2023
Mistranslation of the genetic code by a new family of bacterial transfer RNAs
Schuntermann D, Fischer J, Bile J, Gaier S, Shelley B, Awawdeh A, Jahn M, Hoffman K, Westhof E, Söll D, Clarke C, Vargas-Rodriguez O. Mistranslation of the genetic code by a new family of bacterial transfer RNAs. Journal Of Biological Chemistry 2023, 299: 104852. PMID: 37224963, PMCID: PMC10404621, DOI: 10.1016/j.jbc.2023.104852.Peer-Reviewed Original ResearchConceptsTransfer RNAsAmino acidsBacterial transfer RNAsUnfavorable environmental conditionsProlyl-tRNA synthetaseWrong amino acidPoor substrate specificitySubstrate discriminationGrowth defectTransfer RNAGenetic codePosttranslational modificationsProtein reporterTranslation factorsEnvironmental stressFunctional proteinsSubstrate specificityThreonine codonGenetic informationDistinct isoformsPro mutationAntibiotic carbenicillinEscherichia coliNovel familyEnvironmental conditions
2009
The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation
Palioura S, Sherrer RL, Steitz TA, Söll D, Simonović M. The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation. Science 2009, 325: 321-325. PMID: 19608919, PMCID: PMC2857584, DOI: 10.1126/science.1173755.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBase SequenceBiocatalysisCatalytic DomainCrystallography, X-RayHumansHydrogen BondingModels, MolecularMolecular Sequence DataNucleic Acid ConformationPhosphatesPhosphoserineProtein ConformationProtein MultimerizationProtein Structure, SecondaryRNA, Transfer, Amino Acid-SpecificRNA, Transfer, Amino AcylSelenocysteineConceptsTransfer RNASelenocysteine formationSelenocysteinyl-tRNA synthaseCognate transfer RNAEnzyme active siteTRNA bindingActive siteConformational changesEnzyme assaysAmino acidsFree phosphoserinePhosphoserineSepSecSFinal stepSelenocysteineBiosynthesisComplexesRNAMechanismBindsCrystal structureSynthaseBindingFormationAssaysA Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea
Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Söll D. A Cytidine Deaminase Edits C to U in Transfer RNAs in Archaea. Science 2009, 324: 657-659. PMID: 19407206, PMCID: PMC2857566, DOI: 10.1126/science.1170123.Peer-Reviewed Original ResearchConceptsTransfer RNAArchaeon Methanopyrus kandleriTertiary coreCytidine deaminase domainsTRNA genesTransfer RNAsTHUMP domainProper foldingU editingC deaminationMethanopyrus kandleriTRNA tertiary structureDeaminase domainTertiary structureTRNA tertiary corePosition 8Cytidine deaminaseUnique familyArchaeaRNAsGenesRNAFoldingDomainCrystal structure
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 membersEukarya
1996
Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis
Kumar A, Schaub U, Söll D, Ujwal M. Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis. Trends In Plant Science 1996, 1: 371-376. DOI: 10.1016/s1360-1385(96)80311-6.Peer-Reviewed Original ResearchTransfer RNAConversion of GSAGlu-tRNA reductaseEssential biosynthetic processesVariety of plantsChlorophyll biosynthesisGlu-tRNAHigher plantsProtein biosynthesisBiosynthetic processesBiosynthesisPlantsPivotal stepFirst pivotal stepChloroplastsKey precursorBiosynthesesGenesRNAProteinReductaseChlorophyllEnzymeRegulationAla
1995
Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon
Rogers K, Crescenzo A, Söll D. Aminoacylation of transfer RNAs with 2-thiouridine derivatives in the wobble position of the anticodon. Biochimie 1995, 77: 66-74. PMID: 7541255, DOI: 10.1016/0300-9084(96)88106-5.Peer-Reviewed Original ResearchConceptsEvolution of specificityPost-transcriptional modificationsAnticodon of tRNAAminoacyl-tRNA synthetasesTranslational regulationTransfer RNAWobble positionWobble baseLysine tRNATRNAEscherichia coliAnticodonAminoacylationFirst positionSynthetasesRNAColiRegulationGlutamineModificationDiscoveryGlutamate
1994
Transfer RNA in Its Fourth Decade
RajBhandary U, Söll D. Transfer RNA in Its Fourth Decade. 1994, 1-4. DOI: 10.1128/9781555818333.ch1.Peer-Reviewed Original Research
1993
Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA.
Weygand-Durasević I, Schwob E, Söll D. Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1993, 90: 2010-2014. PMID: 7680483, PMCID: PMC46010, DOI: 10.1073/pnas.90.5.2010.Peer-Reviewed Original ResearchConceptsAmber suppressor tRNASuppressor tRNAEscherichia coli glutaminyl-tRNA synthetaseAcceptor stemAccuracy of aminoacylationGlutaminyl-tRNA synthetaseWild-type enzymeNoncognate complexGlnR mutantTRNA specificityArg-130Amber mutationTransfer RNASuch mutantsMutant enzymesCritical residuesDomain contributesDomain interactionsRecognition specificityTRNAGlu-131MutantsNoncognate tRNAsGlnRCorrect aminoacylation
1992
Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl‐tRNA synthetase: a complete identity set.
Hayase Y, Jahn M, Rogers M, Sylvers L, Koizumi M, Inoue H, Ohtsuka E, Söll D. Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl‐tRNA synthetase: a complete identity set. The EMBO Journal 1992, 11: 4159-4165. PMID: 1396597, PMCID: PMC556926, DOI: 10.1002/j.1460-2075.1992.tb05509.x.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseRecognition of basesSet of tRNAsEscherichia coliCognate aminoacyl-tRNA synthetasesAminoacyl-tRNA synthetasesCorrect aminoacylationRecombinant RNA technologySet of nucleotidesNumber of mutantsGlutamine identityTRNA genesTRNA discriminationTransfer RNAExcellent systemGlnRFunctional importanceSingle deletionSpecific contactsRNA technologyBase changesSpecificity constantAminoacylationSpecific guanosineMutants
1991
Anticodon and acceptor stem nucleotides in tRNAGln are major recognition elements for E. coli glutaminyl-tRNA synthetase
Jahn M, Rogers M, Söll D. Anticodon and acceptor stem nucleotides in tRNAGln are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature 1991, 352: 258-260. PMID: 1857423, DOI: 10.1038/352258a0.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant tRNAsE. coli glutaminyl-tRNA synthetaseEfficient amber suppressorsAminoacyl-tRNA synthetasesCorresponding transfer RNASet of nucleotidesMajor recognition elementGlutamine identityAcceptor stem regionTRNA discriminationTransfer RNAAmber suppressorProtein biosynthesisTRNA moleculesUnmodified tRNACorrect attachmentAnticodon regionTRNAAcceptor stemSimilar kinetic parametersEscherichia coliAmino acidsDifferent synthetasesSpecificity constantTransfer RNA Involvement in Chlorophyll Biosynthesis
O’Neill G, Jahn D, Söll D. Transfer RNA Involvement in Chlorophyll Biosynthesis. Subcellular Biochemistry 1991, 17: 235-264. PMID: 1796486, DOI: 10.1007/978-1-4613-9365-8_11.Peer-Reviewed Original ResearchConceptsTransfer RNARegulation of hemeBranched biosynthetic pathwayPorphyrin biosynthesisBiosynthesis of ALAPhotosynthetic metabolismChlorophyll biosynthesisRNA involvementArchaebacterial kingdomMammalian cellsBiosynthetic pathwayChlorophyll synthesisBacterial systemsBiosynthesisRecent rapid progressPlantsCentral roleAlaHemeTetrapyrrole ringEnzymePathwayFive-carbonProkaryotesExperimental system
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 synthesisBiosynthesisRNAOrganismsAcidCofactorProteinGlutamateEnzymatic addition of guanylate to histidine transfer RNA
Williams J, Cooley L, Söll D. Enzymatic addition of guanylate to histidine transfer RNA. Methods In Enzymology 1990, 181: 451-462. PMID: 2166216, DOI: 10.1016/0076-6879(90)81143-i.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineChromatography, AffinityChromatography, DEAE-CelluloseChromatography, Ion ExchangeDrosophilaElectrophoresis, Polyacrylamide GelGuanosine TriphosphateKineticsNucleotidyltransferasesPhosphorus RadioisotopesRadioisotope Dilution TechniqueRNA, Transfer, Amino Acid-SpecificRNA, Transfer, HisSaccharomyces cerevisiaeSubstrate SpecificityConceptsHistidine tRNATransfer RNABacteriophage T5Yeast enzymeEnzyme migratesUridine residuesExtra nucleotidesLigase mechanismAdditional nucleotidesEnzymatic additionGel filtration chromatographyEnzyme intermediateTRNAAbsolute requirementEnzymeMolecular weightNucleotidesUltrogel AcA 34Filtration chromatographyATPDrosophilaAcA 34Molecular weight markersYeastTitration experiments
1989
Structural Basis for Misaminoacylation by Mutant E. coli Glutaminyl-tRNA Synthetase Enzymes
Perona J, Swanson R, Rould M, Steitz T, Söll D. Structural Basis for Misaminoacylation by Mutant E. coli Glutaminyl-tRNA Synthetase Enzymes. Science 1989, 246: 1152-1154. PMID: 2686030, DOI: 10.1126/science.2686030.Peer-Reviewed Original Research
1988
The 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 pathwaysTRNAAlaProkaryotesSynthetasesRNAEmbryosSpecies
1986
The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA
Schön A, Krupp G, Gough S, Berry-Lowe S, Kannangara C, Söll D. The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature 1986, 322: 281-284. PMID: 3637637, DOI: 10.1038/322281a0.Peer-Reviewed Original ResearchConceptsΔ-aminolevulinatePeptide bond synthesisCognate amino acidMolecules of chlorophyllLow relative molecular massNucleotide sequence analysisRelative molecular massBond synthesisSubsequent reactionChlorophyll biosynthesisTransfer RNAUniversal precursorGlutamate tRNAAminoacyl bondSequence analysisNovel roleSerial affinity chromatographyMolecular massRNAAmino acidsComplete reactionBlue SepharoseAcceptor RNAReduction of glutamateReactionProton NMR Studies of RNA’S and Related Enzymes Using Isotope Labels
Redfield A, Choi B, Griffey R, Jarema M, Rosevear P, Hoben P, Swanson R, Soll D. Proton NMR Studies of RNA’S and Related Enzymes Using Isotope Labels. NATO Science Series A: 1986, 99-112. DOI: 10.1007/978-1-4684-5173-3_9.Peer-Reviewed Original ResearchTransfer RNATRNA synthetasesProton NMRAminoacyl-tRNA synthetasesSmall RNA fragmentsDetails of recognitionProton NMR studiesNitrogen-15 labellingSmall proteinsTRNARNA fragmentsSmall enzymeNMR methodologyRelated enzymesNMR studiesRNANMRSmall moleculesLarge moleculesIsotope labelsSynthetasesImportant moleculesEnzymeNucleic acidsMolecules
1974
N‐(purin‐6‐ylcarbamoyl)threonine: Biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli
Körner A, Söll D. N‐(purin‐6‐ylcarbamoyl)threonine: Biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. FEBS Letters 1974, 39: 301-306. PMID: 4604806, DOI: 10.1016/0014-5793(74)80135-3.Peer-Reviewed Original ResearchMeSH KeywordsAlkaline PhosphataseAmino Acyl-tRNA SynthetasesCarbamatesCarbon RadioisotopesChromatography, DEAE-CelluloseChromatography, Ion ExchangeChromatography, PaperChromatography, Thin LayerElectrophoresis, PaperEscherichia coliIsotope LabelingMutationNitrosoguanidinesPhosphorus RadioisotopesPurine NucleosidesRibonucleasesRNA, BacterialRNA, TransferSpectrophotometry, UltravioletThreonineTime FactorsTritium
1972
N6 - (Δ2 - Isopentenyl) Adenosine: Biosynthesis in vitro in transfer RNA by an enzyme purified from Eschericha coli
Bartz J, Söll D. N6 - (Δ2 - Isopentenyl) Adenosine: Biosynthesis in vitro in transfer RNA by an enzyme purified from Eschericha coli. Biochimie 1972, 54: 31-39. PMID: 4346747, DOI: 10.1016/s0300-9084(72)80035-x.Peer-Reviewed Original Research
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 preparations