Anticodon: The sequential set of three nucleotides in TRANSFER RNA that interacts with its complement in MESSENGER RNA, the CODON, during translation in the ribosome.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.Genetic Code: The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Nucleoside Q: A modified nucleoside which is present in the first position of the anticodon of tRNA-tyrosine, tRNA-histidine, tRNA-asparagine and tRNA-aspartic acid of many organisms. It is believed to play a role in the regulatory function of tRNA. Nucleoside Q can be further modified to nucleoside Q*, which has a mannose or galactose moiety linked to position 4 of its cyclopentenediol moiety.RNA, Transfer, Asn: A transfer RNA which is specific for carrying asparagine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Ala: A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Arg: A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Amino Acyl: Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.Transfer RNA Aminoacylation: The conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Amino Acyl-tRNA Synthetases: A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Transfer, Amino Acid-Specific: A group of transfer RNAs which are specific for carrying each one of the 20 amino acids to the ribosome in preparation for protein synthesis.RNA, Transfer, Ser: A transfer RNA which is specific for carrying serine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Phe: A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.RNA, Transfer, Trp: A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Met: A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).RNA, Transfer, Gly: A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Ile: A transfer RNA which is specific for carrying isoleucine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Glu: A transfer RNA which is specific for carrying glutamic acid to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Asp: A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Val: A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Gln: A transfer RNA which is specific for carrying glutamine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Pro: A transfer RNA which is specific for carrying proline to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, His: A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Thr: A transfer RNA which is specific for carrying threonine to sites on the ribosomes in preparation for protein synthesis.Aminoacylation: A reaction that introduces an aminoacyl group to a molecule. TRANSFER RNA AMINOACYLATION is the first step in GENETIC TRANSLATION.Serine-tRNA Ligase: An enzyme that activates serine with its specific transfer RNA. EC 6.1.1.11.Thiouridine: A photoactivable URIDINE analog that is used as an affinity label.RNA, Transfer, Cys: A transfer RNA which is specific for carrying cysteine to sites on the ribosomes in preparation for protein synthesis.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.Aspartate-tRNA Ligase: An enzyme that activates aspartic acid with its specific transfer RNA. EC 6.1.1.12.Suppression, Genetic: Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.Acylation: The addition of an organic acid radical into a molecule.Tyrosine-tRNA Ligase: An enzyme that activates tyrosine with its specific transfer RNA. EC 6.1.1.1.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.PseudouridineIsopentenyladenosine: N(6)-[delta(3)-isopentenyl]adenosine. Isopentenyl derivative of adenosine which is a member of the cytokinin family of plant growth regulators.Glutamate-tRNA Ligase: An enzyme that activates glutamic acid with its specific transfer RNA. EC 6.1.1.17.Isoleucine-tRNA Ligase: An enzyme that activates isoleucine with its specific transfer RNA. EC 6.1.1.5.Ribonuclease P: An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.Alanine-tRNA Ligase: An enzyme that activates alanine with its specific transfer RNA. EC 6.1.1.7.Guanosine: A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)Phenylalanine-tRNA Ligase: An enzyme that activates phenylalanine with its specific transfer RNA. EC 6.1.1.20.Peptide Elongation Factor Tu: A protein found in bacteria and eukaryotic mitochondria which delivers aminoacyl-tRNA's to the A site of the ribosome. The aminoacyl-tRNA is first bound to a complex of elongation factor Tu containing a molecule of bound GTP. The resulting complex is then bound to the 70S initiation complex. Simultaneously the GTP is hydrolyzed and a Tu-GDP complex is released from the 70S ribosome. The Tu-GTP complex is regenerated from the Tu-GDP complex by the Ts elongation factor and GTP.Lysine-tRNA Ligase: An enzyme that activates lysine with its specific transfer RNA. EC 6.1.1.6.Leucine-tRNA Ligase: An enzyme that activates leucine with its specific transfer RNA. EC 6.1.1.4.RNA Ligase (ATP): An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Tryptophan-tRNA Ligase: An enzyme that activates tryptophan with its specific transfer RNA. EC 6.1.1.2.Kinetics: The rate dynamics in chemical or physical systems.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)RNA Precursors: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.UridineThermus thermophilus: A species of gram-negative, aerobic, rod-shaped bacteria found in hot springs of neutral to alkaline pH, as well as in hot-water heaters.Histidine-tRNA Ligase: An enzyme that activates histidine with its specific transfer RNA. EC 6.1.1.21.Ribonuclease T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Peptide Chain Elongation, Translational: A process of GENETIC TRANSLATION, when an amino acid is transferred from its cognate TRANSFER RNA to the lengthening chain of PEPTIDES.Genes, Suppressor: Genes that have a suppressor allele or suppressor mutation (SUPPRESSION, GENETIC) which cancels the effect of a previous mutation, enabling the wild-type phenotype to be maintained or partially restored. For example, amber suppressors cancel the effect of an AMBER NONSENSE MUTATION.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.RNA Nucleotidyltransferases: Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Threonine-tRNA Ligase: An enzyme that activates threonine with its specific transfer RNA. EC 6.1.1.3.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.RNA Polymerase III: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.Nucleic Acid Precursors: Use for nucleic acid precursors in general or for which there is no specific heading.Valine-tRNA Ligase: An enzyme that activates valine with its specific transfer RNA. EC 6.1.1.9Arginine-tRNA Ligase: An enzyme that activates arginine with its specific transfer RNA. EC 6.1.1.19.Poly U: A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.MERRF Syndrome: A mitochondrial encephalomyopathy characterized clinically by a mixed seizure disorder, myoclonus, progressive ataxia, spasticity, and a mild myopathy. Dysarthria, optic atrophy, growth retardation, deafness, and dementia may also occur. This condition tends to present in childhood and to be transmitted via maternal lineage. Muscle biopsies reveal ragged-red fibers and respiratory chain enzymatic defects. (From Adams et al., Principles of Neurology, 6th ed, p986)Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Phenylalanine: An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.Selenocysteine: A naturally occurring amino acid in both eukaryotic and prokaryotic organisms. It is found in tRNAs and in the catalytic site of some enzymes. The genes for glutathione peroxidase and formate dehydrogenase contain the TGA codon, which codes for this amino acid.RNA, Catalytic: RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Codon, Terminator: Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids.Yeasts: A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.Genes, Bacterial: The functional hereditary units of BACTERIA.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
  • This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2Ile) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. (mit.edu)
  • Ribosome binding experiments show that although the wild-type tRNA2Ile binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. (mit.edu)
  • The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. (mit.edu)
  • Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. (mit.edu)
  • This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. (mit.edu)
  • Evidence for distinct coding properties in tRNA acceptor stems and anticodons, and experimental demonstration that the two synthetase family ATP binding sites can indeed be coded by opposite strands of the same gene supplement these biochemical and bioinformatic data, establishing a solid basis for key intermediates on a path from simple, stereochemically coded, reciprocally catalytic peptide/RNA complexes through the earliest peptide catalysts to contemporary aminoacyl-tRNA synthetases. (nih.gov)
  • Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. (mit.edu)
  • Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. (mit.edu)
  • The Specifier domain of the T box riboswitch contains the Specifier sequence that is complementary to the tRNA anticodon and is flanked by a highly conserved purine nucleotide that could result in a fourth base pair involving the invariant U33 of tRNA. (rice.edu)
  • Motivated by our demonstration that aaRS Urzymes cannot interact with the tRNA anticodon (Figure 8) and the proposal that an operational code in the acceptor stem preceded formation of the canonical genetic code, we investigated the unique coding properties of these two regions in tRNAs. (nih.gov)
  • Transfer RNA (tRNA) modifications enhance the efficiency, specificity and fidelity of translation in all organisms. (prolekare.cz)
  • Transfer RNAs (tRNAs) from all domains of life contain numerous post-transcriptional modifications, many of which are highly conserved. (prolekare.cz)
  • The molecular connection between these cellular/organismal phenotypes and the lack of specific tRNA anticodon modifications is currently unknown. (prolekare.cz)
  • Eventually, sorting deregulated proteins into functional categories may uncover the mechanistic principle of how simultaneous loss of the above tRNA modifications induces such phenotypes. (uni-kassel.de)
  • Together, these efforts may address how functional cross-talk among anticodon stem-loop modifications is able to protect against cellular dysfunctions, which in higher eukaryotes - including our own cells - can translate into formation of cancer or neuropathies as severe as ALS. (uni-kassel.de)
  • Therefore, using budding yeast as a model system, we consider the project and its specific tRNA modification focus is logically linked to the topic of DFG SPP 1784 Chemical Biology of Native Nucleic Acid Modifications and has the potential to provide innovative mechanistic insights into the biological significance of tRNA anticodon modification pathways and their functional cross-talk. (uni-kassel.de)
  • In the yeast Saccharomyces cerevisiae, cytoplasmic tRNAs have an average of 13 modifications, and there are a total of 25 chemically distinct modifications, many of which are highly conserved in different organisms, and of unknown function. (rochester.edu)
  • We recently found evidence that lack of certain modifications can lead to rapid degradation of specific mature tRNAs, suggesting the existence of a quality control pathway that monitors the integrity of tRNA. (rochester.edu)
  • Since modifications have crucial roles in the cell, incorrect modification of a tRNA is likely to have catastrophic effects. (rochester.edu)
  • In addition, we reported pre-tRNA capping, several novel RNA modifications and growth phase-dependent alteration of tRNA modification. (nii.ac.jp)
  • This review summarizes the recent characterization of the biosynthesis of sulfur modifications in tRNA and the novel roles of this modification in cellular functions in various model organisms, with a special emphasis on 2-thiouridine derivatives. (frontiersin.org)
  • This enzyme catalyses the following chemical reaction tRNA uridine38/39 ⇌ {\displaystyle \rightleftharpoons } tRNA pseudouridine38/39 The enzyme from Saccharomyces cerevisiae is active only towards uridine38 and uridine39. (wikipedia.org)
  • We have identified a novel tRNA methyltransferase in Saccharomyces cerevisiae that we designate Trm9. (asm.org)
  • Second, we are defining the mechanisms by which modification enzymes recognize and act on their specific tRNA substrates. (rochester.edu)
  • Motivated by our demonstration that aaRS Urzymes cannot interact with the tRNA anticodon (Figure 8) and the proposal that an operational code in the acceptor stem preceded formation of the canonical genetic code, we investigated the unique coding properties of these two regions in tRNAs. (nih.gov)
  • As such, tRNAs are a necessary component of translation , the biological synthesis of new proteins in accordance with the genetic code . (wikipedia.org)
  • The cleavage occurs in vitro between positions 38 and 39 in an anticodon loop with a 2′,3′-cyclic phosphate end, and is inhibited by a specific immunity protein. (pnas.org)
  • Furthermore, we generated a single mutation of histidine in the C-terminal possible catalytic domain, which caused the loss of the killing activity in vivo together with the tRNA Arg -cleaving activity both in vivo and in vitro . (pnas.org)
  • In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus. (semanticscholar.org)
  • In addition, we show that the F6 gene product can methyl esterify tRNA in vitro, and we have now designated the F6 gene TRM9 . (asm.org)
  • The 5'-UTR of the mRNA forms mutually exclusive anti-terminator or terminator structures depending on whether the tRNA bound is uncharged or charged. (rice.edu)
  • The structures of the three tRNAGly anticodon arms exhibit small differences between one another and there is no evidence that they form the canonical U-turn motif. (rice.edu)
  • The 2.9 Å crystal structure of HIV reverse transcriptase complexed with an anti-AIDS drug and more recently its structure complexed with an RNA pseudo-knot inhibitor as well as future structures with an RNA template and tRNA primer are the starting points for rational design of anti-AIDS drugs. (angelfire.com)
  • Three tRNA-like cloverleaf structures were found in mNCR. (biomedcentral.com)
  • 11. tRNAs are cloverleaf-like structures. (oregonstate.edu)