2022
Ancestral archaea expanded the genetic code with pyrrolysine
Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O’Donoghue P, Söll D, Tharp JM. Ancestral archaea expanded the genetic code with pyrrolysine. Journal Of Biological Chemistry 2022, 298: 102521. PMID: 36152750, PMCID: PMC9630628, DOI: 10.1016/j.jbc.2022.102521.Peer-Reviewed Original ResearchConceptsAminoacylation efficiencyGenetic code expansionDomains of lifePyrrolysyl-tRNA synthetaseTRNA-binding domainFull-length enzymeNoncanonical amino acidsAmino acid substratesMolecular phylogenyDiverse archaeaCoevolutionary historyTRNA sequencesGenetic codeCode expansionDiscriminator basesMethanogenic archaeaMethanosarcina mazeiPylRSSubstrate spectrumTRNAArchaeaMultiple organismsLiving cellsAcid substratesAmino acids
2007
Features of Aminoacyl‐tRNA Synthesis Unique to Archaea
Polycarpo C, Sheppard K, Randau L, Ambrogelly A, Cardoso A, Fukai S, Herring S, Hohn M, Nakamura Y, Oshikane H, Palioura S, Salazar J, Yuan J, Nureki O, Söll D. Features of Aminoacyl‐tRNA Synthesis Unique to Archaea. 2007, 198-208. DOI: 10.1128/9781555815516.ch9.Peer-Reviewed Original ResearchAminoacyl-tRNA synthetasesAmino acidsCognate tRNA speciesCorrect amino acidDomains of lifeAminoacyl-tRNA synthetaseIntron-exon junctionsCorresponding tRNAsNanoarchaeum equitansMethylated thiolsM. jannaschiiMature tRNATRNA speciesGenomic studiesAncient familyBulge motifCysteine synthesisMethanogenic archaeaArchaeaBiosynthetic routeAa-tRNATRNATwo-step pathwayCys-tRNACysSynthetases
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 ionsEucaryotesRNA‐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
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
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 puzzleSppOrthologsArchaeaPhylogenyJannaschiiMutantsLineagesOrganisms
1998
Sequence Divergence of Seryl-tRNA Synthetases in Archaea
Kim H, Vothknecht U, Hedderich R, Celic I, Söll D. Sequence Divergence of Seryl-tRNA Synthetases in Archaea. Journal Of Bacteriology 1998, 180: 6446-6449. PMID: 9851985, PMCID: PMC107743, DOI: 10.1128/jb.180.24.6446-6449.1998.Peer-Reviewed Original ResearchConceptsOpen reading frameM. thermoautotrophicumRelevant open reading frameSeryl-tRNA synthetasesCys-tRNACysCanonical cysteinyl-tRNA synthetaseGel shift experimentsCysteinyl-tRNA synthetaseN-terminal peptide sequenceEscherichia coli tRNASequence divergenceDirect aminoacylationM. jannaschiiMethanococcus jannaschiiGenomic sequencesReading frameSer geneHomologous tRNAsGenomic dataMethanogenic archaeaMethanobacterium thermoautotrophicumShift experimentsEnzymatic propertiesArchaeaSerine