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 ResearchConceptsSelenoprotein productionYeast expression systemSeryl-tRNA synthetaseSite-specific incorporationEukaryotic relativesKingdom FungiSelenocysteine synthaseSelenophosphate synthetaseBiosynthesis pathwayEukaryotic selenoproteinsMetabolic engineeringBiosynthetic pathwayPathway componentsExpression systemReductase enzymeTRNASaccharomycesYeastTranslation componentsSpecific sitesFacile productionUnique chemicalSynthetasePathwayFirst demonstration
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
2013
Back Cover: Rewiring Translation for Elongation Factor Tu‐Dependent Selenocysteine Incorporation (Angew. Chem. Int. Ed. 5/2013)
Aldag C, Bröcker M, Hohn M, Prat L, Hammond G, Plummer A, Söll D. Back Cover: Rewiring Translation for Elongation Factor Tu‐Dependent Selenocysteine Incorporation (Angew. Chem. Int. Ed. 5/2013). Angewandte Chemie International Edition 2013, 52: 1596-1596. DOI: 10.1002/anie.201300063.Peer-Reviewed Original Research
2012
The Mechanism of Pre-transfer Editing in Yeast Mitochondrial Threonyl-tRNA Synthetase*
Ling J, Peterson KM, Simonović I, Söll D, Simonović M. The Mechanism of Pre-transfer Editing in Yeast Mitochondrial Threonyl-tRNA Synthetase*. Journal Of Biological Chemistry 2012, 287: 28518-28525. PMID: 22773845, PMCID: PMC3436575, DOI: 10.1074/jbc.m112.372920.Peer-Reviewed Original ResearchConceptsPre-transfer editingThreonyl-tRNA synthetaseHydrolytic water moleculeFundamental biological processesNormal cellular functionAminoacyl-tRNA synthetasesPost-transfer editingPost-transfer editing activityTranslational fidelityAminoacylation siteCellular functionsAminoacylation active siteBiological processesMST1Conformational changesEditing activitySeryl adenylateAmino acidsSpecialized domainsEditingSerineSites 100SynthetaseActive siteAdenylate
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 preferenceSynthetaseAn unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine
Su D, Lieberman A, Lang BF, Simonović M, Söll D, Ling J. An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Research 2011, 39: 4866-4874. PMID: 21321019, PMCID: PMC3113583, DOI: 10.1093/nar/gkr073.Peer-Reviewed Original ResearchConceptsCUN codonsYeast mitochondriaGenetic codeAlloacceptor tRNA gene recruitmentComprehensive phylogenetic analysisStandard genetic codeThreonyl-tRNA synthetaseHistidyl-tRNA synthetaseGene recruitmentEvolutionary originPhylogenetic analysisRecoding eventBiochemical experimentsFirst nucleotideAnticodon loopMST1CodonFirst clear exampleYeastMitochondriaThreonineSynthetaseCandida albicansGenomeClear example
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
Structure of the unusual seryl‐tRNA synthetase reveals a distinct zinc‐dependent mode of substrate recognition
Bilokapic S, Maier T, Ahel D, Gruic‐Sovulj I, Söll D, Weygand‐Durasevic I, Ban N. Structure of the unusual seryl‐tRNA synthetase reveals a distinct zinc‐dependent mode of substrate recognition. The EMBO Journal 2006, 25: 2498-2509. PMID: 16675947, PMCID: PMC1478180, DOI: 10.1038/sj.emboj.7601129.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid SequenceAnimalsArchaeal ProteinsBinding SitesCrystallography, X-RayDimerizationEnzyme ActivationHumansMethanosarcina barkeriModels, MolecularMolecular Sequence DataMolecular StructureProtein Structure, QuaternarySequence AlignmentSequence Homology, Amino AcidSerineSerine-tRNA LigaseSubstrate SpecificityThreonineConceptsSeryl-tRNA synthetaseTRNA-binding domainMinimal sequence similarityResolution crystal structureAmino acid substratesActive site zinc ionSequence similaritySubstrate recognitionSerRSsSerine substrateMotif 1Methanogenic archaeaMutational analysisProtein ligandsEnzymatic activityArchaeaAminoacyl-tRNA synthetase systemsDistinct mechanismsAbsolute requirementRecognition mechanismSynthetase systemSynthetaseIon ligandsZinc ionsEucaryotesMischarging of M. barkeri tRNAPyl with alanine and serine in vitro
Li D, Polycarpo C, Ambrogelly A, Söll D. Mischarging of M. barkeri tRNAPyl with alanine and serine in vitro. The FASEB Journal 2006, 20: a503-a503. DOI: 10.1096/fasebj.20.4.a503-c.Peer-Reviewed Original ResearchNon-canonical amino acidsSecondary structureCognate tRNA speciesPyrrolysyl-tRNA synthetaseAminoacyl-tRNA synthetaseSimilar secondary structureBovine mitochondriaTRNA speciesAlanine tRNAAnticodon stemAcceptor stemAmino acidsM. barkeriMethanosarcina barkeriSerRSsPyrrolysineMultiple mutationsVariable loopSynthetaseSerineShorter variable loopsSynthetase systemBarkeriAlanineStemRNA‐Dependent Cysteine Biosynthesis in Archaea
Yuan J, Sauerwald A, Zhu W, Major T, Roy H, Palioura S, Jahn D, Whitman W, Yates J, Ibba M, Söll D. RNA‐Dependent Cysteine Biosynthesis in Archaea. The FASEB Journal 2006, 20: a503-a504. DOI: 10.1096/fasebj.20.4.a503-d.Peer-Reviewed Original ResearchCysteine biosynthesisSep-tRNACys-tRNA synthaseCys-tRNACysPhosphoseryl-tRNA synthetaseCysteinyl-tRNA synthetaseCys-tRNAGenetic experimentsSec tRNAMost organismsMethanocaldococcus jannaschiiGenetic codeGenomic analysisEssential enzymeMethanogenic archaeaArchaeaSimilar enzymesO-phosphoserineBiosynthesisOrganismsSynthetaseEnzymePathwaySulfur donorSole route
2005
RNA-Dependent Cysteine Biosynthesis in Archaea
Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR, Ibba M, Söll D. RNA-Dependent Cysteine Biosynthesis in Archaea. Science 2005, 307: 1969-1972. PMID: 15790858, DOI: 10.1126/science.1108329.Peer-Reviewed Original ResearchConceptsCysteine biosynthesisSep-tRNAComparative genomic analysisCys-tRNA synthasePhosphoseryl-tRNA synthetaseCys-tRNACysteine auxotrophyMost organismsMethanocaldococcus jannaschiiMethanococcus maripaludisGenetic codeGenomic analysisEssential enzymeO-phosphoserineBiosynthesisRNA synthetaseOrganismsSepRSSynthetasePartial purificationCysteineSole routeArchaeaSepCysSJannaschii
2004
Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem?
Ambrogelly A, Kamtekar S, Sauerwald A, Ruan B, Tumbula-Hansen D, Kennedy D, Ahel I, Söll D. Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem? Cellular And Molecular Life Sciences 2004, 61: 2437-2445. PMID: 15526152, DOI: 10.1007/s00018-004-4194-9.Peer-Reviewed Original ResearchConceptsMethanogenic archaeaCysteine biosynthesisCellular translation machineryAminoacyl-tRNA synthesisCanonical cysteinyl-tRNA synthetaseAminoacyl-tRNA synthetasesCysteinyl-tRNA synthetaseRecognizable genesTranslation machineryGenome sequenceArchaeaBiosynthesisEssential componentSynthetasesTRNARibosomesGenesMachineryOrganismsSynthetasePossible linkSequenceFormationThe 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
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
Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis
Stathopoulos C, Kim W, Li T, Anderson I, Deutsch B, Palioura S, Whitman W, Söll D. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2001, 98: 14292-14297. PMID: 11717392, PMCID: PMC64675, DOI: 10.1073/pnas.201540498.Peer-Reviewed Original ResearchConceptsCysteinyl-tRNA synthetaseMethanococcus maripaludisArchaeon Methanococcus maripaludisLateral gene transferNormal growth conditionsAminoacyl-tRNA synthetasesAminoacyl-tRNA synthetaseArchaea Methanocaldococcus jannaschiiProlyl-tRNA synthetaseCysS genesCys-tRNAMethanocaldococcus jannaschiiM. maripaludisSynthetase geneIntriguing enzymeMethanothermobacter thermautotrophicusCysteinyl-tRNAKnockout strainProlyl-tRNAGene transferSynthetaseBiochemical analysisVivo translationGrowth conditionsCysRSA 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
A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*
Hamano-Takaku F, Iwama T, Saito-Yano S, Takaku K, Monden Y, Kitabatake M, Söll D, Nishimura S. A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*. Journal Of Biological Chemistry 2000, 275: 40324-40328. PMID: 11006270, DOI: 10.1074/jbc.m003696200.Peer-Reviewed Original ResearchConceptsUnnatural amino acidsTyrosyl-tRNA synthetaseEscherichia coli tyrosyl-tRNA synthetasePosition 130Amino acidsVivo protein biosynthesisE. coli cellsAminoacyl-tRNA formationSingle point mutationTyrRS mutantsCellular proteinsProtein biosynthesisTYR geneMutant enzymesPlasmid libraryReplacement of phenylalanineColi cellsImmense potentialNormal phenotypeEfficient productionPoint mutationsTyrRSProteinPolymerase chain reaction techniqueSynthetaseDomain-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 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 attachment