DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway.

Abstract:

:In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-term RNAi-mediated gene regulation in plants. Here, we present solution structures of individual and concatenated DRB4 dsRBDs and demonstrate modes of dsRNA binding by employing NMR, ITC and site-specific mutagenesis. While both dsRBDs adopt the canonical α-β-β-β-α fold, key structural differences and ms-μs dynamics located at the RNA binding region were observed for dsRBD1. These features favor dsRBD1 to orient itself and make stronger tripartite contact with dsRNA, a feature missing in dsRBD2. Additionally, the inter-domain orientation induced by the linker restricts the mobility of dsRBD2, resulting in the steric hindrance of α1 helix in dsRBD2, and leads in further reduction of its dsRNA binding activity. Our study deciphers functional roles of DRB4 domains by showing that dsRBD1 drives the tasiRNA/siRNA pathway. Furthermore, we identify a potential role of the C-terminal region of DRB4 in protein:protein interaction as it possesses six PxxP motifs, binds to Zn2+ and contains a small structural domain.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Chiliveri SC,Aute R,Rai U,Deshmukh MV

doi

10.1093/nar/gkx481

subject

Has Abstract

pub_date

2017-08-21 00:00:00

pages

8551-8563

issue

14

eissn

0305-1048

issn

1362-4962

pii

3859017

journal_volume

45

pub_type

杂志文章
  • Two non-histone proteins are associated with the promoter region and histone HI with the transcribed region of active hsp-70 genes as revealed by UV-induced DNA-protein crosslinking in vivo.

    abstract::We described here an approach for mapping proteins on any sequence of genomic DNA. UV-induced DNA-protein crosslinking within whole cells and the 'protein image' hybridization technique (1) were applied to test the proteins bound to different regions of the D. melanogaster hsp-70 gene. The histone H1-DNA association w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.4.1031

    authors: Belikov SV,Belgovsky AI,Preobrazhenskaya OV,Karpov VL,Mirzabekov AD

    更新日期:1993-02-25 00:00:00

  • A 'new lease of life': FnCpf1 possesses DNA cleavage activity for genome editing in human cells.

    abstract::Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx783

    authors: Tu M,Lin L,Cheng Y,He X,Sun H,Xie H,Fu J,Liu C,Li J,Chen D,Xi H,Xue D,Liu Q,Zhao J,Gao C,Song Z,Qu J,Gu F

    更新日期:2017-11-02 00:00:00

  • Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5'-terminal regions of cap0-, cap1- and 5'ppp- mRNAs.

    abstract::Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1321

    authors: Kumar P,Sweeney TR,Skabkin MA,Skabkina OV,Hellen CU,Pestova TV

    更新日期:2014-03-01 00:00:00

  • Interaction of N-terminal domain of U1A protein with an RNA stem/loop.

    abstract::The U1A protein is a sequence-specific RNA binding protein found in the U1 snRNP particle where it binds to stem/loop II of U1 snRNA. U1A contains two 'RNP' or 'RRM' (RNA Recognition Motif) domains, which are common to many RNA-binding proteins. The N-terminal RRM has been shown to bind specifically to the U1 RNA stem...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.16.4283

    authors: Hall KB,Stump WT

    更新日期:1992-08-25 00:00:00

  • Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes.

    abstract::Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidop...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp183

    authors: Ziolkowski PA,Koczyk G,Galganski L,Sadowski J

    更新日期:2009-06-01 00:00:00

  • Mutational analysis of the reverse transcriptase and ribonuclease H domains of the human foamy virus.

    abstract::Human foamy or spuma virus (HFV) codes for a distinct set of pol gen products. To determine the minimal requirements for the HFV enzymatic activities, defined residues of the reverse transcriptase (RT) and ribo-nuclease H (RNase H) domain of the HFV pol gene were mutated by site-specific PCR mutagenesis. The mutant ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.14.2621

    authors: Kögel D,Aboud M,Flügel RM

    更新日期:1995-07-25 00:00:00

  • A comprehensive catalog of predicted functional upstream open reading frames in humans.

    abstract::Upstream open reading frames (uORFs) latent in mRNA transcripts are thought to modify translation of coding sequences by altering ribosome activity. Not all uORFs are thought to be active in such a process. To estimate the impact of uORFs on the regulation of translation in humans, we first circumscribed the universe ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky188

    authors: McGillivray P,Ault R,Pawashe M,Kitchen R,Balasubramanian S,Gerstein M

    更新日期:2018-04-20 00:00:00

  • Relative stabilities of DNA three-way, four-way and five-way junctions (multi-helix junction loops): unpaired nucleotides can be stabilizing or destabilizing.

    abstract::Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.12.2212

    authors: Kadrmas JL,Ravin AJ,Leontis NB

    更新日期:1995-06-25 00:00:00

  • Cell type-specific genomics of Drosophila neurons.

    abstract::Many tools are available to analyse genomes but are often challenging to use in a cell type-specific context. We have developed a method similar to the isolation of nuclei tagged in a specific cell type (INTACT) technique [Deal,R.B. and Henikoff,S. (2010) A simple method for gene expression and chromatin profiling of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks671

    authors: Henry GL,Davis FP,Picard S,Eddy SR

    更新日期:2012-10-01 00:00:00

  • Oligomeric properties and DNA binding specificities of repressor isoforms from the Streptomyces bacteriophage phiC31.

    abstract::Three protein isoforms (74, 54 and 42 kDa) are expressed from repressor gene c in the Streptomyces temperate bacteriophage phiC31. Because expression of the two smaller isoforms, 54 and 42 kDa, is sufficient for superinfection immunity, the interaction between these isoforms was studied. The native 42 kDa repressor (N...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.10.2457

    authors: Wilson SE,Smith MC

    更新日期:1998-05-15 00:00:00

  • RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.

    abstract::RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv020

    authors: Suresh V,Liu L,Adjeroh D,Zhou X

    更新日期:2015-02-18 00:00:00

  • The EcoCyc and MetaCyc databases.

    abstract::EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.1.56

    authors: Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

    更新日期:2000-01-01 00:00:00

  • Incorporation of 2'-amido-nucleosides in oligodeoxynucleotides and oligoribonucleotides as a model for 2'-linked conjugates.

    abstract::The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.1.51

    authors: Hendrix C,Devreese B,Rozenski J,van Aerschot A,De Bruyn A,Van Beeumen J,Herdewijn P

    更新日期:1995-01-11 00:00:00

  • Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch.

    abstract::Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particula...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn443

    authors: Greber D,El-Baba MD,Fussenegger M

    更新日期:2008-09-01 00:00:00

  • TFII-I-mediated polymerase pausing antagonizes GLI2 induction by TGFβ.

    abstract::The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa476

    authors: McCleary-Wheeler AL,Paradise BD,Almada LL,Carlson AJ,Marks DL,Vrabel A,Vera RE,Sigafoos AN,Olson RL,Fernandez-Zapico ME

    更新日期:2020-07-27 00:00:00

  • Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator.

    abstract::Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate -1 programmed ribosomal frameshifting (PRF), suggesting -1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by d...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw718

    authors: Lin YH,Chang KY

    更新日期:2016-10-14 00:00:00

  • PLK1 targets CtIP to promote microhomology-mediated end joining.

    abstract::Proper DNA double-strand break (DSB) repair is essential for maintaining genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism, which introduces mutations at break sites and contributes to chromosomal translocations and telomere fusions, thus driving carcinogenesis. Mitotic kin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky810

    authors: Wang H,Qiu Z,Liu B,Wu Y,Ren J,Liu Y,Zhao Y,Wang Y,Hao S,Li Z,Peng B,Xu X

    更新日期:2018-11-16 00:00:00

  • Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation.

    abstract::Reversible methylation of the N6 or N1 position of adenine in RNA has recently been shown to play significant roles in regulating the functions of RNA. RNA can also be alkylated upon exposure to endogenous and exogenous alkylating agents. Here we examined how regio-specific methylation at the hydrogen bonding edge of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx515

    authors: You C,Dai X,Wang Y

    更新日期:2017-09-06 00:00:00

  • Complete disproportionation of duplex poly(dT)*poly(dA) into triplex poly(dT)*poly(dA)*poly(dT) and poly(dA) by coralyne.

    abstract::Coralyne is a small crescent-shaped molecule known to intercalate duplex and triplex DNA. We report that coralyne can cause the complete and irreversible disproportionation of duplex poly(dT)*poly(dA). That is, coralyne causes the strands of duplex poly(dT)*poly(dA) to repartition into equal molar equivalents of tripl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/30.4.983

    authors: Polak M,Hud NV

    更新日期:2002-02-15 00:00:00

  • A novel E4BP4 element drives circadian expression of mPeriod2.

    abstract::Period2 (Per2) is an essential component of the mammalian clock mechanism and robust circadian expression of Per2 is essential for the maintenance of circadian rhythms. Although recent studies have shown that the circadian E2 enhancer (a non-canonical E-box) accounts for most of the circadian transcriptional drive of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl868

    authors: Ohno T,Onishi Y,Ishida N

    更新日期:2007-01-01 00:00:00

  • Assembly of MMTV promoter minichromosomes with positioned nucleosomes precludes NF1 access but not restriction enzyme cleavage.

    abstract::To generate long arrays of nucleosomes within a topologically defined chromatin domain we have assembled minichromosomes on negatively supercoiled plasmid DNA with extracts from Drosophila preblastoderm embryos. These minichromosomes are dynamic substrates for energy-dependent nucleosome remodeling machines that facil...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.16.3657

    authors: Venditti P,Di Croce L,Kauer M,Blank T,Becker PB,Beato M

    更新日期:1998-08-15 00:00:00

  • Update of the Human MitBASE database.

    abstract::Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerne...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.1.143

    authors: Attimonelli M,Cooper JM,D'Elia D,de Montalvo A,De Robertis M,Lehväslaiho H,Malladi SB,Memeo F,Stevens K,Schapira AH,Saccone C

    更新日期:1999-01-01 00:00:00

  • Robust detection of alternative splicing in a population of single cells.

    abstract::Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3' bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome v...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1525

    authors: Welch JD,Hu Y,Prins JF

    更新日期:2016-05-05 00:00:00

  • Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ.

    abstract::The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1280

    authors: Kogure H,Handa Y,Nagata M,Kanai N,Güntert P,Kubota K,Nameki N

    更新日期:2014-03-01 00:00:00

  • Isolation and characterization of the DNA fraction of rat liver chromatin which binds polylysine.

    abstract::The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.5.667

    authors: Arnold EA,Wahn U,Young KE

    更新日期:1975-05-01 00:00:00

  • Absolute quantitative measurement of transcriptional kinetic parameters in vivo.

    abstract::mRNA expression involves transcription initiation, elongation and degradation. In cells, these dynamic processes are highly regulated. However, experimental characterization of the dynamic processes in vivo is difficult due to the paucity of methods capable of direct measurements. We present a highly sensitive and ver...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw596

    authors: Iyer S,Park BR,Kim M

    更新日期:2016-10-14 00:00:00

  • Elements of an archaeal promoter defined by mutational analysis.

    abstract::The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.20.5423

    authors: Hain J,Reiter WD,Hüdepohl U,Zillig W

    更新日期:1992-10-25 00:00:00

  • The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.

    abstract::Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp603

    authors: Uyen NT,Park SY,Choi JW,Lee HJ,Nishi K,Kim JS

    更新日期:2009-11-01 00:00:00

  • Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin.

    abstract::The specific DNA binding ligand netropsin selectively blocks dA-dT base pairs in clusters containing two or more consecutive thymine residues at the dNAase I cleavage sites of DNA. Using CD and UV absorption measurements it is shown, that at various ratios of netropsin to nucleotide concentrations and even at satuatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.13.2999

    authors: Zimmer C,Luck G,Nüske R

    更新日期:1980-07-11 00:00:00

  • Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

    abstract::Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx436

    authors: Redin D,Borgström E,He M,Aghelpasand H,Käller M,Ahmadian A

    更新日期:2017-07-27 00:00:00