2023
Recoding UAG to selenocysteine in Saccharomyces cerevisiae
Hoffman K, Chung C, Mukai T, Krahn N, Jiang H, Balasuriya N, O'Donoghue P, Söll D. Recoding UAG to selenocysteine in Saccharomyces cerevisiae. RNA 2023, 29: 1400-1410. PMID: 37279998, PMCID: PMC10573291, DOI: 10.1261/rna.079658.123.Peer-Reviewed Original ResearchMeSH KeywordsAeromonas salmonicidaCodon, TerminatorHumansNucleic Acid ConformationProtein EngineeringRNA, Transfer, CysSaccharomyces cerevisiaeConceptsSelenoprotein productionYeast expression systemSeryl-tRNA synthetaseSite-specific incorporationEukaryotic relativesKingdom FungiSelenocysteine synthaseSelenophosphate synthetaseBiosynthesis pathwayEukaryotic selenoproteinsMetabolic engineeringBiosynthetic pathwayPathway componentsExpression systemReductase enzymeTRNASaccharomycesYeastTranslation componentsSpecific sitesFacile productionUnique chemicalSynthetasePathwayFirst demonstration
2011
Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase
O’Donoghue P, Sheppard K, Nureki O, Söll D. Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20485-20490. PMID: 22158897, PMCID: PMC3251134, DOI: 10.1073/pnas.1117294108.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acyl-tRNA SynthetasesBase SequenceCodonEscherichia coliEvolution, MolecularGenetic EngineeringKineticsMethanobacteriaceaeModels, MolecularMolecular ConformationMolecular Sequence DataNucleic Acid ConformationPhylogenyProtein Structure, SecondarySequence Homology, Amino AcidConceptsGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesGenetic code engineeringAmino acidsDomains of lifeMost aminoacyl-tRNA synthetasesGlutamyl-tRNA synthetaseCanonical amino acidsBacterial GlnRSTRNA specificityTRNA pairsParticular codonsEvolutionary precursorBiochemical characterizationStem loopGlnRAdditional codonsCAA codonCodonProtein synthesisCAG codonEscherichia coliSpecific enzymesCatalytic preferenceSynthetase
2009
The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation
Palioura S, Sherrer RL, Steitz TA, Söll D, Simonović M. The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation. Science 2009, 325: 321-325. PMID: 19608919, PMCID: PMC2857584, DOI: 10.1126/science.1173755.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBase SequenceBiocatalysisCatalytic DomainCrystallography, X-RayHumansHydrogen BondingModels, MolecularMolecular Sequence DataNucleic Acid ConformationPhosphatesPhosphoserineProtein ConformationProtein MultimerizationProtein Structure, SecondaryRNA, Transfer, Amino Acid-SpecificRNA, Transfer, Amino AcylSelenocysteineConceptsTransfer RNASelenocysteine formationSelenocysteinyl-tRNA synthaseCognate transfer RNAEnzyme active siteTRNA bindingActive siteConformational changesEnzyme assaysAmino acidsFree phosphoserinePhosphoserineSepSecSFinal stepSelenocysteineBiosynthesisComplexesRNAMechanismBindsCrystal structureSynthaseBindingFormationAssaysA Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea
Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Söll D. A Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea. Science 2009, 324: 657-659. PMID: 19407206, PMCID: PMC2857566, DOI: 10.1126/science.1170123.Peer-Reviewed Original ResearchConceptsTransfer RNAArchaeon Methanopyrus kandleriTertiary coreCytidine deaminase domainsTRNA genesTransfer RNAsTHUMP domainProper foldingU editingC deaminationMethanopyrus kandleriTRNA tertiary structureDeaminase domainTertiary structureTRNA tertiary corePosition 8Cytidine deaminaseUnique familyArchaeaRNAsGenesRNAFoldingDomainCrystal structure
2008
Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import
Rubio MA, Rinehart JJ, Krett B, Duvezin-Caubet S, Reichert AS, Söll D, Alfonzo JD. Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 9186-9191. PMID: 18587046, PMCID: PMC2453747, DOI: 10.1073/pnas.0804283105.Peer-Reviewed Original ResearchConceptsProtein importMammalian mitochondriaImport systemSubcellular RNA fractionsMitochondrial tRNA genesMitochondrial electrochemical gradientMitochondrial genomeTRNA genesTranscribed tRNAsHuman mitochondriaDefective mitochondriaProtein factorsFiber cellsHeterologous RNATRNACytosolic factorsSufficient ATPRNA fractionHuman cellsHuman diseasesProtein synthesisMitochondriaElectrochemical gradientOligonucleotide primersVitro system
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
1999
Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis
Ibba M, Sever S, Praetorius-Ibba M, Söll D. Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis. Nucleic Acids Research 1999, 27: 3631-3637. PMID: 10471730, PMCID: PMC148616, DOI: 10.1093/nar/27.18.3631.Peer-Reviewed Original ResearchSubstrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement
Ibba M, Losey H, Kawarabayasi Y, Kikuchi H, Bunjun S, Söll D. Substrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 418-423. PMID: 9892648, PMCID: PMC15151, DOI: 10.1073/pnas.96.2.418.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBase SequenceBorrelia burgdorferi GroupCloning, MolecularDiphosphatesEscherichia coliEvolution, MolecularGenes, ArchaealGenes, BacterialGenetic Complementation TestKineticsLysine-tRNA LigaseMethanococcusMolecular Sequence DataNucleic Acid ConformationPhylogenyRNA, Transfer, Amino AcylSequence Analysis, DNASubstrate SpecificityTranscription, GeneticConceptsClass II LysRSAminoacyl-tRNA synthetasesLysyl-tRNA synthetasesSubstrate recognitionMolecular basisBacterial class IClass II enzymesSequence-specific recognitionGene displacementTranslational apparatusTRNA recognitionEscherichia coli strainsLysRSLysRSsSame nucleotideSynthetasesDiscriminator baseUnrelated typesLysine activationCertain bacteriaII enzymesColi strainsTRNALysClass IEnzyme
1997
When protein engineering confronts the tRNA world
Schimmel P, Söll D. When protein engineering confronts the tRNA world. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 10007-10009. PMID: 9294151, PMCID: PMC33764, DOI: 10.1073/pnas.94.19.10007.Peer-Reviewed Original ResearchAmino Acyl-tRNA SynthetasesMutagenesisNucleic Acid ConformationProtein ConformationProtein EngineeringRNA, Transfer
1996
Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme.
Ibba M, Hong K, Sherman J, Sever S, Söll D. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proceedings Of The National Academy Of Sciences Of The United States Of America 1996, 93: 6953-6958. PMID: 8692925, PMCID: PMC38915, DOI: 10.1073/pnas.93.14.6953.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnimalsBase SequenceBinding SitesCalorimetryCloning, MolecularConsensus SequenceEscherichia coliHumansKineticsModels, StructuralMolecular Sequence DataNucleic Acid ConformationProtein FoldingRecombinant ProteinsRNA, Transfer, GlnSequence Homology, Nucleic AcidConceptsGlutaminyl-tRNA synthetaseAmino acid affinityAmino acid recognitionEscherichia coli glutaminyl-tRNA synthetaseBase pairsIdentity nucleotidesProtein-RNA interactionsDiscriminator baseE. coli tryptophanyl-tRNA synthetaseAminoacyl-tRNA synthetasesSequence-specific interactionsAcid affinityRecognition sitesAbility of tRNATryptophanyl-tRNA synthetaseTRNA specificityNoncognate substratesTranslational fidelityTRNA recognitionBiochemical functionsRNA recognitionCognate tRNATRNAMajor binding siteNoncognate tRNAsGlutaminyl‐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 displaysGeneticsSynthetaseGlutamineMechanismViabilityLactobacillus bulgaricus asparagine synthetase and asparaginyl-tRNA synthetase: coregulation by transcription antitermination?
Kim S, Germond J, Pridmore D, Söll D. Lactobacillus bulgaricus asparagine synthetase and asparaginyl-tRNA synthetase: coregulation by transcription antitermination? Journal Of Bacteriology 1996, 178: 2459-2461. PMID: 8636057, PMCID: PMC177964, DOI: 10.1128/jb.178.8.2459-2461.1996.Peer-Reviewed Original ResearchAmino Acid SequenceAmino Acyl-tRNA SynthetasesAspartate-Ammonia LigaseAspartate-tRNA LigaseBase SequenceGene Expression Regulation, BacterialGenes, BacterialGenetic Complementation TestLactobacillusMolecular Sequence DataNucleic Acid ConformationRNA, Transfer, Amino AcylSequence Homology, Amino AcidTerminator Regions, GeneticTranscription, GeneticAminoacyl-tRNA Synthetases Optimize Both Cognate tRNA Recognition and Discrimination against Noncognate tRNAs †
Sherman J, Söll D. Aminoacyl-tRNA Synthetases Optimize Both Cognate tRNA Recognition and Discrimination against Noncognate tRNAs †. Biochemistry 1996, 35: 601-607. PMID: 8555233, DOI: 10.1021/bi951602b.Peer-Reviewed Original ResearchConceptsTRNA recognitionNoncognate tRNAsEscherichia coli glutaminyl-tRNA synthetaseWild-type GlnRSGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesNucleic acid interactionsGlutamine tRNAFirst base pairMutational analysisSpecific proteinsTRNAGlnRSequence preferenceMutantsBase pairsAcid interactionsDecreased affinityVivoTRNAGlnAffinitySynthetasesProteinSynthetaseCrystal structure
1995
Substrate selection by aminoacyl-tRNA synthetases.
Ibba M, Thomann H, Hong K, Sherman J, Weygand-Durasevic I, Sever S, Stange-Thomann N, Praetorius M, Söll D. Substrate selection by aminoacyl-tRNA synthetases. Nucleic Acids Symposium Series 1995, 40-2. PMID: 8643392.Peer-Reviewed Original Research
1994
A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis.
Stange-Thomann N, Thomann H, Lloyd A, Lyman H, Söll D. A point mutation in Euglena gracilis chloroplast tRNA(Glu) uncouples protein and chlorophyll biosynthesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 7947-7951. PMID: 8058739, PMCID: PMC44521, DOI: 10.1073/pnas.91.17.7947.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde OxidoreductasesAnimalsBase SequenceBlotting, NorthernChlorophyllChloroplastsCloning, MolecularDNADNA PrimersEuglena gracilisIntramolecular TransferasesIsomerasesMolecular Sequence DataNucleic Acid ConformationPoint MutationPolymerase Chain ReactionProtein BiosynthesisRNA, Transfer, GluConceptsEuglena gracilis chloroplastsChlorophyll biosynthesisGlu-tRNA reductaseChlorophyll-deficient mutantsPoint mutationsChloroplast protein synthesisSequence-specific mannerDual-function moleculeC5 pathwayNADPH-dependent reductionSpecific cofactorsGluTRFirst enzymeGene productsUniversal precursorImportant identity elementAminomutase activitySequence analysisE. gracilisSecond enzymeTetrapyrrole pigmentsT-loopProtein synthesisBiosynthesisChloroplastsIdentity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases.
Frugier M, Söll D, Giegé R, Florentz C. Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases. Biochemistry 1994, 33: 9912-21. PMID: 8060999, DOI: 10.1021/bi00199a013.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetasesIdentity nucleotidesHigh-resolution X-ray structuresAminoacyl-tRNA synthetase complexGlutaminyl-tRNA synthetaseAspartyl-tRNA synthetasesAspartyl-tRNA synthetaseGlutamine identityCognate tRNATRNA structureTRNA moleculesTRNAAminoacylation specificitySynthetase complexSpecific aminoacylationConformational changesSynthetasesEscherichia coliYeastSynthetaseNucleotidesE. coliX-ray structureComplex formationColiCoexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli
Weygand-Durasević I, Nalaskowska M, Söll D. Coexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli. Journal Of Bacteriology 1994, 176: 232-239. PMID: 8282701, PMCID: PMC205035, DOI: 10.1128/jb.176.1.232-239.1994.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseYeast seryl-tRNA synthetaseEscherichia coliSerine tRNA geneE. coliConservation of determinantsTRNA genesSchizosaccharomyces pombePrimary transcriptPlasmid promoterAmber suppressionTRNA identityFunctional expressionColiCoexpressionSynthetasePombeGenesPromoterSuppressorTranscriptsOrganismsConservationExpressionEfficient suppression
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 AminoacylationA 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase.
Sylvers L, Rogers K, Shimizu M, Ohtsuka E, Söll D. A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 1993, 32: 3836-41. PMID: 8385989, DOI: 10.1021/bi00066a002.Peer-Reviewed Original ResearchSPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing
Kolman C, Söll D. SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing. Journal Of Bacteriology 1993, 175: 1433-1442. PMID: 8444805, PMCID: PMC193230, DOI: 10.1128/jb.175.5.1433-1442.1993.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBlotting, NorthernIntronsMolecular Sequence DataMutationNucleic Acid ConformationRNA Processing, Post-TranscriptionalRNA SplicingRNA, FungalRNA, TransferSaccharomyces cerevisiaeSequence Homology, Amino AcidSequence Homology, Nucleic AcidTranscription, GeneticConceptsTRNA genesSaccharomyces cerevisiae genesMature suppressor tRNASuppressor tRNA geneOpen reading frameSaccharomyces cerevisiae mutationsCerevisiae genesTRNA splicingSuppression phenotypeTRNA processingChromosome IIIGenetic approachesSuppressor tRNAReading frameGenetic analysisNorthern analysisMutant selectionMutantsNonsense mutationGenesMutationsLEU2Cell levelIncreased synthesisNFS1