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 conditionsEukaryotesPyrrolysineSelenocysteineOrganismsSpeciesBacteriaPathwayAcidDiscovery
2004
The 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
1992
Chloroplast tRNAAsp: nucleotide sequence and variation of in vivo levels during plastid maturation
Schön A, Gough S, Söll D. Chloroplast tRNAAsp: nucleotide sequence and variation of in vivo levels during plastid maturation. Plant Molecular Biology 1992, 20: 601-607. PMID: 1450377, DOI: 10.1007/bf00046445.Peer-Reviewed Original Research
1991
Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNAGln interaction
Enlisch-Peters S, Conley J, Plumbridge J, Leptak C, Söll D, Rogers M. Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNAGln interaction. Biochimie 1991, 73: 1501-1508. PMID: 1725262, DOI: 10.1016/0300-9084(91)90184-3.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseEscherichia coli glutaminyl-tRNA synthetaseClass I aminoacyl-tRNA synthetaseTemperature-sensitive phenotypeAminoacyl-tRNA synthetaseTemperature-sensitive mutantGlutamine identityThree-dimensional structureMutant enzymesGlnRMutantsTerminal adenosineAminoacylation reactionExchange activitySynthetaseMutationsSubsequent assaysPseudorevertantsGlutaminylationTRNAAminoacylationGenesNucleotidesSpeciesColi
1990
The accuracy of aminoacylation — ensuring the fidelity of the genetic code
Söll D. The accuracy of aminoacylation — ensuring the fidelity of the genetic code. Cellular And Molecular Life Sciences 1990, 46: 1089-1096. PMID: 2253707, DOI: 10.1007/bf01936918.Peer-Reviewed Original ResearchConceptsAccuracy of aminoacylationTransfer RNA speciesAminoacyl-tRNA synthetasesMessenger RNA codonRNA speciesProtein biosynthesisGenetic codeProtein interactionsParticular tRNATRNACorrect attachmentBiophysical techniquesRNA codonsAmino acidsSynthetasesSpecific recognitionProper interactionAnticodonBiosynthesisCodonAminoacylationNucleotidesSpeciesEnzymeIdentity elementThe 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
1988
Formation of the chlorophyll precursor delta-aminolevulinic acid in cyanobacteria requires aminoacylation of a tRNAGlu species
O'Neill G, Peterson D, Schön A, Chen M, Söll D. Formation of the chlorophyll precursor delta-aminolevulinic acid in cyanobacteria requires aminoacylation of a tRNAGlu species. Journal Of Bacteriology 1988, 170: 3810-3816. PMID: 2900830, PMCID: PMC211375, DOI: 10.1128/jb.170.9.3810-3816.1988.Peer-Reviewed Original ResearchConceptsPrecursor delta-aminolevulinic acidHigher plantsUnicellular cyanobacterium Synechocystis spGlutamate-1-semialdehyde aminotransferaseCell extractsCyanobacterium Synechocystis spDelta-aminolevulinic acidSouthern blot analysisIdentical primary sequencesSynechocystis spNucleotide modificationsConversion of glutamateGene copiesALA synthesisPrimary sequenceSequence specificityTerminal enzymePolyacrylamide gel electrophoresisChloroplastsEuglena gracilisEscherichia coliSpeciesBlot analysisTRNAGel electrophoresisThe nucleotide sequences of barley cytoplasmic glutamate transfer RNAs and structural features essential for formation of δ-aminolevulinic acid
Peterson D, Schön A, Söll D. The nucleotide sequences of barley cytoplasmic glutamate transfer RNAs and structural features essential for formation of δ-aminolevulinic acid. Plant Molecular Biology 1988, 11: 293-299. PMID: 24272342, DOI: 10.1007/bf00027386.Peer-Reviewed Original ResearchChloroplast aminoacyl-tRNA synthetasesGlu-tRNA reductaseNumber of prokaryotesΔ-aminolevulinic acidMultistep enzymatic pathwayAminoacyl-tRNA synthetasesGlu-tRNATRNA discriminationTransfer RNAALA formationNucleotide sequenceALA synthesisBarley chloroplastsUniversal precursorBarley embryosChloroplastsStructural featuresEnzymatic pathwaysTRNAAlaProkaryotesSynthetasesRNAEmbryosSpeciesProtein 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
Two RNA species co‐purify with RNase P from the fission yeast Schizosaccharomyces pombe.
Krupp G, Cherayil B, Frendewey D, Nishikawa S, Söll D. Two RNA species co‐purify with RNase P from the fission yeast Schizosaccharomyces pombe. The EMBO Journal 1986, 5: 1697-1703. PMID: 3743551, PMCID: PMC1166996, DOI: 10.1002/j.1460-2075.1986.tb04413.x.Peer-Reviewed Original ResearchConceptsM1 RNARNA speciesK RNASecondary structureFission yeast SchizosaccharomycesRNase P activityYeast genomic DNALimited sequence homologyYeast SchizosaccharomycesHaploid genomeSchizosaccharomyces pombeRNase PSingle copySouthern analysisSequence homologyGenomic DNAP activityRNAEscherichia coliHairpin loopSame basic organizationEnzyme activityBasic organizationInactivation experimentsSpecies
1985
Dimeric tRNA gene arrangement in Schizosaccharomyces pombe allows increased expression of the downstream gene
Hottinger-Werlen A, Schaack J, Lapointe J, Mao J, Nichols M, Söll D. Dimeric tRNA gene arrangement in Schizosaccharomyces pombe allows increased expression of the downstream gene. Nucleic Acids Research 1985, 13: 8739-8747. PMID: 3936021, PMCID: PMC318948, DOI: 10.1093/nar/13.24.8739.Peer-Reviewed Original ResearchConceptsTRNASer geneS. pombe genesDimeric arrangementPombe geneTRNA genesGene arrangementSchizosaccharomyces pombeSpecies genesMinor genesTranscription factorsDownstream genesTranscriptional efficiencyCompetitive abilityGenesMinor speciesMajor speciesSpeciesDimeric structureEfficient productionExpressionSchizosaccharomycesPombeTRNASerSaccharomycesSequenceNucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs
Grosjean H, Nicoghosian K, Haumont E, Söll D, Cedergren R. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Research 1985, 13: 5697-5706. PMID: 3898020, PMCID: PMC321899, DOI: 10.1093/nar/13.15.5697.Peer-Reviewed Original ResearchConceptsSerine tRNANucleotide sequenceRecent common ancestorE. coli tRNACodon-anticodon interactionStructure-function relationshipsEubacterial originUCU codonsEvolutionary analysisCommon ancestorD-loopTRNAAnticodon stemSerine familyAnticodonGenesE. coliMinor speciesCodonMajor speciesSpeciesSequenceTRNASerAncestorSerine
1978
Specific transcription of eukaryotic tRNA genes in Xenopus germinal vesicle extracts.
Schmidt O, Mao J, Silverman S, Hovemann B, Söll D. Specific transcription of eukaryotic tRNA genes in Xenopus germinal vesicle extracts. Proceedings Of The National Academy Of Sciences Of The United States Of America 1978, 75: 4819-4823. PMID: 105357, PMCID: PMC336212, DOI: 10.1073/pnas.75.10.4819.Peer-Reviewed Original ResearchConceptsGerminal vesicle extractsTRNA genesRNA speciesVesicle extractsEukaryotic gene transcriptionEukaryotic tRNA genesRegulatory DNA regionsPrecursor tRNA moleculesXenopus germinal vesiclePrecursor tRNAsSpecific transcriptionDNA regionsTRNA biosynthesisTRNA precursorsNucleotide modificationsGene transcriptionTRNA moleculesTranscription systemNucleotide analysisTRNAGerminal vesicleGenesTranscriptionTRNALysSpecies
1977
Regulation of biosynthesis of aminoacyl-tRNA synthetases and of tRNA in Escherichia coli I. Isolation and characterization of a mutant with elevated levels of tRNAGln1
Morgan S, Körner A, Low K, Söll D. Regulation of biosynthesis of aminoacyl-tRNA synthetases and of tRNA in Escherichia coli I. Isolation and characterization of a mutant with elevated levels of tRNAGln1. Journal Of Molecular Biology 1977, 117: 1013-1031. PMID: 24122, DOI: 10.1016/s0022-2836(77)80010-7.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesRegulation of biosynthesisEscherichia coli strainsGlutamine synthetaseSpontaneous revertantsSynthetasesColi strainsMutantsSynthetaseElevated levelsRevertantsI. IsolationTRNABiosynthesisDuplicationSpeciesMutationsGlnTRegulationOverproductionIsolation
1971
Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases
Johnson L, Söll D. Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases. Biopolymers 1971, 10: 2209-2221. PMID: 4940767, DOI: 10.1002/bip.360101114.Peer-Reviewed Original ResearchConceptsSpecific transfer RNAsTRNA-IleTransfer RNAThermal denaturation profilesB. stearothermophilusAminoacyl-tRNA synthetasesDenaturation profilesAminoacylation of tRNAAmino acid acceptor activityTRNA-ValAcceptor activityTRNATertiary structureMycoplasma spBacillus stearothermophilusEscherichia coliAminoacylation reactionStearothermophilusAminoacylationRNASpeciesIleSynthetasesNucleaseSynthetase preparationsPurification of Five Leucine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Heterologous Leucyl-Transfer Ribonucleic Acid Synthetase
Blank H, Söll D. Purification of Five Leucine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Heterologous Leucyl-Transfer Ribonucleic Acid Synthetase. Journal Of Biological Chemistry 1971, 246: 4947-4950. PMID: 4936719, DOI: 10.1016/s0021-9258(18)61954-4.Peer-Reviewed Original ResearchMeSH KeywordsAcylationBase SequenceBenzoatesCarbon IsotopesCarcinomaCell LineChromatography, DEAE-CelluloseChromatography, GelDrug StabilityEscherichia coliGenetic CodeHot TemperatureKineticsLeucineLigasesMouth NeoplasmsNucleic Acid DenaturationPolynucleotidesRibosomesRNA, BacterialRNA, TransferTemplates, GeneticYeastsPurification of an Escherichia coli Leucine Suppressor Transfer Ribonucleic Acid and Its Aminoacylation by the Homologous Leucyl-Transfer Ribonucleic Acid Synthetase
Hayashi H, Söll D. Purification of an Escherichia coli Leucine Suppressor Transfer Ribonucleic Acid and Its Aminoacylation by the Homologous Leucyl-Transfer Ribonucleic Acid Synthetase. Journal Of Biological Chemistry 1971, 246: 4951-4954. PMID: 4941862, DOI: 10.1016/s0021-9258(18)61955-6.Peer-Reviewed Original ResearchMeSH KeywordsAcylationBenzoatesBiological AssayCarbon IsotopesChromatography, DEAE-CelluloseColiphagesEscherichia coliGenetics, MicrobialKineticsLeucineLigasesMutationPeptide BiosynthesisPlant Growth RegulatorsPlants, ToxicPolynucleotidesRNA, TransferSuppression, GeneticTemplates, GeneticTobaccoValineThe nucleotide sequence of two leucine tRNA species from Escherichia coli K12
Blank H, Sőll D. The nucleotide sequence of two leucine tRNA species from Escherichia coli K12. Biochemical And Biophysical Research Communications 1971, 43: 1192-1197. PMID: 4936129, DOI: 10.1016/0006-291x(71)90589-4.Peer-Reviewed Original Research
1970
Purification of Five Serine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Homologous and Heterologous Seryl Transfer Ribonucleic Acid Synthetases
Roy K, Söll D. Purification of Five Serine Transfer Ribonucleic Acid Species from Escherichia coli and Their Acylation by Homologous and Heterologous Seryl Transfer Ribonucleic Acid Synthetases. Journal Of Biological Chemistry 1970, 245: 1394-1400. PMID: 4910052, DOI: 10.1016/s0021-9258(18)63249-1.Peer-Reviewed Original ResearchThe Interaction of Seryl and of Leucyl Transfer Ribonucleic Acid Synthetases with Their Cognate Transfer Ribonucleic Acids
Knowles J, Katze J, Konigsberg W, Söll D. The Interaction of Seryl and of Leucyl Transfer Ribonucleic Acid Synthetases with Their Cognate Transfer Ribonucleic Acids. Journal Of Biological Chemistry 1970, 245: 1407-1415. PMID: 4910800, DOI: 10.1016/s0021-9258(18)63251-x.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseTransfer ribonucleic acidComplex formationTransfer RNA speciesLeucyl-tRNA synthetaseRibonucleic acidRNA speciesCognate tRNAEscherichia coliSynthetaseDensity gradient centrifugationTRNAStable complexesHigh saltGradient centrifugationSpeciesGel filtrationComplexesSerylColiATPEnzymeAcidSerFormation