2022
Measuring the tolerance of the genetic code to altered codon size
DeBenedictis EA, Söll D, Esvelt KM. Measuring the tolerance of the genetic code to altered codon size. ELife 2022, 11: e76941. PMID: 35293861, PMCID: PMC9094753, DOI: 10.7554/elife.76941.Peer-Reviewed Original ResearchConceptsFour-base codonsGenetic codeTRNA mutationsAminoacyl-tRNA synthetasesQuadruplet codonsSingle amino acidCodon translationTriplet codonsTRNA synthetasesSynthetic biologistsCodonTRNAAmino acidsChemical alphabetsMutationsMass spectrometrySynthetasesAnticodonToleranceSynthetic systemsBiologistsTranslationEscherichiaNascent
2014
Exploring the Substrate Range of Wild‐Type Aminoacyl‐tRNA Synthetases
Fan C, Ho JM, Chirathivat N, Söll D, Wang Y. Exploring the Substrate Range of Wild‐Type Aminoacyl‐tRNA Synthetases. ChemBioChem 2014, 15: 1805-1809. PMID: 24890918, PMCID: PMC4133344, DOI: 10.1002/cbic.201402083.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetasesSubstrate rangeDifferent amino acid sitesAmino acidsE. coli tryptophanyl-tRNA synthetaseE. coli aminoacyl-tRNA synthetasesAmino acid sitesCanonical amino acidsNonstandard amino acidsTyrosyl-tRNA synthetaseTryptophanyl-tRNA synthetaseAnticodon sequenceTRNA synthetasesSynthetasesSynthetaseSequenceAnticodonNSAAsTrpRSProteinAminoacylAcid
2012
Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment
Ling J, Peterson KM, Simonović I, Cho C, Söll D, Simonović M. Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 3281-3286. PMID: 22343532, PMCID: PMC3295322, DOI: 10.1073/pnas.1200109109.Peer-Reviewed Original ResearchMeSH KeywordsAeropyrumAmino Acid SequenceAnticodonCatalytic DomainCodonCrystallography, X-RayEscherichia coliEvolution, MolecularLeucineMitochondriaModels, MolecularMolecular Sequence DataProtein ConformationProtein Structure, TertiaryRNA EditingRNA, Transfer, Amino AcylSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentSpecies SpecificityStaphylococcus aureusSubstrate SpecificityThreonineThreonine-tRNA LigaseConceptsThreonyl-tRNA synthetaseAnticodon loopAnticodon sequenceEscherichia coli ThrRSSet of tRNAsDistinct recognition mechanismsAnticodon-binding domainAminoacyl-tRNA synthetasesCUN codonsDetailed structural comparisonCodon reassignmentYeast mitochondriaGenetic codeTRNA isoacceptorsSaccharomyces cerevisiaeIsoacceptor tRNAsEditing domainTRNAMST1Anticodon tripletStructural comparisonNatural tRNAAmino acidsDistinct mechanismsRecognition mechanism
2004
The unusual methanogenic seryl‐tRNA synthetase recognizes tRNASer species from all three kingdoms of life
Bilokapic S, Korencic D, Söll D, Weygand‐Durasevic I. The unusual methanogenic seryl‐tRNA synthetase recognizes tRNASer species from all three kingdoms of life. The FEBS Journal 2004, 271: 694-702. PMID: 14764085, DOI: 10.1111/j.1432-1033.2003.03971.x.Peer-Reviewed Original ResearchMeSH KeywordsAnticodonBase SequenceChromatography, GelDimerizationElectrophoretic Mobility Shift AssayEscherichia coliIsoelectric FocusingMethanococcusMolecular Sequence DataNucleic Acid ConformationProtein BindingRNA, Transfer, Amino AcylRNA, Transfer, SerSerineSerine-tRNA LigaseSubstrate SpecificityTranscription, GeneticYeastsConceptsSeryl-tRNA synthetaseGel mobility shift assaysKingdoms of lifeMobility shift assaysMethanococcus jannaschiiM. maripaludisTRNA recognitionShift assaysTRNARenaturation conditionsGel filtration chromatographyConformation of tRNAComplex formationSpeciesFiltration chromatographySynthetaseDimerizationSerRSsJannaschiiTRNASerIsoacceptorsHomologuesComplementary oligonucleotidesAminoacylationRenaturation
2000
Transfer RNA Identity Change in Anticodon Variants of E. coli tRNAPhe in Vivo
Kim H, Kim I, Söll D, Lee Y. Transfer RNA Identity Change in Anticodon Variants of E. coli tRNAPhe in Vivo. Molecules And Cells 2000, 10: 76-82. PMID: 10774751, DOI: 10.1007/s10059-000-0076-7.Peer-Reviewed Original ResearchConceptsMutant tRNA genesMutant tRNAsTRNA genesAnticodon sequenceAnticodon mutantsHost viabilityE. coliAmino acidsMost aminoacyl-tRNA synthetasesOpal stop codonAminoacyl-tRNA synthetasesSite-directed mutagenesisE. coli tRNAMajor recognition elementAnticodon variantsSuch tRNAsTRNAStop codonAminoacylation specificityAnticodonSimilarity dendrogramVivo evolutionGenesAcceptor specificityAnticodon change
1995
Divergence of glutamate and glutamine aminoacylation pathways: Providing the evolutionary rationale for mischarging
Rogers K, Söll D. Divergence of glutamate and glutamine aminoacylation pathways: Providing the evolutionary rationale for mischarging. Journal Of Molecular Evolution 1995, 40: 476-481. PMID: 7783222, DOI: 10.1007/bf00166615.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseGlutamine tRNAEukaryotic organismsProkaryotic organismsGln-tRNAGlnHorizontal gene transfer eventsGene transfer eventsGlutaminyl-tRNA synthetasesGram-negative eubacteriaGlutamyl-tRNA synthetaseAminoacyl-tRNA synthetasesAminoacyl-tRNA synthetaseFamily of enzymesEukaryotic organellesPool of glutamateAminoacyl-tRNATRNADifferent cellular mechanismsEvolutionary rationaleProtein synthesisOrganismsAmino acidsTransfer eventsCellular mechanismsSynthetaseAminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon
Rogers K, Crescenzo A, Söll D. Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon. Biochimie 1995, 77: 66-74. PMID: 7541255, DOI: 10.1016/0300-9084(96)88106-5.Peer-Reviewed Original ResearchConceptsEvolution of specificityPost-transcriptional modificationsAnticodon of tRNAAminoacyl-tRNA synthetasesTranslational regulationTransfer RNAWobble positionWobble baseLysine tRNATRNAEscherichia coliAnticodonAminoacylationFirst positionSynthetasesRNAColiRegulationGlutamineModificationDiscoveryGlutamate
1994
Connecting Anticodon Recognition with the Active Site of Escherichia coli Glutaminyl-tRNA Synthetase
Weygand-Duraševic I, Rogers M, Söll D. Connecting Anticodon Recognition with the Active Site of Escherichia coli Glutaminyl-tRNA Synthetase. Journal Of Molecular Biology 1994, 240: 111-118. PMID: 8027995, DOI: 10.1006/jmbi.1994.1425.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseAnticodon recognitionMutant enzymesEscherichia coli glutaminyl-tRNA synthetaseOpal suppressor tRNASpecificity constantMutant gene productsWild-type enzymeAmino acid loopExtensive conformational changesActive siteNumber of mutationsSuppressor tRNAGene productsGlnRPathways of communicationSaturation mutagenesisTRNAAcceptor stemAcid loopGenetic selectionConformational changesAnticodonPoor substrateAminoacylationFunctional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase.
Rogers M, Adachi T, Inokuchi H, Söll D. Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 291-295. PMID: 7506418, PMCID: PMC42933, DOI: 10.1073/pnas.91.1.291.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acyl-tRNA SynthetasesAnticodonBacterial ProteinsEscherichia coliGenes, SuppressorModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein Structure, TertiaryRNA, BacterialRNA, TransferStructure-Activity RelationshipSubstrate SpecificityTransfer RNA AminoacylationConceptsEscherichia coli glutaminyl-tRNA synthetaseGlutaminyl-tRNA synthetaseLys-317Genetic selectionOpal suppressorMutant enzymesWild-type GlnRSAsp-235Anticodon-binding domainSingle amino acid changeSite-directed mutagenesisNumber of mutantsAmino acid changesRecognition of tRNAGlnR mutantAnticodon recognitionAdditional mutantsGln mutantGlnRMutantsAcid changesBase pairsSpecificity constantAminoacylationTRNA
1993
Discrimination among tRNAs intermediate in glutamate and glutamine acceptor identity.
Rogers K, Söll D. Discrimination among tRNAs intermediate in glutamate and glutamine acceptor identity. Biochemistry 1993, 32: 14210-9. PMID: 7505112, DOI: 10.1021/bi00214a021.Peer-Reviewed Original ResearchAmino Acyl-tRNA SynthetasesAnticodonBase SequenceBiological EvolutionEscherichia coliGlutamate-tRNA LigaseHydrogen BondingKineticsMolecular Sequence DataNucleic Acid ConformationRNA, BacterialRNA, Transfer, GlnRNA, Transfer, GluStructure-Activity RelationshipSubstrate SpecificityTransfer RNA AminoacylationSelectivity and specificity in the recognition of tRNA by E coli glutaminyl-tRNA synthetase
Rogers M, Weygand-Durašević I, Schwob E, Sherman J, Rogers K, Adachi T, Inokuchi H, Söll D. Selectivity and specificity in the recognition of tRNA by E coli glutaminyl-tRNA synthetase. Biochimie 1993, 75: 1083-1090. PMID: 8199243, DOI: 10.1016/0300-9084(93)90007-f.Peer-Reviewed Original ResearchConceptsOpal suppressor tRNAGlutaminyl-tRNA synthetaseAcceptor stem recognitionSuppressor tRNAEscherichia coli glutaminyl-tRNA synthetaseGenetic selectionAmber suppressor tRNAExtensive mutational analysisRecognition of tRNARNA contactsTRNA transcriptsRelaxed specificityMutational analysisTRNAGlnRAcceptor stemExtensive proteinIndividual functional groupsMutantsSpecific recognitionAnticodonAminoacylationSynthetaseIdentity elementSynthetasesAcceptor stem and anticodon RNA hairpin helix interactions with glutamine tRNA synthetase
Wright D, Martinis S, Jahn M, Söll D, Schimmel P. Acceptor stem and anticodon RNA hairpin helix interactions with glutamine tRNA synthetase. Biochimie 1993, 75: 1041-1049. PMID: 8199240, DOI: 10.1016/0300-9084(93)90003-b.Peer-Reviewed Original ResearchThe recognition of E. coli glutamine tRNA by glutaminyl-tRNA synthetase.
Rogers M, Weygand-Durasević I, Schwob E, Sherman J, Rogers K, Thomann H, Sylvers L, Ohtsuka E, Inokuchi H, Söll D. The recognition of E. coli glutamine tRNA by glutaminyl-tRNA synthetase. Nucleic Acids Symposium Series 1993, 211-3. PMID: 7504247.Peer-Reviewed Original Research
1992
Switching tRNA(Gln) identity from glutamine to tryptophan.
Rogers M, Adachi T, Inokuchi H, Söll D. Switching tRNA(Gln) identity from glutamine to tryptophan. Proceedings Of The National Academy Of Sciences Of The United States Of America 1992, 89: 3463-3467. PMID: 1565639, PMCID: PMC48888, DOI: 10.1073/pnas.89.8.3463.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnticodonBase SequenceBeta-GalactosidaseCloning, MolecularEscherichia coliGenes, BacterialGenes, SuppressorGenes, SyntheticGlutamineMolecular Sequence DataMutagenesis, Site-DirectedNucleic Acid ConformationRNA, Transfer, GlnSuppression, GeneticTetrahydrofolate DehydrogenaseTryptophanConceptsOpal suppressorEscherichia coli glutaminyl-tRNA synthetaseAccuracy of aminoacylationGlutaminyl-tRNA synthetaseN-terminal sequence analysisEfficient suppressorYeast mitochondriaRespective tRNAsUCA anticodonAmber suppressorFol geneUGA codonUGA mutationsSequence analysisAlanine insertionAnticodonGenetic selectionBase pairsBase substitutionsSuppressorTRNATrpRSDihydrofolate reductasePosition 35Mutations
1991
Anticodon and acceptor stem nucleotides in tRNAGln are major recognition elements for E. coli glutaminyl-tRNA synthetase
Jahn M, Rogers M, Söll D. Anticodon and acceptor stem nucleotides in tRNAGln are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature 1991, 352: 258-260. PMID: 1857423, DOI: 10.1038/352258a0.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant tRNAsE. coli glutaminyl-tRNA synthetaseEfficient amber suppressorsAminoacyl-tRNA synthetasesCorresponding transfer RNASet of nucleotidesMajor recognition elementGlutamine identityAcceptor stem regionTRNA discriminationTransfer RNAAmber suppressorProtein biosynthesisTRNA moleculesUnmodified tRNACorrect attachmentAnticodon regionTRNAAcceptor stemSimilar kinetic parametersEscherichia coliAmino acidsDifferent synthetasesSpecificity constant
1989
Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP at 2.8 Å Resolution
Rould M, Perona J, Söll D, Steitz T. Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP at 2.8 Å Resolution. Science 1989, 246: 1135-1142. PMID: 2479982, DOI: 10.1126/science.2479982.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acyl-tRNA SynthetasesAnticodonBase CompositionBase SequenceBinding SitesBiological EvolutionChemical PhenomenaChemistry, PhysicalCrystallizationEscherichia coliMolecular Sequence DataMolecular StructureNucleic Acid ConformationRNA, BacterialRNA, FungalRNA, Transfer, Amino Acid-SpecificRNA, Transfer, GlnX-Ray Diffraction
1988
Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli.
Eggertsson G, Söll D. Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli. Microbiology And Molecular Biology Reviews 1988, 52: 354-74. PMID: 3054467, PMCID: PMC373150, DOI: 10.1128/mr.52.3.354-374.1988.Peer-Reviewed Original Research
1985
supN ochre suppressor gene in Escherichia coli codes for tRNALys
Uemura H, Thorbjarnardóttir S, Gamulin V, Yano J, Andrésson O, Söll D, Eggertsson G. supN ochre suppressor gene in Escherichia coli codes for tRNALys. Journal Of Bacteriology 1985, 163: 1288-1289. PMID: 3897192, PMCID: PMC219277, DOI: 10.1128/jb.163.3.1288-1289.1985.Peer-Reviewed Original ResearchNucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs
Grosjean H, Nicoghosian K, Haumont E, Söll D, Cedergren R. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Research 1985, 13: 5697-5706. PMID: 3898020, PMCID: PMC321899, DOI: 10.1093/nar/13.15.5697.Peer-Reviewed Original ResearchConceptsSerine tRNANucleotide sequenceRecent common ancestorE. coli tRNACodon-anticodon interactionStructure-function relationshipsEubacterial originUCU codonsEvolutionary analysisCommon ancestorD-loopTRNAAnticodon stemSerine familyAnticodonGenesE. coliMinor speciesCodonMajor speciesSpeciesSequenceTRNASerAncestorSerineLeucine tRNA family of Escherichia coli: nucleotide sequence of the supP(Am) suppressor gene
Thorbjarnardóttir S, Dingermann T, Rafnar T, Andrésson O, Söll D, Eggertsson G. Leucine tRNA family of Escherichia coli: nucleotide sequence of the supP(Am) suppressor gene. Journal Of Bacteriology 1985, 161: 219-222. PMID: 2981802, PMCID: PMC214859, DOI: 10.1128/jb.161.1.219-222.1985.Peer-Reviewed Original ResearchConceptsSuppressor allelesLeuX geneAmber suppressor allelesMature coding sequenceLeucyl-tRNA synthetaseSingle base changeTRNA familiesCAA anticodonBox sequenceTermination signalDNA sequencesNucleotide sequenceBacteriophage T4Coding sequenceAminoacyl stemSuppressor geneLoop regionTRNABase changesEscherichia coliGenesE. coliSequenceColiAlleles