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CodonCodon, TerminatorCodon, NonsenseCodon, InitiatorBase SequenceMolecular Sequence DataPeptide Chain Termination, TranslationalPeptide Termination FactorsAmino Acid SequenceProtein BiosynthesisMutationGenetic CodeRNA, MessengerExonsCloning, MolecularFrameshift MutationEscherichia coliRNA, TransferPoint MutationRibosomesSequence Analysis, DNADNA Mutational AnalysisPolymerase Chain ReactionAnticodonPedigreeBase CompositionGenes, BacterialGenesNucleic Acid ConformationReading FramesIntronsSequence AlignmentPseudogenesEvolution, MolecularSequence Homology, Nucleic AcidPlasmidsRestriction MappingOpen Reading FramesSequence Homology, Amino AcidTranscription, GeneticFrameshifting, RibosomalPeptide Chain Initiation, TranslationalSuppression, GeneticAlternative SplicingRNA, Transfer, Amino AcylTerminator Regions, GeneticAllelesEuplotesDNA PrimersDNA, ComplementaryDNASequence DeletionPhenotypePhylogenyRNA SplicingModels, GeneticRNA, BacterialMutation, MissensePolymorphism, Single-Stranded ConformationalBacterial ProteinsPolymorphism, GeneticMutagenesis, Site-DirectedHomozygoteSaccharomyces cerevisiaeGenotypeSelection, GeneticGenes, ViralGenes, OverlappingGenetic VariationRNA EditingOperonGene Expression Regulation, BacterialGenes, rasChromosome MappingCell LineNonsense Mediated mRNA DecayHeterozygoteRNA StabilityAmino Acid Substitution5' Untranslated RegionsConserved SequenceDNA, BacterialRNA Splice SitesRNA, Transfer, TrpProkaryotic CellsGene DeletionSpecies SpecificityParomomycinTryptophanase3' Untranslated RegionsViral ProteinsGenome, ViralBlotting, NorthernOligonucleotide ProbesMutagenesisBlotting, SouthernGene ExpressionSelenoproteinsCiliophoraDNA Restriction Enzymes
Amino acidsMRNARibosomePrematureTripletOpal stop codonsMethionineTranslationalTRNAGeneTermination codonsSequencesTripletsPolypeptide chainRecognitionLysinePeptideNucleotidesReassignmentOchreNoncanonicalBacteriaSignalsRecognizeRibosomalEukaryotesMutationBasesTruncationTranslationOrganismMutationsGeneticVariantsMolecularGenesGenomesSignalPositionTimeClinical
Amino acids6
  • The nuclear genetic code is flexible as illustrated by variant genetic codes that reassign standard stop codons to amino acids. (wikipedia.org)
  • This code either matches an amino acid or tells the cell when it is time to start (start codon) or stop (stop codon) adding amino acids to a polypeptide chain. (biologydictionary.net)
  • Since the discovery of the genetic code and protein translation mechanisms ( 1 ), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages ( 2 - 7 ). (scienceintheclassroom.org)
  • As there are only 20 natural amino acids and 64 codon combinations each amino acid is encoded for by multiple codons. (addgene.org)
  • The codons between the start and stop signals code for the various amino acids of the gene product but do not include any of the three stop codons. (genome.gov)
  • The intron sequences do not code for amino acids and contain internal stop codons. (genome.gov)
MRNA11
  • In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. (nature.com)
  • In particular, upstream open reading frames (uORFs) are segments of 5′UTR mRNA sequences that can initiate and terminate translation upstream of protein-coding start codons. (nature.com)
  • If scanning ribosomes encountering uORFs prematurely initiate translation in the 5′UTR, upon reaching the uORF termination codon the ribosome may dissociate from the mRNA transcript, or the 40 s subunit may resume scanning after the 60 s subunit is lost. (nature.com)
  • A gene encoding an mRNA that has the stop codon redefined as selenocysteine. (virtualflybrain.org)
  • An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)
  • Each time an amino acid is added to a growing polypeptide during protein synthesis, a tRNA anticodon pairs with its complementary codon on the mRNA molecule, ensuring that the appropriate amino acid is inserted into the polypeptide. (genome.gov)
  • A ribosome binds to mRNA with the AUG codon in the P-site and the UUU codon in the A-site. (howstuffworks.com)
  • Upon encountering the stop sequence, the ribosome detaches from the mRNA and splits into its two parts. (howstuffworks.com)
  • Four isoforms of DMT1 have been identified in mammalian cells encoded by a single gene that differ both in their N- and C-terminal sequences with two mRNA isoforms possessing an iron response element (IRE) motif downstream from the stop codon on the message. (cdc.gov)
  • During translation, mRNA molecules are incidentally damaged, leaving the ribosome unable to reach or recognize the stop codon and thus stalled with mRNA and a potentially harmful polypeptide product attached to tRNA in the ribosomal P-site. (lu.se)
  • The ribosome then resumes protein synthesis guided by an mRNA-like portion of the tmRNA which ends with a stop codon and codes for a peptide sequence susceptible to proteolysis, thus allowing the bacteria to salvage stalled ribosomes and degrade ill-defined and potentially harmful protein products. (lu.se)
Ribosome6
  • Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. (nature.com)
  • Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. (nature.com)
  • A stop codon tells the ribosome and transfer DNA that the process can stop and the new polypeptide chain can be released. (biologydictionary.net)
  • An amino acyl-tRNA (anti-codon = UAC) with an attached methionine comes into the P-site of the ribosome. (howstuffworks.com)
  • The ribosome shifts so that the P-site now contains the UUU codon with the attached phenyl-alanine tRNA and the next codon (ACA) now occupies the A-site. (howstuffworks.com)
  • The ribosome shifts down one codon so that the stop sequence is now in the A-site. (howstuffworks.com)
Premature4
  • The most frequent mutation found in 70% of CF patients is F508del, while premature stop mutations are found in about 10% of patients. (biomedcentral.com)
  • More than 1,500 mutations have been described since the discovery of the gene, including premature stop mutations, which are found in about 10% of all CF patients [ 2 ]. (biomedcentral.com)
  • These gene editing technologies were targeted to the first exon of each gene, to induce frameshifts producing premature termination codons. (koreamed.org)
  • Mutations of this gene introduce a premature stop codon and result in truncated protein versions. (medscape.com)
Triplet3
  • In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. (wikipedia.org)
  • A stop codon is a single nucleotide triplet that provides an end-point for protein synthesis. (biologydictionary.net)
  • In 1961, Nirenberg, a biochemist from the National Institute of Arthritic and Metabolic Diseases, described the first base 'triplet,' a set of three nucleotides that make up a codon. (news-medical.net)
Opal stop codons2
  • Similar suppressors are known for ochre and opal stop codons as well. (wikipedia.org)
  • Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages ( 12 - 14 ) and the discovery of a previously unknown reassignment of TGA opal stop codons to glycine ( 4 , 5 , 14 ). (scienceintheclassroom.org)
Methionine5
Translational1
  • Moreover, it has been shown that variants destroying stop codons in translated uORFs are under strong negative selection, presumably because the resultant translational readthrough can decrease start codon recognition and translation initiation at the coding sequence (CDS) 10 . (nature.com)
TRNA4
  • For example, a mutation in the tRNA that recognizes the amber stop codon allows translation to "read through" the codon and produce a full-length protein, thereby recovering the normal form of the protein and "suppressing" the amber mutation. (wikipedia.org)
  • tRNA molecules carrying unnatural aminoacids have been designed to recognize the amber stop codon in bacterial RNA. (wikipedia.org)
  • 2008). Therefore, the goal of this study is to investigate critical residues of RF1 and determine their role in the recognition process of codon specificity or in the hydrolysis of peptidyl-tRNA. (escholarship.org)
  • In Escherichia coli , conventional amber and ochre stop codons can be separately targeted by engineered amber-suppressing Methanocaldococcus jannaschii tyrosyl-tRNA synthetase-tRNA Pyl and ochre-suppressing Methanosarcina maezi pyrrolysyl-tRNA synthetase-tRNA Pyl pairs for coding two different noncanonical amino acids in one protein gene. (springer.com)
Gene3
  • A dual gene reporter system was used to determine the gentamicin-induced readthrough level of the most frequent stop mutations within the CFTR in the French population. (biomedcentral.com)
  • Suppression of stop mutations in the CFTR gene with parenteral gentamicin can be predicted in vitro and is associated with clinical benefit and significant modification of the CFTR-mediated Cl - transport in nasal and sweat gland epithelium. (biomedcentral.com)
  • Using a dual reporter gene assay, we first determined the readthrough level of the most prevalent stop codon mutations in the French CF population after gentamicin incubation. (biomedcentral.com)
Termination codons1
  • In the standard genetic code, there are three different termination codons: There are variations on the standard genetic code, and alternative stop codons have been found in the mitochondrial genomes of vertebrates, Scenedesmus obliquus, and Thraustochytrium. (wikipedia.org)
Sequences3
  • While start codons need nearby sequences or initiation factors to start translation, a stop codon alone is sufficient to initiate termination. (wikipedia.org)
  • To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber , TGA opal , and TAA ochre codons in assembled metagenomes and metatranscriptomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of viral sequences ( Fig. 1A ) ( 15 ). (scienceintheclassroom.org)
  • Using the allele frequency spectrum of SNVs from 71,702 whole genome sequences in gnomAD, we find that SNVs introducing new stop codons, or creating stronger translation termination signals in uORFs are under strong selective constraints within 5′UTRs. (nature.com)
Triplets1
Polypeptide chain2
  • Moreover, the codon partially directing its incorporation in the polypeptide chain was identified as UGA also known as the opal termination codon. (wikipedia.org)
  • Both start and stop codons in DNA and RNA, just as their names suggest, provide start and stop instructions that regulate the length of a polypeptide chain. (biologydictionary.net)
Recognition4
  • Recognition of stop codons in bacteria have been associated with the so-called 'tripeptide anticodon', a highly conserved amino acid motif in RF1 (PxT) and RF2 (SPF). (wikipedia.org)
  • Figure 4: Molecular basis of stop codon recognition by eRF1. (nature.com)
  • Recent crystal structures have allowed the investigation of critical residues in these release factors that may be critical to codon recognition as well as peptide release (Laurberg, et al. (escholarship.org)
  • The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. (nih.gov)
Lysine1
Peptide1
  • At the start codon, peptide synthesis initiates when the 40 s subunit acquires the 60 s subunit with other translation initiation factors. (nature.com)
Nucleotides2
  • A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)
  • Each amino acid is encoded for by 3 nucleotides termed a codon. (addgene.org)
Reassignment1
Ochre1
  • Reminiscent of the usual yellow-orange-brown color associated with amber, this second stop codon was given the name of "ochre", an orange-reddish-brown mineral pigment. (wikipedia.org)
Noncanonical1
  • Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and noncanonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. (scienceintheclassroom.org)
Bacteria1
  • Large scale study of bacteria with a broad range of GC-contents shows that while the frequency of occurrence of TAA is negatively correlated to the GC-content and the frequency of occurrence of TGA is positively correlated to the GC-content, the frequency of occurrence of the TAG stop codon, which is often the minimally used stop codon in a genome, is not influenced by the GC-content. (wikipedia.org)
Signals2
Recognize1
  • By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons 2 . (nature.com)
Ribosomal4
  • stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain. (wikipedia.org)
  • Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. (nature.com)
  • Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. (nature.com)
  • Cap-dependent translation initiation begins when the 40 s ribosomal subunit encounters a start codon as it scans along the 5′UTR. (nature.com)
Eukaryotes2
  • Different mechanisms for overriding the termination function of this codon have been identified in prokaryotes and in eukaryotes. (wikipedia.org)
  • A particular difference between these kingdoms is that cis elements seem restricted to the neighborhood of the UAG codon in prokaryotes while in eukaryotes this restriction is not present. (wikipedia.org)
Mutation1
Bases1
  • All codons are made up of three nucleotide bases and named according to the order of these bases - for example, the stop codon TAG tells us that it is made up of thymine, followed by adenine, followed by guanine. (biologydictionary.net)
Truncation1
  • [ 8 ] Both mutations created stop codons leading to truncation of the PAX3 protein. (medscape.com)
Translation4
  • In vitro aminoglycoside antibiotics (e.g. gentamicin) suppress nonsense mutations located in CFTR permitting translation to continue to the natural termination codon. (biomedcentral.com)
  • Resumption of scanning leads to translation of downstream reading frames only if the necessary translation initiation factors are reacquired by the 40 s subunit before reaching the downstream start codon. (nature.com)
  • Thus, the spatial combination of uORFs and protein-coding start codons can produce different effects on downstream protein translation. (nature.com)
  • The codons UAA, UAG, and UGA are the stop codons that signal the termination of translation. (rhumbarlv.com)
Organism2
Mutations4
  • Pharmacologic suppression of stop mutations within the CFTR may be of benefit to a significant number of patients. (biomedcentral.com)
  • We investigated readthrough efficiency in response to 10 mg/kg once-daily intravenous gentamicin perfusions in patients with and without stop mutations. (biomedcentral.com)
  • Clinical status, NPD and sweat Cl - values did not change in the Y122X patients with no protein expression, in patients with the other stop mutations investigated in vitro and those without stop mutations. (biomedcentral.com)
  • To investigate readthrough efficiency after intravenous gentamicin in CF patients with these mutations, in comparison with patients with other stop mutations and without stop mutations, we tested CFTR expression in nasal cells, evaluated the CFTR-mediated chloride secretion in nasal and sweat gland epithelia, and assessed clinical status. (biomedcentral.com)
Genetic1
  • Seven years after the first codon of the genetic code was described, Nirenberg, Khorana, and Holley received the Nobel Prize in Physiology or Medicine in 1968. (news-medical.net)
Variants2
  • We show that uORF variants introducing new stop codons, or strengthening existing stop codons, are under strong negative selection comparable to protein-coding missense variants. (nature.com)
  • A new category, unsense variation, was introduced to describe variants that do not introduce a stop codon into the variation site, but which lead to different types of changes in the coded protein. (lu.se)
Molecular1
  • The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. (nature.com)
Genes1
  • We expect that, just by chance, there will be some long stretches of DNA that do not contain stop codons yet are not parts of genes. (genome.gov)
Genomes1
  • The purpose of this project is to develop and test large genomes in cells, and that is where it stops," says Nancy Kelley, a fundraiser who is among the authors of the paper and is described as the "lead executive" of the project. (technologyreview.com)
Signal1
  • Eventually, three of the codons - UAG, UAA, and UGA - were found to be STOP codons that signal the end of amino acid chains. (news-medical.net)
Position2
  • physiological and/or anatomical changes are possible if a stop codon is in the wrong position on a DNA or RNA strand, or if the code sequence is changed. (biologydictionary.net)
  • TGA) [TAT ending at position 6705 on + strand];first in-frame stop codon exists 3' of stop position predicted by homology to reference [homology search predicted 5085. (cdc.gov)
Time1
Clinical1
  • Our pilot study was conducted to determine whether intravenous gentamicin suppresses stop codons in CF patients and whether it has clinical benefits. (biomedcentral.com)