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
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
2008
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation
Sherrer RL, O’Donoghue P, Söll D. Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation. Nucleic Acids Research 2008, 36: 1247-1259. PMID: 18174226, PMCID: PMC2275090, DOI: 10.1093/nar/gkm1134.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateAmino Acid SequenceArchaeal ProteinsBinding SitesEvolution, MolecularKineticsMethanococcalesModels, MolecularMutationPhosphotransferasesPhylogenyProtein Structure, TertiaryRNA, Transfer, Amino AcylSequence AlignmentSingle-Strand Specific DNA and RNA EndonucleasesSubstrate SpecificityConceptsATPase active sitePhosphate-binding loopInduced fit mechanismRxxxR motifEvolutionary historyWalker BKinase familyPhylogenetic analysisSep-tRNARelated kinasesPSTKBiochemical characterizationSynthase convertsFit mechanismKinaseATPase activityPlasmodium speciesMotifActive siteSerHigh affinityDecreased activityArchaeaSepSecSSer18
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 linkSequenceFormation
2001
Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales
McCloskey J, Graham D, Zhou S, Crain P, Ibba M, Konisky J, Söll D, Olsen G. Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Research 2001, 29: 4699-4706. PMID: 11713320, PMCID: PMC92529, DOI: 10.1093/nar/29.22.4699.Peer-Reviewed Original ResearchConceptsPost-transcriptional modificationsSmall ribosomal subunit RNA sequencesRibose-methylated nucleosidesClose phylogenetic relationshipArchaeal RNAArchaeal tRNAsPhylogenetic relationshipsMethanococcus jannaschiiMethanococcus maripaludisTransfer RNAPhylogenetic relationsBacterial tRNAsMethanococcus vannieliiPosition 37Methanococcus igneusModification differencesModification patternsTRNAMethanococcus thermolithotrophicusRNA sequencesRNATemperature of growthUnknown structureFamily membersEukaryaGenomics and the evolution of aminoacyl-tRNA synthesis.
Ruan B, Ahel I, Ambrogelly A, Becker H, Bunjun S, Feng L, Tumbula-Hansen D, Ibba M, Korencic D, Kobayashi H, Jacquin-Becker C, Mejlhede N, Min B, Raczniak G, Rinehart J, Stathopoulos C, Li T, Söll D. Genomics and the evolution of aminoacyl-tRNA synthesis. Acta Biochimica Polonica 2001, 48: 313-21. PMID: 11732603, DOI: 10.18388/abp.2001_3917.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthesisAminoacyl-tRNA synthetasesTransfer RNAsAmino acidsMessenger RNAGenetic informationContemporary aminoacyl-tRNA synthetasesDirect protein synthesisNon-canonical routesEvolutionary diversityEvolutionary divergenceCys-tRNANascent polypeptidesRibosome movesAsn-tRNAGln-tRNAWhole genomeAppropriate amino acidsTRNA anticodonSubstrate specificityLys-tRNATrinucleotide codonsNext codonUnexpected levelProtein synthesis
2000
A dual-specificity aminoacyl-tRNA synthetase in the deep-rooted eukaryote Giardia lamblia
Bunjun S, Stathopoulos C, Graham D, Min B, Kitabatake M, Wang A, Wang C, Vivarès C, Weiss L, Söll D. A dual-specificity aminoacyl-tRNA synthetase in the deep-rooted eukaryote Giardia lamblia. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 12997-13002. PMID: 11078517, PMCID: PMC27167, DOI: 10.1073/pnas.230444397.Peer-Reviewed Original ResearchConceptsCys-tRNAAminoacyl-tRNA synthetaseProlyl-tRNA synthetasePrimitive eukaryote Giardia lambliaPro geneEukaryote Giardia lambliaNumber of archaeaAlanyl-tRNA synthetasesCysteinyl-tRNA synthetaseE. coli tRNACysS genesM. jannaschiiMethanococcus jannaschiiMost organismsGenomic sequencesSaccharomyces cerevisiaeCysteinyl-tRNAGene productsPro-tRNATRNA synthetaseDual specificityMethanobacterium thermoautotrophicumProtein synthesisEscherichia coliAmino acidsThe Adaptor hypothesis revisited
Ibba M, Becker H, Stathopoulos C, Tumbula D, Söll D, Ibba M, Becker H, Stathopoulos C, Tumbula D, Söll D. The Adaptor hypothesis revisited. Trends In Biochemical Sciences 2000, 25: 311-316. PMID: 10871880, DOI: 10.1016/s0968-0004(00)01600-5.Peer-Reviewed Original ResearchAminoacyl-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 counterpartsTreesCysteine Biosynthesis Pathway in the ArchaeonMethanosarcina barkeri Encoded by Acquired Bacterial Genes?
Kitabatake M, So M, Tumbula D, Söll D. Cysteine Biosynthesis Pathway in the ArchaeonMethanosarcina barkeri Encoded by Acquired Bacterial Genes? Journal Of Bacteriology 2000, 182: 143-145. PMID: 10613873, PMCID: PMC94250, DOI: 10.1128/jb.182.1.143-145.2000.Peer-Reviewed Original ResearchConceptsCysteine biosynthesis pathwayCysK geneCysteine biosynthesisBiosynthesis pathwayRecent genome dataOpen reading framePyrococcus sppCysE geneBacterial genesMethanococcus jannaschiiGenome dataArchaeoglobus fulgidusReading frameSulfolobus solfataricusThermoplasma acidophilumCysM geneMethanobacterium thermoautotrophicumGenesBiosynthesisPathwayGreat similaritySame functionCysKOrthologsArchaea
1999
Cysteinyl‐tRNA formation: the last puzzle of aminoacyl‐tRNA synthesis
Li T, Graham D, Stathopoulos C, Haney P, Kim H, Vothknecht U, Kitabatake M, Hong K, Eggertsson G, Curnow A, Lin W, Celic I, Whitman W, Söll D. Cysteinyl‐tRNA formation: the last puzzle of aminoacyl‐tRNA synthesis. FEBS Letters 1999, 462: 302-306. PMID: 10622715, DOI: 10.1016/s0014-5793(99)01550-1.Peer-Reviewed Original ResearchConceptsLateral gene transferAminoacyl-tRNA synthesisCysteinyl-tRNA synthetaseEscherichia coli cysteinyl-tRNA synthetaseMolecular phylogenyPyrococcus sppMethanococcus jannaschiiMethanococcus maripaludisM. maripaludisMethanogenic archaeaMethanosarcina sppGene transferCysRSMethanosarcina barkeriGenesSpecific relativeLast puzzleSppOrthologsArchaeaPhylogenyJannaschiiMutantsLineagesOrganismsArchaeal Aminoacyl-tRNA Synthesis: Diversity Replaces Dogma
Tumbula D, Vothknecht U, Kim H, Ibba M, Min B, Li T, Pelaschier J, Stathopoulos C, Becker H, Söll D. Archaeal Aminoacyl-tRNA Synthesis: Diversity Replaces Dogma. Genetics 1999, 152: 1269-1276. PMID: 10430557, PMCID: PMC1460689, DOI: 10.1093/genetics/152.4.1269.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthesisGene transfer eventsPhenylalanyl-tRNA synthetasesLysyl-tRNA synthetaseTransamidation pathwayExtant organismsMethanococcus jannaschiiAsparaginyl-tRNAProtein biosynthesisGenetic codeGene expressionGenome sequencingAminoacyl-tRNAArchaeaMethanobacterium thermoautotrophicumMolecular biologyUnexpected levelNovel pathwayTransfer eventsFaithful translationPathwayJannaschiiSynthetasesBiosynthesisOrganismsSubstrate 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
Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi
Ibba M, Bono J, Rosa P, Söll D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 14383-14388. PMID: 9405621, PMCID: PMC24988, DOI: 10.1073/pnas.94.26.14383.Peer-Reviewed Original ResearchConceptsLysyl-tRNA synthetasesLysyl-tRNA synthetaseOpen reading frameReading frameAminoacyl-tRNA synthetasesLyme disease spirochete Borrelia burgdorferiGroup of enzymesLysyl-tRNA synthetase activityAmino acid levelsBacterial pathogen Borrelia burgdorferiArchaeal kingdomHeterologous expressionProtein biosynthesisGenomic sequencesMRNA translationPathogen Borrelia burgdorferiSignificant similarityLysyl-tRNASynthetasesB. burgdorferiBorrelia burgdorferiEscherichia coliEukaryaSpirochete Borrelia burgdorferiPathogenic spirochetesA Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I Synthetases
Ibba M, Morgan S, Curnow A, Pridmore D, Vothknecht U, Gardner W, Lin W, Woese C, Söll D. A Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I Synthetases. Science 1997, 278: 1119-1122. PMID: 9353192, DOI: 10.1126/science.278.5340.1119.Peer-Reviewed Original ResearchConceptsClass I aminoacyl-tRNA synthetaseCrenarchaeote Sulfolobus solfataricusDinucleotide-binding domainAminoacyl-tRNA synthetasesAmino acid motifsAmino acid sequenceAminoacyl-tRNA synthetaseLysyl-tRNA synthetaseClass II synthetasesEuryarchaeal genomesUnassigned functionMethanococcus jannaschiiMethanococcus maripaludisLysRS proteinsReading frameSulfolobus solfataricusAcid motifAcid sequenceSuch organismsMethanobacterium thermoautotrophicumLysRSProteinSynthetasesSynthetaseRNA synthetase
1990
The RNA component of RNase P in Schizosaccharomyces species
Zimmerly S, Gamulin V, Burkard U, Söll D. The RNA component of RNase P in Schizosaccharomyces species. FEBS Letters 1990, 271: 189-193. PMID: 2226803, DOI: 10.1016/0014-5793(90)80403-6.Peer-Reviewed Original ResearchConceptsSchizosaccharomyces speciesS. pombeS. octosporusFission yeast SchizosaccharomycesSecondary structure modelComparative structural informationYeast SchizosaccharomycesGenes divergeRNase PRelated organismsSingle geneRNA componentNorthern analysisK RNAGenesS. japonicusSpeciesPombeOctosporusRNAStructural informationSequenceSchizosaccharomycesCopurifiesCloning