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
2000
AMINOACYL-tRNA SYNTHESIS
Ibba M, Söll D. AMINOACYL-tRNA SYNTHESIS. Annual Review Of Biochemistry 2000, 69: 617-650. PMID: 10966471, DOI: 10.1146/annurev.biochem.69.1.617.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthesisAmino acidsAminoacyl-tRNA synthetaseEvolutionary facetsWhole-genome sequencingCorresponding tRNAsGenetic codeGenome sequencingAminoacyl-tRNACorresponding anticodonTRNACurrent knowledgeStructural dataRecent studiesAnticodonDetailed pictureAcidSequencingSynthetaseEditingProofreadingSynthesisTranslationDirect attachmentTransfer 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
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 substrateAminoacylation
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
Competition 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 affinityVivoMisacylationAssaysAnticodonBiosynthesisCompetitionSwitching 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 35MutationsCompetition 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
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
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 speciesSpeciesSequenceTRNASerAncestorSerineEscherichia coli supH suppressor: temperature-sensitive missense suppression caused by an anticodon change in tRNASer2
Thorbjarnardóttir S, Uemura H, Dingermann T, Rafnar T, Thorsteinsdóttir S, Söll D, Eggertsson G. Escherichia coli supH suppressor: temperature-sensitive missense suppression caused by an anticodon change in tRNASer2. Journal Of Bacteriology 1985, 161: 207-211. PMID: 3155715, PMCID: PMC214857, DOI: 10.1128/jb.161.1.207-211.1985.Peer-Reviewed Original ResearchConceptsWild-type tRNASingle nucleotide changeWild-type sequenceCAA anticodonMissense suppressorMissense suppressionCUA anticodonDNA sequencesLeucine codonMutant formsInsertion of serineNucleotide changesSuppressor geneAnticodonTRNASupHTRNASer2Anticodon changeCodonSuppressorSequenceTRNASerCloningGenesSerine
1984
The sup8 tRNALeu gene of Schizosaccharomyces pombe has an unusual intervening sequence and reduced pairing in the anticodon stem
Sumner-Smith M, Hottinger H, Willis I, Koch T, Arentzen R, Söll D. The sup8 tRNALeu gene of Schizosaccharomyces pombe has an unusual intervening sequence and reduced pairing in the anticodon stem. Molecular Genetics And Genomics 1984, 197: 447-452. PMID: 6597338, DOI: 10.1007/bf00329941.Peer-Reviewed Original ResearchConceptsTRNA genesS. pombe DNAWild-type alleleAnticodon UCASplicing endonucleaseSuppressor allelesSchizosaccharomyces pombeTRNALeu geneUUA codonTrailer sequencesIntervening sequenceCell-free extractsAnticodon stemRelated sequencesSplice siteBase pairsSecondary structureGenesIsoacceptorsAllelesSequenceStructural requirementsPombeAnticodonSup8The Schizosaccharomyces pombe sup3‐i suppressor recognizes ochre, but not amber codons in vitro and in vivo.
Hottinger H, Stadelmann B, Pearson D, Frendewey D, Kohli J, Söll D. The Schizosaccharomyces pombe sup3‐i suppressor recognizes ochre, but not amber codons in vitro and in vivo. The EMBO Journal 1984, 3: 423-428. PMID: 6370683, PMCID: PMC557361, DOI: 10.1002/j.1460-2075.1984.tb01823.x.Peer-Reviewed Original ResearchConceptsFission yeast Schizosaccharomyces pombeYeast Schizosaccharomyces pombeUGA termination codonVitro translation assaysReadthrough productS. pombeSchizosaccharomyces pombeNonsense mutantsTermination signalOchre suppressorUGA suppressionTranslation assaysAmber codonTermination codonGlobin mRNASup3PombeT substitutionCodonSuppressorPlasmid DNASchizosaccharomycesMutantsVivoAnticodon
1983
Six Schizosaccharomyces pombe tRNA genes including a gene for a tRNA Lys with an intervening sequence which cannot base-pair with the anticodon
Gamulin V, Mao J, Appel B, Sumner-Smith M, Yamao F, Söll D. Six Schizosaccharomyces pombe tRNA genes including a gene for a tRNA Lys with an intervening sequence which cannot base-pair with the anticodon. Nucleic Acids Research 1983, 11: 8537-8546. PMID: 6561518, PMCID: PMC326605, DOI: 10.1093/nar/11.24.8537.Peer-Reviewed Original Research
1982
19 Nucleotide Modification in RNA
Kline L, Söll D. 19 Nucleotide Modification in RNA. The Enzymes 1982, 15: 567-582. DOI: 10.1016/s1874-6047(08)60291-7.Peer-Reviewed Original ResearchRNA base modificationsAnticodon of tRNAComplex nucleotidesNucleotide modificationsAdenosine modificationsEnzymatic modificationRNA chainsBase modificationsEnzymatic stepsAdenosine residuesUracil residuesNucleotidesRNABiochemical evidenceEnzymeModifying groupUracil nucleotidesResiduesGuanine structureFirst positionTRNAAnticodonGeneticsTranscriptsModification