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
2010
Mutations Disrupting Selenocysteine Formation Cause Progressive Cerebello-Cerebral Atrophy
Agamy O, Zeev B, Lev D, Marcus B, Fine D, Su D, Narkis G, Ofir R, Hoffmann C, Leshinsky-Silver E, Flusser H, Sivan S, Söll D, Lerman-Sagie T, Birk OS. Mutations Disrupting Selenocysteine Formation Cause Progressive Cerebello-Cerebral Atrophy. American Journal Of Human Genetics 2010, 87: 538-544. PMID: 20920667, PMCID: PMC2948803, DOI: 10.1016/j.ajhg.2010.09.007.Peer-Reviewed Original Research
2008
Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation
Sherrer RL, O’Donoghue P, Söll D. Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation. Nucleic Acids Research 2008, 36: 1247-1259. PMID: 18174226, PMCID: PMC2275090, DOI: 10.1093/nar/gkm1134.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateAmino Acid SequenceArchaeal ProteinsBinding SitesEvolution, MolecularKineticsMethanococcalesModels, MolecularMutationPhosphotransferasesPhylogenyProtein Structure, TertiaryRNA, Transfer, Amino AcylSequence AlignmentSingle-Strand Specific DNA and RNA EndonucleasesSubstrate SpecificityConceptsATPase active sitePhosphate-binding loopInduced fit mechanismRxxxR motifEvolutionary historyWalker BKinase familyPhylogenetic analysisSep-tRNARelated kinasesPSTKBiochemical characterizationSynthase convertsFit mechanismKinaseATPase activityPlasmodium speciesMotifActive siteSerHigh affinityDecreased activityArchaeaSepSecSSer18
2001
Protein phosphatase 2A: identification in Oryza sativa of the gene encoding the regulatory A subunit
Yu S, Lei H, Chang W, Söll D, Hong G. Protein phosphatase 2A: identification in Oryza sativa of the gene encoding the regulatory A subunit. Plant Molecular Biology 2001, 45: 107-112. PMID: 11247601, DOI: 10.1023/a:1006472722500.Peer-Reviewed Original ResearchConceptsProtein phosphatase 2AAmino acid identitySouthern blot analysisRice genomePP2A proteinPhosphatase 2ABAC libraryRegulatory subunitOryza sativaNicotiana tabacumAcid identityCDNA libraryBp cDNASingle copyGenomic DNAGenesBlot analysisRice proteinRepeat unitsSubunitsProteinArabidopsisIntronsGenomeRPA1
2000
Transfer RNA Identity Change in Anticodon Variants of E. coli tRNAPhe in Vivo
Kim H, Kim I, Söll D, Lee Y. Transfer RNA Identity Change in Anticodon Variants of E. coli tRNAPhe in Vivo. Molecules And Cells 2000, 10: 76-82. PMID: 10774751, DOI: 10.1007/s10059-000-0076-7.Peer-Reviewed Original ResearchConceptsMutant tRNA genesMutant tRNAsTRNA genesAnticodon sequenceAnticodon mutantsHost viabilityE. coliAmino acidsMost aminoacyl-tRNA synthetasesOpal stop codonAminoacyl-tRNA synthetasesSite-directed mutagenesisE. coli tRNAMajor recognition elementAnticodon variantsSuch tRNAsTRNAStop codonAminoacylation specificityAnticodonSimilarity dendrogramVivo evolutionGenesAcceptor specificityAnticodon change
1999
Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A
Jackson K, Söll D. Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A. Molecular Genetics And Genomics 1999, 262: 830-838. PMID: 10628867, DOI: 10.1007/s004380051147.Peer-Reviewed Original ResearchConceptsProtein phosphatase 2APhosphatase 2AHeterotrimeric protein phosphatase 2ARegulatory subunit AProtein phosphatase 2BMultiple signaling pathwaysAuxin transportPhosphatase 2BPP2A activityAntisense transcriptsResponse pathwaysArabidopsis extractsGene productsN-terminusRoot growthSubunit ASignaling pathwaysNovel cyclophilinCyclophilinArabidopsisAltered formsTranscriptsMutationsPathwayEukaryotesTransfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis
Ibba M, Sever S, Praetorius-Ibba M, Söll D. Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis. Nucleic Acids Research 1999, 27: 3631-3637. PMID: 10471730, PMCID: PMC148616, DOI: 10.1093/nar/27.18.3631.Peer-Reviewed Original Research
1998
Root-Growth Behavior of the Arabidopsis Mutantrgr1 1
Mullen J, Turk E, Johnson K, Wolverton C, Ishikawa H, Simmons C, Söll D, Evans M. Root-Growth Behavior of the Arabidopsis Mutantrgr1 1. Plant Physiology 1998, 118: 1139-1145. PMID: 9847088, PMCID: PMC34730, DOI: 10.1104/pp.118.4.1139.Peer-Reviewed Original ResearchMaize mitochondrial seryl-tRNA synthetase recognizes Escherichia coli tRNASer in vivo and in vitro
Rokov J, Söll D, Weygand-Durašević I. Maize mitochondrial seryl-tRNA synthetase recognizes Escherichia coli tRNASer in vivo and in vitro. Plant Molecular Biology 1998, 38: 497-502. PMID: 9747857, DOI: 10.1023/a:1006088516228.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseMitochondrial seryl-tRNA synthetasePutative mature proteinSeryl-tRNA synthetasesEscherichia coliStructure/function relationshipsMature proteinGene sequencesMutant strainSignificant similarityFunctional identityN-terminalYeast tRNAMitochondrial functionFunction relationshipsProteinPoor substrateSynthetaseColiSynthetasesTRNAVivoCDNAMaizeEnzymeRetracing the evolution of amino acid specificity in glutaminyl‐tRNA synthetase
Hong K, Ibba M, Söll D. Retracing the evolution of amino acid specificity in glutaminyl‐tRNA synthetase. FEBS Letters 1998, 434: 149-154. PMID: 9738468, DOI: 10.1016/s0014-5793(98)00968-5.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseTranslational error rateMolecular phylogenetic studiesAmino acid specificityGlutamyl-tRNA synthetaseFirst biochemical evidenceCellular growth ratePhe-90Phylogenetic studiesSynthetase mutantsTyr-240SynthetaseBiochemical evidenceVivo expressionGenesGlutamic acidActive siteGrowth rateMisacylationMutantsMutagenesisDuplicationDiversificationResiduesKey stepMajor Identity Element of Glutamine tRNAs from Bacillus subtilis and Escherichia coli in the Reaction with B. subtilis Glutamyl-tRNA Synthetase
Kim S, Söll D. Major Identity Element of Glutamine tRNAs from Bacillus subtilis and Escherichia coli in the Reaction with B. subtilis Glutamyl-tRNA Synthetase. Molecules And Cells 1998, 8: 459-465. PMID: 9749534, DOI: 10.1016/s1016-8478(23)13451-0.Peer-Reviewed Original Research
1997
Glutaminyl-tRNA synthetase.
Freist W, Gauss D, Ibba M, Söll D. Glutaminyl-tRNA synthetase. Biological Chemistry 1997, 378: 1103-17. PMID: 9372179.Peer-Reviewed Original ResearchConceptsE. coli GlnRSGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseMammalian enzymeCommon ancestorPositive eubacteriaCognate tRNAMultienzyme complexTRNA moleculesGlnRArtificial mutantsAcceptor stemAnticodon loopMolecular massAmino acidsCatalytic siteEnzymeSynthetaseEubacteriaArchaebacteriaTRNAMutantsOrganellesAncestorComplexes
1996
Glutaminyl‐tRNA synthetase: from genetics to molecular recognition
Ibba M, Hong K, Söll D. Glutaminyl‐tRNA synthetase: from genetics to molecular recognition. Genes To Cells 1996, 1: 421-427. PMID: 9078373, DOI: 10.1046/j.1365-2443.1996.d01-255.x.Peer-Reviewed Original ResearchConceptsEscherichia coli glutaminyl-tRNA synthetaseMajority of tRNAsCorrect amino acidGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesSequence-specific interactionsAmino acid recognitionEfficiency of aminoacylationGenetic codeTRNA selectionGlnRTRNAAmino acidsNoncognate tRNAsCellular viabilityStructural studiesMolecular recognitionSynthetasesAminoacylationComplex displaysGeneticsSynthetaseGlutamineMechanismViabilityA mutation in protein phosphatase 2A regulatory subunit A affects auxin transport in Arabidopsis.
Garbers C, DeLong A, Deruére J, Bernasconi P, Söll D. A mutation in protein phosphatase 2A regulatory subunit A affects auxin transport in Arabidopsis. The EMBO Journal 1996, 15: 2115-2124. PMID: 8641277, PMCID: PMC450134, DOI: 10.1002/j.1460-2075.1996.tb00565.x.Peer-Reviewed Original ResearchConceptsProtein phosphatase 2AAuxin transportNaphthylphthalamic acidPhosphatase 2AProtein phosphatase 2A regulatory subunitT-DNA insertionRoot hair developmentT-DNA insertsTemperature-sensitive phenotypeRcn1 mutationROOTS CURLPhytohormone auxinArabidopsis thalianaMutant phenotypeAuxin effluxRCN1 geneRegulatory subunitHypocotyl elongationRoot branchingCell elongationShoot apexMolecular mechanismsHair developmentArabidopsisGrowth curvatureHomologous Expression and Purification of Mutants of an Essential Protein by Reverse Epitope-Tagging
Thomann H, Ibba M, Hong K, Söll D. Homologous Expression and Purification of Mutants of an Essential Protein by Reverse Epitope-Tagging. Bio/Technology 1996, 14: 50-55. PMID: 9636312, DOI: 10.1038/nbt0196-50.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant enzymesEssential enzymeGlutaminyl-tRNA synthetasesWild-type proteinExtrachromosomal genetic elementsEpitope taggingEssential proteinsMutant proteinsHomologous expressionReporter epitopeCell-free extractsGenetic elementsNormal phenotypeBiochemical studiesEnzymatic activityEnzymeProteinSynthetaseProtein contaminationExpressionPurificationMutantsSynthetasesNovel strategy
1995
A novel root gravitropism mutant of Arabidopsis thaliana exhibiting altered auxin physiology
Simmons C, Migliaccio F, Masson P, Caspar T, Söll D. A novel root gravitropism mutant of Arabidopsis thaliana exhibiting altered auxin physiology. Physiologia Plantarum 1995, 93: 790-798. PMID: 11540162, DOI: 10.1111/j.1399-3054.1995.tb05133.x.Peer-Reviewed Original ResearchConceptsGravitropism mutantsPolar auxin transport inhibitorsWild-type rootsLateral root formationAuxin transport inhibitorsInsertional gene inactivationAuxin-resistant mutantsArabidopsis thalianaAuxin physiologyComplementation testsRoot gravitropismRoot hairsRGR1Gene inactivationRoot elongationWild typeMutantsHormone classesRoot formationDichlorophenoxyacetic acidVisible markersMendelian recessiveMap unitsTransport inhibitorsRootsSubstrate selection by aminoacyl-tRNA synthetases.
Ibba M, Thomann H, Hong K, Sherman J, Weygand-Durasevic I, Sever S, Stange-Thomann N, Praetorius M, Söll D. Substrate selection by aminoacyl-tRNA synthetases. Nucleic Acids Symposium Series 1995, 40-2. PMID: 8643392.Peer-Reviewed Original Research
1994
Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases.
Frugier M, Söll D, Giegé R, Florentz C. Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases. Biochemistry 1994, 33: 9912-21. PMID: 8060999, DOI: 10.1021/bi00199a013.Peer-Reviewed Original ResearchConceptsAminoacyl-tRNA synthetasesIdentity nucleotidesHigh-resolution X-ray structuresAminoacyl-tRNA synthetase complexGlutaminyl-tRNA synthetaseAspartyl-tRNA synthetasesAspartyl-tRNA synthetaseGlutamine identityCognate tRNATRNA structureTRNA moleculesTRNAAminoacylation specificitySynthetase complexSpecific aminoacylationConformational changesSynthetasesEscherichia coliYeastSynthetaseNucleotidesE. coliX-ray structureComplex formationColiThiobacillus ferrooxidans tyrosyl-tRNA synthetase functions in vivo in Escherichia coli
Salazar O, Sagredo B, Jedlicki E, Söll D, Weygand-Durasevic I, Orellana O. Thiobacillus ferrooxidans tyrosyl-tRNA synthetase functions in vivo in Escherichia coli. Journal Of Bacteriology 1994, 176: 4409-4415. PMID: 7517395, PMCID: PMC205654, DOI: 10.1128/jb.176.14.4409-4415.1994.Peer-Reviewed Original ResearchMeSH KeywordsAcidithiobacillus thiooxidansAmino Acid SequenceBase SequenceGene Expression Regulation, BacterialGenes, BacterialGenetic Complementation TestMolecular Sequence DataMutationNucleic Acid HybridizationOperonPromoter Regions, GeneticRNA, BacterialRNA, RibosomalRNA, Transfer, TyrSequence Analysis, DNATyrosine-tRNA LigaseConceptsOverall identityTyrosyl-tRNA synthetase geneRho-independent transcription terminatorEscherichia coli TyrRSClass I aminoacyl-tRNA synthetasesRibosomal RNA operonSingle-copy geneAminoacyl-tRNA synthetasesTyrosyl-tRNA synthetasesSouthern blot analysisRNA operonBioleaching of mineralsThermosensitive mutationTranscription unitTranscription terminatorSynthetase genePutative promoterProtein sequencesSynthetase functionE. coli strainsGenesSignature sequencesEscherichia coliAmino acidsDNA probesA Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation
Leong-Morgenthaler P, Oliver S, Hottinger H, Söll D. A Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation. Biochimie 1994, 76: 45-49. PMID: 8031904, DOI: 10.1016/0300-9084(94)90061-2.Peer-Reviewed Original ResearchConceptsNifS-like genesNifS-like proteinsNif gene productsNif proteinsNif genesGene productsNitrogen-fixing bacteriaGroup of enzymesRemarkable sequence homologyCysteine desulfuraseSequence conservationEfficient nitrogen fixationLeucine auxotrophyTransaminase BDiverse functionsSequence homologyNitrogen fixationEscherichia coli strainsProtein productsMetabolic pathwaysAzotobacter vinelandiiGenesB mutationsProteinDissimilar mutations