2023
Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids
Jiang H, Weng J, Wang Y, Tsou J, Chen P, Ko A, Söll D, Tsai M, Wang Y. Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids. Frontiers In Genetics 2023, 14: 1277489. PMID: 37904728, PMCID: PMC10613524, DOI: 10.3389/fgene.2023.1277489.Peer-Reviewed Original ResearchUnique biophysical propertiesTree of lifeAmino acidsSuperfolder green fluorescent proteinGreen fluorescent proteinSubstrate polyspecificityTranslational machinerySynthetic biologistsSmall proteinsFluorescent proteinPhysiological roleRibosomal synthesisProteinBiophysical propertiesKinetic assaysHuman heavy chain ferritinHeavy-chain ferritinPylRSTRNAMutantsAminoacylationPeptidesBiologistsPhysiochemical propertiesMachinery
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
1996
Glutaminyl‐tRNA synthetase: from genetics to molecular recognition
Ibba M, Hong K, Söll D. Glutaminyl‐tRNA synthetase: from genetics to molecular recognition. Genes To Cells 1996, 1: 421-427. PMID: 9078373, DOI: 10.1046/j.1365-2443.1996.d01-255.x.Peer-Reviewed Original ResearchConceptsEscherichia coli glutaminyl-tRNA synthetaseMajority of tRNAsCorrect amino acidGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesSequence-specific interactionsAmino acid recognitionEfficiency of aminoacylationGenetic codeTRNA selectionGlnRTRNAAmino acidsNoncognate tRNAsCellular viabilityStructural studiesMolecular recognitionSynthetasesAminoacylationComplex displaysGeneticsSynthetaseGlutamineMechanismViabilityTransfer RNA‐dependent cognate amino acid recognition by an aminoacyl‐tRNA synthetase.
Hong K, Ibba M, Weygand‐Durasevic I, Rogers M, Thomann H, Söll D. Transfer RNA‐dependent cognate amino acid recognition by an aminoacyl‐tRNA synthetase. The EMBO Journal 1996, 15: 1983-1991. PMID: 8617245, PMCID: PMC450117, DOI: 10.1002/j.1460-2075.1996.tb00549.x.Peer-Reviewed Original ResearchConceptsAmino acid recognitionEscherichia coli glutaminyl-tRNA synthetaseAccuracy of aminoacylationProtein-RNA interactionsRole of tRNAGlutaminyl-tRNA synthetaseAmino acid affinityCharacterization of mutantsAminoacyl-tRNA synthetaseAmino acid activationSpecific interactionsSubstrate recognitionEnzyme active siteGlnRActive siteAcceptor stemTRNAAminoacylationAcid affinityPosition 235TerminusSynthetaseObserved roleGlnTRNAGln
1995
Aminoacylation 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
Selectivity 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 elementSynthetases
1992
Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl‐tRNA synthetase: a complete identity set.
Hayase Y, Jahn M, Rogers M, Sylvers L, Koizumi M, Inoue H, Ohtsuka E, Söll D. Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl‐tRNA synthetase: a complete identity set. The EMBO Journal 1992, 11: 4159-4165. PMID: 1396597, PMCID: PMC556926, DOI: 10.1002/j.1460-2075.1992.tb05509.x.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseRecognition of basesSet of tRNAsEscherichia coliCognate aminoacyl-tRNA synthetasesAminoacyl-tRNA synthetasesCorrect aminoacylationRecombinant RNA technologySet of nucleotidesNumber of mutantsGlutamine identityTRNA genesTRNA discriminationTransfer RNAExcellent systemGlnRFunctional importanceSingle deletionSpecific contactsRNA technologyBase changesSpecificity constantAminoacylationSpecific guanosineMutantsCompetition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation
Sherman J, Rogers M, Söll D. Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation. Nucleic Acids Research 1992, 20: 2847-2852. PMID: 1377381, PMCID: PMC336931, DOI: 10.1093/nar/20.11.2847.Peer-Reviewed Original ResearchConceptsAccuracy of aminoacylationAminoacyl-tRNA synthetasesTyrosyl-tRNA synthetaseE. coli tyrosyl-tRNA synthetaseEscherichia coli tyrosyl-tRNA synthetaseGlutaminyl-tRNA synthetaseLevel of aminoacylationProtein biosynthesisTRNASynthetasesAminoacylationCompetition assaysDiscriminator baseDifferent synthetasesConcurrent overexpressionCorrect aminoacylationSynthetaseFirst baseRelative affinityVivoMisacylationAssaysAnticodonBiosynthesisCompetitionCompetition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation
Sherman J, Rogers M, Söll D. Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation. Nucleic Acids Research 1992, 20: 1547-1552. PMID: 16617497, PMCID: PMC312236, DOI: 10.1093/nar/20.7.1547.Peer-Reviewed Original ResearchAccuracy of aminoacylationAminoacyl-tRNA synthetasesTyrosyl-tRNA synthetaseE. coli tyrosyl-tRNA synthetaseEscherichia coli tyrosyl-tRNA synthetaseGlutaminyl-tRNA synthetaseLevel of aminoacylationProtein biosynthesisTRNASynthetasesAminoacylationCompetition assaysDiscriminator baseDifferent synthetasesConcurrent overexpressionCorrect aminoacylationSynthetaseFirst baseRelative affinityVivoMisacylationAssaysAnticodonBiosynthesisCompetition
1991
Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNAGln interaction
Enlisch-Peters S, Conley J, Plumbridge J, Leptak C, Söll D, Rogers M. Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNAGln interaction. Biochimie 1991, 73: 1501-1508. PMID: 1725262, DOI: 10.1016/0300-9084(91)90184-3.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseEscherichia coli glutaminyl-tRNA synthetaseClass I aminoacyl-tRNA synthetaseTemperature-sensitive phenotypeAminoacyl-tRNA synthetaseTemperature-sensitive mutantGlutamine identityThree-dimensional structureMutant enzymesGlnRMutantsTerminal adenosineAminoacylation reactionExchange activitySynthetaseMutationsSubsequent assaysPseudorevertantsGlutaminylationTRNAAminoacylationGenesNucleotidesSpeciesColi
1990
The accuracy of aminoacylation — ensuring the fidelity of the genetic code
Söll D. The accuracy of aminoacylation — ensuring the fidelity of the genetic code. Cellular And Molecular Life Sciences 1990, 46: 1089-1096. PMID: 2253707, DOI: 10.1007/bf01936918.Peer-Reviewed Original ResearchConceptsAccuracy of aminoacylationTransfer RNA speciesAminoacyl-tRNA synthetasesMessenger RNA codonRNA speciesProtein biosynthesisGenetic codeProtein interactionsParticular tRNATRNACorrect attachmentBiophysical techniquesRNA codonsAmino acidsSynthetasesSpecific recognitionProper interactionAnticodonBiosynthesisCodonAminoacylationNucleotidesSpeciesEnzymeIdentity element
1988
Accuracy of in Vivo Aminoacylation Requires Proper Balance of tRNA and Aminoacyl-tRNA Synthetase
Swanson R, Hoben P, Sumner-Smith M, Uemura H, Watson L, Söll D. Accuracy of in Vivo Aminoacylation Requires Proper Balance of tRNA and Aminoacyl-tRNA Synthetase. Science 1988, 242: 1548-1551. PMID: 3144042, DOI: 10.1126/science.3144042.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetaseAminoacyl-tRNA synthetasesProtein biosynthesisAccuracy of aminoacylationCognate aminoacyl-tRNA synthetaseAmber suppressorVivo aminoacylationGln-tRNA synthetaseCognate tRNATRNAExquisite specificityAminoacylationSynthetaseAccurate aminoacylationSynthetasesBiosynthesisIntracellular concentrationRelative levelsProper balanceComplexed formsSuppressorEscherichiaGln
1971
Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases
Johnson L, Söll D. Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases. Biopolymers 1971, 10: 2209-2221. PMID: 4940767, DOI: 10.1002/bip.360101114.Peer-Reviewed Original ResearchConceptsSpecific transfer RNAsTRNA-IleTransfer RNAThermal denaturation profilesB. stearothermophilusAminoacyl-tRNA synthetasesDenaturation profilesAminoacylation of tRNAAmino acid acceptor activityTRNA-ValAcceptor activityTRNATertiary structureMycoplasma spBacillus stearothermophilusEscherichia coliAminoacylation reactionStearothermophilusAminoacylationRNASpeciesIleSynthetasesNucleaseSynthetase preparationsPurification of an Escherichia coli Leucine Suppressor Transfer Ribonucleic Acid and Its Aminoacylation by the Homologous Leucyl-Transfer Ribonucleic Acid Synthetase
Hayashi H, Söll D. Purification of an Escherichia coli Leucine Suppressor Transfer Ribonucleic Acid and Its Aminoacylation by the Homologous Leucyl-Transfer Ribonucleic Acid Synthetase. Journal Of Biological Chemistry 1971, 246: 4951-4954. PMID: 4941862, DOI: 10.1016/s0021-9258(18)61955-6.Peer-Reviewed Original ResearchMeSH KeywordsAcylationBenzoatesBiological AssayCarbon IsotopesChromatography, DEAE-CelluloseColiphagesEscherichia coliGenetics, MicrobialKineticsLeucineLigasesMutationPeptide BiosynthesisPlant Growth RegulatorsPlants, ToxicPolynucleotidesRNA, TransferSuppression, GeneticTemplates, GeneticTobaccoValine