA library for tissue specific clones without removing those containing repetitive ( SINE ) elements, despite the presence of these elements in the driver population. In a first hybridization excess SINE elements were hybr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.21.4427

    authors: Lin CT,Sargan DR

    更新日期:1997-11-01 00:00:00

  • Intracellular RNA cleavage by the hairpin ribozyme.

    abstract::Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.15.3494

    authors: Seyhan AA,Amaral J,Burke JM

    更新日期:1998-08-01 00:00:00

  • RNAi pathways repress reprogramming of C. elegans germ cells during heat stress.

    abstract::Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa174

    authors: Rogers AK,Phillips CM

    更新日期:2020-05-07 00:00:00

  • Identification of essential domains for Escherichia coli tRNA(leu) aminoacylation and amino acid editing using minimalist RNA molecules.

    abstract::Escherichia coli leucyl-tRNA synthetase (LeuRS) aminoacylates up to six different class II tRNA(leu) molecules. Each has a distinct anticodon and varied nucleotides in other regions of the tRNA. Attempts to construct a minihelix RNA that can be aminoacylated with leucine have been unsuccessful. Herein, we describe the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/30.10.2103

    authors: Larkin DC,Williams AM,Martinis SA,Fox GE

    更新日期:2002-05-15 00:00:00

  • Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3'-A-tract junction.

    abstract::Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer repeated sequence including five inosines we show by uranyl photoprobing that a narrow minor groove varying in phase with the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.17.3497

    authors: Mollegaard NE,Bailly C,Waring MJ,Nielsen PE

    更新日期:1997-09-01 00:00:00

  • Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme.

    abstract::A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1055

    authors: Mustoe AM,Al-Hashimi HM,Brooks CL 3rd

    更新日期:2016-01-08 00:00:00