• We identify an important role for DDX5 in G 1 -S-phase progression where it directly regulates DNA replication factor expression by promoting the recruitment of RNA polymerase II to E2F-regulated gene promoters. (aacrjournals.org)
  • A new yeast poly(A) polymerase complex involved in RNA quality control. (nature.com)
  • In Fungi , it is formed by a RNA Helicase, Mtr4, in addition with a poly(A)polymerase, Trf4 or Trf5 and a RNA-binding zinc knuckle protein, Air1/2. (eu.org)
  • The TRAMP complex consists of a RNA helicase (MTR4), a poly(A)polymerase (Trf4 or Trf5) and a RNA-binding zinc knuckle protein (Air1 or Air2). (eu.org)
  • RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060, PubMed:28790157). (icr.ac.uk)
  • It is not only essential for the maturation of ribosomal RNA (rRNA) and transfer RNA (tRNA) but also the rapid degradation of messenger RNA (mRNA) by hydrolysis reaction. (wikipedia.org)
  • In mRNA degradation, ribonuclease E recognizes and cleaves the single-stranded RNA in A- and U-rich regions. (wikipedia.org)
  • Identified as a prototypic member of the DEAD box family and documented as an ATPase and RNA helicase, p68 plays essential and diverse functions in the control of gene expression ranging from pre-mRNA/rRNA processing and mRNA decay/stability to transcriptional activation and initiation. (gsu.edu)
  • Employing RNA interference and fluorescence in situ hybridization we show that DDX6 colocalizes with endogenous human (h)r15-LOX mRNA to P-body-like RNP granules from which 60S ribosomal subunits are excluded. (researchatlanta.org)
  • 2006). For bait we employed a DICE bearing mRNA and a control mRNA both carrying box-B hairpin sequences (Fig. 1C). (researchatlanta.org)
  • DEAD-box RNA helicases get excited about RNA-dependent cellular procedures including splicing ribosome biogenesis RNA transportation RNA degradation and mRNA translation plus they impact rearrangements of huge RNA buildings or protein-RNA connections (Linder et al. (researchatlanta.org)
  • Conservation of the RNA helicases suggests that mRNA structurome remodelling is a general mechanism for stress-induced translation across kingdoms. (biorxiv.org)
  • N6-methyladenine (m6A) mRNA modification is the most abundant form of posttranscriptional RNA modification in eukaryotes. (biomedcentral.com)
  • More than 60% of all RNA modifications are methylated modifications, and m6A is the most abundant chemical modification in eukaryotic messenger RNA (mRNA). (biomedcentral.com)
  • de la Cruz, J., Kressler, D., Tollervey, D. & Linder, P. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae . (nature.com)
  • In the maturation of rRNA precursor, the substrates for processing are not naked RNAs but somewhat incomplete, unmodified pre-rRNA-ribosomal protein complexes. (wikipedia.org)
  • RNA structural rearrangement reactions and preparation of the used RNA substrates were performed exactly as explained previously (5). (mergullo.net)
  • Anderson, J.T. & Wang, X. Nuclear RNA surveillance: no sign of substrates tailing off. (nature.com)
  • Oligo-adenylated tails are added to aberrant RNA substrates, thus marking them for degradation. (eu.org)
  • While Air1 or Air2 recognizes the RNA substrates, Mtr4 is responsible for unwinding the RNA in order for Trf4 or Trf5 to polyadenylate the substrate ( LaCava,2005 ). (eu.org)
  • DEAH-Box helicase 36 (DHX36), a member of the large DExD/H box helicase family, enzymatically unwinds both G4 DNA and G4 RNA. (bvsalud.org)
  • DbpA RNA binding domain, Helicase conserved C-terminal domain, RNA-binding domain, DEAD/DEAH box helicase domain [InterProScan]. (ntu.edu.sg)
  • Activities of the DEAD box (Asp-Glu-Ala-Asp) family of proteins- including RNA-dependent ATPase and RNA helicase- function in all organisms to sculpt RNA-RNA duplex and RNA-protein complexes, ensuring that necessary rearrangements are rapidly and properly resolved during genetic information processing. (gsu.edu)
  • Wang, X., Jia, H., Jankowsky, E. & Anderson, J.T. Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. (nature.com)
  • We uncovered the functions of ABCE proteins Rli1/ABCE1 and Arb1 in PIC assembly and ribosome biogenesis, and identified the tRNA methyltransferase Gcd10/Gcd14, which contributed to the discovery of the TRAMP-mediated RNA surveillance pathway. (nih.gov)
  • Ribonuclease E is a bacterial ribonuclease that participates in the processing of ribosomal RNA (9S to 5S rRNA) and the chemical degradation of bulk cellular RNA. (wikipedia.org)
  • RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. (nature.com)
  • Callahan, K.P. & Butler, J.S. TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. (nature.com)
  • The TRAMP complex is involved in exosome-mediated degradation of aberrant RNAs and RNA surveillance in the nucleus. (eu.org)
  • Sixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. (biomedcentral.com)
  • Intro p68 and p72/p82 are prototypic users of the DEAD box protein family (1,2) with the isoforms p72 and p82 arising from the gene through the use of different in-frame translation initiation codons (3). (mergullo.net)
  • Here we report on the isolation of five partial gene sequences from gonad tissue cDNA in the functional hermaphrodite scallop Nodipecten subnodosus to be evaluated as reference genes: 18S-rRNA, riboprotein l8 (rp-l8), actin-β (act-β), elongation factor 1α (ef-1α) and alpha-tubulin-α (tub-α). (univ-brest.fr)
  • The least stable gene was tub-α, showing a biased expression profile between sexual regions of the gonad, therefore this gene was analyzed thereafter as a target gene together with vitellogenin (vit) and a DEAD-box RNA helicase (dbx) gene. (univ-brest.fr)
  • In1999 some of the present inventors reported the first use of globaltransposon mutagenesis to experimentally determine the genes notessential for laboratory growth of M. genitalium{A). Since then therehave been numerous other experimental determinations of bacterialessential gene sets using our approach and other methods such as sitedirected gene knockouts and antisense RNA (5- 12). (fullblog.com.ar)
  • PeBoW, a trimeric complex consisting of pescadillo (Pes1), block of proliferation (Bop1), and the WD repeat protein 12 (WDR12), is essential for processing and maturation of mammalian 5.8S and 28S ribosomal RNAs. (cipsm.de)
  • Both pre-16S and pre-23S rRNAs are excised from the primary RNA-protein complex by RNase III, which activates subsequent steps in rRNA maturation by generating 5' monophosphorylated cleavage products. (wikipedia.org)
  • This action helps to facilitate 5' maturation of rRNA by RNase G and make two cleavages to excise pre-5S rRNA. (wikipedia.org)
  • With S1 subdomain, 5' sensing region functions as a substrate-binding site that helps to stabilize the target RNA molecule on one subunit so that the other subunit within a dimer can cleave the RNA of interest. (wikipedia.org)
  • subunit preceding the processing of 32S pre-rRNA. (mergullo.net)
  • Subsequently, we used the Gcd− selection to identify domains/residues in eIF2 and tRNAi, eIF1, eIF1A, eIF3, and residues of 18S rRNA located near the 'P' decoding site of the 40S subunit, that participate in rapid TC recruitment in vivo (Figure 1A). (nih.gov)
  • Among these are energy-consuming enzymes such as GTPases, protein kinases, ATP-dependent RNA helicases, and AAA-type (ATPases associated with various cellular activities) ATPases, which suggests that the energy derived from nucleotide hydrolysis confers directionality to ribosome assembly. (silverchair.com)
  • It has been proposed that ribosome scanning and start codon selection are regulated by elements in the 5' leader sequence, such as RNA primary sequences (for example, the Kozak sequence context), upstream open reading frames (uORFs), secondary structures, and RNA modifications 4 - 7 . (biorxiv.org)
  • Moreover, recent global ribosome-sequencing (Ribo-seq, sequencing of ribosome-protected RNA fragments) studies have shown that uORFs are a prevalent feature in eukaryotic mRNAs, not limited to these few well-studied examples 19 - 21 . (biorxiv.org)
  • RNase E further shortens the 17S precursor of 16S rRNA. (wikipedia.org)
  • The three proteins form a subfamily with related biochemical activities, including an ATP-dependent RNA helicase (4,5), and possibly also related and even redundant cellular functions. (mergullo.net)
  • We discovered many Deceased container proteins and RNA-binding/handling proteins Furthermore. (researchatlanta.org)
  • G4 DNA- and RNA-binding proteins and unwinding helicases associate with and regulate G4s during virtually all processes that involve DNA and RNA. (bvsalud.org)
  • Together with SIRT7, required to prevent R-loop-associated DNA damage and transcription-associated genomic instability: deacetylation by SIRT7 activates the helicase activity, thereby overcoming R-loop-mediated stalling of RNA polymerases (PubMed:28790157). (icr.ac.uk)
  • Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3′-to-5′ translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps. (nature.com)
  • Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1 (By similarity). (icr.ac.uk)
  • Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). (icr.ac.uk)
  • In response to immune induction, uORF-inhibition is alleviated by three Ded1p/DDX3X-homologous RNA helicases which unwind the RNA structures, allowing ribosomes to bypass the inhibitory uORFs and upregulate defence protein production. (biorxiv.org)
  • Applying a mass spectrometric analysis, we identified the DEAD-box helicase DDX27 as stably associated factor of the PeBoW-complex. (cipsm.de)
  • We found that 18S-rRNA was stably expressed independently of the priming method used to reverse transcribe RNA to cDNA, oligo-dT or random hexamer. (univ-brest.fr)
  • G-Quadruplex (G4) DNA (G4 DNA) and RNA (G4 RNA) are secondary nucleic acid structures that have multiple roles in vital cellular processes. (bvsalud.org)
  • The non-covalent binding of Trf4 ( P53632 ) and the DExH-helicase core of Mtr4 ( P47047 , PF00270 ) is mediated by the described motif, which is conserved in both Trf4 ( P53632 ) and Trf5 ( P48561 ) in Fungi . (eu.org)
  • It has been found that the effect of m6A modification on RNA metabolism involves processing, nuclear export, translation and even decay. (biomedcentral.com)
  • Applying RNA chromatography with the DICE as bait combined with hnRNP K immunoprecipitation we specifically purified the DEAD-box RNA helicase 6 (DDX6) that interacts with hnRNP K and hnRNP E1 in a DICE-dependent manner. (researchatlanta.org)
  • 80S ribosomes accumulated in fractions 4-7 while fractions 11-13 contained mainly 18S rRNA of the 40S ribosomal subunits (Fig. 2A). (researchatlanta.org)
  • It is unclear, if/how the RNA-specific biochemical activities of p68 and p72/p82 are involved in these processes as well as with DNA deglycosylation (11), though at least some of the practical complexes formed consist of small RNAs (6,11). (mergullo.net)
  • Required for rRNA 2'-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). (icr.ac.uk)
  • To isolate specific protein-RNA complexes from the pool obtained through glutathione elution hnRNP K immunoprecipitation was performed subsequently. (researchatlanta.org)
  • The distribution of 18S and 28S rRNA was used to analyze the position of ribosomal complexes and mRNPs (Fig. 2A). (researchatlanta.org)
  • In the ribonuclease E, the S1 domain not only aids in the formation of the tetrameric quaternary structure by dimerization but also serves as a substrate-binding site to facilitate RNA hydrolysis by the catalytic domains within this tetrameric enzyme. (wikipedia.org)
  • The cytosolic antiviral innate immune sensor RIG-I distinguishes 5′ tri- or diphosphate containing viral double-stranded (ds) RNA from self-RNA by an incompletely understood mechanism that involves ATP hydrolysis by RIG-I's RNA translocase domain. (cipsm.de)
  • Bernstein, J., Patterson, D.N., Wilson, G.M. & Toth, E.A. Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3′>5′ helicase partner of the nuclear exosome. (nature.com)
  • Schmidt, K. & Butler, J.S. Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity. (nature.com)
  • Bernstein, J. & Toth, E.A. Yeast nuclear RNA processing. (nature.com)
  • van Hoof, A., Lennertz, P. & Parker, R. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. (nature.com)
  • Therefore, LmDDX47 could be a key regulator of midgut homeostasis, regulating 18S rRNA synthesis as well as protein acetylation and crotonylation in the migratory locust. (bvsalud.org)
  • The RNase E catalytic domain binds selectively to 5′-monophosphate RNA termini but has a mode of cleavage in the 3′ to 5′ direction. (wikipedia.org)
  • In the presence of RNA, target RNA binds to the combined S1 subdomain and 5′ sensor in the open configuration. (wikipedia.org)
  • In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. (icr.ac.uk)
  • In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). (icr.ac.uk)
  • Johnson, S.J. & Jackson, R.N. Ski2-like RNA helicase structures: common themes and complex assemblies. (nature.com)
  • Inclusion of Mtr4p within the TRAMP complex increases the rate constant for unwinding initiation but does not change the characteristics of Mtr4p's helicase mechanism. (nature.com)
  • The chemical modification of RNA is a newly discovered epigenetic regulation mechanism in cells and plays a crucial role in a variety of biological processes. (biomedcentral.com)
  • Through the development of m6A RNA sequencing, the relevant molecular mechanism of m6A modification has gradually been revealed. (biomedcentral.com)
  • Also, there is two magnesium ion binding site that mediates cleavage by hydrolytic attack of the RNA backbone and two zinc ion binding site that aids in stabilization of a dimer made of two subunits. (wikipedia.org)
  • We further show that RNA unwinding by Mtr4p requires interaction with upstream RNA duplex. (nature.com)
  • Our data indicate that Mtr4p utilizes a previously unknown unwinding mode that combines aspects of canonical translocating helicases and non-canonical duplex-sensing helicases, thereby restricting directional translocation to duplex regions. (nature.com)
  • Figure 1: Observation of Mtr4p unwinding RNA duplex via high-resolution optical trapping. (nature.com)
  • Figure 2: Mtr4p unwinding rates versus tether tension and nucleotide composition for unwinding the 16-bp RNA hairpin. (nature.com)
  • The 80S ribosomal complex formation was not disturbed by Bupivacaine HCl the box-B hairpin sequences (data not shown). (researchatlanta.org)
  • Cluster identity was assigned based on the top 10 marker genes of each cluster ( Table S2 ), followed by inspection of RNA in situ hybridization patterns. (stowers.org)
  • This recruitment is RNA-dependent and occurs independently of the PeBoW-complex. (cipsm.de)
  • In collaboration with Jon Lorsch's group, we demonstrated that segments/residues in eIF1, eIF1A, tRNAi and 18S rRNA, which are implicated genetically in TC recruitment, also stimulate the rate of this reaction in a fully reconstituted yeast in vitro translation system. (nih.gov)
  • Recent studies have found that non-coding RNAs and post transcriptional modification of RNAs have become the active fields of cancer research. (biomedcentral.com)
  • Figure 4: Observation of TRAMP unwinding RNA. (nature.com)
  • The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. (nature.com)
  • Sloan, K.E., Bohnsack, M.T., Schneider, C. & Watkins, N.J. The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA. (nature.com)
  • RNA processing and surveillance is a mechanisms closely regulated. (eu.org)
  • Schneider, C. & Tollervey, D. Threading the barrel of the RNA exosome. (nature.com)
  • In transcription of plasmids pGEM-U8 and -U14 and recognized according to the Roche DIG Northern Starter Kit manual) or with 32P end-labeled DNA oligonucleotides specific for human being Second internal transcribed spacer (ITS2), 18S, 28S or 5,8S rRNA (29). (mergullo.net)
  • 47904) TATA-box binding family protein CP001857 CDS Arcpr_0059 47991. (go.jp)
  • this complex exists in resting cells with or without poly(I:C) RNA ligand stimulation. (icr.ac.uk)
  • We conclude that DDX27 can interact specifically with the Pes1 and Bop1 but fulfils critical function(s) for proper 3′ end formation of 47S rRNA independently of the PeBoW-complex. (cipsm.de)
  • It also opens a new way of thinking for biomedical scientists, whether RNA modification will be another important factor to regulate the biological development of neoplastic diseases. (biomedcentral.com)
  • RNA helicase activity of Mtr4p is critical for biological functions of the enzyme, but the molecular basis for RNA unwinding is not understood. (nature.com)
  • Enables RNA binding activity. (nih.gov)