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RNARNA, Small InterferingRNA, ViralRNA EditingRNA SplicingRNA, RibosomalRNA, BacterialDNA-Directed RNA PolymerasesRNA VirusesRNA InterferenceRNA, MessengerRNA, Double-StrandedRNA, CatalyticRNA FoldingRNA Polymerase IIRNA, FungalRNA StabilityRNA HelicasesRNA, AntisenseRNA Processing, Post-TranscriptionalRNA, TransferRNA, Small NuclearRNA PrecursorsRNA, UntranslatedNucleic Acid ConformationRNA CapsSequence Analysis, RNARNA, PlantRNA, ProtozoanBase SequenceRNA, NeoplasmRNA Ligase (ATP)DEAD-box RNA HelicasesRNA Polymerase IIIMolecular Sequence DataRNA Polymerase IRNA, NuclearRNA, GuideRNA, Ribosomal, 28SRNA, Ribosomal, 18SRNA-Binding ProteinsRNA, Ribosomal, 23SRNA TransportRNA, Spliced LeaderRNA, SatelliteRNA, Ribosomal, 16SAmino Acid SequenceRNA, ArchaealNucleic Acid HybridizationProtein BiosynthesisCell LineVirus ReplicationEscherichia coliRNA CleavageMutationOligoribonucleotidesRNA, Heterogeneous NuclearTranscription, GeneticRNA, Small CytoplasmicRNA 3' End ProcessingTemplates, GeneticRNA, Small UntranslatedHeLa CellsRibonucleoproteinsRibonucleasesPoly AGenome, ViralRNA, Ribosomal, 5.8SDNARNA, Long NoncodingRNA, Small NucleolarBinding SitesRNA Virus InfectionsProtein BindingRNA, ComplementaryUridinePromoter Regions, GeneticEndoribonucleasesCell NucleusRNA, ChloroplastModels, MolecularPlasmidsReverse Transcriptase Polymerase Chain ReactionKineticsSingle-Strand Specific DNA and RNA EndonucleasesBase PairingRNA, HelminthPlant VirusesDNA PrimersGene Expression RegulationSaccharomyces cerevisiaeTranscription FactorsRNA, Transfer, PheRNA, Transfer, LysRibosomesBlotting, NorthernDNA, ViralPolymerase Chain ReactionOligonucleotidesGene Silencing
Subunit ribosomalProteinRibosomeSubunitsEscherichiaBacterialOperonDomains of the 23S rRNARRNA genesGenesProteinsColiPeptidyl transferase centerBindsSequencesEukaryoticSequenceMethyltransferaseMutationsRibosomesTranslationSynthesisTRNAElongationRibonucleicBacteriaMolecularCytosineHepatitis deltaKineticFunctionalAffectsMotifsMutationStructureViralVirusesDomainSegmentsReactionsRegion
Subunit ribosomal2
  • A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. (embl.de)
  • The sarcin-ricin loop (SRL) is one of the most conserved segments of the large subunit ribosomal RNA (rRNA). (rustbeltrna.org)
Protein20
  • Combinations of the 2661 tion with various mutations in ribosomal protein S12 also demonstrate that elements of both ribosomal subunits work in concert to form this binding site. (nebraska.edu)
  • Clarithromycin inhibits bacterial growth by binding to the 50S ribosomal subunit and inhibiting protein synthesis. (medscape.com)
  • Linezolid inhibits bacterial protein synthesis by binding to bacterial 23S ribosomal RNA of the 50S subunit. (medscape.com)
  • Tigecycline inhibits bacterial protein by binding to the 30S ribosomal subunit. (medscape.com)
  • RL11_THEMA ] This protein binds directly to 23S ribosomal RNA. (proteopedia.org)
  • We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. (proteopedia.org)
  • During its biogenesis KdpD binds to the signal recognition particle (SRP) of Escherichia coli that consists of a 48-kDa protein Ffh and a 4.5S RNA. (nature.com)
  • SRP is universally conserved in its core region that consists of a ribonucleoprotein particle, the SRP RNA (4.5S RNA in E. coli ) and the protein component SRP54 (Ffh in E. coli for "fifty-four-homolog") that binds to the conserved RNA domain IV 4 . (nature.com)
  • They can self-splice without the help of any proteins, whereas nuclear introns are spliced by the spliceosome, an RNA and protein-containing enzyme complex. (jove.com)
  • Parajuli NP, Emmerich A, Mandava CS, Pavlov MY, Sanyal S. 1 Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria. (uu.se)
  • Pang Y., Kovachev P., Sanyal S. , Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s. (uu.se)
  • About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. (embl.de)
  • In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. (embl.de)
  • While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. (embl.de)
  • Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. (embl.de)
  • DNA is the master molecule that ultimately affect the function of RNA and protein. (lynxgen.com)
  • A viral nuclear noncoding RNA binds re-localized poly(A) binding protein and is required for late KSHV gene expression. (uiowa.edu)
  • Importantly, the absence of AtNOL12 alters the expression of many ribosomal protein and ribosome biogenesis genes. (bvsalud.org)
  • Here we present the structure of the Bbu 70S ribosome obtained by single particle cryo-electron microscopy at 2.9 Å resolution, revealing a bound hibernation promotion factor protein and two genetically non-annotated ribosomal proteins bS22 and bL38. (bvsalud.org)
  • The ribosomal protein uL30 in Bbu has an N-terminal α-helical extension, partly resembling the mycobacterial bL37 protein, suggesting evolution of bL37 and a shorter uL30 from a longer uL30 protein. (bvsalud.org)
Ribosome4
  • The 23S rRNA is a 2,904 nucleotide long (in E. coli) component of the large subunit (50S) of the bacterial/archean ribosome and makes up the peptidyl transferase center (PTC). (wikipedia.org)
  • Tapprich, WE & Dahlberg, AE 1990, ' A single base mutation at position 2661 in E. coli 23S ribosomal RNA affects the binding of ternary complex to the ribosome ', EMBO Journal , vol. 9, no. 8, pp. 2649-2655. (nebraska.edu)
  • The only known exception to this is the 23S ribosomal RNA in the bacterial ribosome which catalyzes peptide bond formation. (jove.com)
  • Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site. (uiowa.edu)
Subunits2
  • Peptidyl-tRNA of 50S subunits which binds to the P site preserve eight positions of 23S rRNA from chemical modification. (wikipedia.org)
  • We show that 23S rRNA extracted from ΔSRL subunits can be efficiently reconstituted into 50S subunits. (rustbeltrna.org)
Escherichia3
Bacterial2
  • The chemical structure of bacterial ribosomal RNA. (wikidata.org)
  • To resolve phylogenetic relationships among ries of bacterial clonal complexes by using concatenated isolates, we sequenced 68 isolates from Europe and North sequences of housekeeping genes when within-loci and America at 1 chromosomal locus (16S-23S ribosomal RNA between-loci recombinations are infrequent ( 5 ). (cdc.gov)
Operon2
  • It is located to the 3' side of 23S in the rRNA operon and corresponds to the 3' end of non-fragmented 23S rRNA. (wikipedia.org)
  • Berg K.L. , Squires C. , Squires C.L. Ribosomal RNA operon anti-termination Function of leader and spacer region box B-box A sequences and their conservation in diverse microorganisms. (microbiologyresearch.org)
Domains of the 23S rRNA1
  • Numerous mutations in domains of the 23S rRNA with Peptidyl transferase activity have resulted in antibiotic resistance. (wikipedia.org)
RRNA genes3
  • 23S rRNA genes typically have higher sequence variations, including insertions and/or deletions, compared to other rRNAs. (wikipedia.org)
  • We systematically computed free energy values by exhaustively 'annealing' sequences around the 5′ end and sequences around the 3′ end of both 16S rRNA and 23S rRNA genes, in order to predict potential stem structures. (elsevierpure.com)
  • These loci (rrnA, rrnB and rrnC) were isolated on recombinant lambda clones, and comprised 16S, 23S and 5S rRNA genes closely linked in that order. (microbiologyresearch.org)
Genes2
  • Sequence and primer extension analysis revealed the presence of putative genes encoding tRNA lle and tRNA Ala within the 16S-23S spacer region, as well as a number of potential regulatory features. (microbiologyresearch.org)
  • Baylis H.A. , Bibb M.J. Organization of the ribosomal RNA genes in Streptomjces coelicolor A3(2). (microbiologyresearch.org)
Proteins6
  • The amino-terminal NG domain of SRP is bound to the ribosomal proteins uL23 and uL29, next to the tunnel exit and the carboxy-terminal M domain to the ribosomal 23S RNA 6 . (nature.com)
  • Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. (embl.de)
  • Most of the proteins interact with multiple RNA elements, often from different domains. (embl.de)
  • Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. (embl.de)
  • Exosomes secreted by tumor cells carry molecules of DNA, RNA, and proteins that reflect abnormal cancer status. (lynxgen.com)
  • Modern cells mostly follow the Central Dogma of Molecular Biology , which proposes that genetic information is stored in DNA, that the information is transcribed into RNA, and then translated into proteins. (provingthenegative.com)
Coli4
  • rRNA (16S and 23S Ribosomal Standard from E.coli, Sigma) was purified using the Monarch RNA Cleanup Kit (500 µg, NEB #T2050). (neb.com)
  • crystal structure of e. coli 5-methyluridine methyltransferase ruma in complex with ribosomal rna substrate and s-adenosylhomocysteine. (berkeley.edu)
  • 2008) showed that expression of 23S rRNA lacking the SRL confers a dominant lethal phenotype in E. coli. (rustbeltrna.org)
  • The processing of 16S rRNA and 23S rRNA by RNase III in E.coli is known to involve stem structures formed by both ends of the rRNA. (elsevierpure.com)
Peptidyl transferase center1
  • They bind to different bases of the peptidyl transferase center of 23S RNA. (nih.gov)
Binds1
  • While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. (proteopedia.org)
Sequences3
  • Comparison of 23S and 28S ribosomal RNA sequences across species demonstrate conservation of Helix 26a. (wikipedia.org)
  • Indeed, complementary nucleotide sequences are usually found at both ends of 16S rRNA and 23S rRNA. (elsevierpure.com)
  • This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA. (bvsalud.org)
Eukaryotic1
  • The eukaryotic homolog of the 23S LSU rRNA is the 28S ribosomal RNA, with a region filled by the 5.8S ribosomal RNA. (wikipedia.org)
Sequence4
  • In particular, the 5'-G-A-3'/3'-A-G-5' motif and three of its sequence variants have a relatively high occurrence in 16S and 23S ribosomal RNA. (aaai.org)
  • SRP at the ribosomal exit tunnel scans a nascent chain for bearing a hydrophobic SRP signal sequence 7 . (nature.com)
  • and assignment of the genera Cardiobacterium, Dichelobacter, and Suttonella to Cardio-bacteriaceae fam nov in the gamma division of Proteobacteria based on 16S ribosomal ribonucleic acid sequence comparisons. (microbiologyresearch.org)
  • KF673357 Heterochlorella luteoviridis strain SAG 211-2b 18S ribosomal RNA gene, complete sequence. (uni-goettingen.de)
Methyltransferase1
  • We show that CplR contributes to intrinsic pleuromutilin, lincosamide and streptogramin A resistance in Clostridioides, and demonstrate that C. difficile CplR (CDIF630_02847) synergises with the transposon-encoded 23S ribosomal RNA methyltransferase Erm to grant high levels of antibiotic resistance to the C. difficile 630 clinical isolate. (lu.se)
Mutations3
  • The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. (proteopedia.org)
  • Molecular methods have attractive features for identification of Mycoplasma pneumoniae and its associated resistance mutations in the 23S ribosomal RNA (rRNA) .Hypothesis / Gap Statement. (lynxgen.com)
  • Point mutations in the 23S rRNA detected in 67 (26.9%) of the 249 confirmed M. pneumoniae-positive clinical samples. (lynxgen.com)
Ribosomes1
Translation2
  • The ribosomal peptidyl transferase activity resides in domain V of this rRNA, which is also the most common binding site for antibiotics that inhibit translation, making it a target for ribosomal engineering. (wikipedia.org)
  • Wang W, Li W, Ge X, Yan K, Mandava CS, Sanyal S and Gao N, Loss of a single methylation in 23S rRNA delyas 50S assembly at multiple late stages and impairs translation initiation and elongation. (uu.se)
Synthesis2
  • Synthesis and assembly of ribosomal components are fundamental cellular processes and generally well-conserved within the main groups of organisms. (nord.no)
  • T7 Quick High Yield RNA Synthesis Kit (NEB #E2050) using 1.5-1.8 µg of DNA template for two hours at 37°C. 40 µl of each in vitro transcription IVT) reaction was cleaned up using the Monarch RNA Cleanup Kit (500 µg, T2050) and eluted in 200 µl. (neb.com)
TRNA1
  • However, 23S rRNA positions (G2252, A2451, U2506, and U2585) have a significant function for tRNA binding in the P site of the large ribosomal subunit. (wikipedia.org)
Elongation2
  • Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. (embl.de)
  • Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. (rustbeltrna.org)
Ribonucleic1
  • Noncanonical G.A base pairs play important structural and functional roles in ribonucleic acids (RNA). (aaai.org)
Bacteria1
  • Antibiotic Resistance in Bacteria Caused by Modified Nucleosides in 23S Ribosomal RNA. (wikipedia.org)
Molecular1
  • The 23S ribosomal RNA is composed of six domains forming a complex network of molecular interactions. (wikipedia.org)
Cytosine1
Hepatitis delta1
Kinetic1
  • Kim C, Holm M, Mandava CS, and Sanyal S. 1 , Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation. (uu.se)
Functional1
  • The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit. (rustbeltrna.org)
Affects1
  • García-Ortega L, Alvarez-García E, Gavilanes JG, Martínez-del-Pozo A, Joseph S. Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding. (rustbeltrna.org)
Motifs1
Mutation1
Structure2
  • A detailed view of a ribosomal active site: the structure of the L11-RNA complex. (proteopedia.org)
  • Wimberly BT, Guymon R, McCutcheon JP, White SW, Ramakrishnan V. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. (proteopedia.org)
Viral1
  • The replication process in these viruses produce long RNA carrying multiple units of the viral genome where each unit carries a small ribozymes like hammerhead. (jove.com)
Viruses1
Domain2
  • The 23S rRNA is divided into six secondary structural domains titled I-VI, with the corresponding 5S rRNA being considered domain VII. (wikipedia.org)
  • the E-value for the Ribosomal_L31e domain shown below is 3.1e-43. (embl.de)
Segments1
  • These regularly spaced hammerhead enzymes undergo self-cleavage resulting in breakage of the long RNA into individual genome segments. (jove.com)
Reactions1
  • The Monarch RNA Cleanup Columns (500 µg) are a component of the Monarch RNA Cleanup Kit (500 µg) ( NEB #T2050 ) and can be used to purify up to 500 µg of RNA from enzymatic reactions. (neb.com)
Region1
  • This supports previous findings which indicated that position 2661 is part of a region of 23S rRNA that forms a recognition site for binding of the ternary complex in the ribosomal A site. (nebraska.edu)