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 acidsDiversification of aminoacyl-tRNA synthetase activities via genomic duplication
Krahn N, Söll D, Vargas-Rodriguez O. Diversification of aminoacyl-tRNA synthetase activities via genomic duplication. Frontiers In Physiology 2022, 13: 983245. PMID: 36060688, PMCID: PMC9437257, DOI: 10.3389/fphys.2022.983245.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenomic duplicationSynthetase familyRecent bioinformatic analysisAminoacyl-tRNA synthetase familySynthetic biology applicationsDomains of lifeNew drug targetsAminoacyl-tRNA synthetase activityGene duplicationPhylogenetic diversityEvolutionary eventsGenetic codeBioinformatics analysisImportant bioactive moleculesAdaptive advantageBiological functionsBiological processesBiology applicationsDrug targetsDuplicationAaRSsCatalytic siteSynthetase activityProteinBioactive moleculesUncovering translation roadblocks during the development of a synthetic tRNA
Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Research 2022, 50: 10201-10211. PMID: 35882385, PMCID: PMC9561287, DOI: 10.1093/nar/gkac576.Peer-Reviewed Original ResearchConceptsOrthogonal translation systemGenetic code expansionCode expansionTertiary interactionsNon-canonical amino acidsAminoacyl-tRNA substratesDomains of lifeAminoacyl-tRNA synthetaseTranslation systemSingle nucleotide mutationsSingle-molecule fluorescenceDistinct tRNAsNon-canonical structuresSelenocysteine insertionRibosomal translationTRNARibosomesSynthetic tRNANucleotide mutationsAmino acidsSame organismP siteOrganismsTranslocationTranslation
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
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