2023
Mistranslation of the genetic code by a new family of bacterial transfer RNAs
Schuntermann D, Fischer J, Bile J, Gaier S, Shelley B, Awawdeh A, Jahn M, Hoffman K, Westhof E, Söll D, Clarke C, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. Journal Of Biological Chemistry 2023, 299: 104852. PMID: 37224963, PMCID: PMC10404621, DOI: 10.1016/j.jbc.2023.104852.Peer-Reviewed Original ResearchConceptsTransfer RNAsAmino acidsBacterial transfer RNAsUnfavorable environmental conditionsProlyl-tRNA synthetaseWrong amino acidPoor substrate specificitySubstrate discriminationGrowth defectTransfer RNAGenetic codePosttranslational modificationsProtein reporterTranslation factorsEnvironmental stressFunctional proteinsSubstrate specificityThreonine codonGenetic informationDistinct isoformsPro mutationAntibiotic carbenicillinEscherichia coliNovel familyEnvironmental conditions
2022
Uncovering translation roadblocks during the development of a synthetic tRNA
Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Research 2022, 50: 10201-10211. PMID: 35882385, PMCID: PMC9561287, DOI: 10.1093/nar/gkac576.Peer-Reviewed Original ResearchMeSH KeywordsAmino AcidsAmino Acyl-tRNA SynthetasesNucleotidesProtein BiosynthesisRibosomesRNA, TransferSelenocysteineConceptsOrthogonal translation systemGenetic code expansionCode expansionTertiary interactionsNon-canonical amino acidsAminoacyl-tRNA substratesDomains of lifeAminoacyl-tRNA synthetaseTranslation systemSingle nucleotide mutationsSingle-molecule fluorescenceDistinct tRNAsNon-canonical structuresSelenocysteine insertionRibosomal translationTRNARibosomesSynthetic tRNANucleotide mutationsAmino acidsSame organismP siteOrganismsTranslocationTranslationThe tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism
Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova KS, Koonin EV, Shen Y, Söll D, Fu X. The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic Acids Research 2022, 50: gkac271-. PMID: 35466371, PMCID: PMC9071458, DOI: 10.1093/nar/gkac271.Peer-Reviewed Original ResearchConceptsGenetic code expansionCode expansionDistinct non-canonical amino acidsOrthogonal aminoacyl-tRNA synthetase/tRNA pairsAminoacyl-tRNA synthetase/tRNA pairsPyrrolysyl-tRNA synthetase/Halophilic archaeon Haloferax volcaniiAdditional coding capacityDistinct noncanonical amino acidsNon-canonical amino acidsArchaeon Haloferax volcaniiDiscriminator baseAmino acidsPyrrolysyl-tRNA synthetaseNoncanonical amino acidsSite-specific incorporationMotif 2 loopSingle base changeDistinct tRNAsTRNA pairsHaloferax volcaniiUAA codonGenetic codeDiscriminator basesTRNA structure
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 ResearchMeSH KeywordsAmino AcidsAmino Acyl-tRNA SynthetasesAnticodonEscherichia coliMolecular ConformationSubstrate SpecificityConceptsAminoacyl-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
2013
Aminoacylation of tRNA 2′‐ or 3′‐hydroxyl by phosphoseryl‐ and pyrrolysyl‐tRNA synthetases
Englert M, Moses S, Hohn M, Ling J, O‧Donoghue P, Söll D. Aminoacylation of tRNA 2′‐ or 3′‐hydroxyl by phosphoseryl‐ and pyrrolysyl‐tRNA synthetases. FEBS Letters 2013, 587: 3360-3364. PMID: 24021645, PMCID: PMC3830498, DOI: 10.1016/j.febslet.2013.08.037.Peer-Reviewed Original Research
2002
tRNA‐dependent amino acid discrimination by yeast seryl‐tRNA synthetase
Gruic‐Sovulj I, Landeka I, Söll D, Weygand‐Durasevic I. tRNA‐dependent amino acid discrimination by yeast seryl‐tRNA synthetase. The FEBS Journal 2002, 269: 5271-5279. PMID: 12392560, DOI: 10.1046/j.1432-1033.2002.03241.x.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseYeast seryl-tRNA synthetaseCognate tRNA moleculesAmino acid discriminationAminoacyl-tRNA synthetasesAmino acid substratesSimilar amino acidsAmino acid serineGenetic codeEnzyme active siteTRNA moleculesActive siteYeast SerRSConformational changesAcid substratesAmino acidsSerineSynthetaseStoichiometric analysisDifferent affinitiesEnzymeAccurate translationTRNASerSynthetasesSaccharomyces
2001
Protein synthesis: Twenty three amino acids and counting
Ibba M, Stathopoulos C, Söll D. Protein synthesis: Twenty three amino acids and counting. Current Biology 2001, 11: r563-r565. PMID: 11509255, DOI: 10.1016/s0960-9822(01)00344-x.Peer-Reviewed Original ResearchThe renaissance of aminoacyl‐tRNA synthesis
Ibba M, Söll D. The renaissance of aminoacyl‐tRNA synthesis. EMBO Reports 2001, 2: 382-387. PMID: 11375928, PMCID: PMC1083889, DOI: 10.1093/embo-reports/kve095.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthesisProtein synthesisRole of tRNAEvolutionary diversityStructural biologyMolecular biologistsUnexpected arrayMolecular biologyNew enzymeDecades of studyAmino acidsEssential processTRNABiologyComplete pictureGenomicsAdaptorBiologistsDiversityEnzymePathwayHigh degreeSynthesisNumerous milestones
2000
Domain-specific recruitment of amide amino acids for protein synthesis
Tumbula D, Becker H, Chang W, Söll D. Domain-specific recruitment of amide amino acids for protein synthesis. Nature 2000, 407: 106-110. PMID: 10993083, DOI: 10.1038/35024120.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseAsparaginyl-tRNA synthetaseProtein synthesisAmino acidsAminoacyl-transfer RNAAmino acid metabolismGlu-tRNAGlnAsn-tRNAProtein biosynthesisGln-tRNAArchaeaTRNASynthetaseAmidotransferaseBacteriaAmidotransferasesDirect evidenceDifferent mechanismsBiosynthesisCentral importanceCrucial stepRNAOrganismsDomainCytoplasmAminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process
Woese C, Olsen G, Ibba M, Söll D. Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process. Microbiology And Molecular Biology Reviews 2000, 64: 202-236. PMID: 10704480, PMCID: PMC98992, DOI: 10.1128/mmbr.64.1.202-236.2000.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetasesIndividual aminoacyl-tRNA synthetasesEvolutionary processesAAR geneEvolutionary relationshipsPhylogenetic treeGenetic codeUniversal phylogenetic treeDistant evolutionary pastOrganismal phylogenyOrganismal domainsCodon assignmentsTaxonomic distributionEvolutionary pastHorizontal transferEvolutionary profilesGenetic materialIndividual enzymesEvolutionary perspectiveSynthetasesGenesEnzymeBacteriaModern counterpartsTrees
1992
Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants
Sherman J, Rogers K, Rogers M, Söll D. Synthetase competition and tRNA context determine the in vivo identity of tRNA discriminator mutants. Journal Of Molecular Biology 1992, 228: 1055-1062. PMID: 1474577, DOI: 10.1016/0022-2836(92)90314-a.Peer-Reviewed Original ResearchConceptsAmber suppressorTyrosine tRNAN-terminal protein sequencingGlutamyl-tRNA synthetaseE. coli dihydrofolate reductaseAminoacyl-tRNA synthetasesEffects of mutationsEfficiency of aminoacylationColi dihydrofolate reductaseSite of aminoacylationTyrosine specificityTRNAs exhibitGlutamine tRNAMutagenic analysisProtein sequencingGlutamate tRNAImportant identity elementVivo identityTRNANucleotide substitutionsTRNA identityDiscriminator baseDihydrofolate reductaseMultiple mutationsSynthetases
1977
Studies of the complex between transfer RNA's with complementary anticodons : a direct approach to the "wobble" problem [proceedings].
Grosjean H, Söll D, Crothers D. Studies of the complex between transfer RNA's with complementary anticodons : a direct approach to the "wobble" problem [proceedings]. Archives Of Physiology And Biochemistry 1977, 85: 414-5. PMID: 71115.Peer-Reviewed Original ResearchSuppression of a defective alanyl-tRNA synthetase in Escherichia coli: A compensatory mutation to high alanine affinity
Theall G, Low K, Söll D. Suppression of a defective alanyl-tRNA synthetase in Escherichia coli: A compensatory mutation to high alanine affinity. Molecular Genetics And Genomics 1977, 156: 221-227. PMID: 340903, DOI: 10.1007/bf00283495.Peer-Reviewed Original ResearchConceptsTemperature-resistant revertantsAlanyl-tRNA synthetaseResistant revertantsE. coli mapWild-type enzymeRibosomal proteinsStructural geneGene mapsSynthetase mutantsMutant enzymesParental enzymeCompensatory mutationsTemperature-sensitive characterEscherichia coliAdditional mutationsEnzymeRevertantsSynthetaseMutationsKm valuesAlanineRecAMutantsGenesAffinity
1975
Maturation of a hypermodified nucleoside in transfer RNA
Agris P, Armstrong D, Schäfer K, Söll D. Maturation of a hypermodified nucleoside in transfer RNA. Nucleic Acids Research 1975, 2: 691-699. PMID: 49880, PMCID: PMC343621, DOI: 10.1093/nar/2.5.691.Peer-Reviewed Original Research
1972
Is There a Discriminator Site in Transfer RNA?
Crothers D, Seno T, Söll D. Is There a Discriminator Site in Transfer RNA? Proceedings Of The National Academy Of Sciences Of The United States Of America 1972, 69: 3063-3067. PMID: 4562753, PMCID: PMC389707, DOI: 10.1073/pnas.69.10.3063.Peer-Reviewed Original ResearchGlutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli I. PURIFICATION AND PROPERTIES
Lapointe J, Söll D. Glutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli I. PURIFICATION AND PROPERTIES. Journal Of Biological Chemistry 1972, 247: 4966-4974. PMID: 4341531, DOI: 10.1016/s0021-9258(19)44925-9.Peer-Reviewed Original ResearchAdenosine TriphosphateAlkylationAmino AcidsAmino Acyl-tRNA SynthetasesAnimalsCatalysisCentrifugation, ZonalChromatographyDiphosphatesDrug StabilityElectrophoresisElectrophoresis, DiscEscherichia coliGlutamatesHot TemperatureHydroxyapatitesIsoelectric FocusingMacromolecular SubstancesMolecular WeightOxidation-ReductionPhosphorus IsotopesRabbitsUltracentrifugation
1971
Isolation and Partial Characterization of Temperature-Sensitive Escherichia coli Mutants with Altered Leucyl- and Seryl-Transfer Ribonucleic Acid Synthetases
Low B, Gates F, Goldstein T, Söll D. Isolation and Partial Characterization of Temperature-Sensitive Escherichia coli Mutants with Altered Leucyl- and Seryl-Transfer Ribonucleic Acid Synthetases. Journal Of Bacteriology 1971, 108: 742-750. PMID: 4942762, PMCID: PMC247134, DOI: 10.1128/jb.108.2.742-750.1971.Peer-Reviewed Original ResearchConceptsLeucyl-tRNA synthetaseTemperature-sensitive Escherichia coli mutantsCorresponding genetic lociEscherichia coli mutantsSeryl-tRNA synthetaseTemperature-sensitive mutantColi mutantsGenetic lociBranched-chain amino acidsEscherichia coliAmino acidsConditional growthSynthetaseMutantsPartial characterizationEnzyme
1970
Identification of the Cytokinin-Active Ribonucleosides in Pure Escherichia coli tRNA Species
Bartz J, Söll D, Burrows W, Skoog F. Identification of the Cytokinin-Active Ribonucleosides in Pure Escherichia coli tRNA Species. Proceedings Of The National Academy Of Sciences Of The United States Of America 1970, 67: 1448-1453. PMID: 4922291, PMCID: PMC283372, DOI: 10.1073/pnas.67.3.1448.Peer-Reviewed Original ResearchPurification of Leucyl Transfer Ribonucleic Acid Synthetase from Escherichia coli
Hayashi H, Knowles J, Katze J, Lapointe J, Söll D. Purification of Leucyl Transfer Ribonucleic Acid Synthetase from Escherichia coli. Journal Of Biological Chemistry 1970, 245: 1401-1406. PMID: 4986473, DOI: 10.1016/s0021-9258(18)63250-8.Peer-Reviewed Original ResearchMeSH KeywordsAlkylationAmino AcidsChromatographyChromatography, DEAE-CelluloseDrug StabilityEdetic AcidElectrophoresisEscherichia coliHydrogen-Ion ConcentrationHydroxyapatitesLeucineLigasesMethodsMolecular WeightOxidation-ReductionRNA, BacterialRNA, TransferSodium ChlorideTemperatureTime FactorsUltracentrifugation
1969
Transfer ribonucleic acid from Mycoplasma.
Hayashi H, Fisher H, Soell D. Transfer ribonucleic acid from Mycoplasma. Biochemistry 1969, 8: 3680-6. PMID: 4897946, DOI: 10.1021/bi00837a028.Peer-Reviewed Original ResearchAmino AcidsCarbon IsotopesCell-Free SystemCelluloseChemical PhenomenaChemistryChromatography, Ion ExchangeChromatography, PaperElectrophoresisEscherichia coliFormatesHot TemperatureMethionineMycoplasmaNucleic Acid DenaturationNucleosidesPeptide BiosynthesisPolynucleotidesRNA, BacterialRNA, TransferSpecies SpecificityStimulation, ChemicalTritiumUltracentrifugationUracil Nucleotides