2022
Unconventional genetic code systems in archaea
Meng K, Chung CZ, Söll D, Krahn N. Unconventional genetic code systems in archaea. Frontiers In Microbiology 2022, 13: 1007832. PMID: 36160229, PMCID: PMC9499178, DOI: 10.3389/fmicb.2022.1007832.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsGenetic code systemAmino acidsTRNA-dependent pathwayCanonical amino acidsRare amino acidArchaeal lineagesArchaeal speciesSingle lineageArchaeaMolecular mechanismsThird domainExtreme environmentsRecent discoveryLineagesBiochemical elementsHarsh conditionsEukaryotesPyrrolysineSelenocysteineOrganismsSpeciesBacteriaPathwayAcidDiscoveryUncovering 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
2015
Overcoming Challenges in Engineering the Genetic Code
Lajoie M, Söll D, Church G. Overcoming Challenges in Engineering the Genetic Code. Journal Of Molecular Biology 2015, 428: 1004-1021. PMID: 26348789, PMCID: PMC4779434, DOI: 10.1016/j.jmb.2015.09.003.Peer-Reviewed Original Research
2011
tRNA import into mitochondria: many organisms but not so many mechanisms
Alfonzo J, Randau L, Söll D. tRNA import into mitochondria: many organisms but not so many mechanisms. The FASEB Journal 2011, 25: 311.3-311.3. DOI: 10.1096/fasebj.25.1_supplement.311.3.Peer-Reviewed Original ResearchTRNA importMitochondrial genomeMammalian mitochondriaImport of tRNAsMajority of eukaryotesMitochondrial tRNA mutationsProtein importImport pathwayTRNA genesImport systemAdditional tRNAsTRNA mutationsTRNACellular ATPMitochondriaEukaryotesOrganismsGenomeRat liver mitochondriaLiver mitochondriaImportInnate abilityGenesTrypanosomesCytoplasm
2006
RNA‐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 linkSequenceFormation
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 stepRNAOrganismsDomainCytoplasmOne Polypeptide with Two Aminoacyl-tRNA Synthetase Activities
Stathopoulos C, Li T, Longman R, Vothknecht U, Becker H, Ibba M, Söll D. One Polypeptide with Two Aminoacyl-tRNA Synthetase Activities. Science 2000, 287: 479-482. PMID: 10642548, DOI: 10.1126/science.287.5452.479.Peer-Reviewed Original ResearchConceptsProlyl-tRNA synthetaseProtein synthesisCysteinyl-tRNA synthetase activityAmino-terminal sequenceSynthetase activityAminoacyl-tRNA synthetase activityCertain archaeaEvolutionary originMethanococcus jannaschiiGenome sequenceSubstrate specificityGenetic analysisSuch organismsMessenger RNARNA synthetasesSynthetaseSequenceArchaeaJannaschiiSynthetasesRNAOrganismsPolypeptideProlylProtein
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 translationPathwayJannaschiiSynthetasesBiosynthesisOrganisms
1997
Aminoacyl-tRNA synthesis in Archaea.
Ibba M, Celic I, Curnow A, Kim H, Pelaschier J, Tumbula D, Vothknecht U, Woese C, Söll D. Aminoacyl-tRNA synthesis in Archaea. Nucleic Acids Symposium Series 1997, 305-6. PMID: 9586121.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthesisLysyl-tRNA synthetasesGlutaminyl-tRNA synthetasesArchaeon Haloferax volcaniiArchaeal genomesGlu-tRNAAsn-tRNAHaloferax volcaniiNumber of organismsGln-tRNAGenetic studiesArchaeaAsp-tRNASynthetasesAsparaginylCysteinylEukaryaVolcaniiGenomeGlutaminylOrganismsSequencingBacteriaEnzymeTransamidation
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 mechanismsSynthetase
1994
Coexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli
Weygand-Durasević I, Nalaskowska M, Söll D. Coexpression of eukaryotic tRNASer and yeast seryl-tRNA synthetase leads to functional amber suppression in Escherichia coli. Journal Of Bacteriology 1994, 176: 232-239. PMID: 8282701, PMCID: PMC205035, DOI: 10.1128/jb.176.1.232-239.1994.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseYeast seryl-tRNA synthetaseEscherichia coliSerine tRNA geneE. coliConservation of determinantsTRNA genesSchizosaccharomyces pombePrimary transcriptPlasmid promoterAmber suppressionTRNA identityFunctional expressionColiCoexpressionSynthetasePombeGenesPromoterSuppressorTranscriptsOrganismsConservationExpressionEfficient suppression
1991
The Human Genome Project: a paradigm for information management in the life sciences
Pearson M, Söll D. The Human Genome Project: a paradigm for information management in the life sciences. The FASEB Journal 1991, 5: 35-39. PMID: 1991581, DOI: 10.1096/fasebj.5.1.1991581.Peer-Reviewed Original Research
1990
Transfer RNA and the formation of the heme and chlorophyll precursor, 5-aminolevulinic acid.
O'Neill G, Söll D. Transfer RNA and the formation of the heme and chlorophyll precursor, 5-aminolevulinic acid. BioFactors 1990, 2: 227-35. PMID: 2282139.Peer-Reviewed Original ResearchConceptsGlu-tRNA reductaseSequence-specific recognitionDual-function moleculeNADPH-dependent enzymeThree-step pathwayTransfer RNASpecific cofactorsChlorophyll precursorsLow molecular weight metabolitesNovel roleAmino acidsReduction of glutamatePeptide bond synthesisTRNAWeight metabolitesHemeMetabolic conversionBond synthesisBiosynthesisRNAOrganismsAcidCofactorProteinGlutamate
1988
Protein biosynthesis in organelles requires misaminoacylation of tRNA
Schön A, Kannangara C, Cough S, SÖll D. Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature 1988, 331: 187-190. PMID: 3340166, DOI: 10.1038/331187a0.Peer-Reviewed Original ResearchConceptsProtein biosynthesisOrigin of organellesCrude chloroplast extractAnimal mitochondriaRNA involvementSpecific amidotransferaseTRNA speciesConversion of glutamateBarley chloroplastsChloroplast extractsProtein synthesisTRNAOrganellesSpeciesChloroplastsAminoacylation studiesBiosynthesisAmide donorGlutamineGlnCyanobacteriaAmidotransferaseMisaminoacylationMitochondriaOrganisms
1986
The nucleotide sequence, localization and transcriptional properties of a tRNACUGLeu gene from Drosophila melanogaster
Glew L, Lo R, Recce T, Nichols M, Söll D, Bell J. The nucleotide sequence, localization and transcriptional properties of a tRNACUGLeu gene from Drosophila melanogaster. Gene 1986, 44: 307-314. PMID: 2946625, DOI: 10.1016/0378-1119(86)90195-2.Peer-Reviewed Original Research
1974
15. Aminoacyl-tRNA Synthetases
Söll D, Schimmel P. 15. Aminoacyl-tRNA Synthetases. The Enzymes 1974, 10: 489-538. DOI: 10.1016/s1874-6047(08)60147-x.Peer-Reviewed Original ResearchAminoacyl-tRNA synthetasesEucaryotic organismsSpecific aminoacyl-tRNA synthetasesCorresponding cytoplasmic enzymesFamily of enzymesMitochondrial tRNAsProtein biosynthesisMammalian cellsMammalian virusesSynthetasesCytoplasmic enzymeSeparate proteinsCell extractsTRNAAmino acidsOrganismsCytoplasmSame organismEnzymeOrganellesMitochondriaMachineryProteinKey roleProcaryotes