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
2010
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation
Nureki O, O’Donoghue P, Watanabe N, Ohmori A, Oshikane H, Araiso Y, Sheppard K, Söll D, Ishitani R. Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. Nucleic Acids Research 2010, 38: 7286-7297. PMID: 20601684, PMCID: PMC2978374, DOI: 10.1093/nar/gkq605.Peer-Reviewed Original ResearchConceptsNon-discriminating glutamyl-tRNA synthetaseGlutamyl-tRNA synthetaseND-GluRSEscherichia coli GlnRSFormation of GlnCognate tRNA moleculesGlutaminyl-tRNA synthetaseAnticodon-binding domainEvolutionary predecessorPhylogenetic analysisGenetic codeMolecular basisTRNA moleculesRecognition pocketGlnRGenetic encodingAmino acidsSpecific ligationStructural determinantsKey eventsSynthetaseGluPromiscuous recognitionGluRGln
2006
Saccharomyces cerevisiae imports the cytosolic pathway for Gln‐tRNA synthesis into the mitochondrion
Krett B, Rinehart J, Rubio M, Alfonzo J, Söll D. Saccharomyces cerevisiae imports the cytosolic pathway for Gln‐tRNA synthesis into the mitochondrion. The FASEB Journal 2006, 20: a500-a500. DOI: 10.1096/fasebj.20.4.a500-b.Peer-Reviewed Original ResearchTransamidation pathwayMitochondrial translationGln-tRNAOrganellar protein synthesisYeast mitochondrial DNAGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesAminoacyl-tRNA formationImport mechanismMitochondrial localizationMitochondrial DNAProtein biosynthesisMost bacteriaCytoplasmic componentsAlternate functionsCytosolic pathwayProtein synthesisAmino acidsEssential processMitochondriaTRNAPathwayEukaryotesGlnRArchaea
2003
Non-canonical Eukaryotic Glutaminyl- and Glutamyl-tRNA Synthetases Form Mitochondrial Aminoacyl-tRNA in Trypanosoma brucei *
Rinehart J, Horn EK, Wei D, Söll D, Schneider A. Non-canonical Eukaryotic Glutaminyl- and Glutamyl-tRNA Synthetases Form Mitochondrial Aminoacyl-tRNA in Trypanosoma brucei *. Journal Of Biological Chemistry 2003, 279: 1161-1166. PMID: 14563839, DOI: 10.1074/jbc.m310100200.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseT. bruceiGln-tRNATrypanosoma bruceiInsect stage T. bruceiT. brucei enzymeRespective gene productsAminoacyl-tRNA synthetasesGlutamyl-tRNA synthetase activitySynthetase activityTransamidation pathwayLeishmania mitochondriaBrucei enzymeMitochondrial tRNAsGlu-tRNAProtein biosynthesisAminoacylation experimentsGene productsRNA interferenceTRNABruceiMitochondriaTotal tRNAGlutaminyl
2001
A Single Amidotransferase Forms Asparaginyl-tRNA and Glutaminyl-tRNA in Chlamydia trachomatis *
Raczniak G, Becker H, Min B, Söll D. A Single Amidotransferase Forms Asparaginyl-tRNA and Glutaminyl-tRNA in Chlamydia trachomatis *. Journal Of Biological Chemistry 2001, 276: 45862-45867. PMID: 11585842, DOI: 10.1074/jbc.m109494200.Peer-Reviewed Original ResearchConceptsAsn-tRNAGln-tRNAAminoacyl-tRNAOperon-like arrangementAccurate protein synthesisGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseAminoacyl-tRNA synthetasesAsparaginyl-tRNA synthetaseAspartyl-tRNA synthetaseGat genesAsparaginyl-tRNAGenome sequenceMost bacteriaGlutaminyl-tRNAAmidotransferaseProtein synthesisSynthetasesSynthetaseGenesAmide donorEnzymeAspGluGenomeA dual‐specific Glu‐tRNAGln and Asp‐tRNAAsn amidotransferase is involved in decoding glutamine and asparagine codons in Acidithiobacillus ferrooxidans
Salazar J, Zúñiga R, Raczniak G, Becker H, Söll D, Orellana O. A dual‐specific Glu‐tRNAGln and Asp‐tRNAAsn amidotransferase is involved in decoding glutamine and asparagine codons in Acidithiobacillus ferrooxidans. FEBS Letters 2001, 500: 129-131. PMID: 11445070, DOI: 10.1016/s0014-5793(01)02600-x.Peer-Reviewed Original ResearchConceptsOperon-like structureGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseA. ferrooxidansAsparaginyl-tRNA synthetaseTransamidation pathwayGat genesGlu-tRNAGlnBioleaching of mineralsAsn-tRNAAcidithiobacillus ferrooxidansGln-tRNAAsparagine codonsSynthetase enzymeBacillus subtilisAcidophilic bacteriumEscherichia coliBiochemical analysisAmidotransferaseSynthetaseGenes
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 stepRNAOrganismsDomainCytoplasm
1998
Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis
Curnow A, Tumbula D, Pelaschier J, Min B, Söll D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 12838-12843. PMID: 9789001, PMCID: PMC23620, DOI: 10.1073/pnas.95.22.12838.Peer-Reviewed Original ResearchConceptsDeinococcus radioduransD. radiodurans genomeRadiation-resistant bacterium Deinococcus radioduransBiosynthesis of asparagineGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseBacterium Deinococcus radioduransPresence of AsnRSAsparaginyl-tRNA synthetaseAspartyl-tRNA synthetaseAsn-tRNAAsparagine biosynthesisAsparaginyl-tRNAGenomic sequencesGln-tRNAAsparagine synthetaseBiochemical experimentsTransamidation activityGlutaminyl-tRNAProtein synthesisSingle enzymeSynthetaseRadioduransBiosynthesisGenesRetracing the evolution of amino acid specificity in glutaminyl‐tRNA synthetase
Hong K, Ibba M, Söll D. Retracing the evolution of amino acid specificity in glutaminyl‐tRNA synthetase. FEBS Letters 1998, 434: 149-154. PMID: 9738468, DOI: 10.1016/s0014-5793(98)00968-5.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseTranslational error rateMolecular phylogenetic studiesAmino acid specificityGlutamyl-tRNA synthetaseFirst biochemical evidenceCellular growth ratePhe-90Phylogenetic studiesSynthetase mutantsTyr-240SynthetaseBiochemical evidenceVivo expressionGenesGlutamic acidActive siteGrowth rateMisacylationMutantsMutagenesisDuplicationDiversificationResiduesKey stepThe Terminal Adenosine of tRNAGln Mediates tRNA-Dependent Amino Acid Recognition by Glutaminyl-tRNA Synthetase †
Liu J, Ibba M, Hong K, Söll D. The Terminal Adenosine of tRNAGln Mediates tRNA-Dependent Amino Acid Recognition by Glutaminyl-tRNA Synthetase †. Biochemistry 1998, 37: 9836-9842. PMID: 9657697, DOI: 10.1021/bi980704+.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseAmino acid recognitionEscherichia coli glutaminyl-tRNA synthetaseSequence-specific interactionsDouble-mutant cycle analysisAmino acid glutamineMutant cycle analysisApparent affinityConservative replacementsNonconservative replacementGlutamine bindingKcat/KmTyr211Biochemical studiesNoncognate tRNAsTerminal adenosineSynthetaseGlutamineSpecific interactionsCycle analysisKmAsp66AffinityTRNADramatic decrease
1997
Glutamyl-tRNA sythetase.
Freist W, Gauss D, Söll D, Lapointe J. Glutamyl-tRNA sythetase. Biological Chemistry 1997, 378: 1313-29. PMID: 9426192.Peer-Reviewed Original ResearchConceptsGlutamyl-tRNA synthetaseGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesNegative eubacteriaBacterial glutamyl-tRNA synthetasesATP/PPiHigh molecular mass complexesClass I aminoacyl-tRNA synthetasesCytoplasm of eukaryotesE. coli GlnRSGlutamyl-tRNA synthetasesMolecular mass complexesN-terminal halfC-terminal halfAmino acid residuesDihydrouridine (DHU) armPhylogenetic studiesSpecific amidotransferaseGlutamyl-prolylMass complexesTRNA synthetasesCognate tRNAAcid residuesAcceptor stemSynthetasesGlutaminyl-tRNA synthetase.
Freist W, Gauss D, Ibba M, Söll D. Glutaminyl-tRNA synthetase. Biological Chemistry 1997, 378: 1103-17. PMID: 9372179.Peer-Reviewed Original ResearchConceptsE. coli GlnRSGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseMammalian enzymeCommon ancestorPositive eubacteriaCognate tRNAMultienzyme complexTRNA moleculesGlnRArtificial mutantsAcceptor stemAnticodon loopMolecular massAmino acidsCatalytic siteEnzymeSynthetaseEubacteriaArchaebacteriaTRNAMutantsOrganellesAncestorComplexes
1996
Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase
Kitabatake M, Inokuchi H, Ibba M, Hong K, Söll D. Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase. Molecular Genetics And Genomics 1996, 252: 717-722. PMID: 8917315, DOI: 10.1007/bf02173978.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseWild-type enzymeSubstrate discriminationDouble mutantSubstrate recognition domainThree-dimensional structureAnticodon recognitionSubstrate specificityTRNA bindingGenetic analysisAcceptor stemRecognition domainC171Ternary complexExtensive interactionsMutantsPotential involvementG mutationEnzymeHigh KmSynthetaseMutationsActive siteE222GlnRInteractions 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 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 roleGlnTRNAGlnHomologous Expression and Purification of Mutants of an Essential Protein by Reverse Epitope-Tagging
Thomann H, Ibba M, Hong K, Söll D. Homologous Expression and Purification of Mutants of an Essential Protein by Reverse Epitope-Tagging. Bio/Technology 1996, 14: 50-55. PMID: 9636312, DOI: 10.1038/nbt0196-50.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant enzymesEssential enzymeGlutaminyl-tRNA synthetasesWild-type proteinExtrachromosomal genetic elementsEpitope taggingEssential proteinsMutant proteinsHomologous expressionReporter epitopeCell-free extractsGenetic elementsNormal phenotypeBiochemical studiesEnzymatic activityEnzymeProteinSynthetaseProtein contaminationExpressionPurificationMutantsSynthetasesNovel strategyAminoacyl-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
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 mechanismsSynthetaseSubstrate 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